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commit/galaxy-central: jmchilton: Update to latest Pulsar client.
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9207ecb43d81/ Changeset: 9207ecb43d81 User: jmchilton Date: 2014-09-16 22:29:31 Summary: Update to latest Pulsar client. Updates to Pulsar changeset f8d832fe4896f3fa9e27cc66a2aad7e446b99c2a - see Pulsar (https://github.com/galaxyproject/pulsar) for individual changes. Affected #: 6 files diff -r d682014dc25a03118fd16065cd5900863c9b95f9 -r 9207ecb43d81853da7a58cd5634683dc87991c4f lib/pulsar/client/__init__.py --- a/lib/pulsar/client/__init__.py +++ b/lib/pulsar/client/__init__.py @@ -34,7 +34,7 @@ test_tool = pulsar://http://remotehost:8913 Remember this must be added after the ``[galaxy:tool_runners]`` header -in the ``universe.ini`` file. +in the ``galaxy.ini`` file. """ diff -r d682014dc25a03118fd16065cd5900863c9b95f9 -r 9207ecb43d81853da7a58cd5634683dc87991c4f lib/pulsar/client/amqp_exchange.py --- a/lib/pulsar/client/amqp_exchange.py +++ b/lib/pulsar/client/amqp_exchange.py @@ -85,18 +85,27 @@ if heartbeat_thread: heartbeat_thread.join() sleep(DEFAULT_RECONNECT_CONSUMER_WAIT) + except BaseException: + log.exception("Problem consuming queue, consumer quitting in problematic fashion!") + raise def heartbeat(self, connection): log.debug('AMQP heartbeat thread alive') - while connection.connected: - connection.heartbeat_check() - sleep(DEFAULT_HEARTBEAT_WAIT) + try: + while connection.connected: + connection.heartbeat_check() + sleep(DEFAULT_HEARTBEAT_WAIT) + except BaseException: + log.exception("Problem with heartbeat, leaving heartbeat method in problematic state!") + raise log.debug('AMQP heartbeat thread exiting') def publish(self, name, payload): + key = self.__queue_name(name) + log.debug("Begin publishing to key %s" % key) with self.connection(self.__url) as connection: with pools.producers[connection].acquire() as producer: - key = self.__queue_name(name) + log.debug("Have producer for publishing to key %s" % key) producer.publish( payload, serializer='json', @@ -105,6 +114,7 @@ routing_key=key, **self.__publish_kwds ) + log.debug("Published to key %s" % key) def __publish_errback(self, exc, interval): log.error("Connection error while publishing: %r", exc, exc_info=1) diff -r d682014dc25a03118fd16065cd5900863c9b95f9 -r 9207ecb43d81853da7a58cd5634683dc87991c4f lib/pulsar/client/transport/__init__.py --- a/lib/pulsar/client/transport/__init__.py +++ b/lib/pulsar/client/transport/__init__.py @@ -23,9 +23,16 @@ transport_type = 'curl' return transport_type -# TODO: Provide urllib implementation if these unavailable, -# also explore a requests+poster option. -from .curl import get_file -from .curl import post_file +from .curl import curl_available +from .requests import requests_multipart_post_available +if curl_available: + from .curl import get_file + from .curl import post_file +elif requests_multipart_post_available: + from .requests import get_file + from .requests import post_file +else: + from .poster import get_file + from .poster import post_file __all__ = [get_transport, get_file, post_file] diff -r d682014dc25a03118fd16065cd5900863c9b95f9 -r 9207ecb43d81853da7a58cd5634683dc87991c4f lib/pulsar/client/transport/curl.py --- a/lib/pulsar/client/transport/curl.py +++ b/lib/pulsar/client/transport/curl.py @@ -2,10 +2,11 @@ from cStringIO import StringIO except ImportError: from io import StringIO +curl_available = True try: from pycurl import Curl except ImportError: - pass + curl_available = False from os.path import getsize diff -r d682014dc25a03118fd16065cd5900863c9b95f9 -r 9207ecb43d81853da7a58cd5634683dc87991c4f lib/pulsar/client/transport/poster.py --- /dev/null +++ b/lib/pulsar/client/transport/poster.py @@ -0,0 +1,56 @@ +from __future__ import absolute_import +try: + from urllib2 import urlopen +except ImportError: + from urllib.request import urlopen +try: + from urllib2 import Request +except ImportError: + from urllib.request import Request +try: + from galaxy import eggs + eggs.require("poster") +except ImportError: + pass + +try: + import poster +except ImportError: + poster = None + +POSTER_UNAVAILABLE_MESSAGE = "Pulsar configured to use poster module - but it is unavailable. Please install poster." + +import logging +log = logging.getLogger(__name__) + + +if poster is not None: + poster.streaminghttp.register_openers() + + +def post_file(url, path): + __ensure_poster() + try: + datagen, headers = poster.encode.multipart_encode({"file": open(path, "rb")}) + request = Request(url, datagen, headers) + return urlopen(request).read() + except: + log.exception("problem") + raise + + +def get_file(url, path): + __ensure_poster() + request = Request(url=url) + response = urlopen(request) + with open(path, 'wb') as output: + while True: + buffer = response.read(1024) + if not buffer: + break + output.write(buffer) + + +def __ensure_poster(): + if poster is None: + raise ImportError(POSTER_UNAVAILABLE_MESSAGE) diff -r d682014dc25a03118fd16065cd5900863c9b95f9 -r 9207ecb43d81853da7a58cd5634683dc87991c4f lib/pulsar/client/transport/requests.py --- /dev/null +++ b/lib/pulsar/client/transport/requests.py @@ -0,0 +1,50 @@ +from __future__ import absolute_import +try: + from galaxy import eggs + eggs.require("requets") +except ImportError: + pass + +try: + import requests +except ImportError: + requests = None +requests_multipart_post_available = False +try: + import requests_toolbelt + requests_multipart_post_available = True +except ImportError: + requests_toolbelt = None + + +REQUESTS_UNAVAILABLE_MESSAGE = "Pulsar configured to use requests module - but it is unavailable. Please install requests." +REQUESTS_TOOLBELT_UNAVAILABLE_MESSAGE = "Pulsar configured to use requests_toolbelt module - but it is unavailable. Please install requests_toolbelt." + +import logging +log = logging.getLogger(__name__) + + +def post_file(url, path): + if requests_toolbelt is None: + raise ImportError(REQUESTS_TOOLBELT_UNAVAILABLE_MESSAGE) + + __ensure_requests() + m = requests_toolbelt.MultipartEncoder( + fields={'file': ('filename', open(path, 'rb'))} + ) + requests.post(url, data=m, headers={'Content-Type': m.content_type}) + + +def get_file(url, path): + __ensure_requests() + r = requests.get(url, stream=True) + with open(path, 'wb') as f: + for chunk in r.iter_content(chunk_size=1024): + if chunk: # filter out keep-alive new chunks + f.write(chunk) + f.flush() + + +def __ensure_requests(): + if requests is None: + raise ImportError(REQUESTS_UNAVAILABLE_MESSAGE) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/150df6515fc7/ Changeset: 150df6515fc7 User: natefoo Date: 2014-09-16 20:36:37 Summary: Fix config moves for the Tool Shed. Affected #: 1 file diff -r 5ba632c506feccdaf7d6c334ad82347f1ea92fb8 -r 150df6515fc709b12ba9096bef714967439f2f3a lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -27,6 +27,10 @@ def __init__( self, **kwargs ): self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) + + # Resolve paths of other config files + self.__parse_config_file_options( kwargs ) + # Collect the umask and primary gid from the environment self.umask = os.umask( 077 ) # get the current umask os.umask( self.umask ) # can't get w/o set, so set it back @@ -41,7 +45,6 @@ self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) ) - self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) # Tool stuff @@ -51,8 +54,6 @@ self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() ) - self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) - self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root ) self.builds_file_path = resolve_path( kwargs.get( "builds_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'builds.txt') ), self.root ) self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ), self.root ) @@ -136,6 +137,47 @@ self.citation_cache_data_dir = resolve_path( kwargs.get( "citation_cache_data_dir", "database/tool_shed_citations/data" ), self.root ) self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root ) + def __parse_config_file_options( self, kwargs ): + defaults = dict( + datatypes_config_file = [ 'datatypes_conf.xml', 'config/datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], + shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], + ) + + listify_defaults = dict( + tool_data_table_config_path = [ 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + ) + + for var, defaults in defaults.items(): + if kwargs.get( var, None ) is not None: + path = kwargs.get( var ) + else: + for default in defaults: + if os.path.exists( resolve_path( default, self.root ) ): + path = default + break + else: + path = defaults[-1] + setattr( self, var, resolve_path( path, self.root ) ) + + for var, defaults in listify_defaults.items(): + paths = [] + if kwargs.get( var, None ) is not None: + paths = listify( kwargs.get( var ) ) + else: + for default in defaults: + for path in listify( default ): + if not os.path.exists( resolve_path( path, self.root ) ): + break + else: + paths = listify( default ) + break + else: + paths = listify( defaults[-1] ) + setattr( self, var, [ resolve_path( x, self.root ) for x in paths ] ) + + # Backwards compatibility for names used in too many places to fix + self.datatypes_config = self.datatypes_config_file + def get( self, key, default ): return self.config_dict.get( key, default ) https://bitbucket.org/galaxy/galaxy-central/commits/714857a48c7d/ Changeset: 714857a48c7d User: natefoo Date: 2014-09-16 20:55:38 Summary: Rename tool_shed_wsgi.ini.sample to tool_shed_wsgi.ini, fix static and other errors I created when moving it to config/ in the first place. Affected #: 8 files diff -r 150df6515fc709b12ba9096bef714967439f2f3a -r 714857a48c7d6607e6b7822035ddcf35707672a5 config/tool_shed.ini.sample --- /dev/null +++ b/config/tool_shed.ini.sample @@ -0,0 +1,114 @@ +# ---- HTTP Server ---------------------------------------------------------- + +[server:main] + +use = egg:Paste#http +port = 9009 + +# The address on which to listen. By default, only listen to localhost (the tool shed will not +# be accessible over the network). Use '0.0.0.0' to listen on all available network interfaces. +#host = 0.0.0.0 +host = 127.0.0.1 + +use_threadpool = true +threadpool_workers = 10 +# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +threadpool_kill_thread_limit = 10800 + +# ---- Galaxy Webapps Community Interface ------------------------------------------------- + +[app:main] + +# Specifies the factory for the universe WSGI application +paste.app_factory = galaxy.webapps.tool_shed.buildapp:app_factory +log_level = DEBUG + +# Database connection +database_file = database/community.sqlite +# You may use a SQLAlchemy connection string to specify an external database instead +#database_connection = postgres:///community_test?host=/var/run/postgresql + +# Where the hgweb.config file is stored. The default is the Galaxy installation directory. +#hgweb_config_dir = None + +# Where tool shed repositories are stored. +file_path = database/community_files +# Temporary storage for additional datasets, this should be shared through the cluster +new_file_path = database/tmp + +# File containing old-style genome builds +#builds_file_path = tool-data/shared/ucsc/builds.txt + +# Session support (beaker) +use_beaker_session = True +session_type = memory +session_data_dir = %(here)s/database/beaker_sessions +session_key = galaxysessions +session_secret = changethisinproduction + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +id_secret = changethisinproductiontoo + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy +#use_remote_user = False + +# Configuration for debugging middleware +debug = true +use_lint = false + +# NEVER enable this on a public site (even test or QA) +# use_interactive = true + +# this should be a comma-separated list of valid Galaxy users +#admin_users = user1@example.org,user2@example.org + +# Force everyone to log in (disable anonymous access) +require_login = False + +# path to sendmail +sendmail_path = /usr/sbin/sendmail + +# Number of saved tool test results produced by the install and test framework for each repository. +#num_tool_test_results_saved = 5 + +# For use by email messages sent from the tool shed +#smtp_server = smtp.your_tool_shed_server +#email_from = your_tool_shed_email@server + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = https://wiki.galaxyproject.org/Support + +# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) +## use_heartbeat = True + +# Profiling middleware (cProfile based) +## use_profile = True + +# Enable creation of Galaxy flavor Docker Image +#enable_galaxy_flavor_docker_image = False + +# Use the new iframe / javascript based layout +use_new_layout = true + +# Show a message box under the masthead. +#message_box_visible = False +#message_box_content = None +#message_box_class = info + +# Serving static files (needed if running standalone) +#static_enabled = True +#static_cache_time = 360 +#static_dir = static/ +#static_images_dir = static/images +#static_favicon_dir = static/favicon.ico +#static_scripts_dir = static/scripts/ +#static_style_dir = static/style/blue diff -r 150df6515fc709b12ba9096bef714967439f2f3a -r 714857a48c7d6607e6b7822035ddcf35707672a5 config/tool_shed_wsgi.ini.sample --- a/config/tool_shed_wsgi.ini.sample +++ /dev/null @@ -1,114 +0,0 @@ -# ---- HTTP Server ---------------------------------------------------------- - -[server:main] - -use = egg:Paste#http -port = 9009 - -# The address on which to listen. By default, only listen to localhost (the tool shed will not -# be accessible over the network). Use '0.0.0.0' to listen on all available network interfaces. -#host = 0.0.0.0 -host = 127.0.0.1 - -use_threadpool = true -threadpool_workers = 10 -# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. -threadpool_kill_thread_limit = 10800 - -# ---- Galaxy Webapps Community Interface ------------------------------------------------- - -[app:main] - -# Specifies the factory for the universe WSGI application -paste.app_factory = galaxy.webapps.tool_shed.buildapp:app_factory -log_level = DEBUG - -# Database connection -database_file = database/community.sqlite -# You may use a SQLAlchemy connection string to specify an external database instead -#database_connection = postgres:///community_test?host=/var/run/postgresql - -# Where the hgweb.config file is stored. The default is the Galaxy installation directory. -#hgweb_config_dir = None - -# Where tool shed repositories are stored. -file_path = database/community_files -# Temporary storage for additional datasets, this should be shared through the cluster -new_file_path = database/tmp - -# File containing old-style genome builds -#builds_file_path = tool-data/shared/ucsc/builds.txt - -# Session support (beaker) -use_beaker_session = True -session_type = memory -session_data_dir = %(here)s/database/beaker_sessions -session_key = galaxysessions -session_secret = changethisinproduction - -# -- Users and Security - -# Galaxy encodes various internal values when these values will be output in -# some format (for example, in a URL or cookie). You should set a key to be -# used by the algorithm that encodes and decodes these values. It can be any -# string. If left unchanged, anyone could construct a cookie that would grant -# them access to others' sessions. -id_secret = changethisinproductiontoo - -# User authentication can be delegated to an upstream proxy server (usually -# Apache). The upstream proxy should set a REMOTE_USER header in the request. -# Enabling remote user disables regular logins. For more information, see: -# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy -#use_remote_user = False - -# Configuration for debugging middleware -debug = true -use_lint = false - -# NEVER enable this on a public site (even test or QA) -# use_interactive = true - -# this should be a comma-separated list of valid Galaxy users -#admin_users = user1@example.org,user2@example.org - -# Force everyone to log in (disable anonymous access) -require_login = False - -# path to sendmail -sendmail_path = /usr/sbin/sendmail - -# Number of saved tool test results produced by the install and test framework for each repository. -#num_tool_test_results_saved = 5 - -# For use by email messages sent from the tool shed -#smtp_server = smtp.your_tool_shed_server -#email_from = your_tool_shed_email@server - -# The URL linked by the "Support" link in the "Help" menu. -#support_url = https://wiki.galaxyproject.org/Support - -# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) -## use_heartbeat = True - -# Profiling middleware (cProfile based) -## use_profile = True - -# Enable creation of Galaxy flavor Docker Image -#enable_galaxy_flavor_docker_image = False - -# Use the new iframe / javascript based layout -use_new_layout = true - -# Show a message box under the masthead. -#message_box_visible = False -#message_box_content = None -#message_box_class = info - -# Serving static files (needed if running standalone) -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue diff -r 150df6515fc709b12ba9096bef714967439f2f3a -r 714857a48c7d6607e6b7822035ddcf35707672a5 lib/galaxy/model/orm/scripts.py --- a/lib/galaxy/model/orm/scripts.py +++ b/lib/galaxy/model/orm/scripts.py @@ -31,7 +31,7 @@ "tool_shed": { 'repo': 'lib/galaxy/webapps/tool_shed/model/migrate', - 'config_file': 'tool_shed_wsgi.ini', + 'config_file': 'config/tool_shed.ini', 'default_sqlite_file': './database/community.sqlite', }, "install": @@ -79,7 +79,7 @@ ... p.add_section('app:main') ... p.set('app:main', property, value) ... with open(os.path.join(config_dir, path), 'w') as f: p.write(f) - >>> write_ini('tool_shed_wsgi.ini', 'database_connection', 'sqlite:///pg/testdb1') + >>> write_ini('tool_shed.ini', 'database_connection', 'sqlite:///pg/testdb1') >>> config = get_config(['manage_db.py', 'tool_shed'], cwd=config_dir) >>> config['repo'] 'lib/galaxy/webapps/tool_shed/model/migrate' diff -r 150df6515fc709b12ba9096bef714967439f2f3a -r 714857a48c7d6607e6b7822035ddcf35707672a5 lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -20,7 +20,7 @@ def __init__( self, **kwd ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) self.name = "tool_shed" - # Read the tool_shed_wsgi.ini configuration file and check for errors. + # Read the tool_shed.ini configuration file and check for errors. self.config = config.Configuration( **kwd ) self.config.check() config.configure_logging( self.config ) diff -r 150df6515fc709b12ba9096bef714967439f2f3a -r 714857a48c7d6607e6b7822035ddcf35707672a5 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -220,11 +220,12 @@ # Send to dynamic app by default urlmap["/"] = app # Define static mappings from config - urlmap["/static"] = Static( conf.get( "static_dir" ), cache_time ) - urlmap["/images"] = Static( conf.get( "static_images_dir" ), cache_time ) - urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir" ), cache_time ) - urlmap["/static/style"] = Static( conf.get( "static_style_dir" ), cache_time ) - urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir" ), cache_time ) + urlmap["/static"] = Static( conf.get( "static_dir", "./static/" ), cache_time ) + urlmap["/images"] = Static( conf.get( "static_images_dir", "./static/images" ), cache_time ) + urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir", "./static/scripts/" ), cache_time ) + urlmap["/static/style"] = Static( conf.get( "static_style_dir", "./static/style/blue" ), cache_time ) + urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir", "./static/favicon.ico" ), cache_time ) + urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", "./static/robots.txt" ), cache_time ) # URL mapper becomes the root webapp return urlmap diff -r 150df6515fc709b12ba9096bef714967439f2f3a -r 714857a48c7d6607e6b7822035ddcf35707672a5 lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh --- a/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh @@ -1,8 +1,10 @@ #!/bin/bash +: ${TOOL_SHED_CONFIG_FILE:=config/tool_shed.ini.sample} + stop_err() { echo $1 - python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon + python ./scripts/paster.py serve ${TOOL_SHED_CONFIG_FILE} --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon exit 1 } @@ -14,7 +16,7 @@ log_file="lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap.log" -database_result=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute check_db --config_file tool_shed_wsgi.ini` +database_result=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute check_db --config_file ${TOOL_SHED_CONFIG_FILE}` if [ $? -ne 0 ] ; then stop_err "Unable to bootstrap tool shed. $database_result" @@ -31,8 +33,8 @@ fi if [ $? -eq 0 ] ; then - user_auth=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute admin_user_info --config_file tool_shed_wsgi.ini` - local_shed_url=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute get_url --config_file tool_shed_wsgi.ini` + user_auth=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute admin_user_info --config_file ${TOOL_SHED_CONFIG_FILE}` + local_shed_url=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute get_url --config_file ${TOOL_SHED_CONFIG_FILE}` fi admin_user_name=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$1 }'` @@ -41,18 +43,18 @@ echo -n "Creating user '$admin_user_name' with email address '$admin_user_email'..." -python lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py tool_shed_wsgi.ini >> $log_file +python lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py ${TOOL_SHED_CONFIG_FILE} >> $log_file echo " done." -sed -i "s/#admin_users = user1@example.org,user2@example.org/admin_users = $admin_user_email/" tool_shed_wsgi.ini +sed -i "s/#admin_users = user1@example.org,user2@example.org/admin_users = $admin_user_email/" ${TOOL_SHED_CONFIG_FILE} echo -n "Starting tool shed in order to populate users and categories... " if [ -f tool_shed_bootstrap.pid ] ; then stop_err "A bootstrap process is already running." fi -python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --daemon > /dev/null +python ./scripts/paster.py serve ${TOOL_SHED_CONFIG_FILE} --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --daemon > /dev/null shed_pid=`cat tool_shed_bootstrap.pid` @@ -94,6 +96,6 @@ fi echo "Bootstrap complete, shutting down temporary tool shed process. A log has been saved to tool_shed_bootstrap.log" -python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon +python ./scripts/paster.py serve ${TOOL_SHED_CONFIG_FILE} --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon -exit 0 \ No newline at end of file +exit 0 diff -r 150df6515fc709b12ba9096bef714967439f2f3a -r 714857a48c7d6607e6b7822035ddcf35707672a5 lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --- a/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py @@ -25,7 +25,7 @@ db_file = config_parser.get( 'app:main', 'database_file' ) dburi = "sqlite:///%s?isolation_level=IMMEDIATE" % db_file else: - print 'The database configuration setting is missing from the tool_shed_wsgi.ini file. Add this setting before attempting to bootstrap.' + print 'The database configuration setting is missing from the tool_shed.ini file. Add this setting before attempting to bootstrap.' exit(1) sa_session = None @@ -122,7 +122,7 @@ return 1 parser = argparse.ArgumentParser() -parser.add_argument( '-c', '--config_file', dest='config', action='store', default='tool_shed_wsgi.ini' ) +parser.add_argument( '-c', '--config_file', dest='config', action='store', default='config/tool_shed.ini.sample' ) parser.add_argument( '-e', '--execute', dest='method', action='store', default='check_db' ) args = parser.parse_args() diff -r 150df6515fc709b12ba9096bef714967439f2f3a -r 714857a48c7d6607e6b7822035ddcf35707672a5 run_tool_shed.sh --- a/run_tool_shed.sh +++ b/run_tool_shed.sh @@ -12,4 +12,15 @@ args=`echo $@ | sed "s#-\?-bootstrap_from_tool_shed $tool_shed##"` fi -python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $args +if [ -z "$TOOL_SHED_CONFIG_FILE" ]; then + if [ -f tool_shed_wsgi.ini ]; then + TOOL_SHED_CONFIG_FILE=tool_shed_wsgi.ini + elif [ -f config/tool_shed.ini ]; then + TOOL_SHED_CONFIG_FILE=config/tool_shed.ini + else + TOOL_SHED_CONFIG_FILE=config/tool_shed.ini.sample + fi + export TOOL_SHED_CONFIG_FILE +fi + +python ./scripts/paster.py serve $TOOL_SHED_CONFIG_FILE --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $args https://bitbucket.org/galaxy/galaxy-central/commits/d682014dc25a/ Changeset: d682014dc25a User: natefoo Date: 2014-09-16 20:56:57 Summary: merge. Affected #: 2 files diff -r 714857a48c7d6607e6b7822035ddcf35707672a5 -r d682014dc25a03118fd16065cd5900863c9b95f9 test/api/test_libraries.py --- a/test/api/test_libraries.py +++ b/test/api/test_libraries.py @@ -43,7 +43,7 @@ library_dataset = show().json() self._assert_has_keys( library_dataset, "peek", "data_type" ) assert library_dataset[ "peek" ].find("create_test") >= 0 - assert library_dataset[ "data_type" ] == "txt" + assert library_dataset[ "file_ext" ] == "txt", library_dataset[ "file_ext" ] def _create_folder( self, library ): create_data = dict( diff -r 714857a48c7d6607e6b7822035ddcf35707672a5 -r d682014dc25a03118fd16065cd5900863c9b95f9 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -26,9 +26,9 @@ self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor ) - def test_show_invalid_is_404( self ): - show_response = self._get( "workflow/%s" % self._random_key() ) - self._assert_status_code_is( show_response, 404 ) + def test_show_invalid_key_is_400( self ): + show_response = self._get( "workflows/%s" % self._random_key() ) + self._assert_status_code_is( show_response, 400 ) def test_cannot_show_private_workflow( self ): workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) @@ -134,12 +134,12 @@ run_workflow_response = self._post( "workflows", data=workflow_request ) self._assert_status_code_is( run_workflow_response, 403 ) - def test_404_on_invalid_workflow( self ): + def test_400_on_invalid_workflow_id( self ): workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) workflow_request, history_id = self._setup_workflow_run( workflow ) workflow_request[ "workflow_id" ] = self._random_key() run_workflow_response = self._post( "workflows", data=workflow_request ) - self._assert_status_code_is( run_workflow_response, 404 ) + self._assert_status_code_is( run_workflow_response, 400 ) def test_cannot_run_against_other_users_history( self ): workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) @@ -558,21 +558,6 @@ for step in usage_details[ "steps" ]: self._assert_has_keys( step, "workflow_step_id", "order_index", "id" ) - @skip_without_tool( "cat1" ) - def test_post_job_action( self ): - """ Tests both import and execution of post job actions. - """ - workflow = self.workflow_populator.load_workflow( name="test_for_pja_run", add_pja=True ) - workflow_request, history_id = self._setup_workflow_run( workflow ) - run_workflow_response = self._post( "workflows", data=workflow_request ) - self._assert_status_code_is( run_workflow_response, 200 ) - self.dataset_populator.wait_for_history( history_id, assert_ok=True ) - time.sleep(.1) # Give another little bit of time for rename (needed?) - contents = self._get( "histories/%s/contents" % history_id ).json() - # loading workflow with add_pja=True causes workflow output to be - # renamed to 'the_new_name'. - assert "the_new_name" in map( lambda hda: hda[ "name" ], contents ) - def _invocation_details( self, workflow_id, invocation_id ): invocation_details_response = self._get( "workflows/%s/usage/%s" % ( workflow_id, invocation_id ) ) self._assert_status_code_is( invocation_details_response, 200 ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/24da1a0c57bf/ Changeset: 24da1a0c57bf User: jmchilton Date: 2014-09-16 20:48:39 Summary: Remove newly redundant (and broken) test case. That case was testing rename post job actions without replacements - last week I added a more expansive one with replacements (test_run_with_pja). Affected #: 1 file diff -r 5ba632c506feccdaf7d6c334ad82347f1ea92fb8 -r 24da1a0c57bfe10c42014070ac924dc8c9f09983 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -558,21 +558,6 @@ for step in usage_details[ "steps" ]: self._assert_has_keys( step, "workflow_step_id", "order_index", "id" ) - @skip_without_tool( "cat1" ) - def test_post_job_action( self ): - """ Tests both import and execution of post job actions. - """ - workflow = self.workflow_populator.load_workflow( name="test_for_pja_run", add_pja=True ) - workflow_request, history_id = self._setup_workflow_run( workflow ) - run_workflow_response = self._post( "workflows", data=workflow_request ) - self._assert_status_code_is( run_workflow_response, 200 ) - self.dataset_populator.wait_for_history( history_id, assert_ok=True ) - time.sleep(.1) # Give another little bit of time for rename (needed?) - contents = self._get( "histories/%s/contents" % history_id ).json() - # loading workflow with add_pja=True causes workflow output to be - # renamed to 'the_new_name'. - assert "the_new_name" in map( lambda hda: hda[ "name" ], contents ) - def _invocation_details( self, workflow_id, invocation_id ): invocation_details_response = self._get( "workflows/%s/usage/%s" % ( workflow_id, invocation_id ) ) self._assert_status_code_is( invocation_details_response, 200 ) https://bitbucket.org/galaxy/galaxy-central/commits/9059dbe0db58/ Changeset: 9059dbe0db58 User: jmchilton Date: 2014-09-16 20:48:39 Summary: Update workflow API tests for inability to decode ids being a 400 instead of 404. Sort of torn on what this should actually be I guess. Affected #: 1 file diff -r 24da1a0c57bfe10c42014070ac924dc8c9f09983 -r 9059dbe0db5855a0b58669d69177eb5154b9bf9d test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -26,9 +26,9 @@ self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor ) - def test_show_invalid_is_404( self ): - show_response = self._get( "workflow/%s" % self._random_key() ) - self._assert_status_code_is( show_response, 404 ) + def test_show_invalid_key_is_400( self ): + show_response = self._get( "workflows/%s" % self._random_key() ) + self._assert_status_code_is( show_response, 400 ) def test_cannot_show_private_workflow( self ): workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) @@ -134,12 +134,12 @@ run_workflow_response = self._post( "workflows", data=workflow_request ) self._assert_status_code_is( run_workflow_response, 403 ) - def test_404_on_invalid_workflow( self ): + def test_400_on_invalid_workflow_id( self ): workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) workflow_request, history_id = self._setup_workflow_run( workflow ) workflow_request[ "workflow_id" ] = self._random_key() run_workflow_response = self._post( "workflows", data=workflow_request ) - self._assert_status_code_is( run_workflow_response, 404 ) + self._assert_status_code_is( run_workflow_response, 400 ) def test_cannot_run_against_other_users_history( self ): workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) https://bitbucket.org/galaxy/galaxy-central/commits/eb99162379e6/ Changeset: eb99162379e6 User: jmchilton Date: 2014-09-16 20:48:39 Summary: Fix library API test for format field redefinition in 9d152ed. Affected #: 1 file diff -r 9059dbe0db5855a0b58669d69177eb5154b9bf9d -r eb99162379e6c2d73025c5f8dc9c8f1880f31513 test/api/test_libraries.py --- a/test/api/test_libraries.py +++ b/test/api/test_libraries.py @@ -43,7 +43,7 @@ library_dataset = show().json() self._assert_has_keys( library_dataset, "peek", "data_type" ) assert library_dataset[ "peek" ].find("create_test") >= 0 - assert library_dataset[ "data_type" ] == "txt" + assert library_dataset[ "file_ext" ] == "txt", library_dataset[ "file_ext" ] def _create_folder( self, library ): create_data = dict( Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Client build system: add 'grunt watch' command: automatically copies files from client/galaxy/scripts/ to static/scripts when they change in client/galaxy/scripts; add some missing files and pack scripts
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5ba632c506fe/ Changeset: 5ba632c506fe User: carlfeberhard Date: 2014-09-16 19:42:40 Summary: Client build system: add 'grunt watch' command: automatically copies files from client/galaxy/scripts/ to static/scripts when they change in client/galaxy/scripts; add some missing files and pack scripts Affected #: 6 files diff -r 531bb0abb05e0bdae5026feb5cc980ab98a71527 -r 5ba632c506feccdaf7d6c334ad82347f1ea92fb8 client/GruntFile.js --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -2,8 +2,10 @@ // Project configuration. grunt.initConfig({ - pkg: grunt.file.readJSON('package.json'), + pkg: grunt.file.readJSON( 'package.json' ), + // default task + // use 'grunt copy' to copy the entire <galaxy>/client/galaxy/scripts dir into <galaxy>/static/scripts copy: { main: { expand: true, @@ -11,11 +13,18 @@ src: '**', dest: '../static/scripts/' } + }, + + // use 'grunt watch' (from a new tab in your terminal) to have grunt re-copy changed files automatically + watch: { + // watch for changes in the src dir + files: [ 'galaxy/scripts/**' ], + tasks: [ 'default' ] } - }); - grunt.loadNpmTasks('grunt-contrib-copy'); + grunt.loadNpmTasks( 'grunt-contrib-watch' ); + grunt.loadNpmTasks( 'grunt-contrib-copy'); - grunt.registerTask('default', ['copy']); + grunt.registerTask( 'default', [ 'copy' ] ); }; diff -r 531bb0abb05e0bdae5026feb5cc980ab98a71527 -r 5ba632c506feccdaf7d6c334ad82347f1ea92fb8 client/package.json --- a/client/package.json +++ b/client/package.json @@ -6,6 +6,8 @@ "galaxy" ], "devDependencies": { - "grunt-contrib-copy": "^0.5.0" + "grunt": "^0.4.5", + "grunt-contrib-copy": "^0.5.0", + "grunt-contrib-watch": "^0.6.1" } } diff -r 531bb0abb05e0bdae5026feb5cc980ab98a71527 -r 5ba632c506feccdaf7d6c334ad82347f1ea92fb8 static/scripts/mvc/ui/ui-checkbox.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-checkbox.js @@ -0,0 +1,91 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +var View = Backbone.View.extend({ + // options + optionsDefault: { + value : '', + visible : true, + cls : '', + data : [], + id : Utils.uuid() + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // hide input field + if (!this.options.visible) { + this.$el.hide(); + } + + // set initial value + if (this.options.value) { + this.value(this.options.value); + } + + // current value + this.current = this.options.value; + + // onchange event handler. fires on user activity. + var self = this; + this.$el.find('input').on('change', function() { + self.value(self._getValue()); + }); + }, + + // value + value : function (new_val) { + // get current value + var before = this.current; + + // set new value + if (new_val !== undefined) { + this.$el.find('label').removeClass('active'); + this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); + this.current = new_val; + } + + // check value + var after = this.current; + if (after != before && this.options.onchange) { + this.options.onchange(this.current); + } + + // get and return value + return this.current; + }, + + // get value + _getValue: function() { + var selected = this.$el.find(':checked'); + var value = null; + if (selected.length > 0) { + value = selected.val(); + } + return value; + }, + + // element + _template: function(options) { + var tmpl = '<div class="ui-checkbox">'; + for (key in options.data) { + var pair = options.data[key]; + tmpl += '<input type="checkbox" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + '<br>'; + } + tmpl += '</div>'; + return tmpl; + } +}); + +return { + View : View +}; + +}); diff -r 531bb0abb05e0bdae5026feb5cc980ab98a71527 -r 5ba632c506feccdaf7d6c334ad82347f1ea92fb8 static/scripts/mvc/ui/ui-radiobutton.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-radiobutton.js @@ -0,0 +1,93 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +var View = Backbone.View.extend({ + // options + optionsDefault: { + value : '', + visible : true, + cls : '', + data : [], + id : Utils.uuid() + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // hide input field + if (!this.options.visible) { + this.$el.hide(); + } + + // set initial value + if (this.options.value) { + this.value(this.options.value); + } + + // current value + this.current = this.options.value; + + // onchange event handler. fires on user activity. + var self = this; + this.$el.find('input').on('change', function() { + self.value(self._getValue()); + }); + }, + + // value + value : function (new_val) { + // get current value + var before = this.current; + + // set new value + if (new_val !== undefined) { + this.$el.find('label').removeClass('active'); + this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); + this.current = new_val; + } + + // check value + var after = this.current; + if (after != before && this.options.onchange) { + this.options.onchange(this.current); + } + + // get and return value + return this.current; + }, + + // get value + _getValue: function() { + var selected = this.$el.find(':checked'); + var value = null; + if (selected.length > 0) { + value = selected.val(); + } + return value; + }, + + // element + _template: function(options) { + var tmpl = '<div class="btn-group ui-radiobutton" data-toggle="buttons">'; + for (key in options.data) { + var pair = options.data[key]; + tmpl += '<label class="btn btn-default">' + + '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + + '</label>'; + } + tmpl += '</div>'; + return tmpl; + } +}); + +return { + View : View +}; + +}); diff -r 531bb0abb05e0bdae5026feb5cc980ab98a71527 -r 5ba632c506feccdaf7d6c334ad82347f1ea92fb8 static/scripts/packed/mvc/ui/ui-checkbox.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-checkbox.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="ui-checkbox">';for(key in d.data){var e=d.data[key];c+='<input type="checkbox" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"<br>"}c+="</div>";return c}});return{View:b}}); \ No newline at end of file diff -r 531bb0abb05e0bdae5026feb5cc980ab98a71527 -r 5ba632c506feccdaf7d6c334ad82347f1ea92fb8 static/scripts/packed/mvc/ui/ui-radiobutton.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-radiobutton.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in d.data){var e=d.data[key];c+='<label class="btn btn-default"><input type="radio" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"</label>"}c+="</div>";return c}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Configure dependency resolvers via config/dependencies_resolvers_conf.xml if available.
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/531bb0abb05e/ Changeset: 531bb0abb05e User: jmchilton Date: 2014-09-16 19:20:46 Summary: Configure dependency resolvers via config/dependencies_resolvers_conf.xml if available. Has no sample file but bring the configuration file more inline with others. Affected #: 1 file diff -r 80d68ea889c01357b520ecefc56f86b0a44549fc -r 531bb0abb05e0bdae5026feb5cc980ab98a71527 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -137,7 +137,6 @@ self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ] self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) - self.dependency_resolvers_config_file = resolve_path( kwargs.get( 'dependency_resolvers_config_file', 'dependency_resolvers_conf.xml' ), self.root ) self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) ) self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) ) self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") ) @@ -384,6 +383,7 @@ external_service_type_config_file = [ 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample', 'config/external_service_types_conf.xml.sample' ], job_config_file = [ 'job_conf.xml', 'config/job_conf.xml' ], job_metrics_config_file = [ 'job_metrics_conf.xml', 'config/job_metrics_conf.xml' ], + dependency_resolvers_config_file = [ 'dependency_resolvers_conf.xml', 'config/dependency_resolvers_conf.xml' ], job_resource_params_file = [ 'job_resource_params_conf.xml', 'config/job_resource_params_conf.xml' ], migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], object_store_config_file = [ 'object_store_conf.xml', 'config/object_store_conf.xml' ], Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] 06971b: Swapped out several old slides for new one on land...
by GitHub 16 Sep '14

16 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 06971bcb3d2cb7e58a32543320f7ca4e3cccef8b https://github.com/galaxyproject/usegalaxy-playbook/commit/06971bcb3d2cb7e5… Author: Dave Clements <clements(a)Dave-Clementss-MacBook-Pro.local> Date: 2014-09-15 (Mon, 15 Sep 2014) Changed paths: A files/galaxy/common/static/welcome_img/60PlusOdometer1.png A files/galaxy/common/static/welcome_img/EuropeFall2014_2.png A files/galaxy/common/static/welcome_img/G3_2014_v2.png A files/galaxy/common/static/welcome_img/GCUKisLive.png A files/galaxy/common/static/welcome_img/GalaxyBiostarHelp.png Log Message: ----------- Swapped out several old slides for new one on landing page

1 0

commit/galaxy-central: jmchilton: Fix testing helper bug I introduced with recent workflow testing work.
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/80d68ea889c0/ Changeset: 80d68ea889c0 User: jmchilton Date: 2014-09-16 17:14:27 Summary: Fix testing helper bug I introduced with recent workflow testing work. Affected #: 1 file diff -r 24452bb4c6aa1a77a5d9d55fd76c2c43d47dcb9e -r 80d68ea889c01357b520ecefc56f86b0a44549fc test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -142,9 +142,14 @@ elif "dataset" in kwds: dataset_id = kwds[ "dataset" ][ "id" ] else: - hid = kwds.get( "hid", -1 ) # If not hid, just grab last dataset + hid = kwds.get( "hid", None ) # If not hid, just grab last dataset + if hid: + index = hid - 1 + else: + # No hid specified - just grab most recent element. + index = -1 dataset_contents = self.__get_contents_request( history_id ).json() - dataset_id = dataset_contents[ hid - 1 ][ "id" ] + dataset_id = dataset_contents[ index ][ "id" ] return dataset_id def __get_contents_request( self, history_id, suffix=""): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Fix unit tests I broke.
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/24452bb4c6aa/ Changeset: 24452bb4c6aa User: natefoo Date: 2014-09-16 16:13:08 Summary: Fix unit tests I broke. Affected #: 3 files diff -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 -r 24452bb4c6aa1a77a5d9d55fd76c2c43d47dcb9e buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -107,7 +107,7 @@ done echo "Copying job_conf.xml.sample_basic to job_conf.xml" -cp job_conf.xml.sample_basic job_conf.xml +cp config/job_conf.xml.sample_basic config/job_conf.xml for dir in $DIRS; do if [ ! -d $dir ]; then diff -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 -r 24452bb4c6aa1a77a5d9d55fd76c2c43d47dcb9e lib/galaxy/model/orm/scripts.py --- a/lib/galaxy/model/orm/scripts.py +++ b/lib/galaxy/model/orm/scripts.py @@ -18,7 +18,7 @@ log = logging.getLogger( __name__ ) -DEFAULT_CONFIG_FILE = 'config/galaxy.ini' +DEFAULT_CONFIG_FILE = 'galaxy.ini' DEFAULT_CONFIG_PREFIX = '' DEFAULT_DATABASE = 'galaxy' diff -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 -r 24452bb4c6aa1a77a5d9d55fd76c2c43d47dcb9e test/unit/jobs/test_job_configuration.py --- a/test/unit/jobs/test_job_configuration.py +++ b/test/unit/jobs/test_job_configuration.py @@ -9,8 +9,8 @@ # File would be slightly more readable if contents were embedded directly, but # there are advantages to testing the documentation/examples. -SIMPLE_JOB_CONF = os.path.join( os.path.dirname( __file__ ), "..", "..", "..", "job_conf.xml.sample_basic" ) -ADVANCED_JOB_CONF = os.path.join( os.path.dirname( __file__ ), "..", "..", "..", "job_conf.xml.sample_advanced" ) +SIMPLE_JOB_CONF = os.path.join( os.path.dirname( __file__ ), "..", "..", "..", "config", "job_conf.xml.sample_basic" ) +ADVANCED_JOB_CONF = os.path.join( os.path.dirname( __file__ ), "..", "..", "..", "config", "job_conf.xml.sample_advanced" ) class JobConfXmlParserTestCase( unittest.TestCase ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f535ef20718d/ Changeset: f535ef20718d User: carlfeberhard Date: 2014-09-12 18:23:19 Summary: Client build system: (1st step) duplicate static/scripts at client/scripts (w/o packed), add npm package.json file w/ grunt-contrib-copy dependency, add GruntFile.js w/ single task: copy client/scripts to static/scripts Affected #: 164 files diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f535ef20718d82ab374408d492afa917324a22c5 client/GruntFile.js --- /dev/null +++ b/client/GruntFile.js @@ -0,0 +1,21 @@ +module.exports = function(grunt) { + + // Project configuration. + grunt.initConfig({ + pkg: grunt.file.readJSON('package.json'), + + copy: { + main: { + expand: true, + cwd: 'scripts/', + src: '**', + dest: '../static/scripts/' + } + } + + }); + + grunt.loadNpmTasks('grunt-contrib-copy'); + + grunt.registerTask('default', ['copy']); +}; diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f535ef20718d82ab374408d492afa917324a22c5 client/package.json --- /dev/null +++ b/client/package.json @@ -0,0 +1,11 @@ +{ + "name": "galaxy-client", + "version": "0.1.0", + "description": "Galaxy client application build system", + "keywords": [ + "galaxy" + ], + "devDependencies": { + "grunt-contrib-copy": "^0.5.0" + } +} diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f535ef20718d82ab374408d492afa917324a22c5 client/scripts/base.js --- /dev/null +++ b/client/scripts/base.js @@ -0,0 +1,15 @@ +define( ["libs/backbone/backbone"], function( Backbone ) { + + var Base = function() { + if( this.initialize ) { + this.initialize.apply(this, arguments); + } + }; + Base.extend = Backbone.Model.extend; + + return { + Base: Base, + Backbone: Backbone + }; + +}); \ No newline at end of file diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f535ef20718d82ab374408d492afa917324a22c5 client/scripts/galaxy-app-base.js --- /dev/null +++ b/client/scripts/galaxy-app-base.js @@ -0,0 +1,160 @@ +define([ + 'mvc/user/user-model', + 'utils/metrics-logger', + 'utils/add-logging', + 'utils/localization', + 'bootstrapped-data' +], function( userModel, metricsLogger, addLogging, localize, bootstrapped ){ +// ============================================================================ +/** Base galaxy client-side application. + * Iniitializes: + * logger : the logger/metrics-logger + * localize : the string localizer + * config : the current configuration (any k/v in + * universe_wsgi.ini available from the configuration API) + * user : the current user (as a mvc/user/user-model) + */ +function GalaxyApp( options ){ + var self = this; + return self._init( options || {} ); +} + +// add logging shortcuts for this object +addLogging( GalaxyApp, 'GalaxyApp' ); + +/** default options */ +GalaxyApp.prototype.defaultOptions = { + /** monkey patch attributes from existing window.Galaxy object? */ + patchExisting : true, + /** root url of this app */ + // move to self.root? + root : '/' +}; + +/** initalize options and sub-components */ +GalaxyApp.prototype._init = function init( options ){ + var self = this; + _.extend( self, Backbone.Events ); + + self._processOptions( options ); + self.debug( 'GalaxyApp.options: ', self.options ); + + self._patchGalaxy( window.Galaxy ); + + self._initLogger( options.loggerOptions || {} ); + self.debug( 'GalaxyApp.logger: ', self.logger ); + + self._initLocale(); + self.debug( 'GalaxyApp.localize: ', self.localize ); + + self.config = options.config || bootstrapped.config || {}; + self.debug( 'GalaxyApp.config: ', self.config ); + + self._initUser( options.user || bootstrapped.user || {} ); + self.debug( 'GalaxyApp.user: ', self.user ); + + //TODO: temp + self.trigger( 'ready', self ); + //if( typeof options.onload === 'function' ){ + // options.onload(); + //} + + self._setUpListeners(); + + return self; +}; + +/** add an option from options if the key matches an option in defaultOptions */ +GalaxyApp.prototype._processOptions = function _processOptions( options ){ + var self = this, + defaults = self.defaultOptions; + self.debug( '_processOptions: ', options ); + + self.options = {}; + for( var k in defaults ){ + if( defaults.hasOwnProperty( k ) ){ + self.options[ k ] = ( options.hasOwnProperty( k ) )?( options[ k ] ):( defaults[ k ] ); + } + } + return self; +}; + +/** add an option from options if the key matches an option in defaultOptions */ +GalaxyApp.prototype._patchGalaxy = function _processOptions( patchWith ){ + var self = this; + // in case req or plain script tag order has created a prev. version of the Galaxy obj... + if( self.options.patchExisting && patchWith ){ + self.debug( 'found existing Galaxy object:', patchWith ); + // ...(for now) monkey patch any added attributes that the previous Galaxy may have had + //TODO: move those attributes to more formal assignment in GalaxyApp + for( var k in patchWith ){ + if( patchWith.hasOwnProperty( k ) ){ + self.debug( '\t patching in ' + k + ' to Galaxy' ); + self[ k ] = patchWith[ k ]; + } + } + } +}; + +/** set up the metrics logger (utils/metrics-logger) and pass loggerOptions */ +GalaxyApp.prototype._initLogger = function _initLogger( loggerOptions ){ + var self = this; + self.debug( '_initLogger:', loggerOptions ); + self.logger = new metricsLogger.MetricsLogger( loggerOptions ); + return self; +}; + +/** add the localize fn to this object and the window namespace (as '_l') */ +GalaxyApp.prototype._initLocale = function _initLocale( options ){ + var self = this; + self.debug( '_initLocale:', options ); + self.localize = localize; + // add to window as global shortened alias + window._l = self.localize; + return self; +}; + +/** set up the current user as a Backbone model (mvc/user/user-model) */ +GalaxyApp.prototype._initUser = function _initUser( userJSON ){ + var self = this; + self.debug( '_initUser:', userJSON ); + self.user = new userModel.User( userJSON ); + //TODO: temp - old alias + self.currUser = self.user; + return self; +}; + +/** Set up DOM/jQuery/Backbone event listeners enabled for all pages */ +GalaxyApp.prototype._setUpListeners = function _setUpListeners(){ + var self = this; + + // hook to jq beforeSend to record the most recent ajax call and cache some data about it + /** cached info about the last ajax call made through jQuery */ + self.lastAjax = {}; + $( document ).bind( 'ajaxSend', function( ev, xhr, options ){ + var data = options.data; + try { + data = JSON.parse( data ); + } catch( err ){} + + self.lastAjax = { + url : location.href.slice( 0, -1 ) + options.url, + data : data + }; + //TODO:?? we might somehow manage to *retry* ajax using either this hook or Backbone.sync + }); + +}; + +/** string rep */ +GalaxyApp.prototype.toString = function toString(){ + var userEmail = this.user.get( 'email' ) || '(anonymous)'; + return 'GalaxyApp(' + userEmail + ')'; +}; + + +// ============================================================================ + return { + GalaxyApp : GalaxyApp + }; +}); diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f535ef20718d82ab374408d492afa917324a22c5 client/scripts/galaxy.autocom_tagging.js --- /dev/null +++ b/client/scripts/galaxy.autocom_tagging.js @@ -0,0 +1,368 @@ +/** +* JQuery extension for tagging with autocomplete. +* @author: Jeremy Goecks +* @require: jquery.autocomplete plugin +*/ +// +// Initialize "tag click functions" for tags. +// +function init_tag_click_function(tag_elt, click_func) { + $(tag_elt).find('.tag-name').each( function() { + $(this).click( function() { + var tag_str = $(this).text(); + var tag_name_and_value = tag_str.split(":"); + click_func(tag_name_and_value[0], tag_name_and_value[1]); + return true; + }); + }); +} + +jQuery.fn.autocomplete_tagging = function(options) { + + var defaults = { + get_toggle_link_text_fn: function(tags) { + var text = ""; + var num_tags = obj_length(tags); + if (num_tags > 0) { + text = num_tags + (num_tags > 1 ? " Tags" : " Tag"); + } else { + text = "Add tags"; + } + return text; + }, + tag_click_fn : function (name, value) {}, + editable: true, + input_size: 20, + in_form: false, + tags : {}, + use_toggle_link: true, + item_id: "", + add_tag_img: "", + add_tag_img_rollover: "", + delete_tag_img: "", + ajax_autocomplete_tag_url: "", + ajax_retag_url: "", + ajax_delete_tag_url: "", + ajax_add_tag_url: "" + }; + + var settings = jQuery.extend(defaults, options); + + // + // Initalize object's elements. + // + + // Get elements for this object. For this_obj, assume the last element with the id is the "this"; this is somewhat of a hack to address the problem + // that there may be two tagging elements for a single item if there are both community and individual tags for an element. + var this_obj = $(this); + var tag_area = this_obj.find('.tag-area'); + var toggle_link = this_obj.find('.toggle-link'); + var tag_input_field = this_obj.find('.tag-input'); + var add_tag_button = this_obj.find('.add-tag-button'); + + // Initialize toggle link. + toggle_link.click( function() { + // Take special actions depending on whether toggle is showing or hiding link. + var after_toggle_fn; + if (tag_area.is(":hidden")) { + after_toggle_fn = function() { + // If there are no tags, go right to editing mode by generating a click on the area. + var num_tags = $(this).find('.tag-button').length; + if (num_tags === 0) { + tag_area.click(); + } + }; + } else { + after_toggle_fn = function() { + tag_area.blur(); + }; + } + tag_area.slideToggle("fast", after_toggle_fn); + return $(this); + }); + + // Initialize tag input field. + if (settings.editable) { + tag_input_field.hide(); + } + tag_input_field.keyup( function(e) { + if ( e.keyCode === 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( + ( e.keyCode === 13 ) || // Return Key + ( e.keyCode === 188 ) || // Comma + ( e.keyCode === 32 ) // Space + ) { + // + // Check input. + // + + var new_value = this.value; + + // Suppress space after a ":" + if ( new_value.indexOf(": ", new_value.length - 2) !== -1) { + this.value = new_value.substring(0, new_value.length-1); + return false; + } + + // Remove trigger keys from input. + if ( (e.keyCode === 188) || (e.keyCode === 32) ) { + new_value = new_value.substring( 0 , new_value.length - 1 ); + } + + // Trim whitespace. + new_value = $.trim(new_value); + + // Too short? + if (new_value.length < 2) { + return false; + } + + // + // New tag OK - apply it. + // + + this.value = ""; // Reset text field now that tag is being added + + // Add button for tag after all other tag buttons. + var new_tag_button = build_tag_button(new_value); + var tag_buttons = tag_area.children(".tag-button"); + if (tag_buttons.length !== 0) { + var last_tag_button = tag_buttons.slice(tag_buttons.length-1); + last_tag_button.after(new_tag_button); + } else { + tag_area.prepend(new_tag_button); + } + + // Add tag to internal list. + var tag_name_and_value = new_value.split(":"); + settings.tags[tag_name_and_value[0]] = tag_name_and_value[1]; + + // Update toggle link text. + var new_text = settings.get_toggle_link_text_fn(settings.tags); + toggle_link.text(new_text); + + // Commit tag to server. + var zz = $(this); + $.ajax({ + url: settings.ajax_add_tag_url, + data: { new_tag: new_value }, + error: function() { + // Failed. Roll back changes and show alert. + new_tag_button.remove(); + delete settings.tags[tag_name_and_value[0]]; + var new_text = settings.get_toggle_link_text_fn(settings.tags); + toggle_link.text(new_text); + alert( "Add tag failed" ); + }, + success: function() { + // Flush autocomplete cache because it's not out of date. + // TODO: in the future, we could remove the particular item + // that was chosen from the cache rather than flush it. + zz.data('autocompleter').cacheFlush(); + } + }); + + return false; + } + }); + + // Add autocomplete to input. + var format_item_func = function(key, row_position, num_rows, value, search_term) { + var tag_name_and_value = value.split(":"); + return (tag_name_and_value.length === 1 ? tag_name_and_value[0] : tag_name_and_value[1]); + }; + var autocomplete_options = { selectFirst: false, formatItem: format_item_func, + autoFill: false, highlight: false }; + tag_input_field.autocomplete(settings.ajax_autocomplete_tag_url, autocomplete_options); + + + // Initialize delete tag images for current tags. + this_obj.find('.delete-tag-img').each(function() { + init_delete_tag_image( $(this) ); + }); + + + // Initialize tag click function. + init_tag_click_function($(this), settings.tag_click_fn); + + // Initialize "add tag" button. + add_tag_button.click( function() { + $(this).hide(); + + // Clicking on button is the same as clicking on the tag area. + tag_area.click(); + return false; + }); + + // + // Set up tag area interactions; these are needed only if tags are editable. + // + if (settings.editable) { + // When the tag area blurs, go to "view tag" mode. + tag_area.bind("blur", function(e) { + if (obj_length(settings.tags) > 0) { + add_tag_button.show(); + tag_input_field.hide(); + tag_area.removeClass("active-tag-area"); + // tag_area.addClass("tooltip"); + } else { + // No tags, so do nothing to ensure that input is still visible. + } + }); + + // On click, enable user to add tags. + tag_area.click( function(e) { + var is_active = $(this).hasClass("active-tag-area"); + + // If a "delete image" object was pressed and area is inactive, do nothing. + if ($(e.target).hasClass("delete-tag-img") && !is_active) { + return false; + } + + // If a "tag name" object was pressed and area is inactive, do nothing. + if ($(e.target).hasClass("tag-name") && !is_active) { + return false; + } + + // Remove tooltip. + // $(this).removeClass("tooltip"); + + // Hide add tag button, show tag_input field. Change background to show + // area is active. + $(this).addClass("active-tag-area"); + add_tag_button.hide(); + tag_input_field.show(); + tag_input_field.focus(); + + // Add handler to document that will call blur when the tag area is blurred; + // a tag area is blurred when a user clicks on an element outside the area. + var handle_document_click = function(e) { + var check_click = function(tag_area, target) { + var tag_area_id = tag_area.attr("id"); + // Blur the tag area if the element clicked on is not in the tag area. + if (target !== tag_area) { + tag_area.blur(); + $(window).unbind("click.tagging_blur"); + $(this).addClass("tooltip"); + } + }; + check_click(tag_area, $(e.target)); + }; + // TODO: we should attach the click handler to all frames in order to capture + // clicks outside the frame that this element is in. + //window.parent.document.onclick = handle_document_click; + //var temp = $(window.parent.document.body).contents().find("iframe").html(); + //alert(temp); + //$(document).parent().click(handle_document_click); + $(window).bind("click.tagging_blur", handle_document_click); + + return false; + }); + } + + // If using toggle link, hide the tag area. Otherwise, show the tag area. + if (settings.use_toggle_link) { + tag_area.hide(); + } + + // + // Helper functions. + // + + // + // Collapse tag name + value into a single string. + // + function build_tag_str(tag_name, tag_value) { + return tag_name + ( tag_value ? ":" + tag_value : ""); + } + + + // Initialize a "delete tag image": when click, delete tag from UI and send delete request to server. + function init_delete_tag_image(delete_img) { + $(delete_img).mouseenter( function () { + $(this).attr("src", settings.delete_tag_img_rollover); + }); + $(delete_img).mouseleave( function () { + $(this).attr("src", settings.delete_tag_img); + }); + $(delete_img).click( function () { + // Tag button is image's parent. + var tag_button = $(this).parent(); + + // Get tag name, value. + var tag_name_elt = tag_button.find(".tag-name").eq(0); + var tag_str = tag_name_elt.text(); + var tag_name_and_value = tag_str.split(":"); + var tag_name = tag_name_and_value[0]; + var tag_value = tag_name_and_value[1]; + + var prev_button = tag_button.prev(); + tag_button.remove(); + + // Remove tag from local list for consistency. + delete settings.tags[tag_name]; + + // Update toggle link text. + var new_text = settings.get_toggle_link_text_fn(settings.tags); + toggle_link.text(new_text); + + // Delete tag. + $.ajax({ + url: settings.ajax_delete_tag_url, + data: { tag_name: tag_name }, + error: function() { + // Failed. Roll back changes and show alert. + settings.tags[tag_name] = tag_value; + if (prev_button.hasClass("tag-button")) { + prev_button.after(tag_button); + } else { + tag_area.prepend(tag_button); + } + alert( "Remove tag failed" ); + + toggle_link.text(settings.get_toggle_link_text_fn(settings.tags)); + + // TODO: no idea why it's necessary to set this up again. + delete_img.mouseenter( function () { + $(this).attr("src", settings.delete_tag_img_rollover); + }); + delete_img.mouseleave( function () { + $(this).attr("src", settings.delete_tag_img); + }); + }, + success: function() {} + }); + + return true; + }); + } + + // + // Function that builds a tag button. + // + function build_tag_button(tag_str) { + // Build "delete tag" image. + var delete_img = $("<img/>").attr("src", settings.delete_tag_img).addClass("delete-tag-img"); + init_delete_tag_image(delete_img); + + // Build tag button. + var tag_name_elt = $("<span>").text(tag_str).addClass("tag-name"); + tag_name_elt.click( function() { + var tag_name_and_value = tag_str.split(":"); + settings.tag_click_fn(tag_name_and_value[0], tag_name_and_value[1]); + return true; + }); + + var tag_button = $("<span></span>").addClass("tag-button"); + tag_button.append(tag_name_elt); + // Allow delete only if element is editable. + if (settings.editable) { + tag_button.append(delete_img); + } + + return tag_button; + } + +}; diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f535ef20718d82ab374408d492afa917324a22c5 client/scripts/galaxy.base.js --- /dev/null +++ b/client/scripts/galaxy.base.js @@ -0,0 +1,636 @@ +// requestAnimationFrame polyfill +(function() { + var lastTime = 0; + var vendors = ['ms', 'moz', 'webkit', 'o']; + for(var x = 0; x < vendors.length && !window.requestAnimationFrame; ++x) { + window.requestAnimationFrame = window[vendors[x]+'RequestAnimationFrame']; + window.cancelRequestAnimationFrame = window[vendors[x]+ + 'CancelRequestAnimationFrame']; + } + + if (!window.requestAnimationFrame) + window.requestAnimationFrame = function(callback, element) { + var currTime = new Date().getTime(); + var timeToCall = Math.max(0, 16 - (currTime - lastTime)); + var id = window.setTimeout(function() { callback(currTime + timeToCall); }, + timeToCall); + lastTime = currTime + timeToCall; + return id; + }; + + if (!window.cancelAnimationFrame) + window.cancelAnimationFrame = function(id) { + clearTimeout(id); + }; +}()); + +// IE doesn't implement Array.indexOf +if (!Array.indexOf) { + Array.prototype.indexOf = function(obj) { + for (var i = 0, len = this.length; i < len; i++) { + if (this[i] == obj) { + return i; + } + } + return -1; + }; +} + +// Returns the number of keys (elements) in an array/dictionary. +function obj_length(obj) { + if (obj.length !== undefined) { + return obj.length; + } + + var count = 0; + for (var element in obj) { + count++; + } + return count; +} + +$.fn.makeAbsolute = function(rebase) { + return this.each(function() { + var el = $(this); + var pos = el.position(); + el.css({ + position: "absolute", + marginLeft: 0, marginTop: 0, + top: pos.top, left: pos.left, + right: $(window).width() - ( pos.left + el.width() ) + }); + if (rebase) { + el.remove().appendTo("body"); + } + }); +}; + +/** + * Sets up popupmenu rendering and binds options functions to the appropriate links. + * initial_options is a dict with text describing the option pointing to either (a) a + * function to perform; or (b) another dict with two required keys, 'url' and 'action' (the + * function to perform. (b) is useful for exposing the underlying URL of the option. + */ +function make_popupmenu(button_element, initial_options) { + /* Use the $.data feature to store options with the link element. + This allows options to be changed at a later time + */ + var element_menu_exists = (button_element.data("menu_options")); + button_element.data("menu_options", initial_options); + + // If element already has menu, nothing else to do since HTML and actions are already set. + if (element_menu_exists) { return; } + + button_element.bind("click.show_popup", function(e) { + // Close existing visible menus + $(".popmenu-wrapper").remove(); + + // Need setTimeouts so clicks don't interfere with each other + setTimeout( function() { + // Dynamically generate the wrapper holding all the selectable options of the menu. + var menu_element = $( "<ul class='dropdown-menu' id='" + button_element.attr('id') + "-menu'></ul>" ); + var options = button_element.data("menu_options"); + if (obj_length(options) <= 0) { + $("<li>No Options.</li>").appendTo(menu_element); + } + $.each( options, function( k, v ) { + if (v) { + // Action can be either an anonymous function and a mapped dict. + var action = v.action || v; + menu_element.append( $("<li></li>").append( $("<a>").attr("href", v.url).html(k).click(action) ) ); + } else { + menu_element.append( $("<li></li>").addClass( "head" ).append( $("<a href='#'></a>").html(k) ) ); + } + }); + var wrapper = $( "<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>" ) + .append( menu_element ).appendTo( "body" ); + + var x = e.pageX - wrapper.width() / 2 ; + x = Math.min( x, $(document).scrollLeft() + $(window).width() - $(wrapper).width() - 5 ); + x = Math.max( x, $(document).scrollLeft() + 5 ); + + wrapper.css({ + top: e.pageY, + left: x + }); + }, 10); + + setTimeout( function() { + // Bind click event to current window and all frames to remove any visible menus + // Bind to document object instead of window object for IE compat + var close_popup = function(el) { + $(el).bind("click.close_popup", function() { + $(".popmenu-wrapper").remove(); + el.unbind("click.close_popup"); + }); + }; + close_popup( $(window.document) ); // Current frame + close_popup( $(window.top.document) ); // Parent frame + for (var frame_id = window.top.frames.length; frame_id--;) { // Sibling frames + var frame = $(window.top.frames[frame_id].document); + close_popup(frame); + } + }, 50); + + return false; + }); + +} + +/** + * Convert two seperate (often adjacent) divs into galaxy popupmenu + * - div 1 contains a number of anchors which become the menu options + * - div 1 should have a 'popupmenu' attribute + * - this popupmenu attribute contains the id of div 2 + * - div 2 becomes the 'face' of the popupmenu + * + * NOTE: make_popup_menus finds and operates on all divs with a popupmenu attr (no need to point it at something) + * but (since that selector searches the dom on the page), you can send a parent in + * NOTE: make_popup_menus, and make_popupmenu are horrible names + */ +function make_popup_menus( parent ) { + // find all popupmenu menu divs (divs that contains anchors to be converted to menu options) + // either in the parent or the document if no parent passed + parent = parent || document; + $( parent ).find( "div[popupmenu]" ).each( function() { + var options = {}; + var menu = $(this); + + // find each anchor in the menu, convert them into an options map: { a.text : click_function } + menu.find( "a" ).each( function() { + var link = $(this), + link_dom = link.get(0), + confirmtext = link_dom.getAttribute( "confirm" ), + href = link_dom.getAttribute( "href" ), + target = link_dom.getAttribute( "target" ); + + // no href - no function (gen. a label) + if (!href) { + options[ link.text() ] = null; + + } else { + options[ link.text() ] = { + url: href, + action: function() { + + // if theres confirm text, send the dialog + if ( !confirmtext || confirm( confirmtext ) ) { + // link.click() doesn't use target for some reason, + // so manually do it here. + if (target) { + window.open(href, target); + return false; + } + // For all other links, do the default action. + else { + link.click(); + } + } + } + }; + } + }); + // locate the element with the id corresponding to the menu's popupmenu attr + var box = $( parent ).find( "#" + menu.attr( 'popupmenu' ) ); + + // For menus with clickable link text, make clicking on the link go through instead + // of activating the popup menu + box.find("a").bind("click", function(e) { + e.stopPropagation(); // Stop bubbling so clicking on the link goes through + return true; + }); + + // attach the click events and menu box building to the box element + make_popupmenu(box, options); + box.addClass("popup"); + menu.remove(); + }); +} + +// Alphanumeric/natural sort fn +function naturalSort(a, b) { + // setup temp-scope variables for comparison evauluation + var re = /(-?[0-9\.]+)/g, + x = a.toString().toLowerCase() || '', + y = b.toString().toLowerCase() || '', + nC = String.fromCharCode(0), + xN = x.replace( re, nC + '$1' + nC ).split(nC), + yN = y.replace( re, nC + '$1' + nC ).split(nC), + xD = (new Date(x)).getTime(), + yD = xD ? (new Date(y)).getTime() : null; + // natural sorting of dates + if ( yD ) { + if ( xD < yD ) { return -1; } + else if ( xD > yD ) { return 1; } + } + // natural sorting through split numeric strings and default strings + var oFxNcL, oFyNcL; + for ( var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++ ) { + oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc]; + oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc]; + if (oFxNcL < oFyNcL) { return -1; } + else if (oFxNcL > oFyNcL) { return 1; } + } + return 0; +} + +$.fn.refresh_select2 = function() { + var select_elt = $(this); + var options = { width: "resolve", + closeOnSelect: !select_elt.is("[MULTIPLE]") + }; + return select_elt.select2( options ); +} + +// Replace select box with a text input box + autocomplete. +function replace_big_select_inputs(min_length, max_length, select_elts) { + // To do replace, the select2 plugin must be loaded. + + if (!jQuery.fn.select2) { + return; + } + + // Set default for min_length and max_length + if (min_length === undefined) { + min_length = 20; + } + if (max_length === undefined) { + max_length = 3000; + } + + select_elts = select_elts || $('select'); + + select_elts.each( function() { + var select_elt = $(this).not('[multiple]'); + // Make sure that options is within range. + var num_options = select_elt.find('option').length; + if ( (num_options < min_length) || (num_options > max_length) ) { + return; + } + + if (select_elt.hasClass("no-autocomplete")) { + return; + } + + /* Replaced jQuery.autocomplete with select2, notes: + * - multiple selects are supported + * - the original element is updated with the value, convert_to_values should not be needed + * - events are fired when updating the original element, so refresh_on_change should just work + * + * - should we still sort dbkey fields here? + */ + select_elt.refresh_select2(); + }); +} + +/** + * Make an element with text editable: (a) when user clicks on text, a textbox/area + * is provided for editing; (b) when enter key pressed, element's text is set and on_finish + * is called. + */ +// TODO: use this function to implement async_save_text (implemented below). +$.fn.make_text_editable = function(config_dict) { + // Get config options. + var num_cols = ("num_cols" in config_dict ? config_dict.num_cols : 30), + num_rows = ("num_rows" in config_dict ? config_dict.num_rows : 4), + use_textarea = ("use_textarea" in config_dict ? config_dict.use_textarea : false), + on_finish = ("on_finish" in config_dict ? config_dict.on_finish : null), + help_text = ("help_text" in config_dict ? config_dict.help_text : null); + + // Add element behavior. + var container = $(this); + container.addClass("editable-text").click(function(e) { + // If there's already an input element, editing is active, so do nothing. + if ($(this).children(":input").length > 0) { + return; + } + + container.removeClass("editable-text"); + + // Handler for setting element text. + var set_text = function(new_text) { + container.find(":input").remove(); + + if (new_text !== "") { + container.text(new_text); + } + else { + // No text; need a line so that there is a click target. + container.html("<br>"); + } + container.addClass("editable-text"); + + if (on_finish) { + on_finish(new_text); + } + }; + + // Create input element(s) for editing. + var cur_text = ("cur_text" in config_dict ? config_dict.cur_text : container.text() ), + input_elt, button_elt; + + if (use_textarea) { + input_elt = $("<textarea/>") + .attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text)) + .keyup(function(e) { + if (e.keyCode === 27) { + // Escape key. + set_text(cur_text); + } + }); + button_elt = $("<button/>").text("Done").click(function() { + set_text(input_elt.val()); + // Return false so that click does not propogate to container. + return false; + }); + } + else { + input_elt = $("<input type='text'/>").attr({ value: $.trim(cur_text), size: num_cols }) + .blur(function() { + set_text(cur_text); + }).keyup(function(e) { + if (e.keyCode === 27) { + // Escape key. + $(this).trigger("blur"); + } else if (e.keyCode === 13) { + // Enter key. + set_text($(this).val()); + } + + // Do not propogate event to avoid unwanted side effects. + e.stopPropagation(); + }); + } + + // Replace text with input object(s) and focus & select. + container.text(""); + container.append(input_elt); + if (button_elt) { + container.append(button_elt); + } + input_elt.focus(); + input_elt.select(); + + // Do not propogate to elements below b/c that blurs input and prevents it from being used. + e.stopPropagation(); + }); + + // Add help text if there some. + if (help_text) { + container.attr("title", help_text).tooltip(); + } + + return container; +}; + +/** + * Edit and save text asynchronously. + */ +function async_save_text( click_to_edit_elt, text_elt_id, save_url, + text_parm_name, num_cols, use_textarea, num_rows, on_start, on_finish ) { + // Set defaults if necessary. + if (num_cols === undefined) { + num_cols = 30; + } + if (num_rows === undefined) { + num_rows = 4; + } + + // Set up input element. + $("#" + click_to_edit_elt).click(function() { + // Check if this is already active + if ( $("#renaming-active").length > 0) { + return; + } + var text_elt = $("#" + text_elt_id), + old_text = text_elt.text(), + t; + + if (use_textarea) { + t = $("<textarea></textarea>").attr({ rows: num_rows, cols: num_cols }).text( $.trim(old_text) ); + } else { + t = $("<input type='text'></input>").attr({ value: $.trim(old_text), size: num_cols }); + } + t.attr("id", "renaming-active"); + t.blur( function() { + $(this).remove(); + text_elt.show(); + if (on_finish) { + on_finish(t); + } + }); + t.keyup( function( e ) { + if ( e.keyCode === 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( e.keyCode === 13 ) { + // Enter key submits + var ajax_data = {}; + ajax_data[text_parm_name] = $(this).val(); + $(this).trigger( "blur" ); + $.ajax({ + url: save_url, + data: ajax_data, + error: function() { + alert( "Text editing for elt " + text_elt_id + " failed" ); + // TODO: call finish or no? For now, let's not because error occurred. + }, + success: function(processed_text) { + // Set new text and call finish method. + if (processed_text !== "") { + text_elt.text(processed_text); + } else { + text_elt.html("<em>None</em>"); + } + if (on_finish) { + on_finish(t); + } + } + }); + } + }); + + if (on_start) { + on_start(t); + } + // Replace text with input object and focus & select. + text_elt.hide(); + t.insertAfter(text_elt); + t.focus(); + t.select(); + + return; + }); +} + +function commatize( number ) { + number += ''; // Convert to string + var rgx = /(\d+)(\d{3})/; + while (rgx.test(number)) { + number = number.replace(rgx, '$1' + ',' + '$2'); + } + return number; +} + +// Reset tool search to start state. +function reset_tool_search( initValue ) { + // Function may be called in top frame or in tool_menu_frame; + // in either case, get the tool menu frame. + var tool_menu_frame = $("#galaxy_tools").contents(); + if (tool_menu_frame.length === 0) { + tool_menu_frame = $(document); + } + + // Remove classes that indicate searching is active. + $(this).removeClass("search_active"); + tool_menu_frame.find(".toolTitle").removeClass("search_match"); + + // Reset visibility of tools and labels. + tool_menu_frame.find(".toolSectionBody").hide(); + tool_menu_frame.find(".toolTitle").show(); + tool_menu_frame.find(".toolPanelLabel").show(); + tool_menu_frame.find(".toolSectionWrapper").each( function() { + if ($(this).attr('id') !== 'recently_used_wrapper') { + // Default action. + $(this).show(); + } else if ($(this).hasClass("user_pref_visible")) { + $(this).show(); + } + }); + tool_menu_frame.find("#search-no-results").hide(); + + // Reset search input. + tool_menu_frame.find("#search-spinner").hide(); + if (initValue) { + var search_input = tool_menu_frame.find("#tool-search-query"); + search_input.val("search tools"); + } +} + +// Create GalaxyAsync object. +var GalaxyAsync = function(log_action) { + this.url_dict = {}; + this.log_action = (log_action === undefined ? false : log_action); +}; + +GalaxyAsync.prototype.set_func_url = function( func_name, url ) { + this.url_dict[func_name] = url; +}; + +// Set user preference asynchronously. +GalaxyAsync.prototype.set_user_pref = function( pref_name, pref_value ) { + // Get URL. + var url = this.url_dict[arguments.callee]; + if (url === undefined) { return false; } + $.ajax({ + url: url, + data: { "pref_name" : pref_name, "pref_value" : pref_value }, + error: function() { return false; }, + success: function() { return true; } + }); +}; + +// Log user action asynchronously. +GalaxyAsync.prototype.log_user_action = function( action, context, params ) { + if (!this.log_action) { return; } + + // Get URL. + var url = this.url_dict[arguments.callee]; + if (url === undefined) { return false; } + $.ajax({ + url: url, + data: { "action" : action, "context" : context, "params" : params }, + error: function() { return false; }, + success: function() { return true; } + }); +}; + +// Initialize refresh events. +function init_refresh_on_change () { + $("select[refresh_on_change='true']") + .off('change') + .change(function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + $(document).trigger("convert_to_values"); // Convert autocomplete text to values + select_field.get(0).form.submit(); + }); + + // checkboxes refresh on change + $(":checkbox[refresh_on_change='true']") + .off('click') + .click( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + + // Links with confirmation + $( "a[confirm]" ) + .off('click') + .click( function() { + return confirm( $(this).attr("confirm") ); + }); +}; + +$(document).ready( function() { + + // Refresh events for form fields. + init_refresh_on_change(); + + // Tooltips + if ( $.fn.tooltip ) { + // Put tooltips below items in panel header so that they do not overlap masthead. + $(".unified-panel-header [title]").tooltip( { placement: 'bottom' } ); + + // default tooltip initialization, it will follow the data-placement tag for tooltip location + // and fallback to 'top' if not present + $("[title]").tooltip(); + } + // Make popup menus. + make_popup_menus(); + + // Replace big selects. + replace_big_select_inputs(20, 1500); + + // If galaxy_main frame does not exist and link targets galaxy_main, + // add use_panels=True and set target to self. + $("a").click( function() { + var anchor = $(this); + var galaxy_main_exists = (parent.frames && parent.frames.galaxy_main); + if ( ( anchor.attr( "target" ) == "galaxy_main" ) && ( !galaxy_main_exists ) ) { + var href = anchor.attr("href"); + if (href.indexOf("?") == -1) { + href += "?"; + } + else { + href += "&"; + } + href += "use_panels=True"; + anchor.attr("href", href); + anchor.attr("target", "_self"); + } + return anchor; + }); + +}); diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f535ef20718d82ab374408d492afa917324a22c5 client/scripts/galaxy.frame.js --- /dev/null +++ b/client/scripts/galaxy.frame.js @@ -0,0 +1,173 @@ +// dependencies +define(["galaxy.masthead", "mvc/ui/ui-frames"], function(mod_masthead, Frames) { + +// frame manager +var GalaxyFrame = Backbone.View.extend( +{ + // base element + el_main: 'body', + + // frame active/disabled + active: false, + + // button active + button_active: null, + + // button load + button_load : null, + + // initialize + initialize : function(options) + { + // add to masthead menu + var self = this; + + // create frames + this.frames = new Frames.View({ + visible: false, + }); + + // add activate icon + this.button_active = new mod_masthead.GalaxyMastheadIcon ( + { + icon : 'fa-th', + tooltip : 'Enable/Disable Scratchbook', + onclick : function() { self._activate(); }, + onunload : function() { + if (self.frames.length() > 0) { + return "You opened " + self.frames.length() + " frame(s) which will be lost."; + } + } + }); + + // add to masthead + Galaxy.masthead.append(this.button_active); + + // add load icon + this.button_load = new mod_masthead.GalaxyMastheadIcon ( + { + icon : 'fa-eye', + tooltip : 'Show/Hide Scratchbook', + onclick : function(e) { + if (self.frames.visible) { + self.frames.hide(); + } else { + self.frames.show(); + } + }, + with_number : true + }); + + // add to masthead + Galaxy.masthead.append(this.button_load); + + // create + this.setElement(this.frames.$el); + + // append to main + $(this.el_main).append(this.$el); + + // refresh menu + this.frames.setOnChange(function() { + self._refresh(); + }); + this._refresh(); + }, + + // adds and displays a new frame/window + add: function(options) + { + // open new tab + if (options.target == '_blank') + { + window.open(options.content); + return; + } + + // reload entire window + if (options.target == '_top' || options.target == '_parent' || options.target == '_self') + { + window.location = options.content; + return; + } + + // validate + if (!this.active) + { + // fix url if main frame is unavailable + var $galaxy_main = $(window.parent.document).find('#galaxy_main'); + if (options.target == 'galaxy_main' || options.target == 'center') + { + if ($galaxy_main.length === 0) + { + var href = options.content; + if (href.indexOf('?') == -1) + href += '?'; + else + href += '&'; + href += 'use_panels=True'; + window.location = href; + } else { + $galaxy_main.attr('src', options.content); + } + } else + window.location = options.content; + + // stop + return; + } + + // add to frames view + this.frames.add(options); + }, + + // activate/disable panel + _activate: function () + { + // check + if (this.active) + { + // disable + this.active = false; + + // toggle + this.button_active.untoggle(); + + // hide panel + this.frames.hide(); + } else { + // activate + this.active = true; + + // untoggle + this.button_active.toggle(); + } + }, + + // update frame counter + _refresh: function() + { + // update on screen counter + this.button_load.number(this.frames.length()); + + // check + if(this.frames.length() === 0) + this.button_load.hide(); + else + this.button_load.show(); + + // check + if (this.frames.visible) { + this.button_load.toggle(); + } else { + this.button_load.untoggle(); + } + } +}); + +// return +return { + GalaxyFrame: GalaxyFrame +}; + +}); diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f535ef20718d82ab374408d492afa917324a22c5 client/scripts/galaxy.library.js --- /dev/null +++ b/client/scripts/galaxy.library.js @@ -0,0 +1,159 @@ +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// === MAIN GALAXY LIBRARY MODULE ==== +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM + +define([ + "galaxy.masthead", + "utils/utils", + "libs/toastr", + "mvc/base-mvc", + "mvc/library/library-model", + "mvc/library/library-folderlist-view", + "mvc/library/library-librarylist-view", + "mvc/library/library-librarytoolbar-view", + "mvc/library/library-foldertoolbar-view", + "mvc/library/library-dataset-view", + "mvc/library/library-library-view", + "mvc/library/library-folder-view" + ], +function(mod_masthead, + mod_utils, + mod_toastr, + mod_baseMVC, + mod_library_model, + mod_folderlist_view, + mod_librarylist_view, + mod_librarytoolbar_view, + mod_foldertoolbar_view, + mod_library_dataset_view, + mod_library_library_view, + mod_library_folder_view + ) { + +// ============================================================================ +// ROUTER +var LibraryRouter = Backbone.Router.extend({ + initialize: function() { + this.routesHit = 0; + //keep count of number of routes handled by the application + Backbone.history.on('route', function() { this.routesHit++; }, this); + }, + + routes: { + "" : "libraries", + "library/:library_id/permissions" : "library_permissions", + "folders/:folder_id/permissions" : "folder_permissions", + "folders/:id" : "folder_content", + "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", + "folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions", + "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version", + "folders/:folder_id/download/:format" : "download" + }, + + back: function() { + if(this.routesHit > 1) { + //more than one route hit -> user did not land to current page directly + window.history.back(); + } else { + //otherwise go to the home page. Use replaceState if available so + //the navigation doesn't create an extra history entry + this.navigate('#', {trigger:true, replace:true}); + } + } +}); + +// ============================================================================ +/** session storage for library preferences */ +var LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({ + defaults : { + with_deleted : false, + sort_order : 'asc', + sort_by : 'name' + } +}); + +// ============================================================================ +// Main controller of Galaxy Library +var GalaxyLibrary = Backbone.View.extend({ + + libraryToolbarView: null, + libraryListView: null, + library_router: null, + libraryView: null, + folderToolbarView: null, + folderListView: null, + datasetView: null, + + initialize : function(){ + Galaxy.libraries = this; + + this.preferences = new LibraryPrefs( {id: 'global-lib-prefs'} ); + + this.library_router = new LibraryRouter(); + + this.library_router.on('route:libraries', function() { + Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); + Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); + }); + + this.library_router.on('route:folder_content', function(id) { + if (Galaxy.libraries.folderToolbarView){ + Galaxy.libraries.folderToolbarView.$el.unbind('click'); + } + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); + }); + + this.library_router.on('route:download', function(folder_id, format) { + if ($('#folder_list_body').find(':checked').length === 0) { + mod_toastr.info('You have to select some datasets to download'); + Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + } else { + Galaxy.libraries.folderToolbarView.download(folder_id, format); + Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); + } + }); + + this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); + }); + this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); + }); + + this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); + }); + + this.library_router.on('route:library_permissions', function(library_id){ + if (Galaxy.libraries.libraryView){ + Galaxy.libraries.libraryView.$el.unbind('click'); + } + Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); + }); + + this.library_router.on('route:folder_permissions', function(folder_id){ + if (Galaxy.libraries.folderView){ + Galaxy.libraries.folderView.$el.unbind('click'); + } + Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); + }); + + Backbone.history.start({pushState: false}); + } +}); + +return { + GalaxyApp: GalaxyLibrary +}; + +}); This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/ba66d120d001/ Changeset: ba66d120d001 User: carlfeberhard Date: 2014-09-16 15:05:46 Summary: Merged galaxy/galaxy-central into default Affected #: 85 files diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/galaxy.base.js --- a/client/scripts/galaxy.base.js +++ b/client/scripts/galaxy.base.js @@ -593,6 +593,26 @@ }); }; + +// jQuery plugin to prevent double submission of forms +// Ref: http://stackoverflow.com/questions/2830542/prevent-double-submission-of-for… +jQuery.fn.preventDoubleSubmission = function() { + $(this).on('submit',function(e){ + var $form = $(this); + + if ($form.data('submitted') === true) { + // Previously submitted - don't submit again + e.preventDefault(); + } else { + // Mark it so that the next submit can be ignored + $form.data('submitted', true); + } + }); + + // Keep chainability + return this; +}; + $(document).ready( function() { // Refresh events for form fields. diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/tools/tools-datasets.js --- a/client/scripts/mvc/tools/tools-datasets.js +++ b/client/scripts/mvc/tools/tools-datasets.js @@ -25,21 +25,26 @@ }, // filter datasets by data type - filterType: function(filter_type) { - // return matched datasets - return this.currHistoryContents.filter( function( content ){ - // link details - var history_content_type = content.get( 'history_content_type' ); - var data_type = content.get( 'file_ext'); + filterType: function(options) { + options = options || {}; + return this.currHistoryContents.filter(function(content){ + // match datatypes + var found = false; + for (var i in options.data_types) { + if (content.get('data_type').indexOf(options.data_types[i]) != -1) { + found = true; + break; + } + } - // apply filter - return history_content_type === 'dataset';// && (data_type === filter_type || filter_type === ''); + // final match result + return (content.get('history_content_type') === options.content_type || !options.content_type) && + (found || !options.data_types) && !content.get('deleted'); }); }, // filter datasets by id filter: function(filter_id) { - // return matched datasets return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) ); } }); diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/tools/tools-form.js --- a/client/scripts/mvc/tools/tools-form.js +++ b/client/scripts/mvc/tools/tools-form.js @@ -56,6 +56,12 @@ }); }, + // message + message: function(options) { + $(this.main_el).empty(); + $(this.main_el).append(ToolTemplate.message(options)); + }, + // reset form reset: function() { for (var i in this.element_list) { @@ -63,6 +69,20 @@ } }, + // refresh + refresh: function() { + // recreate tree structure + this.tree.refresh(); + + // trigger change + for (var id in this.field_list) { + this.field_list[id].trigger('change'); + } + + // log + console.debug('tools-form::refresh() - Recreated tree structure. Refresh.'); + }, + // initialize tool form _initializeToolForm: function() { // link this @@ -135,10 +155,6 @@ button_search.$el.hide(); } - // create message - self.message = new Ui.Message(); - self.portlet.append(self.message.$el); - // append form $(self.main_el).append(self.portlet.$el); @@ -174,22 +190,9 @@ // trigger refresh self.refresh(); //self.job_handler.submit(); + self.tree.finalize(); } }); - }, - - // refresh - refresh: function() { - // recreate tree structure - this.tree.refresh(); - - // trigger change - for (var id in this.field_list) { - this.field_list[id].trigger('change'); - } - - // log - console.debug('tools-form::refresh() - Recreated tree structure. Refresh.'); } }); diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/tools/tools-jobs.js --- a/client/scripts/mvc/tools/tools-jobs.js +++ b/client/scripts/mvc/tools/tools-jobs.js @@ -31,12 +31,16 @@ // success handler function(response) { if (!response.outputs || response.outputs.length == 0) { - console.log(response); + console.debug(response); } + self.app.message({ + text : 'A job has been successfully added to the queue. You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.' + }); self._refreshHdas(); }, // error handler function(response) { + console.debug(response); if (response && response.message && response.message.data) { var error_messages = self.app.tree.match(response.message.data); for (var id in error_messages) { diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/tools/tools-section.js --- a/client/scripts/mvc/tools/tools-section.js +++ b/client/scripts/mvc/tools/tools-section.js @@ -16,13 +16,11 @@ // set text this.$el.find('.ui-table-form-error-text').html(text); this.$el.find('.ui-table-form-error').fadeIn(); - this.$el.addClass('ui-table-row-error'); }, // reset reset: function() { this.$el.find('.ui-table-form-error').hide(); - this.$el.removeClass('ui-table-form-error'); }, // template @@ -35,7 +33,7 @@ } // add error - $input.append('<div class="ui-table-form-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>'); + $input.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>'); // add label if (options.label) { @@ -274,7 +272,7 @@ // dataset column case 'data_column': - field = this._field_data_colum(input_def); + field = this._field_select(input_def); break; // conditional select field diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/tools/tools-select-dataset.js --- a/client/scripts/mvc/tools/tools-select-dataset.js +++ b/client/scripts/mvc/tools/tools-select-dataset.js @@ -6,54 +6,6 @@ initialize : function(app, options) { // link this var self = this; - - // get datasets - var datasets = app.datasets.filterType(); - - // configure options fields - var select_data = []; - for (var i in datasets) { - select_data.push({ - label: datasets[i].get('name'), - value: datasets[i].get('id') - }); - } - - // create select field - this.select = new Ui.Select.View({ - data : select_data, - value : select_data[0].value, - onchange : function() { - self.trigger('change'); - } - }); - - // create select field for multiple files - this.select_multiple = new Ui.Select.View({ - multiple : true, - data : select_data, - value : select_data[0].value, - onchange : function() { - self.trigger('change'); - } - }); - - - // create select field for multiple files - this.select_collection = new Ui.Select.View({ - data : select_data, - value : select_data[0].value, - onchange : function() { - self.trigger('change'); - } - }); - - // add change event. fires on trigger - this.on('change', function() { - if (options.onchange) { - options.onchange(self.value()); - } - }); // tabs this.tabs = new Tabs.View({ @@ -62,20 +14,66 @@ } }); - // add tab - this.tabs.add({ - id : 'single', - title : 'Select a dataset', - $el : this.select.$el + // + // datasets + // + var datasets = app.datasets.filterType({ + content_type : 'dataset', + data_types : options.extensions + }); + + // configure options fields + var dataset_options = []; + for (var i in datasets) { + dataset_options.push({ + label: datasets[i].get('name'), + value: datasets[i].get('id') + }); + } + + // select field + this.select_datasets = new Ui.Select.View({ + multiple : true, + data : dataset_options, + value : dataset_options[0] && dataset_options[0].value, + onchange : function() { + self.trigger('change'); + } }); // add tab this.tabs.add({ - id : 'multiple', - title : 'Select multiple datasets', - $el : this.select_multiple.$el + id : 'datasets', + title : 'Select datasets', + $el : this.select_datasets.$el }); - + + // + // collections + // + var collections = app.datasets.filterType({ + content_type : 'collection', + data_types : options.extensions + }); + + // configure options fields + var collection_options = []; + for (var i in collections) { + collection_options.push({ + label: collections[i].get('name'), + value: collections[i].get('id') + }); + } + + // create select field for collections + this.select_collection = new Ui.Select.View({ + data : collection_options, + value : collection_options[0] && collection_options[0].value, + onchange : function() { + self.trigger('change'); + } + }); + // add tab this.tabs.add({ id : 'collection', @@ -85,18 +83,23 @@ // add element this.setElement(this.tabs.$el); + + // add change event. fires on trigger + this.on('change', function() { + if (options.onchange) { + options.onchange(self.value()); + } + }); }, // value value : function (new_value) { var current_tab = this.tabs.current(); switch(current_tab) { - case 'multiple' : - return this.select_multiple.value(); - case 'collection' : + case 'datasets': + return this.select_datasets.value(); + case 'collection': return this.select_collection.value(); - default : - return this.select.value(); } }, diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/tools/tools-template.js --- a/client/scripts/mvc/tools/tools-template.js +++ b/client/scripts/mvc/tools/tools-template.js @@ -13,6 +13,12 @@ citations: function() { return '<div id="citations"></div>'; + }, + + message: function(options) { + return '<div class="donemessagelarge">' + + '<p>' + options.text + '</p>' + + '</div>'; } }; diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/tools/tools-tree.js --- a/client/scripts/mvc/tools/tools-tree.js +++ b/client/scripts/mvc/tools/tools-tree.js @@ -50,8 +50,8 @@ // converter between raw dictionary and job dictionary function convert(identifier, head) { - for (var i in head) { - var node = head[i]; + for (var index in head) { + var node = head[index]; if (node.input) { // get node var input = node.input; @@ -68,9 +68,9 @@ // handle repeats case 'repeat': var index = 0; - for (var j in node) { - if (j.indexOf('section') != -1) { - convert(job_input_id + '_' + index++, node[j]); + for (var i in node) { + if (i.indexOf('section') != -1) { + convert(job_input_id + '_' + index++, node[i]); } } break; @@ -83,20 +83,38 @@ add (job_input_id + '|' + input.test_param.name, input.id, value); // find selected case - for (var j in input.cases) { - if (input.cases[j].value == value) { - convert(job_input_id, head[input.id + '-section-' + j]); + for (var i in input.cases) { + if (input.cases[i].value == value) { + convert(job_input_id, head[input.id + '-section-' + i]); break; } } break; // handle data inputs case 'data': - var value = { - id : self.app.field_list[input.id].value(), - src : 'hda' + // create array for dataset ids + var dataset_selection = null; + + // collect dataset ids from input field + var value = self.app.field_list[input.id].value(); + if (typeof value === 'string') { + dataset_selection = { + id : value, + src : 'hda' + }; + } else { + // create array of dataset dictionaries for api submission + dataset_selection = []; + for (var i in value) { + dataset_selection.push({ + id : value[i], + src : 'hda' + }); + } } - add(job_input_id, input.id, value); + + // add final array to job definition + add(job_input_id, input.id, dataset_selection); break; // handle boolean input case 'boolean': @@ -118,7 +136,7 @@ // start conversion convert('', this.dict); - + console.log(this.job_def); // return result return this.job_def; }, diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/ui/ui-misc.js --- a/client/scripts/mvc/ui/ui-misc.js +++ b/client/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,6 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-checkbox', 'mvc/ui/ui-radiobutton', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, Slider, Checkbox, RadioButton, ButtonMenu, Modal) { +define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], + function(Utils, Select, Slider, Options, ButtonMenu, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -403,8 +403,8 @@ Label : Label, Message : Message, Modal : Modal, - RadioButton : RadioButton, - Checkbox : Checkbox, + RadioButton : Options.RadioButton, + Checkbox : Options.Checkbox, Searchbox : Searchbox, Select : Select, Hidden : Hidden, diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/ui/ui-select-default.js --- a/client/scripts/mvc/ui/ui-select-default.js +++ b/client/scripts/mvc/ui/ui-select-default.js @@ -172,7 +172,7 @@ // check if selected value exists exists: function(value) { - return this.$select.find('option[value=' + value + ']').length > 0; + return this.$select.find('option[value="' + value + '"]').length > 0; }, // change diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/upload/upload-ftp.js --- a/client/scripts/mvc/upload/upload-ftp.js +++ b/client/scripts/mvc/upload/upload-ftp.js @@ -31,10 +31,9 @@ // fill table _fill: function(ftp_files) { - if (ftp_files.length > 0) { // add table - this.$el.find('#upload-ftp-content').html($(this._template_table())); + this.$el.find('#upload-ftp-content').html($(this._templateTable())); // add files to table var size = 0; @@ -48,7 +47,7 @@ this.$el.find('#upload-ftp-disk').html(Utils.bytesToString (size, true)); } else { // add info - this.$el.find('#upload-ftp-content').html($(this._template_info())); + this.$el.find('#upload-ftp-content').html($(this._templateInfo())); } // hide spinner @@ -58,7 +57,7 @@ // add add: function(ftp_file) { // create new item - var $it = $(this._template_row(ftp_file)); + var $it = $(this._templateRow(ftp_file)); // append to table $(this.el).find('tbody').append($it); @@ -118,7 +117,7 @@ }, // template row - _template_row: function(options) { + _templateRow: function(options) { return '<tr>' + '<td><div id="upload-ftp-add"/></td>' + '<td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">' + options.path + '</p></td>' + @@ -128,8 +127,7 @@ }, // load table template - _template_table: function() - { + _templateTable: function() { return '<span style="whitespace: nowrap; float: left;">Available files: </span>' + '<span style="whitespace: nowrap; float: right;">' + '<span class="upload-icon fa fa-file-text-o"/>' + @@ -151,16 +149,14 @@ }, // load table template - _template_info: function() - { + _templateInfo: function() { return '<div class="upload-ftp-warning warningmessage">' + 'Your FTP directory does not contain any files.' + '</div>'; }, // load html template - _template: function() - { + _template: function() { return '<div class="upload-ftp">' + '<div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/>' + '<div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>' + this.app.options.ftp_upload_site + '</strong> using your Galaxy credentials (email address and password).</div>' + diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/upload/upload-row.js --- a/client/scripts/mvc/upload/upload-row.js +++ b/client/scripts/mvc/upload/upload-row.js @@ -214,16 +214,14 @@ // // genome - _refreshGenome: function() - { + _refreshGenome: function() { // update genome info on screen var genome = this.model.get('genome'); this.select_genome.value(genome); }, // progress - _refreshInfo: function() - { + _refreshInfo: function() { // write error message var info = this.model.get('info'); if (info) { @@ -234,8 +232,7 @@ }, // progress - _refreshPercentage : function() - { + _refreshPercentage : function() { var percentage = parseInt(this.model.get('percentage')); this.$el.find('.progress-bar').css({ width : percentage + '%' }); if (percentage != 100) @@ -245,8 +242,7 @@ }, // status - _refreshStatus : function() - { + _refreshStatus : function() { // get element var it = this.$el; @@ -315,8 +311,7 @@ }, // attach file info popup - _showExtensionInfo : function() - { + _showExtensionInfo : function() { // initialize var $el = $(this.el).find('#extension-info'); var extension = this.model.get('extension'); @@ -343,8 +338,7 @@ }, // attach file info popup - _showSettings : function() - { + _showSettings : function() { // check if popover is visible if (!this.settings.visible) { // show popover @@ -371,8 +365,7 @@ }, // template - _template: function(options) - { + _template: function(options) { return '<tr id="upload-item-' + options.id + '" class="upload-item">' + '<td>' + '<div style="position: relative;">' + diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/upload/upload-settings.js --- a/client/scripts/mvc/upload/upload-settings.js +++ b/client/scripts/mvc/upload/upload-settings.js @@ -25,12 +25,12 @@ // ui event: space to tabs this.$el.find('#upload-space-to-tabs').on('click', function() { - self._switch_state('#upload-space-to-tabs', 'space_to_tabs'); + self._switchState('#upload-space-to-tabs', 'space_to_tabs'); }); // ui event: to posix this.$el.find('#upload-to-posix-lines').on('click', function() { - self._switch_state('#upload-to-posix-lines', 'to_posix_lines'); + self._switchState('#upload-to-posix-lines', 'to_posix_lines'); }); // render @@ -45,8 +45,8 @@ // render render: function() { // render states - this._render_state('#upload-space-to-tabs', this.model.get('space_to_tabs')); - this._render_state('#upload-to-posix-lines', this.model.get('to_posix_lines')); + this._renderState('#upload-space-to-tabs', this.model.get('space_to_tabs')); + this._renderState('#upload-to-posix-lines', this.model.get('to_posix_lines')); // disable options var $cover = this.$el.find('#upload-settings-cover'); @@ -58,16 +58,16 @@ }, // switch state - _switch_state: function (element_id, parameter_id) { + _switchState: function (element_id, parameter_id) { if (this.model.get('status') == 'init') { var checked = !this.model.get(parameter_id); this.model.set(parameter_id, checked); - this._render_state(element_id, checked); + this._renderState(element_id, checked); } }, // render state - _render_state: function (element_id, checked) { + _renderState: function (element_id, checked) { // swith icon class var $it = this.$el.find(element_id); $it.removeClass(); @@ -79,8 +79,7 @@ }, // load template - _template: function() - { + _template: function() { return '<div class="upload-settings" style="position: relative;">' + '<div id="upload-settings-cover" class="upload-settings-cover"/>' + '<table class="table table-striped">' + diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 client/scripts/mvc/upload/upload-view.js --- a/client/scripts/mvc/upload/upload-view.js +++ b/client/scripts/mvc/upload/upload-view.js @@ -19,8 +19,7 @@ ) { // galaxy upload -return Backbone.View.extend( -{ +return Backbone.View.extend({ // options options : { nginx_upload_path : '' diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <url>${redirect_url}</url><param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /><param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #else: + $bam_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <url>${redirect_url}</url><param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /><param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #else: + $bgzip_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -794,6 +794,8 @@ if value is not None: if not isinstance( value, list ): value = [ value ] + # We could have an unvalidated value here when e.g. running a workflow. + value = [ val.value if isinstance( val, UnvalidatedValue ) else val for val in value ] field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -417,12 +417,13 @@ query = irmm.get_query_for_setting_metadata_on_repositories( order=False ) # Now reset metadata on all remaining repositories. for repository in query: - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + irmm.set_repository( repository ) + irmm.reset_all_metadata_on_installed_repository() + irmm_invalid_file_tups = irmm.get_invalid_file_tups() + if irmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + irmm_invalid_file_tups, repository, None, as_html=False ) diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1732,20 +1732,21 @@ tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata - irmm = InstalledRepositoryMetadataManager( trans.app ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - irmm.update_in_shed_tool_config( repository ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + repository=repository, + changeset_revision=repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if irmm_metadata_dict != original_metadata_dict: + repository.metadata = irmm_metadata_dict + irmm.update_in_shed_tool_config() trans.install_model.context.add( repository ) trans.install_model.context.flush() message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name @@ -1938,22 +1939,24 @@ dmh.remove_from_data_manager( repository ) # Update the repository metadata. tpm = tool_panel_manager.ToolPanelManager( trans.app ) - irmm = InstalledRepositoryMetadataManager( trans.app, tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=latest_changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + tpm=tpm, + repository=repository, + changeset_revision=latest_changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if 'tools' in irmm_metadata_dict: + tool_panel_dict = irmm_metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() tpm.add_to_tool_panel( repository_name=str( repository.name ), repository_clone_url=repository_clone_url, changeset_revision=str( repository.installed_changeset_revision ), @@ -1963,18 +1966,18 @@ tool_panel_dict=tool_panel_dict, new_install=False ) # Add new Data Manager entries - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( trans.app ) new_data_managers = dmh.install_data_managers( trans.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, repository.get_shed_config_dict( trans.app ), os.path.join( relative_install_dir, name ), repository, repository_tools_tups ) - if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: - new_repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + if 'repository_dependencies' in irmm_metadata_dict or 'tool_dependencies' in irmm_metadata_dict: + new_repository_dependencies_dict = irmm_metadata_dict.get( 'repository_dependencies', {} ) new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] ) - new_tool_dependencies_dict = metadata_dict.get( 'tool_dependencies', {} ) + new_tool_dependencies_dict = irmm_metadata_dict.get( 'tool_dependencies', {} ) if new_repository_dependencies: # [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']] proceed_to_install = False @@ -2017,7 +2020,7 @@ updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), updating=True ) return self.prepare_for_install( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies but did include @@ -2033,12 +2036,12 @@ proceed_to_install = True break if proceed_to_install: - encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) + encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( irmm_metadata_dict.get( 'tool_dependencies', {} ) ) encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), encoded_relative_install_dir=encoded_relative_install_dir, encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, message=message, @@ -2047,7 +2050,7 @@ # Updates received did not include any newly defined repository dependencies or newly defined # tool dependencies that need to be installed. repository = trans.app.update_repository_manager.update_repository_record( repository=repository, - updated_metadata_dict=metadata_dict, + updated_metadata_dict=irmm_metadata_dict, updated_changeset_revision=latest_changeset_revision, updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -429,13 +429,13 @@ def handle_repository( trans, rmm, repository, results ): log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + rmm.set_repository( repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) @@ -451,7 +451,11 @@ status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) results = dict( start_time=start_time, repository_status=[], @@ -511,12 +515,17 @@ results = dict( start_time=start_time, repository_status=[] ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.security.encode_id( repository.id ) ) - if invalid_file_tups: + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -1,6 +1,8 @@ import os, logging from galaxy import web from galaxy.web.base.controller import BaseUIController + +from tool_shed.util.common_util import generate_clone_url_for_repository_in_tool_shed from tool_shed.util.shed_util_common import get_repository_by_name_and_owner from tool_shed.util.hg_util import update_repository from tool_shed.metadata import repository_metadata_manager @@ -47,9 +49,19 @@ # interface will result in a new head being created. repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) # Set metadata using the repository files on disk. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - error_message, status = rmm.set_repository_metadata( trans.request.host, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + changeset_revision=repository.tip( trans.app ), + repository_clone_url=repository_clone_url, + relative_install_dir=repository.repo_path( trans.app ), + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + error_message, status = rmm.set_repository_metadata( trans.request.host ) if status == 'ok' and error_message: log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ ( str( repository.name ), str( repository.user.username ), error_message ) ) diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2759,15 +2759,18 @@ def reset_all_metadata( self, trans, id, **kwd ): """Reset all metadata on the complete changelog for a single repository in the tool shed.""" # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( id ) - if invalid_file_tups: - repository = suc.get_repository_in_tool_shed( trans.app, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_metadata_dict = rmm.get_metadata_dict() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, - metadata_dict ) + rmm_metadata_dict ) status = 'error' else: message = "All repository metadata has been reset. " @@ -2849,10 +2852,10 @@ if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, - **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, **kwd ) if error_message: message = error_message else: diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -263,10 +263,11 @@ ( len( files_to_remove ), upload_point ) else: message += " %d files were removed from the repository root. " % len( files_to_remove ) - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) status, error_message = \ rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, content_alert_str=content_alert_str, **kwd ) if error_message: diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -792,9 +792,10 @@ results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, self.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=self.app, + user=self.user, + repository=repository ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, - repository, content_alert_str=content_alert_str ) if error_message: results_dict[ 'ok' ] = False diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -510,31 +510,33 @@ """ shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) tdtm = data_table_manager.ToolDataTableManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict # Update the tool_shed_repository.tool_shed_status column in the database. tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository ) if tool_shed_status_dict: tool_shed_repository.tool_shed_status = tool_shed_status_dict self.install_model.context.add( tool_shed_repository ) self.install_model.context.flush() - if 'tool_dependencies' in metadata_dict and not reinstalling: + if 'tool_dependencies' in irmm_metadata_dict and not reinstalling: tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) - if 'sample_files' in metadata_dict: - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'sample_files' in irmm_metadata_dict: + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_data_table_conf_filename, tool_data_table_elems = \ tdtm.install_tool_data_tables( tool_shed_repository, tool_index_sample_files ) @@ -543,13 +545,13 @@ None, self.app.config.shed_tool_data_table_config, persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'tools' in irmm_metadata_dict: + tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( irmm_metadata_dict[ 'tools' ], tool_section ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. repository_tools_tups = tdtm.handle_missing_data_table_entry( relative_install_dir, @@ -575,15 +577,15 @@ shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=True ) - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, shed_config_dict, relative_install_dir, tool_shed_repository, repository_tools_tups ) - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: tool_shed_repository.status = self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: tool_shed_repository.includes_datatypes = True @@ -604,7 +606,7 @@ name=tool_shed_repository.name, owner=tool_shed_repository.owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -82,9 +82,12 @@ repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools_for_display_in_tool_panel: tpm = tool_panel_manager.ToolPanelManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, tpm ) - metadata = repository.metadata - repository_tools_tups = irmm.get_repository_tools_tups( metadata ) + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=tpm, + repository=repository, + changeset_revision=repository.changeset_revision, + metadata_dict=repository.metadata ) + repository_tools_tups = irmm.get_repository_tools_tups() # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] tpm.add_to_tool_panel( repository.name, @@ -101,7 +104,7 @@ data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata, + repository.metadata, repository.get_shed_config_dict( self.app ), data_manager_relative_install_dir, repository, diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -19,9 +19,16 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, tpm=None ): - super( InstalledRepositoryMetadataManager, self ).__init__( app ) - self.app = app + def __init__( self, app, tpm=None, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( InstalledRepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=None ) if tpm is None: self.tpm = tool_panel_manager.ToolPanelManager( self.app ) else: @@ -53,15 +60,15 @@ return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) - def get_repository_tools_tups( self, metadata_dict ): + def get_repository_tools_tups( self ): """ Return a list of tuples of the form (relative_path, guid, tool) for each tool defined in the received tool shed repository metadata. """ repository_tools_tups = [] - index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( metadata_dict.get( 'shed_config_filename' ) ) - if 'tools' in metadata_dict: - for tool_dict in metadata_dict[ 'tools' ]: + index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( self.metadata_dict.get( 'shed_config_filename' ) ) + if 'tools' in self.metadata_dict: + for tool_dict in self.metadata_dict[ 'tools' ]: load_relative_path = relative_path = tool_dict.get( 'tool_config', None ) if shed_conf_dict.get( 'tool_path' ): load_relative_path = os.path.join( shed_conf_dict.get( 'tool_path' ), relative_path ) @@ -74,36 +81,21 @@ repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups - def reset_all_metadata_on_installed_repository( self, id ): + def reset_all_metadata_on_installed_repository( self ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" - invalid_file_tups = [] - metadata_dict = {} - repository = repository_util.get_installed_tool_shed_repository( self.app, id ) - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - tool_path, relative_install_dir = repository.get_tool_relative_path( self.app ) - if relative_install_dir: - original_metadata_dict = repository.metadata - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( self.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - self.update_in_shed_tool_config( repository ) - self.app.install_model.context.add( repository ) + if self.relative_install_dir: + original_metadata_dict = self.repository.metadata + self.generate_metadata_for_changeset_revision() + if self.metadata_dict != original_metadata_dict: + self.repository.metadata = self.metadata_dict + self.update_in_shed_tool_config() + self.app.install_model.context.add( self.repository ) self.app.install_model.context.flush() - log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + log.debug( 'Metadata has been reset on repository %s.' % self.repository.name ) else: - log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + log.debug( 'Metadata did not need to be reset on repository %s.' % self.repository.name ) else: - log.debug( 'Error locating installation directory for repository %s.' % repository.name ) - return invalid_file_tups, metadata_dict + log.debug( 'Error locating installation directory for repository %s.' % self.repository.name ) def reset_metadata_on_selected_repositories( self, user, **kwd ): """ @@ -119,19 +111,19 @@ for repository_id in repository_ids: try: repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id ) - owner = str( repository.owner ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_installed_repository() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) log.debug( message ) unsuccessful_count += 1 else: - log.debug( "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), owner ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s" % \ + ( str( repository.name ), str( repository.owner ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) ) @@ -146,32 +138,37 @@ status = 'error' return message, status - def tool_shed_from_repository_clone_url( self, repository_clone_url ): + def set_repository( self, repository ): + super( InstalledRepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) + + def tool_shed_from_repository_clone_url( self ): """Given a repository clone URL, return the tool shed that contains the repository.""" - return common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) + return common_util.remove_protocol_and_user_from_clone_url( cleaned_repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) - def update_in_shed_tool_config( self, repository ): + def update_in_shed_tool_config( self ): """ A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list of config_elems instead of using the in-memory list. """ - shed_conf_dict = repository.get_shed_config_dict( self.app ) + shed_conf_dict = self.repository.get_shed_config_dict( self.app ) shed_tool_conf = shed_conf_dict[ 'config_filename' ] tool_path = shed_conf_dict[ 'tool_path' ] - tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = self.get_repository_tools_tups( repository.metadata ) - clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) - tool_shed = self.tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) - owner = repository.owner + tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( self.repository ) + repository_tools_tups = self.get_repository_tools_tups() + clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + tool_shed = self.tool_shed_from_repository_clone_url() + owner = self.repository.owner if not owner: + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) owner = suc.get_repository_owner( cleaned_repository_clone_url ) guid_to_tool_elem_dict = {} for tool_config_filename, guid, tool in repository_tools_tups: guid_to_tool_elem_dict[ guid ] = self.tpm.generate_tool_elem( tool_shed, - repository.name, - repository.changeset_revision, - repository.owner or '', + self.repository.name, + self.repository.changeset_revision, + self.repository.owner or '', tool_config_filename, tool, None ) diff -r f535ef20718d82ab374408d492afa917324a22c5 -r ba66d120d001d6531300f57f215210056481f368 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -416,21 +416,23 @@ log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) ) finally: lock.release() - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = self.shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = self.shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict self.app.install_model.context.add( tool_shed_repository ) self.app.install_model.context.flush() - has_tool_dependencies = self.__has_tool_dependencies( metadata_dict ) + has_tool_dependencies = self.__has_tool_dependencies( irmm_metadata_dict ) if has_tool_dependencies: # All tool_dependency objects must be created before the tools are processed even if no # tool dependencies will be installed. @@ -440,14 +442,14 @@ set_status=True ) else: tool_dependencies = None - if 'tools' in metadata_dict: + if 'tools' in irmm_metadata_dict: tdtm = data_table_manager.ToolDataTableManager( self.app ) - sample_files = metadata_dict.get( 'sample_files', [] ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) sample_files = [ str( s ) for s in sample_files ] tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically # generated select lists. @@ -491,7 +493,7 @@ if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: @@ -514,7 +516,7 @@ name=tool_shed_repository.name, owner=self.repository_owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/773bae7768c1/ Changeset: 773bae7768c1 User: carlfeberhard Date: 2014-09-16 15:40:13 Summary: Move client/scripts to client/galaxy/scripts Affected #: 325 files diff -r ba66d120d001d6531300f57f215210056481f368 -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 client/GruntFile.js --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -7,7 +7,7 @@ copy: { main: { expand: true, - cwd: 'scripts/', + cwd: 'galaxy/scripts/', src: '**', dest: '../static/scripts/' } diff -r ba66d120d001d6531300f57f215210056481f368 -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 client/galaxy/scripts/base.js --- /dev/null +++ b/client/galaxy/scripts/base.js @@ -0,0 +1,15 @@ +define( ["libs/backbone/backbone"], function( Backbone ) { + + var Base = function() { + if( this.initialize ) { + this.initialize.apply(this, arguments); + } + }; + Base.extend = Backbone.Model.extend; + + return { + Base: Base, + Backbone: Backbone + }; + +}); \ No newline at end of file diff -r ba66d120d001d6531300f57f215210056481f368 -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 client/galaxy/scripts/galaxy-app-base.js --- /dev/null +++ b/client/galaxy/scripts/galaxy-app-base.js @@ -0,0 +1,160 @@ +define([ + 'mvc/user/user-model', + 'utils/metrics-logger', + 'utils/add-logging', + 'utils/localization', + 'bootstrapped-data' +], function( userModel, metricsLogger, addLogging, localize, bootstrapped ){ +// ============================================================================ +/** Base galaxy client-side application. + * Iniitializes: + * logger : the logger/metrics-logger + * localize : the string localizer + * config : the current configuration (any k/v in + * universe_wsgi.ini available from the configuration API) + * user : the current user (as a mvc/user/user-model) + */ +function GalaxyApp( options ){ + var self = this; + return self._init( options || {} ); +} + +// add logging shortcuts for this object +addLogging( GalaxyApp, 'GalaxyApp' ); + +/** default options */ +GalaxyApp.prototype.defaultOptions = { + /** monkey patch attributes from existing window.Galaxy object? */ + patchExisting : true, + /** root url of this app */ + // move to self.root? + root : '/' +}; + +/** initalize options and sub-components */ +GalaxyApp.prototype._init = function init( options ){ + var self = this; + _.extend( self, Backbone.Events ); + + self._processOptions( options ); + self.debug( 'GalaxyApp.options: ', self.options ); + + self._patchGalaxy( window.Galaxy ); + + self._initLogger( options.loggerOptions || {} ); + self.debug( 'GalaxyApp.logger: ', self.logger ); + + self._initLocale(); + self.debug( 'GalaxyApp.localize: ', self.localize ); + + self.config = options.config || bootstrapped.config || {}; + self.debug( 'GalaxyApp.config: ', self.config ); + + self._initUser( options.user || bootstrapped.user || {} ); + self.debug( 'GalaxyApp.user: ', self.user ); + + //TODO: temp + self.trigger( 'ready', self ); + //if( typeof options.onload === 'function' ){ + // options.onload(); + //} + + self._setUpListeners(); + + return self; +}; + +/** add an option from options if the key matches an option in defaultOptions */ +GalaxyApp.prototype._processOptions = function _processOptions( options ){ + var self = this, + defaults = self.defaultOptions; + self.debug( '_processOptions: ', options ); + + self.options = {}; + for( var k in defaults ){ + if( defaults.hasOwnProperty( k ) ){ + self.options[ k ] = ( options.hasOwnProperty( k ) )?( options[ k ] ):( defaults[ k ] ); + } + } + return self; +}; + +/** add an option from options if the key matches an option in defaultOptions */ +GalaxyApp.prototype._patchGalaxy = function _processOptions( patchWith ){ + var self = this; + // in case req or plain script tag order has created a prev. version of the Galaxy obj... + if( self.options.patchExisting && patchWith ){ + self.debug( 'found existing Galaxy object:', patchWith ); + // ...(for now) monkey patch any added attributes that the previous Galaxy may have had + //TODO: move those attributes to more formal assignment in GalaxyApp + for( var k in patchWith ){ + if( patchWith.hasOwnProperty( k ) ){ + self.debug( '\t patching in ' + k + ' to Galaxy' ); + self[ k ] = patchWith[ k ]; + } + } + } +}; + +/** set up the metrics logger (utils/metrics-logger) and pass loggerOptions */ +GalaxyApp.prototype._initLogger = function _initLogger( loggerOptions ){ + var self = this; + self.debug( '_initLogger:', loggerOptions ); + self.logger = new metricsLogger.MetricsLogger( loggerOptions ); + return self; +}; + +/** add the localize fn to this object and the window namespace (as '_l') */ +GalaxyApp.prototype._initLocale = function _initLocale( options ){ + var self = this; + self.debug( '_initLocale:', options ); + self.localize = localize; + // add to window as global shortened alias + window._l = self.localize; + return self; +}; + +/** set up the current user as a Backbone model (mvc/user/user-model) */ +GalaxyApp.prototype._initUser = function _initUser( userJSON ){ + var self = this; + self.debug( '_initUser:', userJSON ); + self.user = new userModel.User( userJSON ); + //TODO: temp - old alias + self.currUser = self.user; + return self; +}; + +/** Set up DOM/jQuery/Backbone event listeners enabled for all pages */ +GalaxyApp.prototype._setUpListeners = function _setUpListeners(){ + var self = this; + + // hook to jq beforeSend to record the most recent ajax call and cache some data about it + /** cached info about the last ajax call made through jQuery */ + self.lastAjax = {}; + $( document ).bind( 'ajaxSend', function( ev, xhr, options ){ + var data = options.data; + try { + data = JSON.parse( data ); + } catch( err ){} + + self.lastAjax = { + url : location.href.slice( 0, -1 ) + options.url, + data : data + }; + //TODO:?? we might somehow manage to *retry* ajax using either this hook or Backbone.sync + }); + +}; + +/** string rep */ +GalaxyApp.prototype.toString = function toString(){ + var userEmail = this.user.get( 'email' ) || '(anonymous)'; + return 'GalaxyApp(' + userEmail + ')'; +}; + + +// ============================================================================ + return { + GalaxyApp : GalaxyApp + }; +}); diff -r ba66d120d001d6531300f57f215210056481f368 -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 client/galaxy/scripts/galaxy.autocom_tagging.js --- /dev/null +++ b/client/galaxy/scripts/galaxy.autocom_tagging.js @@ -0,0 +1,368 @@ +/** +* JQuery extension for tagging with autocomplete. +* @author: Jeremy Goecks +* @require: jquery.autocomplete plugin +*/ +// +// Initialize "tag click functions" for tags. +// +function init_tag_click_function(tag_elt, click_func) { + $(tag_elt).find('.tag-name').each( function() { + $(this).click( function() { + var tag_str = $(this).text(); + var tag_name_and_value = tag_str.split(":"); + click_func(tag_name_and_value[0], tag_name_and_value[1]); + return true; + }); + }); +} + +jQuery.fn.autocomplete_tagging = function(options) { + + var defaults = { + get_toggle_link_text_fn: function(tags) { + var text = ""; + var num_tags = obj_length(tags); + if (num_tags > 0) { + text = num_tags + (num_tags > 1 ? " Tags" : " Tag"); + } else { + text = "Add tags"; + } + return text; + }, + tag_click_fn : function (name, value) {}, + editable: true, + input_size: 20, + in_form: false, + tags : {}, + use_toggle_link: true, + item_id: "", + add_tag_img: "", + add_tag_img_rollover: "", + delete_tag_img: "", + ajax_autocomplete_tag_url: "", + ajax_retag_url: "", + ajax_delete_tag_url: "", + ajax_add_tag_url: "" + }; + + var settings = jQuery.extend(defaults, options); + + // + // Initalize object's elements. + // + + // Get elements for this object. For this_obj, assume the last element with the id is the "this"; this is somewhat of a hack to address the problem + // that there may be two tagging elements for a single item if there are both community and individual tags for an element. + var this_obj = $(this); + var tag_area = this_obj.find('.tag-area'); + var toggle_link = this_obj.find('.toggle-link'); + var tag_input_field = this_obj.find('.tag-input'); + var add_tag_button = this_obj.find('.add-tag-button'); + + // Initialize toggle link. + toggle_link.click( function() { + // Take special actions depending on whether toggle is showing or hiding link. + var after_toggle_fn; + if (tag_area.is(":hidden")) { + after_toggle_fn = function() { + // If there are no tags, go right to editing mode by generating a click on the area. + var num_tags = $(this).find('.tag-button').length; + if (num_tags === 0) { + tag_area.click(); + } + }; + } else { + after_toggle_fn = function() { + tag_area.blur(); + }; + } + tag_area.slideToggle("fast", after_toggle_fn); + return $(this); + }); + + // Initialize tag input field. + if (settings.editable) { + tag_input_field.hide(); + } + tag_input_field.keyup( function(e) { + if ( e.keyCode === 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( + ( e.keyCode === 13 ) || // Return Key + ( e.keyCode === 188 ) || // Comma + ( e.keyCode === 32 ) // Space + ) { + // + // Check input. + // + + var new_value = this.value; + + // Suppress space after a ":" + if ( new_value.indexOf(": ", new_value.length - 2) !== -1) { + this.value = new_value.substring(0, new_value.length-1); + return false; + } + + // Remove trigger keys from input. + if ( (e.keyCode === 188) || (e.keyCode === 32) ) { + new_value = new_value.substring( 0 , new_value.length - 1 ); + } + + // Trim whitespace. + new_value = $.trim(new_value); + + // Too short? + if (new_value.length < 2) { + return false; + } + + // + // New tag OK - apply it. + // + + this.value = ""; // Reset text field now that tag is being added + + // Add button for tag after all other tag buttons. + var new_tag_button = build_tag_button(new_value); + var tag_buttons = tag_area.children(".tag-button"); + if (tag_buttons.length !== 0) { + var last_tag_button = tag_buttons.slice(tag_buttons.length-1); + last_tag_button.after(new_tag_button); + } else { + tag_area.prepend(new_tag_button); + } + + // Add tag to internal list. + var tag_name_and_value = new_value.split(":"); + settings.tags[tag_name_and_value[0]] = tag_name_and_value[1]; + + // Update toggle link text. + var new_text = settings.get_toggle_link_text_fn(settings.tags); + toggle_link.text(new_text); + + // Commit tag to server. + var zz = $(this); + $.ajax({ + url: settings.ajax_add_tag_url, + data: { new_tag: new_value }, + error: function() { + // Failed. Roll back changes and show alert. + new_tag_button.remove(); + delete settings.tags[tag_name_and_value[0]]; + var new_text = settings.get_toggle_link_text_fn(settings.tags); + toggle_link.text(new_text); + alert( "Add tag failed" ); + }, + success: function() { + // Flush autocomplete cache because it's not out of date. + // TODO: in the future, we could remove the particular item + // that was chosen from the cache rather than flush it. + zz.data('autocompleter').cacheFlush(); + } + }); + + return false; + } + }); + + // Add autocomplete to input. + var format_item_func = function(key, row_position, num_rows, value, search_term) { + var tag_name_and_value = value.split(":"); + return (tag_name_and_value.length === 1 ? tag_name_and_value[0] : tag_name_and_value[1]); + }; + var autocomplete_options = { selectFirst: false, formatItem: format_item_func, + autoFill: false, highlight: false }; + tag_input_field.autocomplete(settings.ajax_autocomplete_tag_url, autocomplete_options); + + + // Initialize delete tag images for current tags. + this_obj.find('.delete-tag-img').each(function() { + init_delete_tag_image( $(this) ); + }); + + + // Initialize tag click function. + init_tag_click_function($(this), settings.tag_click_fn); + + // Initialize "add tag" button. + add_tag_button.click( function() { + $(this).hide(); + + // Clicking on button is the same as clicking on the tag area. + tag_area.click(); + return false; + }); + + // + // Set up tag area interactions; these are needed only if tags are editable. + // + if (settings.editable) { + // When the tag area blurs, go to "view tag" mode. + tag_area.bind("blur", function(e) { + if (obj_length(settings.tags) > 0) { + add_tag_button.show(); + tag_input_field.hide(); + tag_area.removeClass("active-tag-area"); + // tag_area.addClass("tooltip"); + } else { + // No tags, so do nothing to ensure that input is still visible. + } + }); + + // On click, enable user to add tags. + tag_area.click( function(e) { + var is_active = $(this).hasClass("active-tag-area"); + + // If a "delete image" object was pressed and area is inactive, do nothing. + if ($(e.target).hasClass("delete-tag-img") && !is_active) { + return false; + } + + // If a "tag name" object was pressed and area is inactive, do nothing. + if ($(e.target).hasClass("tag-name") && !is_active) { + return false; + } + + // Remove tooltip. + // $(this).removeClass("tooltip"); + + // Hide add tag button, show tag_input field. Change background to show + // area is active. + $(this).addClass("active-tag-area"); + add_tag_button.hide(); + tag_input_field.show(); + tag_input_field.focus(); + + // Add handler to document that will call blur when the tag area is blurred; + // a tag area is blurred when a user clicks on an element outside the area. + var handle_document_click = function(e) { + var check_click = function(tag_area, target) { + var tag_area_id = tag_area.attr("id"); + // Blur the tag area if the element clicked on is not in the tag area. + if (target !== tag_area) { + tag_area.blur(); + $(window).unbind("click.tagging_blur"); + $(this).addClass("tooltip"); + } + }; + check_click(tag_area, $(e.target)); + }; + // TODO: we should attach the click handler to all frames in order to capture + // clicks outside the frame that this element is in. + //window.parent.document.onclick = handle_document_click; + //var temp = $(window.parent.document.body).contents().find("iframe").html(); + //alert(temp); + //$(document).parent().click(handle_document_click); + $(window).bind("click.tagging_blur", handle_document_click); + + return false; + }); + } + + // If using toggle link, hide the tag area. Otherwise, show the tag area. + if (settings.use_toggle_link) { + tag_area.hide(); + } + + // + // Helper functions. + // + + // + // Collapse tag name + value into a single string. + // + function build_tag_str(tag_name, tag_value) { + return tag_name + ( tag_value ? ":" + tag_value : ""); + } + + + // Initialize a "delete tag image": when click, delete tag from UI and send delete request to server. + function init_delete_tag_image(delete_img) { + $(delete_img).mouseenter( function () { + $(this).attr("src", settings.delete_tag_img_rollover); + }); + $(delete_img).mouseleave( function () { + $(this).attr("src", settings.delete_tag_img); + }); + $(delete_img).click( function () { + // Tag button is image's parent. + var tag_button = $(this).parent(); + + // Get tag name, value. + var tag_name_elt = tag_button.find(".tag-name").eq(0); + var tag_str = tag_name_elt.text(); + var tag_name_and_value = tag_str.split(":"); + var tag_name = tag_name_and_value[0]; + var tag_value = tag_name_and_value[1]; + + var prev_button = tag_button.prev(); + tag_button.remove(); + + // Remove tag from local list for consistency. + delete settings.tags[tag_name]; + + // Update toggle link text. + var new_text = settings.get_toggle_link_text_fn(settings.tags); + toggle_link.text(new_text); + + // Delete tag. + $.ajax({ + url: settings.ajax_delete_tag_url, + data: { tag_name: tag_name }, + error: function() { + // Failed. Roll back changes and show alert. + settings.tags[tag_name] = tag_value; + if (prev_button.hasClass("tag-button")) { + prev_button.after(tag_button); + } else { + tag_area.prepend(tag_button); + } + alert( "Remove tag failed" ); + + toggle_link.text(settings.get_toggle_link_text_fn(settings.tags)); + + // TODO: no idea why it's necessary to set this up again. + delete_img.mouseenter( function () { + $(this).attr("src", settings.delete_tag_img_rollover); + }); + delete_img.mouseleave( function () { + $(this).attr("src", settings.delete_tag_img); + }); + }, + success: function() {} + }); + + return true; + }); + } + + // + // Function that builds a tag button. + // + function build_tag_button(tag_str) { + // Build "delete tag" image. + var delete_img = $("<img/>").attr("src", settings.delete_tag_img).addClass("delete-tag-img"); + init_delete_tag_image(delete_img); + + // Build tag button. + var tag_name_elt = $("<span>").text(tag_str).addClass("tag-name"); + tag_name_elt.click( function() { + var tag_name_and_value = tag_str.split(":"); + settings.tag_click_fn(tag_name_and_value[0], tag_name_and_value[1]); + return true; + }); + + var tag_button = $("<span></span>").addClass("tag-button"); + tag_button.append(tag_name_elt); + // Allow delete only if element is editable. + if (settings.editable) { + tag_button.append(delete_img); + } + + return tag_button; + } + +}; diff -r ba66d120d001d6531300f57f215210056481f368 -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 client/galaxy/scripts/galaxy.base.js --- /dev/null +++ b/client/galaxy/scripts/galaxy.base.js @@ -0,0 +1,656 @@ +// requestAnimationFrame polyfill +(function() { + var lastTime = 0; + var vendors = ['ms', 'moz', 'webkit', 'o']; + for(var x = 0; x < vendors.length && !window.requestAnimationFrame; ++x) { + window.requestAnimationFrame = window[vendors[x]+'RequestAnimationFrame']; + window.cancelRequestAnimationFrame = window[vendors[x]+ + 'CancelRequestAnimationFrame']; + } + + if (!window.requestAnimationFrame) + window.requestAnimationFrame = function(callback, element) { + var currTime = new Date().getTime(); + var timeToCall = Math.max(0, 16 - (currTime - lastTime)); + var id = window.setTimeout(function() { callback(currTime + timeToCall); }, + timeToCall); + lastTime = currTime + timeToCall; + return id; + }; + + if (!window.cancelAnimationFrame) + window.cancelAnimationFrame = function(id) { + clearTimeout(id); + }; +}()); + +// IE doesn't implement Array.indexOf +if (!Array.indexOf) { + Array.prototype.indexOf = function(obj) { + for (var i = 0, len = this.length; i < len; i++) { + if (this[i] == obj) { + return i; + } + } + return -1; + }; +} + +// Returns the number of keys (elements) in an array/dictionary. +function obj_length(obj) { + if (obj.length !== undefined) { + return obj.length; + } + + var count = 0; + for (var element in obj) { + count++; + } + return count; +} + +$.fn.makeAbsolute = function(rebase) { + return this.each(function() { + var el = $(this); + var pos = el.position(); + el.css({ + position: "absolute", + marginLeft: 0, marginTop: 0, + top: pos.top, left: pos.left, + right: $(window).width() - ( pos.left + el.width() ) + }); + if (rebase) { + el.remove().appendTo("body"); + } + }); +}; + +/** + * Sets up popupmenu rendering and binds options functions to the appropriate links. + * initial_options is a dict with text describing the option pointing to either (a) a + * function to perform; or (b) another dict with two required keys, 'url' and 'action' (the + * function to perform. (b) is useful for exposing the underlying URL of the option. + */ +function make_popupmenu(button_element, initial_options) { + /* Use the $.data feature to store options with the link element. + This allows options to be changed at a later time + */ + var element_menu_exists = (button_element.data("menu_options")); + button_element.data("menu_options", initial_options); + + // If element already has menu, nothing else to do since HTML and actions are already set. + if (element_menu_exists) { return; } + + button_element.bind("click.show_popup", function(e) { + // Close existing visible menus + $(".popmenu-wrapper").remove(); + + // Need setTimeouts so clicks don't interfere with each other + setTimeout( function() { + // Dynamically generate the wrapper holding all the selectable options of the menu. + var menu_element = $( "<ul class='dropdown-menu' id='" + button_element.attr('id') + "-menu'></ul>" ); + var options = button_element.data("menu_options"); + if (obj_length(options) <= 0) { + $("<li>No Options.</li>").appendTo(menu_element); + } + $.each( options, function( k, v ) { + if (v) { + // Action can be either an anonymous function and a mapped dict. + var action = v.action || v; + menu_element.append( $("<li></li>").append( $("<a>").attr("href", v.url).html(k).click(action) ) ); + } else { + menu_element.append( $("<li></li>").addClass( "head" ).append( $("<a href='#'></a>").html(k) ) ); + } + }); + var wrapper = $( "<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>" ) + .append( menu_element ).appendTo( "body" ); + + var x = e.pageX - wrapper.width() / 2 ; + x = Math.min( x, $(document).scrollLeft() + $(window).width() - $(wrapper).width() - 5 ); + x = Math.max( x, $(document).scrollLeft() + 5 ); + + wrapper.css({ + top: e.pageY, + left: x + }); + }, 10); + + setTimeout( function() { + // Bind click event to current window and all frames to remove any visible menus + // Bind to document object instead of window object for IE compat + var close_popup = function(el) { + $(el).bind("click.close_popup", function() { + $(".popmenu-wrapper").remove(); + el.unbind("click.close_popup"); + }); + }; + close_popup( $(window.document) ); // Current frame + close_popup( $(window.top.document) ); // Parent frame + for (var frame_id = window.top.frames.length; frame_id--;) { // Sibling frames + var frame = $(window.top.frames[frame_id].document); + close_popup(frame); + } + }, 50); + + return false; + }); + +} + +/** + * Convert two seperate (often adjacent) divs into galaxy popupmenu + * - div 1 contains a number of anchors which become the menu options + * - div 1 should have a 'popupmenu' attribute + * - this popupmenu attribute contains the id of div 2 + * - div 2 becomes the 'face' of the popupmenu + * + * NOTE: make_popup_menus finds and operates on all divs with a popupmenu attr (no need to point it at something) + * but (since that selector searches the dom on the page), you can send a parent in + * NOTE: make_popup_menus, and make_popupmenu are horrible names + */ +function make_popup_menus( parent ) { + // find all popupmenu menu divs (divs that contains anchors to be converted to menu options) + // either in the parent or the document if no parent passed + parent = parent || document; + $( parent ).find( "div[popupmenu]" ).each( function() { + var options = {}; + var menu = $(this); + + // find each anchor in the menu, convert them into an options map: { a.text : click_function } + menu.find( "a" ).each( function() { + var link = $(this), + link_dom = link.get(0), + confirmtext = link_dom.getAttribute( "confirm" ), + href = link_dom.getAttribute( "href" ), + target = link_dom.getAttribute( "target" ); + + // no href - no function (gen. a label) + if (!href) { + options[ link.text() ] = null; + + } else { + options[ link.text() ] = { + url: href, + action: function() { + + // if theres confirm text, send the dialog + if ( !confirmtext || confirm( confirmtext ) ) { + // link.click() doesn't use target for some reason, + // so manually do it here. + if (target) { + window.open(href, target); + return false; + } + // For all other links, do the default action. + else { + link.click(); + } + } + } + }; + } + }); + // locate the element with the id corresponding to the menu's popupmenu attr + var box = $( parent ).find( "#" + menu.attr( 'popupmenu' ) ); + + // For menus with clickable link text, make clicking on the link go through instead + // of activating the popup menu + box.find("a").bind("click", function(e) { + e.stopPropagation(); // Stop bubbling so clicking on the link goes through + return true; + }); + + // attach the click events and menu box building to the box element + make_popupmenu(box, options); + box.addClass("popup"); + menu.remove(); + }); +} + +// Alphanumeric/natural sort fn +function naturalSort(a, b) { + // setup temp-scope variables for comparison evauluation + var re = /(-?[0-9\.]+)/g, + x = a.toString().toLowerCase() || '', + y = b.toString().toLowerCase() || '', + nC = String.fromCharCode(0), + xN = x.replace( re, nC + '$1' + nC ).split(nC), + yN = y.replace( re, nC + '$1' + nC ).split(nC), + xD = (new Date(x)).getTime(), + yD = xD ? (new Date(y)).getTime() : null; + // natural sorting of dates + if ( yD ) { + if ( xD < yD ) { return -1; } + else if ( xD > yD ) { return 1; } + } + // natural sorting through split numeric strings and default strings + var oFxNcL, oFyNcL; + for ( var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++ ) { + oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc]; + oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc]; + if (oFxNcL < oFyNcL) { return -1; } + else if (oFxNcL > oFyNcL) { return 1; } + } + return 0; +} + +$.fn.refresh_select2 = function() { + var select_elt = $(this); + var options = { width: "resolve", + closeOnSelect: !select_elt.is("[MULTIPLE]") + }; + return select_elt.select2( options ); +} + +// Replace select box with a text input box + autocomplete. +function replace_big_select_inputs(min_length, max_length, select_elts) { + // To do replace, the select2 plugin must be loaded. + + if (!jQuery.fn.select2) { + return; + } + + // Set default for min_length and max_length + if (min_length === undefined) { + min_length = 20; + } + if (max_length === undefined) { + max_length = 3000; + } + + select_elts = select_elts || $('select'); + + select_elts.each( function() { + var select_elt = $(this).not('[multiple]'); + // Make sure that options is within range. + var num_options = select_elt.find('option').length; + if ( (num_options < min_length) || (num_options > max_length) ) { + return; + } + + if (select_elt.hasClass("no-autocomplete")) { + return; + } + + /* Replaced jQuery.autocomplete with select2, notes: + * - multiple selects are supported + * - the original element is updated with the value, convert_to_values should not be needed + * - events are fired when updating the original element, so refresh_on_change should just work + * + * - should we still sort dbkey fields here? + */ + select_elt.refresh_select2(); + }); +} + +/** + * Make an element with text editable: (a) when user clicks on text, a textbox/area + * is provided for editing; (b) when enter key pressed, element's text is set and on_finish + * is called. + */ +// TODO: use this function to implement async_save_text (implemented below). +$.fn.make_text_editable = function(config_dict) { + // Get config options. + var num_cols = ("num_cols" in config_dict ? config_dict.num_cols : 30), + num_rows = ("num_rows" in config_dict ? config_dict.num_rows : 4), + use_textarea = ("use_textarea" in config_dict ? config_dict.use_textarea : false), + on_finish = ("on_finish" in config_dict ? config_dict.on_finish : null), + help_text = ("help_text" in config_dict ? config_dict.help_text : null); + + // Add element behavior. + var container = $(this); + container.addClass("editable-text").click(function(e) { + // If there's already an input element, editing is active, so do nothing. + if ($(this).children(":input").length > 0) { + return; + } + + container.removeClass("editable-text"); + + // Handler for setting element text. + var set_text = function(new_text) { + container.find(":input").remove(); + + if (new_text !== "") { + container.text(new_text); + } + else { + // No text; need a line so that there is a click target. + container.html("<br>"); + } + container.addClass("editable-text"); + + if (on_finish) { + on_finish(new_text); + } + }; + + // Create input element(s) for editing. + var cur_text = ("cur_text" in config_dict ? config_dict.cur_text : container.text() ), + input_elt, button_elt; + + if (use_textarea) { + input_elt = $("<textarea/>") + .attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text)) + .keyup(function(e) { + if (e.keyCode === 27) { + // Escape key. + set_text(cur_text); + } + }); + button_elt = $("<button/>").text("Done").click(function() { + set_text(input_elt.val()); + // Return false so that click does not propogate to container. + return false; + }); + } + else { + input_elt = $("<input type='text'/>").attr({ value: $.trim(cur_text), size: num_cols }) + .blur(function() { + set_text(cur_text); + }).keyup(function(e) { + if (e.keyCode === 27) { + // Escape key. + $(this).trigger("blur"); + } else if (e.keyCode === 13) { + // Enter key. + set_text($(this).val()); + } + + // Do not propogate event to avoid unwanted side effects. + e.stopPropagation(); + }); + } + + // Replace text with input object(s) and focus & select. + container.text(""); + container.append(input_elt); + if (button_elt) { + container.append(button_elt); + } + input_elt.focus(); + input_elt.select(); + + // Do not propogate to elements below b/c that blurs input and prevents it from being used. + e.stopPropagation(); + }); + + // Add help text if there some. + if (help_text) { + container.attr("title", help_text).tooltip(); + } + + return container; +}; + +/** + * Edit and save text asynchronously. + */ +function async_save_text( click_to_edit_elt, text_elt_id, save_url, + text_parm_name, num_cols, use_textarea, num_rows, on_start, on_finish ) { + // Set defaults if necessary. + if (num_cols === undefined) { + num_cols = 30; + } + if (num_rows === undefined) { + num_rows = 4; + } + + // Set up input element. + $("#" + click_to_edit_elt).click(function() { + // Check if this is already active + if ( $("#renaming-active").length > 0) { + return; + } + var text_elt = $("#" + text_elt_id), + old_text = text_elt.text(), + t; + + if (use_textarea) { + t = $("<textarea></textarea>").attr({ rows: num_rows, cols: num_cols }).text( $.trim(old_text) ); + } else { + t = $("<input type='text'></input>").attr({ value: $.trim(old_text), size: num_cols }); + } + t.attr("id", "renaming-active"); + t.blur( function() { + $(this).remove(); + text_elt.show(); + if (on_finish) { + on_finish(t); + } + }); + t.keyup( function( e ) { + if ( e.keyCode === 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( e.keyCode === 13 ) { + // Enter key submits + var ajax_data = {}; + ajax_data[text_parm_name] = $(this).val(); + $(this).trigger( "blur" ); + $.ajax({ + url: save_url, + data: ajax_data, + error: function() { + alert( "Text editing for elt " + text_elt_id + " failed" ); + // TODO: call finish or no? For now, let's not because error occurred. + }, + success: function(processed_text) { + // Set new text and call finish method. + if (processed_text !== "") { + text_elt.text(processed_text); + } else { + text_elt.html("<em>None</em>"); + } + if (on_finish) { + on_finish(t); + } + } + }); + } + }); + + if (on_start) { + on_start(t); + } + // Replace text with input object and focus & select. + text_elt.hide(); + t.insertAfter(text_elt); + t.focus(); + t.select(); + + return; + }); +} + +function commatize( number ) { + number += ''; // Convert to string + var rgx = /(\d+)(\d{3})/; + while (rgx.test(number)) { + number = number.replace(rgx, '$1' + ',' + '$2'); + } + return number; +} + +// Reset tool search to start state. +function reset_tool_search( initValue ) { + // Function may be called in top frame or in tool_menu_frame; + // in either case, get the tool menu frame. + var tool_menu_frame = $("#galaxy_tools").contents(); + if (tool_menu_frame.length === 0) { + tool_menu_frame = $(document); + } + + // Remove classes that indicate searching is active. + $(this).removeClass("search_active"); + tool_menu_frame.find(".toolTitle").removeClass("search_match"); + + // Reset visibility of tools and labels. + tool_menu_frame.find(".toolSectionBody").hide(); + tool_menu_frame.find(".toolTitle").show(); + tool_menu_frame.find(".toolPanelLabel").show(); + tool_menu_frame.find(".toolSectionWrapper").each( function() { + if ($(this).attr('id') !== 'recently_used_wrapper') { + // Default action. + $(this).show(); + } else if ($(this).hasClass("user_pref_visible")) { + $(this).show(); + } + }); + tool_menu_frame.find("#search-no-results").hide(); + + // Reset search input. + tool_menu_frame.find("#search-spinner").hide(); + if (initValue) { + var search_input = tool_menu_frame.find("#tool-search-query"); + search_input.val("search tools"); + } +} + +// Create GalaxyAsync object. +var GalaxyAsync = function(log_action) { + this.url_dict = {}; + this.log_action = (log_action === undefined ? false : log_action); +}; + +GalaxyAsync.prototype.set_func_url = function( func_name, url ) { + this.url_dict[func_name] = url; +}; + +// Set user preference asynchronously. +GalaxyAsync.prototype.set_user_pref = function( pref_name, pref_value ) { + // Get URL. + var url = this.url_dict[arguments.callee]; + if (url === undefined) { return false; } + $.ajax({ + url: url, + data: { "pref_name" : pref_name, "pref_value" : pref_value }, + error: function() { return false; }, + success: function() { return true; } + }); +}; + +// Log user action asynchronously. +GalaxyAsync.prototype.log_user_action = function( action, context, params ) { + if (!this.log_action) { return; } + + // Get URL. + var url = this.url_dict[arguments.callee]; + if (url === undefined) { return false; } + $.ajax({ + url: url, + data: { "action" : action, "context" : context, "params" : params }, + error: function() { return false; }, + success: function() { return true; } + }); +}; + +// Initialize refresh events. +function init_refresh_on_change () { + $("select[refresh_on_change='true']") + .off('change') + .change(function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + $(document).trigger("convert_to_values"); // Convert autocomplete text to values + select_field.get(0).form.submit(); + }); + + // checkboxes refresh on change + $(":checkbox[refresh_on_change='true']") + .off('click') + .click( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + + // Links with confirmation + $( "a[confirm]" ) + .off('click') + .click( function() { + return confirm( $(this).attr("confirm") ); + }); +}; + + +// jQuery plugin to prevent double submission of forms +// Ref: http://stackoverflow.com/questions/2830542/prevent-double-submission-of-for… +jQuery.fn.preventDoubleSubmission = function() { + $(this).on('submit',function(e){ + var $form = $(this); + + if ($form.data('submitted') === true) { + // Previously submitted - don't submit again + e.preventDefault(); + } else { + // Mark it so that the next submit can be ignored + $form.data('submitted', true); + } + }); + + // Keep chainability + return this; +}; + +$(document).ready( function() { + + // Refresh events for form fields. + init_refresh_on_change(); + + // Tooltips + if ( $.fn.tooltip ) { + // Put tooltips below items in panel header so that they do not overlap masthead. + $(".unified-panel-header [title]").tooltip( { placement: 'bottom' } ); + + // default tooltip initialization, it will follow the data-placement tag for tooltip location + // and fallback to 'top' if not present + $("[title]").tooltip(); + } + // Make popup menus. + make_popup_menus(); + + // Replace big selects. + replace_big_select_inputs(20, 1500); + + // If galaxy_main frame does not exist and link targets galaxy_main, + // add use_panels=True and set target to self. + $("a").click( function() { + var anchor = $(this); + var galaxy_main_exists = (parent.frames && parent.frames.galaxy_main); + if ( ( anchor.attr( "target" ) == "galaxy_main" ) && ( !galaxy_main_exists ) ) { + var href = anchor.attr("href"); + if (href.indexOf("?") == -1) { + href += "?"; + } + else { + href += "&"; + } + href += "use_panels=True"; + anchor.attr("href", href); + anchor.attr("target", "_self"); + } + return anchor; + }); + +}); diff -r ba66d120d001d6531300f57f215210056481f368 -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 client/galaxy/scripts/galaxy.frame.js --- /dev/null +++ b/client/galaxy/scripts/galaxy.frame.js @@ -0,0 +1,173 @@ +// dependencies +define(["galaxy.masthead", "mvc/ui/ui-frames"], function(mod_masthead, Frames) { + +// frame manager +var GalaxyFrame = Backbone.View.extend( +{ + // base element + el_main: 'body', + + // frame active/disabled + active: false, + + // button active + button_active: null, + + // button load + button_load : null, + + // initialize + initialize : function(options) + { + // add to masthead menu + var self = this; + + // create frames + this.frames = new Frames.View({ + visible: false, + }); + + // add activate icon + this.button_active = new mod_masthead.GalaxyMastheadIcon ( + { + icon : 'fa-th', + tooltip : 'Enable/Disable Scratchbook', + onclick : function() { self._activate(); }, + onunload : function() { + if (self.frames.length() > 0) { + return "You opened " + self.frames.length() + " frame(s) which will be lost."; + } + } + }); + + // add to masthead + Galaxy.masthead.append(this.button_active); + + // add load icon + this.button_load = new mod_masthead.GalaxyMastheadIcon ( + { + icon : 'fa-eye', + tooltip : 'Show/Hide Scratchbook', + onclick : function(e) { + if (self.frames.visible) { + self.frames.hide(); + } else { + self.frames.show(); + } + }, + with_number : true + }); + + // add to masthead + Galaxy.masthead.append(this.button_load); + + // create + this.setElement(this.frames.$el); + + // append to main + $(this.el_main).append(this.$el); + + // refresh menu + this.frames.setOnChange(function() { + self._refresh(); + }); + this._refresh(); + }, + + // adds and displays a new frame/window + add: function(options) + { + // open new tab + if (options.target == '_blank') + { + window.open(options.content); + return; + } + + // reload entire window + if (options.target == '_top' || options.target == '_parent' || options.target == '_self') + { + window.location = options.content; + return; + } + + // validate + if (!this.active) + { + // fix url if main frame is unavailable + var $galaxy_main = $(window.parent.document).find('#galaxy_main'); + if (options.target == 'galaxy_main' || options.target == 'center') + { + if ($galaxy_main.length === 0) + { + var href = options.content; + if (href.indexOf('?') == -1) + href += '?'; + else + href += '&'; + href += 'use_panels=True'; + window.location = href; + } else { + $galaxy_main.attr('src', options.content); + } + } else + window.location = options.content; + + // stop + return; + } + + // add to frames view + this.frames.add(options); + }, + + // activate/disable panel + _activate: function () + { + // check + if (this.active) + { + // disable + this.active = false; + + // toggle + this.button_active.untoggle(); + + // hide panel + this.frames.hide(); + } else { + // activate + this.active = true; + + // untoggle + this.button_active.toggle(); + } + }, + + // update frame counter + _refresh: function() + { + // update on screen counter + this.button_load.number(this.frames.length()); + + // check + if(this.frames.length() === 0) + this.button_load.hide(); + else + this.button_load.show(); + + // check + if (this.frames.visible) { + this.button_load.toggle(); + } else { + this.button_load.untoggle(); + } + } +}); + +// return +return { + GalaxyFrame: GalaxyFrame +}; + +}); diff -r ba66d120d001d6531300f57f215210056481f368 -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 client/galaxy/scripts/galaxy.library.js --- /dev/null +++ b/client/galaxy/scripts/galaxy.library.js @@ -0,0 +1,159 @@ +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// === MAIN GALAXY LIBRARY MODULE ==== +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM + +define([ + "galaxy.masthead", + "utils/utils", + "libs/toastr", + "mvc/base-mvc", + "mvc/library/library-model", + "mvc/library/library-folderlist-view", + "mvc/library/library-librarylist-view", + "mvc/library/library-librarytoolbar-view", + "mvc/library/library-foldertoolbar-view", + "mvc/library/library-dataset-view", + "mvc/library/library-library-view", + "mvc/library/library-folder-view" + ], +function(mod_masthead, + mod_utils, + mod_toastr, + mod_baseMVC, + mod_library_model, + mod_folderlist_view, + mod_librarylist_view, + mod_librarytoolbar_view, + mod_foldertoolbar_view, + mod_library_dataset_view, + mod_library_library_view, + mod_library_folder_view + ) { + +// ============================================================================ +// ROUTER +var LibraryRouter = Backbone.Router.extend({ + initialize: function() { + this.routesHit = 0; + //keep count of number of routes handled by the application + Backbone.history.on('route', function() { this.routesHit++; }, this); + }, + + routes: { + "" : "libraries", + "library/:library_id/permissions" : "library_permissions", + "folders/:folder_id/permissions" : "folder_permissions", + "folders/:id" : "folder_content", + "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", + "folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions", + "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version", + "folders/:folder_id/download/:format" : "download" + }, + + back: function() { + if(this.routesHit > 1) { + //more than one route hit -> user did not land to current page directly + window.history.back(); + } else { + //otherwise go to the home page. Use replaceState if available so + //the navigation doesn't create an extra history entry + this.navigate('#', {trigger:true, replace:true}); + } + } +}); + +// ============================================================================ +/** session storage for library preferences */ +var LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({ + defaults : { + with_deleted : false, + sort_order : 'asc', + sort_by : 'name' + } +}); + +// ============================================================================ +// Main controller of Galaxy Library +var GalaxyLibrary = Backbone.View.extend({ + + libraryToolbarView: null, + libraryListView: null, + library_router: null, + libraryView: null, + folderToolbarView: null, + folderListView: null, + datasetView: null, + + initialize : function(){ + Galaxy.libraries = this; + + this.preferences = new LibraryPrefs( {id: 'global-lib-prefs'} ); + + this.library_router = new LibraryRouter(); + + this.library_router.on('route:libraries', function() { + Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); + Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); + }); + + this.library_router.on('route:folder_content', function(id) { + if (Galaxy.libraries.folderToolbarView){ + Galaxy.libraries.folderToolbarView.$el.unbind('click'); + } + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); + }); + + this.library_router.on('route:download', function(folder_id, format) { + if ($('#folder_list_body').find(':checked').length === 0) { + mod_toastr.info('You have to select some datasets to download'); + Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + } else { + Galaxy.libraries.folderToolbarView.download(folder_id, format); + Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); + } + }); + + this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); + }); + this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); + }); + + this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); + }); + + this.library_router.on('route:library_permissions', function(library_id){ + if (Galaxy.libraries.libraryView){ + Galaxy.libraries.libraryView.$el.unbind('click'); + } + Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); + }); + + this.library_router.on('route:folder_permissions', function(folder_id){ + if (Galaxy.libraries.folderView){ + Galaxy.libraries.folderView.$el.unbind('click'); + } + Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); + }); + + Backbone.history.start({pushState: false}); + } +}); + +return { + GalaxyApp: GalaxyLibrary +}; + +}); This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/898a4bda2318/ Changeset: 898a4bda2318 User: carlfeberhard Date: 2014-09-16 15:41:35 Summary: Merged galaxy/galaxy-central into default Affected #: 117 files diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 README.txt --- a/README.txt +++ b/README.txt @@ -22,13 +22,13 @@ http://localhost:8080 You may wish to make changes from the default configuration. This can be done -in the universe_wsgi.ini file. Tools can be either installed from the Tool Shed +in the config/galaxy.ini file. Tools can be either installed from the Tool Shed or added manually. For details please see the Galaxy wiki: -https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial. +https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial Not all dependencies are included for the tools provided in the sample tool_conf.xml. A full list of external dependencies is available at: -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies \ No newline at end of file +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -43,15 +43,10 @@ " SAMPLES=" -tool_conf.xml.sample -datatypes_conf.xml.sample -universe_wsgi.ini.sample -tool_data_table_conf.xml.sample -tool_sheds_conf.xml.sample -shed_tool_data_table_conf.xml.sample -migrated_tools_conf.xml.sample -data_manager_conf.xml.sample -shed_data_manager_conf.xml.sample +config/galaxy.ini.sample +config/shed_tool_data_table_conf.xml.sample +config/migrated_tools_conf.xml.sample +config/shed_data_manager_conf.xml.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/shared/ucsc/builds.txt.sample diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 client/galaxy/scripts/galaxy-app-base.js --- a/client/galaxy/scripts/galaxy-app-base.js +++ b/client/galaxy/scripts/galaxy-app-base.js @@ -11,7 +11,7 @@ * logger : the logger/metrics-logger * localize : the string localizer * config : the current configuration (any k/v in - * universe_wsgi.ini available from the configuration API) + * galaxy.ini available from the configuration API) * user : the current user (as a mvc/user/user-model) */ function GalaxyApp( options ){ diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 config/data_manager_conf.xml.sample --- /dev/null +++ b/config/data_manager_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<data_managers> +</data_managers> diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 config/datatypes_conf.xml.sample --- /dev/null +++ b/config/datatypes_conf.xml.sample @@ -0,0 +1,333 @@ +<?xml version="1.0"?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Ab1"/> + <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false" /> + <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true" /> + <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true" /> + <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/> + <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/> + <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM"> + <converter file="bam_to_bai.xml" target_datatype="bai"/> + <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="ucsc/bam.xml" /> + <display file="ensembl/ensembl_bam.xml" /> + <display file="igv/bam.xml" /> + <display file="igb/bam.xml" /> + </datatype> + <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed"> + <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> + <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="bed_to_fli_converter.xml" target_datatype="fli"/> +  + <display file="igb/bed.xml" /> + </datatype> + <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> + <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/bedgraph.xml" /> + </datatype> + <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /> + <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> + </datatype> + <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /> + <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> + <converter file="len_to_linecount.xml" target_datatype="linecount" /> + </datatype> + <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigbed.xml" /> + <display file="igb/bb.xml" /> + </datatype> + <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigwig.xml" /> + <display file="igb/bigwig.xml" /> + </datatype> + <datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> +  + <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> +  + <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/> + <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/> + <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" /> + <datatype extension="data_manager_json" type="galaxy.datatypes.data:Text" mimetype="application/json" subclass="True" display_in_upload="False"/> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" description="A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('>') symbol in the first column. All lines should be shorter than 80 characters." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fasta"> + <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/> + <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/> + <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/> + <converter file="fasta_to_2bit.xml" target_datatype="twobit"/> + <converter file="fasta_to_len.xml" target_datatype="len"/> + </datatype> + <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/> + <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/> + <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/> + <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> +  + </datatype> + <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true" description="GFF lines have nine required fields that must be tab-separated." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF"> + <converter file="gff_to_bed_converter.xml" target_datatype="bed"/> + <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="gff_to_fli_converter.xml" target_datatype="fli"/> + <display file="ensembl/ensembl_gff.xml" inherit="True"/> +  + </datatype> + <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true" description="The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF3"/> + <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/> + <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/> + <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"> + <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /> + </datatype> + <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> + <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> + <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/> + <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order)." > + <converter file="interval_to_bed_converter.xml" target_datatype="bed"/> + <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/> + <converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/> + <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/> +  + <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/> + <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/> + <display file="rviewer/bed.xml" inherit="True"/> + </datatype> + <datatype extension="picard_interval_list" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"> + <converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/> + </datatype> + <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_report" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/> + <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/> + <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/> + <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/> + <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/> + <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/> + <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/> + <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/> + <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/> + <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/> + <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/> + <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/> + <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/> + <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/> + <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/> + <datatype extension="laj" type="galaxy.datatypes.images:Laj"/> + <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true" description="Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.." /> + <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true" description="TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated 'variable=value' pairs. There should be no white space surrounding the '='." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#MAF"> + <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/> + <converter file="maf_to_interval_converter.xml" target_datatype="interval"/> + </datatype> + <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack"> + <display file="ucsc/maf_customtrack.xml" /> + </datatype> + <datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True"> + <converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> + <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/> + <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + </datatype> + <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/> + <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> + <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> + <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/> + <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/> + <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/> + <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/> + <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"> + <converter file="sam_to_bam.xml" target_datatype="bam"/> + <converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> + <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/> + <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/> + <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/> + <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/> + <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/> + <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/> + <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/> + <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"> + <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/> + <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="ucsc/vcf.xml" /> + <display file="igv/vcf.xml" /> + <display file="rviewer/vcf.xml" inherit="True"/> + </datatype> + <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True"/> + <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> + <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true" description="The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Wig"> + <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/> +  + <display file="igb/wig.xml" /> + </datatype> + <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="vcf_bgzip" type_extension="bgzip" subclass="True" > + <display file="igv/vcf.xml" /> + <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/> + </datatype> +  + <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" /> + <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" /> + <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /> +  + <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> +  + <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/> +  + <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/> + <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" /> +  + <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/> +  + <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/> +  + <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/> +  +  + <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true"> + </datatype> + <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/> +  + <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"> + <converter file="lped_to_fped_converter.xml" target_datatype="fped"/> + <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/> + </datatype> +  + <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"> + <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/> + <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/> + </datatype> + <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/> +  + <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/> + <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/> + <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/> + <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/> + <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/> + <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/> +  +  + <datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/> + <datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/> + <datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/> + </registration> + <sniffers> +  + <sniffer type="galaxy.datatypes.tabular:Vcf"/> + <sniffer type="galaxy.datatypes.binary:TwoBit"/> + <sniffer type="galaxy.datatypes.binary:SQlite"/> + <sniffer type="galaxy.datatypes.binary:Bam"/> + <sniffer type="galaxy.datatypes.binary:Sff"/> + <sniffer type="galaxy.datatypes.xml:Phyloxml"/> + <sniffer type="galaxy.datatypes.xml:GenericXml"/> + <sniffer type="galaxy.datatypes.sequence:Maf"/> + <sniffer type="galaxy.datatypes.sequence:Lav"/> + <sniffer type="galaxy.datatypes.sequence:csFasta"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> + <sniffer type="galaxy.datatypes.sequence:Fasta"/> + <sniffer type="galaxy.datatypes.sequence:Fastq"/> + <sniffer type="galaxy.datatypes.interval:Wiggle"/> + <sniffer type="galaxy.datatypes.images:Html"/> + <sniffer type="galaxy.datatypes.images:Pdf"/> + <sniffer type="galaxy.datatypes.sequence:Axt"/> + <sniffer type="galaxy.datatypes.interval:Bed"/> + <sniffer type="galaxy.datatypes.interval:CustomTrack"/> + <sniffer type="galaxy.datatypes.interval:Gtf"/> + <sniffer type="galaxy.datatypes.interval:Gff"/> + <sniffer type="galaxy.datatypes.interval:Gff3"/> + <sniffer type="galaxy.datatypes.tabular:Pileup"/> + <sniffer type="galaxy.datatypes.interval:Interval"/> + <sniffer type="galaxy.datatypes.tabular:Sam"/> + <sniffer type="galaxy.datatypes.data:Newick"/> + <sniffer type="galaxy.datatypes.data:Nexus"/> + <sniffer type="galaxy.datatypes.images:Jpg"/> + <sniffer type="galaxy.datatypes.images:Png"/> + <sniffer type="galaxy.datatypes.images:Tiff"/> + <sniffer type="galaxy.datatypes.images:Bmp"/> + <sniffer type="galaxy.datatypes.images:Gif"/> + <sniffer type="galaxy.datatypes.images:Im"/> + <sniffer type="galaxy.datatypes.images:Pcd"/> + <sniffer type="galaxy.datatypes.images:Pcx"/> + <sniffer type="galaxy.datatypes.images:Ppm"/> + <sniffer type="galaxy.datatypes.images:Psd"/> + <sniffer type="galaxy.datatypes.images:Xbm"/> + <sniffer type="galaxy.datatypes.images:Rgb"/> + <sniffer type="galaxy.datatypes.images:Pbm"/> + <sniffer type="galaxy.datatypes.images:Pgm"/> + <sniffer type="galaxy.datatypes.images:Xpm"/> + <sniffer type="galaxy.datatypes.images:Eps"/> + <sniffer type="galaxy.datatypes.images:Rast"/> +  + </sniffers> + <build_sites> +  + <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/> + <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/> + <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/> + <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/> + <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/> + <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/> + </build_sites> +</datatypes> diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 config/demo_sequencer_wsgi.ini.sample --- /dev/null +++ b/config/demo_sequencer_wsgi.ini.sample @@ -0,0 +1,66 @@ +# ---- HTTP Server ---------------------------------------------------------- + +[server:main] + +use = egg:Paste#http +port = 9011 +host = 0.0.0.0 +use_threadpool = true +threadpool_workers = 10 + +# ---- Galaxy Demo Sequencer Emulator Interface ------------------------------------------------- + +[app:main] + +# Specifies the factory for the universe WSGI application +paste.app_factory = galaxy.webapps.demo_sequencer.buildapp:app_factory +log_level = DEBUG + +# Where dataset files are saved +file_path = database/demo_sequencer_files +# Temporary storage for additional datasets, this should be shared through the cluster +new_file_path = database/tmp + +# Sequencer emulator actions +sequencer_actions_config_file = %(here)s/lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml + +# Session support (beaker) +use_beaker_session = True +session_type = memory +session_data_dir = %(here)s/database/beaker_sessions +session_key = galaxysessions +session_secret = changethisinproduction + +# Galaxy session security +id_secret = changethisinproductiontoo + +# Configuration for debugging middleware +debug = true +use_lint = false + +# NEVER enable this on a public site (even test or QA) +# use_interactive = true + +# this should be a comma-separated list of valid Galaxy users +#admin_users = test(a)bx.psu.edu + +# Force everyone to log in (disable anonymous access) +require_login = False + +# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) +## use_heartbeat = True + +# Profiling middleware (cProfile based) +## use_profile = True + +# Use the new iframe / javascript based layout +use_new_layout = true + +# Serving static files (needed if running standalone) +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 config/external_service_types_conf.xml.sample --- /dev/null +++ b/config/external_service_types_conf.xml.sample @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<external_service_types> + <external_service_type file="simple_unknown_sequencer.xml" visible="False"/> + <external_service_type file="applied_biosystems_solid.xml" visible="True"/> +</external_service_types> diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 config/galaxy.ini.sample --- /dev/null +++ b/config/galaxy.ini.sample @@ -0,0 +1,889 @@ +# +# Galaxy is configured by default to be useable in a single-user development +# environment. To tune the application for a multi-user production +# environment, see the documentation at: +# +# http://usegalaxy.org/production +# + +# Throughout this sample configuration file, except where stated otherwise, +# uncommented values override the default if left unset, whereas commented +# values are set to the default value. Relative paths are relative to the root +# Galaxy directory. +# +# Examples of many of these options are explained in more detail in the wiki: +# +# https://wiki.galaxyproject.org/Admin/Config +# +# Config hackers are encouraged to check there before asking for help. + +# ---- HTTP Server ---------------------------------------------------------- + +# Configuration of the internal HTTP server. + +[server:main] + +# The internal HTTP server to use. Currently only Paste is provided. This +# option is required. +use = egg:Paste#http + +# The port on which to listen. +#port = 8080 + +# The address on which to listen. By default, only listen to localhost (Galaxy +# will not be accessible over the network). Use '0.0.0.0' to listen on all +# available network interfaces. +#host = 127.0.0.1 + +# Use a threadpool for the web server instead of creating a thread for each +# request. +use_threadpool = True + +# Number of threads in the web server thread pool. +#threadpool_workers = 10 + +# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +threadpool_kill_thread_limit = 10800 + +# ---- Filters -------------------------------------------------------------- + +# Filters sit between Galaxy and the HTTP server. + +# These filters are disabled by default. They can be enabled with +# 'filter-with' in the [app:main] section below. + +# Define the gzip filter. +[filter:gzip] +use = egg:Paste#gzip + +# Define the proxy-prefix filter. +[filter:proxy-prefix] +use = egg:PasteDeploy#prefix +prefix = /galaxy + +# ---- Galaxy --------------------------------------------------------------- + +# Configuration of the Galaxy application. + +[app:main] + +# -- Application and filtering + +# The factory for the WSGI application. This should not be changed. +paste.app_factory = galaxy.web.buildapp:app_factory + +# If not running behind a proxy server, you may want to enable gzip compression +# to decrease the size of data transferred over the network. If using a proxy +# server, please enable gzip compression there instead. +#filter-with = gzip + +# If running behind a proxy server and Galaxy is served from a subdirectory, +# enable the proxy-prefix filter and set the prefix in the +# [filter:proxy-prefix] section above. +#filter-with = proxy-prefix + +# If proxy-prefix is enabled and you're running more than one Galaxy instance +# behind one hostname, you will want to set this to the same path as the prefix +# in the filter above. This value becomes the "path" attribute set in the +# cookie so the cookies from each instance will not clobber each other. +#cookie_path = None + +# -- Database + +# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You +# may use a SQLAlchemy connection string to specify an external database +# instead. This string takes many options which are explained in detail in the +# config file documentation. +#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# If the server logs errors about not having enough database pool connections, +# you will want to increase these values, or consider running more Galaxy +# processes. +#database_engine_option_pool_size = 5 +#database_engine_option_max_overflow = 10 + +# If using MySQL and the server logs the error "MySQL server has gone away", +# you will want to set this to some positive value (7200 should work). +#database_engine_option_pool_recycle = -1 + +# If large database query results are causing memory or response time issues in +# the Galaxy process, leave the result on the server instead. This option is +# only available for PostgreSQL and is highly recommended. +#database_engine_option_server_side_cursors = False + +# Log all database transactions, can be useful for debugging and performance +# profiling. Logging is done via Python's 'logging' module under the qualname +# 'galaxy.model.orm.logging_connection_proxy' +#database_query_profiling_proxy = False + +# By default, Galaxy will use the same database to track user data and +# tool shed install data. There are many situtations in which it is +# valuable to seperate these - for instance bootstrapping fresh Galaxy +# instances with pretested installs. The following optin can be used to +# separate the tool shed install database (all other options listed above +# but prefixed with install_ are also available). +#install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# -- Files and directories + +# Dataset files are stored in this directory. +#file_path = database/files + +# Temporary files are stored in this directory. +#new_file_path = database/tmp + +# Tool config files, defines what tools are available in Galaxy. +# Tools can be locally developed or installed from Galaxy tool sheds. +# (config/tool_conf.xml.sample will be used if left unset and +# config/tool_conf.xml does not exist). +#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml + +# Enable / disable checking if any tools defined in the above non-shed tool_config_files +# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool +# Shed. This setting should generally be set to False only for development Galaxy environments +# that are often rebuilt from scratch where migrated tools do not need to be available in the +# Galaxy tool panel. If the following setting remains commented, the default setting will be True. +#check_migrate_tools = True + +# Tool config maintained by tool migration scripts. If you use the migration +# scripts to install tools that have been migrated to the tool shed upon a new +# release, they will be added to this tool config file. +#migrated_tools_config = migrated_tools_conf.xml + +# File that contains the XML section and tool tags from all tool panel config +# files integrated into a single file that defines the tool panel layout. This +# file can be changed by the Galaxy administrator to alter the layout of the +# tool panel. If not present, Galaxy will create it. +#integrated_tool_panel_config = integrated_tool_panel.xml + +# Default path to the directory containing the tools defined in tool_conf.xml. +# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. +#tool_path = tools + +# Path to the directory in which tool dependencies are placed. This is used by +# the tool shed to install dependencies and can also be used by administrators +# to manually install or link to dependencies. For details, see: +# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies +# If this option is not set to a valid path, installing tools with dependencies +# from the Tool Shed will fail. +#tool_dependency_dir = None + +# File containing the Galaxy Tool Sheds that should be made available to +# install from in the admin interface (.sample used if default does not exist). +#tool_sheds_config_file = config/tool_sheds_conf.xml + +# Enable automatic polling of relative tool sheds to see if any updates +# are available for installed repositories. Ideally only one Galaxy +# server process should be able to check for repository updates. The +# setting for hours_between_check should be an integer between 1 and 24. +#enable_tool_shed_check = False +#hours_between_check = 12 + +# Enable use of an in-memory registry with bi-directional relationships +# between repositories (i.e., in addition to lists of dependencies for a +# repository, keep an in-memory registry of dependent items for each repository. +#manage_dependency_relationships = False + +# XML config file that contains data table entries for the +# ToolDataTableManager. This file is manually # maintained by the Galaxy +# administrator (.sample used if default does not exist). +#tool_data_table_config_path = config/tool_data_table_conf.xml + +# XML config file that contains additional data table entries for the ToolDataTableManager. This file +# is automatically generated based on the current installed tool shed repositories that contain valid +# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically +# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. +#shed_tool_data_table_config = config/shed_tool_data_table_conf.xml + +# Directory where data used by tools is located, see the samples in that +# directory and the wiki for help: +# https://wiki.galaxyproject.org/Admin/DataIntegration +#tool_data_path = tool-data + +# File containing old-style genome builds +#builds_file_path = tool-data/shared/ucsc/builds.txt + +# Directory where chrom len files are kept, currently mainly used by trackster +#len_file_path = tool-data/shared/ucsc/chrom + +# Datatypes config file, defines what data (file) types are available in +# Galaxy (.sample is used if default does not exist). +#datatypes_config_file = config/datatypes_conf.xml + +# Disable the 'Auto-detect' option for file uploads +#datatypes_disable_auto = False + +# Visualizations config directory: where to look for individual visualization plugins. +# The path is relative to the Galaxy root dir. To use an absolute path begin the path +# with '/'. Defaults to "config/plugins/visualizations". +#visualization_plugins_directory = config/plugins/visualizations + +# Each job is given a unique empty directory as its current working directory. +# This option defines in what parent directory those directories will be +# created. +#job_working_directory = database/job_working_directory + +# If using a cluster, Galaxy will write job scripts and stdout/stderr to this +# directory. +#cluster_files_directory = database/pbs + +# Mako templates are compiled as needed and cached for reuse, this directory is +# used for the cache +#template_cache_path = database/compiled_templates + +# Citation related caching. Tool citations information maybe fetched from +# external sources such as http://dx.doi.org/ by Galaxy - the following parameters +# can be used to control the caching used to store this information. +#citation_cache_type = file +#citation_cache_data_dir = database/citations/data +#citation_cache_lock_dir = database/citations/lock + +# External service types config file, defines what types of external_services configurations +# are available in Galaxy (.sample is used if default does not exist). +#external_service_type_config_file = config/external_service_types_conf.xml + +# Path to the directory containing the external_service_types defined in the config. +#external_service_type_path = external_service_types + +# Tools with a number of outputs not known until runtime can write these +# outputs to a directory for collection by Galaxy when the job is done. +# Previously, this directory was new_file_path, but using one global directory +# can cause performance problems, so using job_working_directory ('.' or cwd +# when a job is run) is encouraged. By default, both are checked to avoid +# breaking existing tools. +#collect_outputs_from = new_file_path,job_working_directory + +# -- Data Storage (Object Store) +# +# Configuration file for the object store +# If this is set and exists, it overrides any other objectstore settings. +# object_store_config_file = config/object_store_conf.xml + +# Object store backend module (valid options are: disk, s3, swift, irods, +# distributed, hierarchical) +#object_store = disk + +# *Extremely* old Galaxy instances created datasets at the root of the +# `file_path` defined above. If your Galaxy instance has datasets at the root +# (instead of in directories composed by hashing the dataset id), you should +# enable this option to allow Galaxy to find them. +#object_store_check_old_style = False + +# Credentials used by certain (s3, swift) object store backends +#os_access_key = <your cloud object store access key> +#os_secret_key = <your cloud object store secret key> +#os_bucket_name = <name of an existing object store bucket or container> + +# If using 'swift' object store, you must specify the following connection +# properties +#os_host = swift.rc.nectar.org.au +#os_port = 8888 +#os_is_secure = False +#os_conn_path = / + +# Reduced redundancy can be used only with the 's3' object store +#os_use_reduced_redundancy = False + +# Path to cache directory for object store backends that utilize a cache (s3, +# swift, irods) +#object_store_cache_path = database/files/ + +# Size (in GB) that the cache used by object store should be limited to. +# If the value is not specified, the cache size will be limited only by the +# file system size. +#object_store_cache_size = 100 + +# Configuration file for the distributed object store, if object_store = +# distributed. See the sample at distributed_object_store_conf.xml.sample +#distributed_object_store_config_file = None + + +# -- Mail and notification + +# Galaxy sends mail for various things: Subscribing users to the mailing list +# if they request it, emailing password resets, notification from the Galaxy +# Sample Tracking system, reporting dataset errors, and sending activation emails. +# To do this, it needs to send mail through an SMTP server, which you may define here (host:port). +# Galaxy will automatically try STARTTLS but will continue upon failure. +#smtp_server = None + +# If your SMTP server requires a username and password, you can provide them +# here (password in cleartext here, but if your server supports STARTTLS it +# will be sent over the network encrypted). +#smtp_username = None +#smtp_password = None + +# If your SMTP server requires SSL from the beginning of the connection +# smtp_ssl = False + +# On the user registration form, users may choose to join the mailing list. +# This is the address of the list they'll be subscribed to. +#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu + +# Datasets in an error state include a link to report the error. Those reports +# will be sent to this address. Error reports are disabled if no address is set. +# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter. +#error_email_to = None + +# Activation email is used as a sender ('from' field) for the account activation mail. +# We recommend using string in the following format: Galaxy Project <galaxy-no-reply(a)example.com> +#activation_email = None + +# URL of the support resource for the galaxy instance. Used in activation emails. +#instance_resource_url = http://wiki.galaxyproject.org/ + +# E-mail domains blacklist is used for filtering out users that are using disposable email address +# during the registration. If their address domain matches any domain in the BL they are refused the registration. +#blacklist_file = config/disposable_email_blacklist.conf + +# Registration warning message is used to discourage people from registering multiple accounts. Applies mostly for the main Galaxy instance. +# If no message specified the warning box will not be shown. +#registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. + +# When users opt to reset passwords, new ones are created, this option +# specifies the length of these passwords. +#reset_password_length = 15 + + +# -- Account activation + +# This is user account activation feature global flag. If set to "False" the rest of the Account +# activation configuration is ignored and user activation is disabled (a.k.a. accounts are active since registration). +# Note the activation is also not working in case the smtp server is not defined. +#user_activation_on = False + +# Activation grace period. Activation is not forced (login is not disabled) until +# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content). +# In hours. Default is 3. Enter 0 to disable grace period. +# Users with OpenID logins have grace period forever. +#activation_grace_period = 0 + +# Used for warning box for inactive accounts (unable to run jobs). +# In use only if activation_grace_period is set. +#inactivity_box_content = Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address. + + +# -- Display sites + +# Galaxy can display data at various external browsers. These options specify +# which browsers should be available. URLs and builds available at these +# browsers are defined in the specifield files. + +# If use_remote_user = True, display application servers will be denied access +# to Galaxy and so displaying datasets in these sites will fail. +# display_servers contains a list of hostnames which should be allowed to +# bypass security to display datasets. Please be aware that there are security +# implications if this is allowed. More details (including required changes to +# the proxy server config) are available in the Apache proxy documentation on +# the wiki. +# +# The list of servers in this sample config are for the UCSC Main, Test and +# Archaea browsers, but the default if left commented is to not allow any +# display sites to bypass security (you must uncomment the line below to allow +# them). +#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… + +# To disable the old-style display applications that are hardcoded into datatype classes, +# set enable_old_display_applications = False. +# This may be desirable due to using the new-style, XML-defined, display applications that +# have been defined for many of the datatypes that have the old-style. +# There is also a potential security concern with the old-style applications, +# where a malicious party could provide a link that appears to reference the Galaxy server, +# but contains a redirect to a third-party server, tricking a Galaxy user to access said +# site. +#enable_old_display_applications = True + +# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. + +use_nglims = False +nglims_config_file = tool-data/nglims.yaml + +# -- UI Localization + +# Show a message box under the masthead. +#message_box_visible = False +#message_box_content = None +#message_box_class = info + +# Append "/{brand}" to the "Galaxy" text in the masthead. +#brand = None + +# Format string used when showing date and time information. +# The string may contain: +# - the directives used by Python time.strftime() function (see http://docs.python.org/2/library/time.html#time.strftime ), +# - $locale (complete format string for the server locale), +# - $iso8601 (complete format string as specified by ISO 8601 international standard). +# pretty_datetime_format = $locale (UTC) + +# The URL of the page to display in Galaxy's middle pane when loaded. This can be +# an absolute or relative URL. +#welcome_url = /static/welcome.html + +# The URL linked by the "Galaxy/brand" text. +#logo_url = / + +# The URL linked by the "Wiki" link in the "Help" menu. +#wiki_url = http://wiki.galaxyproject.org/ + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.galaxyproject.org/Support + +# The URL linked by the "How to Cite Galaxy" link in the "Help" menu. +#citation_url = http://wiki.galaxyproject.org/CitingGalaxy + +#The URL linked by the "Search" link in the "Help" menu. +#search_url = http://galaxyproject.org/search/usegalaxy/ + +#The URL linked by the "Mailing Lists" link in the "Help" menu. +#mailing_lists_url = http://wiki.galaxyproject.org/MailingLists + +#The URL linked by the "Videos" link in the "Help" menu. +#videos_url = http://vimeo.com/galaxyproject + +# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well +# as on the user registration and login forms and in the activation emails. +#terms_url = None + +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +# The Galaxy Q&A site is under development; when the site is done, this URL +# will be set and uncommented. +#qa_url = + +# Serve static content, which must be enabled if you're not serving it via a +# proxy server. These options should be self explanatory and so are not +# documented individually. You can use these paths (or ones in the proxy +# server) to point to your own styles. +#static_enabled = True +#static_cache_time = 360 +#static_dir = static/ +#static_images_dir = static/images +#static_favicon_dir = static/favicon.ico +#static_scripts_dir = static/scripts/ +#static_style_dir = static/june_2007_style/blue +#static_robots_txt = static/robots.txt + +# Pack javascript at launch (/static/scripts/*.js) +# This only happens if the modified timestamp of the source .js is newer +# than the version (if it exists) in /static/scripts/packed/ +# Note that this requires java > 1.4 for executing yuicompressor.jar +#pack_scripts = False + +# Cloud Launch + +#enable_cloud_launch = False +#cloudlaunch_default_ami = ami-a7dbf6ce + +# Incremental Display Options + +#display_chunk_size = 65536 + +# -- Advanced proxy features + +# For help on configuring the Advanced proxy features, see: +# http://usegalaxy.org/production + +# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set +# this to True to inform Galaxy that mod_xsendfile is enabled upstream. +#apache_xsendfile = False + +# The same download handling can be done by nginx using X-Accel-Redirect. This +# should be set to the path defined in the nginx config as an internal redirect +# with access to Galaxy's data files (see documentation linked above). +#nginx_x_accel_redirect_base = False + +# nginx can make use of mod_zip to create zip files containing multiple library +# files. If using X-Accel-Redirect, this can be the same value as that option. +#nginx_x_archive_files_base = False + +# If using compression in the upstream proxy server, use this option to disable +# gzipping of library .tar.gz and .zip archives, since the proxy server will do +# it faster on the fly. +#upstream_gzip = False + +# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. +# Configuration for this is complex and explained in detail in the +# documentation linked above. The upload store is a temporary directory in +# which files uploaded by the upload module will be placed. +#nginx_upload_store = False + +# This value overrides the action set on the file upload form, e.g. the web +# path where the nginx_upload_module has been configured to intercept upload +# requests. +#nginx_upload_path = False + +# -- Logging and Debugging + +# Verbosity of console log messages. Acceptable values can be found here: +# http://docs.python.org/library/logging.html#logging-levels +#log_level = DEBUG + +# Print database operations to the server log (warning, quite verbose!). +#database_engine_option_echo = False + +# Print database pool operations to the server log (warning, quite verbose!). +#database_engine_option_echo_pool = False + +# Turn on logging of application events and some user events to the database. +#log_events = True + +# Turn on logging of user actions to the database. Actions currently logged are +# grid views, tool searches, and use of "recently" used tools menu. The +# log_events and log_actions functionality will eventually be merged. +#log_actions = True + +# Sanitize All HTML Tool Output +# By default, all tool output served as 'text/html' will be sanitized +# thoroughly. This can be disabled if you have special tools that require +# unaltered output. +#sanitize_all_html = True + +# By default Galaxy will serve non-HTML tool output that may potentially +# contain browser executable JavaScript content as plain text. This will for +# instance cause SVG datasets to not render properly and so may be disabled +# by setting the following option to True. +#serve_xss_vulnerable_mimetypes = False + +# Debug enables access to various config options useful for development and +# debugging: use_lint, use_profile, use_printdebug and use_interactive. It +# also causes the files used by PBS/SGE (submission script, output, and error) +# to remain on disk after the job is complete. Debug mode is disabled if +# commented, but is uncommented by default in the sample config. +debug = True + +# Check for WSGI compliance. +#use_lint = False + +# Run the Python profiler on each request. +#use_profile = False + +# Intercept print statements and show them on the returned page. +#use_printdebug = True + +# Enable live debugging in your browser. This should NEVER be enabled on a +# public site. Enabled in the sample config for development. +use_interactive = True + +# Write thread status periodically to 'heartbeat.log', (careful, uses disk +# space rapidly!). Useful to determine why your processes may be consuming a +# lot of CPU. +#use_heartbeat = False + +# Enable the memory debugging interface (careful, negatively impacts server +# performance). +#use_memdump = False + +# -- Data Libraries + +# These library upload options are described in much more detail in the wiki: +# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles + +# Add an option to the library upload form which allows administrators to +# upload a directory of files. +#library_import_dir = None + +# Add an option to the library upload form which allows authorized +# non-administrators to upload a directory of files. The configured directory +# must contain sub-directories named the same as the non-admin user's Galaxy +# login ( email ). The non-admin user is restricted to uploading files or +# sub-directories of files contained in their directory. +#user_library_import_dir = None + +# Add an option to the admin library upload tool allowing admins to paste +# filesystem paths to files and directories in a box, and these paths will be +# added to a library. Set to True to enable. Please note the security +# implication that this will give Galaxy Admins access to anything your Galaxy +# user has access to. +#allow_library_path_paste = False + +# Users may choose to download multiple files from a library in an archive. By +# default, Galaxy allows users to select from a few different archive formats +# if testing shows that Galaxy is able to create files using these formats. +# Specific formats can be disabled with this option, separate more than one +# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. +#disable_library_comptypes = + +# Some sequencer integration features in beta allow you to automatically +# transfer datasets. This is done using a lightweight transfer manager which +# runs outside of Galaxy (but is spawned by it automatically). Galaxy will +# communicate with this manager over the port specified here. +#transfer_manager_port = 8163 + +# Search data libraries with whoosh +#enable_whoosh_library_search = True +# Whoosh indexes are stored in this directory. +#whoosh_index_dir = database/whoosh_indexes + +# Search data libraries with lucene +#enable_lucene_library_search = False +# maxiumum file size to index for searching, in MB +#fulltext_max_size = 500 +#fulltext_noindex_filetypes = bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger +# base URL of server providing search functionality using lucene +#fulltext_url = http://localhost:8081 + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +#id_secret = USING THE DEFAULT IS NOT SECURE! + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy +#use_remote_user = False + +# If use_remote_user is enabled and your external authentication +# method just returns bare usernames, set a default mail domain to be appended +# to usernames, to become your Galaxy usernames (email addresses). +#remote_user_maildomain = None + +# If use_remote_user is enabled, the header that the upstream proxy provides +# the remote username in defaults to HTTP_REMOTE_USER (the 'HTTP_' is prepended +# by WSGI). This option allows you to change the header. Note, you still need +# to prepend 'HTTP_' to the header in this option, but your proxy server should +# *not* include 'HTTP_' at the beginning of the header name. +#remote_user_header = HTTP_REMOTE_USER + +# If use_remote_user is enabled, you can set this to a URL that will log your +# users out. +#remote_user_logout_href = None + +# If your proxy and/or authentication source does not normalize e-mail +# addresses or user names being passed to Galaxy - set the following option +# to True to force these to lower case. +#normalize_remote_user_email = False + +# Administrative users - set this to a comma-separated list of valid Galaxy +# users (email addresses). These users will have access to the Admin section +# of the server, and will have access to create users, groups, roles, +# libraries, and more. For more information, see: +# https://wiki.galaxyproject.org/Admin/Interface +#admin_users = None + +# Force everyone to log in (disable anonymous access). +#require_login = False + +# Allow unregistered users to create new accounts (otherwise, they will have to +# be created by an admin). +#allow_user_creation = True + +# Allow administrators to delete accounts. +#allow_user_deletion = False + +# Allow administrators to log in as other users (useful for debugging) +#allow_user_impersonation = False + +# Allow users to remove their datasets from disk immediately (otherwise, +# datasets will be removed after a time period specified by an administrator in +# the cleanup scripts run via cron) +#allow_user_dataset_purge = False + +# By default, users' data will be public, but setting this to True will cause +# it to be private. Does not affect existing users and data, only ones created +# after this option is set. Users may still change their default back to +# public. +#new_user_dataset_access_role_default_private = False + +# -- Beta features + +# Enable Galaxy to communicate directly with a sequencer +#enable_sequencer_communication = False + +# Enable authentication via OpenID. Allows users to log in to their Galaxy +# account by authenticating with an OpenID provider. +#enable_openid = False +# .sample used if default does not exist +#openid_config_file = config/openid_conf.xml +#openid_consumer_cache_path = database/openid_consumer_cache + +# Optional list of email addresses of API users who can make calls on behalf of +# other users +#api_allow_run_as = None + +# Master key that allows many API admin actions to be used without actually +# having a defined admin user in the database/config. Only set this if you need +# to bootstrap Galaxy, you probably do not want to set this on public servers. +#master_api_key = changethis + +# Enable tool tags (associating tools with tags). This has its own option +# since its implementation has a few performance implications on startup for +# large servers. +#enable_tool_tags = False + +# Enable a feature when running workflows. When enabled, default datasets +# are selected for "Set at Runtime" inputs from the history such that the +# same input will not be selected twice, unless there are more inputs than +# compatible datasets in the history. +# When False, the most recently added compatible item in the history will +# be used for each "Set at Runtime" input, independent of others in the Workflow +#enable_unique_workflow_defaults = False + +# The URL to the myExperiment instance being used (omit scheme but include port) +#myexperiment_url = www.myexperiment.org:80 + +# Enable Galaxy's "Upload via FTP" interface. You'll need to install and +# configure an FTP server (we've used ProFTPd since it can use Galaxy's +# database for authentication) and set the following two options. + +# This should point to a directory containing subdirectories matching users' +# email addresses, where Galaxy will look for files. +#ftp_upload_dir = None + +# This should be the hostname of your FTP server, which will be provided to +# users in the help text. +#ftp_upload_site = None + +# Enable enforcement of quotas. Quotas can be set from the Admin interface. +#enable_quotas = False + +# This option allows users to see the full path of datasets via the "View +# Details" option in the history. Administrators can always see this. +#expose_dataset_path = False + +# Data manager configuration options +# Allow non-admin users to view available Data Manager options +#enable_data_manager_user_view = False +# File where Data Managers are configured (.sample used if default does not +# exist) +#data_manager_config_file = config/data_manager_conf.xml +# File where Tool Shed based Data Managers are configured +#shed_data_manager_config_file = config/shed_data_manager_conf.xml +# Directory to store Data Manager based tool-data; defaults to tool_data_path +#galaxy_data_manager_data_path = tool-data + +# -- Job Execution + +# To increase performance of job execution and the web interface, you can +# separate Galaxy into multiple processes. There are more than one way to do +# this, and they are explained in detail in the documentation: +# +# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling + +# By default, Galaxy manages and executes jobs from within a single process and +# notifies itself of new jobs via in-memory queues. Jobs are run locally on +# the system on which Galaxy is started. Advanced job running capabilities can +# be configured through the job configuration file. +#job_config_file = config/job_conf.xml + +# In multiprocess configurations, notification between processes about new jobs +# is done via the database. In single process configurations, this is done in +# memory, which is a bit quicker. Galaxy tries to automatically determine +# which method it should used based on your handler configuration in the job +# config file, but you can explicitly override this behavior by setting the +# following option to True or False. +#track_jobs_in_database = None + +# This enables splitting of jobs into tasks, if specified by the particular tool config. +# This is a new feature and not recommended for production servers yet. +#use_tasked_jobs = False +#local_task_queue_workers = 2 + +# Enable job recovery (if Galaxy is restarted while cluster jobs are running, +# it can "recover" them when it starts). This is not safe to use if you are +# running more than one Galaxy server using the same database. +#enable_job_recovery = True + +# Although it is fairly reliable, setting metadata can occasionally fail. In +# these instances, you can choose to retry setting it internally or leave it in +# a failed state (since retrying internally may cause the Galaxy process to be +# unresponsive). If this option is set to False, the user will be given the +# option to retry externally, or set metadata manually (when possible). +#retry_metadata_internally = True + +# If (for example) you run on a cluster and your datasets (by default, +# database/files/) are mounted read-only, this option will override tool output +# paths to write outputs to the working directory instead, and the job manager +# will move the outputs to their proper place in the dataset directory on the +# Galaxy server after the job completes. +#outputs_to_working_directory = False + +# If your network filesystem's caching prevents the Galaxy server from seeing +# the job's stdout and stderr files when it completes, you can retry reading +# these files. The job runner will retry the number of times specified below, +# waiting 1 second between tries. For NFS, you may want to try the -noac mount +# option (Linux) or -actimeo=0 (Solaris). +#retry_job_output_collection = 0 + +# Clean up various bits of jobs left on the filesystem after completion. These +# bits include the job working directory, external metadata temporary files, +# and DRM stdout and stderr files (if using a DRM). Possible values are: +# always, onsuccess, never +#cleanup_job = always + +# File to source to set up the environment when running jobs. By default, the +# environment in which the Galaxy server starts is used when running jobs +# locally, and the environment set up per the DRM's submission method and +# policy is used when running jobs on a cluster (try testing with `qsub` on the +# command line). environment_setup_file can be set to the path of a file on +# the cluster that should be sourced by the user to set up the environment +# prior to running tools. This can be especially useful for running jobs as +# the actual user, to remove the need to configure each user's environment +# individually. +#environment_setup_file = None + + +# Optional file containing job resource data entry fields definition. +# These fields will be presented to users in the tool forms and allow them to +# overwrite default job resources such as number of processors, memory, and walltime. +#job_resource_params_file = config/job_resource_params_conf.xml + +# If using job concurrency limits (configured in job_config_file), several +# extra database queries must be performed to determine the number of jobs a +# user has dispatched to a given destination. By default, these queries will +# happen for every job that is waiting to run, but if cache_user_job_count is +# set to True, it will only happen once per iteration of the handler queue. +# Although better for performance due to reduced queries, the tradeoff is a +# greater possibility that jobs will be dispatched past the configured limits +# if running many handlers. +#cache_user_job_count = False + +# ToolBox filtering +# Modules from lib/galaxy/tools/filters/ can be specified in the following lines. +# tool_* filters will be applied for all users and can not be changed by them. +# user_tool_* filters will be shown under user preferences and can be toogled +# on and off by runtime +#tool_filters +#tool_label_filters +#tool_section_filters +#user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode +#user_tool_section_filters = examples:restrict_text +#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode + +# Galaxy Application Internal Message Queue + +# Galaxy uses AMQP internally TODO more documentation on what for. +# For examples, see http://ask.github.io/kombu/userguide/connections.html +# +# Without specifying anything here, galaxy will first attempt to use your +# specified database_connection above. If that's not specified either, Galaxy +# will automatically create and use a separate sqlite database located in your +# <galaxy>/database folder (indicated in the commented out line below). + +#amqp_internal_connection = sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE + + + +# ---- Galaxy External Message Queue ------------------------------------------------- + +# Galaxy uses AMQ protocol to receive messages from external sources like +# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +# For Galaxy to receive messages from a message queue the RabbitMQ server has +# to be set up with a user account and other parameters listed below. The 'host' +# and 'port' fields should point to where the RabbitMQ server is running. + +[galaxy_amqp] + +#host = 127.0.0.1 +#port = 5672 +#userid = galaxy +#password = galaxy +#virtual_host = galaxy_messaging_engine +#queue = galaxy_queue +#exchange = galaxy_exchange +#routing_key = bar_code_scanner +#rabbitmqctl_path = /path/to/rabbitmqctl + diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 config/job_conf.xml.sample_advanced --- /dev/null +++ b/config/job_conf.xml.sample_advanced @@ -0,0 +1,482 @@ +<?xml version="1.0"?> +<job_conf> + <plugins workers="4"> +  + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> + <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/> + <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> +  + <param id="invalidjobexception_state">ok</param> + <param id="invalidjobexception_retries">0</param> + <param id="internalexception_state">ok</param> + <param id="internalexception_retries">0</param> + </plugin> + <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> +  + <param id="drmaa_library_path">/sge/lib/libdrmaa.so</param> + </plugin> + <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> + <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> + <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> + <plugin id="dynamic" type="runner"> +  + <param id="rules_module">galaxy.jobs.rules</param> + </plugin> +  + <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"> +  +  + +  +  + </plugin> + <plugin id="pulsar_mq" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner"> +  + <param id="amqp_url">amqp://guest:guest@localhost:5672//</param> +  + <param id="galaxy_url">http://localhost:8080</param> +  +  +  +  +  +  +  +  +  + </plugin> + <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner"> +  + </plugin> + </plugins> + <handlers default="handlers"> +  + <handler id="handler0" tags="handlers"/> + <handler id="handler1" tags="handlers"/> +  + <handler id="sge_handler"> + <plugin id="sge"/> + </handler> + <handler id="special_handler0" tags="special_handlers"/> + <handler id="special_handler1" tags="special_handlers"/> + <handler id="trackster_handler"/> + </handlers> + <destinations default="local"> +  + <destination id="local" runner="local"/> + <destination id="multicore_local" runner="local"> + <param id="local_slots">4</param> +  + <param id="embed_metadata_in_job">True</param> +  + <job_metrics /> +  + </destination> + <destination id="docker_local" runner="local"> + <param id="docker_enabled">true</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + +  +  + +  +  + + </destination> + <destination id="pbs" runner="pbs" tags="mycluster"/> + <destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"> +  + <param id="Resource_List">walltime=72:00:00</param> + </destination> + <destination id="remote_cluster" runner="drmaa" tags="longjobs"/> + <destination id="java_cluster" runner="drmaa"> +  + <env id="_JAVA_OPTIONS">-Xmx=6GB</env> + <env id="ANOTHER_OPTION" raw="true">'5'</env> + <env file="/mnt/java_cluster/environment_setup.sh" /> + <env exec="module load javastuff/2.10" /> +  + </destination> + <destination id="real_user_cluster" runner="drmaa"> +  + <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> + <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> + <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> + </destination> + <destination id="dynamic" runner="dynamic"> +  + <param id="function">foo</param> + </destination> + <destination id="load_balance" runner="dynamic"> + <param id="type">choose_one</param> +  + <param id="destination_ids">cluster1,cluster2,cluster3</param> + </destination> + <destination id="load_balance_with_data_locality" runner="dynamic"> +  + <param id="type">choose_one</param> + <param id="destination_ids">cluster1,cluster2,cluster3</param> + <param id="hash_by">workflow_invocation,history</param> + </destination> + <destination id="burst_out" runner="dynamic"> +  + <param id="type">burst</param> + <param id="from_destination_ids">local_cluster_8_core,local_cluster_1_core,local_cluster_16_core</param> + <param id="to_destination_id">shared_cluster_8_core</param> + <param id="num_jobs">50</param> +  + </destination> + <destination id="docker_dispatch" runner="dynamic"> +  + <param id="type">docker_dispatch</param> + <param id="docker_destination_id">docker_cluster</param> + <param id="default_destination_id">normal_cluster</param> + </destination> + <destination id="secure_pulsar_rest_dest" runner="pulsar_rest"> + <param id="url">https://examle.com:8913/</param> +  + <param id="private_token">123456789changeme</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + </destination> + <destination id="pulsar_mq_dest" runner="amqp_pulsar" > +  + <param id="jobs_directory">/path/to/remote/pulsar/files/staging/</param> +  + </destination> + <destination id="ssh_torque" runner="cli"> + <param id="shell_plugin">SecureShell</param> + <param id="job_plugin">Torque</param> + <param id="shell_username">foo</param> + <param id="shell_hostname">foo.example.org</param> + <param id="job_Resource_List">walltime=24:00:00,ncpus=4</param> + </destination> + +  + <destination id="ssh_slurm" runner="cli"> + <param id="shell_plugin">SecureShell</param> + <param id="job_plugin">Slurm</param> + <param id="shell_username">foo</param> + <param id="shell_hostname">my_host</param> + <param id="job_time">2:00:00</param> + <param id="job_ncpus">4</param> + <param id="job_partition">my_partition</param> + </destination> + + <destination id="condor" runner="condor"> +  + <param id="request_cpus">8</param> + </destination> + +  + <destination id="short_fast" runner="slurm"> + <param id="nativeSpecification">--time=00:05:00 --nodes=1</param> + <resubmit condition="walltime_reached" destination="long_slow" handler="sge_handler" /> + </destination> + <destination id="long_slow" runner="sge"> +  + <param id="nativeSpecification">-l h_rt=96:00:00</param> + </destination> + + </destinations> + <resources default="default"> +  + <group id="default"></group> + <group id="memoryonly">memory</group> + <group id="all">processors,memory,time,project</group> + </resources> + <tools> +  + <tool id="foo" handler="trackster_handler"> + <param id="source">trackster</param> + </tool> + <tool id="bar" destination="dynamic"/> +  + <tool id="longbar" destination="dynamic" resources="all" /> + <tool id="baz" handler="special_handlers" destination="bigmem"/> + </tools> + <limits> +  +  + <limit type="registered_user_concurrent_jobs">2</limit> +  + <limit type="anonymous_user_concurrent_jobs">1</limit> +  + <limit type="destination_user_concurrent_jobs" id="local">1</limit> + <limit type="destination_user_concurrent_jobs" tag="mycluster">2</limit> + <limit type="destination_user_concurrent_jobs" tag="longjobs">1</limit> +  + <limit type="destination_total_concurrent_jobs" id="local">16</limit> + <limit type="destination_total_concurrent_jobs" tag="longjobs">100</limit> +  + <limit type="walltime">24:00:00</limit> +  + <limit type="output_size">10GB</limit> + </limits> +</job_conf> diff -r 773bae7768c1fed8d6fcd2e2c374fc0245ed06f4 -r 898a4bda231824bc0453d5e593e0b86a9e1004e9 config/job_conf.xml.sample_basic --- /dev/null +++ b/config/job_conf.xml.sample_basic @@ -0,0 +1,13 @@ +<?xml version="1.0"?> + +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"/> + </destinations> +</job_conf> This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Set config file vars to the option's value, not the option's name... Thanks Dave B.
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8f43c3bc008/ Changeset: f8f43c3bc008 User: natefoo Date: 2014-09-16 15:36:21 Summary: Set config file vars to the option's value, not the option's name... Thanks Dave B. Affected #: 1 file diff -r 5f90a490e9971685945081cbed681c961932a4fd -r f8f43c3bc008c102537e4a6afbb8508f2ea98797 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -400,7 +400,7 @@ for var, defaults in defaults.items(): if kwargs.get( var, None ) is not None: - path = var + path = kwargs.get( var ) else: for default in defaults: if os.path.exists( resolve_path( default, self.root ) ): @@ -413,7 +413,7 @@ for var, defaults in listify_defaults.items(): paths = [] if kwargs.get( var, None ) is not None: - paths = listify( var ) + paths = listify( kwargs.get( var ) ) else: for default in defaults: for path in listify( default ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 8 new changesets
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

8 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e4daf2910a99/ Changeset: e4daf2910a99 User: natefoo Date: 2014-09-15 17:28:18 Summary: Move samples configs to config subdirectory. Affected #: 44 files diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/data_manager_conf.xml.sample --- /dev/null +++ b/config/data_manager_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<data_managers> +</data_managers> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/datatypes_conf.xml.sample --- /dev/null +++ b/config/datatypes_conf.xml.sample @@ -0,0 +1,333 @@ +<?xml version="1.0"?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Ab1"/> + <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false" /> + <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true" /> + <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true" /> + <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/> + <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/> + <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM"> + <converter file="bam_to_bai.xml" target_datatype="bai"/> + <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="ucsc/bam.xml" /> + <display file="ensembl/ensembl_bam.xml" /> + <display file="igv/bam.xml" /> + <display file="igb/bam.xml" /> + </datatype> + <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed"> + <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> + <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="bed_to_fli_converter.xml" target_datatype="fli"/> +  + <display file="igb/bed.xml" /> + </datatype> + <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> + <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/bedgraph.xml" /> + </datatype> + <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /> + <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> + </datatype> + <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /> + <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> + <converter file="len_to_linecount.xml" target_datatype="linecount" /> + </datatype> + <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigbed.xml" /> + <display file="igb/bb.xml" /> + </datatype> + <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigwig.xml" /> + <display file="igb/bigwig.xml" /> + </datatype> + <datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> +  + <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> +  + <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/> + <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/> + <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" /> + <datatype extension="data_manager_json" type="galaxy.datatypes.data:Text" mimetype="application/json" subclass="True" display_in_upload="False"/> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" description="A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('>') symbol in the first column. All lines should be shorter than 80 characters." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fasta"> + <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/> + <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/> + <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/> + <converter file="fasta_to_2bit.xml" target_datatype="twobit"/> + <converter file="fasta_to_len.xml" target_datatype="len"/> + </datatype> + <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/> + <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/> + <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/> + <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> +  + </datatype> + <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true" description="GFF lines have nine required fields that must be tab-separated." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF"> + <converter file="gff_to_bed_converter.xml" target_datatype="bed"/> + <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="gff_to_fli_converter.xml" target_datatype="fli"/> + <display file="ensembl/ensembl_gff.xml" inherit="True"/> +  + </datatype> + <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true" description="The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF3"/> + <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/> + <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/> + <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"> + <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /> + </datatype> + <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> + <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> + <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/> + <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order)." > + <converter file="interval_to_bed_converter.xml" target_datatype="bed"/> + <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/> + <converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/> + <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/> +  + <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/> + <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/> + <display file="rviewer/bed.xml" inherit="True"/> + </datatype> + <datatype extension="picard_interval_list" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"> + <converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/> + </datatype> + <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_report" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/> + <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/> + <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/> + <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/> + <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/> + <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/> + <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/> + <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/> + <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/> + <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/> + <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/> + <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/> + <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/> + <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/> + <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/> + <datatype extension="laj" type="galaxy.datatypes.images:Laj"/> + <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true" description="Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.." /> + <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true" description="TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated 'variable=value' pairs. There should be no white space surrounding the '='." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#MAF"> + <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/> + <converter file="maf_to_interval_converter.xml" target_datatype="interval"/> + </datatype> + <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack"> + <display file="ucsc/maf_customtrack.xml" /> + </datatype> + <datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True"> + <converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> + <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/> + <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + </datatype> + <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/> + <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> + <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> + <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/> + <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/> + <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/> + <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/> + <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"> + <converter file="sam_to_bam.xml" target_datatype="bam"/> + <converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> + <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/> + <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/> + <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/> + <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/> + <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/> + <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/> + <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/> + <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"> + <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/> + <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="ucsc/vcf.xml" /> + <display file="igv/vcf.xml" /> + <display file="rviewer/vcf.xml" inherit="True"/> + </datatype> + <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True"/> + <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> + <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true" description="The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Wig"> + <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/> +  + <display file="igb/wig.xml" /> + </datatype> + <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="vcf_bgzip" type_extension="bgzip" subclass="True" > + <display file="igv/vcf.xml" /> + <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/> + </datatype> +  + <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" /> + <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" /> + <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /> +  + <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> +  + <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/> +  + <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/> + <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" /> +  + <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/> +  + <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/> +  + <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/> +  +  + <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true"> + </datatype> + <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/> +  + <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"> + <converter file="lped_to_fped_converter.xml" target_datatype="fped"/> + <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/> + </datatype> +  + <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"> + <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/> + <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/> + </datatype> + <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/> +  + <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/> + <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/> + <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/> + <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/> + <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/> + <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/> +  +  + <datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/> + <datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/> + <datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/> + </registration> + <sniffers> +  + <sniffer type="galaxy.datatypes.tabular:Vcf"/> + <sniffer type="galaxy.datatypes.binary:TwoBit"/> + <sniffer type="galaxy.datatypes.binary:SQlite"/> + <sniffer type="galaxy.datatypes.binary:Bam"/> + <sniffer type="galaxy.datatypes.binary:Sff"/> + <sniffer type="galaxy.datatypes.xml:Phyloxml"/> + <sniffer type="galaxy.datatypes.xml:GenericXml"/> + <sniffer type="galaxy.datatypes.sequence:Maf"/> + <sniffer type="galaxy.datatypes.sequence:Lav"/> + <sniffer type="galaxy.datatypes.sequence:csFasta"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> + <sniffer type="galaxy.datatypes.sequence:Fasta"/> + <sniffer type="galaxy.datatypes.sequence:Fastq"/> + <sniffer type="galaxy.datatypes.interval:Wiggle"/> + <sniffer type="galaxy.datatypes.images:Html"/> + <sniffer type="galaxy.datatypes.images:Pdf"/> + <sniffer type="galaxy.datatypes.sequence:Axt"/> + <sniffer type="galaxy.datatypes.interval:Bed"/> + <sniffer type="galaxy.datatypes.interval:CustomTrack"/> + <sniffer type="galaxy.datatypes.interval:Gtf"/> + <sniffer type="galaxy.datatypes.interval:Gff"/> + <sniffer type="galaxy.datatypes.interval:Gff3"/> + <sniffer type="galaxy.datatypes.tabular:Pileup"/> + <sniffer type="galaxy.datatypes.interval:Interval"/> + <sniffer type="galaxy.datatypes.tabular:Sam"/> + <sniffer type="galaxy.datatypes.data:Newick"/> + <sniffer type="galaxy.datatypes.data:Nexus"/> + <sniffer type="galaxy.datatypes.images:Jpg"/> + <sniffer type="galaxy.datatypes.images:Png"/> + <sniffer type="galaxy.datatypes.images:Tiff"/> + <sniffer type="galaxy.datatypes.images:Bmp"/> + <sniffer type="galaxy.datatypes.images:Gif"/> + <sniffer type="galaxy.datatypes.images:Im"/> + <sniffer type="galaxy.datatypes.images:Pcd"/> + <sniffer type="galaxy.datatypes.images:Pcx"/> + <sniffer type="galaxy.datatypes.images:Ppm"/> + <sniffer type="galaxy.datatypes.images:Psd"/> + <sniffer type="galaxy.datatypes.images:Xbm"/> + <sniffer type="galaxy.datatypes.images:Rgb"/> + <sniffer type="galaxy.datatypes.images:Pbm"/> + <sniffer type="galaxy.datatypes.images:Pgm"/> + <sniffer type="galaxy.datatypes.images:Xpm"/> + <sniffer type="galaxy.datatypes.images:Eps"/> + <sniffer type="galaxy.datatypes.images:Rast"/> +  + </sniffers> + <build_sites> +  + <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/> + <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/> + <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/> + <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/> + <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/> + <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/> + </build_sites> +</datatypes> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/demo_sequencer_wsgi.ini.sample --- /dev/null +++ b/config/demo_sequencer_wsgi.ini.sample @@ -0,0 +1,66 @@ +# ---- HTTP Server ---------------------------------------------------------- + +[server:main] + +use = egg:Paste#http +port = 9011 +host = 0.0.0.0 +use_threadpool = true +threadpool_workers = 10 + +# ---- Galaxy Demo Sequencer Emulator Interface ------------------------------------------------- + +[app:main] + +# Specifies the factory for the universe WSGI application +paste.app_factory = galaxy.webapps.demo_sequencer.buildapp:app_factory +log_level = DEBUG + +# Where dataset files are saved +file_path = database/demo_sequencer_files +# Temporary storage for additional datasets, this should be shared through the cluster +new_file_path = database/tmp + +# Sequencer emulator actions +sequencer_actions_config_file = %(here)s/lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml + +# Session support (beaker) +use_beaker_session = True +session_type = memory +session_data_dir = %(here)s/database/beaker_sessions +session_key = galaxysessions +session_secret = changethisinproduction + +# Galaxy session security +id_secret = changethisinproductiontoo + +# Configuration for debugging middleware +debug = true +use_lint = false + +# NEVER enable this on a public site (even test or QA) +# use_interactive = true + +# this should be a comma-separated list of valid Galaxy users +#admin_users = test(a)bx.psu.edu + +# Force everyone to log in (disable anonymous access) +require_login = False + +# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) +## use_heartbeat = True + +# Profiling middleware (cProfile based) +## use_profile = True + +# Use the new iframe / javascript based layout +use_new_layout = true + +# Serving static files (needed if running standalone) +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/external_service_types_conf.xml.sample --- /dev/null +++ b/config/external_service_types_conf.xml.sample @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<external_service_types> + <external_service_type file="simple_unknown_sequencer.xml" visible="False"/> + <external_service_type file="applied_biosystems_solid.xml" visible="True"/> +</external_service_types> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/job_conf.xml.sample_advanced --- /dev/null +++ b/config/job_conf.xml.sample_advanced @@ -0,0 +1,482 @@ +<?xml version="1.0"?> +<job_conf> + <plugins workers="4"> +  + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> + <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/> + <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> +  + <param id="invalidjobexception_state">ok</param> + <param id="invalidjobexception_retries">0</param> + <param id="internalexception_state">ok</param> + <param id="internalexception_retries">0</param> + </plugin> + <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> +  + <param id="drmaa_library_path">/sge/lib/libdrmaa.so</param> + </plugin> + <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> + <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> + <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> + <plugin id="dynamic" type="runner"> +  + <param id="rules_module">galaxy.jobs.rules</param> + </plugin> +  + <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"> +  +  + +  +  + </plugin> + <plugin id="pulsar_mq" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner"> +  + <param id="amqp_url">amqp://guest:guest@localhost:5672//</param> +  + <param id="galaxy_url">http://localhost:8080</param> +  +  +  +  +  +  +  +  +  + </plugin> + <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner"> +  + </plugin> + </plugins> + <handlers default="handlers"> +  + <handler id="handler0" tags="handlers"/> + <handler id="handler1" tags="handlers"/> +  + <handler id="sge_handler"> + <plugin id="sge"/> + </handler> + <handler id="special_handler0" tags="special_handlers"/> + <handler id="special_handler1" tags="special_handlers"/> + <handler id="trackster_handler"/> + </handlers> + <destinations default="local"> +  + <destination id="local" runner="local"/> + <destination id="multicore_local" runner="local"> + <param id="local_slots">4</param> +  + <param id="embed_metadata_in_job">True</param> +  + <job_metrics /> +  + </destination> + <destination id="docker_local" runner="local"> + <param id="docker_enabled">true</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + +  +  + +  +  + + </destination> + <destination id="pbs" runner="pbs" tags="mycluster"/> + <destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"> +  + <param id="Resource_List">walltime=72:00:00</param> + </destination> + <destination id="remote_cluster" runner="drmaa" tags="longjobs"/> + <destination id="java_cluster" runner="drmaa"> +  + <env id="_JAVA_OPTIONS">-Xmx=6GB</env> + <env id="ANOTHER_OPTION" raw="true">'5'</env> + <env file="/mnt/java_cluster/environment_setup.sh" /> + <env exec="module load javastuff/2.10" /> +  + </destination> + <destination id="real_user_cluster" runner="drmaa"> +  + <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> + <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> + <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> + </destination> + <destination id="dynamic" runner="dynamic"> +  + <param id="function">foo</param> + </destination> + <destination id="load_balance" runner="dynamic"> + <param id="type">choose_one</param> +  + <param id="destination_ids">cluster1,cluster2,cluster3</param> + </destination> + <destination id="load_balance_with_data_locality" runner="dynamic"> +  + <param id="type">choose_one</param> + <param id="destination_ids">cluster1,cluster2,cluster3</param> + <param id="hash_by">workflow_invocation,history</param> + </destination> + <destination id="burst_out" runner="dynamic"> +  + <param id="type">burst</param> + <param id="from_destination_ids">local_cluster_8_core,local_cluster_1_core,local_cluster_16_core</param> + <param id="to_destination_id">shared_cluster_8_core</param> + <param id="num_jobs">50</param> +  + </destination> + <destination id="docker_dispatch" runner="dynamic"> +  + <param id="type">docker_dispatch</param> + <param id="docker_destination_id">docker_cluster</param> + <param id="default_destination_id">normal_cluster</param> + </destination> + <destination id="secure_pulsar_rest_dest" runner="pulsar_rest"> + <param id="url">https://examle.com:8913/</param> +  + <param id="private_token">123456789changeme</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + </destination> + <destination id="pulsar_mq_dest" runner="amqp_pulsar" > +  + <param id="jobs_directory">/path/to/remote/pulsar/files/staging/</param> +  + </destination> + <destination id="ssh_torque" runner="cli"> + <param id="shell_plugin">SecureShell</param> + <param id="job_plugin">Torque</param> + <param id="shell_username">foo</param> + <param id="shell_hostname">foo.example.org</param> + <param id="job_Resource_List">walltime=24:00:00,ncpus=4</param> + </destination> + +  + <destination id="ssh_slurm" runner="cli"> + <param id="shell_plugin">SecureShell</param> + <param id="job_plugin">Slurm</param> + <param id="shell_username">foo</param> + <param id="shell_hostname">my_host</param> + <param id="job_time">2:00:00</param> + <param id="job_ncpus">4</param> + <param id="job_partition">my_partition</param> + </destination> + + <destination id="condor" runner="condor"> +  + <param id="request_cpus">8</param> + </destination> + +  + <destination id="short_fast" runner="slurm"> + <param id="nativeSpecification">--time=00:05:00 --nodes=1</param> + <resubmit condition="walltime_reached" destination="long_slow" handler="sge_handler" /> + </destination> + <destination id="long_slow" runner="sge"> +  + <param id="nativeSpecification">-l h_rt=96:00:00</param> + </destination> + + </destinations> + <resources default="default"> +  + <group id="default"></group> + <group id="memoryonly">memory</group> + <group id="all">processors,memory,time,project</group> + </resources> + <tools> +  + <tool id="foo" handler="trackster_handler"> + <param id="source">trackster</param> + </tool> + <tool id="bar" destination="dynamic"/> +  + <tool id="longbar" destination="dynamic" resources="all" /> + <tool id="baz" handler="special_handlers" destination="bigmem"/> + </tools> + <limits> +  +  + <limit type="registered_user_concurrent_jobs">2</limit> +  + <limit type="anonymous_user_concurrent_jobs">1</limit> +  + <limit type="destination_user_concurrent_jobs" id="local">1</limit> + <limit type="destination_user_concurrent_jobs" tag="mycluster">2</limit> + <limit type="destination_user_concurrent_jobs" tag="longjobs">1</limit> +  + <limit type="destination_total_concurrent_jobs" id="local">16</limit> + <limit type="destination_total_concurrent_jobs" tag="longjobs">100</limit> +  + <limit type="walltime">24:00:00</limit> +  + <limit type="output_size">10GB</limit> + </limits> +</job_conf> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/job_conf.xml.sample_basic --- /dev/null +++ b/config/job_conf.xml.sample_basic @@ -0,0 +1,13 @@ +<?xml version="1.0"?> + +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"/> + </destinations> +</job_conf> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/job_metrics_conf.xml.sample --- /dev/null +++ b/config/job_metrics_conf.xml.sample @@ -0,0 +1,124 @@ +<?xml version="1.0"?> + +<job_metrics> +  + +  + <core /> + +  +  +  +  + +  +  + +  +  + +  +  +  +  + +  +  +</job_metrics> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/job_resource_params_conf.xml.sample --- /dev/null +++ b/config/job_resource_params_conf.xml.sample @@ -0,0 +1,6 @@ +<parameters> + <param label="Processors" name="processors" type="integer" size="2" min="1" max="64" value="" help="Number of processing cores, 'ppn' value (1-64). Leave blank to use default value." /> + <param label="Memory" name="memory" type="integer" size="3" min="1" max="256" value="" help="Memory size in gigabytes, 'pmem' value (1-256). Leave blank to use default value." /> + <param label="Time" name="time" type="integer" size="3" min="1" max="744" value="" help="Maximum job time in hours, 'walltime' value (1-744). Leave blank to use default value." /> + <param label="Project" name="project" type="text" value="" help="Project to assign resource allocation to. Leave blank to use default value." /> +</parameters> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/migrated_tools_conf.xml.sample --- /dev/null +++ b/config/migrated_tools_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<toolbox tool_path="../shed_tools"> +</toolbox> \ No newline at end of file diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/object_store_conf.xml.sample --- /dev/null +++ b/config/object_store_conf.xml.sample @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<object_store type="hierarchical"> + <backends> + <object_store type="distributed" id="primary" order="0"> + <backends> + <backend id="files1" type="disk" weight="1"> + <files_dir path="database/files1"/> + <extra_dir type="temp" path="database/tmp1"/> + <extra_dir type="job_work" path="database/job_working_directory1"/> + </backend> + <backend id="files2" type="disk" weight="1"> + <files_dir path="database/files2"/> + <extra_dir type="temp" path="database/tmp2"/> + <extra_dir type="job_work" path="database/job_working_directory2"/> + </backend> + </backends> + </object_store> + <object_store type="disk" id="secondary" order="1"> + <files_dir path="database/files3"/> + <extra_dir type="temp" path="database/tmp3"/> + <extra_dir type="job_work" path="database/job_working_directory3"/> + </object_store> +  + </backends> +</object_store> + diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/openid_conf.xml.sample --- /dev/null +++ b/config/openid_conf.xml.sample @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<openid> + <provider file="google.xml" /> + <provider file="yahoo.xml" /> + <provider file="aol.xml" /> + <provider file="launchpad.xml" /> + <provider file="genomespace.xml" /> +</openid> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/reports_wsgi.ini.sample --- /dev/null +++ b/config/reports_wsgi.ini.sample @@ -0,0 +1,69 @@ +# ---- HTTP Server ---------------------------------------------------------- + +[server:main] + +use = egg:Paste#http +port = 9001 +host = 127.0.0.1 +use_threadpool = true +threadpool_workers = 10 + +# ---- Galaxy Webapps Report Interface ------------------------------------------------- + +[app:main] + +# Specifies the factory for the universe WSGI application +paste.app_factory = galaxy.webapps.reports.buildapp:app_factory +log_level = DEBUG + +# Database connection +# Galaxy reports are intended for production Galaxy instances, so sqlite is not supported. +# You may use a SQLAlchemy connection string to specify an external database. +# database_connection = postgres:///galaxy_test?user=postgres&password=postgres + +# Where dataset files are saved +file_path = database/files +# Temporary storage for additional datasets, this should be shared through the cluster +new_file_path = database/tmp + +# Session support (beaker) +use_beaker_session = True +session_type = memory +session_data_dir = %(here)s/database/beaker_sessions +session_key = galaxysessions +session_secret = changethisinproduction + +# Configuration for debugging middleware +# debug = true +use_lint = false + +# NEVER enable this on a public site (even test or QA) +# use_interactive = true + +# path to sendmail +sendmail_path = /usr/sbin/sendmail + +# Address to join mailing list +mailing_join_addr = galaxy-user-join(a)bx.psu.edu + +# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) +## use_heartbeat = True + +# Profiling middleware (cProfile based) +## use_profile = True + +# Mail +# smtp_server = yourserver(a)yourfacility.edu +# error_email_to = your_bugs(a)bx.psu.edu + +# Use the new iframe / javascript based layout +use_new_layout = true + +# Serving static files (needed if running standalone) +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/shed_data_manager_conf.xml.sample --- /dev/null +++ b/config/shed_data_manager_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<data_managers> +</data_managers> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/shed_tool_conf.xml.sample --- /dev/null +++ b/config/shed_tool_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<toolbox tool_path="../shed_tools"> +</toolbox> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/shed_tool_data_table_conf.xml.sample --- /dev/null +++ b/config/shed_tool_data_table_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<tables> +</tables> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/tool_conf.xml.main --- /dev/null +++ b/config/tool_conf.xml.main @@ -0,0 +1,134 @@ +<?xml version='1.0' encoding='utf-8'?> +<toolbox> + <section id="getext" name="Get Data"> + <tool file="data_source/upload.xml" /> + <tool file="data_source/ucsc_tablebrowser.xml" /> + <tool file="data_source/ucsc_tablebrowser_archaea.xml" /> + <tool file="data_source/ebi_sra.xml" /> + <tool file="data_source/biomart.xml" /> + <tool file="data_source/gramene_mart.xml" /> + <tool file="data_source/flymine.xml" /> + <tool file="data_source/fly_modencode.xml" /> + <tool file="data_source/modmine.xml" /> + <tool file="data_source/mousemine.xml" /> + <tool file="data_source/ratmine.xml" /> + <tool file="data_source/yeastmine.xml" /> + <tool file="data_source/worm_modencode.xml" /> + <tool file="data_source/wormbase.xml" /> + <tool file="data_source/eupathdb.xml" /> + <tool file="genomespace/genomespace_file_browser_prod.xml" /> + <tool file="genomespace/genomespace_importer.xml" /> + </section> + <section id="send" name="Send Data"> + <tool file="genomespace/genomespace_exporter.xml" /> + </section> + <section id="liftOver" name="Lift-Over"> + <tool file="extract/liftOver_wrapper.xml" /> + </section> + <section id="textutil" name="Text Manipulation"> + <tool file="filters/fixedValueColumn.xml" /> + <tool file="filters/catWrapper.xml" /> + <tool file="filters/condense_characters.xml" /> + <tool file="filters/convert_characters.xml" /> + <tool file="filters/mergeCols.xml" /> + <tool file="filters/CreateInterval.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/changeCase.xml" /> + <tool file="filters/pasteWrapper.xml" /> + <tool file="filters/remove_beginning.xml" /> + <tool file="filters/randomlines.xml" /> + <tool file="filters/headWrapper.xml" /> + <tool file="filters/tailWrapper.xml" /> + <tool file="filters/trimmer.xml" /> + <tool file="filters/wc_gnu.xml" /> + <tool file="filters/secure_hash_message_digest.xml" /> + </section> + <section id="convert" name="Convert Formats"> + <tool file="filters/bed2gff.xml" /> + <tool file="filters/gff2bed.xml" /> + <tool file="maf/maf_to_bed.xml" /> + <tool file="maf/maf_to_interval.xml" /> + <tool file="maf/maf_to_fasta.xml" /> + <tool file="filters/sff_extractor.xml" /> + <tool file="filters/wig_to_bigwig.xml" /> + <tool file="filters/bed_to_bigbed.xml" /> + </section> + <section id="filter" name="Filter and Sort"> + <tool file="stats/filtering.xml" /> + <tool file="filters/sorter.xml" /> + <tool file="filters/grep.xml" /> + <label id="gff" text="GFF" /> + <tool file="filters/gff/extract_GFF_Features.xml" /> + <tool file="filters/gff/gff_filter_by_attribute.xml" /> + <tool file="filters/gff/gff_filter_by_feature_count.xml" /> + <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /> + </section> + <section id="group" name="Join, Subtract and Group"> + <tool file="filters/joiner.xml" /> + <tool file="filters/compare.xml" /> + <tool file="stats/grouping.xml" /> + </section> + <section id="features" name="Extract Features"> + <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> + </section> + <section id="fetchSeq" name="Fetch Sequences"> + <tool file="extract/extract_genomic_dna.xml" /> + </section> + <section id="fetchAlign" name="Fetch Alignments"> + <tool file="maf/interval2maf_pairwise.xml" /> + <tool file="maf/interval2maf.xml" /> + <tool file="maf/interval_maf_to_merged_fasta.xml" /> + <tool file="maf/genebed_maf_to_fasta.xml" /> + <tool file="maf/maf_stats.xml" /> + <tool file="maf/maf_thread_for_species.xml" /> + <tool file="maf/maf_limit_to_species.xml" /> + <tool file="maf/maf_limit_size.xml" /> + <tool file="maf/maf_by_block_number.xml" /> + <tool file="maf/maf_filter.xml" /> + <tool file="maf/maf_reverse_complement.xml" /> + </section> + <section id="scores" name="Get Genomic Scores"> + <tool file="filters/wiggle_to_simple.xml" /> + <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> + </section> + <section id="stats" name="Statistics"> + <tool file="stats/gsummary.xml" /> + <tool file="filters/uniq.xml" /> + </section> + <section id="plots" name="Graph/Display Data"> + <tool file="plotting/boxplot.xml" /> + <tool file="maf/vcf_to_maf_customtrack.xml" /> + <tool file="mutation/visualize.xml" /> + </section> + <section id="hgv" name="Phenotype Association"> + <tool file="evolution/codingSnps.xml" /> + <tool file="evolution/add_scores.xml" /> + <tool file="phenotype_association/sift.xml" /> + <tool file="phenotype_association/linkToGProfile.xml" /> + <tool file="phenotype_association/linkToDavid.xml" /> + <tool file="phenotype_association/ldtools.xml" /> + <tool file="phenotype_association/pass.xml" /> + <tool file="phenotype_association/gpass.xml" /> + <tool file="phenotype_association/beam.xml" /> + <tool file="phenotype_association/lps.xml" /> + <tool file="phenotype_association/master2pg.xml" /> + </section> + <label id="ngs" text="NGS Toolbox Beta" /> + <section id="cshl_library_information" name="NGS: QC and manipulation"> + <label id="illumina" text="Illumina data" /> + <label id="454" text="Roche-454 data" /> + <label id="solid" text="AB-SOLiD data" /> + <tool file="next_gen_conversion/solid2fastq.xml" /> + <tool file="solid_tools/solid_qual_stats.xml" /> + <tool file="solid_tools/solid_qual_boxplot.xml" /> + <label id="generic_fastq" text="Generic FASTQ manipulation" /> + <label id="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" /> + </section> + <section id="ngs_mapping" name="NGS: Mapping"> + <label id="illumina" text="Illumina" /> + <label id="roche_454" text="Roche-454" /> + <label id="ab_solid" text="AB-SOLiD" /> + </section> + <section id="samtools" name="NGS: SAM Tools"> + </section> +</toolbox> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/tool_conf.xml.sample --- /dev/null +++ b/config/tool_conf.xml.sample @@ -0,0 +1,186 @@ +<?xml version='1.0' encoding='utf-8'?> +<toolbox> + <section id="getext" name="Get Data"> + <tool file="data_source/upload.xml" /> + <tool file="data_source/ucsc_tablebrowser.xml" /> + <tool file="data_source/ucsc_tablebrowser_test.xml" /> + <tool file="data_source/ucsc_tablebrowser_archaea.xml" /> + <tool file="data_source/ebi_sra.xml" /> + <tool file="data_source/microbial_import.xml" /> + <tool file="data_source/biomart.xml" /> + <tool file="data_source/biomart_test.xml" /> + <tool file="data_source/cbi_rice_mart.xml" /> + <tool file="data_source/gramene_mart.xml" /> + <tool file="data_source/fly_modencode.xml" /> + <tool file="data_source/flymine.xml" /> + <tool file="data_source/flymine_test.xml" /> + <tool file="data_source/modmine.xml" /> + <tool file="data_source/mousemine.xml" /> + <tool file="data_source/ratmine.xml" /> + <tool file="data_source/yeastmine.xml" /> + <tool file="data_source/metabolicmine.xml" /> + <tool file="data_source/worm_modencode.xml" /> + <tool file="data_source/wormbase.xml" /> + <tool file="data_source/wormbase_test.xml" /> + <tool file="data_source/eupathdb.xml" /> + <tool file="data_source/hbvar.xml" /> + <tool file="genomespace/genomespace_file_browser_prod.xml" /> + <tool file="genomespace/genomespace_importer.xml" /> + <tool file="validation/fix_errors.xml" /> + </section> + <section id="send" name="Send Data"> + <tool file="genomespace/genomespace_exporter.xml" /> + </section> + <section id="liftOver" name="Lift-Over"> + <tool file="extract/liftOver_wrapper.xml" /> + </section> + <section id="textutil" name="Text Manipulation"> + <tool file="filters/fixedValueColumn.xml" /> + <tool file="filters/catWrapper.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/mergeCols.xml" /> + <tool file="filters/convert_characters.xml" /> + <tool file="filters/CreateInterval.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/changeCase.xml" /> + <tool file="filters/pasteWrapper.xml" /> + <tool file="filters/remove_beginning.xml" /> + <tool file="filters/randomlines.xml" /> + <tool file="filters/headWrapper.xml" /> + <tool file="filters/tailWrapper.xml" /> + <tool file="filters/trimmer.xml" /> + <tool file="filters/wc_gnu.xml" /> + <tool file="filters/secure_hash_message_digest.xml" /> + </section> + <section id="filter" name="Filter and Sort"> + <tool file="stats/filtering.xml" /> + <tool file="filters/sorter.xml" /> + <tool file="filters/grep.xml" /> + + <label id="gff" text="GFF" /> + <tool file="filters/gff/extract_GFF_Features.xml" /> + <tool file="filters/gff/gff_filter_by_attribute.xml" /> + <tool file="filters/gff/gff_filter_by_feature_count.xml" /> + <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /> + </section> + <section id="group" name="Join, Subtract and Group"> + <tool file="filters/joiner.xml" /> + <tool file="filters/compare.xml" /> + <tool file="stats/grouping.xml" /> + </section> + <section id="convert" name="Convert Formats"> + <tool file="filters/axt_to_concat_fasta.xml" /> + <tool file="filters/axt_to_fasta.xml" /> + <tool file="filters/axt_to_lav.xml" /> + <tool file="filters/bed2gff.xml" /> + <tool file="filters/gff2bed.xml" /> + <tool file="filters/lav_to_bed.xml" /> + <tool file="maf/maf_to_bed.xml" /> + <tool file="maf/maf_to_interval.xml" /> + <tool file="maf/maf_to_fasta.xml" /> + <tool file="filters/wiggle_to_simple.xml" /> + <tool file="filters/sff_extractor.xml" /> + <tool file="filters/gtf2bedgraph.xml" /> + <tool file="filters/wig_to_bigwig.xml" /> + <tool file="filters/bed_to_bigbed.xml" /> + </section> + <section id="features" name="Extract Features"> + <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> + </section> + <section id="fetchSeq" name="Fetch Sequences"> + <tool file="extract/extract_genomic_dna.xml" /> + </section> + <section id="fetchAlign" name="Fetch Alignments"> + <tool file="maf/interval2maf_pairwise.xml" /> + <tool file="maf/interval2maf.xml" /> + <tool file="maf/maf_split_by_species.xml" /> + <tool file="maf/interval_maf_to_merged_fasta.xml" /> + <tool file="maf/genebed_maf_to_fasta.xml" /> + <tool file="maf/maf_stats.xml" /> + <tool file="maf/maf_thread_for_species.xml" /> + <tool file="maf/maf_limit_to_species.xml" /> + <tool file="maf/maf_limit_size.xml" /> + <tool file="maf/maf_by_block_number.xml" /> + <tool file="maf/maf_reverse_complement.xml" /> + <tool file="maf/maf_filter.xml" /> + </section> + <section id="scores" name="Get Genomic Scores"> + <tool file="filters/wiggle_to_simple.xml" /> + <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> + </section> + <section id="stats" name="Statistics"> + <tool file="stats/gsummary.xml" /> + <tool file="filters/uniq.xml" /> + </section> + <section id="plots" name="Graph/Display Data"> + <tool file="plotting/bar_chart.xml" /> + <tool file="plotting/boxplot.xml" /> + <tool file="visualization/LAJ.xml" /> + <tool file="maf/vcf_to_maf_customtrack.xml" /> + <tool file="mutation/visualize.xml" /> + </section> + <section id="hyphy" name="Evolution"> + <tool file="evolution/codingSnps.xml" /> + <tool file="evolution/add_scores.xml" /> + </section> + <section id="motifs" name="Motif Tools"> + <tool file="meme/meme.xml" /> + <tool file="meme/fimo.xml" /> + </section> + <section id="NGS_QC" name="NGS: QC and manipulation"> + + <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /> + + <label id="illumina" text="Illumina fastq" /> + + <label id="454" text="Roche-454 data" /> + <label id="solid" text="AB-SOLiD data" /> + <tool file="next_gen_conversion/solid2fastq.xml" /> + <tool file="solid_tools/solid_qual_stats.xml" /> + <tool file="solid_tools/solid_qual_boxplot.xml" /> + + <label id="generic_fastq" text="Generic FASTQ manipulation" /> + + <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /> + </section> +  + <section id="solexa_tools" name="NGS: Mapping"> + <tool file="sr_mapping/bfast_wrapper.xml" /> + <tool file="sr_mapping/PerM.xml" /> + <tool file="sr_mapping/srma_wrapper.xml" /> + <tool file="sr_mapping/mosaik.xml" /> + </section> + <section id="ngs-rna-tools" name="NGS: RNA Analysis"> + + <label id="rna_seq" text="RNA-seq" /> + <label id="filtering" text="Filtering" /> + </section> + <section id="samtools" name="NGS: SAM Tools"> + </section> + <section id="ngs-simulation" name="NGS: Simulation"> + <tool file="ngs_simulation/ngs_simulation.xml" /> + </section> + <section id="hgv" name="Phenotype Association"> + <tool file="evolution/codingSnps.xml" /> + <tool file="evolution/add_scores.xml" /> + <tool file="phenotype_association/sift.xml" /> + <tool file="phenotype_association/linkToGProfile.xml" /> + <tool file="phenotype_association/linkToDavid.xml" /> + <tool file="phenotype_association/ldtools.xml" /> + <tool file="phenotype_association/pass.xml" /> + <tool file="phenotype_association/gpass.xml" /> + <tool file="phenotype_association/beam.xml" /> + <tool file="phenotype_association/lps.xml" /> + <tool file="phenotype_association/master2pg.xml" /> + </section> +</toolbox> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/tool_data_table_conf.xml.sample --- /dev/null +++ b/config/tool_data_table_conf.xml.sample @@ -0,0 +1,63 @@ + +<tables> +  + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +  + <table name="bfast_indexes" comment_char="#"> + <columns>value, dbkey, formats, name, path</columns> + <file path="tool-data/bfast_indexes.loc" /> + </table> +  + <table name="blastdb_p" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb_p.loc" /> + </table> +  + <table name="bwa_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwa_index.loc" /> + </table> +  + <table name="bwa_indexes_color" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwa_index_color.loc" /> + </table> +  + <table name="indexed_maf_files"> + <columns>name, value, dbkey, species</columns> + <file path="tool-data/maf_index.loc" /> + </table> +  + <table name="ngs_sim_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/ngs_sim_fasta.loc" /> + </table> +  + <table name="perm_base_indexes" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/perm_base_index.loc" /> + </table> +  + <table name="perm_color_indexes" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/perm_color_index.loc" /> + </table> +  + <table name="picard_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/picard_index.loc" /> + </table> +  + <table name="srma_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/picard_index.loc" /> + </table> +  + <table name="mosaik_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/mosaik_index.loc" /> + </table> +</tables> diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/tool_shed_wsgi.ini.sample --- /dev/null +++ b/config/tool_shed_wsgi.ini.sample @@ -0,0 +1,114 @@ +# ---- HTTP Server ---------------------------------------------------------- + +[server:main] + +use = egg:Paste#http +port = 9009 + +# The address on which to listen. By default, only listen to localhost (the tool shed will not +# be accessible over the network). Use '0.0.0.0' to listen on all available network interfaces. +#host = 0.0.0.0 +host = 127.0.0.1 + +use_threadpool = true +threadpool_workers = 10 +# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +threadpool_kill_thread_limit = 10800 + +# ---- Galaxy Webapps Community Interface ------------------------------------------------- + +[app:main] + +# Specifies the factory for the universe WSGI application +paste.app_factory = galaxy.webapps.tool_shed.buildapp:app_factory +log_level = DEBUG + +# Database connection +database_file = database/community.sqlite +# You may use a SQLAlchemy connection string to specify an external database instead +#database_connection = postgres:///community_test?host=/var/run/postgresql + +# Where the hgweb.config file is stored. The default is the Galaxy installation directory. +#hgweb_config_dir = None + +# Where tool shed repositories are stored. +file_path = database/community_files +# Temporary storage for additional datasets, this should be shared through the cluster +new_file_path = database/tmp + +# File containing old-style genome builds +#builds_file_path = tool-data/shared/ucsc/builds.txt + +# Session support (beaker) +use_beaker_session = True +session_type = memory +session_data_dir = %(here)s/database/beaker_sessions +session_key = galaxysessions +session_secret = changethisinproduction + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +id_secret = changethisinproductiontoo + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy +#use_remote_user = False + +# Configuration for debugging middleware +debug = true +use_lint = false + +# NEVER enable this on a public site (even test or QA) +# use_interactive = true + +# this should be a comma-separated list of valid Galaxy users +#admin_users = user1@example.org,user2@example.org + +# Force everyone to log in (disable anonymous access) +require_login = False + +# path to sendmail +sendmail_path = /usr/sbin/sendmail + +# Number of saved tool test results produced by the install and test framework for each repository. +#num_tool_test_results_saved = 5 + +# For use by email messages sent from the tool shed +#smtp_server = smtp.your_tool_shed_server +#email_from = your_tool_shed_email@server + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = https://wiki.galaxyproject.org/Support + +# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) +## use_heartbeat = True + +# Profiling middleware (cProfile based) +## use_profile = True + +# Enable creation of Galaxy flavor Docker Image +#enable_galaxy_flavor_docker_image = False + +# Use the new iframe / javascript based layout +use_new_layout = true + +# Show a message box under the masthead. +#message_box_visible = False +#message_box_content = None +#message_box_class = info + +# Serving static files (needed if running standalone) +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r e4daf2910a9989eda0efe2b532adb860999532c3 config/tool_sheds_conf.xml.sample --- /dev/null +++ b/config/tool_sheds_conf.xml.sample @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<tool_sheds> + <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> + <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> +</tool_sheds> This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/21fb6c2f4349/ Changeset: 21fb6c2f4349 User: natefoo Date: 2014-09-15 20:34:40 Summary: Rename universe_wsgi.ini to galaxy.ini Affected #: 2 files diff -r e4daf2910a9989eda0efe2b532adb860999532c3 -r 21fb6c2f4349c358321b9344b9dbda20264b78fb config/galaxy.ini.sample --- /dev/null +++ b/config/galaxy.ini.sample @@ -0,0 +1,882 @@ +# +# Galaxy is configured by default to be useable in a single-user development +# environment. To tune the application for a multi-user production +# environment, see the documentation at: +# +# http://usegalaxy.org/production +# + +# Throughout this sample configuration file, except where stated otherwise, +# uncommented values override the default if left unset, whereas commented +# values are set to the default value. +# Examples of many of these options are explained in more detail in the wiki: +# +# https://wiki.galaxyproject.org/Admin/Config +# +# Config hackers are encouraged to check there before asking for help. + +# ---- HTTP Server ---------------------------------------------------------- + +# Configuration of the internal HTTP server. + +[server:main] + +# The internal HTTP server to use. Currently only Paste is provided. This +# option is required. +use = egg:Paste#http + +# The port on which to listen. +#port = 8080 + +# The address on which to listen. By default, only listen to localhost (Galaxy +# will not be accessible over the network). Use '0.0.0.0' to listen on all +# available network interfaces. +#host = 127.0.0.1 + +# Use a threadpool for the web server instead of creating a thread for each +# request. +use_threadpool = True + +# Number of threads in the web server thread pool. +#threadpool_workers = 10 + +# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +threadpool_kill_thread_limit = 10800 + +# ---- Filters -------------------------------------------------------------- + +# Filters sit between Galaxy and the HTTP server. + +# These filters are disabled by default. They can be enabled with +# 'filter-with' in the [app:main] section below. + +# Define the gzip filter. +[filter:gzip] +use = egg:Paste#gzip + +# Define the proxy-prefix filter. +[filter:proxy-prefix] +use = egg:PasteDeploy#prefix +prefix = /galaxy + +# ---- Galaxy --------------------------------------------------------------- + +# Configuration of the Galaxy application. + +[app:main] + +# -- Application and filtering + +# The factory for the WSGI application. This should not be changed. +paste.app_factory = galaxy.web.buildapp:app_factory + +# If not running behind a proxy server, you may want to enable gzip compression +# to decrease the size of data transferred over the network. If using a proxy +# server, please enable gzip compression there instead. +#filter-with = gzip + +# If running behind a proxy server and Galaxy is served from a subdirectory, +# enable the proxy-prefix filter and set the prefix in the +# [filter:proxy-prefix] section above. +#filter-with = proxy-prefix + +# If proxy-prefix is enabled and you're running more than one Galaxy instance +# behind one hostname, you will want to set this to the same path as the prefix +# in the filter above. This value becomes the "path" attribute set in the +# cookie so the cookies from each instance will not clobber each other. +#cookie_path = None + +# -- Database + +# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You +# may use a SQLAlchemy connection string to specify an external database +# instead. This string takes many options which are explained in detail in the +# config file documentation. +#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# If the server logs errors about not having enough database pool connections, +# you will want to increase these values, or consider running more Galaxy +# processes. +#database_engine_option_pool_size = 5 +#database_engine_option_max_overflow = 10 + +# If using MySQL and the server logs the error "MySQL server has gone away", +# you will want to set this to some positive value (7200 should work). +#database_engine_option_pool_recycle = -1 + +# If large database query results are causing memory or response time issues in +# the Galaxy process, leave the result on the server instead. This option is +# only available for PostgreSQL and is highly recommended. +#database_engine_option_server_side_cursors = False + +# Log all database transactions, can be useful for debugging and performance +# profiling. Logging is done via Python's 'logging' module under the qualname +# 'galaxy.model.orm.logging_connection_proxy' +#database_query_profiling_proxy = False + +# By default, Galaxy will use the same database to track user data and +# tool shed install data. There are many situtations in which it is +# valuable to seperate these - for instance bootstrapping fresh Galaxy +# instances with pretested installs. The following optin can be used to +# separate the tool shed install database (all other options listed above +# but prefixed with install_ are also available). +#install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# -- Files and directories + +# Dataset files are stored in this directory. +#file_path = database/files + +# Temporary files are stored in this directory. +#new_file_path = database/tmp + +# Tool config files, defines what tools are available in Galaxy. +# Tools can be locally developed or installed from Galaxy tool sheds. +#tool_config_file = tool_conf.xml,shed_tool_conf.xml + +# Enable / disable checking if any tools defined in the above non-shed tool_config_files +# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool +# Shed. This setting should generally be set to False only for development Galaxy environments +# that are often rebuilt from scratch where migrated tools do not need to be available in the +# Galaxy tool panel. If the following setting remains commented, the default setting will be True. +#check_migrate_tools = True + +# Tool config maintained by tool migration scripts. If you use the migration +# scripts to install tools that have been migrated to the tool shed upon a new +# release, they will be added to this tool config file. +#migrated_tools_config = migrated_tools_conf.xml + +# File that contains the XML section and tool tags from all tool panel config +# files integrated into a single file that defines the tool panel layout. This +# file can be changed by the Galaxy administrator to alter the layout of the +# tool panel. If not present, Galaxy will create it. +#integrated_tool_panel_config = integrated_tool_panel.xml + +# Default path to the directory containing the tools defined in tool_conf.xml. +# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. +#tool_path = tools + +# Path to the directory in which tool dependencies are placed. This is used by +# the tool shed to install dependencies and can also be used by administrators +# to manually install or link to dependencies. For details, see: +# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies +# If this option is not set to a valid path, installing tools with dependencies +# from the Tool Shed will fail. +#tool_dependency_dir = None + +# File containing the Galaxy Tool Sheds that should be made available to +# install from in the admin interface +#tool_sheds_config_file = tool_sheds_conf.xml + +# Enable automatic polling of relative tool sheds to see if any updates +# are available for installed repositories. Ideally only one Galaxy +# server process should be able to check for repository updates. The +# setting for hours_between_check should be an integer between 1 and 24. +#enable_tool_shed_check = False +#hours_between_check = 12 + +# Enable use of an in-memory registry with bi-directional relationships +# between repositories (i.e., in addition to lists of dependencies for a +# repository, keep an in-memory registry of dependent items for each repository. +#manage_dependency_relationships = False + +# XML config file that contains data table entries for the ToolDataTableManager. This file is manually +# maintained by the Galaxy administrator. +#tool_data_table_config_path = tool_data_table_conf.xml + +# XML config file that contains additional data table entries for the ToolDataTableManager. This file +# is automatically generated based on the current installed tool shed repositories that contain valid +# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically +# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. +#shed_tool_data_table_config = shed_tool_data_table_conf.xml + +# Directory where data used by tools is located, see the samples in that +# directory and the wiki for help: +# https://wiki.galaxyproject.org/Admin/DataIntegration +#tool_data_path = tool-data + +# File containing old-style genome builds +#builds_file_path = tool-data/shared/ucsc/builds.txt + +# Directory where chrom len files are kept, currently mainly used by trackster +#len_file_path = tool-data/shared/ucsc/chrom + +# Datatypes config file, defines what data (file) types are available in +# Galaxy. +#datatypes_config_file = config/datatypes_conf.xml + +# Disable the 'Auto-detect' option for file uploads +#datatypes_disable_auto = False + +# Visualizations config directory: where to look for individual visualization plugins. +# The path is relative to the Galaxy root dir. To use an absolute path begin the path +# with '/'. Defaults to "config/plugins/visualizations". +#visualization_plugins_directory = config/plugins/visualizations + +# Each job is given a unique empty directory as its current working directory. +# This option defines in what parent directory those directories will be +# created. +#job_working_directory = database/job_working_directory + +# If using a cluster, Galaxy will write job scripts and stdout/stderr to this +# directory. +#cluster_files_directory = database/pbs + +# Mako templates are compiled as needed and cached for reuse, this directory is +# used for the cache +#template_cache_path = database/compiled_templates + +# Citation related caching. Tool citations information maybe fetched from +# external sources such as http://dx.doi.org/ by Galaxy - the following parameters +# can be used to control the caching used to store this information. +#citation_cache_type = file +#citation_cache_data_dir = database/citations/data +#citation_cache_lock_dir = database/citations/lock + +# External service types config file, defines what types of external_services configurations +# are available in Galaxy. +#external_service_type_config_file = config/external_service_types_conf.xml + +# Path to the directory containing the external_service_types defined in the config. +#external_service_type_path = external_service_types + +# Tools with a number of outputs not known until runtime can write these +# outputs to a directory for collection by Galaxy when the job is done. +# Previously, this directory was new_file_path, but using one global directory +# can cause performance problems, so using job_working_directory ('.' or cwd +# when a job is run) is encouraged. By default, both are checked to avoid +# breaking existing tools. +#collect_outputs_from = new_file_path,job_working_directory + +# -- Data Storage (Object Store) +# +# Configuration file for the object store +# If this is set and exists, it overrides any other objectstore settings. +# object_store_config_file = object_store_conf.xml + +# Object store backend module (valid options are: disk, s3, swift, irods, +# distributed, hierarchical) +#object_store = disk + +# *Extremely* old Galaxy instances created datasets at the root of the +# `file_path` defined above. If your Galaxy instance has datasets at the root +# (instead of in directories composed by hashing the dataset id), you should +# enable this option to allow Galaxy to find them. +#object_store_check_old_style = False + +# Credentials used by certain (s3, swift) object store backends +#os_access_key = <your cloud object store access key> +#os_secret_key = <your cloud object store secret key> +#os_bucket_name = <name of an existing object store bucket or container> + +# If using 'swift' object store, you must specify the following connection +# properties +#os_host = swift.rc.nectar.org.au +#os_port = 8888 +#os_is_secure = False +#os_conn_path = / + +# Reduced redundancy can be used only with the 's3' object store +#os_use_reduced_redundancy = False + +# Path to cache directory for object store backends that utilize a cache (s3, +# swift, irods) +#object_store_cache_path = database/files/ + +# Size (in GB) that the cache used by object store should be limited to. +# If the value is not specified, the cache size will be limited only by the +# file system size. +#object_store_cache_size = 100 + +# Configuration file for the distributed object store, if object_store = +# distributed. See the sample at distributed_object_store_conf.xml.sample +#distributed_object_store_config_file = None + + +# -- Mail and notification + +# Galaxy sends mail for various things: Subscribing users to the mailing list +# if they request it, emailing password resets, notification from the Galaxy +# Sample Tracking system, reporting dataset errors, and sending activation emails. +# To do this, it needs to send mail through an SMTP server, which you may define here (host:port). +# Galaxy will automatically try STARTTLS but will continue upon failure. +#smtp_server = None + +# If your SMTP server requires a username and password, you can provide them +# here (password in cleartext here, but if your server supports STARTTLS it +# will be sent over the network encrypted). +#smtp_username = None +#smtp_password = None + +# If your SMTP server requires SSL from the beginning of the connection +# smtp_ssl = False + +# On the user registration form, users may choose to join the mailing list. +# This is the address of the list they'll be subscribed to. +#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu + +# Datasets in an error state include a link to report the error. Those reports +# will be sent to this address. Error reports are disabled if no address is set. +# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter. +#error_email_to = None + +# Activation email is used as a sender ('from' field) for the account activation mail. +# We recommend using string in the following format: Galaxy Project <galaxy-no-reply(a)example.com> +#activation_email = None + +# URL of the support resource for the galaxy instance. Used in activation emails. +#instance_resource_url = http://wiki.galaxyproject.org/ + +# E-mail domains blacklist is used for filtering out users that are using disposable email address +# during the registration. If their address domain matches any domain in the BL they are refused the registration. +#blacklist_file = config/disposable_email_blacklist.conf + +# Registration warning message is used to discourage people from registering multiple accounts. Applies mostly for the main Galaxy instance. +# If no message specified the warning box will not be shown. +#registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. + +# When users opt to reset passwords, new ones are created, this option +# specifies the length of these passwords. +#reset_password_length = 15 + + +# -- Account activation + +# This is user account activation feature global flag. If set to "False" the rest of the Account +# activation configuration is ignored and user activation is disabled (a.k.a. accounts are active since registration). +# Note the activation is also not working in case the smtp server is not defined. +#user_activation_on = False + +# Activation grace period. Activation is not forced (login is not disabled) until +# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content). +# In hours. Default is 3. Enter 0 to disable grace period. +# Users with OpenID logins have grace period forever. +#activation_grace_period = 0 + +# Used for warning box for inactive accounts (unable to run jobs). +# In use only if activation_grace_period is set. +#inactivity_box_content = Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address. + + +# -- Display sites + +# Galaxy can display data at various external browsers. These options specify +# which browsers should be available. URLs and builds available at these +# browsers are defined in the specifield files. + +# If use_remote_user = True, display application servers will be denied access +# to Galaxy and so displaying datasets in these sites will fail. +# display_servers contains a list of hostnames which should be allowed to +# bypass security to display datasets. Please be aware that there are security +# implications if this is allowed. More details (including required changes to +# the proxy server config) are available in the Apache proxy documentation on +# the wiki. +# +# The list of servers in this sample config are for the UCSC Main, Test and +# Archaea browsers, but the default if left commented is to not allow any +# display sites to bypass security (you must uncomment the line below to allow +# them). +#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… + +# To disable the old-style display applications that are hardcoded into datatype classes, +# set enable_old_display_applications = False. +# This may be desirable due to using the new-style, XML-defined, display applications that +# have been defined for many of the datatypes that have the old-style. +# There is also a potential security concern with the old-style applications, +# where a malicious party could provide a link that appears to reference the Galaxy server, +# but contains a redirect to a third-party server, tricking a Galaxy user to access said +# site. +#enable_old_display_applications = True + +# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. + +use_nglims = False +nglims_config_file = tool-data/nglims.yaml + +# -- UI Localization + +# Show a message box under the masthead. +#message_box_visible = False +#message_box_content = None +#message_box_class = info + +# Append "/{brand}" to the "Galaxy" text in the masthead. +#brand = None + +# Format string used when showing date and time information. +# The string may contain: +# - the directives used by Python time.strftime() function (see http://docs.python.org/2/library/time.html#time.strftime ), +# - $locale (complete format string for the server locale), +# - $iso8601 (complete format string as specified by ISO 8601 international standard). +# pretty_datetime_format = $locale (UTC) + +# The URL of the page to display in Galaxy's middle pane when loaded. This can be +# an absolute or relative URL. +#welcome_url = /static/welcome.html + +# The URL linked by the "Galaxy/brand" text. +#logo_url = / + +# The URL linked by the "Wiki" link in the "Help" menu. +#wiki_url = http://wiki.galaxyproject.org/ + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.galaxyproject.org/Support + +# The URL linked by the "How to Cite Galaxy" link in the "Help" menu. +#citation_url = http://wiki.galaxyproject.org/CitingGalaxy + +#The URL linked by the "Search" link in the "Help" menu. +#search_url = http://galaxyproject.org/search/usegalaxy/ + +#The URL linked by the "Mailing Lists" link in the "Help" menu. +#mailing_lists_url = http://wiki.galaxyproject.org/MailingLists + +#The URL linked by the "Videos" link in the "Help" menu. +#videos_url = http://vimeo.com/galaxyproject + +# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well +# as on the user registration and login forms and in the activation emails. +#terms_url = None + +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +# The Galaxy Q&A site is under development; when the site is done, this URL +# will be set and uncommented. +#qa_url = + +# Serve static content, which must be enabled if you're not serving it via a +# proxy server. These options should be self explanatory and so are not +# documented individually. You can use these paths (or ones in the proxy +# server) to point to your own styles. +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue +static_robots_txt = %(here)s/static/robots.txt + +# Pack javascript at launch (/static/scripts/*.js) +# This only happens if the modified timestamp of the source .js is newer +# than the version (if it exists) in /static/scripts/packed/ +# Note that this requires java > 1.4 for executing yuicompressor.jar +#pack_scripts = False + +# Cloud Launch + +#enable_cloud_launch = False +#cloudlaunch_default_ami = ami-a7dbf6ce + +# Incremental Display Options + +#display_chunk_size = 65536 + +# -- Advanced proxy features + +# For help on configuring the Advanced proxy features, see: +# http://usegalaxy.org/production + +# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set +# this to True to inform Galaxy that mod_xsendfile is enabled upstream. +#apache_xsendfile = False + +# The same download handling can be done by nginx using X-Accel-Redirect. This +# should be set to the path defined in the nginx config as an internal redirect +# with access to Galaxy's data files (see documentation linked above). +#nginx_x_accel_redirect_base = False + +# nginx can make use of mod_zip to create zip files containing multiple library +# files. If using X-Accel-Redirect, this can be the same value as that option. +#nginx_x_archive_files_base = False + +# If using compression in the upstream proxy server, use this option to disable +# gzipping of library .tar.gz and .zip archives, since the proxy server will do +# it faster on the fly. +#upstream_gzip = False + +# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. +# Configuration for this is complex and explained in detail in the +# documentation linked above. The upload store is a temporary directory in +# which files uploaded by the upload module will be placed. +#nginx_upload_store = False + +# This value overrides the action set on the file upload form, e.g. the web +# path where the nginx_upload_module has been configured to intercept upload +# requests. +#nginx_upload_path = False + +# -- Logging and Debugging + +# Verbosity of console log messages. Acceptable values can be found here: +# http://docs.python.org/library/logging.html#logging-levels +#log_level = DEBUG + +# Print database operations to the server log (warning, quite verbose!). +#database_engine_option_echo = False + +# Print database pool operations to the server log (warning, quite verbose!). +#database_engine_option_echo_pool = False + +# Turn on logging of application events and some user events to the database. +#log_events = True + +# Turn on logging of user actions to the database. Actions currently logged are +# grid views, tool searches, and use of "recently" used tools menu. The +# log_events and log_actions functionality will eventually be merged. +#log_actions = True + +# Sanitize All HTML Tool Output +# By default, all tool output served as 'text/html' will be sanitized +# thoroughly. This can be disabled if you have special tools that require +# unaltered output. +#sanitize_all_html = True + +# By default Galaxy will serve non-HTML tool output that may potentially +# contain browser executable JavaScript content as plain text. This will for +# instance cause SVG datasets to not render properly and so may be disabled +# by setting the following option to True. +#serve_xss_vulnerable_mimetypes = False + +# Debug enables access to various config options useful for development and +# debugging: use_lint, use_profile, use_printdebug and use_interactive. It +# also causes the files used by PBS/SGE (submission script, output, and error) +# to remain on disk after the job is complete. Debug mode is disabled if +# commented, but is uncommented by default in the sample config. +debug = True + +# Check for WSGI compliance. +#use_lint = False + +# Run the Python profiler on each request. +#use_profile = False + +# Intercept print statements and show them on the returned page. +#use_printdebug = True + +# Enable live debugging in your browser. This should NEVER be enabled on a +# public site. Enabled in the sample config for development. +use_interactive = True + +# Write thread status periodically to 'heartbeat.log', (careful, uses disk +# space rapidly!). Useful to determine why your processes may be consuming a +# lot of CPU. +#use_heartbeat = False + +# Enable the memory debugging interface (careful, negatively impacts server +# performance). +#use_memdump = False + +# -- Data Libraries + +# These library upload options are described in much more detail in the wiki: +# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles + +# Add an option to the library upload form which allows administrators to +# upload a directory of files. +#library_import_dir = None + +# Add an option to the library upload form which allows authorized +# non-administrators to upload a directory of files. The configured directory +# must contain sub-directories named the same as the non-admin user's Galaxy +# login ( email ). The non-admin user is restricted to uploading files or +# sub-directories of files contained in their directory. +#user_library_import_dir = None + +# Add an option to the admin library upload tool allowing admins to paste +# filesystem paths to files and directories in a box, and these paths will be +# added to a library. Set to True to enable. Please note the security +# implication that this will give Galaxy Admins access to anything your Galaxy +# user has access to. +#allow_library_path_paste = False + +# Users may choose to download multiple files from a library in an archive. By +# default, Galaxy allows users to select from a few different archive formats +# if testing shows that Galaxy is able to create files using these formats. +# Specific formats can be disabled with this option, separate more than one +# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. +#disable_library_comptypes = + +# Some sequencer integration features in beta allow you to automatically +# transfer datasets. This is done using a lightweight transfer manager which +# runs outside of Galaxy (but is spawned by it automatically). Galaxy will +# communicate with this manager over the port specified here. +#transfer_manager_port = 8163 + +# Search data libraries with whoosh +#enable_whoosh_library_search = True +# Whoosh indexes are stored in this directory. +#whoosh_index_dir = database/whoosh_indexes + +# Search data libraries with lucene +#enable_lucene_library_search = False +# maxiumum file size to index for searching, in MB +#fulltext_max_size = 500 +#fulltext_noindex_filetypes = bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger +# base URL of server providing search functionality using lucene +#fulltext_url = http://localhost:8081 + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +#id_secret = USING THE DEFAULT IS NOT SECURE! + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy +#use_remote_user = False + +# If use_remote_user is enabled and your external authentication +# method just returns bare usernames, set a default mail domain to be appended +# to usernames, to become your Galaxy usernames (email addresses). +#remote_user_maildomain = None + +# If use_remote_user is enabled, the header that the upstream proxy provides +# the remote username in defaults to HTTP_REMOTE_USER (the 'HTTP_' is prepended +# by WSGI). This option allows you to change the header. Note, you still need +# to prepend 'HTTP_' to the header in this option, but your proxy server should +# *not* include 'HTTP_' at the beginning of the header name. +#remote_user_header = HTTP_REMOTE_USER + +# If use_remote_user is enabled, you can set this to a URL that will log your +# users out. +#remote_user_logout_href = None + +# If your proxy and/or authentication source does not normalize e-mail +# addresses or user names being passed to Galaxy - set the following option +# to True to force these to lower case. +#normalize_remote_user_email = False + +# Administrative users - set this to a comma-separated list of valid Galaxy +# users (email addresses). These users will have access to the Admin section +# of the server, and will have access to create users, groups, roles, +# libraries, and more. For more information, see: +# https://wiki.galaxyproject.org/Admin/Interface +#admin_users = None + +# Force everyone to log in (disable anonymous access). +#require_login = False + +# Allow unregistered users to create new accounts (otherwise, they will have to +# be created by an admin). +#allow_user_creation = True + +# Allow administrators to delete accounts. +#allow_user_deletion = False + +# Allow administrators to log in as other users (useful for debugging) +#allow_user_impersonation = False + +# Allow users to remove their datasets from disk immediately (otherwise, +# datasets will be removed after a time period specified by an administrator in +# the cleanup scripts run via cron) +#allow_user_dataset_purge = False + +# By default, users' data will be public, but setting this to True will cause +# it to be private. Does not affect existing users and data, only ones created +# after this option is set. Users may still change their default back to +# public. +#new_user_dataset_access_role_default_private = False + +# -- Beta features + +# Enable Galaxy to communicate directly with a sequencer +#enable_sequencer_communication = False + +# Enable authentication via OpenID. Allows users to log in to their Galaxy +# account by authenticating with an OpenID provider. +#enable_openid = False +#openid_config_file = openid_conf.xml +#openid_consumer_cache_path = database/openid_consumer_cache + +# Optional list of email addresses of API users who can make calls on behalf of +# other users +#api_allow_run_as = None + +# Master key that allows many API admin actions to be used without actually +# having a defined admin user in the database/config. Only set this if you need +# to bootstrap Galaxy, you probably do not want to set this on public servers. +#master_api_key = changethis + +# Enable tool tags (associating tools with tags). This has its own option +# since its implementation has a few performance implications on startup for +# large servers. +#enable_tool_tags = False + +# Enable a feature when running workflows. When enabled, default datasets +# are selected for "Set at Runtime" inputs from the history such that the +# same input will not be selected twice, unless there are more inputs than +# compatible datasets in the history. +# When False, the most recently added compatible item in the history will +# be used for each "Set at Runtime" input, independent of others in the Workflow +#enable_unique_workflow_defaults = False + +# The URL to the myExperiment instance being used (omit scheme but include port) +#myexperiment_url = www.myexperiment.org:80 + +# Enable Galaxy's "Upload via FTP" interface. You'll need to install and +# configure an FTP server (we've used ProFTPd since it can use Galaxy's +# database for authentication) and set the following two options. + +# This should point to a directory containing subdirectories matching users' +# email addresses, where Galaxy will look for files. +#ftp_upload_dir = None + +# This should be the hostname of your FTP server, which will be provided to +# users in the help text. +#ftp_upload_site = None + +# Enable enforcement of quotas. Quotas can be set from the Admin interface. +#enable_quotas = False + +# This option allows users to see the full path of datasets via the "View +# Details" option in the history. Administrators can always see this. +#expose_dataset_path = False + +# Data manager configuration options +# Allow non-admin users to view available Data Manager options +#enable_data_manager_user_view = False +# File where Data Managers are configured +#data_manager_config_file = config/data_manager_conf.xml +# File where Tool Shed based Data Managers are configured +#shed_data_manager_config_file = shed_data_manager_conf.xml +# Directory to store Data Manager based tool-data; defaults to tool_data_path +#galaxy_data_manager_data_path = tool-data + +# -- Job Execution + +# To increase performance of job execution and the web interface, you can +# separate Galaxy into multiple processes. There are more than one way to do +# this, and they are explained in detail in the documentation: +# +# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling + +# By default, Galaxy manages and executes jobs from within a single process and +# notifies itself of new jobs via in-memory queues. Jobs are run locally on +# the system on which Galaxy is started. Advanced job running capabilities can +# be configured through the job configuration file. +#job_config_file = job_conf.xml + +# In multiprocess configurations, notification between processes about new jobs +# is done via the database. In single process configurations, this is done in +# memory, which is a bit quicker. Galaxy tries to automatically determine +# which method it should used based on your handler configuration in the job +# config file, but you can explicitly override this behavior by setting the +# following option to True or False. +#track_jobs_in_database = None + +# This enables splitting of jobs into tasks, if specified by the particular tool config. +# This is a new feature and not recommended for production servers yet. +#use_tasked_jobs = False +#local_task_queue_workers = 2 + +# Enable job recovery (if Galaxy is restarted while cluster jobs are running, +# it can "recover" them when it starts). This is not safe to use if you are +# running more than one Galaxy server using the same database. +#enable_job_recovery = True + +# Although it is fairly reliable, setting metadata can occasionally fail. In +# these instances, you can choose to retry setting it internally or leave it in +# a failed state (since retrying internally may cause the Galaxy process to be +# unresponsive). If this option is set to False, the user will be given the +# option to retry externally, or set metadata manually (when possible). +#retry_metadata_internally = True + +# If (for example) you run on a cluster and your datasets (by default, +# database/files/) are mounted read-only, this option will override tool output +# paths to write outputs to the working directory instead, and the job manager +# will move the outputs to their proper place in the dataset directory on the +# Galaxy server after the job completes. +#outputs_to_working_directory = False + +# If your network filesystem's caching prevents the Galaxy server from seeing +# the job's stdout and stderr files when it completes, you can retry reading +# these files. The job runner will retry the number of times specified below, +# waiting 1 second between tries. For NFS, you may want to try the -noac mount +# option (Linux) or -actimeo=0 (Solaris). +#retry_job_output_collection = 0 + +# Clean up various bits of jobs left on the filesystem after completion. These +# bits include the job working directory, external metadata temporary files, +# and DRM stdout and stderr files (if using a DRM). Possible values are: +# always, onsuccess, never +#cleanup_job = always + +# File to source to set up the environment when running jobs. By default, the +# environment in which the Galaxy server starts is used when running jobs +# locally, and the environment set up per the DRM's submission method and +# policy is used when running jobs on a cluster (try testing with `qsub` on the +# command line). environment_setup_file can be set to the path of a file on +# the cluster that should be sourced by the user to set up the environment +# prior to running tools. This can be especially useful for running jobs as +# the actual user, to remove the need to configure each user's environment +# individually. +#environment_setup_file = None + + +# Optional file containing job resource data entry fields definition. +# These fields will be presented to users in the tool forms and allow them to +# overwrite default job resources such as number of processors, memory, and walltime. +#job_resource_params_file = job_resource_params_conf.xml + +# If using job concurrency limits (configured in job_config_file), several +# extra database queries must be performed to determine the number of jobs a +# user has dispatched to a given destination. By default, these queries will +# happen for every job that is waiting to run, but if cache_user_job_count is +# set to True, it will only happen once per iteration of the handler queue. +# Although better for performance due to reduced queries, the tradeoff is a +# greater possibility that jobs will be dispatched past the configured limits +# if running many handlers. +#cache_user_job_count = False + +# ToolBox filtering +# Modules from lib/galaxy/tools/filters/ can be specified in the following lines. +# tool_* filters will be applied for all users and can not be changed by them. +# user_tool_* filters will be shown under user preferences and can be toogled +# on and off by runtime +#tool_filters +#tool_label_filters +#tool_section_filters +#user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode +#user_tool_section_filters = examples:restrict_text +#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode + +# Galaxy Application Internal Message Queue + +# Galaxy uses AMQP internally TODO more documentation on what for. +# For examples, see http://ask.github.io/kombu/userguide/connections.html +# +# Without specifying anything here, galaxy will first attempt to use your +# specified database_connection above. If that's not specified either, Galaxy +# will automatically create and use a separate sqlite database located in your +# <galaxy>/database folder (indicated in the commented out line below). + +#amqp_internal_connection = sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE + + + +# ---- Galaxy External Message Queue ------------------------------------------------- + +# Galaxy uses AMQ protocol to receive messages from external sources like +# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +# For Galaxy to receive messages from a message queue the RabbitMQ server has +# to be set up with a user account and other parameters listed below. The 'host' +# and 'port' fields should point to where the RabbitMQ server is running. + +[galaxy_amqp] + +#host = 127.0.0.1 +#port = 5672 +#userid = galaxy +#password = galaxy +#virtual_host = galaxy_messaging_engine +#queue = galaxy_queue +#exchange = galaxy_exchange +#routing_key = bar_code_scanner +#rabbitmqctl_path = /path/to/rabbitmqctl + diff -r e4daf2910a9989eda0efe2b532adb860999532c3 -r 21fb6c2f4349c358321b9344b9dbda20264b78fb config/universe_wsgi.ini.sample --- a/config/universe_wsgi.ini.sample +++ /dev/null @@ -1,882 +0,0 @@ -# -# Galaxy is configured by default to be useable in a single-user development -# environment. To tune the application for a multi-user production -# environment, see the documentation at: -# -# http://usegalaxy.org/production -# - -# Throughout this sample configuration file, except where stated otherwise, -# uncommented values override the default if left unset, whereas commented -# values are set to the default value. -# Examples of many of these options are explained in more detail in the wiki: -# -# https://wiki.galaxyproject.org/Admin/Config -# -# Config hackers are encouraged to check there before asking for help. - -# ---- HTTP Server ---------------------------------------------------------- - -# Configuration of the internal HTTP server. - -[server:main] - -# The internal HTTP server to use. Currently only Paste is provided. This -# option is required. -use = egg:Paste#http - -# The port on which to listen. -#port = 8080 - -# The address on which to listen. By default, only listen to localhost (Galaxy -# will not be accessible over the network). Use '0.0.0.0' to listen on all -# available network interfaces. -#host = 127.0.0.1 - -# Use a threadpool for the web server instead of creating a thread for each -# request. -use_threadpool = True - -# Number of threads in the web server thread pool. -#threadpool_workers = 10 - -# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. -threadpool_kill_thread_limit = 10800 - -# ---- Filters -------------------------------------------------------------- - -# Filters sit between Galaxy and the HTTP server. - -# These filters are disabled by default. They can be enabled with -# 'filter-with' in the [app:main] section below. - -# Define the gzip filter. -[filter:gzip] -use = egg:Paste#gzip - -# Define the proxy-prefix filter. -[filter:proxy-prefix] -use = egg:PasteDeploy#prefix -prefix = /galaxy - -# ---- Galaxy --------------------------------------------------------------- - -# Configuration of the Galaxy application. - -[app:main] - -# -- Application and filtering - -# The factory for the WSGI application. This should not be changed. -paste.app_factory = galaxy.web.buildapp:app_factory - -# If not running behind a proxy server, you may want to enable gzip compression -# to decrease the size of data transferred over the network. If using a proxy -# server, please enable gzip compression there instead. -#filter-with = gzip - -# If running behind a proxy server and Galaxy is served from a subdirectory, -# enable the proxy-prefix filter and set the prefix in the -# [filter:proxy-prefix] section above. -#filter-with = proxy-prefix - -# If proxy-prefix is enabled and you're running more than one Galaxy instance -# behind one hostname, you will want to set this to the same path as the prefix -# in the filter above. This value becomes the "path" attribute set in the -# cookie so the cookies from each instance will not clobber each other. -#cookie_path = None - -# -- Database - -# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You -# may use a SQLAlchemy connection string to specify an external database -# instead. This string takes many options which are explained in detail in the -# config file documentation. -#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE - -# If the server logs errors about not having enough database pool connections, -# you will want to increase these values, or consider running more Galaxy -# processes. -#database_engine_option_pool_size = 5 -#database_engine_option_max_overflow = 10 - -# If using MySQL and the server logs the error "MySQL server has gone away", -# you will want to set this to some positive value (7200 should work). -#database_engine_option_pool_recycle = -1 - -# If large database query results are causing memory or response time issues in -# the Galaxy process, leave the result on the server instead. This option is -# only available for PostgreSQL and is highly recommended. -#database_engine_option_server_side_cursors = False - -# Log all database transactions, can be useful for debugging and performance -# profiling. Logging is done via Python's 'logging' module under the qualname -# 'galaxy.model.orm.logging_connection_proxy' -#database_query_profiling_proxy = False - -# By default, Galaxy will use the same database to track user data and -# tool shed install data. There are many situtations in which it is -# valuable to seperate these - for instance bootstrapping fresh Galaxy -# instances with pretested installs. The following optin can be used to -# separate the tool shed install database (all other options listed above -# but prefixed with install_ are also available). -#install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE - -# -- Files and directories - -# Dataset files are stored in this directory. -#file_path = database/files - -# Temporary files are stored in this directory. -#new_file_path = database/tmp - -# Tool config files, defines what tools are available in Galaxy. -# Tools can be locally developed or installed from Galaxy tool sheds. -#tool_config_file = tool_conf.xml,shed_tool_conf.xml - -# Enable / disable checking if any tools defined in the above non-shed tool_config_files -# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool -# Shed. This setting should generally be set to False only for development Galaxy environments -# that are often rebuilt from scratch where migrated tools do not need to be available in the -# Galaxy tool panel. If the following setting remains commented, the default setting will be True. -#check_migrate_tools = True - -# Tool config maintained by tool migration scripts. If you use the migration -# scripts to install tools that have been migrated to the tool shed upon a new -# release, they will be added to this tool config file. -#migrated_tools_config = migrated_tools_conf.xml - -# File that contains the XML section and tool tags from all tool panel config -# files integrated into a single file that defines the tool panel layout. This -# file can be changed by the Galaxy administrator to alter the layout of the -# tool panel. If not present, Galaxy will create it. -#integrated_tool_panel_config = integrated_tool_panel.xml - -# Default path to the directory containing the tools defined in tool_conf.xml. -# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. -#tool_path = tools - -# Path to the directory in which tool dependencies are placed. This is used by -# the tool shed to install dependencies and can also be used by administrators -# to manually install or link to dependencies. For details, see: -# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies -# If this option is not set to a valid path, installing tools with dependencies -# from the Tool Shed will fail. -#tool_dependency_dir = None - -# File containing the Galaxy Tool Sheds that should be made available to -# install from in the admin interface -#tool_sheds_config_file = tool_sheds_conf.xml - -# Enable automatic polling of relative tool sheds to see if any updates -# are available for installed repositories. Ideally only one Galaxy -# server process should be able to check for repository updates. The -# setting for hours_between_check should be an integer between 1 and 24. -#enable_tool_shed_check = False -#hours_between_check = 12 - -# Enable use of an in-memory registry with bi-directional relationships -# between repositories (i.e., in addition to lists of dependencies for a -# repository, keep an in-memory registry of dependent items for each repository. -#manage_dependency_relationships = False - -# XML config file that contains data table entries for the ToolDataTableManager. This file is manually -# maintained by the Galaxy administrator. -#tool_data_table_config_path = tool_data_table_conf.xml - -# XML config file that contains additional data table entries for the ToolDataTableManager. This file -# is automatically generated based on the current installed tool shed repositories that contain valid -# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically -# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. -#shed_tool_data_table_config = shed_tool_data_table_conf.xml - -# Directory where data used by tools is located, see the samples in that -# directory and the wiki for help: -# https://wiki.galaxyproject.org/Admin/DataIntegration -#tool_data_path = tool-data - -# File containing old-style genome builds -#builds_file_path = tool-data/shared/ucsc/builds.txt - -# Directory where chrom len files are kept, currently mainly used by trackster -#len_file_path = tool-data/shared/ucsc/chrom - -# Datatypes config file, defines what data (file) types are available in -# Galaxy. -#datatypes_config_file = datatypes_conf.xml - -# Disable the 'Auto-detect' option for file uploads -#datatypes_disable_auto = False - -# Visualizations config directory: where to look for individual visualization plugins. -# The path is relative to the Galaxy root dir. To use an absolute path begin the path -# with '/'. Defaults to "config/plugins/visualizations". -#visualization_plugins_directory = config/plugins/visualizations - -# Each job is given a unique empty directory as its current working directory. -# This option defines in what parent directory those directories will be -# created. -#job_working_directory = database/job_working_directory - -# If using a cluster, Galaxy will write job scripts and stdout/stderr to this -# directory. -#cluster_files_directory = database/pbs - -# Mako templates are compiled as needed and cached for reuse, this directory is -# used for the cache -#template_cache_path = database/compiled_templates - -# Citation related caching. Tool citations information maybe fetched from -# external sources such as http://dx.doi.org/ by Galaxy - the following parameters -# can be used to control the caching used to store this information. -#citation_cache_type = file -#citation_cache_data_dir = database/citations/data -#citation_cache_lock_dir = database/citations/lock - -# External service types config file, defines what types of external_services configurations -# are available in Galaxy. -#external_service_type_config_file = external_service_types_conf.xml - -# Path to the directory containing the external_service_types defined in the config. -#external_service_type_path = external_service_types - -# Tools with a number of outputs not known until runtime can write these -# outputs to a directory for collection by Galaxy when the job is done. -# Previously, this directory was new_file_path, but using one global directory -# can cause performance problems, so using job_working_directory ('.' or cwd -# when a job is run) is encouraged. By default, both are checked to avoid -# breaking existing tools. -#collect_outputs_from = new_file_path,job_working_directory - -# -- Data Storage (Object Store) -# -# Configuration file for the object store -# If this is set and exists, it overrides any other objectstore settings. -# object_store_config_file = object_store_conf.xml - -# Object store backend module (valid options are: disk, s3, swift, irods, -# distributed, hierarchical) -#object_store = disk - -# *Extremely* old Galaxy instances created datasets at the root of the -# `file_path` defined above. If your Galaxy instance has datasets at the root -# (instead of in directories composed by hashing the dataset id), you should -# enable this option to allow Galaxy to find them. -#object_store_check_old_style = False - -# Credentials used by certain (s3, swift) object store backends -#os_access_key = <your cloud object store access key> -#os_secret_key = <your cloud object store secret key> -#os_bucket_name = <name of an existing object store bucket or container> - -# If using 'swift' object store, you must specify the following connection -# properties -#os_host = swift.rc.nectar.org.au -#os_port = 8888 -#os_is_secure = False -#os_conn_path = / - -# Reduced redundancy can be used only with the 's3' object store -#os_use_reduced_redundancy = False - -# Path to cache directory for object store backends that utilize a cache (s3, -# swift, irods) -#object_store_cache_path = database/files/ - -# Size (in GB) that the cache used by object store should be limited to. -# If the value is not specified, the cache size will be limited only by the -# file system size. -#object_store_cache_size = 100 - -# Configuration file for the distributed object store, if object_store = -# distributed. See the sample at distributed_object_store_conf.xml.sample -#distributed_object_store_config_file = None - - -# -- Mail and notification - -# Galaxy sends mail for various things: Subscribing users to the mailing list -# if they request it, emailing password resets, notification from the Galaxy -# Sample Tracking system, reporting dataset errors, and sending activation emails. -# To do this, it needs to send mail through an SMTP server, which you may define here (host:port). -# Galaxy will automatically try STARTTLS but will continue upon failure. -#smtp_server = None - -# If your SMTP server requires a username and password, you can provide them -# here (password in cleartext here, but if your server supports STARTTLS it -# will be sent over the network encrypted). -#smtp_username = None -#smtp_password = None - -# If your SMTP server requires SSL from the beginning of the connection -# smtp_ssl = False - -# On the user registration form, users may choose to join the mailing list. -# This is the address of the list they'll be subscribed to. -#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu - -# Datasets in an error state include a link to report the error. Those reports -# will be sent to this address. Error reports are disabled if no address is set. -# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter. -#error_email_to = None - -# Activation email is used as a sender ('from' field) for the account activation mail. -# We recommend using string in the following format: Galaxy Project <galaxy-no-reply(a)example.com> -#activation_email = None - -# URL of the support resource for the galaxy instance. Used in activation emails. -#instance_resource_url = http://wiki.galaxyproject.org/ - -# E-mail domains blacklist is used for filtering out users that are using disposable email address -# during the registration. If their address domain matches any domain in the BL they are refused the registration. -#blacklist_file = config/disposable_email_blacklist.conf - -# Registration warning message is used to discourage people from registering multiple accounts. Applies mostly for the main Galaxy instance. -# If no message specified the warning box will not be shown. -#registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. - -# When users opt to reset passwords, new ones are created, this option -# specifies the length of these passwords. -#reset_password_length = 15 - - -# -- Account activation - -# This is user account activation feature global flag. If set to "False" the rest of the Account -# activation configuration is ignored and user activation is disabled (a.k.a. accounts are active since registration). -# Note the activation is also not working in case the smtp server is not defined. -#user_activation_on = False - -# Activation grace period. Activation is not forced (login is not disabled) until -# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content). -# In hours. Default is 3. Enter 0 to disable grace period. -# Users with OpenID logins have grace period forever. -#activation_grace_period = 0 - -# Used for warning box for inactive accounts (unable to run jobs). -# In use only if activation_grace_period is set. -#inactivity_box_content = Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address. - - -# -- Display sites - -# Galaxy can display data at various external browsers. These options specify -# which browsers should be available. URLs and builds available at these -# browsers are defined in the specifield files. - -# If use_remote_user = True, display application servers will be denied access -# to Galaxy and so displaying datasets in these sites will fail. -# display_servers contains a list of hostnames which should be allowed to -# bypass security to display datasets. Please be aware that there are security -# implications if this is allowed. More details (including required changes to -# the proxy server config) are available in the Apache proxy documentation on -# the wiki. -# -# The list of servers in this sample config are for the UCSC Main, Test and -# Archaea browsers, but the default if left commented is to not allow any -# display sites to bypass security (you must uncomment the line below to allow -# them). -#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… - -# To disable the old-style display applications that are hardcoded into datatype classes, -# set enable_old_display_applications = False. -# This may be desirable due to using the new-style, XML-defined, display applications that -# have been defined for many of the datatypes that have the old-style. -# There is also a potential security concern with the old-style applications, -# where a malicious party could provide a link that appears to reference the Galaxy server, -# but contains a redirect to a third-party server, tricking a Galaxy user to access said -# site. -#enable_old_display_applications = True - -# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. - -use_nglims = False -nglims_config_file = tool-data/nglims.yaml - -# -- UI Localization - -# Show a message box under the masthead. -#message_box_visible = False -#message_box_content = None -#message_box_class = info - -# Append "/{brand}" to the "Galaxy" text in the masthead. -#brand = None - -# Format string used when showing date and time information. -# The string may contain: -# - the directives used by Python time.strftime() function (see http://docs.python.org/2/library/time.html#time.strftime ), -# - $locale (complete format string for the server locale), -# - $iso8601 (complete format string as specified by ISO 8601 international standard). -# pretty_datetime_format = $locale (UTC) - -# The URL of the page to display in Galaxy's middle pane when loaded. This can be -# an absolute or relative URL. -#welcome_url = /static/welcome.html - -# The URL linked by the "Galaxy/brand" text. -#logo_url = / - -# The URL linked by the "Wiki" link in the "Help" menu. -#wiki_url = http://wiki.galaxyproject.org/ - -# The URL linked by the "Support" link in the "Help" menu. -#support_url = http://wiki.galaxyproject.org/Support - -# The URL linked by the "How to Cite Galaxy" link in the "Help" menu. -#citation_url = http://wiki.galaxyproject.org/CitingGalaxy - -#The URL linked by the "Search" link in the "Help" menu. -#search_url = http://galaxyproject.org/search/usegalaxy/ - -#The URL linked by the "Mailing Lists" link in the "Help" menu. -#mailing_lists_url = http://wiki.galaxyproject.org/MailingLists - -#The URL linked by the "Videos" link in the "Help" menu. -#videos_url = http://vimeo.com/galaxyproject - -# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well -# as on the user registration and login forms and in the activation emails. -#terms_url = None - -# The URL linked by the "Galaxy Q&A" link in the "Help" menu -# The Galaxy Q&A site is under development; when the site is done, this URL -# will be set and uncommented. -#qa_url = - -# Serve static content, which must be enabled if you're not serving it via a -# proxy server. These options should be self explanatory and so are not -# documented individually. You can use these paths (or ones in the proxy -# server) to point to your own styles. -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue -static_robots_txt = %(here)s/static/robots.txt - -# Pack javascript at launch (/static/scripts/*.js) -# This only happens if the modified timestamp of the source .js is newer -# than the version (if it exists) in /static/scripts/packed/ -# Note that this requires java > 1.4 for executing yuicompressor.jar -#pack_scripts = False - -# Cloud Launch - -#enable_cloud_launch = False -#cloudlaunch_default_ami = ami-a7dbf6ce - -# Incremental Display Options - -#display_chunk_size = 65536 - -# -- Advanced proxy features - -# For help on configuring the Advanced proxy features, see: -# http://usegalaxy.org/production - -# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set -# this to True to inform Galaxy that mod_xsendfile is enabled upstream. -#apache_xsendfile = False - -# The same download handling can be done by nginx using X-Accel-Redirect. This -# should be set to the path defined in the nginx config as an internal redirect -# with access to Galaxy's data files (see documentation linked above). -#nginx_x_accel_redirect_base = False - -# nginx can make use of mod_zip to create zip files containing multiple library -# files. If using X-Accel-Redirect, this can be the same value as that option. -#nginx_x_archive_files_base = False - -# If using compression in the upstream proxy server, use this option to disable -# gzipping of library .tar.gz and .zip archives, since the proxy server will do -# it faster on the fly. -#upstream_gzip = False - -# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. -# Configuration for this is complex and explained in detail in the -# documentation linked above. The upload store is a temporary directory in -# which files uploaded by the upload module will be placed. -#nginx_upload_store = False - -# This value overrides the action set on the file upload form, e.g. the web -# path where the nginx_upload_module has been configured to intercept upload -# requests. -#nginx_upload_path = False - -# -- Logging and Debugging - -# Verbosity of console log messages. Acceptable values can be found here: -# http://docs.python.org/library/logging.html#logging-levels -#log_level = DEBUG - -# Print database operations to the server log (warning, quite verbose!). -#database_engine_option_echo = False - -# Print database pool operations to the server log (warning, quite verbose!). -#database_engine_option_echo_pool = False - -# Turn on logging of application events and some user events to the database. -#log_events = True - -# Turn on logging of user actions to the database. Actions currently logged are -# grid views, tool searches, and use of "recently" used tools menu. The -# log_events and log_actions functionality will eventually be merged. -#log_actions = True - -# Sanitize All HTML Tool Output -# By default, all tool output served as 'text/html' will be sanitized -# thoroughly. This can be disabled if you have special tools that require -# unaltered output. -#sanitize_all_html = True - -# By default Galaxy will serve non-HTML tool output that may potentially -# contain browser executable JavaScript content as plain text. This will for -# instance cause SVG datasets to not render properly and so may be disabled -# by setting the following option to True. -#serve_xss_vulnerable_mimetypes = False - -# Debug enables access to various config options useful for development and -# debugging: use_lint, use_profile, use_printdebug and use_interactive. It -# also causes the files used by PBS/SGE (submission script, output, and error) -# to remain on disk after the job is complete. Debug mode is disabled if -# commented, but is uncommented by default in the sample config. -debug = True - -# Check for WSGI compliance. -#use_lint = False - -# Run the Python profiler on each request. -#use_profile = False - -# Intercept print statements and show them on the returned page. -#use_printdebug = True - -# Enable live debugging in your browser. This should NEVER be enabled on a -# public site. Enabled in the sample config for development. -use_interactive = True - -# Write thread status periodically to 'heartbeat.log', (careful, uses disk -# space rapidly!). Useful to determine why your processes may be consuming a -# lot of CPU. -#use_heartbeat = False - -# Enable the memory debugging interface (careful, negatively impacts server -# performance). -#use_memdump = False - -# -- Data Libraries - -# These library upload options are described in much more detail in the wiki: -# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles - -# Add an option to the library upload form which allows administrators to -# upload a directory of files. -#library_import_dir = None - -# Add an option to the library upload form which allows authorized -# non-administrators to upload a directory of files. The configured directory -# must contain sub-directories named the same as the non-admin user's Galaxy -# login ( email ). The non-admin user is restricted to uploading files or -# sub-directories of files contained in their directory. -#user_library_import_dir = None - -# Add an option to the admin library upload tool allowing admins to paste -# filesystem paths to files and directories in a box, and these paths will be -# added to a library. Set to True to enable. Please note the security -# implication that this will give Galaxy Admins access to anything your Galaxy -# user has access to. -#allow_library_path_paste = False - -# Users may choose to download multiple files from a library in an archive. By -# default, Galaxy allows users to select from a few different archive formats -# if testing shows that Galaxy is able to create files using these formats. -# Specific formats can be disabled with this option, separate more than one -# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. -#disable_library_comptypes = - -# Some sequencer integration features in beta allow you to automatically -# transfer datasets. This is done using a lightweight transfer manager which -# runs outside of Galaxy (but is spawned by it automatically). Galaxy will -# communicate with this manager over the port specified here. -#transfer_manager_port = 8163 - -# Search data libraries with whoosh -#enable_whoosh_library_search = True -# Whoosh indexes are stored in this directory. -#whoosh_index_dir = database/whoosh_indexes - -# Search data libraries with lucene -#enable_lucene_library_search = False -# maxiumum file size to index for searching, in MB -#fulltext_max_size = 500 -#fulltext_noindex_filetypes = bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger -# base URL of server providing search functionality using lucene -#fulltext_url = http://localhost:8081 - -# -- Users and Security - -# Galaxy encodes various internal values when these values will be output in -# some format (for example, in a URL or cookie). You should set a key to be -# used by the algorithm that encodes and decodes these values. It can be any -# string. If left unchanged, anyone could construct a cookie that would grant -# them access to others' sessions. -#id_secret = USING THE DEFAULT IS NOT SECURE! - -# User authentication can be delegated to an upstream proxy server (usually -# Apache). The upstream proxy should set a REMOTE_USER header in the request. -# Enabling remote user disables regular logins. For more information, see: -# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy -#use_remote_user = False - -# If use_remote_user is enabled and your external authentication -# method just returns bare usernames, set a default mail domain to be appended -# to usernames, to become your Galaxy usernames (email addresses). -#remote_user_maildomain = None - -# If use_remote_user is enabled, the header that the upstream proxy provides -# the remote username in defaults to HTTP_REMOTE_USER (the 'HTTP_' is prepended -# by WSGI). This option allows you to change the header. Note, you still need -# to prepend 'HTTP_' to the header in this option, but your proxy server should -# *not* include 'HTTP_' at the beginning of the header name. -#remote_user_header = HTTP_REMOTE_USER - -# If use_remote_user is enabled, you can set this to a URL that will log your -# users out. -#remote_user_logout_href = None - -# If your proxy and/or authentication source does not normalize e-mail -# addresses or user names being passed to Galaxy - set the following option -# to True to force these to lower case. -#normalize_remote_user_email = False - -# Administrative users - set this to a comma-separated list of valid Galaxy -# users (email addresses). These users will have access to the Admin section -# of the server, and will have access to create users, groups, roles, -# libraries, and more. For more information, see: -# https://wiki.galaxyproject.org/Admin/Interface -#admin_users = None - -# Force everyone to log in (disable anonymous access). -#require_login = False - -# Allow unregistered users to create new accounts (otherwise, they will have to -# be created by an admin). -#allow_user_creation = True - -# Allow administrators to delete accounts. -#allow_user_deletion = False - -# Allow administrators to log in as other users (useful for debugging) -#allow_user_impersonation = False - -# Allow users to remove their datasets from disk immediately (otherwise, -# datasets will be removed after a time period specified by an administrator in -# the cleanup scripts run via cron) -#allow_user_dataset_purge = False - -# By default, users' data will be public, but setting this to True will cause -# it to be private. Does not affect existing users and data, only ones created -# after this option is set. Users may still change their default back to -# public. -#new_user_dataset_access_role_default_private = False - -# -- Beta features - -# Enable Galaxy to communicate directly with a sequencer -#enable_sequencer_communication = False - -# Enable authentication via OpenID. Allows users to log in to their Galaxy -# account by authenticating with an OpenID provider. -#enable_openid = False -#openid_config_file = openid_conf.xml -#openid_consumer_cache_path = database/openid_consumer_cache - -# Optional list of email addresses of API users who can make calls on behalf of -# other users -#api_allow_run_as = None - -# Master key that allows many API admin actions to be used without actually -# having a defined admin user in the database/config. Only set this if you need -# to bootstrap Galaxy, you probably do not want to set this on public servers. -#master_api_key = changethis - -# Enable tool tags (associating tools with tags). This has its own option -# since its implementation has a few performance implications on startup for -# large servers. -#enable_tool_tags = False - -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - -# The URL to the myExperiment instance being used (omit scheme but include port) -#myexperiment_url = www.myexperiment.org:80 - -# Enable Galaxy's "Upload via FTP" interface. You'll need to install and -# configure an FTP server (we've used ProFTPd since it can use Galaxy's -# database for authentication) and set the following two options. - -# This should point to a directory containing subdirectories matching users' -# email addresses, where Galaxy will look for files. -#ftp_upload_dir = None - -# This should be the hostname of your FTP server, which will be provided to -# users in the help text. -#ftp_upload_site = None - -# Enable enforcement of quotas. Quotas can be set from the Admin interface. -#enable_quotas = False - -# This option allows users to see the full path of datasets via the "View -# Details" option in the history. Administrators can always see this. -#expose_dataset_path = False - -# Data manager configuration options -# Allow non-admin users to view available Data Manager options -#enable_data_manager_user_view = False -# File where Data Managers are configured -#data_manager_config_file = data_manager_conf.xml -# File where Tool Shed based Data Managers are configured -#shed_data_manager_config_file = shed_data_manager_conf.xml -# Directory to store Data Manager based tool-data; defaults to tool_data_path -#galaxy_data_manager_data_path = tool-data - -# -- Job Execution - -# To increase performance of job execution and the web interface, you can -# separate Galaxy into multiple processes. There are more than one way to do -# this, and they are explained in detail in the documentation: -# -# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling - -# By default, Galaxy manages and executes jobs from within a single process and -# notifies itself of new jobs via in-memory queues. Jobs are run locally on -# the system on which Galaxy is started. Advanced job running capabilities can -# be configured through the job configuration file. -#job_config_file = job_conf.xml - -# In multiprocess configurations, notification between processes about new jobs -# is done via the database. In single process configurations, this is done in -# memory, which is a bit quicker. Galaxy tries to automatically determine -# which method it should used based on your handler configuration in the job -# config file, but you can explicitly override this behavior by setting the -# following option to True or False. -#track_jobs_in_database = None - -# This enables splitting of jobs into tasks, if specified by the particular tool config. -# This is a new feature and not recommended for production servers yet. -#use_tasked_jobs = False -#local_task_queue_workers = 2 - -# Enable job recovery (if Galaxy is restarted while cluster jobs are running, -# it can "recover" them when it starts). This is not safe to use if you are -# running more than one Galaxy server using the same database. -#enable_job_recovery = True - -# Although it is fairly reliable, setting metadata can occasionally fail. In -# these instances, you can choose to retry setting it internally or leave it in -# a failed state (since retrying internally may cause the Galaxy process to be -# unresponsive). If this option is set to False, the user will be given the -# option to retry externally, or set metadata manually (when possible). -#retry_metadata_internally = True - -# If (for example) you run on a cluster and your datasets (by default, -# database/files/) are mounted read-only, this option will override tool output -# paths to write outputs to the working directory instead, and the job manager -# will move the outputs to their proper place in the dataset directory on the -# Galaxy server after the job completes. -#outputs_to_working_directory = False - -# If your network filesystem's caching prevents the Galaxy server from seeing -# the job's stdout and stderr files when it completes, you can retry reading -# these files. The job runner will retry the number of times specified below, -# waiting 1 second between tries. For NFS, you may want to try the -noac mount -# option (Linux) or -actimeo=0 (Solaris). -#retry_job_output_collection = 0 - -# Clean up various bits of jobs left on the filesystem after completion. These -# bits include the job working directory, external metadata temporary files, -# and DRM stdout and stderr files (if using a DRM). Possible values are: -# always, onsuccess, never -#cleanup_job = always - -# File to source to set up the environment when running jobs. By default, the -# environment in which the Galaxy server starts is used when running jobs -# locally, and the environment set up per the DRM's submission method and -# policy is used when running jobs on a cluster (try testing with `qsub` on the -# command line). environment_setup_file can be set to the path of a file on -# the cluster that should be sourced by the user to set up the environment -# prior to running tools. This can be especially useful for running jobs as -# the actual user, to remove the need to configure each user's environment -# individually. -#environment_setup_file = None - - -# Optional file containing job resource data entry fields definition. -# These fields will be presented to users in the tool forms and allow them to -# overwrite default job resources such as number of processors, memory, and walltime. -#job_resource_params_file = job_resource_params_conf.xml - -# If using job concurrency limits (configured in job_config_file), several -# extra database queries must be performed to determine the number of jobs a -# user has dispatched to a given destination. By default, these queries will -# happen for every job that is waiting to run, but if cache_user_job_count is -# set to True, it will only happen once per iteration of the handler queue. -# Although better for performance due to reduced queries, the tradeoff is a -# greater possibility that jobs will be dispatched past the configured limits -# if running many handlers. -#cache_user_job_count = False - -# ToolBox filtering -# Modules from lib/galaxy/tools/filters/ can be specified in the following lines. -# tool_* filters will be applied for all users and can not be changed by them. -# user_tool_* filters will be shown under user preferences and can be toogled -# on and off by runtime -#tool_filters -#tool_label_filters -#tool_section_filters -#user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode -#user_tool_section_filters = examples:restrict_text -#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode - -# Galaxy Application Internal Message Queue - -# Galaxy uses AMQP internally TODO more documentation on what for. -# For examples, see http://ask.github.io/kombu/userguide/connections.html -# -# Without specifying anything here, galaxy will first attempt to use your -# specified database_connection above. If that's not specified either, Galaxy -# will automatically create and use a separate sqlite database located in your -# <galaxy>/database folder (indicated in the commented out line below). - -#amqp_internal_connection = sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE - - - -# ---- Galaxy External Message Queue ------------------------------------------------- - -# Galaxy uses AMQ protocol to receive messages from external sources like -# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -# For Galaxy to receive messages from a message queue the RabbitMQ server has -# to be set up with a user account and other parameters listed below. The 'host' -# and 'port' fields should point to where the RabbitMQ server is running. - -[galaxy_amqp] - -#host = 127.0.0.1 -#port = 5672 -#userid = galaxy -#password = galaxy -#virtual_host = galaxy_messaging_engine -#queue = galaxy_queue -#exchange = galaxy_exchange -#routing_key = bar_code_scanner -#rabbitmqctl_path = /path/to/rabbitmqctl - https://bitbucket.org/galaxy/galaxy-central/commits/bbf9c5f5fdaf/ Changeset: bbf9c5f5fdaf User: natefoo Date: 2014-09-15 22:43:22 Summary: Handle backwards compatibility for old config file locations. Affected #: 2 files diff -r 21fb6c2f4349c358321b9344b9dbda20264b78fb -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -112,7 +112,7 @@ if self.config.enable_openid: from galaxy.web.framework import openid_manager self.openid_manager = openid_manager.OpenIDManager( self.config.openid_consumer_cache_path ) - self.openid_providers = OpenIDProviders.from_file( self.config.openid_config ) + self.openid_providers = OpenIDProviders.from_file( self.config.openid_config_file ) else: self.openid_providers = OpenIDProviders() # Start the heartbeat process if configured and available diff -r 21fb6c2f4349c358321b9344b9dbda20264b78fb -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -38,6 +38,10 @@ def __init__( self, **kwargs ): self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) + + # Resolve paths of other config files + self.__parse_config_file_options( kwargs ) + # Collect the umask and primary gid from the environment self.umask = os.umask( 077 ) # get the current umask os.umask( self.umask ) # can't get w/o set, so set it back @@ -66,9 +70,7 @@ self.cookie_path = kwargs.get( "cookie_path", "/" ) # Galaxy OpenID settings self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) - self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' ) self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) ) - self.tool_sheds_config = kwargs.get( 'tool_sheds_config_file', 'tool_sheds_conf.xml' ) self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) ) self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) @@ -77,13 +79,6 @@ self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) # The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution # and moved to the tool shed. - self.migrated_tools_config = resolve_path( kwargs.get( 'migrated_tools_config', 'migrated_tools_conf.xml' ), self.root ) - if 'tool_config_file' in kwargs: - tcf = kwargs[ 'tool_config_file' ] - elif 'tool_config_files' in kwargs: - tcf = kwargs[ 'tool_config_files' ] - else: - tcf = 'tool_conf.xml,shed_tool_conf.xml' self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root ) self.tool_filters = listify( kwargs.get( "tool_filters", [] ), do_strip=True ) self.tool_label_filters = listify( kwargs.get( "tool_label_filters", [] ), do_strip=True ) @@ -93,7 +88,6 @@ self.user_label_filters = listify( kwargs.get( "user_tool_label_filters", [] ), do_strip=True ) self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) - self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ] # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have # been migrated from the Galaxy code distribution to the Tool Shed. self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) ) @@ -102,8 +96,6 @@ self.shed_tool_data_path = resolve_path( self.shed_tool_data_path, self.root ) else: self.shed_tool_data_path = self.tool_data_path - self.tool_data_table_config_path = [ resolve_path( x, self.root ) for x in kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ).split( ',' ) ] - self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) @@ -127,8 +119,6 @@ self.hours_between_check = 12 self.update_integrated_tool_panel = kwargs.get( "update_integrated_tool_panel", True ) self.enable_data_manager_user_view = string_as_bool( kwargs.get( "enable_data_manager_user_view", "False" ) ) - self.data_manager_config_file = resolve_path( kwargs.get('data_manager_config_file', 'data_manager_conf.xml' ), self.root ) - self.shed_data_manager_config_file = resolve_path( kwargs.get('shed_data_manager_config_file', 'shed_data_manager_conf.xml' ), self.root ) self.galaxy_data_manager_data_path = kwargs.get( 'galaxy_data_manager_data_path', self.tool_data_path ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) @@ -148,9 +138,6 @@ self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) self.dependency_resolvers_config_file = resolve_path( kwargs.get( 'dependency_resolvers_config_file', 'dependency_resolvers_conf.xml' ), self.root ) - self.job_metrics_config_file = resolve_path( kwargs.get( 'job_metrics_config_file', 'job_metrics_conf.xml' ), self.root ) - self.job_config_file = resolve_path( kwargs.get( 'job_config_file', 'job_conf.xml' ), self.root ) - self.job_resource_params_file = resolve_path( kwargs.get( 'job_resource_params_file', 'job_resource_params_conf.xml' ), self.root ) self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) ) self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) ) self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") ) @@ -195,7 +182,6 @@ self.start_job_runners = listify(kwargs.get( 'start_job_runners', '' )) self.expose_dataset_path = string_as_bool( kwargs.get( 'expose_dataset_path', 'False' ) ) # External Service types used in sample tracking - self.external_service_type_config_file = resolve_path( kwargs.get( 'external_service_type_config_file', 'external_service_types_conf.xml' ), self.root ) self.external_service_type_path = resolve_path( kwargs.get( 'external_service_type_path', 'external_service_types' ), self.root ) # Tasked job runner. self.use_tasked_jobs = string_as_bool( kwargs.get( 'use_tasked_jobs', False ) ) @@ -282,9 +268,6 @@ self.os_is_secure = string_as_bool( kwargs.get( 'os_is_secure', True ) ) self.os_conn_path = kwargs.get( 'os_conn_path', '/' ) self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 )) - self.object_store_config_file = kwargs.get( 'object_store_config_file', None ) - if self.object_store_config_file is not None: - self.object_store_config_file = resolve_path( self.object_store_config_file, self.root ) self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None ) if self.distributed_object_store_config_file is not None: self.distributed_object_store_config_file = resolve_path( self.distributed_object_store_config_file, self.root ) @@ -326,7 +309,6 @@ # Store per-tool runner configs self.tool_handlers = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_handlers', 'name' ) self.tool_runners = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_runners', 'url' ) - self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) # Cloud configuration options self.enable_cloud_launch = string_as_bool( kwargs.get( 'enable_cloud_launch', False ) ) self.cloudlaunch_default_ami = kwargs.get( 'cloudlaunch_default_ami', 'ami-a7dbf6ce' ) @@ -392,6 +374,64 @@ else: return None + def __parse_config_file_options( self, kwargs ): + """ + Backwards compatibility for config files moved to the config/ dir. + """ + defaults = dict( + data_manager_config_file = [ 'data_manager_conf.xml', 'config/data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ], + datatypes_config_file = [ 'datatypes_conf.xml', 'config/datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], + external_service_type_config_file = [ 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample', 'config/external_service_types_conf.xml.sample' ], + job_config_file = [ 'job_conf.xml', 'config/job_conf.xml' ], + job_metrics_config_file = [ 'job_metrics_conf.xml', 'config/job_metrics_conf.xml' ], + job_resource_params_file = [ 'job_resource_params_conf.xml', 'config/job_resource_params_conf.xml' ], + migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], + object_store_config_file = [ 'object_store_conf.xml', 'config/object_store_conf.xml' ], + openid_config_file = [ 'openid_conf.xml', 'config/openid_conf.xml' 'config/openid_conf.xml.sample' ], + shed_data_manager_config_file = [ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], + shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], + tool_sheds_config_file = [ 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], + ) + + listify_defaults = dict( + tool_data_table_config_path = [ 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + tool_config_file = [ 'tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml,config/shed_tool_conf.xml', 'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ] + ) + + for var, defaults in defaults.items(): + if kwargs.get( var, None ) is not None: + path = var + else: + for default in defaults: + if os.path.exists( resolve_path( default, self.root ) ): + path = default + break + else: + path = defaults[-1] + print( "Using config '%s' at: %s" % ( var, path ) ) + setattr( self, var, resolve_path( path, self.root ) ) + + for var, defaults in listify_defaults.items(): + paths = [] + if kwargs.get( var, None ) is not None: + paths = listify( var ) + else: + for default in defaults: + for path in listify( default ): + if not os.path.exists( resolve_path( path, self.root ) ): + break + else: + paths = listify( default ) + break + else: + paths = listify( defaults[-1] ) + print( "Using config '%s' at: %s" % ( var, ', '.join( paths ) ) ) + setattr( self, var, [ resolve_path( x, self.root ) for x in paths ] ) + + # Backwards compatibility for names used in too many places to fix + self.datatypes_config = self.datatypes_config_file + self.tool_configs = self.tool_config_file + def __read_tool_job_config( self, global_conf_parser, section, key ): try: tool_runners_config = global_conf_parser.items( section ) @@ -633,8 +673,8 @@ import tool_shed.tool_shed_registry # Set up the tool sheds registry - if os.path.isfile( self.config.tool_sheds_config ): - self.tool_shed_registry = tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) + if os.path.isfile( self.config.tool_sheds_config_file ): + self.tool_shed_registry = tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config_file ) else: self.tool_shed_registry = None https://bitbucket.org/galaxy/galaxy-central/commits/70d2dff1297d/ Changeset: 70d2dff1297d User: natefoo Date: 2014-09-15 22:43:51 Summary: Rename universe_wsgi.ini -> galaxy.ini everywhere. Affected #: 75 files diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb README.txt --- a/README.txt +++ b/README.txt @@ -22,13 +22,13 @@ http://localhost:8080 You may wish to make changes from the default configuration. This can be done -in the universe_wsgi.ini file. Tools can be either installed from the Tool Shed +in the config/galaxy.ini file. Tools can be either installed from the Tool Shed or added manually. For details please see the Galaxy wiki: -https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial. +https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial Not all dependencies are included for the tools provided in the sample tool_conf.xml. A full list of external dependencies is available at: -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies \ No newline at end of file +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -43,15 +43,10 @@ " SAMPLES=" -tool_conf.xml.sample -datatypes_conf.xml.sample -universe_wsgi.ini.sample -tool_data_table_conf.xml.sample -tool_sheds_conf.xml.sample -shed_tool_data_table_conf.xml.sample -migrated_tools_conf.xml.sample -data_manager_conf.xml.sample -shed_data_manager_conf.xml.sample +config/galaxy.ini.sample +config/shed_tool_data_table_conf.xml.sample +config/migrated_tools_conf.xml.sample +config/shed_data_manager_conf.xml.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/shared/ucsc/builds.txt.sample diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -318,10 +318,10 @@ applications and the URL to those sites. The `display` attributes on the `ucsc` and `gbrowse` sites replace the - `ucsc_display_sites` and `gbrowse_display_sites` options in - universe_wsgi.ini. Because these are used by "old-style" display - applications, their types cannot change if you want the old-style display - links for these sites to work. + `ucsc_display_sites` and `gbrowse_display_sites` options in galaxy.ini. + Because these are used by "old-style" display applications, their types + cannot change if you want the old-style display links for these sites to + work. --><site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/><site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/> diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -8,7 +8,9 @@ # Throughout this sample configuration file, except where stated otherwise, # uncommented values override the default if left unset, whereas commented -# values are set to the default value. +# values are set to the default value. Relative paths are relative to the root +# Galaxy directory. +# # Examples of many of these options are explained in more detail in the wiki: # # https://wiki.galaxyproject.org/Admin/Config @@ -132,7 +134,9 @@ # Tool config files, defines what tools are available in Galaxy. # Tools can be locally developed or installed from Galaxy tool sheds. -#tool_config_file = tool_conf.xml,shed_tool_conf.xml +# (config/tool_conf.xml.sample will be used if left unset and +# config/tool_conf.xml does not exist). +#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml # Enable / disable checking if any tools defined in the above non-shed tool_config_files # (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool @@ -165,8 +169,8 @@ #tool_dependency_dir = None # File containing the Galaxy Tool Sheds that should be made available to -# install from in the admin interface -#tool_sheds_config_file = tool_sheds_conf.xml +# install from in the admin interface (.sample used if default does not exist). +#tool_sheds_config_file = config/tool_sheds_conf.xml # Enable automatic polling of relative tool sheds to see if any updates # are available for installed repositories. Ideally only one Galaxy @@ -180,15 +184,16 @@ # repository, keep an in-memory registry of dependent items for each repository. #manage_dependency_relationships = False -# XML config file that contains data table entries for the ToolDataTableManager. This file is manually -# maintained by the Galaxy administrator. -#tool_data_table_config_path = tool_data_table_conf.xml +# XML config file that contains data table entries for the +# ToolDataTableManager. This file is manually # maintained by the Galaxy +# administrator (.sample used if default does not exist). +#tool_data_table_config_path = config/tool_data_table_conf.xml # XML config file that contains additional data table entries for the ToolDataTableManager. This file # is automatically generated based on the current installed tool shed repositories that contain valid # tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically # added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. -#shed_tool_data_table_config = shed_tool_data_table_conf.xml +#shed_tool_data_table_config = config/shed_tool_data_table_conf.xml # Directory where data used by tools is located, see the samples in that # directory and the wiki for help: @@ -202,7 +207,7 @@ #len_file_path = tool-data/shared/ucsc/chrom # Datatypes config file, defines what data (file) types are available in -# Galaxy. +# Galaxy (.sample is used if default does not exist). #datatypes_config_file = config/datatypes_conf.xml # Disable the 'Auto-detect' option for file uploads @@ -234,7 +239,7 @@ #citation_cache_lock_dir = database/citations/lock # External service types config file, defines what types of external_services configurations -# are available in Galaxy. +# are available in Galaxy (.sample is used if default does not exist). #external_service_type_config_file = config/external_service_types_conf.xml # Path to the directory containing the external_service_types defined in the config. @@ -252,7 +257,7 @@ # # Configuration file for the object store # If this is set and exists, it overrides any other objectstore settings. -# object_store_config_file = object_store_conf.xml +# object_store_config_file = config/object_store_conf.xml # Object store backend module (valid options are: disk, s3, swift, irods, # distributed, hierarchical) @@ -448,14 +453,14 @@ # proxy server. These options should be self explanatory and so are not # documented individually. You can use these paths (or ones in the proxy # server) to point to your own styles. -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue -static_robots_txt = %(here)s/static/robots.txt +#static_enabled = True +#static_cache_time = 360 +#static_dir = static/ +#static_images_dir = static/images +#static_favicon_dir = static/favicon.ico +#static_scripts_dir = static/scripts/ +#static_style_dir = static/june_2007_style/blue +#static_robots_txt = static/robots.txt # Pack javascript at launch (/static/scripts/*.js) # This only happens if the modified timestamp of the source .js is newer @@ -691,7 +696,8 @@ # Enable authentication via OpenID. Allows users to log in to their Galaxy # account by authenticating with an OpenID provider. #enable_openid = False -#openid_config_file = openid_conf.xml +# .sample used if default does not exist +#openid_config_file = config/openid_conf.xml #openid_consumer_cache_path = database/openid_consumer_cache # Optional list of email addresses of API users who can make calls on behalf of @@ -741,10 +747,11 @@ # Data manager configuration options # Allow non-admin users to view available Data Manager options #enable_data_manager_user_view = False -# File where Data Managers are configured +# File where Data Managers are configured (.sample used if default does not +# exist) #data_manager_config_file = config/data_manager_conf.xml # File where Tool Shed based Data Managers are configured -#shed_data_manager_config_file = shed_data_manager_conf.xml +#shed_data_manager_config_file = config/shed_data_manager_conf.xml # Directory to store Data Manager based tool-data; defaults to tool_data_path #galaxy_data_manager_data_path = tool-data @@ -760,7 +767,7 @@ # notifies itself of new jobs via in-memory queues. Jobs are run locally on # the system on which Galaxy is started. Advanced job running capabilities can # be configured through the job configuration file. -#job_config_file = job_conf.xml +#job_config_file = config/job_conf.xml # In multiprocess configurations, notification between processes about new jobs # is done via the database. In single process configurations, this is done in @@ -822,7 +829,7 @@ # Optional file containing job resource data entry fields definition. # These fields will be presented to users in the tool forms and allow them to # overwrite default job resources such as number of processors, memory, and walltime. -#job_resource_params_file = job_resource_params_conf.xml +#job_resource_params_file = config/job_resource_params_conf.xml # If using job concurrency limits (configured in job_config_file), several # extra database queries must be performed to determine the number of jobs a diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -86,7 +86,7 @@ </plugins><handlers default="handlers"><handler id="handler0" tags="handlers"/><handler id="handler1" tags="handlers"/> @@ -148,7 +148,7 @@ This configuration allows any docker instance to write to any Galaxy file - for greater isolation set outputs_to_working_directory in - universe_wsgi.ini. This will cause $defaults to allow writing to much + galaxy.ini. This will cause $defaults to allow writing to much less. It will then expand as follows: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb config/plugins/visualizations/README.txt --- a/config/plugins/visualizations/README.txt +++ b/config/plugins/visualizations/README.txt @@ -8,9 +8,8 @@ the user when they click the 'visualizations' icon for a dataset in their history panel. -The framework must be enabled in your 'universe_wsgi.ini' file by -uncommenting (and having a valid path for) the -'visualizations_plugin_directory' entry. +The framework must be enabled in your 'galaxy.ini' file by uncommenting (and +having a valid path for) the 'visualizations_plugin_directory' entry. For more information, see http://wiki.galaxyproject.org/VisualizationsRegistry diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb config/tool_conf.xml.main --- a/config/tool_conf.xml.main +++ b/config/tool_conf.xml.main @@ -98,7 +98,6 @@ <section id="plots" name="Graph/Display Data"><tool file="plotting/boxplot.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /> - <tool file="mutation/visualize.xml" /></section><section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /> diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb config/tool_conf.xml.sample --- a/config/tool_conf.xml.sample +++ b/config/tool_conf.xml.sample @@ -117,7 +117,6 @@ <tool file="plotting/boxplot.xml" /><tool file="visualization/LAJ.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /> - <tool file="mutation/visualize.xml" /></section><section id="hyphy" name="Evolution"><tool file="evolution/codingSnps.xml" /> diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb contrib/galaxy.debian-init --- a/contrib/galaxy.debian-init +++ b/contrib/galaxy.debian-init @@ -17,7 +17,7 @@ GROUP="nogroup" DIR="/home/galaxy/galaxy_dist/" PYTHON="/usr/bin/python" -OPTS="-ES ./scripts/paster.py serve --log-file /home/galaxy/galaxy.log universe_wsgi.ini" +OPTS="./scripts/paster.py serve --log-file /home/galaxy/galaxy.log config/galaxy.ini" PIDFILE="/var/run/galaxy.pid" case "${1:-''}" in diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb contrib/galaxy_config_merger.py --- /dev/null +++ b/contrib/galaxy_config_merger.py @@ -0,0 +1,87 @@ +#! /usr/bin/env python +''' +galaxy_config_merger.py + +Created by Anne Pajon on 31 Jan 2012 + +Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute. + +This source file is licensed under the Academic Free License version +3.0 available at http://www.opensource.org/licenses/AFL-3.0. + +Permission is hereby granted to reproduce, translate, adapt, alter, +transform, modify, or arrange this source file (the "Original Work"); +to distribute or communicate copies of it under any license of your +choice that does not contradict the terms and conditions; to perform +or display the Original Work publicly. + +THE ORIGINAL WORK IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS +AND WITHOUT WARRANTY, EITHER EXPRESS OR IMPLIED, INCLUDING, WITHOUT +LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY OR +FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY OF +THE ORIGINAL WORK IS WITH YOU. + +Script for merging specific local Galaxy config galaxy.ini.cri with default Galaxy galaxy.ini.sample +''' +import ConfigParser +import sys +import optparse +import logging + +def main(): + # logging configuration + logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO) + + # get the options + parser = optparse.OptionParser() + parser.add_option("-s", "--sample", dest="sample", action="store", help="path to Galaxy galaxy.ini.sample file") + parser.add_option("-c", "--config", dest="config", action="store", help="path to your own galaxy.ini file") + parser.add_option("-o", "--output", dest="output", action="store", help="path to the new merged galaxy.ini.new file") + (options, args) = parser.parse_args() + + for option in ['sample', 'config']: + if getattr(options, option) == None: + print "Please supply a --%s parameter.\n" % (option) + parser.print_help() + sys.exit() + + config_sample = ConfigParser.RawConfigParser() + config_sample.read(options.sample) + config_sample_content = open(options.sample, 'r').read() + + config = ConfigParser.RawConfigParser() + config.read(options.config) + + logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample)) + logging.info("---------- DIFFERENCE ANALYSIS BEGIN ----------") + for section in config.sections(): + if not config_sample.has_section(section): + logging.warning("-MISSING- section [%s] not found in sample file. It will be ignored." % section) + else: + for (name, value) in config.items(section): + if not config_sample.has_option(section, name): + if not "#%s" % name in config_sample_content: + logging.warning("-MISSING- section [%s] option '%s' not found in sample file. It will be ignored." % (section, name)) + else: + logging.info("-notset- section [%s] option '%s' not set in sample file. It will be added." % (section, name)) + config_sample.set(section, name, value) + else: + if not config_sample.get(section, name) == value: + logging.info("- diff - section [%s] option '%s' has different value ('%s':'%s'). It will be modified." % (section, name, config_sample.get(section, name), value)) + config_sample.set(section, name, value) + logging.info("---------- DIFFERENCE ANALYSIS END ----------") + + if options.output: + outputfile = open(options.output, 'w') + config_sample.write(outputfile) + outputfile.close() + else: + #print "----------" + #config_sample.write(sys.stdout) + #print "----------" + logging.info("use -o OUTPUT to write the merged configuration into a file.") + + logging.info("read Galaxy galaxy.ini.sample for detailed information.") + +if __name__ == '__main__': + main() diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb contrib/universe_merger.py --- a/contrib/universe_merger.py +++ /dev/null @@ -1,87 +0,0 @@ -#! /usr/bin/env python -''' -universe_merger.py - -Created by Anne Pajon on 31 Jan 2012 - -Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute. - -This source file is licensed under the Academic Free License version -3.0 available at http://www.opensource.org/licenses/AFL-3.0. - -Permission is hereby granted to reproduce, translate, adapt, alter, -transform, modify, or arrange this source file (the "Original Work"); -to distribute or communicate copies of it under any license of your -choice that does not contradict the terms and conditions; to perform -or display the Original Work publicly. - -THE ORIGINAL WORK IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS -AND WITHOUT WARRANTY, EITHER EXPRESS OR IMPLIED, INCLUDING, WITHOUT -LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY OR -FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY OF -THE ORIGINAL WORK IS WITH YOU. - -Script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample -''' -import ConfigParser -import sys -import optparse -import logging - -def main(): - # logging configuration - logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO) - - # get the options - parser = optparse.OptionParser() - parser.add_option("-s", "--sample", dest="sample", action="store", help="path to Galaxy universe_wsgi.ini.sample file") - parser.add_option("-c", "--config", dest="config", action="store", help="path to your own universe_wsgi.ini file") - parser.add_option("-o", "--output", dest="output", action="store", help="path to the new merged universe_wsgi.ini.new file") - (options, args) = parser.parse_args() - - for option in ['sample', 'config']: - if getattr(options, option) == None: - print "Please supply a --%s parameter.\n" % (option) - parser.print_help() - sys.exit() - - config_sample = ConfigParser.RawConfigParser() - config_sample.read(options.sample) - config_sample_content = open(options.sample, 'r').read() - - config = ConfigParser.RawConfigParser() - config.read(options.config) - - logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample)) - logging.info("---------- DIFFERENCE ANALYSIS BEGIN ----------") - for section in config.sections(): - if not config_sample.has_section(section): - logging.warning("-MISSING- section [%s] not found in sample file. It will be ignored." % section) - else: - for (name, value) in config.items(section): - if not config_sample.has_option(section, name): - if not "#%s" % name in config_sample_content: - logging.warning("-MISSING- section [%s] option '%s' not found in sample file. It will be ignored." % (section, name)) - else: - logging.info("-notset- section [%s] option '%s' not set in sample file. It will be added." % (section, name)) - config_sample.set(section, name, value) - else: - if not config_sample.get(section, name) == value: - logging.info("- diff - section [%s] option '%s' has different value ('%s':'%s'). It will be modified." % (section, name, config_sample.get(section, name), value)) - config_sample.set(section, name, value) - logging.info("---------- DIFFERENCE ANALYSIS END ----------") - - if options.output: - outputfile = open(options.output, 'w') - config_sample.write(outputfile) - outputfile.close() - else: - #print "----------" - #config_sample.write(sys.stdout) - #print "----------" - logging.info("use -o OUTPUT to write the merged configuration into a file.") - - logging.info("read Galaxy universe_wsgi.ini.sample for detailed information.") - -if __name__ == '__main__': - main() diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb doc/source/lib/galaxy.webapps.galaxy.api.rst --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -91,7 +91,7 @@ about a particular dataset. For a more comprehensive Data Library example, set the following option in your -universe_wsgi.ini as well, and restart galaxy again:: +galaxy.ini as well, and restart galaxy again:: admin_users = you(a)example.org library_import_dir = /path/to/some/directory diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -267,7 +267,7 @@ log.debug('Done loading job configuration') def __parse_job_conf_legacy(self): - """Loads the old-style job configuration from options in the galaxy config file (by default, universe_wsgi.ini). + """Loads the old-style job configuration from options in the galaxy config file (by default, config/galaxy.ini). """ log.debug('Loading job configuration from %s' % self.app.config.config_file) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/jobs/metrics/instrumenters/core.py --- a/lib/galaxy/jobs/metrics/instrumenters/core.py +++ b/lib/galaxy/jobs/metrics/instrumenters/core.py @@ -20,7 +20,7 @@ elif key == RUNTIME_SECONDS_KEY: return ( "Job Runtime (Wall Clock)", formatting.seconds_to_str( value ) ) else: - # TODO: Use localized version of this from universe_wsgi.ini + # TODO: Use localized version of this from galaxy.ini title = "Job Start Time" if key == START_EPOCH_KEY else "Job End Time" return (title, time.strftime( '%Y-%m-%d %H:%M:%S', time.localtime( value ) ) ) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -542,7 +542,7 @@ metadata_kwds['output_fnames'] = outputs metadata_kwds['compute_tmp_dir'] = working_directory metadata_kwds['config_root'] = remote_galaxy_home - default_config_file = os.path.join(remote_galaxy_home, 'universe_wsgi.ini') + default_config_file = os.path.join(remote_galaxy_home, 'galaxy.ini') metadata_kwds['config_file'] = remote_system_properties.get('galaxy_config_file', default_config_file) metadata_kwds['dataset_files_path'] = remote_system_properties.get('galaxy_dataset_files_path', None) if LwrJobRunner.__use_remote_datatypes_conf( client ): diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -14,22 +14,22 @@ for information on how to configure Galaxy to interact with the LWR. Galaxy also supports an older, less rich configuration of job runners directly -in its main ``universe_wsgi.ini`` file. The following section describes how to +in its main ``galaxy.ini`` file. The following section describes how to configure Galaxy to communicate with the LWR in this legacy mode. Legacy ------ A Galaxy tool can be configured to be executed remotely via LWR by -adding a line to the ``universe_wsgi.ini`` file under the -``galaxy:tool_runners`` section with the format:: +adding a line to the ``galaxy.ini`` file under the ``galaxy:tool_runners`` +section with the format:: <tool_id> = lwr://http://<lwr_host>:<lwr_port> As an example, if a host named remotehost is running the LWR server application on port ``8913``, then the tool with id ``test_tool`` can be configured to run remotely on remotehost by adding the following -line to ``universe.ini``:: +line to ``galaxy.ini``:: test_tool = lwr://http://remotehost:8913 diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/jobs/runners/pulsar.py --- a/lib/galaxy/jobs/runners/pulsar.py +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -558,7 +558,7 @@ metadata_kwds['output_fnames'] = outputs metadata_kwds['compute_tmp_dir'] = working_directory metadata_kwds['config_root'] = remote_galaxy_home - default_config_file = os.path.join(remote_galaxy_home, 'universe_wsgi.ini') + default_config_file = os.path.join(remote_galaxy_home, 'config/galaxy.ini') metadata_kwds['config_file'] = remote_system_properties.get('galaxy_config_file', default_config_file) metadata_kwds['dataset_files_path'] = remote_system_properties.get('galaxy_dataset_files_path', None) if PulsarJobRunner.__use_remote_datatypes_conf( client ): diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -105,7 +105,7 @@ db_schema = schema.ControlledSchema( engine, migrate_repository ) if migrate_repository.versions.latest != db_schema.version: config_arg = '' - if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: + if os.path.abspath( os.path.join( os.getcwd(), 'config', 'galaxy.ini' ) ) != galaxy_config_file: config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) raise Exception( "Your database has version '%d' but this code expects version '%d'. Please backup your database and then migrate the schema by running 'sh manage_db.sh%s upgrade'." % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/model/orm/scripts.py --- a/lib/galaxy/model/orm/scripts.py +++ b/lib/galaxy/model/orm/scripts.py @@ -18,7 +18,7 @@ log = logging.getLogger( __name__ ) -DEFAULT_CONFIG_FILE = 'universe_wsgi.ini' +DEFAULT_CONFIG_FILE = 'config/galaxy.ini' DEFAULT_CONFIG_PREFIX = '' DEFAULT_DATABASE = 'galaxy' @@ -85,7 +85,7 @@ 'lib/galaxy/webapps/tool_shed/model/migrate' >>> config['db_url'] 'sqlite:///pg/testdb1' - >>> write_ini('universe_wsgi.ini', 'database_file', 'moo.sqlite') + >>> write_ini('galaxy.ini', 'database_file', 'moo.sqlite') >>> config = get_config(['manage_db.py'], cwd=config_dir) >>> config['db_url'] 'sqlite:///moo.sqlite?isolation_level=IMMEDIATE' diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -596,7 +596,7 @@ Depending on the configuration setting, invoke the appropriate object store """ - if config_xml is None and config.object_store_config_file: + if config_xml is None and os.path.exists( config.object_store_config_file ): # This is a top level invocation of build_object_store_from_config, and # we have an object_store_conf.xml -- read the .xml and build # accordingly diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -49,7 +49,7 @@ self._parse_config_xml(config_xml) self._configure_connection() self.bucket = self._get_bucket(self.bucket) - # Clean cache only if value is set in universe_wsgi.ini + # Clean cache only if value is set in galaxy.ini if self.cache_size != -1: # Convert GBs to bytes for comparison self.cache_size = self.cache_size * 1073741824 diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/tools/filters/examples.py --- a/lib/galaxy/tools/filters/examples.py +++ b/lib/galaxy/tools/filters/examples.py @@ -32,7 +32,7 @@ users. This can be enabled by renaming this file to examples.py and adding - the following to the ``app:main`` section of ``universe_wsgi.ini``: + the following to the ``app:main`` section of ``galaxy.ini``: tool_filters = examples:restrict_upload_to_admins """ @@ -46,7 +46,7 @@ This tool filter will disable all gatk tools when enabled. This can be enabled by renaming this file to examples.py and adding the following to the - ``app:main`` section of ``universe_wsgi.ini``: + ``app:main`` section of ``galaxy.ini``: tool_filters = examples:disable_gatk """ @@ -59,7 +59,7 @@ which tool sections. Anonymous users will only be able to view the "Get Data" tool section (with id getext). This can be enabled by renaming this file to examples.py and adding the following to the ``app:main`` section of - ``universe_wsgi.ini``: + ``galaxy.ini``: tool_section_filters = examples:explicit_user_mapping """ @@ -82,7 +82,7 @@ This tool filter will disable all tools with the string alpha appearing in the version for all users except those explicitly appearing in the DEVELOPERS list defined above. This can be enabled by renaming this file to examples.py and - adding the following to the ``app:main`` section of ``universe_wsgi.ini``: + adding the following to the ``app:main`` section of ``galaxy.ini``: tool_filters = examples:restrict_development_tools """ @@ -98,7 +98,7 @@ the URL the user is making the request to. This could allow a single Galaxy instance to seem like several different instances hosting different tools based on the URL used to access the Galxy. This can be enabled by renaming this file to examples.py and adding - the following to the ``app:main`` section of ``universe_wsgi.ini``: + the following to the ``app:main`` section of ``galaxy.ini``: tool_section_filters = examples:per_host_tool_sections """ diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/tools/filters/examples.py.sample --- a/lib/galaxy/tools/filters/examples.py.sample +++ b/lib/galaxy/tools/filters/examples.py.sample @@ -6,7 +6,7 @@ """ This tool filter will hide the upload tool from all users except admin users. This can be enabled by renaming this file to examples.py and adding - the following to the ``app:main`` section of ``universe_wsgi.ini``: + the following to the ``app:main`` section of ``galaxy.ini``: tool_filters = examples:restrict_upload_to_admins """ @@ -19,7 +19,7 @@ """ This tool filter will disable all gatk tools when enabled. This can be enabled by renaming this file to examples.py and adding the following to the - ``app:main`` section of ``universe_wsgi.ini``: + ``app:main`` section of ``galaxy.ini``: tool_filters = examples:disable_gatk """ @@ -32,7 +32,7 @@ which tool sections. Anonymous users will only be able to view the "Get Data" tool section (with id getext). This can be enabled by renaming this file to examples.py and adding the following to the ``app:main`` section of - ``universe_wsgi.ini``: + ``galaxy.ini``: tool_section_filters = examples:explicit_user_mapping """ @@ -55,7 +55,7 @@ This tool filter will disable all tools with the string alpha appearing in the version for all users except those explicitly appearing in the DEVELOPERS list defined above. This can be enabled by renaming this file to examples.py and - adding the following to the ``app:main`` section of ``universe_wsgi.ini``: + adding the following to the ``app:main`` section of ``galaxy.ini``: tool_filters = examples:restrict_development_tools """ @@ -71,7 +71,7 @@ the URL the user is making the request to. This could allow a single Galaxy instance to seem like several different instances hosting different tools based on the URL used to access the Galxy. This can be enabled by renaming this file to examples.py and adding - the following to the ``app:main`` section of ``universe_wsgi.ini``: + the following to the ``app:main`` section of ``galaxy.ini``: tool_section_filters = examples:per_host_tool_sections """ diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1027,7 +1027,7 @@ @web.require_admin def memdump( self, trans, ids = 'None', sorts = 'None', pages = 'None', new_id = None, new_sort = None, **kwd ): if self.app.memdump is None: - return trans.show_error_message( "Memdump is not enabled (set <code>use_memdump = True</code> in universe_wsgi.ini)" ) + return trans.show_error_message( "Memdump is not enabled (set <code>use_memdump = True</code> in galaxy.ini)" ) heap = self.app.memdump.get() p = util.Params( kwd ) msg = None diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -27,7 +27,7 @@ def get_message_for_no_shed_tool_config(): # This Galaxy instance is not configured with a shed-related tool panel configuration file. - message = 'The tool_config_file setting in universe_wsgi.ini must include at least one shed tool configuration file name with a <toolbox> ' + message = 'The tool_config_file setting in galaxy.ini must include at least one shed tool configuration file name with a <toolbox> ' message += 'tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to ' message += 'automatically install tools from a tool shed into Galaxy (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is ' message += '<toolbox tool_path="../shed_tools">). For details, see the "Installation of Galaxy tool shed repository tools into a local ' @@ -229,7 +229,7 @@ :param install_tool_dependencies (optional): Set to True if you want to install tool dependencies defined for the specified repository being installed. The default setting is False. :param shed_tool_conf (optional): The shed-related tool panel configuration file configured in the "tool_config_file" setting in the Galaxy config file - (e.g., universe_wsgi.ini). At least one shed-related tool panel config file is required to be configured. Setting + (e.g., galaxy.ini). At least one shed-related tool panel config file is required to be configured. Setting this parameter to a specific file enables you to choose where the specified repository will be installed because the tool_path attribute of the <toolbox> from the specified file is used as the installation location (e.g., <toolbox tool_path="../shed_tools">). If this parameter is not set, a shed-related tool panel configuration @@ -283,7 +283,7 @@ :param install_tool_dependencies (optional): Set to True if you want to install tool dependencies defined for the specified repository being installed. The default setting is False. :param shed_tool_conf (optional): The shed-related tool panel configuration file configured in the "tool_config_file" setting in the Galaxy config file - (e.g., universe_wsgi.ini). At least one shed-related tool panel config file is required to be configured. Setting + (e.g., galaxy.ini). At least one shed-related tool panel config file is required to be configured. Setting this parameter to a specific file enables you to choose where the specified repository will be installed because the tool_path attribute of the <toolbox> from the specified file is used as the installation location (e.g., <toolbox tool_path="../shed_tools">). If this parameter is not set, a shed-related tool panel configuration diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -616,7 +616,7 @@ if includes_tool_dependencies: message = "Tool dependencies defined in this repository can be automatically installed if you set " message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file " - message += "(universe_wsgi.ini) and restart your Galaxy server." + message += "(galaxy.ini) and restart your Galaxy server." status = "warning" install_tool_dependencies_check_box_checked = False else: @@ -865,7 +865,7 @@ message = 'All selected tool dependencies are already installed.' status = 'error' else: - message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) ' + message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) ' message += ' and restart your Galaxy server to install tool dependencies.' status = 'error' installed_tool_dependencies_select_field = \ @@ -934,7 +934,7 @@ kwd[ 'message' ] = 'All selected tool dependencies are already installed.' kwd[ 'status' ] = 'error' else: - message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) ' + message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) ' message += ' and restart your Galaxy server to install tool dependencies.' kwd[ 'message' ] = message kwd[ 'status' ] = 'error' @@ -969,7 +969,7 @@ @web.require_admin def prepare_for_install( self, trans, **kwd ): if not suc.have_shed_tool_conf_for_install( trans.app ): - message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one ' + message = 'The <b>tool_config_file</b> setting in <b>galaxy.ini</b> must include at least one ' message += 'shed tool configuration file name with a <b><toolbox></b> tag that includes a <b>tool_path</b> ' message += 'attribute value which is a directory relative to the Galaxy installation directory in order ' message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> ' @@ -1213,7 +1213,7 @@ if includes_tool_dependencies: message = "Tool dependencies defined in this repository can be automatically installed if you set " message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file " - message += "(universe_wsgi.ini) and restart your Galaxy server before installing the repository." + message += "(galaxy.ini) and restart your Galaxy server before installing the repository." status = "warning" install_tool_dependencies_check_box_checked = False else: @@ -1681,7 +1681,7 @@ if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " - message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository. " + message += "setting in your Galaxy config file (galaxy.ini) and restart your Galaxy server before installing the repository. " status = "warning" install_tool_dependencies_check_box_checked = False else: diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1192,13 +1192,13 @@ def toolbox_filters( self, trans, cntrller, **kwd ): """ Sets the user's default filters for the toolbox. - Toolbox filters are specified in universe_wsgi.ini. + Toolbox filters are specified in galaxy.ini. The user can activate them and the choice is stored in user_preferences. """ def get_filter_mapping( db_filters, config_filters ): """ - Compare the allowed filters from the universe_wsgi.ini config file with the previously saved or default filters from the database. + Compare the allowed filters from the galaxy.ini config file with the previously saved or default filters from the database. We need that to toogle the checkboxes for the formular in the right way. Furthermore we extract all information associated to a filter to display them in the formular. """ diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -793,7 +793,7 @@ # validate name vs. registry registry = trans.app.visualizations_registry if not registry: - raise HTTPNotFound( 'No visualization registry (possibly disabled in universe_wsgi.ini)' ) + raise HTTPNotFound( 'No visualization registry (possibly disabled in galaxy.ini)' ) if visualization_name not in registry.plugins: raise HTTPNotFound( 'Unknown or invalid visualization: ' + visualization_name ) # or redirect to list? diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/pulsar/client/__init__.py --- a/lib/pulsar/client/__init__.py +++ b/lib/pulsar/client/__init__.py @@ -10,26 +10,26 @@ Galaxy job runners are configured in Galaxy's ``job_conf.xml`` file. See ``job_conf.xml.sample_advanced`` in your Galaxy code base or on -`Bitbucket <https://bitbucket.org/galaxy/galaxy-dist/src/tip/job_conf.xml.sample_advanc…>`_ +`Bitbucket <https://bitbucket.org/galaxy/galaxy-dist/src/tip/config/job_conf.xml.sample…>`_ for information on how to configure Galaxy to interact with the Pulsar. Galaxy also supports an older, less rich configuration of job runners directly -in its main ``universe_wsgi.ini`` file. The following section describes how to +in its main ``galaxy.ini`` file. The following section describes how to configure Galaxy to communicate with the Pulsar in this legacy mode. Legacy ------ A Galaxy tool can be configured to be executed remotely via Pulsar by -adding a line to the ``universe_wsgi.ini`` file under the -``galaxy:tool_runners`` section with the format:: +adding a line to the ``galaxy.ini`` file under the ``galaxy:tool_runners`` +section with the format:: <tool_id> = pulsar://http://<pulsar_host>:<pulsar_port> As an example, if a host named remotehost is running the Pulsar server application on port ``8913``, then the tool with id ``test_tool`` can be configured to run remotely on remotehost by adding the following -line to ``universe.ini``:: +line to ``galaxy.ini``:: test_tool = pulsar://http://remotehost:8913 diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -726,7 +726,7 @@ if self.app.config.tool_dependency_dir is None: no_tool_dependency_dir_message = "Tool dependencies can be automatically installed only if you set " no_tool_dependency_dir_message += "the value of your 'tool_dependency_dir' setting in your Galaxy " - no_tool_dependency_dir_message += "configuration file (universe_wsgi.ini) and restart your Galaxy server. " + no_tool_dependency_dir_message += "configuration file (galaxy.ini) and restart your Galaxy server. " raise exceptions.ConfigDoesNotAllowException( no_tool_dependency_dir_message ) new_tool_panel_section_label = install_options.get( 'new_tool_panel_section_label', '' ) shed_tool_conf = install_options.get( 'shed_tool_conf', None ) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -71,7 +71,7 @@ have_tool_dependencies = True break config_arg = '' - if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: + if os.path.abspath( os.path.join( os.getcwd(), 'galaxy.ini' ) ) != galaxy_config_file: config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) if not app.config.running_functional_tests: if tool_shed_accessible: diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/tool_shed/galaxy_install/migrate/common.py --- a/lib/tool_shed/galaxy_install/migrate/common.py +++ b/lib/tool_shed/galaxy_install/migrate/common.py @@ -10,7 +10,7 @@ def __init__( self, tools_migration_config ): install_dependencies = 'install_dependencies' in sys.argv - galaxy_config_file = 'universe_wsgi.ini' + galaxy_config_file = 'galaxy.ini' self.name = 'galaxy' if '-c' in sys.argv: pos = sys.argv.index( '-c' ) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -50,7 +50,7 @@ # to install but print informative error message. if install_dependencies and app.config.tool_dependency_dir is None: message = 'You are attempting to install tool dependencies but do not have a value ' - message += 'for "tool_dependency_dir" set in your universe_wsgi.ini file. Set this ' + message += 'for "tool_dependency_dir" set in your galaxy.ini file. Set this ' message += 'location value to the path where you want tool dependencies installed and ' message += 'rerun the migration script.' raise Exception( message ) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -16,7 +16,13 @@ fi } -servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` + +CONFIG_FILE=config/galaxy.ini +if [ ! -f $CONFIG_FILE ]; then + CONFIG_FILE=universe_wsgi.ini +fi + +servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $CONFIG_FILE | xargs echo` for server in $servers; do # If there's a pid @@ -31,7 +37,7 @@ echo "$server not running" fi # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ + python ./scripts/paster.py serve $CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ # Wait for the server to start sleep 1 # Grab the new pid diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb run.sh --- a/run.sh +++ b/run.sh @@ -18,8 +18,13 @@ python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" fi +CONFIG_FILE=config/galaxy.ini +if [ ! -f $CONFIG_FILE ]; then + CONFIG_FILE=universe_wsgi.ini +fi + if [ -n "$GALAXY_RUN_ALL" ]; then - servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` + servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $CONFIG_FILE | xargs echo` daemon=`echo "$@" | grep -q daemon` if [ $? -ne 0 ]; then echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon` or `--stop-daemon` arguments to run.sh' @@ -27,8 +32,8 @@ fi for server in $servers; do echo "Handling $server with log file $server.log..." - python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + python ./scripts/paster.py serve $CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ done else - python ./scripts/paster.py serve universe_wsgi.ini $@ + python ./scripts/paster.py serve $CONFIG_FILE $@ fi diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/api/README --- a/scripts/api/README +++ b/scripts/api/README @@ -1,7 +1,7 @@ This is not documentation. These are hints and examples to get you started until the documentation is written. -Set these options in universe_wsgi.ini and start the server: +Set these options in galaxy.ini and start the server: admin_users = you(a)example.org library_import_dir = /path/to/some/directory diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/build_universe_config.py --- a/scripts/build_universe_config.py +++ b/scripts/build_universe_config.py @@ -20,7 +20,7 @@ ## TODO: Expand enviroment variables here, that would ## also make Galaxy much easier to configure. - destination= "universe_wsgi.ini" + destination= "config/galaxy.ini" if len(argv) > 2: destination = argv[2] diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/check_eggs.py --- a/scripts/check_eggs.py +++ b/scripts/check_eggs.py @@ -10,7 +10,7 @@ from optparse import OptionParser parser = OptionParser() -parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' ) +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default='config/galaxy.ini' ) parser.add_option( '-q', '--quiet', dest='quiet', action="store_true", help='Quiet (no output, only set return code)', default=False ) ( options, args ) = parser.parse_args() @@ -23,7 +23,7 @@ root.addHandler( logging.StreamHandler( sys.stdout ) ) config_arg = '' -if options.config != 'universe_wsgi.ini': +if options.config != 'config/galaxy.ini': config_arg = '-c %s' % options.config lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/admin_cleanup_datasets.py --- a/scripts/cleanup_datasets/admin_cleanup_datasets.py +++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py @@ -9,11 +9,11 @@ script originally distributed with Galaxy. Basic Usage: - admin_cleanup_datasets.py universe_wsgi.ini -d 60 \ + admin_cleanup_datasets.py galaxy.ini -d 60 \ --template=email_template.txt Required Arguments: - config_file - the Galaxy configuration file (universe_wsgi.ini) + config_file - the Galaxy configuration file (galaxy.ini) Optional Arguments: -d --days - number of days old the dataset must be (default: 60) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/delete_datasets.sh --- a/scripts/cleanup_datasets/delete_datasets.sh +++ b/scripts/cleanup_datasets/delete_datasets.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -6 -r $@ >> ./scripts/cleanup_datasets/delete_datasets.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./config/galaxy.ini -d 10 -6 -r $@ >> ./scripts/cleanup_datasets/delete_datasets.log diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/delete_userless_histories.sh --- a/scripts/cleanup_datasets/delete_userless_histories.sh +++ b/scripts/cleanup_datasets/delete_userless_histories.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./config/galaxy.ini -d 10 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -61,10 +61,10 @@ self.action_names.append(name) def __parse_args(self): - default_config = os.path.abspath(os.path.join(galaxy_root, 'universe_wsgi.ini')) + default_config = os.path.abspath(os.path.join(galaxy_root, 'config', 'galaxy.ini')) parser = OptionParser() - parser.add_option('-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default=default_config) + parser.add_option('-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=default_config) parser.add_option('-d', '--debug', action='store_true', dest='debug', help='Enable debug logging', default=False) parser.add_option('--dry-run', action='store_true', dest='dry_run', help="Dry run (rollback all transactions)", default=False) parser.add_option('--force-retry', action='store_true', dest='force_retry', help="Retry file removals (on applicable actions)", default=False) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/populate_uuid.sh --- a/scripts/cleanup_datasets/populate_uuid.sh +++ b/scripts/cleanup_datasets/populate_uuid.sh @@ -2,4 +2,4 @@ cd `dirname $0`/../.. export PYTHONPATH=./lib/ -python ./scripts/cleanup_datasets/populate_uuid.py ./universe_wsgi.ini $@ \ No newline at end of file +python ./scripts/cleanup_datasets/populate_uuid.py ./config/galaxy.ini $@ diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/purge_datasets.sh --- a/scripts/cleanup_datasets/purge_datasets.sh +++ b/scripts/cleanup_datasets/purge_datasets.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./config/galaxy.ini -d 10 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/purge_folders.sh --- a/scripts/cleanup_datasets/purge_folders.sh +++ b/scripts/cleanup_datasets/purge_folders.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./config/galaxy.ini -d 10 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/purge_histories.sh --- a/scripts/cleanup_datasets/purge_histories.sh +++ b/scripts/cleanup_datasets/purge_histories.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./config/galaxy.ini -d 10 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/purge_libraries.sh --- a/scripts/cleanup_datasets/purge_libraries.sh +++ b/scripts/cleanup_datasets/purge_libraries.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./config/galaxy.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/cleanup_datasets/update_metadata.sh --- a/scripts/cleanup_datasets/update_metadata.sh +++ b/scripts/cleanup_datasets/update_metadata.sh @@ -6,4 +6,4 @@ . ./scripts/get_python.sh . ./setup_paths.sh -$GALAXY_PYTHON ./scripts/cleanup_datasets/update_metadata.py ./universe_wsgi.ini $@ +$GALAXY_PYTHON ./scripts/cleanup_datasets/update_metadata.py ./config/galaxy.ini $@ diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/common_startup.sh --- a/scripts/common_startup.sh +++ b/scripts/common_startup.sh @@ -10,21 +10,11 @@ done SAMPLES=" - tool_shed_wsgi.ini.sample - datatypes_conf.xml.sample - external_service_types_conf.xml.sample - migrated_tools_conf.xml.sample - reports_wsgi.ini.sample - shed_tool_conf.xml.sample - tool_conf.xml.sample - shed_tool_data_table_conf.xml.sample - tool_data_table_conf.xml.sample - tool_sheds_conf.xml.sample - data_manager_conf.xml.sample - shed_data_manager_conf.xml.sample - openid_conf.xml.sample - job_metrics_conf.xml.sample - universe_wsgi.ini.sample + config/galaxy.ini.sample + config/migrated_tools_conf.xml.sample + config/shed_tool_conf.xml.sample + config/shed_tool_data_table_conf.xml.sample + config/shed_data_manager_conf.xml.sample lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/ucsc/ucsc_build_sites.txt.sample diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/create_db.py --- a/scripts/create_db.py +++ b/scripts/create_db.py @@ -1,19 +1,19 @@ """ Creates the initial galaxy database schema using the settings defined in -universe_wsgi.ini. +config/galaxy.ini. This script is also wrapped by create_db.sh. .. note: pass '-c /location/to/your_config.ini' for non-standard ini file locations. -.. note: if no database_connection is set in universe_wsgi.ini, the default, -sqlite database will be constructed. - Using the database_file setting in universe_wsgi.ini will create the file - at the settings location (??) +.. note: if no database_connection is set in galaxy.ini, the default, sqlite +database will be constructed. + Using the database_file setting in galaxy.ini will create the file at the + settings location (??) -.. seealso: universe_wsgi.ini, specifically the settings: database_connection -and database file +.. seealso: galaxy.ini, specifically the settings: database_connection and +database file """ import sys diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/data_libraries/build_lucene_index.py --- a/scripts/data_libraries/build_lucene_index.py +++ b/scripts/data_libraries/build_lucene_index.py @@ -3,8 +3,8 @@ Build index for full-text lucene search of files in data libraries. Requires a full text search server and configuration settings in -universe_wsgi.ini. See the lucene settings in the data library -search section for more details. +galaxy.ini. See the lucene settings in the data library search section for more +details. Run from the ~/scripts/data_libraries directory: %sh build_lucene_index.sh @@ -32,7 +32,7 @@ ignore_exts = gconfig.get( "fulltext_noindex_filetypes", "" ).split( "," ) search_url = gconfig.get( "fulltext_url", None ) if not search_url: - raise ValueError( "Need to specify search functionality in universe_wsgi.ini" ) + raise ValueError( "Need to specify search functionality in galaxy.ini" ) dataset_file = create_dataset_file( get_lddas( sa_session, max_size, ignore_exts ) ) try: build_index( search_url, dataset_file ) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/data_libraries/build_lucene_index.sh --- a/scripts/data_libraries/build_lucene_index.sh +++ b/scripts/data_libraries/build_lucene_index.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/data_libraries/build_lucene_index.py ./universe_wsgi.ini +python ./scripts/data_libraries/build_lucene_index.py ./config/galaxy.ini diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/data_libraries/build_whoosh_index.py --- a/scripts/data_libraries/build_whoosh_index.py +++ b/scripts/data_libraries/build_whoosh_index.py @@ -2,8 +2,8 @@ """ Build index for full-text whoosh search of files in data libraries. -Requires configuration settings in universe_wsgi.ini. See the whoosh settings -in the data library search section for more details. +Requires configuration settings in galaxy.ini. See the whoosh settings in the +data library search section for more details. Run from the ~/scripts/data_libraries directory: %sh build_whoosh_index.sh diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/data_libraries/build_whoosh_index.sh --- a/scripts/data_libraries/build_whoosh_index.sh +++ b/scripts/data_libraries/build_whoosh_index.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/data_libraries/build_whoosh_index.py ./universe_wsgi.ini +python ./scripts/data_libraries/build_whoosh_index.py ./config/galaxy.ini diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/fetch_eggs.py --- a/scripts/fetch_eggs.py +++ b/scripts/fetch_eggs.py @@ -9,7 +9,7 @@ from optparse import OptionParser parser = OptionParser() -parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' ) +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default='config/galaxy.ini' ) parser.add_option( '-e', '--egg-name', dest='egg_name', help='Egg name (as defined in eggs.ini) to fetch, or "all" for all eggs, even those not needed by your configuration' ) parser.add_option( '-p', '--platform', dest='platform', help='Fetch for a specific platform (by default, eggs are fetched for *this* platform' ) ( options, args ) = parser.parse_args() @@ -49,7 +49,7 @@ print "%s %s is installed at %s" % ( dist.project_name, dist.version, dist.location ) except EggNotFetchable, e: config_arg = '' - if options.config != 'universe_wsgi.ini': + if options.config != 'config/galaxy.ini': config_arg = '-c %s ' % options.config try: assert options.egg_name != 'all' diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -100,7 +100,7 @@ """ cwd = os.getcwd() static_dir = os.path.join( cwd, 'static' ) - #TODO: these should be copied from universe_wsgi.ini + #TODO: these should be copied from config/galaxy.ini return dict( #TODO: static_enabled needed here? static_enabled=True, @@ -398,8 +398,8 @@ for label in kwargs: config_tuple = label, kwargs[ label ] config_items.append( config_tuple ) - # Write a temporary file, based on universe_wsgi.ini.sample, using the configuration options defined above. - generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) + # Write a temporary file, based on config/galaxy.ini.sample, using the configuration options defined above. + generate_config_file( 'config/galaxy.ini.sample', galaxy_config_file, config_items ) # Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh. kwargs[ 'global_conf' ] = get_webapp_global_conf() kwargs[ 'global_conf' ][ '__file__' ] = galaxy_config_file diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/helper.py --- a/scripts/helper.py +++ b/scripts/helper.py @@ -9,10 +9,10 @@ from ConfigParser import ConfigParser from optparse import OptionParser -default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'universe_wsgi.ini') ) +default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'config/galaxy.ini') ) parser = OptionParser() -parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default=default_config ) +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=default_config ) parser.add_option( '-e', '--encode-id', dest='encode_id', help='Encode an ID' ) parser.add_option( '-d', '--decode-id', dest='decode_id', help='Decode an ID' ) parser.add_option( '--hda', dest='hda_id', help='Display HistoryDatasetAssociation info' ) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/make_egg_packager.py --- a/scripts/make_egg_packager.py +++ b/scripts/make_egg_packager.py @@ -4,7 +4,7 @@ from optparse import OptionParser parser = OptionParser() -parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' ) +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default='config/galaxy.ini' ) parser.add_option( '-p', '--platform', dest='platform', help='Fetch for a specific platform (by default, eggs are fetched for *this* platform' ) ( options, args ) = parser.parse_args() diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -22,7 +22,7 @@ log = logging.getLogger( __name__ ) -config_file = read_config_file_arg( sys.argv, 'universe_wsgi.ini' ) +config_file = read_config_file_arg( sys.argv, 'config/galaxy.ini' ) if not os.path.exists( config_file ): print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file sys.exit( 1 ) @@ -31,7 +31,7 @@ cp = SafeConfigParser() cp.read( config_file ) -if config_file == 'universe_wsgi.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ: +if config_file == 'config/galaxy.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ: # Running functional tests. db_url = os.environ[ 'GALAXY_TEST_DBURI' ] elif cp.has_option( "app:main", "install_database_connection" ): diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/others/incorrect_gops_jobs.sh --- a/scripts/others/incorrect_gops_jobs.sh +++ b/scripts/others/incorrect_gops_jobs.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/others/incorrect_gops_jobs.py ./universe_wsgi.ini >> ./scripts/others/incorrect_gops_jobs.log +python ./scripts/others/incorrect_gops_jobs.py ./config/galaxy.ini >> ./scripts/others/incorrect_gops_jobs.log diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/others/incorrect_gops_join_jobs.sh --- a/scripts/others/incorrect_gops_join_jobs.sh +++ b/scripts/others/incorrect_gops_join_jobs.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/others/incorrect_gops_join_jobs.py ./universe_wsgi.ini >> ./scripts/others/incorrect_gops_join_jobs.log +python ./scripts/others/incorrect_gops_join_jobs.py ./config/galaxy.ini >> ./scripts/others/incorrect_gops_join_jobs.log diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/scramble.py --- a/scripts/scramble.py +++ b/scripts/scramble.py @@ -2,7 +2,7 @@ from optparse import OptionParser parser = OptionParser() -parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' ) +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default='config/galaxy.ini' ) parser.add_option( '-e', '--egg-name', dest='egg_name', help='Egg name (as defined in eggs.ini) to fetch, or "all" for all eggs, even those not needed by your configuration' ) ( options, args ) = parser.parse_args() @@ -36,7 +36,7 @@ sys.exit( 1 ) for dependency in egg.dependencies: config_arg = '' - if options.config != 'universe_wsgi.ini': + if options.config != 'config/galaxy.ini': config_arg = '-c %s' % options.config print "Checking %s dependency: %s" % ( egg.name, dependency ) try: diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/set_dataset_sizes.py --- a/scripts/set_dataset_sizes.py +++ b/scripts/set_dataset_sizes.py @@ -4,10 +4,10 @@ from ConfigParser import ConfigParser from optparse import OptionParser -default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'universe_wsgi.ini') ) +default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'config/galaxy.ini') ) parser = OptionParser() -parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default=default_config ) +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=default_config ) ( options, args ) = parser.parse_args() def init(): diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/set_user_disk_usage.py --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -4,10 +4,10 @@ from ConfigParser import ConfigParser from optparse import OptionParser -default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'universe_wsgi.ini') ) +default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'config/galaxy.ini') ) parser = OptionParser() -parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default=default_config ) +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=default_config ) parser.add_option( '-u', '--username', dest='username', help='Username of user to update', default='all' ) parser.add_option( '-e', '--email', dest='email', help='Email address of user to update', default='all' ) parser.add_option( '--dry-run', dest='dryrun', help='Dry run (show changes but do not save to database)', action='store_true', default=False ) diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/sync_reports_config.py --- a/scripts/sync_reports_config.py +++ b/scripts/sync_reports_config.py @@ -5,13 +5,13 @@ MAIN_SECTION = "app:main" def sync(): - # Add or replace the relevant properites from universe_wsgi.ini + # Add or replace the relevant properites from galaxy.ini # into reports_wsgi.ini - reports_config_file = "reports_wsgi.ini" + reports_config_file = "config/reports_wsgi.ini" if len(argv) > 1: reports_config_file = argv[1] - universe_config_file = "universe_wsgi.ini" + universe_config_file = "config/galaxy.ini" if len(argv) > 2: universe_config_file = argv[2] diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb scripts/transfer.py --- a/scripts/transfer.py +++ b/scripts/transfer.py @@ -41,8 +41,8 @@ """ def __init__( self ): self.parser = optparse.OptionParser() - self.parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', - default=os.path.abspath( os.path.join( galaxy_root, 'universe_wsgi.ini' ) ) ) + self.parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', + default=os.path.abspath( os.path.join( galaxy_root, 'config/galaxy.ini' ) ) ) self.parser.add_option( '-d', '--debug', action='store_true', dest='debug', help="Debug (don't detach)" ) self.parser.add_option( '-s', '--slow', action='store_true', dest='slow', help="Transfer slowly (for debugging)" ) self.opts = None diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb static/scripts/galaxy-app-base.js --- a/static/scripts/galaxy-app-base.js +++ b/static/scripts/galaxy-app-base.js @@ -11,7 +11,7 @@ * logger : the logger/metrics-logger * localize : the string localizer * config : the current configuration (any k/v in - * universe_wsgi.ini available from the configuration API) + * galaxy.ini available from the configuration API) * user : the current user (as a mvc/user/user-model) */ function GalaxyApp( options ){ diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -45,7 +45,7 @@ ## ---------------------------------------------------------------------------- <%def name="get_config_dict()"> - ## Return a dictionary of universe_wsgi.ini settings + ## Return a dictionary of galaxy.ini settings <% config_dict = {} try: diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -220,13 +220,13 @@ }; // ------------------------------------------------------------------- Admin -/** Gets the admin user data from spaceghost if set and checks the universe_wsgi.ini file for the email. +/** Gets the admin user data from spaceghost if set and checks the galaxy.ini file for the email. * @returns {Object|null} the admin data object (email, pasword, username) - * or null if no admin is set in both the universe_wsgi.ini and spaceghost. + * or null if no admin is set in both the galaxy.ini and spaceghost. */ User.prototype.getAdminData = function getAdminData(){ //TODO: this might be better inside sg - // check for the setting in sg and the universe_wsgi.ini file + // check for the setting in sg and the galaxy.ini file var adminData = this.spaceghost.options.adminUser, iniAdminEmails = this.spaceghost.getUniverseSetting( 'admin_users' ); iniAdminEmails = ( iniAdminEmails )? diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -1141,12 +1141,12 @@ return read.match( regex ); }; -/** Read a configuration setting from the universe_wsgi.ini file. +/** Read a configuration setting from the galaxy.ini file. * @param {String} iniKey the setting key to find * @returns {String} value from file for iniKey (or null if not found or commented out) */ SpaceGhost.prototype.getUniverseSetting = function getUniverseSetting( iniKey ){ - var iniFilepath = '../../universe_wsgi.ini', + var iniFilepath = '../../config/galaxy.ini', regex = new RegExp( '^([#]*)\\\s*' + iniKey + '\\\s*=\\\s*(.*)$', 'm' ), match = this.searchFile( iniFilepath, regex ); this.debug( 'regex: ' + regex ); diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb test/functional/tools/README.txt --- a/test/functional/tools/README.txt +++ b/test/functional/tools/README.txt @@ -10,6 +10,6 @@ to ensure these tools get loaded during the testing process. Finally, to play around witht these tools interactively - simply -replace the 'universe_wsgi.ini' option 'tool_config_file' with: +replace the 'galaxy.ini' option 'tool_config_file' with: tool_config_file = test/functional/tools/samples_tool_conf.xml diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -453,7 +453,7 @@ """ cwd = os.getcwd() static_dir = os.path.join( cwd, 'static' ) - #TODO: these should be copied from universe_wsgi.ini + #TODO: these should be copied from galaxy.ini #TODO: static_enabled needed here? return dict( static_enabled = True, static_cache_time = 360, diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -495,8 +495,8 @@ for label in kwargs: config_tuple = label, kwargs[ label ] config_items.append( config_tuple ) - # Write a temporary file, based on universe_wsgi.ini.sample, using the configuration options defined above. - generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) + # Write a temporary file, based on galaxy.ini.sample, using the configuration options defined above. + generate_config_file( 'config/galaxy.ini.sample', galaxy_config_file, config_items ) # kwargs must be a list when passed to the Galaxy webapp (i.e., UniverseApplication). # The following is used to set metadata externally. kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -347,8 +347,8 @@ for label in kwargs: config_tuple = label, kwargs[ label ] config_items.append( config_tuple ) - # Write a temporary file, based on universe_wsgi.ini.sample, using the configuration options defined above. - generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) + # Write a temporary file, based on galaxy.ini.sample, using the configuration options defined above. + generate_config_file( 'config/galaxy.ini.sample', galaxy_config_file, config_items ) kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] # Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh. kwargs[ 'global_conf' ] = install_and_test_base_util.get_webapp_global_conf() diff -r bbf9c5f5fdaf96fd02639f3342e47d4eecae8a4f -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -94,7 +94,7 @@ """ cwd = os.getcwd() static_dir = os.path.join( cwd, 'static' ) - #TODO: these should be copied from universe_wsgi.ini + #TODO: these should be copied from galaxy.ini return dict( #TODO: static_enabled needed here? static_enabled = True, @@ -356,7 +356,7 @@ if not os.environ.get( 'GALAXY_SHED_DATA_MANAGER_CONF' ): open( galaxy_shed_data_manager_conf_file, 'wb' ).write( shed_data_manager_conf_xml_template ) galaxy_global_conf = get_webapp_global_conf() - galaxy_global_conf[ '__file__' ] = 'universe_wsgi.ini.sample' + galaxy_global_conf[ '__file__' ] = 'config/galaxy.ini.sample' kwargs = dict( allow_user_creation = True, allow_user_deletion = True, https://bitbucket.org/galaxy/galaxy-central/commits/aeca0d388e83/ Changeset: aeca0d388e83 User: natefoo Date: 2014-09-15 22:52:50 Summary: Bug fixes to scripts for config subdir. Affected #: 3 files diff -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 scripts/helper.py --- a/scripts/helper.py +++ b/scripts/helper.py @@ -26,8 +26,7 @@ sys.exit( 1 ) options.config = os.path.abspath( options.config ) -os.chdir( os.path.dirname( options.config ) ) -sys.path.append( 'lib' ) +sys.path.append( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) from galaxy import eggs import pkg_resources @@ -35,7 +34,7 @@ config = ConfigParser( dict( file_path = 'database/files', id_secret = 'USING THE DEFAULT IS NOT SECURE!', database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) ) -config.read( os.path.basename( options.config ) ) +config.read( options.config ) from galaxy.web import security from galaxy.model import mapping diff -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 scripts/set_dataset_sizes.py --- a/scripts/set_dataset_sizes.py +++ b/scripts/set_dataset_sizes.py @@ -13,15 +13,14 @@ def init(): options.config = os.path.abspath( options.config ) - os.chdir( os.path.dirname( options.config ) ) - sys.path.append( 'lib' ) + sys.path.append( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) from galaxy import eggs import pkg_resources config = ConfigParser( dict( file_path = 'database/files', database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) ) - config.read( os.path.basename( options.config ) ) + config.read( options.config ) from galaxy.model import mapping diff -r 70d2dff1297db4c5462c6c9889e290790d3ae5bb -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 scripts/set_user_disk_usage.py --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -21,8 +21,7 @@ if options.email == 'all': options.email = None - os.chdir( os.path.dirname( options.config ) ) - sys.path.append( 'lib' ) + sys.path.append( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) from galaxy import eggs import pkg_resources @@ -35,7 +34,7 @@ config_parser = ConfigParser( dict( here = os.getcwd(), database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) ) - config_parser.read( os.path.basename( options.config ) ) + config_parser.read( options.config ) config_dict = {} for key, value in config_parser.items( "app:main" ): https://bitbucket.org/galaxy/galaxy-central/commits/14d243c7069e/ Changeset: 14d243c7069e User: natefoo Date: 2014-09-15 22:57:28 Summary: merge. Affected #: 34 files diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -794,6 +794,8 @@ if value is not None: if not isinstance( value, list ): value = [ value ] + # We could have an unvalidated value here when e.g. running a workflow. + value = [ val.value if isinstance( val, UnvalidatedValue ) else val for val in value ] field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -417,12 +417,13 @@ query = irmm.get_query_for_setting_metadata_on_repositories( order=False ) # Now reset metadata on all remaining repositories. for repository in query: - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + irmm.set_repository( repository ) + irmm.reset_all_metadata_on_installed_repository() + irmm_invalid_file_tups = irmm.get_invalid_file_tups() + if irmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + irmm_invalid_file_tups, repository, None, as_html=False ) diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1732,20 +1732,21 @@ tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata - irmm = InstalledRepositoryMetadataManager( trans.app ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - irmm.update_in_shed_tool_config( repository ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + repository=repository, + changeset_revision=repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if irmm_metadata_dict != original_metadata_dict: + repository.metadata = irmm_metadata_dict + irmm.update_in_shed_tool_config() trans.install_model.context.add( repository ) trans.install_model.context.flush() message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name @@ -1938,22 +1939,24 @@ dmh.remove_from_data_manager( repository ) # Update the repository metadata. tpm = tool_panel_manager.ToolPanelManager( trans.app ) - irmm = InstalledRepositoryMetadataManager( trans.app, tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=latest_changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + tpm=tpm, + repository=repository, + changeset_revision=latest_changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if 'tools' in irmm_metadata_dict: + tool_panel_dict = irmm_metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() tpm.add_to_tool_panel( repository_name=str( repository.name ), repository_clone_url=repository_clone_url, changeset_revision=str( repository.installed_changeset_revision ), @@ -1963,18 +1966,18 @@ tool_panel_dict=tool_panel_dict, new_install=False ) # Add new Data Manager entries - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( trans.app ) new_data_managers = dmh.install_data_managers( trans.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, repository.get_shed_config_dict( trans.app ), os.path.join( relative_install_dir, name ), repository, repository_tools_tups ) - if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: - new_repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + if 'repository_dependencies' in irmm_metadata_dict or 'tool_dependencies' in irmm_metadata_dict: + new_repository_dependencies_dict = irmm_metadata_dict.get( 'repository_dependencies', {} ) new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] ) - new_tool_dependencies_dict = metadata_dict.get( 'tool_dependencies', {} ) + new_tool_dependencies_dict = irmm_metadata_dict.get( 'tool_dependencies', {} ) if new_repository_dependencies: # [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']] proceed_to_install = False @@ -2017,7 +2020,7 @@ updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), updating=True ) return self.prepare_for_install( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies but did include @@ -2033,12 +2036,12 @@ proceed_to_install = True break if proceed_to_install: - encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) + encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( irmm_metadata_dict.get( 'tool_dependencies', {} ) ) encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), encoded_relative_install_dir=encoded_relative_install_dir, encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, message=message, @@ -2047,7 +2050,7 @@ # Updates received did not include any newly defined repository dependencies or newly defined # tool dependencies that need to be installed. repository = trans.app.update_repository_manager.update_repository_record( repository=repository, - updated_metadata_dict=metadata_dict, + updated_metadata_dict=irmm_metadata_dict, updated_changeset_revision=latest_changeset_revision, updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -429,13 +429,13 @@ def handle_repository( trans, rmm, repository, results ): log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + rmm.set_repository( repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) @@ -451,7 +451,11 @@ status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) results = dict( start_time=start_time, repository_status=[], @@ -511,12 +515,17 @@ results = dict( start_time=start_time, repository_status=[] ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.security.encode_id( repository.id ) ) - if invalid_file_tups: + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -1,6 +1,8 @@ import os, logging from galaxy import web from galaxy.web.base.controller import BaseUIController + +from tool_shed.util.common_util import generate_clone_url_for_repository_in_tool_shed from tool_shed.util.shed_util_common import get_repository_by_name_and_owner from tool_shed.util.hg_util import update_repository from tool_shed.metadata import repository_metadata_manager @@ -47,9 +49,19 @@ # interface will result in a new head being created. repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) # Set metadata using the repository files on disk. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - error_message, status = rmm.set_repository_metadata( trans.request.host, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + changeset_revision=repository.tip( trans.app ), + repository_clone_url=repository_clone_url, + relative_install_dir=repository.repo_path( trans.app ), + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + error_message, status = rmm.set_repository_metadata( trans.request.host ) if status == 'ok' and error_message: log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ ( str( repository.name ), str( repository.user.username ), error_message ) ) diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2759,15 +2759,18 @@ def reset_all_metadata( self, trans, id, **kwd ): """Reset all metadata on the complete changelog for a single repository in the tool shed.""" # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( id ) - if invalid_file_tups: - repository = suc.get_repository_in_tool_shed( trans.app, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_metadata_dict = rmm.get_metadata_dict() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, - metadata_dict ) + rmm_metadata_dict ) status = 'error' else: message = "All repository metadata has been reset. " @@ -2849,10 +2852,10 @@ if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, - **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, **kwd ) if error_message: message = error_message else: diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -263,10 +263,11 @@ ( len( files_to_remove ), upload_point ) else: message += " %d files were removed from the repository root. " % len( files_to_remove ) - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) status, error_message = \ rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, content_alert_str=content_alert_str, **kwd ) if error_message: diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -792,9 +792,10 @@ results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, self.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=self.app, + user=self.user, + repository=repository ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, - repository, content_alert_str=content_alert_str ) if error_message: results_dict[ 'ok' ] = False diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -510,31 +510,33 @@ """ shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) tdtm = data_table_manager.ToolDataTableManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict # Update the tool_shed_repository.tool_shed_status column in the database. tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository ) if tool_shed_status_dict: tool_shed_repository.tool_shed_status = tool_shed_status_dict self.install_model.context.add( tool_shed_repository ) self.install_model.context.flush() - if 'tool_dependencies' in metadata_dict and not reinstalling: + if 'tool_dependencies' in irmm_metadata_dict and not reinstalling: tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) - if 'sample_files' in metadata_dict: - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'sample_files' in irmm_metadata_dict: + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_data_table_conf_filename, tool_data_table_elems = \ tdtm.install_tool_data_tables( tool_shed_repository, tool_index_sample_files ) @@ -543,13 +545,13 @@ None, self.app.config.shed_tool_data_table_config, persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'tools' in irmm_metadata_dict: + tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( irmm_metadata_dict[ 'tools' ], tool_section ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. repository_tools_tups = tdtm.handle_missing_data_table_entry( relative_install_dir, @@ -575,15 +577,15 @@ shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=True ) - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, shed_config_dict, relative_install_dir, tool_shed_repository, repository_tools_tups ) - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: tool_shed_repository.status = self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: tool_shed_repository.includes_datatypes = True @@ -604,7 +606,7 @@ name=tool_shed_repository.name, owner=tool_shed_repository.owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -82,9 +82,12 @@ repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools_for_display_in_tool_panel: tpm = tool_panel_manager.ToolPanelManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, tpm ) - metadata = repository.metadata - repository_tools_tups = irmm.get_repository_tools_tups( metadata ) + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=tpm, + repository=repository, + changeset_revision=repository.changeset_revision, + metadata_dict=repository.metadata ) + repository_tools_tups = irmm.get_repository_tools_tups() # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] tpm.add_to_tool_panel( repository.name, @@ -101,7 +104,7 @@ data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata, + repository.metadata, repository.get_shed_config_dict( self.app ), data_manager_relative_install_dir, repository, diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -19,9 +19,16 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, tpm=None ): - super( InstalledRepositoryMetadataManager, self ).__init__( app ) - self.app = app + def __init__( self, app, tpm=None, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( InstalledRepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=None ) if tpm is None: self.tpm = tool_panel_manager.ToolPanelManager( self.app ) else: @@ -53,15 +60,15 @@ return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) - def get_repository_tools_tups( self, metadata_dict ): + def get_repository_tools_tups( self ): """ Return a list of tuples of the form (relative_path, guid, tool) for each tool defined in the received tool shed repository metadata. """ repository_tools_tups = [] - index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( metadata_dict.get( 'shed_config_filename' ) ) - if 'tools' in metadata_dict: - for tool_dict in metadata_dict[ 'tools' ]: + index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( self.metadata_dict.get( 'shed_config_filename' ) ) + if 'tools' in self.metadata_dict: + for tool_dict in self.metadata_dict[ 'tools' ]: load_relative_path = relative_path = tool_dict.get( 'tool_config', None ) if shed_conf_dict.get( 'tool_path' ): load_relative_path = os.path.join( shed_conf_dict.get( 'tool_path' ), relative_path ) @@ -74,36 +81,21 @@ repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups - def reset_all_metadata_on_installed_repository( self, id ): + def reset_all_metadata_on_installed_repository( self ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" - invalid_file_tups = [] - metadata_dict = {} - repository = repository_util.get_installed_tool_shed_repository( self.app, id ) - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - tool_path, relative_install_dir = repository.get_tool_relative_path( self.app ) - if relative_install_dir: - original_metadata_dict = repository.metadata - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( self.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - self.update_in_shed_tool_config( repository ) - self.app.install_model.context.add( repository ) + if self.relative_install_dir: + original_metadata_dict = self.repository.metadata + self.generate_metadata_for_changeset_revision() + if self.metadata_dict != original_metadata_dict: + self.repository.metadata = self.metadata_dict + self.update_in_shed_tool_config() + self.app.install_model.context.add( self.repository ) self.app.install_model.context.flush() - log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + log.debug( 'Metadata has been reset on repository %s.' % self.repository.name ) else: - log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + log.debug( 'Metadata did not need to be reset on repository %s.' % self.repository.name ) else: - log.debug( 'Error locating installation directory for repository %s.' % repository.name ) - return invalid_file_tups, metadata_dict + log.debug( 'Error locating installation directory for repository %s.' % self.repository.name ) def reset_metadata_on_selected_repositories( self, user, **kwd ): """ @@ -119,19 +111,19 @@ for repository_id in repository_ids: try: repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id ) - owner = str( repository.owner ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_installed_repository() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) log.debug( message ) unsuccessful_count += 1 else: - log.debug( "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), owner ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s" % \ + ( str( repository.name ), str( repository.owner ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) ) @@ -146,32 +138,37 @@ status = 'error' return message, status - def tool_shed_from_repository_clone_url( self, repository_clone_url ): + def set_repository( self, repository ): + super( InstalledRepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) + + def tool_shed_from_repository_clone_url( self ): """Given a repository clone URL, return the tool shed that contains the repository.""" - return common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) + return common_util.remove_protocol_and_user_from_clone_url( cleaned_repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) - def update_in_shed_tool_config( self, repository ): + def update_in_shed_tool_config( self ): """ A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list of config_elems instead of using the in-memory list. """ - shed_conf_dict = repository.get_shed_config_dict( self.app ) + shed_conf_dict = self.repository.get_shed_config_dict( self.app ) shed_tool_conf = shed_conf_dict[ 'config_filename' ] tool_path = shed_conf_dict[ 'tool_path' ] - tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = self.get_repository_tools_tups( repository.metadata ) - clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) - tool_shed = self.tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) - owner = repository.owner + tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( self.repository ) + repository_tools_tups = self.get_repository_tools_tups() + clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + tool_shed = self.tool_shed_from_repository_clone_url() + owner = self.repository.owner if not owner: + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) owner = suc.get_repository_owner( cleaned_repository_clone_url ) guid_to_tool_elem_dict = {} for tool_config_filename, guid, tool in repository_tools_tups: guid_to_tool_elem_dict[ guid ] = self.tpm.generate_tool_elem( tool_shed, - repository.name, - repository.changeset_revision, - repository.owner or '', + self.repository.name, + self.repository.changeset_revision, + self.repository.owner or '', tool_config_filename, tool, None ) diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -416,21 +416,23 @@ log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) ) finally: lock.release() - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = self.shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = self.shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict self.app.install_model.context.add( tool_shed_repository ) self.app.install_model.context.flush() - has_tool_dependencies = self.__has_tool_dependencies( metadata_dict ) + has_tool_dependencies = self.__has_tool_dependencies( irmm_metadata_dict ) if has_tool_dependencies: # All tool_dependency objects must be created before the tools are processed even if no # tool dependencies will be installed. @@ -440,14 +442,14 @@ set_status=True ) else: tool_dependencies = None - if 'tools' in metadata_dict: + if 'tools' in irmm_metadata_dict: tdtm = data_table_manager.ToolDataTableManager( self.app ) - sample_files = metadata_dict.get( 'sample_files', [] ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) sample_files = [ str( s ) for s in sample_files ] tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically # generated select lists. @@ -491,7 +493,7 @@ if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: @@ -514,7 +516,7 @@ name=tool_shed_repository.name, owner=self.repository_owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -27,31 +27,89 @@ class MetadataGenerator( object ): - def __init__( self, app ): + def __init__( self, app, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None, user=None ): self.app = app + self.user = user + self.repository = repository + if self.app.name == 'galaxy': + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.changeset_revision + else: + self.changeset_revision = changeset_revision + + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + if self.repository is not None: + self.shed_config_dict = self.repository.get_shed_config_dict( self.app ) + else: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_files_directory( self.app ) + if metadata_dict is None: + # Shed related tool panel configs are only relevant to Galaxy. + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + self.metadata_dict = metadata_dict + else: + # We're in the Tool Shed. + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.tip( self.app ) + else: + self.changeset_revision = changeset_revision + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = \ + common_util.generate_clone_url_for_repository_in_tool_shed( self.user, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + relative_install_dir = self.repository.repo_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_path( self.app ) + if metadata_dict is None: + self.metadata_dict = {} + else: + self.metadata_dict = metadata_dict + self.relative_install_dir = relative_install_dir + self.repository_files_dir = repository_files_dir + self.resetting_all_metadata_on_repository = resetting_all_metadata_on_repository + self.updating_installed_repository = updating_installed_repository + self.persist = persist + self.invalid_file_tups = [] self.sa_session = app.model.context.current self.NOT_TOOL_CONFIGS = [ suc.DATATYPES_CONFIG_FILENAME, - rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, - rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, - suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] + rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, + rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, + suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] - def generate_data_manager_metadata( self, repository, repo_dir, data_manager_config_filename, metadata_dict, + def generate_data_manager_metadata( self, repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None ): """ Update the received metadata_dict with information from the parsed data_manager_config_filename. """ if data_manager_config_filename is None: return metadata_dict - repo_path = repository.repo_path( self.app ) + repo_path = self.repository.repo_path( self.app ) try: # Galaxy Side. - repo_files_directory = repository.repo_files_directory( self.app ) + repo_files_directory = self.repository.repo_files_directory( self.app ) repo_dir = repo_files_directory - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) except AttributeError: # Tool Shed side. repo_files_directory = repo_path - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( None, repository ) relative_data_manager_dir = util.relpath( os.path.split( data_manager_config_filename )[0], repo_dir ) rel_data_manager_config_filename = os.path.join( relative_data_manager_dir, os.path.split( data_manager_config_filename )[1] ) @@ -91,7 +149,7 @@ # FIXME: default behavior is to fall back to tool.name. data_manager_name = data_manager_elem.get( 'name', data_manager_id ) version = data_manager_elem.get( 'version', DataManager.DEFAULT_VERSION ) - guid = self.generate_guid_for_object( repository_clone_url, DataManager.GUID_TYPE, data_manager_id, version ) + guid = self.generate_guid_for_object( DataManager.GUID_TYPE, data_manager_id, version ) data_tables = [] if tool_file is None: log.error( 'Data Manager entry is missing tool_file attribute in "%s".' % ( data_manager_config_filename ) ) @@ -130,8 +188,7 @@ log.debug( 'Loaded Data Manager tool_files: %s' % ( tool_file ) ) return metadata_dict - def generate_datatypes_metadata( self, tv, repository, repository_clone_url, repository_files_dir, datatypes_config, - metadata_dict ): + def generate_datatypes_metadata( self, tv, repository_files_dir, datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree, error_message = xml_util.parse_xml( datatypes_config ) if tree is None: @@ -180,11 +237,11 @@ tool_config_path = hg_util.get_config_from_disk( tool_config, repository_files_dir ) full_path = os.path.abspath( tool_config_path ) tool, valid, error_message = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), full_path ) + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: guid = None else: - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) converter_dict = dict( tool_config=tool_config, guid=guid, target_datatype=target_datatype ) @@ -226,76 +283,70 @@ valid_tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return valid_tool_dependencies_dict - def generate_guid_for_object( self, repository_clone_url, guid_type, obj_id, version ): - tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) + def generate_guid_for_object( self, guid_type, obj_id, version ): + tmp_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) return '%s/%s/%s/%s' % ( tmp_url, guid_type, obj_id, version ) - def generate_metadata_for_changeset_revision( self, repository, changeset_revision, repository_clone_url, - shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, - persist=False ): + def generate_metadata_for_changeset_revision( self ): """ Generate metadata for a repository using its files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access - that changeset revision's disk files, so the value of repository_files_dir will not - always be repository.repo_path( self.app ) (it could be an absolute path to a temporary - directory containing a clone). If it is an absolute path, the value of relative_install_dir + that changeset revision's disk files, so the value of self.repository_files_dir will not + always be self.repository.repo_path( self.app ) (it could be an absolute path to a temporary + directory containing a clone). If it is an absolute path, the value of self.relative_install_dir must contain repository.repo_path( self.app ). - The value of persist will be True when the installed repository contains a valid + The value of self.persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by self.app.config.shed_tool_data_table_config. """ tv = tool_validator.ToolValidator( self.app ) - if shed_config_dict is None: - shed_config_dict = {} - if updating_installed_repository: + if self.shed_config_dict is None: + self.shed_config_dict = {} + if self.updating_installed_repository: # Keep the original tool shed repository metadata if setting metadata on a repository # installed into a local Galaxy instance for which we have pulled updates. - original_repository_metadata = repository.metadata + original_repository_metadata = self.repository.metadata else: original_repository_metadata = None - readme_file_names = readme_util.get_readme_file_names( str( repository.name ) ) + readme_file_names = readme_util.get_readme_file_names( str( self.repository.name ) ) if self.app.name == 'galaxy': # Shed related tool panel configs are only relevant to Galaxy. - metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } + metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename' ) } else: metadata_dict = {} readme_files = [] - invalid_file_tups = [] invalid_tool_configs = [] tool_dependencies_config = None original_tool_data_path = self.app.config.tool_data_path original_tool_data_table_config_path = self.app.config.tool_data_table_config_path - if resetting_all_metadata_on_repository: - if not relative_install_dir: - raise Exception( "The value of repository.repo_path must be sent when resetting all metadata on a repository." ) + if self.resetting_all_metadata_on_repository: + if not self.relative_install_dir: + raise Exception( "The value of self.repository.repo_path must be set when resetting all metadata on a repository." ) # Keep track of the location where the repository is temporarily cloned so that we can - # strip the path when setting metadata. The value of repository_files_dir is the full - # path to the temporary directory to which the repository was cloned. - work_dir = repository_files_dir - files_dir = repository_files_dir + # strip the path when setting metadata. The value of self.repository_files_dir is the + # full path to the temporary directory to which self.repository was cloned. + work_dir = self.repository_files_dir + files_dir = self.repository_files_dir # Since we're working from a temporary directory, we can safely copy sample files included # in the repository to the repository root. - self.app.config.tool_data_path = repository_files_dir - self.app.config.tool_data_table_config_path = repository_files_dir + self.app.config.tool_data_path = self.repository_files_dir + self.app.config.tool_data_table_config_path = self.repository_files_dir else: # Use a temporary working directory to copy all sample files. work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-gmfcr" ) # All other files are on disk in the repository's repo_path, which is the value of - # relative_install_dir. - files_dir = relative_install_dir - if shed_config_dict.get( 'tool_path' ): - files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) + # self.relative_install_dir. + files_dir = self.relative_install_dir + if self.shed_config_dict.get( 'tool_path' ): + files_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], files_dir ) self.app.config.tool_data_path = work_dir #FIXME: Thread safe? self.app.config.tool_data_table_config_path = work_dir # Handle proprietary datatypes, if any. datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) if datatypes_config: metadata_dict = self.generate_datatypes_metadata( tv, - repository, - repository_clone_url, files_dir, datatypes_config, metadata_dict ) @@ -303,9 +354,8 @@ # the repository's metadata. sample_file_metadata_paths, sample_file_copy_paths = \ self.get_sample_files_from_disk( repository_files_dir=files_dir, - tool_path=shed_config_dict.get( 'tool_path' ), - relative_install_dir=relative_install_dir, - resetting_all_metadata_on_repository=resetting_all_metadata_on_repository ) + tool_path=self.shed_config_dict.get( 'tool_path' ), + relative_install_dir=self.relative_install_dir ) if sample_file_metadata_paths: metadata_dict[ 'sample_files' ] = sample_file_metadata_paths # Copy all sample files included in the repository to a single directory location so we @@ -322,7 +372,7 @@ shed_tool_data_table_config=self.app.config.shed_tool_data_table_config, persist=False ) if error_message: - invalid_file_tups.append( ( filename, error_message ) ) + self.invalid_file_tups.append( ( filename, error_message ) ) for root, dirs, files in os.walk( files_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: @@ -333,18 +383,16 @@ path_to_repository_dependencies_config = os.path.join( root, name ) metadata_dict, error_message = \ self.generate_repository_dependency_metadata( path_to_repository_dependencies_config, - metadata_dict, - updating_installed_repository=updating_installed_repository ) + metadata_dict ) if error_message: - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) # See if we have one or more READ_ME files. elif name.lower() in readme_file_names: relative_path_to_readme = self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) readme_files.append( relative_path_to_readme ) # See if we have a tool config. elif name not in self.NOT_TOOL_CONFIGS and name.endswith( '.xml' ): @@ -365,12 +413,12 @@ is_tool = element_tree_root.tag == 'tool' if is_tool: tool, valid, error_message = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: if not valid: invalid_tool_configs.append( name ) - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) else: invalid_files_and_errors_tups = \ tv.check_tool_input_params( files_dir, @@ -387,17 +435,15 @@ relative_path_to_tool_config = \ self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) metadata_dict = self.generate_tool_metadata( relative_path_to_tool_config, tool, - repository_clone_url, metadata_dict ) else: for tup in invalid_files_and_errors_tups: - invalid_file_tups.append( tup ) + self.invalid_file_tups.append( tup ) # Find all exported workflows. elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) @@ -421,11 +467,10 @@ metadata_dict ) # Handle any data manager entries data_manager_config = hg_util.get_config_from_disk( suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir ) - metadata_dict = self.generate_data_manager_metadata( repository, - files_dir, + metadata_dict = self.generate_data_manager_metadata( files_dir, data_manager_config, metadata_dict, - shed_config_dict=shed_config_dict ) + shed_config_dict=self.shed_config_dict ) if readme_files: metadata_dict[ 'readme_files' ] = readme_files @@ -433,21 +478,18 @@ tool_dependencies_config = hg_util.get_config_from_disk( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, files_dir ) if tool_dependencies_config: metadata_dict, error_message = \ - self.generate_tool_dependency_metadata( repository, - changeset_revision, - repository_clone_url, - tool_dependencies_config, + self.generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict, original_repository_metadata=original_repository_metadata ) if error_message: - invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) + self.invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs + self.metadata_dict = metadata_dict # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. self.app.config.tool_data_path = original_tool_data_path self.app.config.tool_data_table_config_path = original_tool_data_table_config_path basic_util.remove_dir( work_dir ) - return metadata_dict, invalid_file_tups def generate_package_dependency_metadata( self, elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict ): """ @@ -475,8 +517,7 @@ # where a tool dependency definition is considered invalid. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=False ) + only_if_compiling_contained_td=False ) elif sub_elem.tag == 'install': package_install_version = sub_elem.get( 'version', '1.0' ) if package_install_version == '1.0': @@ -509,8 +550,7 @@ # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) elif action_elem.tag == 'action': # <action type="set_environment_for_install"> # <repository changeset_revision="b107b91b3574" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://localhost:9009"> @@ -522,8 +562,7 @@ # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) if requirements_dict: dependency_key = '%s/%s' % ( package_name, package_version ) if repository_dependency_is_valid: @@ -538,8 +577,7 @@ repository_dependency_is_valid, \ error_message - def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict, - updating_installed_repository=False ): + def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict ): """ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method is called from the tool shed as well as from Galaxy. @@ -560,8 +598,7 @@ for repository_elem in root.findall( 'repository' ): repository_dependency_tup, repository_dependency_is_valid, err_msg = \ self.handle_repository_elem( repository_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=updating_installed_repository ) + only_if_compiling_contained_td=False ) if repository_dependency_is_valid: valid_repository_dependency_tups.append( repository_dependency_tup ) else: @@ -585,10 +622,10 @@ metadata_dict[ 'repository_dependencies' ] = valid_repository_dependencies_dict return metadata_dict, error_message - def generate_tool_metadata( self, tool_config, tool, repository_clone_url, metadata_dict ): + def generate_tool_metadata( self, tool_config, tool, metadata_dict ): """Update the received metadata_dict with changes that have been applied to the received tool.""" # Generate the guid. - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) # Handle tool.requirements. tool_requirements = [] for tool_requirement in tool.requirements: @@ -667,11 +704,10 @@ metadata_dict[ 'tools' ] = [ tool_dict ] return metadata_dict - def generate_tool_dependency_metadata( self, repository, changeset_revision, repository_clone_url, tool_dependencies_config, - metadata_dict, original_repository_metadata=None ): + def generate_tool_dependency_metadata( self, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for - at least one tool in the repository, then update the received metadata_dict with information from the + at least one tool in self.repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ error_message = '' @@ -738,7 +774,7 @@ # into a Galaxy instance, so handle changes to tool dependencies appropriately. irm = self.app.installed_repository_manager updated_tool_dependency_names, deleted_tool_dependency_names = \ - irm.handle_existing_tool_dependencies_that_changed_in_update( repository, + irm.handle_existing_tool_dependencies_that_changed_in_update( self.repository, original_valid_tool_dependencies_dict, valid_tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = valid_tool_dependencies_dict @@ -769,9 +805,14 @@ metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ] return metadata_dict - def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict, - resetting_all_metadata_on_repository ): - if resetting_all_metadata_on_repository: + def get_invalid_file_tups( self ): + return self.invalid_file_tups + + def get_metadata_dict( self ): + return self.metadata_dict + + def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict ): + if self.resetting_all_metadata_on_repository: full_path_to_file = os.path.join( root, name ) stripped_path_to_file = full_path_to_file.replace( work_dir, '' ) if stripped_path_to_file.startswith( '/' ): @@ -785,9 +826,8 @@ relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] return relative_path_to_file - def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None, - resetting_all_metadata_on_repository=False ): - if resetting_all_metadata_on_repository: + def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None ): + if self.resetting_all_metadata_on_repository: # Keep track of the location where the repository is temporarily cloned so that we can strip # it when setting metadata. work_dir = repository_files_dir @@ -797,7 +837,7 @@ if root.find( '.hg' ) < 0: for name in files: if name.endswith( '.sample' ): - if resetting_all_metadata_on_repository: + if self.resetting_all_metadata_on_repository: full_path_to_sample_file = os.path.join( root, name ) stripped_path_to_sample_file = full_path_to_sample_file.replace( work_dir, '' ) if stripped_path_to_sample_file.startswith( '/' ): @@ -816,7 +856,7 @@ sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths - def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False, updating_installed_repository=False ): + def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False ): """ Process the received repository_elem which is a <repository> tag either from a repository_dependencies.xml file or a tool_dependencies.xml file. If the former, @@ -832,7 +872,7 @@ changeset_revision = repository_elem.get( 'changeset_revision', None ) prior_installation_required = str( repository_elem.get( 'prior_installation_required', False ) ) if self.app.name == 'galaxy': - if updating_installed_repository: + if self.updating_installed_repository: pass else: # We're installing a repository into Galaxy, so make sure its contained repository @@ -889,12 +929,12 @@ updated_changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed # repository, so it will not yet be installed. Return the tuple for later # installation. return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed repository, # so it will not yet be installed. Return the tuple for later installation. return repository_dependency_tup, is_valid, error_message @@ -1006,6 +1046,46 @@ return False return True + def set_changeset_revision( self, changeset_revision ): + self.changeset_revision = changeset_revision + + def set_relative_install_dir( self, relative_install_dir ): + self.relative_install_dir = relative_install_dir + + def set_repository( self, repository, relative_install_dir=None, changeset_revision=None ): + self.repository = repository + # Shed related tool panel configs are only relevant to Galaxy. + if self.app.name == 'galaxy': + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.changeset_revision ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = repository.get_shed_config_dict( self.app ) + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + if relative_install_dir is None and self.repository is not None: + relative_install_dir = repository.repo_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.tip( self.app ) ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = {} + self.metadata_dict = {} + self.set_relative_install_dir( relative_install_dir ) + self.set_repository_files_dir() + self.resetting_all_metadata_on_repository = False + self.updating_installed_repository = False + self.persist = False + self.invalid_file_tups = [] + + def set_repository_clone_url( self, repository_clone_url ): + self.repository_clone_url = repository_clone_url + + def set_repository_files_dir( self, repository_files_dir=None ): + self.repository_files_dir = repository_files_dir + def update_repository_dependencies_metadata( self, metadata, repository_dependency_tups, is_valid, description ): if is_valid: repository_dependencies_dict = metadata.get( 'repository_dependencies', None ) diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c lib/tool_shed/metadata/repository_metadata_manager.py --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -22,8 +22,16 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, user ): - super( RepositoryMetadataManager, self ).__init__( app ) + def __init__( self, app, user, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( RepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=user ) self.app = app self.user = user # Repository metadata comparisons for changeset revisions. @@ -62,7 +70,7 @@ repositories_select_field.add_option( option_label, option_value ) return repositories_select_field - def clean_repository_metadata( self, id, changeset_revisions ): + def clean_repository_metadata( self, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have # a changeset_revision that is not in changeset_revisions. We sometimes see multiple # records with the same changeset revision value - no idea how this happens. We'll @@ -71,7 +79,7 @@ changeset_revisions_checked = [] for repository_metadata in \ self.sa_session.query( self.app.model.RepositoryMetadata ) \ - .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.app.security.decode_id( id ) ) \ + .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.repository.id ) \ .order_by( self.app.model.RepositoryMetadata.table.c.changeset_revision, self.app.model.RepositoryMetadata.table.c.update_time.desc() ): changeset_revision = repository_metadata.changeset_revision @@ -79,15 +87,14 @@ self.sa_session.delete( repository_metadata ) self.sa_session.flush() - def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, - current_changeset_revision, current_metadata_dict ): + def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict ): """ Compare the contents of two changeset revisions to determine if a new repository metadata revision should be created. """ # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. - # This changeset_revision is an ancestor of current_changeset_revision which is associated - # with current_metadata_dict. A new repository_metadata record will be created only + # This changeset_revision is an ancestor of self.changeset_revision which is associated + # with self.metadata_dict. A new repository_metadata record will be created only # when this method returns the constant value self.NOT_EQUAL_AND_NOT_SUBSET. ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] ) ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) @@ -99,16 +106,16 @@ ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', {} ) ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] ) ancestor_data_manager = ancestor_metadata_dict.get( 'data_manager', {} ) - current_datatypes = current_metadata_dict.get( 'datatypes', [] ) - current_tools = current_metadata_dict.get( 'tools', [] ) + current_datatypes = self.metadata_dict.get( 'datatypes', [] ) + current_tools = self.metadata_dict.get( 'tools', [] ) current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ] current_guids.sort() - current_readme_files = current_metadata_dict.get( 'readme_files', [] ) - current_repository_dependencies_dict = current_metadata_dict.get( 'repository_dependencies', {} ) + current_readme_files = self.metadata_dict.get( 'readme_files', [] ) + current_repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) current_repository_dependencies = current_repository_dependencies_dict.get( 'repository_dependencies', [] ) - current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', {} ) - current_workflows = current_metadata_dict.get( 'workflows', [] ) - current_data_manager = current_metadata_dict.get( 'data_manager', {} ) + current_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', {} ) + current_workflows = self.metadata_dict.get( 'workflows', [] ) + current_data_manager = self.metadata_dict.get( 'data_manager', {} ) # Handle case where no metadata exists for either changeset. no_datatypes = not ancestor_datatypes and not current_datatypes no_readme_files = not ancestor_readme_files and not current_readme_files @@ -334,7 +341,7 @@ return self.SUBSET return self.NOT_EQUAL_AND_NOT_SUBSET - def create_or_update_repository_metadata( self, id, repository, changeset_revision, metadata_dict ): + def create_or_update_repository_metadata( self, changeset_revision, metadata_dict ): """Create or update a repository_metadatqa record in the tool shed.""" has_repository_dependencies = False has_repository_dependencies_only_if_compiling_contained_td = False @@ -364,7 +371,9 @@ downloadable = True else: downloadable = False - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.app.security.encode_id( self.repository.id ), + changeset_revision ) if repository_metadata: # A repository metadata record already exists with the received changeset_revision, # so we don't need to check the skip_tool_test table. @@ -381,7 +390,7 @@ # need to update the skip_tool_test table. check_skip_tool_test = True repository_metadata = \ - self.app.model.RepositoryMetadata( repository_id=repository.id, + self.app.model.RepositoryMetadata( repository_id=self.repository.id, changeset_revision=changeset_revision, metadata=metadata_dict, downloadable=downloadable, @@ -407,7 +416,7 @@ # if it is contained in the skip_tool_test table. If it is, but is not associated # with a repository_metadata record, reset that skip_tool_test record to the newly # created repository_metadata record. - repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) + repo = hg_util.get_repo_for_repository( self.app, repository=self.repository, repo_path=None, create=False ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) skip_tool_test = self.get_skip_tool_test_by_changeset_revision( changeset_hash ) @@ -531,16 +540,16 @@ .filter( self.app.model.SkipToolTest.table.c.initial_changeset_revision == changeset_revision ) \ .first() - def new_datatypes_metadata_required( self, repository_metadata, metadata_dict ): + def new_datatypes_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each datatype in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if - the last saved metadata record can be updated for datatypes instead. + in self.metadata_dict to determine if a new repository_metadata table record is required + or if the last saved metadata record can be updated for datatypes instead. """ # Datatypes are stored in metadata as a list of dictionaries that looks like: # [{'dtype': 'galaxy.datatypes.data:Text', 'subclass': 'True', 'extension': 'acedb'}] - if 'datatypes' in metadata_dict: - current_datatypes = metadata_dict[ 'datatypes' ] + if 'datatypes' in self.metadata_dict: + current_datatypes = self.metadata_dict[ 'datatypes' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -564,37 +573,31 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for datatypes, so a new repository_metadata + # self.metadata_dict includes no metadata for datatypes, so a new repository_metadata # table record is not needed. return False - def new_metadata_required_for_utilities( self, repository, new_tip_metadata_dict ): + def new_metadata_required_for_utilities( self ): """ - Galaxy utilities currently consist of datatypes, repository_dependency definitions, - tools, tool_dependency definitions and exported Galaxy workflows. This method compares - the last stored repository_metadata record associated with the received repository against - the contents of the received new_tip_metadata_dict and returns True or False for the union - set of Galaxy utilities contained in both metadata dictionaries. The metadata contained - in new_tip_metadata_dict may not be a subset of that contained in the last stored - repository_metadata record associated with the received repository because one or more - Galaxy utilities may have been deleted from the repository in the new tip. + This method compares the last stored repository_metadata record associated with self.repository + against the contents of self.metadata_dict and returns True or False for the union set of Galaxy + utilities contained in both metadata dictionaries. The metadata contained in self.metadata_dict + may not be a subset of that contained in the last stored repository_metadata record associated with + self.repository because one or more Galaxy utilities may have been deleted from self.repository in + the new tip. """ repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) - datatypes_required = self.new_datatypes_metadata_required( repository_metadata, - new_tip_metadata_dict ) + datatypes_required = self.new_datatypes_metadata_required( repository_metadata ) # Uncomment the following if we decide that README files should affect how installable # repository revisions are defined. See the NOTE in the compare_readme_files() method. - # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata, - # new_tip_metadata_dict ) + # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata ) repository_dependencies_required = \ - self.new_repository_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - tools_required = self.new_tool_metadata_required( repository_metadata, new_tip_metadata_dict ) - tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - workflows_required = self.new_workflow_metadata_required( repository_metadata, new_tip_metadata_dict ) + self.new_repository_dependency_metadata_required( repository_metadata ) + tools_required = self.new_tool_metadata_required( repository_metadata ) + tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata ) + workflows_required = self.new_workflow_metadata_required( repository_metadata ) if datatypes_required or \ repository_dependencies_required or \ tools_required or \ @@ -603,17 +606,17 @@ return True return False - def new_readme_files_metadata_required( self, repository_metadata, metadata_dict ): + def new_readme_files_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each readme file in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if the - last saved metadata record can be updated for readme files instead. + in self.metadata_dict to determine if a new repository_metadata table record is required or + if the last saved metadata record can be updated for readme files instead. """ # Repository README files are kind of a special case because they have no effect on reproducibility. # We'll simply inspect the file names to determine if any that exist in the saved metadata are - # eliminated from the new metadata in the received metadata_dict. - if 'readme_files' in metadata_dict: - current_readme_files = metadata_dict[ 'readme_files' ] + # eliminated from the new metadata in self.metadata_dict. + if 'readme_files' in self.metadata_dict: + current_readme_files = self.metadata_dict[ 'readme_files' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -638,14 +641,14 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for readme_files, so a new repository_metadata + # self.metadata_dict includes no metadata for readme_files, so a new repository_metadata # table record is not needed. return False - def new_repository_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_repository_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each repository dependency in the repository - with the new metadata in metadata_dict to determine if a new repository_metadata + with the new metadata in self.metadata_dict to determine if a new repository_metadata table record is required or if the last saved metadata record can be updated for repository_dependencies instead. """ @@ -653,9 +656,9 @@ metadata = repository_metadata.metadata if 'repository_dependencies' in metadata: saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] - new_repository_dependencies_metadata = metadata_dict.get( 'repository_dependencies', None ) + new_repository_dependencies_metadata = self.metadata_dict.get( 'repository_dependencies', None ) if new_repository_dependencies_metadata: - new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] + new_repository_dependencies = self.metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] # TODO: We used to include the following here to handle the case where repository # dependency definitions were deleted. However this erroneously returned True in # cases where is should not have done so. This usually occurred where multiple single @@ -682,21 +685,21 @@ else: return False else: - if 'repository_dependencies' in metadata_dict: + if 'repository_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata record. return True else: - # The received metadata_dict includes no metadata for repository dependencies, so - # a new repository_metadata record is not needed. + # self.metadata_dict includes no metadata for repository dependencies, so a new repository_metadata + # record is not needed. return False - def new_tool_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool in the repository with the new metadata in - metadata_dict to determine if a new repository_metadata table record is required, or if + self.metadata_dict to determine if a new repository_metadata table record is required, or if the last saved metadata record can be updated instead. """ - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -704,9 +707,9 @@ saved_tool_ids = [] # The metadata for one or more tools was successfully generated in the past # for this repository, so we first compare the version string for each tool id - # in metadata_dict with what was previously saved to see if we need to create + # in self.metadata_dict with what was previously saved to see if we need to create # a new table record or if we can simply update the existing record. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: for saved_tool_metadata_dict in metadata[ 'tools' ]: if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids: saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] ) @@ -714,10 +717,10 @@ if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: return True # So far, a new metadata record is not required, but we still have to check to see if - # any new tool ids exist in metadata_dict that are not in the saved metadata. We do + # any new tool ids exist in self.metadata_dict that are not in the saved metadata. We do # this because if a new tarball was uploaded to a repository that included tools, it # may have removed existing tool files if they were not included in the uploaded tarball. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: return True return False @@ -733,22 +736,22 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for tools, so a new repository_metadata table + # self.metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False - def new_tool_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool dependency in the repository with the new - metadata in metadata_dict to determine if a new repository_metadata table record is required - or if the last saved metadata record can be updated for tool_dependencies instead. + metadata in self.metadata_dict to determine if a new repository_metadata table record is + required or if the last saved metadata record can be updated for tool_dependencies instead. """ if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tool_dependencies' in metadata: saved_tool_dependencies = metadata[ 'tool_dependencies' ] - new_tool_dependencies = metadata_dict.get( 'tool_dependencies', None ) + new_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', None ) if new_tool_dependencies: # TODO: We used to include the following here to handle the case where # tool dependency definitions were deleted. However, this erroneously @@ -777,22 +780,22 @@ # in the repository, so we can update the existing repository metadata. return False else: - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata # record. return True else: - # The received metadata_dict includes no metadata for tool dependencies, so a new - # repository_metadata record is not needed. + # self.metadata_dict includes no metadata for tool dependencies, so a new repository_metadata + # record is not needed. return False - def new_workflow_metadata_required( self, repository_metadata, metadata_dict ): + def new_workflow_metadata_required( self, repository_metadata ): """ Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of exported workflows. If this changes at some future time, this method should be enhanced accordingly. """ - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: if repository_metadata: # The repository has metadata, so update the workflows value - # no new record is needed. @@ -801,17 +804,17 @@ # There is no saved repository metadata, so we need to create a # new repository_metadata table record. return True - # The received metadata_dict includes no metadata for workflows, so a new + # self.metadata_dict includes no metadata for workflows, so a new # repository_metadata table record is not needed. return False - def reset_all_metadata_on_repository_in_tool_shed( self, id ): + def reset_all_metadata_on_repository_in_tool_shed( self ): """Reset all metadata on a single repository in a tool shed.""" - repository = suc.get_repository_in_tool_shed( self.app, id ) - log.debug( "Resetting all metadata on repository: %s" % repository.name ) - repo_dir = repository.repo_path( self.app ) - repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) + log.debug( "Resetting all metadata on repository: %s" % self.repository.name ) + repo = hg_util.get_repo_for_repository( self.app, + repository=None, + repo_path=self.repository.repo_path( self.app ), + create=False ) # The list of changeset_revisions refers to repository_metadata records that have been created # or updated. When the following loop completes, we'll delete all repository_metadata records # for this repository that do not have a changeset_revision value in this list. @@ -822,33 +825,22 @@ metadata_dict = None ancestor_changeset_revision = None ancestor_metadata_dict = None - invalid_file_tups = [] - for changeset in repository.get_changesets_for_setting_metadata( self.app ): + for changeset in self.repository.get_changesets_for_setting_metadata( self.app ): work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ramorits" ) - current_changeset_revision = str( repo.changectx( changeset ) ) ctx = repo.changectx( changeset ) log.debug( "Cloning repository changeset revision: %s", str( ctx.rev() ) ) - cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) + cloned_ok, error_message = hg_util.clone_repository( self.repository_clone_url, work_dir, str( ctx.rev() ) ) if cloned_ok: log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) - current_metadata_dict, invalid_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=current_changeset_revision, - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=work_dir, - resetting_all_metadata_on_repository=True, - updating_installed_repository=False, - persist=False ) - # We'll only display error messages for the repository tip (it may be better to display error - # messages for each installable changeset revision). - if current_changeset_revision == repository.tip( self.app ): - invalid_file_tups.extend( invalid_tups ) - if current_metadata_dict: + self.set_changeset_revision( str( repo.changectx( changeset ) ) ) + self.set_relative_install_dir( work_dir ) + self.set_repository_files_dir( work_dir ) + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: if metadata_changeset_revision is None and metadata_dict is None: # We're at the first change set in the change log. - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict if ancestor_changeset_revision: # Compare metadata from ancestor and current. The value of comparison will be one of: # self.NO_METADATA - no metadata for either ancestor or current, so continue from current @@ -856,66 +848,56 @@ # self.SUBSET - ancestor metadata is a subset of current metadata, so continue from current # self.NOT_EQUAL_AND_NOT_SUBSET - ancestor metadata is neither equal to nor a subset of current # metadata, so persist ancestor metadata. - comparison = self.compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) + comparison = self.compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict ) if comparison in [ self.NO_METADATA, self.EQUAL, self.SUBSET ]: - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict elif comparison == self.NOT_EQUAL_AND_NOT_SUBSET: metadata_changeset_revision = ancestor_changeset_revision metadata_dict = ancestor_metadata_dict - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict else: # We're at the beginning of the change log. - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict if not ctx.children(): - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None elif ancestor_metadata_dict: - # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + # We reach here only if self.metadata_dict is empty and ancestor_metadata_dict is not. if not ctx.children(): # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None basic_util.remove_dir( work_dir ) # Delete all repository_metadata records for this repository that do not have a changeset_revision # value in changeset_revisions. - self.clean_repository_metadata( id, changeset_revisions ) + self.clean_repository_metadata( changeset_revisions ) # Set tool version information for all downloadable changeset revisions. Get the list of changeset # revisions from the changelog. - self.reset_all_tool_versions( id, repo ) + self.reset_all_tool_versions( repo ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} - return invalid_file_tups, metadata_dict - def reset_all_tool_versions( self, id, repo ): + def reset_all_tool_versions( self, repo ): """Reset tool version lineage for those changeset revisions that include valid tools.""" + encoded_repository_id = self.app.security.encode_id( self.repository.id ) changeset_revisions_that_contain_tools = [] for changeset in repo.changelog: changeset_revision = str( repo.changectx( changeset ) ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -926,7 +908,9 @@ # { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. for index, changeset_revision in enumerate( changeset_revisions_that_contain_tools ): tool_versions_dict = {} - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) metadata = repository_metadata.metadata tool_dicts = metadata[ 'tools' ] if index == 0: @@ -937,7 +921,7 @@ tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] else: for tool_dict in tool_dicts: - parent_id = self.get_parent_id( id, + parent_id = self.get_parent_id( encoded_repository_id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], @@ -962,11 +946,11 @@ for repository_id in repository_ids: try: repository = suc.get_repository_in_tool_shed( self.app, repository_id ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_repository_in_tool_shed() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) @@ -974,7 +958,7 @@ unsuccessful_count += 1 else: log.debug( "Successfully reset metadata on repository %s owned by %s" % \ - ( str( repository.name ), str( repository.user.username ) ) ) + ( str( repository.name ), str( repository.user.username ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s" % str( repository.name ) ) @@ -989,75 +973,68 @@ status = 'error' return message, status - def set_repository_metadata( self, host, repository, content_alert_str='', **kwd ): + def set_repository( self, repository ): + super( RepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) + + def set_repository_metadata( self, host, content_alert_str='', **kwd ): """ - Set metadata using the repository's current disk files, returning specific error + Set metadata using the self.repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. """ message = '' status = 'done' - encoded_id = self.app.security.encode_id( repository.id ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) - repo_dir = repository.repo_path( self.app ) + encoded_id = self.app.security.encode_id( self.repository.id ) + repo_dir = self.repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.tip( self.app ), - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - if metadata_dict: + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: repository_metadata = None - repository_type_class = self.app.repository_types_registry.get_class_by_label( repository.type ) + repository_type_class = self.app.repository_types_registry.get_class_by_label( self.repository.type ) tip_only = isinstance( repository_type_class, TipOnly ) - if not tip_only and self.new_metadata_required_for_utilities( repository, metadata_dict ): + if not tip_only and self.new_metadata_required_for_utilities(): # Create a new repository_metadata table row. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: + if len( self.repository.downloadable_revisions ) == 1: suc.handle_email_alerts( self.app, host, - repository, + self.repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: - # Update the latest stored repository metadata with the contents and attributes of metadata_dict. + # Update the latest stored repository metadata with the contents and attributes of self.metadata_dict. repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) if repository_metadata: - downloadable = metadata_util.is_downloadable( metadata_dict ) + downloadable = metadata_util.is_downloadable( self.metadata_dict ) # Update the last saved repository_metadata table row. - repository_metadata.changeset_revision = repository.tip( self.app ) - repository_metadata.metadata = metadata_dict + repository_metadata.changeset_revision = self.repository.tip( self.app ) + repository_metadata.metadata = self.metadata_dict repository_metadata.downloadable = downloadable - if 'datatypes' in metadata_dict: + if 'datatypes' in self.metadata_dict: repository_metadata.includes_datatypes = True else: repository_metadata.includes_datatypes = False # We don't store information about the special type of repository dependency that is needed only for # compiling a tool dependency defined for the dependent repository. - repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ suc.get_repository_dependency_types( repository_dependencies ) repository_metadata.has_repository_dependencies = has_repository_dependencies - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: repository_metadata.includes_tool_dependencies = True else: repository_metadata.includes_tool_dependencies = False - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: repository_metadata.includes_tools = True else: repository_metadata.includes_tools = False - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: repository_metadata.includes_workflows = True else: repository_metadata.includes_workflows = False @@ -1070,11 +1047,9 @@ self.sa_session.flush() else: # There are no metadata records associated with the repository. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) - if 'tools' in metadata_dict and repository_metadata and status != 'error': + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) + if 'tools' in self.metadata_dict and repository_metadata and status != 'error': # Set tool versions on the new downloadable change set. The order of the list of changesets is # critical, so we use the repo's changelog. changeset_revisions = [] @@ -1083,25 +1058,22 @@ if suc.get_repository_metadata_by_changeset_revision( self.app, encoded_id, changeset_revision ): changeset_revisions.append( changeset_revision ) self.add_tool_versions( encoded_id, repository_metadata, changeset_revisions ) - elif len( repo ) == 1 and not invalid_file_tups: + elif len( repo ) == 1 and not self.invalid_file_tups: message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % \ - str( repository.tip( self.app ) ) + str( self.repository.tip( self.app ) ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" - if invalid_file_tups: + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, - repository, - metadata_dict ) + self.invalid_file_tups, + self.repository, + self.metadata_dict ) status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} return message, status - def set_repository_metadata_due_to_new_tip( self, host, repository, content_alert_str=None, **kwd ): - """Set metadata on the repository tip in the tool shed.""" - error_message, status = self.set_repository_metadata( host, - repository, - content_alert_str=content_alert_str, - **kwd ) + def set_repository_metadata_due_to_new_tip( self, host, content_alert_str=None, **kwd ): + """Set metadata on the tip of self.repository in the tool shed.""" + error_message, status = self.set_repository_metadata( host, content_alert_str=content_alert_str, **kwd ) return status, error_message diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c run_galaxy_listener.sh --- a/run_galaxy_listener.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0` -python scripts/galaxy_messaging/server/amqp_consumer.py --config-file=universe_wsgi.ini --http-server-section=server:main 2>&1 \ No newline at end of file diff -r aeca0d388e83f87ca74bbbb093746b2f74f93b86 -r 14d243c7069ea33df70635bb4208b39970db951c scripts/cleanup_datasets/delete_datasets_main.sh --- a/scripts/cleanup_datasets/delete_datasets_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -6 -r $@ >> ./scripts/cleanup_datasets/delete_datasets.log This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/87a5903ec2c4/ Changeset: 87a5903ec2c4 User: natefoo Date: 2014-09-16 04:12:18 Summary: Don't create galaxy.ini, just use the sample if galaxy.ini does not exist. Also fix startup when galaxy.ini.sample. Fixes the universe_wsgi.ini skipping problem Dannon found. Affected #: 4 files diff -r 14d243c7069ea33df70635bb4208b39970db951c -r 87a5903ec2c4fafbee4b75c903de6ab594f91384 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -408,7 +408,6 @@ break else: path = defaults[-1] - print( "Using config '%s' at: %s" % ( var, path ) ) setattr( self, var, resolve_path( path, self.root ) ) for var, defaults in listify_defaults.items(): @@ -425,7 +424,6 @@ break else: paths = listify( defaults[-1] ) - print( "Using config '%s' at: %s" % ( var, ', '.join( paths ) ) ) setattr( self, var, [ resolve_path( x, self.root ) for x in paths ] ) # Backwards compatibility for names used in too many places to fix diff -r 14d243c7069ea33df70635bb4208b39970db951c -r 87a5903ec2c4fafbee4b75c903de6ab594f91384 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -17,12 +17,12 @@ } -CONFIG_FILE=config/galaxy.ini -if [ ! -f $CONFIG_FILE ]; then - CONFIG_FILE=universe_wsgi.ini +GALAXY_CONFIG_FILE=config/galaxy.ini +if [ ! -f $GALAXY_CONFIG_FILE ]; then + GALAXY_CONFIG_FILE=universe_wsgi.ini fi -servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $CONFIG_FILE | xargs echo` +servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` for server in $servers; do # If there's a pid @@ -37,7 +37,7 @@ echo "$server not running" fi # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve $CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ # Wait for the server to start sleep 1 # Grab the new pid diff -r 14d243c7069ea33df70635bb4208b39970db951c -r 87a5903ec2c4fafbee4b75c903de6ab594f91384 run.sh --- a/run.sh +++ b/run.sh @@ -18,13 +18,19 @@ python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" fi -CONFIG_FILE=config/galaxy.ini -if [ ! -f $CONFIG_FILE ]; then - CONFIG_FILE=universe_wsgi.ini +if [ -z "$GALAXY_CONFIG_FILE" ]; then + if [ -f universe_wsgi.ini ]; then + GALAXY_CONFIG_FILE=universe_wsgi.ini + elif [ -f config/galaxy.ini ]; then + GALAXY_CONFIG_FILE=universe_wsgi.ini + else + GALAXY_CONFIG_FILE=config/galaxy.ini.sample + fi + export GALAXY_CONFIG_FILE fi if [ -n "$GALAXY_RUN_ALL" ]; then - servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $CONFIG_FILE | xargs echo` + servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` daemon=`echo "$@" | grep -q daemon` if [ $? -ne 0 ]; then echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon` or `--stop-daemon` arguments to run.sh' @@ -32,8 +38,8 @@ fi for server in $servers; do echo "Handling $server with log file $server.log..." - python ./scripts/paster.py serve $CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ done else - python ./scripts/paster.py serve $CONFIG_FILE $@ + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE $@ fi diff -r 14d243c7069ea33df70635bb4208b39970db951c -r 87a5903ec2c4fafbee4b75c903de6ab594f91384 scripts/common_startup.sh --- a/scripts/common_startup.sh +++ b/scripts/common_startup.sh @@ -10,7 +10,6 @@ done SAMPLES=" - config/galaxy.ini.sample config/migrated_tools_conf.xml.sample config/shed_tool_conf.xml.sample config/shed_tool_data_table_conf.xml.sample @@ -35,11 +34,13 @@ done fi +: ${GALAXY_CONFIG_FILE:=config/galaxy.ini.sample} + if [ $FETCH_EGGS -eq 1 ]; then - python ./scripts/check_eggs.py -q + python ./scripts/check_eggs.py -q -c $GALAXY_CONFIG_FILE if [ $? -ne 0 ]; then echo "Some eggs are out of date, attempting to fetch..." - python ./scripts/fetch_eggs.py + python ./scripts/fetch_eggs.py -c $GALAXY_CONFIG_FILE if [ $? -eq 0 ]; then echo "Fetch successful." else https://bitbucket.org/galaxy/galaxy-central/commits/5f90a490e997/ Changeset: 5f90a490e997 User: dannon Date: 2014-09-16 15:08:35 Summary: Merged in natefoo/galaxy-central (pull request #495) Clean up the root directory and rename universe_wsgi.ini Affected #: 116 files diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd README.txt --- a/README.txt +++ b/README.txt @@ -22,13 +22,13 @@ http://localhost:8080 You may wish to make changes from the default configuration. This can be done -in the universe_wsgi.ini file. Tools can be either installed from the Tool Shed +in the config/galaxy.ini file. Tools can be either installed from the Tool Shed or added manually. For details please see the Galaxy wiki: -https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial. +https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial Not all dependencies are included for the tools provided in the sample tool_conf.xml. A full list of external dependencies is available at: -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies \ No newline at end of file +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -43,15 +43,10 @@ " SAMPLES=" -tool_conf.xml.sample -datatypes_conf.xml.sample -universe_wsgi.ini.sample -tool_data_table_conf.xml.sample -tool_sheds_conf.xml.sample -shed_tool_data_table_conf.xml.sample -migrated_tools_conf.xml.sample -data_manager_conf.xml.sample -shed_data_manager_conf.xml.sample +config/galaxy.ini.sample +config/shed_tool_data_table_conf.xml.sample +config/migrated_tools_conf.xml.sample +config/shed_data_manager_conf.xml.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/shared/ucsc/builds.txt.sample diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/data_manager_conf.xml.sample --- /dev/null +++ b/config/data_manager_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<data_managers> +</data_managers> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/datatypes_conf.xml.sample --- /dev/null +++ b/config/datatypes_conf.xml.sample @@ -0,0 +1,333 @@ +<?xml version="1.0"?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Ab1"/> + <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false" /> + <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true" /> + <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true" /> + <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/> + <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/> + <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM"> + <converter file="bam_to_bai.xml" target_datatype="bai"/> + <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="ucsc/bam.xml" /> + <display file="ensembl/ensembl_bam.xml" /> + <display file="igv/bam.xml" /> + <display file="igb/bam.xml" /> + </datatype> + <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed"> + <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> + <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="bed_to_fli_converter.xml" target_datatype="fli"/> +  + <display file="igb/bed.xml" /> + </datatype> + <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> + <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/bedgraph.xml" /> + </datatype> + <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /> + <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> + </datatype> + <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /> + <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> + <converter file="len_to_linecount.xml" target_datatype="linecount" /> + </datatype> + <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigbed.xml" /> + <display file="igb/bb.xml" /> + </datatype> + <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigwig.xml" /> + <display file="igb/bigwig.xml" /> + </datatype> + <datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> +  + <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> +  + <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/> + <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/> + <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" /> + <datatype extension="data_manager_json" type="galaxy.datatypes.data:Text" mimetype="application/json" subclass="True" display_in_upload="False"/> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" description="A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('>') symbol in the first column. All lines should be shorter than 80 characters." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fasta"> + <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/> + <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/> + <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/> + <converter file="fasta_to_2bit.xml" target_datatype="twobit"/> + <converter file="fasta_to_len.xml" target_datatype="len"/> + </datatype> + <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/> + <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/> + <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/> + <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> +  + </datatype> + <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true" description="GFF lines have nine required fields that must be tab-separated." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF"> + <converter file="gff_to_bed_converter.xml" target_datatype="bed"/> + <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="gff_to_fli_converter.xml" target_datatype="fli"/> + <display file="ensembl/ensembl_gff.xml" inherit="True"/> +  + </datatype> + <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true" description="The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF3"/> + <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/> + <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/> + <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"> + <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /> + </datatype> + <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> + <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> + <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/> + <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order)." > + <converter file="interval_to_bed_converter.xml" target_datatype="bed"/> + <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/> + <converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/> + <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/> +  + <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/> + <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/> + <display file="rviewer/bed.xml" inherit="True"/> + </datatype> + <datatype extension="picard_interval_list" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"> + <converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/> + </datatype> + <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_report" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/> + <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/> + <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/> + <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/> + <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/> + <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/> + <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/> + <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/> + <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/> + <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/> + <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/> + <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/> + <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/> + <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/> + <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/> + <datatype extension="laj" type="galaxy.datatypes.images:Laj"/> + <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true" description="Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.." /> + <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true" description="TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated 'variable=value' pairs. There should be no white space surrounding the '='." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#MAF"> + <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/> + <converter file="maf_to_interval_converter.xml" target_datatype="interval"/> + </datatype> + <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack"> + <display file="ucsc/maf_customtrack.xml" /> + </datatype> + <datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True"> + <converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> + <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/> + <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + </datatype> + <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/> + <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> + <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> + <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/> + <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/> + <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/> + <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/> + <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"> + <converter file="sam_to_bam.xml" target_datatype="bam"/> + <converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> + <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/> + <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/> + <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/> + <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/> + <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/> + <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/> + <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/> + <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"> + <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/> + <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="ucsc/vcf.xml" /> + <display file="igv/vcf.xml" /> + <display file="rviewer/vcf.xml" inherit="True"/> + </datatype> + <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True"/> + <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> + <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true" description="The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Wig"> + <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/> +  + <display file="igb/wig.xml" /> + </datatype> + <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="vcf_bgzip" type_extension="bgzip" subclass="True" > + <display file="igv/vcf.xml" /> + <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/> + </datatype> +  + <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" /> + <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" /> + <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /> +  + <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> +  + <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/> +  + <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/> + <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" /> +  + <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/> +  + <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/> +  + <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/> +  +  + <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true"> + </datatype> + <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/> +  + <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"> + <converter file="lped_to_fped_converter.xml" target_datatype="fped"/> + <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/> + </datatype> +  + <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"> + <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/> + <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/> + </datatype> + <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/> +  + <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/> + <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/> + <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/> + <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/> + <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/> + <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/> +  +  + <datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/> + <datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/> + <datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/> + </registration> + <sniffers> +  + <sniffer type="galaxy.datatypes.tabular:Vcf"/> + <sniffer type="galaxy.datatypes.binary:TwoBit"/> + <sniffer type="galaxy.datatypes.binary:SQlite"/> + <sniffer type="galaxy.datatypes.binary:Bam"/> + <sniffer type="galaxy.datatypes.binary:Sff"/> + <sniffer type="galaxy.datatypes.xml:Phyloxml"/> + <sniffer type="galaxy.datatypes.xml:GenericXml"/> + <sniffer type="galaxy.datatypes.sequence:Maf"/> + <sniffer type="galaxy.datatypes.sequence:Lav"/> + <sniffer type="galaxy.datatypes.sequence:csFasta"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> + <sniffer type="galaxy.datatypes.sequence:Fasta"/> + <sniffer type="galaxy.datatypes.sequence:Fastq"/> + <sniffer type="galaxy.datatypes.interval:Wiggle"/> + <sniffer type="galaxy.datatypes.images:Html"/> + <sniffer type="galaxy.datatypes.images:Pdf"/> + <sniffer type="galaxy.datatypes.sequence:Axt"/> + <sniffer type="galaxy.datatypes.interval:Bed"/> + <sniffer type="galaxy.datatypes.interval:CustomTrack"/> + <sniffer type="galaxy.datatypes.interval:Gtf"/> + <sniffer type="galaxy.datatypes.interval:Gff"/> + <sniffer type="galaxy.datatypes.interval:Gff3"/> + <sniffer type="galaxy.datatypes.tabular:Pileup"/> + <sniffer type="galaxy.datatypes.interval:Interval"/> + <sniffer type="galaxy.datatypes.tabular:Sam"/> + <sniffer type="galaxy.datatypes.data:Newick"/> + <sniffer type="galaxy.datatypes.data:Nexus"/> + <sniffer type="galaxy.datatypes.images:Jpg"/> + <sniffer type="galaxy.datatypes.images:Png"/> + <sniffer type="galaxy.datatypes.images:Tiff"/> + <sniffer type="galaxy.datatypes.images:Bmp"/> + <sniffer type="galaxy.datatypes.images:Gif"/> + <sniffer type="galaxy.datatypes.images:Im"/> + <sniffer type="galaxy.datatypes.images:Pcd"/> + <sniffer type="galaxy.datatypes.images:Pcx"/> + <sniffer type="galaxy.datatypes.images:Ppm"/> + <sniffer type="galaxy.datatypes.images:Psd"/> + <sniffer type="galaxy.datatypes.images:Xbm"/> + <sniffer type="galaxy.datatypes.images:Rgb"/> + <sniffer type="galaxy.datatypes.images:Pbm"/> + <sniffer type="galaxy.datatypes.images:Pgm"/> + <sniffer type="galaxy.datatypes.images:Xpm"/> + <sniffer type="galaxy.datatypes.images:Eps"/> + <sniffer type="galaxy.datatypes.images:Rast"/> +  + </sniffers> + <build_sites> +  + <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/> + <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/> + <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/> + <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/> + <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/> + <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/> + </build_sites> +</datatypes> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/demo_sequencer_wsgi.ini.sample --- /dev/null +++ b/config/demo_sequencer_wsgi.ini.sample @@ -0,0 +1,66 @@ +# ---- HTTP Server ---------------------------------------------------------- + +[server:main] + +use = egg:Paste#http +port = 9011 +host = 0.0.0.0 +use_threadpool = true +threadpool_workers = 10 + +# ---- Galaxy Demo Sequencer Emulator Interface ------------------------------------------------- + +[app:main] + +# Specifies the factory for the universe WSGI application +paste.app_factory = galaxy.webapps.demo_sequencer.buildapp:app_factory +log_level = DEBUG + +# Where dataset files are saved +file_path = database/demo_sequencer_files +# Temporary storage for additional datasets, this should be shared through the cluster +new_file_path = database/tmp + +# Sequencer emulator actions +sequencer_actions_config_file = %(here)s/lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml + +# Session support (beaker) +use_beaker_session = True +session_type = memory +session_data_dir = %(here)s/database/beaker_sessions +session_key = galaxysessions +session_secret = changethisinproduction + +# Galaxy session security +id_secret = changethisinproductiontoo + +# Configuration for debugging middleware +debug = true +use_lint = false + +# NEVER enable this on a public site (even test or QA) +# use_interactive = true + +# this should be a comma-separated list of valid Galaxy users +#admin_users = test(a)bx.psu.edu + +# Force everyone to log in (disable anonymous access) +require_login = False + +# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) +## use_heartbeat = True + +# Profiling middleware (cProfile based) +## use_profile = True + +# Use the new iframe / javascript based layout +use_new_layout = true + +# Serving static files (needed if running standalone) +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/external_service_types_conf.xml.sample --- /dev/null +++ b/config/external_service_types_conf.xml.sample @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<external_service_types> + <external_service_type file="simple_unknown_sequencer.xml" visible="False"/> + <external_service_type file="applied_biosystems_solid.xml" visible="True"/> +</external_service_types> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/galaxy.ini.sample --- /dev/null +++ b/config/galaxy.ini.sample @@ -0,0 +1,889 @@ +# +# Galaxy is configured by default to be useable in a single-user development +# environment. To tune the application for a multi-user production +# environment, see the documentation at: +# +# http://usegalaxy.org/production +# + +# Throughout this sample configuration file, except where stated otherwise, +# uncommented values override the default if left unset, whereas commented +# values are set to the default value. Relative paths are relative to the root +# Galaxy directory. +# +# Examples of many of these options are explained in more detail in the wiki: +# +# https://wiki.galaxyproject.org/Admin/Config +# +# Config hackers are encouraged to check there before asking for help. + +# ---- HTTP Server ---------------------------------------------------------- + +# Configuration of the internal HTTP server. + +[server:main] + +# The internal HTTP server to use. Currently only Paste is provided. This +# option is required. +use = egg:Paste#http + +# The port on which to listen. +#port = 8080 + +# The address on which to listen. By default, only listen to localhost (Galaxy +# will not be accessible over the network). Use '0.0.0.0' to listen on all +# available network interfaces. +#host = 127.0.0.1 + +# Use a threadpool for the web server instead of creating a thread for each +# request. +use_threadpool = True + +# Number of threads in the web server thread pool. +#threadpool_workers = 10 + +# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +threadpool_kill_thread_limit = 10800 + +# ---- Filters -------------------------------------------------------------- + +# Filters sit between Galaxy and the HTTP server. + +# These filters are disabled by default. They can be enabled with +# 'filter-with' in the [app:main] section below. + +# Define the gzip filter. +[filter:gzip] +use = egg:Paste#gzip + +# Define the proxy-prefix filter. +[filter:proxy-prefix] +use = egg:PasteDeploy#prefix +prefix = /galaxy + +# ---- Galaxy --------------------------------------------------------------- + +# Configuration of the Galaxy application. + +[app:main] + +# -- Application and filtering + +# The factory for the WSGI application. This should not be changed. +paste.app_factory = galaxy.web.buildapp:app_factory + +# If not running behind a proxy server, you may want to enable gzip compression +# to decrease the size of data transferred over the network. If using a proxy +# server, please enable gzip compression there instead. +#filter-with = gzip + +# If running behind a proxy server and Galaxy is served from a subdirectory, +# enable the proxy-prefix filter and set the prefix in the +# [filter:proxy-prefix] section above. +#filter-with = proxy-prefix + +# If proxy-prefix is enabled and you're running more than one Galaxy instance +# behind one hostname, you will want to set this to the same path as the prefix +# in the filter above. This value becomes the "path" attribute set in the +# cookie so the cookies from each instance will not clobber each other. +#cookie_path = None + +# -- Database + +# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You +# may use a SQLAlchemy connection string to specify an external database +# instead. This string takes many options which are explained in detail in the +# config file documentation. +#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# If the server logs errors about not having enough database pool connections, +# you will want to increase these values, or consider running more Galaxy +# processes. +#database_engine_option_pool_size = 5 +#database_engine_option_max_overflow = 10 + +# If using MySQL and the server logs the error "MySQL server has gone away", +# you will want to set this to some positive value (7200 should work). +#database_engine_option_pool_recycle = -1 + +# If large database query results are causing memory or response time issues in +# the Galaxy process, leave the result on the server instead. This option is +# only available for PostgreSQL and is highly recommended. +#database_engine_option_server_side_cursors = False + +# Log all database transactions, can be useful for debugging and performance +# profiling. Logging is done via Python's 'logging' module under the qualname +# 'galaxy.model.orm.logging_connection_proxy' +#database_query_profiling_proxy = False + +# By default, Galaxy will use the same database to track user data and +# tool shed install data. There are many situtations in which it is +# valuable to seperate these - for instance bootstrapping fresh Galaxy +# instances with pretested installs. The following optin can be used to +# separate the tool shed install database (all other options listed above +# but prefixed with install_ are also available). +#install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# -- Files and directories + +# Dataset files are stored in this directory. +#file_path = database/files + +# Temporary files are stored in this directory. +#new_file_path = database/tmp + +# Tool config files, defines what tools are available in Galaxy. +# Tools can be locally developed or installed from Galaxy tool sheds. +# (config/tool_conf.xml.sample will be used if left unset and +# config/tool_conf.xml does not exist). +#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml + +# Enable / disable checking if any tools defined in the above non-shed tool_config_files +# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool +# Shed. This setting should generally be set to False only for development Galaxy environments +# that are often rebuilt from scratch where migrated tools do not need to be available in the +# Galaxy tool panel. If the following setting remains commented, the default setting will be True. +#check_migrate_tools = True + +# Tool config maintained by tool migration scripts. If you use the migration +# scripts to install tools that have been migrated to the tool shed upon a new +# release, they will be added to this tool config file. +#migrated_tools_config = migrated_tools_conf.xml + +# File that contains the XML section and tool tags from all tool panel config +# files integrated into a single file that defines the tool panel layout. This +# file can be changed by the Galaxy administrator to alter the layout of the +# tool panel. If not present, Galaxy will create it. +#integrated_tool_panel_config = integrated_tool_panel.xml + +# Default path to the directory containing the tools defined in tool_conf.xml. +# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. +#tool_path = tools + +# Path to the directory in which tool dependencies are placed. This is used by +# the tool shed to install dependencies and can also be used by administrators +# to manually install or link to dependencies. For details, see: +# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies +# If this option is not set to a valid path, installing tools with dependencies +# from the Tool Shed will fail. +#tool_dependency_dir = None + +# File containing the Galaxy Tool Sheds that should be made available to +# install from in the admin interface (.sample used if default does not exist). +#tool_sheds_config_file = config/tool_sheds_conf.xml + +# Enable automatic polling of relative tool sheds to see if any updates +# are available for installed repositories. Ideally only one Galaxy +# server process should be able to check for repository updates. The +# setting for hours_between_check should be an integer between 1 and 24. +#enable_tool_shed_check = False +#hours_between_check = 12 + +# Enable use of an in-memory registry with bi-directional relationships +# between repositories (i.e., in addition to lists of dependencies for a +# repository, keep an in-memory registry of dependent items for each repository. +#manage_dependency_relationships = False + +# XML config file that contains data table entries for the +# ToolDataTableManager. This file is manually # maintained by the Galaxy +# administrator (.sample used if default does not exist). +#tool_data_table_config_path = config/tool_data_table_conf.xml + +# XML config file that contains additional data table entries for the ToolDataTableManager. This file +# is automatically generated based on the current installed tool shed repositories that contain valid +# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically +# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. +#shed_tool_data_table_config = config/shed_tool_data_table_conf.xml + +# Directory where data used by tools is located, see the samples in that +# directory and the wiki for help: +# https://wiki.galaxyproject.org/Admin/DataIntegration +#tool_data_path = tool-data + +# File containing old-style genome builds +#builds_file_path = tool-data/shared/ucsc/builds.txt + +# Directory where chrom len files are kept, currently mainly used by trackster +#len_file_path = tool-data/shared/ucsc/chrom + +# Datatypes config file, defines what data (file) types are available in +# Galaxy (.sample is used if default does not exist). +#datatypes_config_file = config/datatypes_conf.xml + +# Disable the 'Auto-detect' option for file uploads +#datatypes_disable_auto = False + +# Visualizations config directory: where to look for individual visualization plugins. +# The path is relative to the Galaxy root dir. To use an absolute path begin the path +# with '/'. Defaults to "config/plugins/visualizations". +#visualization_plugins_directory = config/plugins/visualizations + +# Each job is given a unique empty directory as its current working directory. +# This option defines in what parent directory those directories will be +# created. +#job_working_directory = database/job_working_directory + +# If using a cluster, Galaxy will write job scripts and stdout/stderr to this +# directory. +#cluster_files_directory = database/pbs + +# Mako templates are compiled as needed and cached for reuse, this directory is +# used for the cache +#template_cache_path = database/compiled_templates + +# Citation related caching. Tool citations information maybe fetched from +# external sources such as http://dx.doi.org/ by Galaxy - the following parameters +# can be used to control the caching used to store this information. +#citation_cache_type = file +#citation_cache_data_dir = database/citations/data +#citation_cache_lock_dir = database/citations/lock + +# External service types config file, defines what types of external_services configurations +# are available in Galaxy (.sample is used if default does not exist). +#external_service_type_config_file = config/external_service_types_conf.xml + +# Path to the directory containing the external_service_types defined in the config. +#external_service_type_path = external_service_types + +# Tools with a number of outputs not known until runtime can write these +# outputs to a directory for collection by Galaxy when the job is done. +# Previously, this directory was new_file_path, but using one global directory +# can cause performance problems, so using job_working_directory ('.' or cwd +# when a job is run) is encouraged. By default, both are checked to avoid +# breaking existing tools. +#collect_outputs_from = new_file_path,job_working_directory + +# -- Data Storage (Object Store) +# +# Configuration file for the object store +# If this is set and exists, it overrides any other objectstore settings. +# object_store_config_file = config/object_store_conf.xml + +# Object store backend module (valid options are: disk, s3, swift, irods, +# distributed, hierarchical) +#object_store = disk + +# *Extremely* old Galaxy instances created datasets at the root of the +# `file_path` defined above. If your Galaxy instance has datasets at the root +# (instead of in directories composed by hashing the dataset id), you should +# enable this option to allow Galaxy to find them. +#object_store_check_old_style = False + +# Credentials used by certain (s3, swift) object store backends +#os_access_key = <your cloud object store access key> +#os_secret_key = <your cloud object store secret key> +#os_bucket_name = <name of an existing object store bucket or container> + +# If using 'swift' object store, you must specify the following connection +# properties +#os_host = swift.rc.nectar.org.au +#os_port = 8888 +#os_is_secure = False +#os_conn_path = / + +# Reduced redundancy can be used only with the 's3' object store +#os_use_reduced_redundancy = False + +# Path to cache directory for object store backends that utilize a cache (s3, +# swift, irods) +#object_store_cache_path = database/files/ + +# Size (in GB) that the cache used by object store should be limited to. +# If the value is not specified, the cache size will be limited only by the +# file system size. +#object_store_cache_size = 100 + +# Configuration file for the distributed object store, if object_store = +# distributed. See the sample at distributed_object_store_conf.xml.sample +#distributed_object_store_config_file = None + + +# -- Mail and notification + +# Galaxy sends mail for various things: Subscribing users to the mailing list +# if they request it, emailing password resets, notification from the Galaxy +# Sample Tracking system, reporting dataset errors, and sending activation emails. +# To do this, it needs to send mail through an SMTP server, which you may define here (host:port). +# Galaxy will automatically try STARTTLS but will continue upon failure. +#smtp_server = None + +# If your SMTP server requires a username and password, you can provide them +# here (password in cleartext here, but if your server supports STARTTLS it +# will be sent over the network encrypted). +#smtp_username = None +#smtp_password = None + +# If your SMTP server requires SSL from the beginning of the connection +# smtp_ssl = False + +# On the user registration form, users may choose to join the mailing list. +# This is the address of the list they'll be subscribed to. +#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu + +# Datasets in an error state include a link to report the error. Those reports +# will be sent to this address. Error reports are disabled if no address is set. +# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter. +#error_email_to = None + +# Activation email is used as a sender ('from' field) for the account activation mail. +# We recommend using string in the following format: Galaxy Project <galaxy-no-reply(a)example.com> +#activation_email = None + +# URL of the support resource for the galaxy instance. Used in activation emails. +#instance_resource_url = http://wiki.galaxyproject.org/ + +# E-mail domains blacklist is used for filtering out users that are using disposable email address +# during the registration. If their address domain matches any domain in the BL they are refused the registration. +#blacklist_file = config/disposable_email_blacklist.conf + +# Registration warning message is used to discourage people from registering multiple accounts. Applies mostly for the main Galaxy instance. +# If no message specified the warning box will not be shown. +#registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. + +# When users opt to reset passwords, new ones are created, this option +# specifies the length of these passwords. +#reset_password_length = 15 + + +# -- Account activation + +# This is user account activation feature global flag. If set to "False" the rest of the Account +# activation configuration is ignored and user activation is disabled (a.k.a. accounts are active since registration). +# Note the activation is also not working in case the smtp server is not defined. +#user_activation_on = False + +# Activation grace period. Activation is not forced (login is not disabled) until +# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content). +# In hours. Default is 3. Enter 0 to disable grace period. +# Users with OpenID logins have grace period forever. +#activation_grace_period = 0 + +# Used for warning box for inactive accounts (unable to run jobs). +# In use only if activation_grace_period is set. +#inactivity_box_content = Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address. + + +# -- Display sites + +# Galaxy can display data at various external browsers. These options specify +# which browsers should be available. URLs and builds available at these +# browsers are defined in the specifield files. + +# If use_remote_user = True, display application servers will be denied access +# to Galaxy and so displaying datasets in these sites will fail. +# display_servers contains a list of hostnames which should be allowed to +# bypass security to display datasets. Please be aware that there are security +# implications if this is allowed. More details (including required changes to +# the proxy server config) are available in the Apache proxy documentation on +# the wiki. +# +# The list of servers in this sample config are for the UCSC Main, Test and +# Archaea browsers, but the default if left commented is to not allow any +# display sites to bypass security (you must uncomment the line below to allow +# them). +#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… + +# To disable the old-style display applications that are hardcoded into datatype classes, +# set enable_old_display_applications = False. +# This may be desirable due to using the new-style, XML-defined, display applications that +# have been defined for many of the datatypes that have the old-style. +# There is also a potential security concern with the old-style applications, +# where a malicious party could provide a link that appears to reference the Galaxy server, +# but contains a redirect to a third-party server, tricking a Galaxy user to access said +# site. +#enable_old_display_applications = True + +# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. + +use_nglims = False +nglims_config_file = tool-data/nglims.yaml + +# -- UI Localization + +# Show a message box under the masthead. +#message_box_visible = False +#message_box_content = None +#message_box_class = info + +# Append "/{brand}" to the "Galaxy" text in the masthead. +#brand = None + +# Format string used when showing date and time information. +# The string may contain: +# - the directives used by Python time.strftime() function (see http://docs.python.org/2/library/time.html#time.strftime ), +# - $locale (complete format string for the server locale), +# - $iso8601 (complete format string as specified by ISO 8601 international standard). +# pretty_datetime_format = $locale (UTC) + +# The URL of the page to display in Galaxy's middle pane when loaded. This can be +# an absolute or relative URL. +#welcome_url = /static/welcome.html + +# The URL linked by the "Galaxy/brand" text. +#logo_url = / + +# The URL linked by the "Wiki" link in the "Help" menu. +#wiki_url = http://wiki.galaxyproject.org/ + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.galaxyproject.org/Support + +# The URL linked by the "How to Cite Galaxy" link in the "Help" menu. +#citation_url = http://wiki.galaxyproject.org/CitingGalaxy + +#The URL linked by the "Search" link in the "Help" menu. +#search_url = http://galaxyproject.org/search/usegalaxy/ + +#The URL linked by the "Mailing Lists" link in the "Help" menu. +#mailing_lists_url = http://wiki.galaxyproject.org/MailingLists + +#The URL linked by the "Videos" link in the "Help" menu. +#videos_url = http://vimeo.com/galaxyproject + +# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well +# as on the user registration and login forms and in the activation emails. +#terms_url = None + +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +# The Galaxy Q&A site is under development; when the site is done, this URL +# will be set and uncommented. +#qa_url = + +# Serve static content, which must be enabled if you're not serving it via a +# proxy server. These options should be self explanatory and so are not +# documented individually. You can use these paths (or ones in the proxy +# server) to point to your own styles. +#static_enabled = True +#static_cache_time = 360 +#static_dir = static/ +#static_images_dir = static/images +#static_favicon_dir = static/favicon.ico +#static_scripts_dir = static/scripts/ +#static_style_dir = static/june_2007_style/blue +#static_robots_txt = static/robots.txt + +# Pack javascript at launch (/static/scripts/*.js) +# This only happens if the modified timestamp of the source .js is newer +# than the version (if it exists) in /static/scripts/packed/ +# Note that this requires java > 1.4 for executing yuicompressor.jar +#pack_scripts = False + +# Cloud Launch + +#enable_cloud_launch = False +#cloudlaunch_default_ami = ami-a7dbf6ce + +# Incremental Display Options + +#display_chunk_size = 65536 + +# -- Advanced proxy features + +# For help on configuring the Advanced proxy features, see: +# http://usegalaxy.org/production + +# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set +# this to True to inform Galaxy that mod_xsendfile is enabled upstream. +#apache_xsendfile = False + +# The same download handling can be done by nginx using X-Accel-Redirect. This +# should be set to the path defined in the nginx config as an internal redirect +# with access to Galaxy's data files (see documentation linked above). +#nginx_x_accel_redirect_base = False + +# nginx can make use of mod_zip to create zip files containing multiple library +# files. If using X-Accel-Redirect, this can be the same value as that option. +#nginx_x_archive_files_base = False + +# If using compression in the upstream proxy server, use this option to disable +# gzipping of library .tar.gz and .zip archives, since the proxy server will do +# it faster on the fly. +#upstream_gzip = False + +# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. +# Configuration for this is complex and explained in detail in the +# documentation linked above. The upload store is a temporary directory in +# which files uploaded by the upload module will be placed. +#nginx_upload_store = False + +# This value overrides the action set on the file upload form, e.g. the web +# path where the nginx_upload_module has been configured to intercept upload +# requests. +#nginx_upload_path = False + +# -- Logging and Debugging + +# Verbosity of console log messages. Acceptable values can be found here: +# http://docs.python.org/library/logging.html#logging-levels +#log_level = DEBUG + +# Print database operations to the server log (warning, quite verbose!). +#database_engine_option_echo = False + +# Print database pool operations to the server log (warning, quite verbose!). +#database_engine_option_echo_pool = False + +# Turn on logging of application events and some user events to the database. +#log_events = True + +# Turn on logging of user actions to the database. Actions currently logged are +# grid views, tool searches, and use of "recently" used tools menu. The +# log_events and log_actions functionality will eventually be merged. +#log_actions = True + +# Sanitize All HTML Tool Output +# By default, all tool output served as 'text/html' will be sanitized +# thoroughly. This can be disabled if you have special tools that require +# unaltered output. +#sanitize_all_html = True + +# By default Galaxy will serve non-HTML tool output that may potentially +# contain browser executable JavaScript content as plain text. This will for +# instance cause SVG datasets to not render properly and so may be disabled +# by setting the following option to True. +#serve_xss_vulnerable_mimetypes = False + +# Debug enables access to various config options useful for development and +# debugging: use_lint, use_profile, use_printdebug and use_interactive. It +# also causes the files used by PBS/SGE (submission script, output, and error) +# to remain on disk after the job is complete. Debug mode is disabled if +# commented, but is uncommented by default in the sample config. +debug = True + +# Check for WSGI compliance. +#use_lint = False + +# Run the Python profiler on each request. +#use_profile = False + +# Intercept print statements and show them on the returned page. +#use_printdebug = True + +# Enable live debugging in your browser. This should NEVER be enabled on a +# public site. Enabled in the sample config for development. +use_interactive = True + +# Write thread status periodically to 'heartbeat.log', (careful, uses disk +# space rapidly!). Useful to determine why your processes may be consuming a +# lot of CPU. +#use_heartbeat = False + +# Enable the memory debugging interface (careful, negatively impacts server +# performance). +#use_memdump = False + +# -- Data Libraries + +# These library upload options are described in much more detail in the wiki: +# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles + +# Add an option to the library upload form which allows administrators to +# upload a directory of files. +#library_import_dir = None + +# Add an option to the library upload form which allows authorized +# non-administrators to upload a directory of files. The configured directory +# must contain sub-directories named the same as the non-admin user's Galaxy +# login ( email ). The non-admin user is restricted to uploading files or +# sub-directories of files contained in their directory. +#user_library_import_dir = None + +# Add an option to the admin library upload tool allowing admins to paste +# filesystem paths to files and directories in a box, and these paths will be +# added to a library. Set to True to enable. Please note the security +# implication that this will give Galaxy Admins access to anything your Galaxy +# user has access to. +#allow_library_path_paste = False + +# Users may choose to download multiple files from a library in an archive. By +# default, Galaxy allows users to select from a few different archive formats +# if testing shows that Galaxy is able to create files using these formats. +# Specific formats can be disabled with this option, separate more than one +# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. +#disable_library_comptypes = + +# Some sequencer integration features in beta allow you to automatically +# transfer datasets. This is done using a lightweight transfer manager which +# runs outside of Galaxy (but is spawned by it automatically). Galaxy will +# communicate with this manager over the port specified here. +#transfer_manager_port = 8163 + +# Search data libraries with whoosh +#enable_whoosh_library_search = True +# Whoosh indexes are stored in this directory. +#whoosh_index_dir = database/whoosh_indexes + +# Search data libraries with lucene +#enable_lucene_library_search = False +# maxiumum file size to index for searching, in MB +#fulltext_max_size = 500 +#fulltext_noindex_filetypes = bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger +# base URL of server providing search functionality using lucene +#fulltext_url = http://localhost:8081 + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +#id_secret = USING THE DEFAULT IS NOT SECURE! + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy +#use_remote_user = False + +# If use_remote_user is enabled and your external authentication +# method just returns bare usernames, set a default mail domain to be appended +# to usernames, to become your Galaxy usernames (email addresses). +#remote_user_maildomain = None + +# If use_remote_user is enabled, the header that the upstream proxy provides +# the remote username in defaults to HTTP_REMOTE_USER (the 'HTTP_' is prepended +# by WSGI). This option allows you to change the header. Note, you still need +# to prepend 'HTTP_' to the header in this option, but your proxy server should +# *not* include 'HTTP_' at the beginning of the header name. +#remote_user_header = HTTP_REMOTE_USER + +# If use_remote_user is enabled, you can set this to a URL that will log your +# users out. +#remote_user_logout_href = None + +# If your proxy and/or authentication source does not normalize e-mail +# addresses or user names being passed to Galaxy - set the following option +# to True to force these to lower case. +#normalize_remote_user_email = False + +# Administrative users - set this to a comma-separated list of valid Galaxy +# users (email addresses). These users will have access to the Admin section +# of the server, and will have access to create users, groups, roles, +# libraries, and more. For more information, see: +# https://wiki.galaxyproject.org/Admin/Interface +#admin_users = None + +# Force everyone to log in (disable anonymous access). +#require_login = False + +# Allow unregistered users to create new accounts (otherwise, they will have to +# be created by an admin). +#allow_user_creation = True + +# Allow administrators to delete accounts. +#allow_user_deletion = False + +# Allow administrators to log in as other users (useful for debugging) +#allow_user_impersonation = False + +# Allow users to remove their datasets from disk immediately (otherwise, +# datasets will be removed after a time period specified by an administrator in +# the cleanup scripts run via cron) +#allow_user_dataset_purge = False + +# By default, users' data will be public, but setting this to True will cause +# it to be private. Does not affect existing users and data, only ones created +# after this option is set. Users may still change their default back to +# public. +#new_user_dataset_access_role_default_private = False + +# -- Beta features + +# Enable Galaxy to communicate directly with a sequencer +#enable_sequencer_communication = False + +# Enable authentication via OpenID. Allows users to log in to their Galaxy +# account by authenticating with an OpenID provider. +#enable_openid = False +# .sample used if default does not exist +#openid_config_file = config/openid_conf.xml +#openid_consumer_cache_path = database/openid_consumer_cache + +# Optional list of email addresses of API users who can make calls on behalf of +# other users +#api_allow_run_as = None + +# Master key that allows many API admin actions to be used without actually +# having a defined admin user in the database/config. Only set this if you need +# to bootstrap Galaxy, you probably do not want to set this on public servers. +#master_api_key = changethis + +# Enable tool tags (associating tools with tags). This has its own option +# since its implementation has a few performance implications on startup for +# large servers. +#enable_tool_tags = False + +# Enable a feature when running workflows. When enabled, default datasets +# are selected for "Set at Runtime" inputs from the history such that the +# same input will not be selected twice, unless there are more inputs than +# compatible datasets in the history. +# When False, the most recently added compatible item in the history will +# be used for each "Set at Runtime" input, independent of others in the Workflow +#enable_unique_workflow_defaults = False + +# The URL to the myExperiment instance being used (omit scheme but include port) +#myexperiment_url = www.myexperiment.org:80 + +# Enable Galaxy's "Upload via FTP" interface. You'll need to install and +# configure an FTP server (we've used ProFTPd since it can use Galaxy's +# database for authentication) and set the following two options. + +# This should point to a directory containing subdirectories matching users' +# email addresses, where Galaxy will look for files. +#ftp_upload_dir = None + +# This should be the hostname of your FTP server, which will be provided to +# users in the help text. +#ftp_upload_site = None + +# Enable enforcement of quotas. Quotas can be set from the Admin interface. +#enable_quotas = False + +# This option allows users to see the full path of datasets via the "View +# Details" option in the history. Administrators can always see this. +#expose_dataset_path = False + +# Data manager configuration options +# Allow non-admin users to view available Data Manager options +#enable_data_manager_user_view = False +# File where Data Managers are configured (.sample used if default does not +# exist) +#data_manager_config_file = config/data_manager_conf.xml +# File where Tool Shed based Data Managers are configured +#shed_data_manager_config_file = config/shed_data_manager_conf.xml +# Directory to store Data Manager based tool-data; defaults to tool_data_path +#galaxy_data_manager_data_path = tool-data + +# -- Job Execution + +# To increase performance of job execution and the web interface, you can +# separate Galaxy into multiple processes. There are more than one way to do +# this, and they are explained in detail in the documentation: +# +# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling + +# By default, Galaxy manages and executes jobs from within a single process and +# notifies itself of new jobs via in-memory queues. Jobs are run locally on +# the system on which Galaxy is started. Advanced job running capabilities can +# be configured through the job configuration file. +#job_config_file = config/job_conf.xml + +# In multiprocess configurations, notification between processes about new jobs +# is done via the database. In single process configurations, this is done in +# memory, which is a bit quicker. Galaxy tries to automatically determine +# which method it should used based on your handler configuration in the job +# config file, but you can explicitly override this behavior by setting the +# following option to True or False. +#track_jobs_in_database = None + +# This enables splitting of jobs into tasks, if specified by the particular tool config. +# This is a new feature and not recommended for production servers yet. +#use_tasked_jobs = False +#local_task_queue_workers = 2 + +# Enable job recovery (if Galaxy is restarted while cluster jobs are running, +# it can "recover" them when it starts). This is not safe to use if you are +# running more than one Galaxy server using the same database. +#enable_job_recovery = True + +# Although it is fairly reliable, setting metadata can occasionally fail. In +# these instances, you can choose to retry setting it internally or leave it in +# a failed state (since retrying internally may cause the Galaxy process to be +# unresponsive). If this option is set to False, the user will be given the +# option to retry externally, or set metadata manually (when possible). +#retry_metadata_internally = True + +# If (for example) you run on a cluster and your datasets (by default, +# database/files/) are mounted read-only, this option will override tool output +# paths to write outputs to the working directory instead, and the job manager +# will move the outputs to their proper place in the dataset directory on the +# Galaxy server after the job completes. +#outputs_to_working_directory = False + +# If your network filesystem's caching prevents the Galaxy server from seeing +# the job's stdout and stderr files when it completes, you can retry reading +# these files. The job runner will retry the number of times specified below, +# waiting 1 second between tries. For NFS, you may want to try the -noac mount +# option (Linux) or -actimeo=0 (Solaris). +#retry_job_output_collection = 0 + +# Clean up various bits of jobs left on the filesystem after completion. These +# bits include the job working directory, external metadata temporary files, +# and DRM stdout and stderr files (if using a DRM). Possible values are: +# always, onsuccess, never +#cleanup_job = always + +# File to source to set up the environment when running jobs. By default, the +# environment in which the Galaxy server starts is used when running jobs +# locally, and the environment set up per the DRM's submission method and +# policy is used when running jobs on a cluster (try testing with `qsub` on the +# command line). environment_setup_file can be set to the path of a file on +# the cluster that should be sourced by the user to set up the environment +# prior to running tools. This can be especially useful for running jobs as +# the actual user, to remove the need to configure each user's environment +# individually. +#environment_setup_file = None + + +# Optional file containing job resource data entry fields definition. +# These fields will be presented to users in the tool forms and allow them to +# overwrite default job resources such as number of processors, memory, and walltime. +#job_resource_params_file = config/job_resource_params_conf.xml + +# If using job concurrency limits (configured in job_config_file), several +# extra database queries must be performed to determine the number of jobs a +# user has dispatched to a given destination. By default, these queries will +# happen for every job that is waiting to run, but if cache_user_job_count is +# set to True, it will only happen once per iteration of the handler queue. +# Although better for performance due to reduced queries, the tradeoff is a +# greater possibility that jobs will be dispatched past the configured limits +# if running many handlers. +#cache_user_job_count = False + +# ToolBox filtering +# Modules from lib/galaxy/tools/filters/ can be specified in the following lines. +# tool_* filters will be applied for all users and can not be changed by them. +# user_tool_* filters will be shown under user preferences and can be toogled +# on and off by runtime +#tool_filters +#tool_label_filters +#tool_section_filters +#user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode +#user_tool_section_filters = examples:restrict_text +#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode + +# Galaxy Application Internal Message Queue + +# Galaxy uses AMQP internally TODO more documentation on what for. +# For examples, see http://ask.github.io/kombu/userguide/connections.html +# +# Without specifying anything here, galaxy will first attempt to use your +# specified database_connection above. If that's not specified either, Galaxy +# will automatically create and use a separate sqlite database located in your +# <galaxy>/database folder (indicated in the commented out line below). + +#amqp_internal_connection = sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE + + + +# ---- Galaxy External Message Queue ------------------------------------------------- + +# Galaxy uses AMQ protocol to receive messages from external sources like +# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +# For Galaxy to receive messages from a message queue the RabbitMQ server has +# to be set up with a user account and other parameters listed below. The 'host' +# and 'port' fields should point to where the RabbitMQ server is running. + +[galaxy_amqp] + +#host = 127.0.0.1 +#port = 5672 +#userid = galaxy +#password = galaxy +#virtual_host = galaxy_messaging_engine +#queue = galaxy_queue +#exchange = galaxy_exchange +#routing_key = bar_code_scanner +#rabbitmqctl_path = /path/to/rabbitmqctl + diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/job_conf.xml.sample_advanced --- /dev/null +++ b/config/job_conf.xml.sample_advanced @@ -0,0 +1,482 @@ +<?xml version="1.0"?> +<job_conf> + <plugins workers="4"> +  + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> + <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/> + <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> +  + <param id="invalidjobexception_state">ok</param> + <param id="invalidjobexception_retries">0</param> + <param id="internalexception_state">ok</param> + <param id="internalexception_retries">0</param> + </plugin> + <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> +  + <param id="drmaa_library_path">/sge/lib/libdrmaa.so</param> + </plugin> + <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> + <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> + <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> + <plugin id="dynamic" type="runner"> +  + <param id="rules_module">galaxy.jobs.rules</param> + </plugin> +  + <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"> +  +  + +  +  + </plugin> + <plugin id="pulsar_mq" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner"> +  + <param id="amqp_url">amqp://guest:guest@localhost:5672//</param> +  + <param id="galaxy_url">http://localhost:8080</param> +  +  +  +  +  +  +  +  +  + </plugin> + <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner"> +  + </plugin> + </plugins> + <handlers default="handlers"> +  + <handler id="handler0" tags="handlers"/> + <handler id="handler1" tags="handlers"/> +  + <handler id="sge_handler"> + <plugin id="sge"/> + </handler> + <handler id="special_handler0" tags="special_handlers"/> + <handler id="special_handler1" tags="special_handlers"/> + <handler id="trackster_handler"/> + </handlers> + <destinations default="local"> +  + <destination id="local" runner="local"/> + <destination id="multicore_local" runner="local"> + <param id="local_slots">4</param> +  + <param id="embed_metadata_in_job">True</param> +  + <job_metrics /> +  + </destination> + <destination id="docker_local" runner="local"> + <param id="docker_enabled">true</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + +  +  + +  +  + + </destination> + <destination id="pbs" runner="pbs" tags="mycluster"/> + <destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"> +  + <param id="Resource_List">walltime=72:00:00</param> + </destination> + <destination id="remote_cluster" runner="drmaa" tags="longjobs"/> + <destination id="java_cluster" runner="drmaa"> +  + <env id="_JAVA_OPTIONS">-Xmx=6GB</env> + <env id="ANOTHER_OPTION" raw="true">'5'</env> + <env file="/mnt/java_cluster/environment_setup.sh" /> + <env exec="module load javastuff/2.10" /> +  + </destination> + <destination id="real_user_cluster" runner="drmaa"> +  + <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> + <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> + <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> + </destination> + <destination id="dynamic" runner="dynamic"> +  + <param id="function">foo</param> + </destination> + <destination id="load_balance" runner="dynamic"> + <param id="type">choose_one</param> +  + <param id="destination_ids">cluster1,cluster2,cluster3</param> + </destination> + <destination id="load_balance_with_data_locality" runner="dynamic"> +  + <param id="type">choose_one</param> + <param id="destination_ids">cluster1,cluster2,cluster3</param> + <param id="hash_by">workflow_invocation,history</param> + </destination> + <destination id="burst_out" runner="dynamic"> +  + <param id="type">burst</param> + <param id="from_destination_ids">local_cluster_8_core,local_cluster_1_core,local_cluster_16_core</param> + <param id="to_destination_id">shared_cluster_8_core</param> + <param id="num_jobs">50</param> +  + </destination> + <destination id="docker_dispatch" runner="dynamic"> +  + <param id="type">docker_dispatch</param> + <param id="docker_destination_id">docker_cluster</param> + <param id="default_destination_id">normal_cluster</param> + </destination> + <destination id="secure_pulsar_rest_dest" runner="pulsar_rest"> + <param id="url">https://examle.com:8913/</param> +  + <param id="private_token">123456789changeme</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + </destination> + <destination id="pulsar_mq_dest" runner="amqp_pulsar" > +  + <param id="jobs_directory">/path/to/remote/pulsar/files/staging/</param> +  + </destination> + <destination id="ssh_torque" runner="cli"> + <param id="shell_plugin">SecureShell</param> + <param id="job_plugin">Torque</param> + <param id="shell_username">foo</param> + <param id="shell_hostname">foo.example.org</param> + <param id="job_Resource_List">walltime=24:00:00,ncpus=4</param> + </destination> + +  + <destination id="ssh_slurm" runner="cli"> + <param id="shell_plugin">SecureShell</param> + <param id="job_plugin">Slurm</param> + <param id="shell_username">foo</param> + <param id="shell_hostname">my_host</param> + <param id="job_time">2:00:00</param> + <param id="job_ncpus">4</param> + <param id="job_partition">my_partition</param> + </destination> + + <destination id="condor" runner="condor"> +  + <param id="request_cpus">8</param> + </destination> + +  + <destination id="short_fast" runner="slurm"> + <param id="nativeSpecification">--time=00:05:00 --nodes=1</param> + <resubmit condition="walltime_reached" destination="long_slow" handler="sge_handler" /> + </destination> + <destination id="long_slow" runner="sge"> +  + <param id="nativeSpecification">-l h_rt=96:00:00</param> + </destination> + + </destinations> + <resources default="default"> +  + <group id="default"></group> + <group id="memoryonly">memory</group> + <group id="all">processors,memory,time,project</group> + </resources> + <tools> +  + <tool id="foo" handler="trackster_handler"> + <param id="source">trackster</param> + </tool> + <tool id="bar" destination="dynamic"/> +  + <tool id="longbar" destination="dynamic" resources="all" /> + <tool id="baz" handler="special_handlers" destination="bigmem"/> + </tools> + <limits> +  +  + <limit type="registered_user_concurrent_jobs">2</limit> +  + <limit type="anonymous_user_concurrent_jobs">1</limit> +  + <limit type="destination_user_concurrent_jobs" id="local">1</limit> + <limit type="destination_user_concurrent_jobs" tag="mycluster">2</limit> + <limit type="destination_user_concurrent_jobs" tag="longjobs">1</limit> +  + <limit type="destination_total_concurrent_jobs" id="local">16</limit> + <limit type="destination_total_concurrent_jobs" tag="longjobs">100</limit> +  + <limit type="walltime">24:00:00</limit> +  + <limit type="output_size">10GB</limit> + </limits> +</job_conf> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/job_conf.xml.sample_basic --- /dev/null +++ b/config/job_conf.xml.sample_basic @@ -0,0 +1,13 @@ +<?xml version="1.0"?> + +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"/> + </destinations> +</job_conf> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/job_metrics_conf.xml.sample --- /dev/null +++ b/config/job_metrics_conf.xml.sample @@ -0,0 +1,124 @@ +<?xml version="1.0"?> + +<job_metrics> +  + +  + <core /> + +  +  +  +  + +  +  + +  +  + +  +  +  +  + +  +  +</job_metrics> This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in natefoo/galaxy-central (pull request #495)
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f90a490e997/ Changeset: 5f90a490e997 User: dannon Date: 2014-09-16 15:08:35 Summary: Merged in natefoo/galaxy-central (pull request #495) Clean up the root directory and rename universe_wsgi.ini Affected #: 116 files diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd README.txt --- a/README.txt +++ b/README.txt @@ -22,13 +22,13 @@ http://localhost:8080 You may wish to make changes from the default configuration. This can be done -in the universe_wsgi.ini file. Tools can be either installed from the Tool Shed +in the config/galaxy.ini file. Tools can be either installed from the Tool Shed or added manually. For details please see the Galaxy wiki: -https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial. +https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial Not all dependencies are included for the tools provided in the sample tool_conf.xml. A full list of external dependencies is available at: -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies \ No newline at end of file +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -43,15 +43,10 @@ " SAMPLES=" -tool_conf.xml.sample -datatypes_conf.xml.sample -universe_wsgi.ini.sample -tool_data_table_conf.xml.sample -tool_sheds_conf.xml.sample -shed_tool_data_table_conf.xml.sample -migrated_tools_conf.xml.sample -data_manager_conf.xml.sample -shed_data_manager_conf.xml.sample +config/galaxy.ini.sample +config/shed_tool_data_table_conf.xml.sample +config/migrated_tools_conf.xml.sample +config/shed_data_manager_conf.xml.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/shared/ucsc/builds.txt.sample diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/data_manager_conf.xml.sample --- /dev/null +++ b/config/data_manager_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<data_managers> +</data_managers> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/datatypes_conf.xml.sample --- /dev/null +++ b/config/datatypes_conf.xml.sample @@ -0,0 +1,333 @@ +<?xml version="1.0"?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Ab1"/> + <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false" /> + <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true" /> + <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true" /> + <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/> + <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/> + <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM"> + <converter file="bam_to_bai.xml" target_datatype="bai"/> + <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="ucsc/bam.xml" /> + <display file="ensembl/ensembl_bam.xml" /> + <display file="igv/bam.xml" /> + <display file="igb/bam.xml" /> + </datatype> + <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed"> + <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> + <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="bed_to_fli_converter.xml" target_datatype="fli"/> +  + <display file="igb/bed.xml" /> + </datatype> + <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> + <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/bedgraph.xml" /> + </datatype> + <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /> + <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> + </datatype> + <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /> + <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> + <converter file="len_to_linecount.xml" target_datatype="linecount" /> + </datatype> + <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigbed.xml" /> + <display file="igb/bb.xml" /> + </datatype> + <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigwig.xml" /> + <display file="igb/bigwig.xml" /> + </datatype> + <datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> +  + <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> +  + <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/> + <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/> + <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" /> + <datatype extension="data_manager_json" type="galaxy.datatypes.data:Text" mimetype="application/json" subclass="True" display_in_upload="False"/> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" description="A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('>') symbol in the first column. All lines should be shorter than 80 characters." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fasta"> + <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/> + <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/> + <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/> + <converter file="fasta_to_2bit.xml" target_datatype="twobit"/> + <converter file="fasta_to_len.xml" target_datatype="len"/> + </datatype> + <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/> + <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/> + <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/> + <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> +  + </datatype> + <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true" description="GFF lines have nine required fields that must be tab-separated." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF"> + <converter file="gff_to_bed_converter.xml" target_datatype="bed"/> + <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="gff_to_fli_converter.xml" target_datatype="fli"/> + <display file="ensembl/ensembl_gff.xml" inherit="True"/> +  + </datatype> + <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true" description="The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF3"/> + <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/> + <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/> + <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"> + <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /> + </datatype> + <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> + <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> + <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/> + <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order)." > + <converter file="interval_to_bed_converter.xml" target_datatype="bed"/> + <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/> + <converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/> + <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/> +  + <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/> + <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/> + <display file="rviewer/bed.xml" inherit="True"/> + </datatype> + <datatype extension="picard_interval_list" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"> + <converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/> + </datatype> + <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_report" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/> + <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/> + <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/> + <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/> + <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/> + <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/> + <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/> + <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/> + <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/> + <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/> + <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/> + <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/> + <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/> + <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/> + <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/> + <datatype extension="laj" type="galaxy.datatypes.images:Laj"/> + <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true" description="Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.." /> + <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true" description="TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated 'variable=value' pairs. There should be no white space surrounding the '='." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#MAF"> + <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/> + <converter file="maf_to_interval_converter.xml" target_datatype="interval"/> + </datatype> + <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack"> + <display file="ucsc/maf_customtrack.xml" /> + </datatype> + <datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True"> + <converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> + <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/> + <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + </datatype> + <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/> + <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> + <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> + <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/> + <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/> + <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/> + <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/> + <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"> + <converter file="sam_to_bam.xml" target_datatype="bam"/> + <converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype> + <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/> + <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/> + <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/> + <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/> + <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/> + <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/> + <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/> + <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"> + <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/> + <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="ucsc/vcf.xml" /> + <display file="igv/vcf.xml" /> + <display file="rviewer/vcf.xml" inherit="True"/> + </datatype> + <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True"/> + <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> + <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true" description="The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Wig"> + <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/> +  + <display file="igb/wig.xml" /> + </datatype> + <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="vcf_bgzip" type_extension="bgzip" subclass="True" > + <display file="igv/vcf.xml" /> + <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/> + </datatype> +  + <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" /> + <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" /> + <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /> +  + <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> +  + <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/> +  + <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/> + <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" /> +  + <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/> +  + <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/> +  + <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/> +  +  + <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true"> + </datatype> + <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/> +  + <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"> + <converter file="lped_to_fped_converter.xml" target_datatype="fped"/> + <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/> + </datatype> +  + <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"> + <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/> + <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/> + </datatype> + <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/> +  + <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/> + <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/> + <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/> + <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/> + <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/> + <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/> +  +  + <datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/> + <datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/> + <datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/> + </registration> + <sniffers> +  + <sniffer type="galaxy.datatypes.tabular:Vcf"/> + <sniffer type="galaxy.datatypes.binary:TwoBit"/> + <sniffer type="galaxy.datatypes.binary:SQlite"/> + <sniffer type="galaxy.datatypes.binary:Bam"/> + <sniffer type="galaxy.datatypes.binary:Sff"/> + <sniffer type="galaxy.datatypes.xml:Phyloxml"/> + <sniffer type="galaxy.datatypes.xml:GenericXml"/> + <sniffer type="galaxy.datatypes.sequence:Maf"/> + <sniffer type="galaxy.datatypes.sequence:Lav"/> + <sniffer type="galaxy.datatypes.sequence:csFasta"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> + <sniffer type="galaxy.datatypes.sequence:Fasta"/> + <sniffer type="galaxy.datatypes.sequence:Fastq"/> + <sniffer type="galaxy.datatypes.interval:Wiggle"/> + <sniffer type="galaxy.datatypes.images:Html"/> + <sniffer type="galaxy.datatypes.images:Pdf"/> + <sniffer type="galaxy.datatypes.sequence:Axt"/> + <sniffer type="galaxy.datatypes.interval:Bed"/> + <sniffer type="galaxy.datatypes.interval:CustomTrack"/> + <sniffer type="galaxy.datatypes.interval:Gtf"/> + <sniffer type="galaxy.datatypes.interval:Gff"/> + <sniffer type="galaxy.datatypes.interval:Gff3"/> + <sniffer type="galaxy.datatypes.tabular:Pileup"/> + <sniffer type="galaxy.datatypes.interval:Interval"/> + <sniffer type="galaxy.datatypes.tabular:Sam"/> + <sniffer type="galaxy.datatypes.data:Newick"/> + <sniffer type="galaxy.datatypes.data:Nexus"/> + <sniffer type="galaxy.datatypes.images:Jpg"/> + <sniffer type="galaxy.datatypes.images:Png"/> + <sniffer type="galaxy.datatypes.images:Tiff"/> + <sniffer type="galaxy.datatypes.images:Bmp"/> + <sniffer type="galaxy.datatypes.images:Gif"/> + <sniffer type="galaxy.datatypes.images:Im"/> + <sniffer type="galaxy.datatypes.images:Pcd"/> + <sniffer type="galaxy.datatypes.images:Pcx"/> + <sniffer type="galaxy.datatypes.images:Ppm"/> + <sniffer type="galaxy.datatypes.images:Psd"/> + <sniffer type="galaxy.datatypes.images:Xbm"/> + <sniffer type="galaxy.datatypes.images:Rgb"/> + <sniffer type="galaxy.datatypes.images:Pbm"/> + <sniffer type="galaxy.datatypes.images:Pgm"/> + <sniffer type="galaxy.datatypes.images:Xpm"/> + <sniffer type="galaxy.datatypes.images:Eps"/> + <sniffer type="galaxy.datatypes.images:Rast"/> +  + </sniffers> + <build_sites> +  + <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/> + <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/> + <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/> + <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/> + <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/> + <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/> + </build_sites> +</datatypes> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/demo_sequencer_wsgi.ini.sample --- /dev/null +++ b/config/demo_sequencer_wsgi.ini.sample @@ -0,0 +1,66 @@ +# ---- HTTP Server ---------------------------------------------------------- + +[server:main] + +use = egg:Paste#http +port = 9011 +host = 0.0.0.0 +use_threadpool = true +threadpool_workers = 10 + +# ---- Galaxy Demo Sequencer Emulator Interface ------------------------------------------------- + +[app:main] + +# Specifies the factory for the universe WSGI application +paste.app_factory = galaxy.webapps.demo_sequencer.buildapp:app_factory +log_level = DEBUG + +# Where dataset files are saved +file_path = database/demo_sequencer_files +# Temporary storage for additional datasets, this should be shared through the cluster +new_file_path = database/tmp + +# Sequencer emulator actions +sequencer_actions_config_file = %(here)s/lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml + +# Session support (beaker) +use_beaker_session = True +session_type = memory +session_data_dir = %(here)s/database/beaker_sessions +session_key = galaxysessions +session_secret = changethisinproduction + +# Galaxy session security +id_secret = changethisinproductiontoo + +# Configuration for debugging middleware +debug = true +use_lint = false + +# NEVER enable this on a public site (even test or QA) +# use_interactive = true + +# this should be a comma-separated list of valid Galaxy users +#admin_users = test(a)bx.psu.edu + +# Force everyone to log in (disable anonymous access) +require_login = False + +# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) +## use_heartbeat = True + +# Profiling middleware (cProfile based) +## use_profile = True + +# Use the new iframe / javascript based layout +use_new_layout = true + +# Serving static files (needed if running standalone) +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/external_service_types_conf.xml.sample --- /dev/null +++ b/config/external_service_types_conf.xml.sample @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<external_service_types> + <external_service_type file="simple_unknown_sequencer.xml" visible="False"/> + <external_service_type file="applied_biosystems_solid.xml" visible="True"/> +</external_service_types> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/galaxy.ini.sample --- /dev/null +++ b/config/galaxy.ini.sample @@ -0,0 +1,889 @@ +# +# Galaxy is configured by default to be useable in a single-user development +# environment. To tune the application for a multi-user production +# environment, see the documentation at: +# +# http://usegalaxy.org/production +# + +# Throughout this sample configuration file, except where stated otherwise, +# uncommented values override the default if left unset, whereas commented +# values are set to the default value. Relative paths are relative to the root +# Galaxy directory. +# +# Examples of many of these options are explained in more detail in the wiki: +# +# https://wiki.galaxyproject.org/Admin/Config +# +# Config hackers are encouraged to check there before asking for help. + +# ---- HTTP Server ---------------------------------------------------------- + +# Configuration of the internal HTTP server. + +[server:main] + +# The internal HTTP server to use. Currently only Paste is provided. This +# option is required. +use = egg:Paste#http + +# The port on which to listen. +#port = 8080 + +# The address on which to listen. By default, only listen to localhost (Galaxy +# will not be accessible over the network). Use '0.0.0.0' to listen on all +# available network interfaces. +#host = 127.0.0.1 + +# Use a threadpool for the web server instead of creating a thread for each +# request. +use_threadpool = True + +# Number of threads in the web server thread pool. +#threadpool_workers = 10 + +# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +threadpool_kill_thread_limit = 10800 + +# ---- Filters -------------------------------------------------------------- + +# Filters sit between Galaxy and the HTTP server. + +# These filters are disabled by default. They can be enabled with +# 'filter-with' in the [app:main] section below. + +# Define the gzip filter. +[filter:gzip] +use = egg:Paste#gzip + +# Define the proxy-prefix filter. +[filter:proxy-prefix] +use = egg:PasteDeploy#prefix +prefix = /galaxy + +# ---- Galaxy --------------------------------------------------------------- + +# Configuration of the Galaxy application. + +[app:main] + +# -- Application and filtering + +# The factory for the WSGI application. This should not be changed. +paste.app_factory = galaxy.web.buildapp:app_factory + +# If not running behind a proxy server, you may want to enable gzip compression +# to decrease the size of data transferred over the network. If using a proxy +# server, please enable gzip compression there instead. +#filter-with = gzip + +# If running behind a proxy server and Galaxy is served from a subdirectory, +# enable the proxy-prefix filter and set the prefix in the +# [filter:proxy-prefix] section above. +#filter-with = proxy-prefix + +# If proxy-prefix is enabled and you're running more than one Galaxy instance +# behind one hostname, you will want to set this to the same path as the prefix +# in the filter above. This value becomes the "path" attribute set in the +# cookie so the cookies from each instance will not clobber each other. +#cookie_path = None + +# -- Database + +# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You +# may use a SQLAlchemy connection string to specify an external database +# instead. This string takes many options which are explained in detail in the +# config file documentation. +#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# If the server logs errors about not having enough database pool connections, +# you will want to increase these values, or consider running more Galaxy +# processes. +#database_engine_option_pool_size = 5 +#database_engine_option_max_overflow = 10 + +# If using MySQL and the server logs the error "MySQL server has gone away", +# you will want to set this to some positive value (7200 should work). +#database_engine_option_pool_recycle = -1 + +# If large database query results are causing memory or response time issues in +# the Galaxy process, leave the result on the server instead. This option is +# only available for PostgreSQL and is highly recommended. +#database_engine_option_server_side_cursors = False + +# Log all database transactions, can be useful for debugging and performance +# profiling. Logging is done via Python's 'logging' module under the qualname +# 'galaxy.model.orm.logging_connection_proxy' +#database_query_profiling_proxy = False + +# By default, Galaxy will use the same database to track user data and +# tool shed install data. There are many situtations in which it is +# valuable to seperate these - for instance bootstrapping fresh Galaxy +# instances with pretested installs. The following optin can be used to +# separate the tool shed install database (all other options listed above +# but prefixed with install_ are also available). +#install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# -- Files and directories + +# Dataset files are stored in this directory. +#file_path = database/files + +# Temporary files are stored in this directory. +#new_file_path = database/tmp + +# Tool config files, defines what tools are available in Galaxy. +# Tools can be locally developed or installed from Galaxy tool sheds. +# (config/tool_conf.xml.sample will be used if left unset and +# config/tool_conf.xml does not exist). +#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml + +# Enable / disable checking if any tools defined in the above non-shed tool_config_files +# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool +# Shed. This setting should generally be set to False only for development Galaxy environments +# that are often rebuilt from scratch where migrated tools do not need to be available in the +# Galaxy tool panel. If the following setting remains commented, the default setting will be True. +#check_migrate_tools = True + +# Tool config maintained by tool migration scripts. If you use the migration +# scripts to install tools that have been migrated to the tool shed upon a new +# release, they will be added to this tool config file. +#migrated_tools_config = migrated_tools_conf.xml + +# File that contains the XML section and tool tags from all tool panel config +# files integrated into a single file that defines the tool panel layout. This +# file can be changed by the Galaxy administrator to alter the layout of the +# tool panel. If not present, Galaxy will create it. +#integrated_tool_panel_config = integrated_tool_panel.xml + +# Default path to the directory containing the tools defined in tool_conf.xml. +# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. +#tool_path = tools + +# Path to the directory in which tool dependencies are placed. This is used by +# the tool shed to install dependencies and can also be used by administrators +# to manually install or link to dependencies. For details, see: +# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies +# If this option is not set to a valid path, installing tools with dependencies +# from the Tool Shed will fail. +#tool_dependency_dir = None + +# File containing the Galaxy Tool Sheds that should be made available to +# install from in the admin interface (.sample used if default does not exist). +#tool_sheds_config_file = config/tool_sheds_conf.xml + +# Enable automatic polling of relative tool sheds to see if any updates +# are available for installed repositories. Ideally only one Galaxy +# server process should be able to check for repository updates. The +# setting for hours_between_check should be an integer between 1 and 24. +#enable_tool_shed_check = False +#hours_between_check = 12 + +# Enable use of an in-memory registry with bi-directional relationships +# between repositories (i.e., in addition to lists of dependencies for a +# repository, keep an in-memory registry of dependent items for each repository. +#manage_dependency_relationships = False + +# XML config file that contains data table entries for the +# ToolDataTableManager. This file is manually # maintained by the Galaxy +# administrator (.sample used if default does not exist). +#tool_data_table_config_path = config/tool_data_table_conf.xml + +# XML config file that contains additional data table entries for the ToolDataTableManager. This file +# is automatically generated based on the current installed tool shed repositories that contain valid +# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically +# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. +#shed_tool_data_table_config = config/shed_tool_data_table_conf.xml + +# Directory where data used by tools is located, see the samples in that +# directory and the wiki for help: +# https://wiki.galaxyproject.org/Admin/DataIntegration +#tool_data_path = tool-data + +# File containing old-style genome builds +#builds_file_path = tool-data/shared/ucsc/builds.txt + +# Directory where chrom len files are kept, currently mainly used by trackster +#len_file_path = tool-data/shared/ucsc/chrom + +# Datatypes config file, defines what data (file) types are available in +# Galaxy (.sample is used if default does not exist). +#datatypes_config_file = config/datatypes_conf.xml + +# Disable the 'Auto-detect' option for file uploads +#datatypes_disable_auto = False + +# Visualizations config directory: where to look for individual visualization plugins. +# The path is relative to the Galaxy root dir. To use an absolute path begin the path +# with '/'. Defaults to "config/plugins/visualizations". +#visualization_plugins_directory = config/plugins/visualizations + +# Each job is given a unique empty directory as its current working directory. +# This option defines in what parent directory those directories will be +# created. +#job_working_directory = database/job_working_directory + +# If using a cluster, Galaxy will write job scripts and stdout/stderr to this +# directory. +#cluster_files_directory = database/pbs + +# Mako templates are compiled as needed and cached for reuse, this directory is +# used for the cache +#template_cache_path = database/compiled_templates + +# Citation related caching. Tool citations information maybe fetched from +# external sources such as http://dx.doi.org/ by Galaxy - the following parameters +# can be used to control the caching used to store this information. +#citation_cache_type = file +#citation_cache_data_dir = database/citations/data +#citation_cache_lock_dir = database/citations/lock + +# External service types config file, defines what types of external_services configurations +# are available in Galaxy (.sample is used if default does not exist). +#external_service_type_config_file = config/external_service_types_conf.xml + +# Path to the directory containing the external_service_types defined in the config. +#external_service_type_path = external_service_types + +# Tools with a number of outputs not known until runtime can write these +# outputs to a directory for collection by Galaxy when the job is done. +# Previously, this directory was new_file_path, but using one global directory +# can cause performance problems, so using job_working_directory ('.' or cwd +# when a job is run) is encouraged. By default, both are checked to avoid +# breaking existing tools. +#collect_outputs_from = new_file_path,job_working_directory + +# -- Data Storage (Object Store) +# +# Configuration file for the object store +# If this is set and exists, it overrides any other objectstore settings. +# object_store_config_file = config/object_store_conf.xml + +# Object store backend module (valid options are: disk, s3, swift, irods, +# distributed, hierarchical) +#object_store = disk + +# *Extremely* old Galaxy instances created datasets at the root of the +# `file_path` defined above. If your Galaxy instance has datasets at the root +# (instead of in directories composed by hashing the dataset id), you should +# enable this option to allow Galaxy to find them. +#object_store_check_old_style = False + +# Credentials used by certain (s3, swift) object store backends +#os_access_key = <your cloud object store access key> +#os_secret_key = <your cloud object store secret key> +#os_bucket_name = <name of an existing object store bucket or container> + +# If using 'swift' object store, you must specify the following connection +# properties +#os_host = swift.rc.nectar.org.au +#os_port = 8888 +#os_is_secure = False +#os_conn_path = / + +# Reduced redundancy can be used only with the 's3' object store +#os_use_reduced_redundancy = False + +# Path to cache directory for object store backends that utilize a cache (s3, +# swift, irods) +#object_store_cache_path = database/files/ + +# Size (in GB) that the cache used by object store should be limited to. +# If the value is not specified, the cache size will be limited only by the +# file system size. +#object_store_cache_size = 100 + +# Configuration file for the distributed object store, if object_store = +# distributed. See the sample at distributed_object_store_conf.xml.sample +#distributed_object_store_config_file = None + + +# -- Mail and notification + +# Galaxy sends mail for various things: Subscribing users to the mailing list +# if they request it, emailing password resets, notification from the Galaxy +# Sample Tracking system, reporting dataset errors, and sending activation emails. +# To do this, it needs to send mail through an SMTP server, which you may define here (host:port). +# Galaxy will automatically try STARTTLS but will continue upon failure. +#smtp_server = None + +# If your SMTP server requires a username and password, you can provide them +# here (password in cleartext here, but if your server supports STARTTLS it +# will be sent over the network encrypted). +#smtp_username = None +#smtp_password = None + +# If your SMTP server requires SSL from the beginning of the connection +# smtp_ssl = False + +# On the user registration form, users may choose to join the mailing list. +# This is the address of the list they'll be subscribed to. +#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu + +# Datasets in an error state include a link to report the error. Those reports +# will be sent to this address. Error reports are disabled if no address is set. +# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter. +#error_email_to = None + +# Activation email is used as a sender ('from' field) for the account activation mail. +# We recommend using string in the following format: Galaxy Project <galaxy-no-reply(a)example.com> +#activation_email = None + +# URL of the support resource for the galaxy instance. Used in activation emails. +#instance_resource_url = http://wiki.galaxyproject.org/ + +# E-mail domains blacklist is used for filtering out users that are using disposable email address +# during the registration. If their address domain matches any domain in the BL they are refused the registration. +#blacklist_file = config/disposable_email_blacklist.conf + +# Registration warning message is used to discourage people from registering multiple accounts. Applies mostly for the main Galaxy instance. +# If no message specified the warning box will not be shown. +#registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. + +# When users opt to reset passwords, new ones are created, this option +# specifies the length of these passwords. +#reset_password_length = 15 + + +# -- Account activation + +# This is user account activation feature global flag. If set to "False" the rest of the Account +# activation configuration is ignored and user activation is disabled (a.k.a. accounts are active since registration). +# Note the activation is also not working in case the smtp server is not defined. +#user_activation_on = False + +# Activation grace period. Activation is not forced (login is not disabled) until +# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content). +# In hours. Default is 3. Enter 0 to disable grace period. +# Users with OpenID logins have grace period forever. +#activation_grace_period = 0 + +# Used for warning box for inactive accounts (unable to run jobs). +# In use only if activation_grace_period is set. +#inactivity_box_content = Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address. + + +# -- Display sites + +# Galaxy can display data at various external browsers. These options specify +# which browsers should be available. URLs and builds available at these +# browsers are defined in the specifield files. + +# If use_remote_user = True, display application servers will be denied access +# to Galaxy and so displaying datasets in these sites will fail. +# display_servers contains a list of hostnames which should be allowed to +# bypass security to display datasets. Please be aware that there are security +# implications if this is allowed. More details (including required changes to +# the proxy server config) are available in the Apache proxy documentation on +# the wiki. +# +# The list of servers in this sample config are for the UCSC Main, Test and +# Archaea browsers, but the default if left commented is to not allow any +# display sites to bypass security (you must uncomment the line below to allow +# them). +#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… + +# To disable the old-style display applications that are hardcoded into datatype classes, +# set enable_old_display_applications = False. +# This may be desirable due to using the new-style, XML-defined, display applications that +# have been defined for many of the datatypes that have the old-style. +# There is also a potential security concern with the old-style applications, +# where a malicious party could provide a link that appears to reference the Galaxy server, +# but contains a redirect to a third-party server, tricking a Galaxy user to access said +# site. +#enable_old_display_applications = True + +# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. + +use_nglims = False +nglims_config_file = tool-data/nglims.yaml + +# -- UI Localization + +# Show a message box under the masthead. +#message_box_visible = False +#message_box_content = None +#message_box_class = info + +# Append "/{brand}" to the "Galaxy" text in the masthead. +#brand = None + +# Format string used when showing date and time information. +# The string may contain: +# - the directives used by Python time.strftime() function (see http://docs.python.org/2/library/time.html#time.strftime ), +# - $locale (complete format string for the server locale), +# - $iso8601 (complete format string as specified by ISO 8601 international standard). +# pretty_datetime_format = $locale (UTC) + +# The URL of the page to display in Galaxy's middle pane when loaded. This can be +# an absolute or relative URL. +#welcome_url = /static/welcome.html + +# The URL linked by the "Galaxy/brand" text. +#logo_url = / + +# The URL linked by the "Wiki" link in the "Help" menu. +#wiki_url = http://wiki.galaxyproject.org/ + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.galaxyproject.org/Support + +# The URL linked by the "How to Cite Galaxy" link in the "Help" menu. +#citation_url = http://wiki.galaxyproject.org/CitingGalaxy + +#The URL linked by the "Search" link in the "Help" menu. +#search_url = http://galaxyproject.org/search/usegalaxy/ + +#The URL linked by the "Mailing Lists" link in the "Help" menu. +#mailing_lists_url = http://wiki.galaxyproject.org/MailingLists + +#The URL linked by the "Videos" link in the "Help" menu. +#videos_url = http://vimeo.com/galaxyproject + +# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well +# as on the user registration and login forms and in the activation emails. +#terms_url = None + +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +# The Galaxy Q&A site is under development; when the site is done, this URL +# will be set and uncommented. +#qa_url = + +# Serve static content, which must be enabled if you're not serving it via a +# proxy server. These options should be self explanatory and so are not +# documented individually. You can use these paths (or ones in the proxy +# server) to point to your own styles. +#static_enabled = True +#static_cache_time = 360 +#static_dir = static/ +#static_images_dir = static/images +#static_favicon_dir = static/favicon.ico +#static_scripts_dir = static/scripts/ +#static_style_dir = static/june_2007_style/blue +#static_robots_txt = static/robots.txt + +# Pack javascript at launch (/static/scripts/*.js) +# This only happens if the modified timestamp of the source .js is newer +# than the version (if it exists) in /static/scripts/packed/ +# Note that this requires java > 1.4 for executing yuicompressor.jar +#pack_scripts = False + +# Cloud Launch + +#enable_cloud_launch = False +#cloudlaunch_default_ami = ami-a7dbf6ce + +# Incremental Display Options + +#display_chunk_size = 65536 + +# -- Advanced proxy features + +# For help on configuring the Advanced proxy features, see: +# http://usegalaxy.org/production + +# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set +# this to True to inform Galaxy that mod_xsendfile is enabled upstream. +#apache_xsendfile = False + +# The same download handling can be done by nginx using X-Accel-Redirect. This +# should be set to the path defined in the nginx config as an internal redirect +# with access to Galaxy's data files (see documentation linked above). +#nginx_x_accel_redirect_base = False + +# nginx can make use of mod_zip to create zip files containing multiple library +# files. If using X-Accel-Redirect, this can be the same value as that option. +#nginx_x_archive_files_base = False + +# If using compression in the upstream proxy server, use this option to disable +# gzipping of library .tar.gz and .zip archives, since the proxy server will do +# it faster on the fly. +#upstream_gzip = False + +# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. +# Configuration for this is complex and explained in detail in the +# documentation linked above. The upload store is a temporary directory in +# which files uploaded by the upload module will be placed. +#nginx_upload_store = False + +# This value overrides the action set on the file upload form, e.g. the web +# path where the nginx_upload_module has been configured to intercept upload +# requests. +#nginx_upload_path = False + +# -- Logging and Debugging + +# Verbosity of console log messages. Acceptable values can be found here: +# http://docs.python.org/library/logging.html#logging-levels +#log_level = DEBUG + +# Print database operations to the server log (warning, quite verbose!). +#database_engine_option_echo = False + +# Print database pool operations to the server log (warning, quite verbose!). +#database_engine_option_echo_pool = False + +# Turn on logging of application events and some user events to the database. +#log_events = True + +# Turn on logging of user actions to the database. Actions currently logged are +# grid views, tool searches, and use of "recently" used tools menu. The +# log_events and log_actions functionality will eventually be merged. +#log_actions = True + +# Sanitize All HTML Tool Output +# By default, all tool output served as 'text/html' will be sanitized +# thoroughly. This can be disabled if you have special tools that require +# unaltered output. +#sanitize_all_html = True + +# By default Galaxy will serve non-HTML tool output that may potentially +# contain browser executable JavaScript content as plain text. This will for +# instance cause SVG datasets to not render properly and so may be disabled +# by setting the following option to True. +#serve_xss_vulnerable_mimetypes = False + +# Debug enables access to various config options useful for development and +# debugging: use_lint, use_profile, use_printdebug and use_interactive. It +# also causes the files used by PBS/SGE (submission script, output, and error) +# to remain on disk after the job is complete. Debug mode is disabled if +# commented, but is uncommented by default in the sample config. +debug = True + +# Check for WSGI compliance. +#use_lint = False + +# Run the Python profiler on each request. +#use_profile = False + +# Intercept print statements and show them on the returned page. +#use_printdebug = True + +# Enable live debugging in your browser. This should NEVER be enabled on a +# public site. Enabled in the sample config for development. +use_interactive = True + +# Write thread status periodically to 'heartbeat.log', (careful, uses disk +# space rapidly!). Useful to determine why your processes may be consuming a +# lot of CPU. +#use_heartbeat = False + +# Enable the memory debugging interface (careful, negatively impacts server +# performance). +#use_memdump = False + +# -- Data Libraries + +# These library upload options are described in much more detail in the wiki: +# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles + +# Add an option to the library upload form which allows administrators to +# upload a directory of files. +#library_import_dir = None + +# Add an option to the library upload form which allows authorized +# non-administrators to upload a directory of files. The configured directory +# must contain sub-directories named the same as the non-admin user's Galaxy +# login ( email ). The non-admin user is restricted to uploading files or +# sub-directories of files contained in their directory. +#user_library_import_dir = None + +# Add an option to the admin library upload tool allowing admins to paste +# filesystem paths to files and directories in a box, and these paths will be +# added to a library. Set to True to enable. Please note the security +# implication that this will give Galaxy Admins access to anything your Galaxy +# user has access to. +#allow_library_path_paste = False + +# Users may choose to download multiple files from a library in an archive. By +# default, Galaxy allows users to select from a few different archive formats +# if testing shows that Galaxy is able to create files using these formats. +# Specific formats can be disabled with this option, separate more than one +# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. +#disable_library_comptypes = + +# Some sequencer integration features in beta allow you to automatically +# transfer datasets. This is done using a lightweight transfer manager which +# runs outside of Galaxy (but is spawned by it automatically). Galaxy will +# communicate with this manager over the port specified here. +#transfer_manager_port = 8163 + +# Search data libraries with whoosh +#enable_whoosh_library_search = True +# Whoosh indexes are stored in this directory. +#whoosh_index_dir = database/whoosh_indexes + +# Search data libraries with lucene +#enable_lucene_library_search = False +# maxiumum file size to index for searching, in MB +#fulltext_max_size = 500 +#fulltext_noindex_filetypes = bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger +# base URL of server providing search functionality using lucene +#fulltext_url = http://localhost:8081 + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +#id_secret = USING THE DEFAULT IS NOT SECURE! + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy +#use_remote_user = False + +# If use_remote_user is enabled and your external authentication +# method just returns bare usernames, set a default mail domain to be appended +# to usernames, to become your Galaxy usernames (email addresses). +#remote_user_maildomain = None + +# If use_remote_user is enabled, the header that the upstream proxy provides +# the remote username in defaults to HTTP_REMOTE_USER (the 'HTTP_' is prepended +# by WSGI). This option allows you to change the header. Note, you still need +# to prepend 'HTTP_' to the header in this option, but your proxy server should +# *not* include 'HTTP_' at the beginning of the header name. +#remote_user_header = HTTP_REMOTE_USER + +# If use_remote_user is enabled, you can set this to a URL that will log your +# users out. +#remote_user_logout_href = None + +# If your proxy and/or authentication source does not normalize e-mail +# addresses or user names being passed to Galaxy - set the following option +# to True to force these to lower case. +#normalize_remote_user_email = False + +# Administrative users - set this to a comma-separated list of valid Galaxy +# users (email addresses). These users will have access to the Admin section +# of the server, and will have access to create users, groups, roles, +# libraries, and more. For more information, see: +# https://wiki.galaxyproject.org/Admin/Interface +#admin_users = None + +# Force everyone to log in (disable anonymous access). +#require_login = False + +# Allow unregistered users to create new accounts (otherwise, they will have to +# be created by an admin). +#allow_user_creation = True + +# Allow administrators to delete accounts. +#allow_user_deletion = False + +# Allow administrators to log in as other users (useful for debugging) +#allow_user_impersonation = False + +# Allow users to remove their datasets from disk immediately (otherwise, +# datasets will be removed after a time period specified by an administrator in +# the cleanup scripts run via cron) +#allow_user_dataset_purge = False + +# By default, users' data will be public, but setting this to True will cause +# it to be private. Does not affect existing users and data, only ones created +# after this option is set. Users may still change their default back to +# public. +#new_user_dataset_access_role_default_private = False + +# -- Beta features + +# Enable Galaxy to communicate directly with a sequencer +#enable_sequencer_communication = False + +# Enable authentication via OpenID. Allows users to log in to their Galaxy +# account by authenticating with an OpenID provider. +#enable_openid = False +# .sample used if default does not exist +#openid_config_file = config/openid_conf.xml +#openid_consumer_cache_path = database/openid_consumer_cache + +# Optional list of email addresses of API users who can make calls on behalf of +# other users +#api_allow_run_as = None + +# Master key that allows many API admin actions to be used without actually +# having a defined admin user in the database/config. Only set this if you need +# to bootstrap Galaxy, you probably do not want to set this on public servers. +#master_api_key = changethis + +# Enable tool tags (associating tools with tags). This has its own option +# since its implementation has a few performance implications on startup for +# large servers. +#enable_tool_tags = False + +# Enable a feature when running workflows. When enabled, default datasets +# are selected for "Set at Runtime" inputs from the history such that the +# same input will not be selected twice, unless there are more inputs than +# compatible datasets in the history. +# When False, the most recently added compatible item in the history will +# be used for each "Set at Runtime" input, independent of others in the Workflow +#enable_unique_workflow_defaults = False + +# The URL to the myExperiment instance being used (omit scheme but include port) +#myexperiment_url = www.myexperiment.org:80 + +# Enable Galaxy's "Upload via FTP" interface. You'll need to install and +# configure an FTP server (we've used ProFTPd since it can use Galaxy's +# database for authentication) and set the following two options. + +# This should point to a directory containing subdirectories matching users' +# email addresses, where Galaxy will look for files. +#ftp_upload_dir = None + +# This should be the hostname of your FTP server, which will be provided to +# users in the help text. +#ftp_upload_site = None + +# Enable enforcement of quotas. Quotas can be set from the Admin interface. +#enable_quotas = False + +# This option allows users to see the full path of datasets via the "View +# Details" option in the history. Administrators can always see this. +#expose_dataset_path = False + +# Data manager configuration options +# Allow non-admin users to view available Data Manager options +#enable_data_manager_user_view = False +# File where Data Managers are configured (.sample used if default does not +# exist) +#data_manager_config_file = config/data_manager_conf.xml +# File where Tool Shed based Data Managers are configured +#shed_data_manager_config_file = config/shed_data_manager_conf.xml +# Directory to store Data Manager based tool-data; defaults to tool_data_path +#galaxy_data_manager_data_path = tool-data + +# -- Job Execution + +# To increase performance of job execution and the web interface, you can +# separate Galaxy into multiple processes. There are more than one way to do +# this, and they are explained in detail in the documentation: +# +# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling + +# By default, Galaxy manages and executes jobs from within a single process and +# notifies itself of new jobs via in-memory queues. Jobs are run locally on +# the system on which Galaxy is started. Advanced job running capabilities can +# be configured through the job configuration file. +#job_config_file = config/job_conf.xml + +# In multiprocess configurations, notification between processes about new jobs +# is done via the database. In single process configurations, this is done in +# memory, which is a bit quicker. Galaxy tries to automatically determine +# which method it should used based on your handler configuration in the job +# config file, but you can explicitly override this behavior by setting the +# following option to True or False. +#track_jobs_in_database = None + +# This enables splitting of jobs into tasks, if specified by the particular tool config. +# This is a new feature and not recommended for production servers yet. +#use_tasked_jobs = False +#local_task_queue_workers = 2 + +# Enable job recovery (if Galaxy is restarted while cluster jobs are running, +# it can "recover" them when it starts). This is not safe to use if you are +# running more than one Galaxy server using the same database. +#enable_job_recovery = True + +# Although it is fairly reliable, setting metadata can occasionally fail. In +# these instances, you can choose to retry setting it internally or leave it in +# a failed state (since retrying internally may cause the Galaxy process to be +# unresponsive). If this option is set to False, the user will be given the +# option to retry externally, or set metadata manually (when possible). +#retry_metadata_internally = True + +# If (for example) you run on a cluster and your datasets (by default, +# database/files/) are mounted read-only, this option will override tool output +# paths to write outputs to the working directory instead, and the job manager +# will move the outputs to their proper place in the dataset directory on the +# Galaxy server after the job completes. +#outputs_to_working_directory = False + +# If your network filesystem's caching prevents the Galaxy server from seeing +# the job's stdout and stderr files when it completes, you can retry reading +# these files. The job runner will retry the number of times specified below, +# waiting 1 second between tries. For NFS, you may want to try the -noac mount +# option (Linux) or -actimeo=0 (Solaris). +#retry_job_output_collection = 0 + +# Clean up various bits of jobs left on the filesystem after completion. These +# bits include the job working directory, external metadata temporary files, +# and DRM stdout and stderr files (if using a DRM). Possible values are: +# always, onsuccess, never +#cleanup_job = always + +# File to source to set up the environment when running jobs. By default, the +# environment in which the Galaxy server starts is used when running jobs +# locally, and the environment set up per the DRM's submission method and +# policy is used when running jobs on a cluster (try testing with `qsub` on the +# command line). environment_setup_file can be set to the path of a file on +# the cluster that should be sourced by the user to set up the environment +# prior to running tools. This can be especially useful for running jobs as +# the actual user, to remove the need to configure each user's environment +# individually. +#environment_setup_file = None + + +# Optional file containing job resource data entry fields definition. +# These fields will be presented to users in the tool forms and allow them to +# overwrite default job resources such as number of processors, memory, and walltime. +#job_resource_params_file = config/job_resource_params_conf.xml + +# If using job concurrency limits (configured in job_config_file), several +# extra database queries must be performed to determine the number of jobs a +# user has dispatched to a given destination. By default, these queries will +# happen for every job that is waiting to run, but if cache_user_job_count is +# set to True, it will only happen once per iteration of the handler queue. +# Although better for performance due to reduced queries, the tradeoff is a +# greater possibility that jobs will be dispatched past the configured limits +# if running many handlers. +#cache_user_job_count = False + +# ToolBox filtering +# Modules from lib/galaxy/tools/filters/ can be specified in the following lines. +# tool_* filters will be applied for all users and can not be changed by them. +# user_tool_* filters will be shown under user preferences and can be toogled +# on and off by runtime +#tool_filters +#tool_label_filters +#tool_section_filters +#user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode +#user_tool_section_filters = examples:restrict_text +#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode + +# Galaxy Application Internal Message Queue + +# Galaxy uses AMQP internally TODO more documentation on what for. +# For examples, see http://ask.github.io/kombu/userguide/connections.html +# +# Without specifying anything here, galaxy will first attempt to use your +# specified database_connection above. If that's not specified either, Galaxy +# will automatically create and use a separate sqlite database located in your +# <galaxy>/database folder (indicated in the commented out line below). + +#amqp_internal_connection = sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE + + + +# ---- Galaxy External Message Queue ------------------------------------------------- + +# Galaxy uses AMQ protocol to receive messages from external sources like +# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +# For Galaxy to receive messages from a message queue the RabbitMQ server has +# to be set up with a user account and other parameters listed below. The 'host' +# and 'port' fields should point to where the RabbitMQ server is running. + +[galaxy_amqp] + +#host = 127.0.0.1 +#port = 5672 +#userid = galaxy +#password = galaxy +#virtual_host = galaxy_messaging_engine +#queue = galaxy_queue +#exchange = galaxy_exchange +#routing_key = bar_code_scanner +#rabbitmqctl_path = /path/to/rabbitmqctl + diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/job_conf.xml.sample_advanced --- /dev/null +++ b/config/job_conf.xml.sample_advanced @@ -0,0 +1,482 @@ +<?xml version="1.0"?> +<job_conf> + <plugins workers="4"> +  + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> + <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/> + <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> +  + <param id="invalidjobexception_state">ok</param> + <param id="invalidjobexception_retries">0</param> + <param id="internalexception_state">ok</param> + <param id="internalexception_retries">0</param> + </plugin> + <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> +  + <param id="drmaa_library_path">/sge/lib/libdrmaa.so</param> + </plugin> + <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> + <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> + <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> + <plugin id="dynamic" type="runner"> +  + <param id="rules_module">galaxy.jobs.rules</param> + </plugin> +  + <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"> +  +  + +  +  + </plugin> + <plugin id="pulsar_mq" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner"> +  + <param id="amqp_url">amqp://guest:guest@localhost:5672//</param> +  + <param id="galaxy_url">http://localhost:8080</param> +  +  +  +  +  +  +  +  +  + </plugin> + <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner"> +  + </plugin> + </plugins> + <handlers default="handlers"> +  + <handler id="handler0" tags="handlers"/> + <handler id="handler1" tags="handlers"/> +  + <handler id="sge_handler"> + <plugin id="sge"/> + </handler> + <handler id="special_handler0" tags="special_handlers"/> + <handler id="special_handler1" tags="special_handlers"/> + <handler id="trackster_handler"/> + </handlers> + <destinations default="local"> +  + <destination id="local" runner="local"/> + <destination id="multicore_local" runner="local"> + <param id="local_slots">4</param> +  + <param id="embed_metadata_in_job">True</param> +  + <job_metrics /> +  + </destination> + <destination id="docker_local" runner="local"> + <param id="docker_enabled">true</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + +  +  + +  +  + + </destination> + <destination id="pbs" runner="pbs" tags="mycluster"/> + <destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"> +  + <param id="Resource_List">walltime=72:00:00</param> + </destination> + <destination id="remote_cluster" runner="drmaa" tags="longjobs"/> + <destination id="java_cluster" runner="drmaa"> +  + <env id="_JAVA_OPTIONS">-Xmx=6GB</env> + <env id="ANOTHER_OPTION" raw="true">'5'</env> + <env file="/mnt/java_cluster/environment_setup.sh" /> + <env exec="module load javastuff/2.10" /> +  + </destination> + <destination id="real_user_cluster" runner="drmaa"> +  + <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> + <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> + <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> + </destination> + <destination id="dynamic" runner="dynamic"> +  + <param id="function">foo</param> + </destination> + <destination id="load_balance" runner="dynamic"> + <param id="type">choose_one</param> +  + <param id="destination_ids">cluster1,cluster2,cluster3</param> + </destination> + <destination id="load_balance_with_data_locality" runner="dynamic"> +  + <param id="type">choose_one</param> + <param id="destination_ids">cluster1,cluster2,cluster3</param> + <param id="hash_by">workflow_invocation,history</param> + </destination> + <destination id="burst_out" runner="dynamic"> +  + <param id="type">burst</param> + <param id="from_destination_ids">local_cluster_8_core,local_cluster_1_core,local_cluster_16_core</param> + <param id="to_destination_id">shared_cluster_8_core</param> + <param id="num_jobs">50</param> +  + </destination> + <destination id="docker_dispatch" runner="dynamic"> +  + <param id="type">docker_dispatch</param> + <param id="docker_destination_id">docker_cluster</param> + <param id="default_destination_id">normal_cluster</param> + </destination> + <destination id="secure_pulsar_rest_dest" runner="pulsar_rest"> + <param id="url">https://examle.com:8913/</param> +  + <param id="private_token">123456789changeme</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + </destination> + <destination id="pulsar_mq_dest" runner="amqp_pulsar" > +  + <param id="jobs_directory">/path/to/remote/pulsar/files/staging/</param> +  + </destination> + <destination id="ssh_torque" runner="cli"> + <param id="shell_plugin">SecureShell</param> + <param id="job_plugin">Torque</param> + <param id="shell_username">foo</param> + <param id="shell_hostname">foo.example.org</param> + <param id="job_Resource_List">walltime=24:00:00,ncpus=4</param> + </destination> + +  + <destination id="ssh_slurm" runner="cli"> + <param id="shell_plugin">SecureShell</param> + <param id="job_plugin">Slurm</param> + <param id="shell_username">foo</param> + <param id="shell_hostname">my_host</param> + <param id="job_time">2:00:00</param> + <param id="job_ncpus">4</param> + <param id="job_partition">my_partition</param> + </destination> + + <destination id="condor" runner="condor"> +  + <param id="request_cpus">8</param> + </destination> + +  + <destination id="short_fast" runner="slurm"> + <param id="nativeSpecification">--time=00:05:00 --nodes=1</param> + <resubmit condition="walltime_reached" destination="long_slow" handler="sge_handler" /> + </destination> + <destination id="long_slow" runner="sge"> +  + <param id="nativeSpecification">-l h_rt=96:00:00</param> + </destination> + + </destinations> + <resources default="default"> +  + <group id="default"></group> + <group id="memoryonly">memory</group> + <group id="all">processors,memory,time,project</group> + </resources> + <tools> +  + <tool id="foo" handler="trackster_handler"> + <param id="source">trackster</param> + </tool> + <tool id="bar" destination="dynamic"/> +  + <tool id="longbar" destination="dynamic" resources="all" /> + <tool id="baz" handler="special_handlers" destination="bigmem"/> + </tools> + <limits> +  +  + <limit type="registered_user_concurrent_jobs">2</limit> +  + <limit type="anonymous_user_concurrent_jobs">1</limit> +  + <limit type="destination_user_concurrent_jobs" id="local">1</limit> + <limit type="destination_user_concurrent_jobs" tag="mycluster">2</limit> + <limit type="destination_user_concurrent_jobs" tag="longjobs">1</limit> +  + <limit type="destination_total_concurrent_jobs" id="local">16</limit> + <limit type="destination_total_concurrent_jobs" tag="longjobs">100</limit> +  + <limit type="walltime">24:00:00</limit> +  + <limit type="output_size">10GB</limit> + </limits> +</job_conf> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/job_conf.xml.sample_basic --- /dev/null +++ b/config/job_conf.xml.sample_basic @@ -0,0 +1,13 @@ +<?xml version="1.0"?> + +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"/> + </destinations> +</job_conf> diff -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 -r 5f90a490e9971685945081cbed681c961932a4fd config/job_metrics_conf.xml.sample --- /dev/null +++ b/config/job_metrics_conf.xml.sample @@ -0,0 +1,124 @@ +<?xml version="1.0"?> + +<job_metrics> +  + +  + <core /> + +  +  +  +  + +  +  + +  +  + +  +  +  +  + +  +  +</job_metrics> This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Update tag latest_2014.08.11 for changeset 2c0a15d8d6b4
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/65d1a7c363e9/ Changeset: 65d1a7c363e9 Branch: stable User: natefoo Date: 2014-09-16 15:00:31 Summary: Update tag latest_2014.08.11 for changeset 2c0a15d8d6b4 Affected #: 1 file diff -r 2c0a15d8d6b4a98295df6f3b614bb54da452d1d9 -r 65d1a7c363e95b1af3ba81655c3965d5b8917af0 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -e8453771b1dbfe462974b63216e00752fb8c4097 latest_2014.08.11 +2c0a15d8d6b4a98295df6f3b614bb54da452d1d9 latest_2014.08.11 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Ui: Fix checkbox border
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/76a4156aefd3/ Changeset: 76a4156aefd3 User: guerler Date: 2014-09-16 09:09:18 Summary: Ui: Fix checkbox border Affected #: 2 files diff -r 05d002ec72e1c99317d32d976b4aae6450227de4 -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -148,7 +148,7 @@ .form-control::-moz-placeholder{color:#999} .form-control:-ms-input-placeholder{color:#999} .form-control::-webkit-input-placeholder{color:#999} -.form-control,.ui-form-slider .ui-form-slider-text,.ui-input,.ui-textarea{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} +.form-control,.ui-checkbox,.ui-form-slider .ui-form-slider-text,.ui-input,.ui-textarea{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} .form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee} textarea.form-control{height:auto} .form-group{margin-bottom:15px} @@ -1279,6 +1279,7 @@ .upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px} .upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop} .ui-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px} +.ui-checkbox{height:100% !important} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} .ui-form-slider .ui-form-slider-text{width:100px;float:left} .ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px} diff -r 05d002ec72e1c99317d32d976b4aae6450227de4 -r 76a4156aefd3e7076571f18e9199dde1fb05b0f3 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -5,6 +5,11 @@ padding: 5px; } +.ui-checkbox { + &:extend(.form-control); + height: 100% !important; +} + .ui-table-form-error { display: none; .ui-table-form-error-text { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Ui: Add packed script, fix attributes
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/05d002ec72e1/ Changeset: 05d002ec72e1 User: guerler Date: 2014-09-16 08:42:09 Summary: Ui: Add packed script, fix attributes Affected #: 2 files diff -r 673228acc8abfeb724c3e5306ff5b2da24d70858 -r 05d002ec72e1c99317d32d976b4aae6450227de4 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -3,22 +3,17 @@ /** base class for options based ui elements **/ var OptionsBase = Backbone.View.extend({ - // settings - settings : { - multiple : false - }, - - // options - optionsDefault: { - value : [], - visible : true, - data : [], - id : Utils.uuid(), - empty : 'No data available' - }, - // initialize initialize: function(options) { + // options + this.optionsDefault = { + value : [], + visible : true, + data : [], + id : Utils.uuid(), + empty : 'No data available' + }; + // configure options this.options = Utils.merge(options, this.optionsDefault); @@ -123,7 +118,7 @@ } // return multiple or single value - if (this.settings.multiple) { + if (this.options.multiple) { var values = []; selected.each(function() { values.push($(this).val()); @@ -145,7 +140,7 @@ Checkbox.View = OptionsBase.extend({ // initialize initialize: function(options) { - this.settings.multiple = true; + options.multiple = true; OptionsBase.prototype.initialize.call(this, options); }, @@ -196,8 +191,9 @@ value: function (new_val) { // set new value if (new_val !== undefined) { + this.$el.find('input').prop('checked', false); this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); + this.$el.find('[value="' + new_val + '"]').prop('checked', true).closest('label').addClass('active'); } // get and return value @@ -206,7 +202,7 @@ // template for options _templateOption: function(pair) { - return '<label class="btn btn-default">' + + return '<label class="ui-option btn btn-default">' + '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '">' + pair.label + '</label>'; }, diff -r 673228acc8abfeb724c3e5306ff5b2da24d70858 -r 05d002ec72e1c99317d32d976b4aae6450227de4 static/scripts/packed/mvc/ui/ui-options.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(f){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(f,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var e=this;this.on("change",function(){e._change()})},update:function(f){var h=this._getValue();this.$el.find(".ui-option").remove();for(var g in f){this.$el.append(this._templateOption(f[g]))}var e=this;this.$el.find("input").on("change",function(){e.value(e._getValue());e._change()});this._refresh();this.value(h)},exists:function(f){if(typeof f==="string"){f=[f]}for(var e in f){if(this.$el.find('input[value="'+f[e]+'"]').length>0){return true}}return false},first:function(){var e=this.$el.find("input");if(e.length>0){return e.val()}else{return undefined}},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){this.$el.find(".ui-error").remove();var e=this.$el.find("input").length;if(e==0){this.$el.append(this._templateEmpty())}},_getValue:function(){var f=this.$el.find(":checked");if(f.length==0){return null}if(this.options.multiple){var e=[];f.each(function(){e.push($(this).val())});return e}else{return f.val()}},_templateEmpty:function(){return'<div class="ui-error">'+this.options.empty+"</div>"}});var c={};c.View=a.extend({initialize:function(e){e.multiple=true;a.prototype.initialize.call(this,e)},value:function(e){if(typeof e==="string"){e=[e]}if(e!==undefined){this.$el.find("input").prop("checked",false);for(var f in e){this.$el.find("input[value="+e[f]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(e){return'<div class="ui-option"><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br></div>"},_template:function(){return'<div class="ui-checkbox"/>'}});var d={};d.View=a.extend({initialize:function(e){a.prototype.initialize.call(this,e)},value:function(e){if(e!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+e+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(e){return'<label class="ui-option btn btn-default"><input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>"},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Checkbox:c,RadioButton:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Ui: Unify checkboxes and radio buttons, extend functionality, Upload: Fix code style, ToolForm: Extend dataset filtering
by commits-noreply＠bitbucket.org 16 Sep '14

16 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/673228acc8ab/ Changeset: 673228acc8ab User: guerler Date: 2014-09-16 07:46:17 Summary: Ui: Unify checkboxes and radio buttons, extend functionality, Upload: Fix code style, ToolForm: Extend dataset filtering Affected #: 31 files diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/tools/tools-datasets.js --- a/static/scripts/mvc/tools/tools-datasets.js +++ b/static/scripts/mvc/tools/tools-datasets.js @@ -25,21 +25,26 @@ }, // filter datasets by data type - filterType: function(filter_type) { - // return matched datasets - return this.currHistoryContents.filter( function( content ){ - // link details - var history_content_type = content.get( 'history_content_type' ); - var data_type = content.get( 'file_ext'); + filterType: function(options) { + options = options || {}; + return this.currHistoryContents.filter(function(content){ + // match datatypes + var found = false; + for (var i in options.data_types) { + if (content.get('data_type').indexOf(options.data_types[i]) != -1) { + found = true; + break; + } + } - // apply filter - return history_content_type === 'dataset';// && (data_type === filter_type || filter_type === ''); + // final match result + return (content.get('history_content_type') === options.content_type || !options.content_type) && + (found || !options.data_types) && !content.get('deleted'); }); }, // filter datasets by id filter: function(filter_id) { - // return matched datasets return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) ); } }); diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -56,6 +56,12 @@ }); }, + // message + message: function(options) { + $(this.main_el).empty(); + $(this.main_el).append(ToolTemplate.message(options)); + }, + // reset form reset: function() { for (var i in this.element_list) { @@ -63,6 +69,20 @@ } }, + // refresh + refresh: function() { + // recreate tree structure + this.tree.refresh(); + + // trigger change + for (var id in this.field_list) { + this.field_list[id].trigger('change'); + } + + // log + console.debug('tools-form::refresh() - Recreated tree structure. Refresh.'); + }, + // initialize tool form _initializeToolForm: function() { // link this @@ -135,10 +155,6 @@ button_search.$el.hide(); } - // create message - self.message = new Ui.Message(); - self.portlet.append(self.message.$el); - // append form $(self.main_el).append(self.portlet.$el); @@ -174,22 +190,9 @@ // trigger refresh self.refresh(); //self.job_handler.submit(); + self.tree.finalize(); } }); - }, - - // refresh - refresh: function() { - // recreate tree structure - this.tree.refresh(); - - // trigger change - for (var id in this.field_list) { - this.field_list[id].trigger('change'); - } - - // log - console.debug('tools-form::refresh() - Recreated tree structure. Refresh.'); } }); diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -31,12 +31,16 @@ // success handler function(response) { if (!response.outputs || response.outputs.length == 0) { - console.log(response); + console.debug(response); } + self.app.message({ + text : 'A job has been successfully added to the queue. You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.' + }); self._refreshHdas(); }, // error handler function(response) { + console.debug(response); if (response && response.message && response.message.data) { var error_messages = self.app.tree.match(response.message.data); for (var id in error_messages) { diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -16,13 +16,11 @@ // set text this.$el.find('.ui-table-form-error-text').html(text); this.$el.find('.ui-table-form-error').fadeIn(); - this.$el.addClass('ui-table-row-error'); }, // reset reset: function() { this.$el.find('.ui-table-form-error').hide(); - this.$el.removeClass('ui-table-form-error'); }, // template @@ -35,7 +33,7 @@ } // add error - $input.append('<div class="ui-table-form-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>'); + $input.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>'); // add label if (options.label) { @@ -274,7 +272,7 @@ // dataset column case 'data_column': - field = this._field_data_colum(input_def); + field = this._field_select(input_def); break; // conditional select field diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/tools/tools-select-dataset.js --- a/static/scripts/mvc/tools/tools-select-dataset.js +++ b/static/scripts/mvc/tools/tools-select-dataset.js @@ -6,54 +6,6 @@ initialize : function(app, options) { // link this var self = this; - - // get datasets - var datasets = app.datasets.filterType(); - - // configure options fields - var select_data = []; - for (var i in datasets) { - select_data.push({ - label: datasets[i].get('name'), - value: datasets[i].get('id') - }); - } - - // create select field - this.select = new Ui.Select.View({ - data : select_data, - value : select_data[0].value, - onchange : function() { - self.trigger('change'); - } - }); - - // create select field for multiple files - this.select_multiple = new Ui.Select.View({ - multiple : true, - data : select_data, - value : select_data[0].value, - onchange : function() { - self.trigger('change'); - } - }); - - - // create select field for multiple files - this.select_collection = new Ui.Select.View({ - data : select_data, - value : select_data[0].value, - onchange : function() { - self.trigger('change'); - } - }); - - // add change event. fires on trigger - this.on('change', function() { - if (options.onchange) { - options.onchange(self.value()); - } - }); // tabs this.tabs = new Tabs.View({ @@ -62,20 +14,66 @@ } }); - // add tab - this.tabs.add({ - id : 'single', - title : 'Select a dataset', - $el : this.select.$el + // + // datasets + // + var datasets = app.datasets.filterType({ + content_type : 'dataset', + data_types : options.extensions + }); + + // configure options fields + var dataset_options = []; + for (var i in datasets) { + dataset_options.push({ + label: datasets[i].get('name'), + value: datasets[i].get('id') + }); + } + + // select field + this.select_datasets = new Ui.Select.View({ + multiple : true, + data : dataset_options, + value : dataset_options[0] && dataset_options[0].value, + onchange : function() { + self.trigger('change'); + } }); // add tab this.tabs.add({ - id : 'multiple', - title : 'Select multiple datasets', - $el : this.select_multiple.$el + id : 'datasets', + title : 'Select datasets', + $el : this.select_datasets.$el }); - + + // + // collections + // + var collections = app.datasets.filterType({ + content_type : 'collection', + data_types : options.extensions + }); + + // configure options fields + var collection_options = []; + for (var i in collections) { + collection_options.push({ + label: collections[i].get('name'), + value: collections[i].get('id') + }); + } + + // create select field for collections + this.select_collection = new Ui.Select.View({ + data : collection_options, + value : collection_options[0] && collection_options[0].value, + onchange : function() { + self.trigger('change'); + } + }); + // add tab this.tabs.add({ id : 'collection', @@ -85,18 +83,23 @@ // add element this.setElement(this.tabs.$el); + + // add change event. fires on trigger + this.on('change', function() { + if (options.onchange) { + options.onchange(self.value()); + } + }); }, // value value : function (new_value) { var current_tab = this.tabs.current(); switch(current_tab) { - case 'multiple' : - return this.select_multiple.value(); - case 'collection' : + case 'datasets': + return this.select_datasets.value(); + case 'collection': return this.select_collection.value(); - default : - return this.select.value(); } }, diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -13,6 +13,12 @@ citations: function() { return '<div id="citations"></div>'; + }, + + message: function(options) { + return '<div class="donemessagelarge">' + + '<p>' + options.text + '</p>' + + '</div>'; } }; diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -50,8 +50,8 @@ // converter between raw dictionary and job dictionary function convert(identifier, head) { - for (var i in head) { - var node = head[i]; + for (var index in head) { + var node = head[index]; if (node.input) { // get node var input = node.input; @@ -68,9 +68,9 @@ // handle repeats case 'repeat': var index = 0; - for (var j in node) { - if (j.indexOf('section') != -1) { - convert(job_input_id + '_' + index++, node[j]); + for (var i in node) { + if (i.indexOf('section') != -1) { + convert(job_input_id + '_' + index++, node[i]); } } break; @@ -83,20 +83,38 @@ add (job_input_id + '|' + input.test_param.name, input.id, value); // find selected case - for (var j in input.cases) { - if (input.cases[j].value == value) { - convert(job_input_id, head[input.id + '-section-' + j]); + for (var i in input.cases) { + if (input.cases[i].value == value) { + convert(job_input_id, head[input.id + '-section-' + i]); break; } } break; // handle data inputs case 'data': - var value = { - id : self.app.field_list[input.id].value(), - src : 'hda' + // create array for dataset ids + var dataset_selection = null; + + // collect dataset ids from input field + var value = self.app.field_list[input.id].value(); + if (typeof value === 'string') { + dataset_selection = { + id : value, + src : 'hda' + }; + } else { + // create array of dataset dictionaries for api submission + dataset_selection = []; + for (var i in value) { + dataset_selection.push({ + id : value[i], + src : 'hda' + }); + } } - add(job_input_id, input.id, value); + + // add final array to job definition + add(job_input_id, input.id, dataset_selection); break; // handle boolean input case 'boolean': @@ -118,7 +136,7 @@ // start conversion convert('', this.dict); - + console.log(this.job_def); // return result return this.job_def; }, diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/ui/ui-checkbox.js --- a/static/scripts/mvc/ui/ui-checkbox.js +++ /dev/null @@ -1,91 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// plugin -var View = Backbone.View.extend({ - // options - optionsDefault: { - value : '', - visible : true, - cls : '', - data : [], - id : Utils.uuid() - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // hide input field - if (!this.options.visible) { - this.$el.hide(); - } - - // set initial value - if (this.options.value) { - this.value(this.options.value); - } - - // current value - this.current = this.options.value; - - // onchange event handler. fires on user activity. - var self = this; - this.$el.find('input').on('change', function() { - self.value(self._getValue()); - }); - }, - - // value - value : function (new_val) { - // get current value - var before = this.current; - - // set new value - if (new_val !== undefined) { - this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); - this.current = new_val; - } - - // check value - var after = this.current; - if (after != before && this.options.onchange) { - this.options.onchange(this.current); - } - - // get and return value - return this.current; - }, - - // get value - _getValue: function() { - var selected = this.$el.find(':checked'); - var value = null; - if (selected.length > 0) { - value = selected.val(); - } - return value; - }, - - // element - _template: function(options) { - var tmpl = '<div class="ui-checkbox">'; - for (key in options.data) { - var pair = options.data[key]; - tmpl += '<input type="checkbox" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + '<br>'; - } - tmpl += '</div>'; - return tmpl; - } -}); - -return { - View : View -}; - -}); diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,6 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-checkbox', 'mvc/ui/ui-radiobutton', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, Slider, Checkbox, RadioButton, ButtonMenu, Modal) { +define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], + function(Utils, Select, Slider, Options, ButtonMenu, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -403,8 +403,8 @@ Label : Label, Message : Message, Modal : Modal, - RadioButton : RadioButton, - Checkbox : Checkbox, + RadioButton : Options.RadioButton, + Checkbox : Options.Checkbox, Searchbox : Searchbox, Select : Select, Hidden : Hidden, diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/ui/ui-options.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-options.js @@ -0,0 +1,225 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +/** base class for options based ui elements **/ +var OptionsBase = Backbone.View.extend({ + // settings + settings : { + multiple : false + }, + + // options + optionsDefault: { + value : [], + visible : true, + data : [], + id : Utils.uuid(), + empty : 'No data available' + }, + + // initialize + initialize: function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // hide input field + if (!this.options.visible) { + this.$el.hide(); + } + + // initialize data + this.update(this.options.data); + + // set initial value + if (this.options.value) { + this.value(this.options.value); + } + + // add change event. fires on trigger + var self = this; + this.on('change', function() { + self._change(); + }); + }, + + // update options + update: function(options) { + // backup current value + var current = this._getValue(); + + // remove all options + this.$el.find('.ui-option').remove(); + + // add new options + for (var key in options) { + this.$el.append(this._templateOption(options[key])); + } + + // add change events + var self = this; + this.$el.find('input').on('change', function() { + self.value(self._getValue()); + self._change(); + }); + + // refresh + this._refresh(); + + // set previous value + this.value(current); + }, + + // check if selected value exists (or any if multiple) + exists: function(value) { + if (typeof value === 'string') { + value = [value]; + } + for (var i in value) { + if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { + return true; + } + } + return false; + }, + + // first + first: function() { + var options = this.$el.find('input'); + if (options.length > 0) { + return options.val(); + } else { + return undefined; + } + }, + + // change + _change: function() { + if (this.options.onchange) { + this.options.onchange(this._getValue()); + } + }, + + // refresh + _refresh: function() { + // remove placeholder + this.$el.find('.ui-error').remove(); + + // count remaining options + var remaining = this.$el.find('input').length; + if (remaining == 0) { + this.$el.append(this._templateEmpty()); + } + }, + + // get value + _getValue: function() { + // get selected values + var selected = this.$el.find(':checked'); + if (selected.length == 0) { + return null; + } + + // return multiple or single value + if (this.settings.multiple) { + var values = []; + selected.each(function() { + values.push($(this).val()); + }); + return values; + } else { + return selected.val(); + } + }, + + // template for options + _templateEmpty: function() { + return '<div class="ui-error">' + this.options.empty + '</div>'; + } +}); + +/** checkbox options field **/ +var Checkbox = {}; +Checkbox.View = OptionsBase.extend({ + // initialize + initialize: function(options) { + this.settings.multiple = true; + OptionsBase.prototype.initialize.call(this, options); + }, + + // value + value: function (new_val) { + // check if its an array + if (typeof new_val === 'string') { + new_val = [new_val]; + } + + // set new value + if (new_val !== undefined) { + // reset selection + this.$el.find('input').prop('checked', false); + + // update to new selection + for (var i in new_val) { + this.$el.find('input[value=' + new_val[i] + ']').prop('checked', true); + }; + } + + // get and return value + return this._getValue(); + }, + + // template for options + _templateOption: function(pair) { + return '<div class="ui-option">' + + '<input type="checkbox" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + + '</div>'; + }, + + // template + _template: function() { + return '<div class="ui-checkbox"/>'; + } +}); + +/** radio button options field **/ +var RadioButton = {}; +RadioButton.View = OptionsBase.extend({ + // initialize + initialize: function(options) { + OptionsBase.prototype.initialize.call(this, options); + }, + + // value + value: function (new_val) { + // set new value + if (new_val !== undefined) { + this.$el.find('label').removeClass('active'); + this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); + } + + // get and return value + return this._getValue(); + }, + + // template for options + _templateOption: function(pair) { + return '<label class="btn btn-default">' + + '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '">' + pair.label + + '</label>'; + }, + + // template + _template: function() { + return '<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'; + } +}); + +return { + Checkbox : Checkbox, + RadioButton : RadioButton +}; + +}); diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/ui/ui-radiobutton.js --- a/static/scripts/mvc/ui/ui-radiobutton.js +++ /dev/null @@ -1,93 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// plugin -var View = Backbone.View.extend({ - // options - optionsDefault: { - value : '', - visible : true, - cls : '', - data : [], - id : Utils.uuid() - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // hide input field - if (!this.options.visible) { - this.$el.hide(); - } - - // set initial value - if (this.options.value) { - this.value(this.options.value); - } - - // current value - this.current = this.options.value; - - // onchange event handler. fires on user activity. - var self = this; - this.$el.find('input').on('change', function() { - self.value(self._getValue()); - }); - }, - - // value - value : function (new_val) { - // get current value - var before = this.current; - - // set new value - if (new_val !== undefined) { - this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); - this.current = new_val; - } - - // check value - var after = this.current; - if (after != before && this.options.onchange) { - this.options.onchange(this.current); - } - - // get and return value - return this.current; - }, - - // get value - _getValue: function() { - var selected = this.$el.find(':checked'); - var value = null; - if (selected.length > 0) { - value = selected.val(); - } - return value; - }, - - // element - _template: function(options) { - var tmpl = '<div class="btn-group ui-radiobutton" data-toggle="buttons">'; - for (key in options.data) { - var pair = options.data[key]; - tmpl += '<label class="btn btn-default">' + - '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + - '</label>'; - } - tmpl += '</div>'; - return tmpl; - } -}); - -return { - View : View -}; - -}); diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -172,7 +172,7 @@ // check if selected value exists exists: function(value) { - return this.$select.find('option[value=' + value + ']').length > 0; + return this.$select.find('option[value="' + value + '"]').length > 0; }, // change diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/upload/upload-ftp.js --- a/static/scripts/mvc/upload/upload-ftp.js +++ b/static/scripts/mvc/upload/upload-ftp.js @@ -31,10 +31,9 @@ // fill table _fill: function(ftp_files) { - if (ftp_files.length > 0) { // add table - this.$el.find('#upload-ftp-content').html($(this._template_table())); + this.$el.find('#upload-ftp-content').html($(this._templateTable())); // add files to table var size = 0; @@ -48,7 +47,7 @@ this.$el.find('#upload-ftp-disk').html(Utils.bytesToString (size, true)); } else { // add info - this.$el.find('#upload-ftp-content').html($(this._template_info())); + this.$el.find('#upload-ftp-content').html($(this._templateInfo())); } // hide spinner @@ -58,7 +57,7 @@ // add add: function(ftp_file) { // create new item - var $it = $(this._template_row(ftp_file)); + var $it = $(this._templateRow(ftp_file)); // append to table $(this.el).find('tbody').append($it); @@ -118,7 +117,7 @@ }, // template row - _template_row: function(options) { + _templateRow: function(options) { return '<tr>' + '<td><div id="upload-ftp-add"/></td>' + '<td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">' + options.path + '</p></td>' + @@ -128,8 +127,7 @@ }, // load table template - _template_table: function() - { + _templateTable: function() { return '<span style="whitespace: nowrap; float: left;">Available files: </span>' + '<span style="whitespace: nowrap; float: right;">' + '<span class="upload-icon fa fa-file-text-o"/>' + @@ -151,16 +149,14 @@ }, // load table template - _template_info: function() - { + _templateInfo: function() { return '<div class="upload-ftp-warning warningmessage">' + 'Your FTP directory does not contain any files.' + '</div>'; }, // load html template - _template: function() - { + _template: function() { return '<div class="upload-ftp">' + '<div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/>' + '<div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>' + this.app.options.ftp_upload_site + '</strong> using your Galaxy credentials (email address and password).</div>' + diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -214,16 +214,14 @@ // // genome - _refreshGenome: function() - { + _refreshGenome: function() { // update genome info on screen var genome = this.model.get('genome'); this.select_genome.value(genome); }, // progress - _refreshInfo: function() - { + _refreshInfo: function() { // write error message var info = this.model.get('info'); if (info) { @@ -234,8 +232,7 @@ }, // progress - _refreshPercentage : function() - { + _refreshPercentage : function() { var percentage = parseInt(this.model.get('percentage')); this.$el.find('.progress-bar').css({ width : percentage + '%' }); if (percentage != 100) @@ -245,8 +242,7 @@ }, // status - _refreshStatus : function() - { + _refreshStatus : function() { // get element var it = this.$el; @@ -315,8 +311,7 @@ }, // attach file info popup - _showExtensionInfo : function() - { + _showExtensionInfo : function() { // initialize var $el = $(this.el).find('#extension-info'); var extension = this.model.get('extension'); @@ -343,8 +338,7 @@ }, // attach file info popup - _showSettings : function() - { + _showSettings : function() { // check if popover is visible if (!this.settings.visible) { // show popover @@ -371,8 +365,7 @@ }, // template - _template: function(options) - { + _template: function(options) { return '<tr id="upload-item-' + options.id + '" class="upload-item">' + '<td>' + '<div style="position: relative;">' + diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/upload/upload-settings.js --- a/static/scripts/mvc/upload/upload-settings.js +++ b/static/scripts/mvc/upload/upload-settings.js @@ -25,12 +25,12 @@ // ui event: space to tabs this.$el.find('#upload-space-to-tabs').on('click', function() { - self._switch_state('#upload-space-to-tabs', 'space_to_tabs'); + self._switchState('#upload-space-to-tabs', 'space_to_tabs'); }); // ui event: to posix this.$el.find('#upload-to-posix-lines').on('click', function() { - self._switch_state('#upload-to-posix-lines', 'to_posix_lines'); + self._switchState('#upload-to-posix-lines', 'to_posix_lines'); }); // render @@ -45,8 +45,8 @@ // render render: function() { // render states - this._render_state('#upload-space-to-tabs', this.model.get('space_to_tabs')); - this._render_state('#upload-to-posix-lines', this.model.get('to_posix_lines')); + this._renderState('#upload-space-to-tabs', this.model.get('space_to_tabs')); + this._renderState('#upload-to-posix-lines', this.model.get('to_posix_lines')); // disable options var $cover = this.$el.find('#upload-settings-cover'); @@ -58,16 +58,16 @@ }, // switch state - _switch_state: function (element_id, parameter_id) { + _switchState: function (element_id, parameter_id) { if (this.model.get('status') == 'init') { var checked = !this.model.get(parameter_id); this.model.set(parameter_id, checked); - this._render_state(element_id, checked); + this._renderState(element_id, checked); } }, // render state - _render_state: function (element_id, checked) { + _renderState: function (element_id, checked) { // swith icon class var $it = this.$el.find(element_id); $it.removeClass(); @@ -79,8 +79,7 @@ }, // load template - _template: function() - { + _template: function() { return '<div class="upload-settings" style="position: relative;">' + '<div id="upload-settings-cover" class="upload-settings-cover"/>' + '<table class="table table-striped">' + diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -19,8 +19,7 @@ ) { // galaxy upload -return Backbone.View.extend( -{ +return Backbone.View.extend({ // options options : { nginx_upload_path : '' diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/tools/tools-datasets.js --- a/static/scripts/packed/mvc/tools/tools-datasets.js +++ b/static/scripts/packed/mvc/tools/tools-datasets.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-contents"],function(a){return Backbone.Model.extend({initialize:function(c){this.currHistoryContents=new a.HistoryContents({});this.currHistoryContents.historyId=c.history_id;var b=this;var d=this.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request failed.")})},filterType:function(b){return this.currHistoryContents.filter(function(c){var d=c.get("history_content_type");var e=c.get("file_ext");return d==="dataset"})},filter:function(b){return _.first(this.currHistoryContents.filter(function(c){return c.get("id")===b}))}})}); \ No newline at end of file +define(["mvc/history/history-contents"],function(a){return Backbone.Model.extend({initialize:function(c){this.currHistoryContents=new a.HistoryContents({});this.currHistoryContents.historyId=c.history_id;var b=this;var d=this.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request failed.")})},filterType:function(b){b=b||{};return this.currHistoryContents.filter(function(d){var e=false;for(var c in b.data_types){if(d.get("data_type").indexOf(b.data_types[c])!=-1){e=true;break}}return(d.get("history_content_type")===b.content_type||!b.content_type)&&(e||!b.data_types)&&!d.get("deleted")})},filter:function(b){return _.first(this.currHistoryContents.filter(function(c){return c.get("id")===b}))}})}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(h,l,j,a,f,d,i,k,c,g){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(n){var m=this;this.options=n;this.model=new e({id:n.id});this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.datasets=new i({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},_initializeToolForm:function(){var n=this;var o=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var p=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});this.model.fetch({error:function(q){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");n.portlet=new h.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),buttons:{execute:new l.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){n.job_handler.submit()}})},operations:{button_question:o,button_search:p,button_share:m}});if(!n.options.biostar_url){o.$el.hide();p.$el.hide()}n.message=new l.Message();n.portlet.append(n.message.$el);$(n.main_el).append(n.portlet.$el);if(n.options.help!=""){$(n.main_el).append(d.help(n.options.help))}if(n.options.citations){$(n.main_el).append(d.citations());var q=new j.ToolCitationCollection();q.tool_id=n.options.id;var r=new a.CitationListView({collection:q});r.render();q.fetch()}n.setElement(n.portlet.content());n.section=new k.View(n,{inputs:n.model.get("inputs")});n.portlet.append(n.section.$el);n.refresh()}})},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")}});return{View:b}}); \ No newline at end of file +define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(h,l,j,a,f,d,i,k,c,g){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(n){var m=this;this.options=n;this.model=new e({id:n.id});this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.datasets=new i({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.main_el).empty();$(this.main_el).append(d.message(m))},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")},_initializeToolForm:function(){var n=this;var o=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var p=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});this.model.fetch({error:function(q){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");n.portlet=new h.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),buttons:{execute:new l.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){n.job_handler.submit()}})},operations:{button_question:o,button_search:p,button_share:m}});if(!n.options.biostar_url){o.$el.hide();p.$el.hide()}$(n.main_el).append(n.portlet.$el);if(n.options.help!=""){$(n.main_el).append(d.help(n.options.help))}if(n.options.citations){$(n.main_el).append(d.citations());var q=new j.ToolCitationCollection();q.tool_id=n.options.id;var r=new a.CitationListView({collection:q});r.render();q.fetch()}n.setElement(n.portlet.content());n.section=new k.View(n,{inputs:n.model.get("inputs")});n.portlet.append(n.section.$el);n.refresh();n.tree.finalize()}})}});return{View:b}}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c,b){this.app=c;this.options=a.merge(b,this.optionsDefault)},submit:function(){var b=this;var c={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();a.request("POST",galaxy_config.root+"api/tools",c,function(d){if(!d.outputs||d.outputs.length==0){console.log(d)}b._refreshHdas()},function(d){if(d&&d.message&&d.message.data){var g=b.app.tree.match(d.message.data);for(var f in g){var e=g[f];if(!e){e="Please verify this parameter."}b.app.element_list[f].error(e)}}})},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c,b){this.app=c;this.options=a.merge(b,this.optionsDefault)},submit:function(){var b=this;var c={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();a.request("POST",galaxy_config.root+"api/tools",c,function(d){if(!d.outputs||d.outputs.length==0){console.debug(d)}b.app.message({text:"A job has been successfully added to the queue. You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered."});b._refreshHdas()},function(d){console.debug(d);if(d&&d.message&&d.message.data){var g=b.app.tree.match(d.message.data);for(var f in g){var e=g[f];if(!e){e="Please verify this parameter."}b.app.element_list[f].error(e)}}})},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-select-dataset"],function(d,b,g,a,c){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-table-row-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-table-form-error")},_template:function(h){var i;if(h.highlight){i=$('<div class="ui-table-element ui-table-form-section"/>')}else{i=$('<div class="ui-table-element"/>')}i.append('<div class="ui-table-form-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});var m=new e({label:"",help:h.help,$el:n.$el,highlight:true});this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var m=new a.View({title_new:"Add "+h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);m.show(i);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el,highlight:true});this.table.add(n.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_data_colum(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_field_conditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(h){var i=this;var j=h.id;return new c.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_field_select:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.RadioButton;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_data_colum:function(h){return new g.Select.View({id:"field-"+h.id,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min||0,max:h.max||1000,step:i})},_field_hidden:function(h){return new g.Hidden({id:"field-"+h.id})},_field_boolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-select-dataset"],function(d,b,g,a,c){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn()},reset:function(){this.$el.find(".ui-table-form-error").hide()},_template:function(h){var i;if(h.highlight){i=$('<div class="ui-table-element ui-table-form-section"/>')}else{i=$('<div class="ui-table-element"/>')}i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});var m=new e({label:"",help:h.help,$el:n.$el,highlight:true});this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var m=new a.View({title_new:"Add "+h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);m.show(i);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el,highlight:true});this.table.add(n.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_field_conditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(h){var i=this;var j=h.id;return new c.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_field_select:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.RadioButton;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_data_colum:function(h){return new g.Select.View({id:"field-"+h.id,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min||0,max:h.max||1000,step:i})},_field_hidden:function(h){return new g.Hidden({id:"field-"+h.id})},_field_boolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/tools/tools-select-dataset.js --- a/static/scripts/packed/mvc/tools/tools-select-dataset.js +++ b/static/scripts/packed/mvc/tools/tools-select-dataset.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(b,d,a){var c=Backbone.View.extend({initialize:function(k,f){var e=this;var h=k.datasets.filterType();var j=[];for(var g in h){j.push({label:h[g].get("name"),value:h[g].get("id")})}this.select=new d.Select.View({data:j,value:j[0].value,onchange:function(){e.trigger("change")}});this.select_multiple=new d.Select.View({multiple:true,data:j,value:j[0].value,onchange:function(){e.trigger("change")}});this.select_collection=new d.Select.View({data:j,value:j[0].value,onchange:function(){e.trigger("change")}});this.on("change",function(){if(f.onchange){f.onchange(e.value())}});this.tabs=new a.View({onchange:function(){e.trigger("change")}});this.tabs.add({id:"single",title:"Select a dataset",$el:this.select.$el});this.tabs.add({id:"multiple",title:"Select multiple datasets",$el:this.select_multiple.$el});this.tabs.add({id:"collection",title:"Select a dataset collection",$el:this.select_collection.$el});this.setElement(this.tabs.$el)},value:function(e){var f=this.tabs.current();switch(f){case"multiple":return this.select_multiple.value();case"collection":return this.select_collection.value();default:return this.select.value()}},update:function(e){this.select.update(e)}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(b,d,a){var c=Backbone.View.extend({initialize:function(m,g){var f=this;this.tabs=new a.View({onchange:function(){f.trigger("change")}});var k=m.datasets.filterType({content_type:"dataset",data_types:g.extensions});var j=[];for(var h in k){j.push({label:k[h].get("name"),value:k[h].get("id")})}this.select_datasets=new d.Select.View({multiple:true,data:j,value:j[0]&&j[0].value,onchange:function(){f.trigger("change")}});this.tabs.add({id:"datasets",title:"Select datasets",$el:this.select_datasets.$el});var l=m.datasets.filterType({content_type:"collection",data_types:g.extensions});var e=[];for(var h in l){e.push({label:l[h].get("name"),value:l[h].get("id")})}this.select_collection=new d.Select.View({data:e,value:e[0]&&e[0].value,onchange:function(){f.trigger("change")}});this.tabs.add({id:"collection",title:"Select a dataset collection",$el:this.select_collection.$el});this.setElement(this.tabs.$el);this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},value:function(e){var f=this.tabs.current();switch(f){case"datasets":return this.select_datasets.value();case"collection":return this.select_collection.value()}},update:function(e){this.select.update(e)}});return{View:c}}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},message:function(a){return'<div class="donemessagelarge"><p>'+a.text+"</p></div>"}}}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(k,l){for(var f in l){var d=l[f];if(d.input){var m=d.input;var h=k;if(k!=""){h+="|"}h+=m.name;switch(m.type){case"repeat":var g=0;for(var e in d){if(e.indexOf("section")!=-1){b(h+"_"+g++,d[e])}}break;case"conditional":var n=a.app.field_list[m.id].value();c(h+"|"+m.test_param.name,m.id,n);for(var e in m.cases){if(m.cases[e].value==n){b(h,l[m.id+"-section-"+e]);break}}break;case"data":var n={id:a.app.field_list[m.id].value(),src:"hda"};c(h,m.id,n);break;case"boolean":var n=a.app.field_list[m.id].value();if(n==="true"){n=m.truevalue}else{n=m.falsevalue}c(h,m.id,n);break;default:c(h,m.id,a.app.field_list[m.id].value())}}}}b("",this.dict);return this.job_def},match:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")||$(i).hasClass("tab-pane")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(h,j){for(var f in j){var d=j[f];if(d.input){var k=d.input;var g=h;if(h!=""){g+="|"}g+=k.name;switch(k.type){case"repeat":var f=0;for(var e in d){if(e.indexOf("section")!=-1){b(g+"_"+f++,d[e])}}break;case"conditional":var l=a.app.field_list[k.id].value();c(g+"|"+k.test_param.name,k.id,l);for(var e in k.cases){if(k.cases[e].value==l){b(g,j[k.id+"-section-"+e]);break}}break;case"data":var m=null;var l=a.app.field_list[k.id].value();if(typeof l==="string"){m={id:l,src:"hda"}}else{m=[];for(var e in l){m.push({id:l[e],src:"hda"})}}c(g,k.id,m);break;case"boolean":var l=a.app.field_list[k.id].value();if(l==="true"){l=k.truevalue}else{l=k.falsevalue}c(g,k.id,l);break;default:c(g,k.id,a.app.field_list[k.id].value())}}}}b("",this.dict);console.log(this.job_def);return this.job_def},match:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")||$(i).hasClass("tab-pane")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/ui/ui-checkbox.js --- a/static/scripts/packed/mvc/ui/ui-checkbox.js +++ /dev/null @@ -1,1 +0,0 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="ui-checkbox">';for(key in d.data){var e=d.data[key];c+='<input type="checkbox" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"<br>"}c+="</div>";return c}});return{View:b}}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/ui/ui-misc.js --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(l,b,f,e,m,q,n){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(r){return'<img class="ui-image '+r.cls+'" src="'+r.url+'"/>'}});var k=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},title:function(r){this.$el.html(r)},_template:function(r){return'<label class="ui-label '+r.cls+'">'+r.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){return'<div><span class="fa '+r.icon+'" class="ui-icon"/> '+r.title+"</div>"}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick);$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s='<button id="'+r.id+'" type="submit" style="float: '+r.floating+';" type="button" class="ui-button '+r.cls+'">';if(r.icon){s+='<i class="icon fa '+r.icon+'"></i> '}s+=r.title+"</button>";return s}});var i=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick);$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s="";if(r.title){s="width: auto;"}var t='<div id="'+r.id+'" style="float: '+r.floating+"; "+s+'" class="ui-button-icon '+r.cls+'">';if(r.title){t+='<div class="button"><i class="icon fa '+r.icon+'"/> <span class="title">'+r.title+"</span></div>"}else{t+='<i class="icon fa '+r.icon+'"/>'}t+="</div>";return t}});var g=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick)},_template:function(r){return'<div><a href="javascript:void(0)" class="ui-anchor '+r.cls+'">'+r.title+"</a></div>"}});var o=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement("<div></div>")},update:function(s){this.options=l.merge(s,this.optionsDefault);if(s.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(s.message);this.$el.fadeIn();if(!s.persistent){var r=this;window.setTimeout(function(){if(r.$el.is(":visible")){r.$el.fadeOut()}else{r.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(r){return'<div class="ui-message alert alert-'+r.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(s){this.options=l.merge(s,this.optionsDefault);this.setElement(this._template(this.options));var r=this;if(this.options.onclick){this.$el.on("submit",function(u){var t=r.$el.find("#search");r.options.onclick(t.val())})}},_template:function(r){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+r.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var j=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(s){this.options=l.merge(s,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var r=this;this.$el.on("input",function(){if(r.options.onchange){r.options.onchange(r.$el.val())}})},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){if(r.area){return'<textarea id="'+r.id+'" class="ui-textarea '+r.cls+'"></textarea>'}else{return'<input id="'+r.id+'" type="'+r.type+'" value="'+r.value+'" placeholder="'+r.placeholder+'" class="ui-input '+r.cls+'">'}}});var p=Backbone.View.extend({optionsDefault:{value:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){return'<hidden id="'+r.id+'" value="'+r.value+'"/>'}});return{Anchor:g,Button:h,ButtonIcon:i,ButtonMenu:q,Icon:c,Image:d,Input:j,Label:k,Message:o,Modal:n,RadioButton:m,Checkbox:e,Searchbox:a,Select:b,Hidden:p,Slider:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,n,p,l){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'<label class="ui-label '+q.cls+'">'+q.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/> '+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick);$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='<button id="'+q.id+'" type="submit" style="float: '+q.floating+';" type="button" class="ui-button '+q.cls+'">';if(q.icon){r+='<i class="icon fa '+q.icon+'"></i> '}r+=q.title+"</button>";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick);$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="ui-button-icon '+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/> <span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'<div><a href="javascript:void(0)" class="ui-anchor '+q.cls+'">'+q.title+"</a></div>"}});var m=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=k.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){if(q.area){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'"></textarea>'}else{return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}}});var o=Backbone.View.extend({optionsDefault:{value:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<hidden id="'+q.id+'" value="'+q.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:i,Label:j,Message:m,Modal:l,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Searchbox:a,Select:b,Hidden:o,Slider:e}}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/ui/ui-radiobutton.js --- a/static/scripts/packed/mvc/ui/ui-radiobutton.js +++ /dev/null @@ -1,1 +0,0 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in d.data){var e=d.data[key];c+='<label class="btn btn-default"><input type="radio" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"</label>"}c+="</div>";return c}});return{View:b}}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find("option[value="+c+"]").length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/upload/upload-ftp.js --- a/static/scripts/packed/mvc/upload/upload-ftp.js +++ b/static/scripts/packed/mvc/upload/upload-ftp.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());a.get(galaxy_config.root+"api/ftp_files",function(d){b._fill(d)})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(c){if(c.length>0){this.$el.find("#upload-ftp-content").html($(this._template_table()));var b=0;for(key in c){this.add(c[key]);b+=c[key].size}this.$el.find("#upload-ftp-number").html(c.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(b,true))}else{this.$el.find("#upload-ftp-content").html($(this._template_info()))}this.$el.find("#upload-ftp-wait").hide()},add:function(e){var d=$(this._template_row(e));$(this.el).find("tbody").append(d);var c="";if(this._find(e)){c=this.options.class_remove}else{c=this.options.class_add}d.find("#upload-ftp-add").addClass(c);var b=this;d.find("#upload-ftp-add").on("click",function(){var f=b._find(e);$(this).removeClass();if(!f){b.app.uploadbox.add([{mode:"ftp",name:e.path,size:e.size,path:e.path}]);$(this).addClass(b.options.class_remove)}else{b.app.collection.remove(f);$(this).addClass(b.options.class_add)}})},_find:function(f){var c=this.app.collection.where({file_path:f.path});var b=null;for(var d in c){var e=c[d];if(e.get("status")=="init"&&e.get("file_mode")=="ftp"){b=e.get("id")}}return b},_template_row:function(b){return'<tr><td><div id="upload-ftp-add"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+b.path+'</p></td><td style="white-space: nowrap;">'+a.bytesToString(b.size)+'</td><td style="white-space: nowrap;">'+b.ctime+"</td></tr>"},_template_table:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_template_info:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());a.get(galaxy_config.root+"api/ftp_files",function(d){b._fill(d)})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(c){if(c.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var b=0;for(key in c){this.add(c[key]);b+=c[key].size}this.$el.find("#upload-ftp-number").html(c.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(b,true))}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},add:function(e){var d=$(this._templateRow(e));$(this.el).find("tbody").append(d);var c="";if(this._find(e)){c=this.options.class_remove}else{c=this.options.class_add}d.find("#upload-ftp-add").addClass(c);var b=this;d.find("#upload-ftp-add").on("click",function(){var f=b._find(e);$(this).removeClass();if(!f){b.app.uploadbox.add([{mode:"ftp",name:e.path,size:e.size,path:e.path}]);$(this).addClass(b.options.class_remove)}else{b.app.collection.remove(f);$(this).addClass(b.options.class_add)}})},_find:function(f){var c=this.app.collection.where({file_path:f.path});var b=null;for(var d in c){var e=c[d];if(e.get("status")=="init"&&e.get("file_mode")=="ftp"){b=e.get("id")}}return b},_templateRow:function(b){return'<tr><td><div id="upload-ftp-add"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+b.path+'</p></td><td style="white-space: nowrap;">'+a.bytesToString(b.size)+'</td><td style="white-space: nowrap;">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/scripts/packed/mvc/upload/upload-settings.js --- a/static/scripts/packed/mvc/upload/upload-settings.js +++ b/static/scripts/packed/mvc/upload/upload-settings.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_check:"upload-icon-button fa fa-check-square-o",class_uncheck:"upload-icon-button fa fa-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());this.model=this.app.model;this.$el.find("#upload-space-to-tabs").on("click",function(){b._switch_state("#upload-space-to-tabs","space_to_tabs")});this.$el.find("#upload-to-posix-lines").on("click",function(){b._switch_state("#upload-to-posix-lines","to_posix_lines")});this.render()},events:{mousedown:function(b){b.preventDefault()}},render:function(){this._render_state("#upload-space-to-tabs",this.model.get("space_to_tabs"));this._render_state("#upload-to-posix-lines",this.model.get("to_posix_lines"));var b=this.$el.find("#upload-settings-cover");if(this.model.get("status")!="init"){b.show()}else{b.hide()}},_switch_state:function(c,b){if(this.model.get("status")=="init"){var d=!this.model.get(b);this.model.set(b,d);this._render_state(c,d)}},_render_state:function(b,d){var c=this.$el.find(b);c.removeClass();if(d){c.addClass(this.options.class_check)}else{c.addClass(this.options.class_uncheck)}},_template:function(){return'<div class="upload-settings" style="position: relative;"><div id="upload-settings-cover" class="upload-settings-cover"/><table class="table table-striped"><tbody><tr><td><div id="upload-space-to-tabs"/></td><td>Convert spaces to tabs</td></tr><tr><td><div id="upload-to-posix-lines"/></td><td>Use POSIX standard</td></tr></tbody></table></div>'}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_check:"upload-icon-button fa fa-check-square-o",class_uncheck:"upload-icon-button fa fa-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());this.model=this.app.model;this.$el.find("#upload-space-to-tabs").on("click",function(){b._switchState("#upload-space-to-tabs","space_to_tabs")});this.$el.find("#upload-to-posix-lines").on("click",function(){b._switchState("#upload-to-posix-lines","to_posix_lines")});this.render()},events:{mousedown:function(b){b.preventDefault()}},render:function(){this._renderState("#upload-space-to-tabs",this.model.get("space_to_tabs"));this._renderState("#upload-to-posix-lines",this.model.get("to_posix_lines"));var b=this.$el.find("#upload-settings-cover");if(this.model.get("status")!="init"){b.show()}else{b.hide()}},_switchState:function(c,b){if(this.model.get("status")=="init"){var d=!this.model.get(b);this.model.set(b,d);this._renderState(c,d)}},_renderState:function(b,d){var c=this.$el.find(b);c.removeClass();if(d){c.addClass(this.options.class_check)}else{c.addClass(this.options.class_uncheck)}},_template:function(){return'<div class="upload-settings" style="position: relative;"><div id="upload-settings-cover" class="upload-settings-cover"/><table class="table table-striped"><tbody><tr><td><div id="upload-space-to-tabs"/></td><td>Convert spaces to tabs</td></tr><tr><td><div id="upload-to-posix-lines"/></td><td>Use POSIX standard</td></tr></tbody></table></div>'}})}); \ No newline at end of file diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1278,7 +1278,7 @@ .upload-ftp .upload-ftp-help{margin-bottom:10px} .upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px} .upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop} -.ui-table-row-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px} +.ui-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} .ui-form-slider .ui-form-slider-text{width:100px;float:left} .ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px} diff -r cb6dffff27973cff0afd22d9907e675fea948113 -r 673228acc8abfeb724c3e5306ff5b2da24d70858 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -1,4 +1,4 @@ -.ui-table-row-error { +.ui-error { -moz-border-radius: @border-radius-base; border-radius: @border-radius-base; background: @state-danger-bg; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] e7ba88: Use XSEDE Community account for Stampede, but it c...
by GitHub 15 Sep '14

15 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e7ba88e04a5575f5f68d1c52b649fd3ffc332e29 https://github.com/galaxyproject/usegalaxy-playbook/commit/e7ba88e04a5575f5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-15 (Mon, 15 Sep 2014) Changed paths: M stage/inventory Log Message: ----------- Use XSEDE Community account for Stampede, but it can't log in to login5, so use login1 for deployment. Commit: f0a8043ac0cb95980aa1b5a0107f4400d00f0cfd https://github.com/galaxyproject/usegalaxy-playbook/commit/f0a8043ac0cb9598… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-15 (Mon, 15 Sep 2014) Changed paths: M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml A files/galaxy/usegalaxy.org/dynamic_rules/roundup_stampede_select.py M production/group_vars/galaxyservers.yml A production/group_vars/pulsarservers.yml A production/host_vars/login5.stampede.tacc.utexas.edu.yml M production/inventory A production/secret_vars/pulsarservers.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Deploy Pulsar for Main. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/14926e345bc4...…

1 0

commit/galaxy-central: davebgx: Merged in greg/gvk-galaxy-central (pull request #485)
by commits-noreply＠bitbucket.org 15 Sep '14

15 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cb6dffff2797/ Changeset: cb6dffff2797 User: davebgx Date: 2014-09-15 22:34:18 Summary: Merged in greg/gvk-galaxy-central (pull request #485) Encapsulate the Tool Shed's metadata generator. Affected #: 13 files diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -417,12 +417,13 @@ query = irmm.get_query_for_setting_metadata_on_repositories( order=False ) # Now reset metadata on all remaining repositories. for repository in query: - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + irmm.set_repository( repository ) + irmm.reset_all_metadata_on_installed_repository() + irmm_invalid_file_tups = irmm.get_invalid_file_tups() + if irmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + irmm_invalid_file_tups, repository, None, as_html=False ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1732,20 +1732,21 @@ tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata - irmm = InstalledRepositoryMetadataManager( trans.app ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - irmm.update_in_shed_tool_config( repository ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + repository=repository, + changeset_revision=repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if irmm_metadata_dict != original_metadata_dict: + repository.metadata = irmm_metadata_dict + irmm.update_in_shed_tool_config() trans.install_model.context.add( repository ) trans.install_model.context.flush() message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name @@ -1938,22 +1939,24 @@ dmh.remove_from_data_manager( repository ) # Update the repository metadata. tpm = tool_panel_manager.ToolPanelManager( trans.app ) - irmm = InstalledRepositoryMetadataManager( trans.app, tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=latest_changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + tpm=tpm, + repository=repository, + changeset_revision=latest_changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if 'tools' in irmm_metadata_dict: + tool_panel_dict = irmm_metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() tpm.add_to_tool_panel( repository_name=str( repository.name ), repository_clone_url=repository_clone_url, changeset_revision=str( repository.installed_changeset_revision ), @@ -1963,18 +1966,18 @@ tool_panel_dict=tool_panel_dict, new_install=False ) # Add new Data Manager entries - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( trans.app ) new_data_managers = dmh.install_data_managers( trans.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, repository.get_shed_config_dict( trans.app ), os.path.join( relative_install_dir, name ), repository, repository_tools_tups ) - if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: - new_repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + if 'repository_dependencies' in irmm_metadata_dict or 'tool_dependencies' in irmm_metadata_dict: + new_repository_dependencies_dict = irmm_metadata_dict.get( 'repository_dependencies', {} ) new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] ) - new_tool_dependencies_dict = metadata_dict.get( 'tool_dependencies', {} ) + new_tool_dependencies_dict = irmm_metadata_dict.get( 'tool_dependencies', {} ) if new_repository_dependencies: # [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']] proceed_to_install = False @@ -2017,7 +2020,7 @@ updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), updating=True ) return self.prepare_for_install( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies but did include @@ -2033,12 +2036,12 @@ proceed_to_install = True break if proceed_to_install: - encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) + encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( irmm_metadata_dict.get( 'tool_dependencies', {} ) ) encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), encoded_relative_install_dir=encoded_relative_install_dir, encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, message=message, @@ -2047,7 +2050,7 @@ # Updates received did not include any newly defined repository dependencies or newly defined # tool dependencies that need to be installed. repository = trans.app.update_repository_manager.update_repository_record( repository=repository, - updated_metadata_dict=metadata_dict, + updated_metadata_dict=irmm_metadata_dict, updated_changeset_revision=latest_changeset_revision, updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -429,13 +429,13 @@ def handle_repository( trans, rmm, repository, results ): log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + rmm.set_repository( repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) @@ -451,7 +451,11 @@ status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) results = dict( start_time=start_time, repository_status=[], @@ -511,12 +515,17 @@ results = dict( start_time=start_time, repository_status=[] ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.security.encode_id( repository.id ) ) - if invalid_file_tups: + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -1,6 +1,8 @@ import os, logging from galaxy import web from galaxy.web.base.controller import BaseUIController + +from tool_shed.util.common_util import generate_clone_url_for_repository_in_tool_shed from tool_shed.util.shed_util_common import get_repository_by_name_and_owner from tool_shed.util.hg_util import update_repository from tool_shed.metadata import repository_metadata_manager @@ -47,9 +49,19 @@ # interface will result in a new head being created. repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) # Set metadata using the repository files on disk. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - error_message, status = rmm.set_repository_metadata( trans.request.host, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + changeset_revision=repository.tip( trans.app ), + repository_clone_url=repository_clone_url, + relative_install_dir=repository.repo_path( trans.app ), + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + error_message, status = rmm.set_repository_metadata( trans.request.host ) if status == 'ok' and error_message: log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ ( str( repository.name ), str( repository.user.username ), error_message ) ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2759,15 +2759,18 @@ def reset_all_metadata( self, trans, id, **kwd ): """Reset all metadata on the complete changelog for a single repository in the tool shed.""" # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( id ) - if invalid_file_tups: - repository = suc.get_repository_in_tool_shed( trans.app, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_metadata_dict = rmm.get_metadata_dict() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, - metadata_dict ) + rmm_metadata_dict ) status = 'error' else: message = "All repository metadata has been reset. " @@ -2849,10 +2852,10 @@ if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, - **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, **kwd ) if error_message: message = error_message else: diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -263,10 +263,11 @@ ( len( files_to_remove ), upload_point ) else: message += " %d files were removed from the repository root. " % len( files_to_remove ) - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) status, error_message = \ rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, content_alert_str=content_alert_str, **kwd ) if error_message: diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -792,9 +792,10 @@ results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, self.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=self.app, + user=self.user, + repository=repository ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, - repository, content_alert_str=content_alert_str ) if error_message: results_dict[ 'ok' ] = False diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -510,31 +510,33 @@ """ shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) tdtm = data_table_manager.ToolDataTableManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict # Update the tool_shed_repository.tool_shed_status column in the database. tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository ) if tool_shed_status_dict: tool_shed_repository.tool_shed_status = tool_shed_status_dict self.install_model.context.add( tool_shed_repository ) self.install_model.context.flush() - if 'tool_dependencies' in metadata_dict and not reinstalling: + if 'tool_dependencies' in irmm_metadata_dict and not reinstalling: tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) - if 'sample_files' in metadata_dict: - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'sample_files' in irmm_metadata_dict: + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_data_table_conf_filename, tool_data_table_elems = \ tdtm.install_tool_data_tables( tool_shed_repository, tool_index_sample_files ) @@ -543,13 +545,13 @@ None, self.app.config.shed_tool_data_table_config, persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'tools' in irmm_metadata_dict: + tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( irmm_metadata_dict[ 'tools' ], tool_section ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. repository_tools_tups = tdtm.handle_missing_data_table_entry( relative_install_dir, @@ -575,15 +577,15 @@ shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=True ) - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, shed_config_dict, relative_install_dir, tool_shed_repository, repository_tools_tups ) - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: tool_shed_repository.status = self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: tool_shed_repository.includes_datatypes = True @@ -604,7 +606,7 @@ name=tool_shed_repository.name, owner=tool_shed_repository.owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -82,9 +82,12 @@ repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools_for_display_in_tool_panel: tpm = tool_panel_manager.ToolPanelManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, tpm ) - metadata = repository.metadata - repository_tools_tups = irmm.get_repository_tools_tups( metadata ) + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=tpm, + repository=repository, + changeset_revision=repository.changeset_revision, + metadata_dict=repository.metadata ) + repository_tools_tups = irmm.get_repository_tools_tups() # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] tpm.add_to_tool_panel( repository.name, @@ -101,7 +104,7 @@ data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata, + repository.metadata, repository.get_shed_config_dict( self.app ), data_manager_relative_install_dir, repository, diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -19,9 +19,16 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, tpm=None ): - super( InstalledRepositoryMetadataManager, self ).__init__( app ) - self.app = app + def __init__( self, app, tpm=None, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( InstalledRepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=None ) if tpm is None: self.tpm = tool_panel_manager.ToolPanelManager( self.app ) else: @@ -53,15 +60,15 @@ return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) - def get_repository_tools_tups( self, metadata_dict ): + def get_repository_tools_tups( self ): """ Return a list of tuples of the form (relative_path, guid, tool) for each tool defined in the received tool shed repository metadata. """ repository_tools_tups = [] - index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( metadata_dict.get( 'shed_config_filename' ) ) - if 'tools' in metadata_dict: - for tool_dict in metadata_dict[ 'tools' ]: + index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( self.metadata_dict.get( 'shed_config_filename' ) ) + if 'tools' in self.metadata_dict: + for tool_dict in self.metadata_dict[ 'tools' ]: load_relative_path = relative_path = tool_dict.get( 'tool_config', None ) if shed_conf_dict.get( 'tool_path' ): load_relative_path = os.path.join( shed_conf_dict.get( 'tool_path' ), relative_path ) @@ -74,36 +81,21 @@ repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups - def reset_all_metadata_on_installed_repository( self, id ): + def reset_all_metadata_on_installed_repository( self ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" - invalid_file_tups = [] - metadata_dict = {} - repository = repository_util.get_installed_tool_shed_repository( self.app, id ) - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - tool_path, relative_install_dir = repository.get_tool_relative_path( self.app ) - if relative_install_dir: - original_metadata_dict = repository.metadata - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( self.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - self.update_in_shed_tool_config( repository ) - self.app.install_model.context.add( repository ) + if self.relative_install_dir: + original_metadata_dict = self.repository.metadata + self.generate_metadata_for_changeset_revision() + if self.metadata_dict != original_metadata_dict: + self.repository.metadata = self.metadata_dict + self.update_in_shed_tool_config() + self.app.install_model.context.add( self.repository ) self.app.install_model.context.flush() - log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + log.debug( 'Metadata has been reset on repository %s.' % self.repository.name ) else: - log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + log.debug( 'Metadata did not need to be reset on repository %s.' % self.repository.name ) else: - log.debug( 'Error locating installation directory for repository %s.' % repository.name ) - return invalid_file_tups, metadata_dict + log.debug( 'Error locating installation directory for repository %s.' % self.repository.name ) def reset_metadata_on_selected_repositories( self, user, **kwd ): """ @@ -119,19 +111,19 @@ for repository_id in repository_ids: try: repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id ) - owner = str( repository.owner ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_installed_repository() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) log.debug( message ) unsuccessful_count += 1 else: - log.debug( "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), owner ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s" % \ + ( str( repository.name ), str( repository.owner ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) ) @@ -146,32 +138,37 @@ status = 'error' return message, status - def tool_shed_from_repository_clone_url( self, repository_clone_url ): + def set_repository( self, repository ): + super( InstalledRepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) + + def tool_shed_from_repository_clone_url( self ): """Given a repository clone URL, return the tool shed that contains the repository.""" - return common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) + return common_util.remove_protocol_and_user_from_clone_url( cleaned_repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) - def update_in_shed_tool_config( self, repository ): + def update_in_shed_tool_config( self ): """ A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list of config_elems instead of using the in-memory list. """ - shed_conf_dict = repository.get_shed_config_dict( self.app ) + shed_conf_dict = self.repository.get_shed_config_dict( self.app ) shed_tool_conf = shed_conf_dict[ 'config_filename' ] tool_path = shed_conf_dict[ 'tool_path' ] - tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = self.get_repository_tools_tups( repository.metadata ) - clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) - tool_shed = self.tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) - owner = repository.owner + tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( self.repository ) + repository_tools_tups = self.get_repository_tools_tups() + clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + tool_shed = self.tool_shed_from_repository_clone_url() + owner = self.repository.owner if not owner: + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) owner = suc.get_repository_owner( cleaned_repository_clone_url ) guid_to_tool_elem_dict = {} for tool_config_filename, guid, tool in repository_tools_tups: guid_to_tool_elem_dict[ guid ] = self.tpm.generate_tool_elem( tool_shed, - repository.name, - repository.changeset_revision, - repository.owner or '', + self.repository.name, + self.repository.changeset_revision, + self.repository.owner or '', tool_config_filename, tool, None ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -416,21 +416,23 @@ log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) ) finally: lock.release() - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = self.shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = self.shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict self.app.install_model.context.add( tool_shed_repository ) self.app.install_model.context.flush() - has_tool_dependencies = self.__has_tool_dependencies( metadata_dict ) + has_tool_dependencies = self.__has_tool_dependencies( irmm_metadata_dict ) if has_tool_dependencies: # All tool_dependency objects must be created before the tools are processed even if no # tool dependencies will be installed. @@ -440,14 +442,14 @@ set_status=True ) else: tool_dependencies = None - if 'tools' in metadata_dict: + if 'tools' in irmm_metadata_dict: tdtm = data_table_manager.ToolDataTableManager( self.app ) - sample_files = metadata_dict.get( 'sample_files', [] ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) sample_files = [ str( s ) for s in sample_files ] tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically # generated select lists. @@ -491,7 +493,7 @@ if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: @@ -514,7 +516,7 @@ name=tool_shed_repository.name, owner=self.repository_owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -27,31 +27,89 @@ class MetadataGenerator( object ): - def __init__( self, app ): + def __init__( self, app, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None, user=None ): self.app = app + self.user = user + self.repository = repository + if self.app.name == 'galaxy': + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.changeset_revision + else: + self.changeset_revision = changeset_revision + + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + if self.repository is not None: + self.shed_config_dict = self.repository.get_shed_config_dict( self.app ) + else: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_files_directory( self.app ) + if metadata_dict is None: + # Shed related tool panel configs are only relevant to Galaxy. + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + self.metadata_dict = metadata_dict + else: + # We're in the Tool Shed. + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.tip( self.app ) + else: + self.changeset_revision = changeset_revision + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = \ + common_util.generate_clone_url_for_repository_in_tool_shed( self.user, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + relative_install_dir = self.repository.repo_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_path( self.app ) + if metadata_dict is None: + self.metadata_dict = {} + else: + self.metadata_dict = metadata_dict + self.relative_install_dir = relative_install_dir + self.repository_files_dir = repository_files_dir + self.resetting_all_metadata_on_repository = resetting_all_metadata_on_repository + self.updating_installed_repository = updating_installed_repository + self.persist = persist + self.invalid_file_tups = [] self.sa_session = app.model.context.current self.NOT_TOOL_CONFIGS = [ suc.DATATYPES_CONFIG_FILENAME, - rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, - rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, - suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] + rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, + rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, + suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] - def generate_data_manager_metadata( self, repository, repo_dir, data_manager_config_filename, metadata_dict, + def generate_data_manager_metadata( self, repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None ): """ Update the received metadata_dict with information from the parsed data_manager_config_filename. """ if data_manager_config_filename is None: return metadata_dict - repo_path = repository.repo_path( self.app ) + repo_path = self.repository.repo_path( self.app ) try: # Galaxy Side. - repo_files_directory = repository.repo_files_directory( self.app ) + repo_files_directory = self.repository.repo_files_directory( self.app ) repo_dir = repo_files_directory - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) except AttributeError: # Tool Shed side. repo_files_directory = repo_path - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( None, repository ) relative_data_manager_dir = util.relpath( os.path.split( data_manager_config_filename )[0], repo_dir ) rel_data_manager_config_filename = os.path.join( relative_data_manager_dir, os.path.split( data_manager_config_filename )[1] ) @@ -91,7 +149,7 @@ # FIXME: default behavior is to fall back to tool.name. data_manager_name = data_manager_elem.get( 'name', data_manager_id ) version = data_manager_elem.get( 'version', DataManager.DEFAULT_VERSION ) - guid = self.generate_guid_for_object( repository_clone_url, DataManager.GUID_TYPE, data_manager_id, version ) + guid = self.generate_guid_for_object( DataManager.GUID_TYPE, data_manager_id, version ) data_tables = [] if tool_file is None: log.error( 'Data Manager entry is missing tool_file attribute in "%s".' % ( data_manager_config_filename ) ) @@ -130,8 +188,7 @@ log.debug( 'Loaded Data Manager tool_files: %s' % ( tool_file ) ) return metadata_dict - def generate_datatypes_metadata( self, tv, repository, repository_clone_url, repository_files_dir, datatypes_config, - metadata_dict ): + def generate_datatypes_metadata( self, tv, repository_files_dir, datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree, error_message = xml_util.parse_xml( datatypes_config ) if tree is None: @@ -180,11 +237,11 @@ tool_config_path = hg_util.get_config_from_disk( tool_config, repository_files_dir ) full_path = os.path.abspath( tool_config_path ) tool, valid, error_message = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), full_path ) + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: guid = None else: - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) converter_dict = dict( tool_config=tool_config, guid=guid, target_datatype=target_datatype ) @@ -226,76 +283,70 @@ valid_tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return valid_tool_dependencies_dict - def generate_guid_for_object( self, repository_clone_url, guid_type, obj_id, version ): - tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) + def generate_guid_for_object( self, guid_type, obj_id, version ): + tmp_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) return '%s/%s/%s/%s' % ( tmp_url, guid_type, obj_id, version ) - def generate_metadata_for_changeset_revision( self, repository, changeset_revision, repository_clone_url, - shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, - persist=False ): + def generate_metadata_for_changeset_revision( self ): """ Generate metadata for a repository using its files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access - that changeset revision's disk files, so the value of repository_files_dir will not - always be repository.repo_path( self.app ) (it could be an absolute path to a temporary - directory containing a clone). If it is an absolute path, the value of relative_install_dir + that changeset revision's disk files, so the value of self.repository_files_dir will not + always be self.repository.repo_path( self.app ) (it could be an absolute path to a temporary + directory containing a clone). If it is an absolute path, the value of self.relative_install_dir must contain repository.repo_path( self.app ). - The value of persist will be True when the installed repository contains a valid + The value of self.persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by self.app.config.shed_tool_data_table_config. """ tv = tool_validator.ToolValidator( self.app ) - if shed_config_dict is None: - shed_config_dict = {} - if updating_installed_repository: + if self.shed_config_dict is None: + self.shed_config_dict = {} + if self.updating_installed_repository: # Keep the original tool shed repository metadata if setting metadata on a repository # installed into a local Galaxy instance for which we have pulled updates. - original_repository_metadata = repository.metadata + original_repository_metadata = self.repository.metadata else: original_repository_metadata = None - readme_file_names = readme_util.get_readme_file_names( str( repository.name ) ) + readme_file_names = readme_util.get_readme_file_names( str( self.repository.name ) ) if self.app.name == 'galaxy': # Shed related tool panel configs are only relevant to Galaxy. - metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } + metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename' ) } else: metadata_dict = {} readme_files = [] - invalid_file_tups = [] invalid_tool_configs = [] tool_dependencies_config = None original_tool_data_path = self.app.config.tool_data_path original_tool_data_table_config_path = self.app.config.tool_data_table_config_path - if resetting_all_metadata_on_repository: - if not relative_install_dir: - raise Exception( "The value of repository.repo_path must be sent when resetting all metadata on a repository." ) + if self.resetting_all_metadata_on_repository: + if not self.relative_install_dir: + raise Exception( "The value of self.repository.repo_path must be set when resetting all metadata on a repository." ) # Keep track of the location where the repository is temporarily cloned so that we can - # strip the path when setting metadata. The value of repository_files_dir is the full - # path to the temporary directory to which the repository was cloned. - work_dir = repository_files_dir - files_dir = repository_files_dir + # strip the path when setting metadata. The value of self.repository_files_dir is the + # full path to the temporary directory to which self.repository was cloned. + work_dir = self.repository_files_dir + files_dir = self.repository_files_dir # Since we're working from a temporary directory, we can safely copy sample files included # in the repository to the repository root. - self.app.config.tool_data_path = repository_files_dir - self.app.config.tool_data_table_config_path = repository_files_dir + self.app.config.tool_data_path = self.repository_files_dir + self.app.config.tool_data_table_config_path = self.repository_files_dir else: # Use a temporary working directory to copy all sample files. work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-gmfcr" ) # All other files are on disk in the repository's repo_path, which is the value of - # relative_install_dir. - files_dir = relative_install_dir - if shed_config_dict.get( 'tool_path' ): - files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) + # self.relative_install_dir. + files_dir = self.relative_install_dir + if self.shed_config_dict.get( 'tool_path' ): + files_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], files_dir ) self.app.config.tool_data_path = work_dir #FIXME: Thread safe? self.app.config.tool_data_table_config_path = work_dir # Handle proprietary datatypes, if any. datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) if datatypes_config: metadata_dict = self.generate_datatypes_metadata( tv, - repository, - repository_clone_url, files_dir, datatypes_config, metadata_dict ) @@ -303,9 +354,8 @@ # the repository's metadata. sample_file_metadata_paths, sample_file_copy_paths = \ self.get_sample_files_from_disk( repository_files_dir=files_dir, - tool_path=shed_config_dict.get( 'tool_path' ), - relative_install_dir=relative_install_dir, - resetting_all_metadata_on_repository=resetting_all_metadata_on_repository ) + tool_path=self.shed_config_dict.get( 'tool_path' ), + relative_install_dir=self.relative_install_dir ) if sample_file_metadata_paths: metadata_dict[ 'sample_files' ] = sample_file_metadata_paths # Copy all sample files included in the repository to a single directory location so we @@ -322,7 +372,7 @@ shed_tool_data_table_config=self.app.config.shed_tool_data_table_config, persist=False ) if error_message: - invalid_file_tups.append( ( filename, error_message ) ) + self.invalid_file_tups.append( ( filename, error_message ) ) for root, dirs, files in os.walk( files_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: @@ -333,18 +383,16 @@ path_to_repository_dependencies_config = os.path.join( root, name ) metadata_dict, error_message = \ self.generate_repository_dependency_metadata( path_to_repository_dependencies_config, - metadata_dict, - updating_installed_repository=updating_installed_repository ) + metadata_dict ) if error_message: - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) # See if we have one or more READ_ME files. elif name.lower() in readme_file_names: relative_path_to_readme = self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) readme_files.append( relative_path_to_readme ) # See if we have a tool config. elif name not in self.NOT_TOOL_CONFIGS and name.endswith( '.xml' ): @@ -365,12 +413,12 @@ is_tool = element_tree_root.tag == 'tool' if is_tool: tool, valid, error_message = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: if not valid: invalid_tool_configs.append( name ) - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) else: invalid_files_and_errors_tups = \ tv.check_tool_input_params( files_dir, @@ -387,17 +435,15 @@ relative_path_to_tool_config = \ self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) metadata_dict = self.generate_tool_metadata( relative_path_to_tool_config, tool, - repository_clone_url, metadata_dict ) else: for tup in invalid_files_and_errors_tups: - invalid_file_tups.append( tup ) + self.invalid_file_tups.append( tup ) # Find all exported workflows. elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) @@ -421,11 +467,10 @@ metadata_dict ) # Handle any data manager entries data_manager_config = hg_util.get_config_from_disk( suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir ) - metadata_dict = self.generate_data_manager_metadata( repository, - files_dir, + metadata_dict = self.generate_data_manager_metadata( files_dir, data_manager_config, metadata_dict, - shed_config_dict=shed_config_dict ) + shed_config_dict=self.shed_config_dict ) if readme_files: metadata_dict[ 'readme_files' ] = readme_files @@ -433,21 +478,18 @@ tool_dependencies_config = hg_util.get_config_from_disk( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, files_dir ) if tool_dependencies_config: metadata_dict, error_message = \ - self.generate_tool_dependency_metadata( repository, - changeset_revision, - repository_clone_url, - tool_dependencies_config, + self.generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict, original_repository_metadata=original_repository_metadata ) if error_message: - invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) + self.invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs + self.metadata_dict = metadata_dict # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. self.app.config.tool_data_path = original_tool_data_path self.app.config.tool_data_table_config_path = original_tool_data_table_config_path basic_util.remove_dir( work_dir ) - return metadata_dict, invalid_file_tups def generate_package_dependency_metadata( self, elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict ): """ @@ -475,8 +517,7 @@ # where a tool dependency definition is considered invalid. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=False ) + only_if_compiling_contained_td=False ) elif sub_elem.tag == 'install': package_install_version = sub_elem.get( 'version', '1.0' ) if package_install_version == '1.0': @@ -509,8 +550,7 @@ # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) elif action_elem.tag == 'action': # <action type="set_environment_for_install"> # <repository changeset_revision="b107b91b3574" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://localhost:9009"> @@ -522,8 +562,7 @@ # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) if requirements_dict: dependency_key = '%s/%s' % ( package_name, package_version ) if repository_dependency_is_valid: @@ -538,8 +577,7 @@ repository_dependency_is_valid, \ error_message - def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict, - updating_installed_repository=False ): + def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict ): """ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method is called from the tool shed as well as from Galaxy. @@ -560,8 +598,7 @@ for repository_elem in root.findall( 'repository' ): repository_dependency_tup, repository_dependency_is_valid, err_msg = \ self.handle_repository_elem( repository_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=updating_installed_repository ) + only_if_compiling_contained_td=False ) if repository_dependency_is_valid: valid_repository_dependency_tups.append( repository_dependency_tup ) else: @@ -585,10 +622,10 @@ metadata_dict[ 'repository_dependencies' ] = valid_repository_dependencies_dict return metadata_dict, error_message - def generate_tool_metadata( self, tool_config, tool, repository_clone_url, metadata_dict ): + def generate_tool_metadata( self, tool_config, tool, metadata_dict ): """Update the received metadata_dict with changes that have been applied to the received tool.""" # Generate the guid. - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) # Handle tool.requirements. tool_requirements = [] for tool_requirement in tool.requirements: @@ -667,11 +704,10 @@ metadata_dict[ 'tools' ] = [ tool_dict ] return metadata_dict - def generate_tool_dependency_metadata( self, repository, changeset_revision, repository_clone_url, tool_dependencies_config, - metadata_dict, original_repository_metadata=None ): + def generate_tool_dependency_metadata( self, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for - at least one tool in the repository, then update the received metadata_dict with information from the + at least one tool in self.repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ error_message = '' @@ -738,7 +774,7 @@ # into a Galaxy instance, so handle changes to tool dependencies appropriately. irm = self.app.installed_repository_manager updated_tool_dependency_names, deleted_tool_dependency_names = \ - irm.handle_existing_tool_dependencies_that_changed_in_update( repository, + irm.handle_existing_tool_dependencies_that_changed_in_update( self.repository, original_valid_tool_dependencies_dict, valid_tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = valid_tool_dependencies_dict @@ -769,9 +805,14 @@ metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ] return metadata_dict - def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict, - resetting_all_metadata_on_repository ): - if resetting_all_metadata_on_repository: + def get_invalid_file_tups( self ): + return self.invalid_file_tups + + def get_metadata_dict( self ): + return self.metadata_dict + + def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict ): + if self.resetting_all_metadata_on_repository: full_path_to_file = os.path.join( root, name ) stripped_path_to_file = full_path_to_file.replace( work_dir, '' ) if stripped_path_to_file.startswith( '/' ): @@ -785,9 +826,8 @@ relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] return relative_path_to_file - def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None, - resetting_all_metadata_on_repository=False ): - if resetting_all_metadata_on_repository: + def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None ): + if self.resetting_all_metadata_on_repository: # Keep track of the location where the repository is temporarily cloned so that we can strip # it when setting metadata. work_dir = repository_files_dir @@ -797,7 +837,7 @@ if root.find( '.hg' ) < 0: for name in files: if name.endswith( '.sample' ): - if resetting_all_metadata_on_repository: + if self.resetting_all_metadata_on_repository: full_path_to_sample_file = os.path.join( root, name ) stripped_path_to_sample_file = full_path_to_sample_file.replace( work_dir, '' ) if stripped_path_to_sample_file.startswith( '/' ): @@ -816,7 +856,7 @@ sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths - def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False, updating_installed_repository=False ): + def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False ): """ Process the received repository_elem which is a <repository> tag either from a repository_dependencies.xml file or a tool_dependencies.xml file. If the former, @@ -832,7 +872,7 @@ changeset_revision = repository_elem.get( 'changeset_revision', None ) prior_installation_required = str( repository_elem.get( 'prior_installation_required', False ) ) if self.app.name == 'galaxy': - if updating_installed_repository: + if self.updating_installed_repository: pass else: # We're installing a repository into Galaxy, so make sure its contained repository @@ -889,12 +929,12 @@ updated_changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed # repository, so it will not yet be installed. Return the tuple for later # installation. return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed repository, # so it will not yet be installed. Return the tuple for later installation. return repository_dependency_tup, is_valid, error_message @@ -1006,6 +1046,46 @@ return False return True + def set_changeset_revision( self, changeset_revision ): + self.changeset_revision = changeset_revision + + def set_relative_install_dir( self, relative_install_dir ): + self.relative_install_dir = relative_install_dir + + def set_repository( self, repository, relative_install_dir=None, changeset_revision=None ): + self.repository = repository + # Shed related tool panel configs are only relevant to Galaxy. + if self.app.name == 'galaxy': + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.changeset_revision ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = repository.get_shed_config_dict( self.app ) + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + if relative_install_dir is None and self.repository is not None: + relative_install_dir = repository.repo_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.tip( self.app ) ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = {} + self.metadata_dict = {} + self.set_relative_install_dir( relative_install_dir ) + self.set_repository_files_dir() + self.resetting_all_metadata_on_repository = False + self.updating_installed_repository = False + self.persist = False + self.invalid_file_tups = [] + + def set_repository_clone_url( self, repository_clone_url ): + self.repository_clone_url = repository_clone_url + + def set_repository_files_dir( self, repository_files_dir=None ): + self.repository_files_dir = repository_files_dir + def update_repository_dependencies_metadata( self, metadata, repository_dependency_tups, is_valid, description ): if is_valid: repository_dependencies_dict = metadata.get( 'repository_dependencies', None ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/metadata/repository_metadata_manager.py --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -22,8 +22,16 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, user ): - super( RepositoryMetadataManager, self ).__init__( app ) + def __init__( self, app, user, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( RepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=user ) self.app = app self.user = user # Repository metadata comparisons for changeset revisions. @@ -62,7 +70,7 @@ repositories_select_field.add_option( option_label, option_value ) return repositories_select_field - def clean_repository_metadata( self, id, changeset_revisions ): + def clean_repository_metadata( self, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have # a changeset_revision that is not in changeset_revisions. We sometimes see multiple # records with the same changeset revision value - no idea how this happens. We'll @@ -71,7 +79,7 @@ changeset_revisions_checked = [] for repository_metadata in \ self.sa_session.query( self.app.model.RepositoryMetadata ) \ - .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.app.security.decode_id( id ) ) \ + .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.repository.id ) \ .order_by( self.app.model.RepositoryMetadata.table.c.changeset_revision, self.app.model.RepositoryMetadata.table.c.update_time.desc() ): changeset_revision = repository_metadata.changeset_revision @@ -79,15 +87,14 @@ self.sa_session.delete( repository_metadata ) self.sa_session.flush() - def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, - current_changeset_revision, current_metadata_dict ): + def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict ): """ Compare the contents of two changeset revisions to determine if a new repository metadata revision should be created. """ # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. - # This changeset_revision is an ancestor of current_changeset_revision which is associated - # with current_metadata_dict. A new repository_metadata record will be created only + # This changeset_revision is an ancestor of self.changeset_revision which is associated + # with self.metadata_dict. A new repository_metadata record will be created only # when this method returns the constant value self.NOT_EQUAL_AND_NOT_SUBSET. ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] ) ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) @@ -99,16 +106,16 @@ ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', {} ) ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] ) ancestor_data_manager = ancestor_metadata_dict.get( 'data_manager', {} ) - current_datatypes = current_metadata_dict.get( 'datatypes', [] ) - current_tools = current_metadata_dict.get( 'tools', [] ) + current_datatypes = self.metadata_dict.get( 'datatypes', [] ) + current_tools = self.metadata_dict.get( 'tools', [] ) current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ] current_guids.sort() - current_readme_files = current_metadata_dict.get( 'readme_files', [] ) - current_repository_dependencies_dict = current_metadata_dict.get( 'repository_dependencies', {} ) + current_readme_files = self.metadata_dict.get( 'readme_files', [] ) + current_repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) current_repository_dependencies = current_repository_dependencies_dict.get( 'repository_dependencies', [] ) - current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', {} ) - current_workflows = current_metadata_dict.get( 'workflows', [] ) - current_data_manager = current_metadata_dict.get( 'data_manager', {} ) + current_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', {} ) + current_workflows = self.metadata_dict.get( 'workflows', [] ) + current_data_manager = self.metadata_dict.get( 'data_manager', {} ) # Handle case where no metadata exists for either changeset. no_datatypes = not ancestor_datatypes and not current_datatypes no_readme_files = not ancestor_readme_files and not current_readme_files @@ -334,7 +341,7 @@ return self.SUBSET return self.NOT_EQUAL_AND_NOT_SUBSET - def create_or_update_repository_metadata( self, id, repository, changeset_revision, metadata_dict ): + def create_or_update_repository_metadata( self, changeset_revision, metadata_dict ): """Create or update a repository_metadatqa record in the tool shed.""" has_repository_dependencies = False has_repository_dependencies_only_if_compiling_contained_td = False @@ -364,7 +371,9 @@ downloadable = True else: downloadable = False - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.app.security.encode_id( self.repository.id ), + changeset_revision ) if repository_metadata: # A repository metadata record already exists with the received changeset_revision, # so we don't need to check the skip_tool_test table. @@ -381,7 +390,7 @@ # need to update the skip_tool_test table. check_skip_tool_test = True repository_metadata = \ - self.app.model.RepositoryMetadata( repository_id=repository.id, + self.app.model.RepositoryMetadata( repository_id=self.repository.id, changeset_revision=changeset_revision, metadata=metadata_dict, downloadable=downloadable, @@ -407,7 +416,7 @@ # if it is contained in the skip_tool_test table. If it is, but is not associated # with a repository_metadata record, reset that skip_tool_test record to the newly # created repository_metadata record. - repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) + repo = hg_util.get_repo_for_repository( self.app, repository=self.repository, repo_path=None, create=False ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) skip_tool_test = self.get_skip_tool_test_by_changeset_revision( changeset_hash ) @@ -531,16 +540,16 @@ .filter( self.app.model.SkipToolTest.table.c.initial_changeset_revision == changeset_revision ) \ .first() - def new_datatypes_metadata_required( self, repository_metadata, metadata_dict ): + def new_datatypes_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each datatype in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if - the last saved metadata record can be updated for datatypes instead. + in self.metadata_dict to determine if a new repository_metadata table record is required + or if the last saved metadata record can be updated for datatypes instead. """ # Datatypes are stored in metadata as a list of dictionaries that looks like: # [{'dtype': 'galaxy.datatypes.data:Text', 'subclass': 'True', 'extension': 'acedb'}] - if 'datatypes' in metadata_dict: - current_datatypes = metadata_dict[ 'datatypes' ] + if 'datatypes' in self.metadata_dict: + current_datatypes = self.metadata_dict[ 'datatypes' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -564,37 +573,31 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for datatypes, so a new repository_metadata + # self.metadata_dict includes no metadata for datatypes, so a new repository_metadata # table record is not needed. return False - def new_metadata_required_for_utilities( self, repository, new_tip_metadata_dict ): + def new_metadata_required_for_utilities( self ): """ - Galaxy utilities currently consist of datatypes, repository_dependency definitions, - tools, tool_dependency definitions and exported Galaxy workflows. This method compares - the last stored repository_metadata record associated with the received repository against - the contents of the received new_tip_metadata_dict and returns True or False for the union - set of Galaxy utilities contained in both metadata dictionaries. The metadata contained - in new_tip_metadata_dict may not be a subset of that contained in the last stored - repository_metadata record associated with the received repository because one or more - Galaxy utilities may have been deleted from the repository in the new tip. + This method compares the last stored repository_metadata record associated with self.repository + against the contents of self.metadata_dict and returns True or False for the union set of Galaxy + utilities contained in both metadata dictionaries. The metadata contained in self.metadata_dict + may not be a subset of that contained in the last stored repository_metadata record associated with + self.repository because one or more Galaxy utilities may have been deleted from self.repository in + the new tip. """ repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) - datatypes_required = self.new_datatypes_metadata_required( repository_metadata, - new_tip_metadata_dict ) + datatypes_required = self.new_datatypes_metadata_required( repository_metadata ) # Uncomment the following if we decide that README files should affect how installable # repository revisions are defined. See the NOTE in the compare_readme_files() method. - # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata, - # new_tip_metadata_dict ) + # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata ) repository_dependencies_required = \ - self.new_repository_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - tools_required = self.new_tool_metadata_required( repository_metadata, new_tip_metadata_dict ) - tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - workflows_required = self.new_workflow_metadata_required( repository_metadata, new_tip_metadata_dict ) + self.new_repository_dependency_metadata_required( repository_metadata ) + tools_required = self.new_tool_metadata_required( repository_metadata ) + tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata ) + workflows_required = self.new_workflow_metadata_required( repository_metadata ) if datatypes_required or \ repository_dependencies_required or \ tools_required or \ @@ -603,17 +606,17 @@ return True return False - def new_readme_files_metadata_required( self, repository_metadata, metadata_dict ): + def new_readme_files_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each readme file in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if the - last saved metadata record can be updated for readme files instead. + in self.metadata_dict to determine if a new repository_metadata table record is required or + if the last saved metadata record can be updated for readme files instead. """ # Repository README files are kind of a special case because they have no effect on reproducibility. # We'll simply inspect the file names to determine if any that exist in the saved metadata are - # eliminated from the new metadata in the received metadata_dict. - if 'readme_files' in metadata_dict: - current_readme_files = metadata_dict[ 'readme_files' ] + # eliminated from the new metadata in self.metadata_dict. + if 'readme_files' in self.metadata_dict: + current_readme_files = self.metadata_dict[ 'readme_files' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -638,14 +641,14 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for readme_files, so a new repository_metadata + # self.metadata_dict includes no metadata for readme_files, so a new repository_metadata # table record is not needed. return False - def new_repository_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_repository_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each repository dependency in the repository - with the new metadata in metadata_dict to determine if a new repository_metadata + with the new metadata in self.metadata_dict to determine if a new repository_metadata table record is required or if the last saved metadata record can be updated for repository_dependencies instead. """ @@ -653,9 +656,9 @@ metadata = repository_metadata.metadata if 'repository_dependencies' in metadata: saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] - new_repository_dependencies_metadata = metadata_dict.get( 'repository_dependencies', None ) + new_repository_dependencies_metadata = self.metadata_dict.get( 'repository_dependencies', None ) if new_repository_dependencies_metadata: - new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] + new_repository_dependencies = self.metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] # TODO: We used to include the following here to handle the case where repository # dependency definitions were deleted. However this erroneously returned True in # cases where is should not have done so. This usually occurred where multiple single @@ -682,21 +685,21 @@ else: return False else: - if 'repository_dependencies' in metadata_dict: + if 'repository_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata record. return True else: - # The received metadata_dict includes no metadata for repository dependencies, so - # a new repository_metadata record is not needed. + # self.metadata_dict includes no metadata for repository dependencies, so a new repository_metadata + # record is not needed. return False - def new_tool_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool in the repository with the new metadata in - metadata_dict to determine if a new repository_metadata table record is required, or if + self.metadata_dict to determine if a new repository_metadata table record is required, or if the last saved metadata record can be updated instead. """ - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -704,9 +707,9 @@ saved_tool_ids = [] # The metadata for one or more tools was successfully generated in the past # for this repository, so we first compare the version string for each tool id - # in metadata_dict with what was previously saved to see if we need to create + # in self.metadata_dict with what was previously saved to see if we need to create # a new table record or if we can simply update the existing record. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: for saved_tool_metadata_dict in metadata[ 'tools' ]: if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids: saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] ) @@ -714,10 +717,10 @@ if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: return True # So far, a new metadata record is not required, but we still have to check to see if - # any new tool ids exist in metadata_dict that are not in the saved metadata. We do + # any new tool ids exist in self.metadata_dict that are not in the saved metadata. We do # this because if a new tarball was uploaded to a repository that included tools, it # may have removed existing tool files if they were not included in the uploaded tarball. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: return True return False @@ -733,22 +736,22 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for tools, so a new repository_metadata table + # self.metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False - def new_tool_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool dependency in the repository with the new - metadata in metadata_dict to determine if a new repository_metadata table record is required - or if the last saved metadata record can be updated for tool_dependencies instead. + metadata in self.metadata_dict to determine if a new repository_metadata table record is + required or if the last saved metadata record can be updated for tool_dependencies instead. """ if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tool_dependencies' in metadata: saved_tool_dependencies = metadata[ 'tool_dependencies' ] - new_tool_dependencies = metadata_dict.get( 'tool_dependencies', None ) + new_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', None ) if new_tool_dependencies: # TODO: We used to include the following here to handle the case where # tool dependency definitions were deleted. However, this erroneously @@ -777,22 +780,22 @@ # in the repository, so we can update the existing repository metadata. return False else: - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata # record. return True else: - # The received metadata_dict includes no metadata for tool dependencies, so a new - # repository_metadata record is not needed. + # self.metadata_dict includes no metadata for tool dependencies, so a new repository_metadata + # record is not needed. return False - def new_workflow_metadata_required( self, repository_metadata, metadata_dict ): + def new_workflow_metadata_required( self, repository_metadata ): """ Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of exported workflows. If this changes at some future time, this method should be enhanced accordingly. """ - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: if repository_metadata: # The repository has metadata, so update the workflows value - # no new record is needed. @@ -801,17 +804,17 @@ # There is no saved repository metadata, so we need to create a # new repository_metadata table record. return True - # The received metadata_dict includes no metadata for workflows, so a new + # self.metadata_dict includes no metadata for workflows, so a new # repository_metadata table record is not needed. return False - def reset_all_metadata_on_repository_in_tool_shed( self, id ): + def reset_all_metadata_on_repository_in_tool_shed( self ): """Reset all metadata on a single repository in a tool shed.""" - repository = suc.get_repository_in_tool_shed( self.app, id ) - log.debug( "Resetting all metadata on repository: %s" % repository.name ) - repo_dir = repository.repo_path( self.app ) - repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) + log.debug( "Resetting all metadata on repository: %s" % self.repository.name ) + repo = hg_util.get_repo_for_repository( self.app, + repository=None, + repo_path=self.repository.repo_path( self.app ), + create=False ) # The list of changeset_revisions refers to repository_metadata records that have been created # or updated. When the following loop completes, we'll delete all repository_metadata records # for this repository that do not have a changeset_revision value in this list. @@ -822,33 +825,22 @@ metadata_dict = None ancestor_changeset_revision = None ancestor_metadata_dict = None - invalid_file_tups = [] - for changeset in repository.get_changesets_for_setting_metadata( self.app ): + for changeset in self.repository.get_changesets_for_setting_metadata( self.app ): work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ramorits" ) - current_changeset_revision = str( repo.changectx( changeset ) ) ctx = repo.changectx( changeset ) log.debug( "Cloning repository changeset revision: %s", str( ctx.rev() ) ) - cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) + cloned_ok, error_message = hg_util.clone_repository( self.repository_clone_url, work_dir, str( ctx.rev() ) ) if cloned_ok: log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) - current_metadata_dict, invalid_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=current_changeset_revision, - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=work_dir, - resetting_all_metadata_on_repository=True, - updating_installed_repository=False, - persist=False ) - # We'll only display error messages for the repository tip (it may be better to display error - # messages for each installable changeset revision). - if current_changeset_revision == repository.tip( self.app ): - invalid_file_tups.extend( invalid_tups ) - if current_metadata_dict: + self.set_changeset_revision( str( repo.changectx( changeset ) ) ) + self.set_relative_install_dir( work_dir ) + self.set_repository_files_dir( work_dir ) + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: if metadata_changeset_revision is None and metadata_dict is None: # We're at the first change set in the change log. - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict if ancestor_changeset_revision: # Compare metadata from ancestor and current. The value of comparison will be one of: # self.NO_METADATA - no metadata for either ancestor or current, so continue from current @@ -856,66 +848,56 @@ # self.SUBSET - ancestor metadata is a subset of current metadata, so continue from current # self.NOT_EQUAL_AND_NOT_SUBSET - ancestor metadata is neither equal to nor a subset of current # metadata, so persist ancestor metadata. - comparison = self.compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) + comparison = self.compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict ) if comparison in [ self.NO_METADATA, self.EQUAL, self.SUBSET ]: - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict elif comparison == self.NOT_EQUAL_AND_NOT_SUBSET: metadata_changeset_revision = ancestor_changeset_revision metadata_dict = ancestor_metadata_dict - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict else: # We're at the beginning of the change log. - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict if not ctx.children(): - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None elif ancestor_metadata_dict: - # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + # We reach here only if self.metadata_dict is empty and ancestor_metadata_dict is not. if not ctx.children(): # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None basic_util.remove_dir( work_dir ) # Delete all repository_metadata records for this repository that do not have a changeset_revision # value in changeset_revisions. - self.clean_repository_metadata( id, changeset_revisions ) + self.clean_repository_metadata( changeset_revisions ) # Set tool version information for all downloadable changeset revisions. Get the list of changeset # revisions from the changelog. - self.reset_all_tool_versions( id, repo ) + self.reset_all_tool_versions( repo ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} - return invalid_file_tups, metadata_dict - def reset_all_tool_versions( self, id, repo ): + def reset_all_tool_versions( self, repo ): """Reset tool version lineage for those changeset revisions that include valid tools.""" + encoded_repository_id = self.app.security.encode_id( self.repository.id ) changeset_revisions_that_contain_tools = [] for changeset in repo.changelog: changeset_revision = str( repo.changectx( changeset ) ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -926,7 +908,9 @@ # { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. for index, changeset_revision in enumerate( changeset_revisions_that_contain_tools ): tool_versions_dict = {} - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) metadata = repository_metadata.metadata tool_dicts = metadata[ 'tools' ] if index == 0: @@ -937,7 +921,7 @@ tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] else: for tool_dict in tool_dicts: - parent_id = self.get_parent_id( id, + parent_id = self.get_parent_id( encoded_repository_id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], @@ -962,11 +946,11 @@ for repository_id in repository_ids: try: repository = suc.get_repository_in_tool_shed( self.app, repository_id ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_repository_in_tool_shed() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) @@ -974,7 +958,7 @@ unsuccessful_count += 1 else: log.debug( "Successfully reset metadata on repository %s owned by %s" % \ - ( str( repository.name ), str( repository.user.username ) ) ) + ( str( repository.name ), str( repository.user.username ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s" % str( repository.name ) ) @@ -989,75 +973,68 @@ status = 'error' return message, status - def set_repository_metadata( self, host, repository, content_alert_str='', **kwd ): + def set_repository( self, repository ): + super( RepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) + + def set_repository_metadata( self, host, content_alert_str='', **kwd ): """ - Set metadata using the repository's current disk files, returning specific error + Set metadata using the self.repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. """ message = '' status = 'done' - encoded_id = self.app.security.encode_id( repository.id ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) - repo_dir = repository.repo_path( self.app ) + encoded_id = self.app.security.encode_id( self.repository.id ) + repo_dir = self.repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.tip( self.app ), - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - if metadata_dict: + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: repository_metadata = None - repository_type_class = self.app.repository_types_registry.get_class_by_label( repository.type ) + repository_type_class = self.app.repository_types_registry.get_class_by_label( self.repository.type ) tip_only = isinstance( repository_type_class, TipOnly ) - if not tip_only and self.new_metadata_required_for_utilities( repository, metadata_dict ): + if not tip_only and self.new_metadata_required_for_utilities(): # Create a new repository_metadata table row. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: + if len( self.repository.downloadable_revisions ) == 1: suc.handle_email_alerts( self.app, host, - repository, + self.repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: - # Update the latest stored repository metadata with the contents and attributes of metadata_dict. + # Update the latest stored repository metadata with the contents and attributes of self.metadata_dict. repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) if repository_metadata: - downloadable = metadata_util.is_downloadable( metadata_dict ) + downloadable = metadata_util.is_downloadable( self.metadata_dict ) # Update the last saved repository_metadata table row. - repository_metadata.changeset_revision = repository.tip( self.app ) - repository_metadata.metadata = metadata_dict + repository_metadata.changeset_revision = self.repository.tip( self.app ) + repository_metadata.metadata = self.metadata_dict repository_metadata.downloadable = downloadable - if 'datatypes' in metadata_dict: + if 'datatypes' in self.metadata_dict: repository_metadata.includes_datatypes = True else: repository_metadata.includes_datatypes = False # We don't store information about the special type of repository dependency that is needed only for # compiling a tool dependency defined for the dependent repository. - repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ suc.get_repository_dependency_types( repository_dependencies ) repository_metadata.has_repository_dependencies = has_repository_dependencies - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: repository_metadata.includes_tool_dependencies = True else: repository_metadata.includes_tool_dependencies = False - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: repository_metadata.includes_tools = True else: repository_metadata.includes_tools = False - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: repository_metadata.includes_workflows = True else: repository_metadata.includes_workflows = False @@ -1070,11 +1047,9 @@ self.sa_session.flush() else: # There are no metadata records associated with the repository. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) - if 'tools' in metadata_dict and repository_metadata and status != 'error': + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) + if 'tools' in self.metadata_dict and repository_metadata and status != 'error': # Set tool versions on the new downloadable change set. The order of the list of changesets is # critical, so we use the repo's changelog. changeset_revisions = [] @@ -1083,25 +1058,22 @@ if suc.get_repository_metadata_by_changeset_revision( self.app, encoded_id, changeset_revision ): changeset_revisions.append( changeset_revision ) self.add_tool_versions( encoded_id, repository_metadata, changeset_revisions ) - elif len( repo ) == 1 and not invalid_file_tups: + elif len( repo ) == 1 and not self.invalid_file_tups: message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % \ - str( repository.tip( self.app ) ) + str( self.repository.tip( self.app ) ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" - if invalid_file_tups: + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, - repository, - metadata_dict ) + self.invalid_file_tups, + self.repository, + self.metadata_dict ) status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} return message, status - def set_repository_metadata_due_to_new_tip( self, host, repository, content_alert_str=None, **kwd ): - """Set metadata on the repository tip in the tool shed.""" - error_message, status = self.set_repository_metadata( host, - repository, - content_alert_str=content_alert_str, - **kwd ) + def set_repository_metadata_due_to_new_tip( self, host, content_alert_str=None, **kwd ): + """Set metadata on the tip of self.repository in the tool shed.""" + error_message, status = self.set_repository_metadata( host, content_alert_str=content_alert_str, **kwd ) return status, error_message Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Sep '14

15 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fc09985c6c56/ Changeset: fc09985c6c56 User: greg Date: 2014-09-04 19:14:00 Summary: Encapsulate the Tool Shed's metadata generator. Affected #: 13 files diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -417,12 +417,13 @@ query = irmm.get_query_for_setting_metadata_on_repositories( order=False ) # Now reset metadata on all remaining repositories. for repository in query: - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + irmm.set_repository( repository ) + irmm.reset_all_metadata_on_installed_repository() + irmm_invalid_file_tups = irmm.get_invalid_file_tups() + if irmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + irmm_invalid_file_tups, repository, None, as_html=False ) diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1732,20 +1732,21 @@ tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata - irmm = InstalledRepositoryMetadataManager( trans.app ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - irmm.update_in_shed_tool_config( repository ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + repository=repository, + changeset_revision=repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if irmm_metadata_dict != original_metadata_dict: + repository.metadata = irmm_metadata_dict + irmm.update_in_shed_tool_config() trans.install_model.context.add( repository ) trans.install_model.context.flush() message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name @@ -1938,22 +1939,24 @@ dmh.remove_from_data_manager( repository ) # Update the repository metadata. tpm = tool_panel_manager.ToolPanelManager( trans.app ) - irmm = InstalledRepositoryMetadataManager( trans.app, tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=latest_changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + tpm=tpm, + repository=repository, + changeset_revision=latest_changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if 'tools' in irmm_metadata_dict: + tool_panel_dict = irmm_metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() tpm.add_to_tool_panel( repository_name=str( repository.name ), repository_clone_url=repository_clone_url, changeset_revision=str( repository.installed_changeset_revision ), @@ -1963,18 +1966,18 @@ tool_panel_dict=tool_panel_dict, new_install=False ) # Add new Data Manager entries - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( trans.app ) new_data_managers = dmh.install_data_managers( trans.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, repository.get_shed_config_dict( trans.app ), os.path.join( relative_install_dir, name ), repository, repository_tools_tups ) - if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: - new_repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + if 'repository_dependencies' in irmm_metadata_dict or 'tool_dependencies' in irmm_metadata_dict: + new_repository_dependencies_dict = irmm_metadata_dict.get( 'repository_dependencies', {} ) new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] ) - new_tool_dependencies_dict = metadata_dict.get( 'tool_dependencies', {} ) + new_tool_dependencies_dict = irmm_metadata_dict.get( 'tool_dependencies', {} ) if new_repository_dependencies: # [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']] proceed_to_install = False @@ -2017,7 +2020,7 @@ updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), updating=True ) return self.prepare_for_install( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies but did include @@ -2033,12 +2036,12 @@ proceed_to_install = True break if proceed_to_install: - encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) + encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( irmm_metadata_dict.get( 'tool_dependencies', {} ) ) encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), encoded_relative_install_dir=encoded_relative_install_dir, encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, message=message, @@ -2047,7 +2050,7 @@ # Updates received did not include any newly defined repository dependencies or newly defined # tool dependencies that need to be installed. repository = trans.app.update_repository_manager.update_repository_record( repository=repository, - updated_metadata_dict=metadata_dict, + updated_metadata_dict=irmm_metadata_dict, updated_changeset_revision=latest_changeset_revision, updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -429,13 +429,13 @@ def handle_repository( trans, rmm, repository, results ): log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + rmm.set_repository( repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) @@ -451,7 +451,11 @@ status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) results = dict( start_time=start_time, repository_status=[], @@ -511,12 +515,17 @@ results = dict( start_time=start_time, repository_status=[] ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.security.encode_id( repository.id ) ) - if invalid_file_tups: + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -1,6 +1,8 @@ import os, logging from galaxy import web from galaxy.web.base.controller import BaseUIController + +from tool_shed.util.common_util import generate_clone_url_for_repository_in_tool_shed from tool_shed.util.shed_util_common import get_repository_by_name_and_owner from tool_shed.util.hg_util import update_repository from tool_shed.metadata import repository_metadata_manager @@ -47,9 +49,19 @@ # interface will result in a new head being created. repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) # Set metadata using the repository files on disk. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - error_message, status = rmm.set_repository_metadata( trans.request.host, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + changeset_revision=repository.tip( trans.app ), + repository_clone_url=repository_clone_url, + relative_install_dir=repository.repo_path( trans.app ), + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + error_message, status = rmm.set_repository_metadata( trans.request.host ) if status == 'ok' and error_message: log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ ( str( repository.name ), str( repository.user.username ), error_message ) ) diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2759,15 +2759,18 @@ def reset_all_metadata( self, trans, id, **kwd ): """Reset all metadata on the complete changelog for a single repository in the tool shed.""" # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( id ) - if invalid_file_tups: - repository = suc.get_repository_in_tool_shed( trans.app, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_metadata_dict = rmm.get_metadata_dict() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, - metadata_dict ) + rmm_metadata_dict ) status = 'error' else: message = "All repository metadata has been reset. " @@ -2849,10 +2852,10 @@ if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, - **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, **kwd ) if error_message: message = error_message else: diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -263,10 +263,11 @@ ( len( files_to_remove ), upload_point ) else: message += " %d files were removed from the repository root. " % len( files_to_remove ) - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) status, error_message = \ rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, content_alert_str=content_alert_str, **kwd ) if error_message: diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -792,9 +792,10 @@ results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, self.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=self.app, + user=self.user, + repository=repository ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, - repository, content_alert_str=content_alert_str ) if error_message: results_dict[ 'ok' ] = False diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -510,31 +510,33 @@ """ shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) tdtm = data_table_manager.ToolDataTableManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict # Update the tool_shed_repository.tool_shed_status column in the database. tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository ) if tool_shed_status_dict: tool_shed_repository.tool_shed_status = tool_shed_status_dict self.install_model.context.add( tool_shed_repository ) self.install_model.context.flush() - if 'tool_dependencies' in metadata_dict and not reinstalling: + if 'tool_dependencies' in irmm_metadata_dict and not reinstalling: tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) - if 'sample_files' in metadata_dict: - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'sample_files' in irmm_metadata_dict: + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_data_table_conf_filename, tool_data_table_elems = \ tdtm.install_tool_data_tables( tool_shed_repository, tool_index_sample_files ) @@ -543,13 +545,13 @@ None, self.app.config.shed_tool_data_table_config, persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'tools' in irmm_metadata_dict: + tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( irmm_metadata_dict[ 'tools' ], tool_section ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. repository_tools_tups = tdtm.handle_missing_data_table_entry( relative_install_dir, @@ -575,15 +577,15 @@ shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=True ) - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, shed_config_dict, relative_install_dir, tool_shed_repository, repository_tools_tups ) - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: tool_shed_repository.status = self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: tool_shed_repository.includes_datatypes = True @@ -604,7 +606,7 @@ name=tool_shed_repository.name, owner=tool_shed_repository.owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -82,9 +82,12 @@ repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools_for_display_in_tool_panel: tpm = tool_panel_manager.ToolPanelManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, tpm ) - metadata = repository.metadata - repository_tools_tups = irmm.get_repository_tools_tups( metadata ) + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=tpm, + repository=repository, + changeset_revision=repository.changeset_revision, + metadata_dict=repository.metadata ) + repository_tools_tups = irmm.get_repository_tools_tups() # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] tpm.add_to_tool_panel( repository.name, @@ -101,7 +104,7 @@ data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata, + repository.metadata, repository.get_shed_config_dict( self.app ), data_manager_relative_install_dir, repository, diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -19,9 +19,16 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, tpm=None ): - super( InstalledRepositoryMetadataManager, self ).__init__( app ) - self.app = app + def __init__( self, app, tpm=None, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( InstalledRepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=None ) if tpm is None: self.tpm = tool_panel_manager.ToolPanelManager( self.app ) else: @@ -53,15 +60,15 @@ return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) - def get_repository_tools_tups( self, metadata_dict ): + def get_repository_tools_tups( self ): """ Return a list of tuples of the form (relative_path, guid, tool) for each tool defined in the received tool shed repository metadata. """ repository_tools_tups = [] - index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( metadata_dict.get( 'shed_config_filename' ) ) - if 'tools' in metadata_dict: - for tool_dict in metadata_dict[ 'tools' ]: + index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( self.metadata_dict.get( 'shed_config_filename' ) ) + if 'tools' in self.metadata_dict: + for tool_dict in self.metadata_dict[ 'tools' ]: load_relative_path = relative_path = tool_dict.get( 'tool_config', None ) if shed_conf_dict.get( 'tool_path' ): load_relative_path = os.path.join( shed_conf_dict.get( 'tool_path' ), relative_path ) @@ -74,36 +81,21 @@ repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups - def reset_all_metadata_on_installed_repository( self, id ): + def reset_all_metadata_on_installed_repository( self ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" - invalid_file_tups = [] - metadata_dict = {} - repository = repository_util.get_installed_tool_shed_repository( self.app, id ) - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - tool_path, relative_install_dir = repository.get_tool_relative_path( self.app ) - if relative_install_dir: - original_metadata_dict = repository.metadata - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( self.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - self.update_in_shed_tool_config( repository ) - self.app.install_model.context.add( repository ) + if self.relative_install_dir: + original_metadata_dict = self.repository.metadata + self.generate_metadata_for_changeset_revision() + if self.metadata_dict != original_metadata_dict: + self.repository.metadata = self.metadata_dict + self.update_in_shed_tool_config() + self.app.install_model.context.add( self.repository ) self.app.install_model.context.flush() - log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + log.debug( 'Metadata has been reset on repository %s.' % self.repository.name ) else: - log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + log.debug( 'Metadata did not need to be reset on repository %s.' % self.repository.name ) else: - log.debug( 'Error locating installation directory for repository %s.' % repository.name ) - return invalid_file_tups, metadata_dict + log.debug( 'Error locating installation directory for repository %s.' % self.repository.name ) def reset_metadata_on_selected_repositories( self, user, **kwd ): """ @@ -119,19 +111,19 @@ for repository_id in repository_ids: try: repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id ) - owner = str( repository.owner ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_installed_repository() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) log.debug( message ) unsuccessful_count += 1 else: - log.debug( "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), owner ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s" % \ + ( str( repository.name ), str( repository.owner ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) ) @@ -146,32 +138,37 @@ status = 'error' return message, status - def tool_shed_from_repository_clone_url( self, repository_clone_url ): + def set_repository( self, repository ): + super( InstalledRepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) + + def tool_shed_from_repository_clone_url( self ): """Given a repository clone URL, return the tool shed that contains the repository.""" - return common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) + return common_util.remove_protocol_and_user_from_clone_url( cleaned_repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) - def update_in_shed_tool_config( self, repository ): + def update_in_shed_tool_config( self ): """ A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list of config_elems instead of using the in-memory list. """ - shed_conf_dict = repository.get_shed_config_dict( self.app ) + shed_conf_dict = self.repository.get_shed_config_dict( self.app ) shed_tool_conf = shed_conf_dict[ 'config_filename' ] tool_path = shed_conf_dict[ 'tool_path' ] - tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = self.get_repository_tools_tups( repository.metadata ) - clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) - tool_shed = self.tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) - owner = repository.owner + tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( self.repository ) + repository_tools_tups = self.get_repository_tools_tups() + clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + tool_shed = self.tool_shed_from_repository_clone_url() + owner = self.repository.owner if not owner: + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) owner = suc.get_repository_owner( cleaned_repository_clone_url ) guid_to_tool_elem_dict = {} for tool_config_filename, guid, tool in repository_tools_tups: guid_to_tool_elem_dict[ guid ] = self.tpm.generate_tool_elem( tool_shed, - repository.name, - repository.changeset_revision, - repository.owner or '', + self.repository.name, + self.repository.changeset_revision, + self.repository.owner or '', tool_config_filename, tool, None ) diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -416,21 +416,23 @@ log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) ) finally: lock.release() - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = self.shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = self.shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict self.app.install_model.context.add( tool_shed_repository ) self.app.install_model.context.flush() - has_tool_dependencies = self.__has_tool_dependencies( metadata_dict ) + has_tool_dependencies = self.__has_tool_dependencies( irmm_metadata_dict ) if has_tool_dependencies: # All tool_dependency objects must be created before the tools are processed even if no # tool dependencies will be installed. @@ -440,14 +442,14 @@ set_status=True ) else: tool_dependencies = None - if 'tools' in metadata_dict: + if 'tools' in irmm_metadata_dict: tdtm = data_table_manager.ToolDataTableManager( self.app ) - sample_files = metadata_dict.get( 'sample_files', [] ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) sample_files = [ str( s ) for s in sample_files ] tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically # generated select lists. @@ -491,7 +493,7 @@ if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: @@ -514,7 +516,7 @@ name=tool_shed_repository.name, owner=self.repository_owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -27,31 +27,89 @@ class MetadataGenerator( object ): - def __init__( self, app ): + def __init__( self, app, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None, user=None ): self.app = app + self.user = user + self.repository = repository + if self.app.name == 'galaxy': + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.changeset_revision + else: + self.changeset_revision = changeset_revision + + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + if self.repository is not None: + self.shed_config_dict = self.repository.get_shed_config_dict( self.app ) + else: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_files_directory( self.app ) + if metadata_dict is None: + # Shed related tool panel configs are only relevant to Galaxy. + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + self.metadata_dict = metadata_dict + else: + # We're in the Tool Shed. + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.tip( self.app ) + else: + self.changeset_revision = changeset_revision + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = \ + common_util.generate_clone_url_for_repository_in_tool_shed( self.user, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + relative_install_dir = self.repository.repo_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_path( self.app ) + if metadata_dict is None: + self.metadata_dict = {} + else: + self.metadata_dict = metadata_dict + self.relative_install_dir = relative_install_dir + self.repository_files_dir = repository_files_dir + self.resetting_all_metadata_on_repository = resetting_all_metadata_on_repository + self.updating_installed_repository = updating_installed_repository + self.persist = persist + self.invalid_file_tups = [] self.sa_session = app.model.context.current self.NOT_TOOL_CONFIGS = [ suc.DATATYPES_CONFIG_FILENAME, - rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, - rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, - suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] + rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, + rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, + suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] - def generate_data_manager_metadata( self, repository, repo_dir, data_manager_config_filename, metadata_dict, + def generate_data_manager_metadata( self, repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None ): """ Update the received metadata_dict with information from the parsed data_manager_config_filename. """ if data_manager_config_filename is None: return metadata_dict - repo_path = repository.repo_path( self.app ) + repo_path = self.repository.repo_path( self.app ) try: # Galaxy Side. - repo_files_directory = repository.repo_files_directory( self.app ) + repo_files_directory = self.repository.repo_files_directory( self.app ) repo_dir = repo_files_directory - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) except AttributeError: # Tool Shed side. repo_files_directory = repo_path - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( None, repository ) relative_data_manager_dir = util.relpath( os.path.split( data_manager_config_filename )[0], repo_dir ) rel_data_manager_config_filename = os.path.join( relative_data_manager_dir, os.path.split( data_manager_config_filename )[1] ) @@ -91,7 +149,7 @@ # FIXME: default behavior is to fall back to tool.name. data_manager_name = data_manager_elem.get( 'name', data_manager_id ) version = data_manager_elem.get( 'version', DataManager.DEFAULT_VERSION ) - guid = self.generate_guid_for_object( repository_clone_url, DataManager.GUID_TYPE, data_manager_id, version ) + guid = self.generate_guid_for_object( DataManager.GUID_TYPE, data_manager_id, version ) data_tables = [] if tool_file is None: log.error( 'Data Manager entry is missing tool_file attribute in "%s".' % ( data_manager_config_filename ) ) @@ -130,8 +188,7 @@ log.debug( 'Loaded Data Manager tool_files: %s' % ( tool_file ) ) return metadata_dict - def generate_datatypes_metadata( self, tv, repository, repository_clone_url, repository_files_dir, datatypes_config, - metadata_dict ): + def generate_datatypes_metadata( self, tv, repository_files_dir, datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree, error_message = xml_util.parse_xml( datatypes_config ) if tree is None: @@ -180,11 +237,11 @@ tool_config_path = hg_util.get_config_from_disk( tool_config, repository_files_dir ) full_path = os.path.abspath( tool_config_path ) tool, valid, error_message = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), full_path ) + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: guid = None else: - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) converter_dict = dict( tool_config=tool_config, guid=guid, target_datatype=target_datatype ) @@ -226,76 +283,70 @@ valid_tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return valid_tool_dependencies_dict - def generate_guid_for_object( self, repository_clone_url, guid_type, obj_id, version ): - tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) + def generate_guid_for_object( self, guid_type, obj_id, version ): + tmp_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) return '%s/%s/%s/%s' % ( tmp_url, guid_type, obj_id, version ) - def generate_metadata_for_changeset_revision( self, repository, changeset_revision, repository_clone_url, - shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, - persist=False ): + def generate_metadata_for_changeset_revision( self ): """ Generate metadata for a repository using its files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access - that changeset revision's disk files, so the value of repository_files_dir will not - always be repository.repo_path( self.app ) (it could be an absolute path to a temporary - directory containing a clone). If it is an absolute path, the value of relative_install_dir + that changeset revision's disk files, so the value of self.repository_files_dir will not + always be self.repository.repo_path( self.app ) (it could be an absolute path to a temporary + directory containing a clone). If it is an absolute path, the value of self.relative_install_dir must contain repository.repo_path( self.app ). - The value of persist will be True when the installed repository contains a valid + The value of self.persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by self.app.config.shed_tool_data_table_config. """ tv = tool_validator.ToolValidator( self.app ) - if shed_config_dict is None: - shed_config_dict = {} - if updating_installed_repository: + if self.shed_config_dict is None: + self.shed_config_dict = {} + if self.updating_installed_repository: # Keep the original tool shed repository metadata if setting metadata on a repository # installed into a local Galaxy instance for which we have pulled updates. - original_repository_metadata = repository.metadata + original_repository_metadata = self.repository.metadata else: original_repository_metadata = None - readme_file_names = readme_util.get_readme_file_names( str( repository.name ) ) + readme_file_names = readme_util.get_readme_file_names( str( self.repository.name ) ) if self.app.name == 'galaxy': # Shed related tool panel configs are only relevant to Galaxy. - metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } + metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename' ) } else: metadata_dict = {} readme_files = [] - invalid_file_tups = [] invalid_tool_configs = [] tool_dependencies_config = None original_tool_data_path = self.app.config.tool_data_path original_tool_data_table_config_path = self.app.config.tool_data_table_config_path - if resetting_all_metadata_on_repository: - if not relative_install_dir: - raise Exception( "The value of repository.repo_path must be sent when resetting all metadata on a repository." ) + if self.resetting_all_metadata_on_repository: + if not self.relative_install_dir: + raise Exception( "The value of self.repository.repo_path must be set when resetting all metadata on a repository." ) # Keep track of the location where the repository is temporarily cloned so that we can - # strip the path when setting metadata. The value of repository_files_dir is the full - # path to the temporary directory to which the repository was cloned. - work_dir = repository_files_dir - files_dir = repository_files_dir + # strip the path when setting metadata. The value of self.repository_files_dir is the + # full path to the temporary directory to which self.repository was cloned. + work_dir = self.repository_files_dir + files_dir = self.repository_files_dir # Since we're working from a temporary directory, we can safely copy sample files included # in the repository to the repository root. - self.app.config.tool_data_path = repository_files_dir - self.app.config.tool_data_table_config_path = repository_files_dir + self.app.config.tool_data_path = self.repository_files_dir + self.app.config.tool_data_table_config_path = self.repository_files_dir else: # Use a temporary working directory to copy all sample files. work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-gmfcr" ) # All other files are on disk in the repository's repo_path, which is the value of - # relative_install_dir. - files_dir = relative_install_dir - if shed_config_dict.get( 'tool_path' ): - files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) + # self.relative_install_dir. + files_dir = self.relative_install_dir + if self.shed_config_dict.get( 'tool_path' ): + files_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], files_dir ) self.app.config.tool_data_path = work_dir #FIXME: Thread safe? self.app.config.tool_data_table_config_path = work_dir # Handle proprietary datatypes, if any. datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) if datatypes_config: metadata_dict = self.generate_datatypes_metadata( tv, - repository, - repository_clone_url, files_dir, datatypes_config, metadata_dict ) @@ -303,9 +354,8 @@ # the repository's metadata. sample_file_metadata_paths, sample_file_copy_paths = \ self.get_sample_files_from_disk( repository_files_dir=files_dir, - tool_path=shed_config_dict.get( 'tool_path' ), - relative_install_dir=relative_install_dir, - resetting_all_metadata_on_repository=resetting_all_metadata_on_repository ) + tool_path=self.shed_config_dict.get( 'tool_path' ), + relative_install_dir=self.relative_install_dir ) if sample_file_metadata_paths: metadata_dict[ 'sample_files' ] = sample_file_metadata_paths # Copy all sample files included in the repository to a single directory location so we @@ -322,7 +372,7 @@ shed_tool_data_table_config=self.app.config.shed_tool_data_table_config, persist=False ) if error_message: - invalid_file_tups.append( ( filename, error_message ) ) + self.invalid_file_tups.append( ( filename, error_message ) ) for root, dirs, files in os.walk( files_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: @@ -333,18 +383,16 @@ path_to_repository_dependencies_config = os.path.join( root, name ) metadata_dict, error_message = \ self.generate_repository_dependency_metadata( path_to_repository_dependencies_config, - metadata_dict, - updating_installed_repository=updating_installed_repository ) + metadata_dict ) if error_message: - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) # See if we have one or more READ_ME files. elif name.lower() in readme_file_names: relative_path_to_readme = self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) readme_files.append( relative_path_to_readme ) # See if we have a tool config. elif name not in self.NOT_TOOL_CONFIGS and name.endswith( '.xml' ): @@ -365,12 +413,12 @@ is_tool = element_tree_root.tag == 'tool' if is_tool: tool, valid, error_message = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: if not valid: invalid_tool_configs.append( name ) - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) else: invalid_files_and_errors_tups = \ tv.check_tool_input_params( files_dir, @@ -387,17 +435,15 @@ relative_path_to_tool_config = \ self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) metadata_dict = self.generate_tool_metadata( relative_path_to_tool_config, tool, - repository_clone_url, metadata_dict ) else: for tup in invalid_files_and_errors_tups: - invalid_file_tups.append( tup ) + self.invalid_file_tups.append( tup ) # Find all exported workflows. elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) @@ -421,11 +467,10 @@ metadata_dict ) # Handle any data manager entries data_manager_config = hg_util.get_config_from_disk( suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir ) - metadata_dict = self.generate_data_manager_metadata( repository, - files_dir, + metadata_dict = self.generate_data_manager_metadata( files_dir, data_manager_config, metadata_dict, - shed_config_dict=shed_config_dict ) + shed_config_dict=self.shed_config_dict ) if readme_files: metadata_dict[ 'readme_files' ] = readme_files @@ -433,21 +478,18 @@ tool_dependencies_config = hg_util.get_config_from_disk( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, files_dir ) if tool_dependencies_config: metadata_dict, error_message = \ - self.generate_tool_dependency_metadata( repository, - changeset_revision, - repository_clone_url, - tool_dependencies_config, + self.generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict, original_repository_metadata=original_repository_metadata ) if error_message: - invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) + self.invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs + self.metadata_dict = metadata_dict # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. self.app.config.tool_data_path = original_tool_data_path self.app.config.tool_data_table_config_path = original_tool_data_table_config_path basic_util.remove_dir( work_dir ) - return metadata_dict, invalid_file_tups def generate_package_dependency_metadata( self, elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict ): """ @@ -475,8 +517,7 @@ # where a tool dependency definition is considered invalid. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=False ) + only_if_compiling_contained_td=False ) elif sub_elem.tag == 'install': package_install_version = sub_elem.get( 'version', '1.0' ) if package_install_version == '1.0': @@ -509,8 +550,7 @@ # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) elif action_elem.tag == 'action': # <action type="set_environment_for_install"> # <repository changeset_revision="b107b91b3574" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://localhost:9009"> @@ -522,8 +562,7 @@ # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) if requirements_dict: dependency_key = '%s/%s' % ( package_name, package_version ) if repository_dependency_is_valid: @@ -538,8 +577,7 @@ repository_dependency_is_valid, \ error_message - def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict, - updating_installed_repository=False ): + def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict ): """ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method is called from the tool shed as well as from Galaxy. @@ -560,8 +598,7 @@ for repository_elem in root.findall( 'repository' ): repository_dependency_tup, repository_dependency_is_valid, err_msg = \ self.handle_repository_elem( repository_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=updating_installed_repository ) + only_if_compiling_contained_td=False ) if repository_dependency_is_valid: valid_repository_dependency_tups.append( repository_dependency_tup ) else: @@ -585,10 +622,10 @@ metadata_dict[ 'repository_dependencies' ] = valid_repository_dependencies_dict return metadata_dict, error_message - def generate_tool_metadata( self, tool_config, tool, repository_clone_url, metadata_dict ): + def generate_tool_metadata( self, tool_config, tool, metadata_dict ): """Update the received metadata_dict with changes that have been applied to the received tool.""" # Generate the guid. - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) # Handle tool.requirements. tool_requirements = [] for tool_requirement in tool.requirements: @@ -667,11 +704,10 @@ metadata_dict[ 'tools' ] = [ tool_dict ] return metadata_dict - def generate_tool_dependency_metadata( self, repository, changeset_revision, repository_clone_url, tool_dependencies_config, - metadata_dict, original_repository_metadata=None ): + def generate_tool_dependency_metadata( self, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for - at least one tool in the repository, then update the received metadata_dict with information from the + at least one tool in self.repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ error_message = '' @@ -738,7 +774,7 @@ # into a Galaxy instance, so handle changes to tool dependencies appropriately. irm = self.app.installed_repository_manager updated_tool_dependency_names, deleted_tool_dependency_names = \ - irm.handle_existing_tool_dependencies_that_changed_in_update( repository, + irm.handle_existing_tool_dependencies_that_changed_in_update( self.repository, original_valid_tool_dependencies_dict, valid_tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = valid_tool_dependencies_dict @@ -769,9 +805,14 @@ metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ] return metadata_dict - def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict, - resetting_all_metadata_on_repository ): - if resetting_all_metadata_on_repository: + def get_invalid_file_tups( self ): + return self.invalid_file_tups + + def get_metadata_dict( self ): + return self.metadata_dict + + def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict ): + if self.resetting_all_metadata_on_repository: full_path_to_file = os.path.join( root, name ) stripped_path_to_file = full_path_to_file.replace( work_dir, '' ) if stripped_path_to_file.startswith( '/' ): @@ -785,9 +826,8 @@ relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] return relative_path_to_file - def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None, - resetting_all_metadata_on_repository=False ): - if resetting_all_metadata_on_repository: + def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None ): + if self.resetting_all_metadata_on_repository: # Keep track of the location where the repository is temporarily cloned so that we can strip # it when setting metadata. work_dir = repository_files_dir @@ -797,7 +837,7 @@ if root.find( '.hg' ) < 0: for name in files: if name.endswith( '.sample' ): - if resetting_all_metadata_on_repository: + if self.resetting_all_metadata_on_repository: full_path_to_sample_file = os.path.join( root, name ) stripped_path_to_sample_file = full_path_to_sample_file.replace( work_dir, '' ) if stripped_path_to_sample_file.startswith( '/' ): @@ -816,7 +856,7 @@ sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths - def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False, updating_installed_repository=False ): + def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False ): """ Process the received repository_elem which is a <repository> tag either from a repository_dependencies.xml file or a tool_dependencies.xml file. If the former, @@ -832,7 +872,7 @@ changeset_revision = repository_elem.get( 'changeset_revision', None ) prior_installation_required = str( repository_elem.get( 'prior_installation_required', False ) ) if self.app.name == 'galaxy': - if updating_installed_repository: + if self.updating_installed_repository: pass else: # We're installing a repository into Galaxy, so make sure its contained repository @@ -889,12 +929,12 @@ updated_changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed # repository, so it will not yet be installed. Return the tuple for later # installation. return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed repository, # so it will not yet be installed. Return the tuple for later installation. return repository_dependency_tup, is_valid, error_message @@ -1006,6 +1046,46 @@ return False return True + def set_changeset_revision( self, changeset_revision ): + self.changeset_revision = changeset_revision + + def set_relative_install_dir( self, relative_install_dir ): + self.relative_install_dir = relative_install_dir + + def set_repository( self, repository, relative_install_dir=None, changeset_revision=None ): + self.repository = repository + # Shed related tool panel configs are only relevant to Galaxy. + if self.app.name == 'galaxy': + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.changeset_revision ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = repository.get_shed_config_dict( self.app ) + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + if relative_install_dir is None and self.repository is not None: + relative_install_dir = repository.repo_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.tip( self.app ) ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = {} + self.metadata_dict = {} + self.set_relative_install_dir( relative_install_dir ) + self.set_repository_files_dir() + self.resetting_all_metadata_on_repository = False + self.updating_installed_repository = False + self.persist = False + self.invalid_file_tups = [] + + def set_repository_clone_url( self, repository_clone_url ): + self.repository_clone_url = repository_clone_url + + def set_repository_files_dir( self, repository_files_dir=None ): + self.repository_files_dir = repository_files_dir + def update_repository_dependencies_metadata( self, metadata, repository_dependency_tups, is_valid, description ): if is_valid: repository_dependencies_dict = metadata.get( 'repository_dependencies', None ) diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r fc09985c6c5641e6cdb709e6461e4a6ea115c0f8 lib/tool_shed/metadata/repository_metadata_manager.py --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -22,8 +22,16 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, user ): - super( RepositoryMetadataManager, self ).__init__( app ) + def __init__( self, app, user, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( RepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=user ) self.app = app self.user = user # Repository metadata comparisons for changeset revisions. @@ -62,7 +70,7 @@ repositories_select_field.add_option( option_label, option_value ) return repositories_select_field - def clean_repository_metadata( self, id, changeset_revisions ): + def clean_repository_metadata( self, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have # a changeset_revision that is not in changeset_revisions. We sometimes see multiple # records with the same changeset revision value - no idea how this happens. We'll @@ -71,7 +79,7 @@ changeset_revisions_checked = [] for repository_metadata in \ self.sa_session.query( self.app.model.RepositoryMetadata ) \ - .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.app.security.decode_id( id ) ) \ + .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.repository.id ) \ .order_by( self.app.model.RepositoryMetadata.table.c.changeset_revision, self.app.model.RepositoryMetadata.table.c.update_time.desc() ): changeset_revision = repository_metadata.changeset_revision @@ -79,15 +87,14 @@ self.sa_session.delete( repository_metadata ) self.sa_session.flush() - def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, - current_changeset_revision, current_metadata_dict ): + def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict ): """ Compare the contents of two changeset revisions to determine if a new repository metadata revision should be created. """ # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. - # This changeset_revision is an ancestor of current_changeset_revision which is associated - # with current_metadata_dict. A new repository_metadata record will be created only + # This changeset_revision is an ancestor of self.changeset_revision which is associated + # with self.metadata_dict. A new repository_metadata record will be created only # when this method returns the constant value self.NOT_EQUAL_AND_NOT_SUBSET. ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] ) ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) @@ -99,16 +106,16 @@ ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', {} ) ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] ) ancestor_data_manager = ancestor_metadata_dict.get( 'data_manager', {} ) - current_datatypes = current_metadata_dict.get( 'datatypes', [] ) - current_tools = current_metadata_dict.get( 'tools', [] ) + current_datatypes = self.metadata_dict.get( 'datatypes', [] ) + current_tools = self.metadata_dict.get( 'tools', [] ) current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ] current_guids.sort() - current_readme_files = current_metadata_dict.get( 'readme_files', [] ) - current_repository_dependencies_dict = current_metadata_dict.get( 'repository_dependencies', {} ) + current_readme_files = self.metadata_dict.get( 'readme_files', [] ) + current_repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) current_repository_dependencies = current_repository_dependencies_dict.get( 'repository_dependencies', [] ) - current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', {} ) - current_workflows = current_metadata_dict.get( 'workflows', [] ) - current_data_manager = current_metadata_dict.get( 'data_manager', {} ) + current_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', {} ) + current_workflows = self.metadata_dict.get( 'workflows', [] ) + current_data_manager = self.metadata_dict.get( 'data_manager', {} ) # Handle case where no metadata exists for either changeset. no_datatypes = not ancestor_datatypes and not current_datatypes no_readme_files = not ancestor_readme_files and not current_readme_files @@ -334,7 +341,7 @@ return self.SUBSET return self.NOT_EQUAL_AND_NOT_SUBSET - def create_or_update_repository_metadata( self, id, repository, changeset_revision, metadata_dict ): + def create_or_update_repository_metadata( self, changeset_revision, metadata_dict ): """Create or update a repository_metadatqa record in the tool shed.""" has_repository_dependencies = False has_repository_dependencies_only_if_compiling_contained_td = False @@ -364,7 +371,9 @@ downloadable = True else: downloadable = False - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.app.security.encode_id( self.repository.id ), + changeset_revision ) if repository_metadata: # A repository metadata record already exists with the received changeset_revision, # so we don't need to check the skip_tool_test table. @@ -381,7 +390,7 @@ # need to update the skip_tool_test table. check_skip_tool_test = True repository_metadata = \ - self.app.model.RepositoryMetadata( repository_id=repository.id, + self.app.model.RepositoryMetadata( repository_id=self.repository.id, changeset_revision=changeset_revision, metadata=metadata_dict, downloadable=downloadable, @@ -407,7 +416,7 @@ # if it is contained in the skip_tool_test table. If it is, but is not associated # with a repository_metadata record, reset that skip_tool_test record to the newly # created repository_metadata record. - repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) + repo = hg_util.get_repo_for_repository( self.app, repository=self.repository, repo_path=None, create=False ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) skip_tool_test = self.get_skip_tool_test_by_changeset_revision( changeset_hash ) @@ -531,16 +540,16 @@ .filter( self.app.model.SkipToolTest.table.c.initial_changeset_revision == changeset_revision ) \ .first() - def new_datatypes_metadata_required( self, repository_metadata, metadata_dict ): + def new_datatypes_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each datatype in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if - the last saved metadata record can be updated for datatypes instead. + in self.metadata_dict to determine if a new repository_metadata table record is required + or if the last saved metadata record can be updated for datatypes instead. """ # Datatypes are stored in metadata as a list of dictionaries that looks like: # [{'dtype': 'galaxy.datatypes.data:Text', 'subclass': 'True', 'extension': 'acedb'}] - if 'datatypes' in metadata_dict: - current_datatypes = metadata_dict[ 'datatypes' ] + if 'datatypes' in self.metadata_dict: + current_datatypes = self.metadata_dict[ 'datatypes' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -564,37 +573,31 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for datatypes, so a new repository_metadata + # self.metadata_dict includes no metadata for datatypes, so a new repository_metadata # table record is not needed. return False - def new_metadata_required_for_utilities( self, repository, new_tip_metadata_dict ): + def new_metadata_required_for_utilities( self ): """ - Galaxy utilities currently consist of datatypes, repository_dependency definitions, - tools, tool_dependency definitions and exported Galaxy workflows. This method compares - the last stored repository_metadata record associated with the received repository against - the contents of the received new_tip_metadata_dict and returns True or False for the union - set of Galaxy utilities contained in both metadata dictionaries. The metadata contained - in new_tip_metadata_dict may not be a subset of that contained in the last stored - repository_metadata record associated with the received repository because one or more - Galaxy utilities may have been deleted from the repository in the new tip. + This method compares the last stored repository_metadata record associated with self.repository + against the contents of self.metadata_dict and returns True or False for the union set of Galaxy + utilities contained in both metadata dictionaries. The metadata contained in self.metadata_dict + may not be a subset of that contained in the last stored repository_metadata record associated with + self.repository because one or more Galaxy utilities may have been deleted from self.repository in + the new tip. """ repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) - datatypes_required = self.new_datatypes_metadata_required( repository_metadata, - new_tip_metadata_dict ) + datatypes_required = self.new_datatypes_metadata_required( repository_metadata ) # Uncomment the following if we decide that README files should affect how installable # repository revisions are defined. See the NOTE in the compare_readme_files() method. - # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata, - # new_tip_metadata_dict ) + # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata ) repository_dependencies_required = \ - self.new_repository_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - tools_required = self.new_tool_metadata_required( repository_metadata, new_tip_metadata_dict ) - tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - workflows_required = self.new_workflow_metadata_required( repository_metadata, new_tip_metadata_dict ) + self.new_repository_dependency_metadata_required( repository_metadata ) + tools_required = self.new_tool_metadata_required( repository_metadata ) + tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata ) + workflows_required = self.new_workflow_metadata_required( repository_metadata ) if datatypes_required or \ repository_dependencies_required or \ tools_required or \ @@ -603,17 +606,17 @@ return True return False - def new_readme_files_metadata_required( self, repository_metadata, metadata_dict ): + def new_readme_files_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each readme file in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if the - last saved metadata record can be updated for readme files instead. + in self.metadata_dict to determine if a new repository_metadata table record is required or + if the last saved metadata record can be updated for readme files instead. """ # Repository README files are kind of a special case because they have no effect on reproducibility. # We'll simply inspect the file names to determine if any that exist in the saved metadata are - # eliminated from the new metadata in the received metadata_dict. - if 'readme_files' in metadata_dict: - current_readme_files = metadata_dict[ 'readme_files' ] + # eliminated from the new metadata in self.metadata_dict. + if 'readme_files' in self.metadata_dict: + current_readme_files = self.metadata_dict[ 'readme_files' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -638,14 +641,14 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for readme_files, so a new repository_metadata + # self.metadata_dict includes no metadata for readme_files, so a new repository_metadata # table record is not needed. return False - def new_repository_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_repository_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each repository dependency in the repository - with the new metadata in metadata_dict to determine if a new repository_metadata + with the new metadata in self.metadata_dict to determine if a new repository_metadata table record is required or if the last saved metadata record can be updated for repository_dependencies instead. """ @@ -653,9 +656,9 @@ metadata = repository_metadata.metadata if 'repository_dependencies' in metadata: saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] - new_repository_dependencies_metadata = metadata_dict.get( 'repository_dependencies', None ) + new_repository_dependencies_metadata = self.metadata_dict.get( 'repository_dependencies', None ) if new_repository_dependencies_metadata: - new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] + new_repository_dependencies = self.metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] # TODO: We used to include the following here to handle the case where repository # dependency definitions were deleted. However this erroneously returned True in # cases where is should not have done so. This usually occurred where multiple single @@ -682,21 +685,21 @@ else: return False else: - if 'repository_dependencies' in metadata_dict: + if 'repository_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata record. return True else: - # The received metadata_dict includes no metadata for repository dependencies, so - # a new repository_metadata record is not needed. + # self.metadata_dict includes no metadata for repository dependencies, so a new repository_metadata + # record is not needed. return False - def new_tool_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool in the repository with the new metadata in - metadata_dict to determine if a new repository_metadata table record is required, or if + self.metadata_dict to determine if a new repository_metadata table record is required, or if the last saved metadata record can be updated instead. """ - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -704,9 +707,9 @@ saved_tool_ids = [] # The metadata for one or more tools was successfully generated in the past # for this repository, so we first compare the version string for each tool id - # in metadata_dict with what was previously saved to see if we need to create + # in self.metadata_dict with what was previously saved to see if we need to create # a new table record or if we can simply update the existing record. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: for saved_tool_metadata_dict in metadata[ 'tools' ]: if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids: saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] ) @@ -714,10 +717,10 @@ if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: return True # So far, a new metadata record is not required, but we still have to check to see if - # any new tool ids exist in metadata_dict that are not in the saved metadata. We do + # any new tool ids exist in self.metadata_dict that are not in the saved metadata. We do # this because if a new tarball was uploaded to a repository that included tools, it # may have removed existing tool files if they were not included in the uploaded tarball. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: return True return False @@ -733,22 +736,22 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for tools, so a new repository_metadata table + # self.metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False - def new_tool_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool dependency in the repository with the new - metadata in metadata_dict to determine if a new repository_metadata table record is required - or if the last saved metadata record can be updated for tool_dependencies instead. + metadata in self.metadata_dict to determine if a new repository_metadata table record is + required or if the last saved metadata record can be updated for tool_dependencies instead. """ if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tool_dependencies' in metadata: saved_tool_dependencies = metadata[ 'tool_dependencies' ] - new_tool_dependencies = metadata_dict.get( 'tool_dependencies', None ) + new_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', None ) if new_tool_dependencies: # TODO: We used to include the following here to handle the case where # tool dependency definitions were deleted. However, this erroneously @@ -777,22 +780,22 @@ # in the repository, so we can update the existing repository metadata. return False else: - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata # record. return True else: - # The received metadata_dict includes no metadata for tool dependencies, so a new - # repository_metadata record is not needed. + # self.metadata_dict includes no metadata for tool dependencies, so a new repository_metadata + # record is not needed. return False - def new_workflow_metadata_required( self, repository_metadata, metadata_dict ): + def new_workflow_metadata_required( self, repository_metadata ): """ Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of exported workflows. If this changes at some future time, this method should be enhanced accordingly. """ - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: if repository_metadata: # The repository has metadata, so update the workflows value - # no new record is needed. @@ -801,17 +804,17 @@ # There is no saved repository metadata, so we need to create a # new repository_metadata table record. return True - # The received metadata_dict includes no metadata for workflows, so a new + # self.metadata_dict includes no metadata for workflows, so a new # repository_metadata table record is not needed. return False - def reset_all_metadata_on_repository_in_tool_shed( self, id ): + def reset_all_metadata_on_repository_in_tool_shed( self ): """Reset all metadata on a single repository in a tool shed.""" - repository = suc.get_repository_in_tool_shed( self.app, id ) - log.debug( "Resetting all metadata on repository: %s" % repository.name ) - repo_dir = repository.repo_path( self.app ) - repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) + log.debug( "Resetting all metadata on repository: %s" % self.repository.name ) + repo = hg_util.get_repo_for_repository( self.app, + repository=None, + repo_path=self.repository.repo_path( self.app ), + create=False ) # The list of changeset_revisions refers to repository_metadata records that have been created # or updated. When the following loop completes, we'll delete all repository_metadata records # for this repository that do not have a changeset_revision value in this list. @@ -822,33 +825,22 @@ metadata_dict = None ancestor_changeset_revision = None ancestor_metadata_dict = None - invalid_file_tups = [] - for changeset in repository.get_changesets_for_setting_metadata( self.app ): + for changeset in self.repository.get_changesets_for_setting_metadata( self.app ): work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ramorits" ) - current_changeset_revision = str( repo.changectx( changeset ) ) ctx = repo.changectx( changeset ) log.debug( "Cloning repository changeset revision: %s", str( ctx.rev() ) ) - cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) + cloned_ok, error_message = hg_util.clone_repository( self.repository_clone_url, work_dir, str( ctx.rev() ) ) if cloned_ok: log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) - current_metadata_dict, invalid_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=current_changeset_revision, - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=work_dir, - resetting_all_metadata_on_repository=True, - updating_installed_repository=False, - persist=False ) - # We'll only display error messages for the repository tip (it may be better to display error - # messages for each installable changeset revision). - if current_changeset_revision == repository.tip( self.app ): - invalid_file_tups.extend( invalid_tups ) - if current_metadata_dict: + self.set_changeset_revision( str( repo.changectx( changeset ) ) ) + self.set_relative_install_dir( work_dir ) + self.set_repository_files_dir( work_dir ) + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: if metadata_changeset_revision is None and metadata_dict is None: # We're at the first change set in the change log. - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict if ancestor_changeset_revision: # Compare metadata from ancestor and current. The value of comparison will be one of: # self.NO_METADATA - no metadata for either ancestor or current, so continue from current @@ -856,66 +848,56 @@ # self.SUBSET - ancestor metadata is a subset of current metadata, so continue from current # self.NOT_EQUAL_AND_NOT_SUBSET - ancestor metadata is neither equal to nor a subset of current # metadata, so persist ancestor metadata. - comparison = self.compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) + comparison = self.compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict ) if comparison in [ self.NO_METADATA, self.EQUAL, self.SUBSET ]: - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict elif comparison == self.NOT_EQUAL_AND_NOT_SUBSET: metadata_changeset_revision = ancestor_changeset_revision metadata_dict = ancestor_metadata_dict - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict else: # We're at the beginning of the change log. - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict if not ctx.children(): - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None elif ancestor_metadata_dict: - # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + # We reach here only if self.metadata_dict is empty and ancestor_metadata_dict is not. if not ctx.children(): # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None basic_util.remove_dir( work_dir ) # Delete all repository_metadata records for this repository that do not have a changeset_revision # value in changeset_revisions. - self.clean_repository_metadata( id, changeset_revisions ) + self.clean_repository_metadata( changeset_revisions ) # Set tool version information for all downloadable changeset revisions. Get the list of changeset # revisions from the changelog. - self.reset_all_tool_versions( id, repo ) + self.reset_all_tool_versions( repo ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} - return invalid_file_tups, metadata_dict - def reset_all_tool_versions( self, id, repo ): + def reset_all_tool_versions( self, repo ): """Reset tool version lineage for those changeset revisions that include valid tools.""" + encoded_repository_id = self.app.security.encode_id( self.repository.id ) changeset_revisions_that_contain_tools = [] for changeset in repo.changelog: changeset_revision = str( repo.changectx( changeset ) ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -926,7 +908,9 @@ # { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. for index, changeset_revision in enumerate( changeset_revisions_that_contain_tools ): tool_versions_dict = {} - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) metadata = repository_metadata.metadata tool_dicts = metadata[ 'tools' ] if index == 0: @@ -937,7 +921,7 @@ tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] else: for tool_dict in tool_dicts: - parent_id = self.get_parent_id( id, + parent_id = self.get_parent_id( encoded_repository_id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], @@ -962,11 +946,11 @@ for repository_id in repository_ids: try: repository = suc.get_repository_in_tool_shed( self.app, repository_id ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_repository_in_tool_shed() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) @@ -974,7 +958,7 @@ unsuccessful_count += 1 else: log.debug( "Successfully reset metadata on repository %s owned by %s" % \ - ( str( repository.name ), str( repository.user.username ) ) ) + ( str( repository.name ), str( repository.user.username ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s" % str( repository.name ) ) @@ -989,75 +973,68 @@ status = 'error' return message, status - def set_repository_metadata( self, host, repository, content_alert_str='', **kwd ): + def set_repository( self, repository ): + super( RepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) + + def set_repository_metadata( self, host, content_alert_str='', **kwd ): """ - Set metadata using the repository's current disk files, returning specific error + Set metadata using the self.repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. """ message = '' status = 'done' - encoded_id = self.app.security.encode_id( repository.id ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) - repo_dir = repository.repo_path( self.app ) + encoded_id = self.app.security.encode_id( self.repository.id ) + repo_dir = self.repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.tip( self.app ), - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - if metadata_dict: + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: repository_metadata = None - repository_type_class = self.app.repository_types_registry.get_class_by_label( repository.type ) + repository_type_class = self.app.repository_types_registry.get_class_by_label( self.repository.type ) tip_only = isinstance( repository_type_class, TipOnly ) - if not tip_only and self.new_metadata_required_for_utilities( repository, metadata_dict ): + if not tip_only and self.new_metadata_required_for_utilities(): # Create a new repository_metadata table row. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: + if len( self.repository.downloadable_revisions ) == 1: suc.handle_email_alerts( self.app, host, - repository, + self.repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: - # Update the latest stored repository metadata with the contents and attributes of metadata_dict. + # Update the latest stored repository metadata with the contents and attributes of self.metadata_dict. repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) if repository_metadata: - downloadable = metadata_util.is_downloadable( metadata_dict ) + downloadable = metadata_util.is_downloadable( self.metadata_dict ) # Update the last saved repository_metadata table row. - repository_metadata.changeset_revision = repository.tip( self.app ) - repository_metadata.metadata = metadata_dict + repository_metadata.changeset_revision = self.repository.tip( self.app ) + repository_metadata.metadata = self.metadata_dict repository_metadata.downloadable = downloadable - if 'datatypes' in metadata_dict: + if 'datatypes' in self.metadata_dict: repository_metadata.includes_datatypes = True else: repository_metadata.includes_datatypes = False # We don't store information about the special type of repository dependency that is needed only for # compiling a tool dependency defined for the dependent repository. - repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ suc.get_repository_dependency_types( repository_dependencies ) repository_metadata.has_repository_dependencies = has_repository_dependencies - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: repository_metadata.includes_tool_dependencies = True else: repository_metadata.includes_tool_dependencies = False - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: repository_metadata.includes_tools = True else: repository_metadata.includes_tools = False - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: repository_metadata.includes_workflows = True else: repository_metadata.includes_workflows = False @@ -1070,11 +1047,9 @@ self.sa_session.flush() else: # There are no metadata records associated with the repository. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) - if 'tools' in metadata_dict and repository_metadata and status != 'error': + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) + if 'tools' in self.metadata_dict and repository_metadata and status != 'error': # Set tool versions on the new downloadable change set. The order of the list of changesets is # critical, so we use the repo's changelog. changeset_revisions = [] @@ -1083,25 +1058,22 @@ if suc.get_repository_metadata_by_changeset_revision( self.app, encoded_id, changeset_revision ): changeset_revisions.append( changeset_revision ) self.add_tool_versions( encoded_id, repository_metadata, changeset_revisions ) - elif len( repo ) == 1 and not invalid_file_tups: + elif len( repo ) == 1 and not self.invalid_file_tups: message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % \ - str( repository.tip( self.app ) ) + str( self.repository.tip( self.app ) ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" - if invalid_file_tups: + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, - repository, - metadata_dict ) + self.invalid_file_tups, + self.repository, + self.metadata_dict ) status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} return message, status - def set_repository_metadata_due_to_new_tip( self, host, repository, content_alert_str=None, **kwd ): - """Set metadata on the repository tip in the tool shed.""" - error_message, status = self.set_repository_metadata( host, - repository, - content_alert_str=content_alert_str, - **kwd ) + def set_repository_metadata_due_to_new_tip( self, host, content_alert_str=None, **kwd ): + """Set metadata on the tip of self.repository in the tool shed.""" + error_message, status = self.set_repository_metadata( host, content_alert_str=content_alert_str, **kwd ) return status, error_message https://bitbucket.org/galaxy/galaxy-central/commits/cb6dffff2797/ Changeset: cb6dffff2797 User: davebgx Date: 2014-09-15 22:34:18 Summary: Merged in greg/gvk-galaxy-central (pull request #485) Encapsulate the Tool Shed's metadata generator. Affected #: 13 files diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -417,12 +417,13 @@ query = irmm.get_query_for_setting_metadata_on_repositories( order=False ) # Now reset metadata on all remaining repositories. for repository in query: - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + irmm.set_repository( repository ) + irmm.reset_all_metadata_on_installed_repository() + irmm_invalid_file_tups = irmm.get_invalid_file_tups() + if irmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + irmm_invalid_file_tups, repository, None, as_html=False ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1732,20 +1732,21 @@ tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata - irmm = InstalledRepositoryMetadataManager( trans.app ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - irmm.update_in_shed_tool_config( repository ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + repository=repository, + changeset_revision=repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if irmm_metadata_dict != original_metadata_dict: + repository.metadata = irmm_metadata_dict + irmm.update_in_shed_tool_config() trans.install_model.context.add( repository ) trans.install_model.context.flush() message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name @@ -1938,22 +1939,24 @@ dmh.remove_from_data_manager( repository ) # Update the repository metadata. tpm = tool_panel_manager.ToolPanelManager( trans.app ) - irmm = InstalledRepositoryMetadataManager( trans.app, tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=latest_changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + tpm=tpm, + repository=repository, + changeset_revision=latest_changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if 'tools' in irmm_metadata_dict: + tool_panel_dict = irmm_metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() tpm.add_to_tool_panel( repository_name=str( repository.name ), repository_clone_url=repository_clone_url, changeset_revision=str( repository.installed_changeset_revision ), @@ -1963,18 +1966,18 @@ tool_panel_dict=tool_panel_dict, new_install=False ) # Add new Data Manager entries - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( trans.app ) new_data_managers = dmh.install_data_managers( trans.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, repository.get_shed_config_dict( trans.app ), os.path.join( relative_install_dir, name ), repository, repository_tools_tups ) - if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: - new_repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + if 'repository_dependencies' in irmm_metadata_dict or 'tool_dependencies' in irmm_metadata_dict: + new_repository_dependencies_dict = irmm_metadata_dict.get( 'repository_dependencies', {} ) new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] ) - new_tool_dependencies_dict = metadata_dict.get( 'tool_dependencies', {} ) + new_tool_dependencies_dict = irmm_metadata_dict.get( 'tool_dependencies', {} ) if new_repository_dependencies: # [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']] proceed_to_install = False @@ -2017,7 +2020,7 @@ updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), updating=True ) return self.prepare_for_install( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies but did include @@ -2033,12 +2036,12 @@ proceed_to_install = True break if proceed_to_install: - encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) + encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( irmm_metadata_dict.get( 'tool_dependencies', {} ) ) encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), encoded_relative_install_dir=encoded_relative_install_dir, encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, message=message, @@ -2047,7 +2050,7 @@ # Updates received did not include any newly defined repository dependencies or newly defined # tool dependencies that need to be installed. repository = trans.app.update_repository_manager.update_repository_record( repository=repository, - updated_metadata_dict=metadata_dict, + updated_metadata_dict=irmm_metadata_dict, updated_changeset_revision=latest_changeset_revision, updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -429,13 +429,13 @@ def handle_repository( trans, rmm, repository, results ): log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) - repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + rmm.set_repository( repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) @@ -451,7 +451,11 @@ status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) results = dict( start_time=start_time, repository_status=[], @@ -511,12 +515,17 @@ results = dict( start_time=start_time, repository_status=[] ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.security.encode_id( repository.id ) ) - if invalid_file_tups: + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -1,6 +1,8 @@ import os, logging from galaxy import web from galaxy.web.base.controller import BaseUIController + +from tool_shed.util.common_util import generate_clone_url_for_repository_in_tool_shed from tool_shed.util.shed_util_common import get_repository_by_name_and_owner from tool_shed.util.hg_util import update_repository from tool_shed.metadata import repository_metadata_manager @@ -47,9 +49,19 @@ # interface will result in a new head being created. repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) # Set metadata using the repository files on disk. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - error_message, status = rmm.set_repository_metadata( trans.request.host, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + changeset_revision=repository.tip( trans.app ), + repository_clone_url=repository_clone_url, + relative_install_dir=repository.repo_path( trans.app ), + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + error_message, status = rmm.set_repository_metadata( trans.request.host ) if status == 'ok' and error_message: log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ ( str( repository.name ), str( repository.user.username ), error_message ) ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2759,15 +2759,18 @@ def reset_all_metadata( self, trans, id, **kwd ): """Reset all metadata on the complete changelog for a single repository in the tool shed.""" # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( id ) - if invalid_file_tups: - repository = suc.get_repository_in_tool_shed( trans.app, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_metadata_dict = rmm.get_metadata_dict() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, - metadata_dict ) + rmm_metadata_dict ) status = 'error' else: message = "All repository metadata has been reset. " @@ -2849,10 +2852,10 @@ if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, - **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, **kwd ) if error_message: message = error_message else: diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -263,10 +263,11 @@ ( len( files_to_remove ), upload_point ) else: message += " %d files were removed from the repository root. " % len( files_to_remove ) - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) status, error_message = \ rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, content_alert_str=content_alert_str, **kwd ) if error_message: diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -792,9 +792,10 @@ results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, self.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=self.app, + user=self.user, + repository=repository ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, - repository, content_alert_str=content_alert_str ) if error_message: results_dict[ 'ok' ] = False diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -510,31 +510,33 @@ """ shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) tdtm = data_table_manager.ToolDataTableManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict # Update the tool_shed_repository.tool_shed_status column in the database. tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository ) if tool_shed_status_dict: tool_shed_repository.tool_shed_status = tool_shed_status_dict self.install_model.context.add( tool_shed_repository ) self.install_model.context.flush() - if 'tool_dependencies' in metadata_dict and not reinstalling: + if 'tool_dependencies' in irmm_metadata_dict and not reinstalling: tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) - if 'sample_files' in metadata_dict: - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'sample_files' in irmm_metadata_dict: + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_data_table_conf_filename, tool_data_table_elems = \ tdtm.install_tool_data_tables( tool_shed_repository, tool_index_sample_files ) @@ -543,13 +545,13 @@ None, self.app.config.shed_tool_data_table_config, persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'tools' in irmm_metadata_dict: + tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( irmm_metadata_dict[ 'tools' ], tool_section ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. repository_tools_tups = tdtm.handle_missing_data_table_entry( relative_install_dir, @@ -575,15 +577,15 @@ shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=True ) - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, shed_config_dict, relative_install_dir, tool_shed_repository, repository_tools_tups ) - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: tool_shed_repository.status = self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: tool_shed_repository.includes_datatypes = True @@ -604,7 +606,7 @@ name=tool_shed_repository.name, owner=tool_shed_repository.owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -82,9 +82,12 @@ repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools_for_display_in_tool_panel: tpm = tool_panel_manager.ToolPanelManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, tpm ) - metadata = repository.metadata - repository_tools_tups = irmm.get_repository_tools_tups( metadata ) + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=tpm, + repository=repository, + changeset_revision=repository.changeset_revision, + metadata_dict=repository.metadata ) + repository_tools_tups = irmm.get_repository_tools_tups() # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] tpm.add_to_tool_panel( repository.name, @@ -101,7 +104,7 @@ data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata, + repository.metadata, repository.get_shed_config_dict( self.app ), data_manager_relative_install_dir, repository, diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -19,9 +19,16 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, tpm=None ): - super( InstalledRepositoryMetadataManager, self ).__init__( app ) - self.app = app + def __init__( self, app, tpm=None, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( InstalledRepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=None ) if tpm is None: self.tpm = tool_panel_manager.ToolPanelManager( self.app ) else: @@ -53,15 +60,15 @@ return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) - def get_repository_tools_tups( self, metadata_dict ): + def get_repository_tools_tups( self ): """ Return a list of tuples of the form (relative_path, guid, tool) for each tool defined in the received tool shed repository metadata. """ repository_tools_tups = [] - index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( metadata_dict.get( 'shed_config_filename' ) ) - if 'tools' in metadata_dict: - for tool_dict in metadata_dict[ 'tools' ]: + index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( self.metadata_dict.get( 'shed_config_filename' ) ) + if 'tools' in self.metadata_dict: + for tool_dict in self.metadata_dict[ 'tools' ]: load_relative_path = relative_path = tool_dict.get( 'tool_config', None ) if shed_conf_dict.get( 'tool_path' ): load_relative_path = os.path.join( shed_conf_dict.get( 'tool_path' ), relative_path ) @@ -74,36 +81,21 @@ repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups - def reset_all_metadata_on_installed_repository( self, id ): + def reset_all_metadata_on_installed_repository( self ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" - invalid_file_tups = [] - metadata_dict = {} - repository = repository_util.get_installed_tool_shed_repository( self.app, id ) - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - tool_path, relative_install_dir = repository.get_tool_relative_path( self.app ) - if relative_install_dir: - original_metadata_dict = repository.metadata - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( self.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - self.update_in_shed_tool_config( repository ) - self.app.install_model.context.add( repository ) + if self.relative_install_dir: + original_metadata_dict = self.repository.metadata + self.generate_metadata_for_changeset_revision() + if self.metadata_dict != original_metadata_dict: + self.repository.metadata = self.metadata_dict + self.update_in_shed_tool_config() + self.app.install_model.context.add( self.repository ) self.app.install_model.context.flush() - log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + log.debug( 'Metadata has been reset on repository %s.' % self.repository.name ) else: - log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + log.debug( 'Metadata did not need to be reset on repository %s.' % self.repository.name ) else: - log.debug( 'Error locating installation directory for repository %s.' % repository.name ) - return invalid_file_tups, metadata_dict + log.debug( 'Error locating installation directory for repository %s.' % self.repository.name ) def reset_metadata_on_selected_repositories( self, user, **kwd ): """ @@ -119,19 +111,19 @@ for repository_id in repository_ids: try: repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id ) - owner = str( repository.owner ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_installed_repository() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) log.debug( message ) unsuccessful_count += 1 else: - log.debug( "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), owner ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s" % \ + ( str( repository.name ), str( repository.owner ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) ) @@ -146,32 +138,37 @@ status = 'error' return message, status - def tool_shed_from_repository_clone_url( self, repository_clone_url ): + def set_repository( self, repository ): + super( InstalledRepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) + + def tool_shed_from_repository_clone_url( self ): """Given a repository clone URL, return the tool shed that contains the repository.""" - return common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) + return common_util.remove_protocol_and_user_from_clone_url( cleaned_repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) - def update_in_shed_tool_config( self, repository ): + def update_in_shed_tool_config( self ): """ A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list of config_elems instead of using the in-memory list. """ - shed_conf_dict = repository.get_shed_config_dict( self.app ) + shed_conf_dict = self.repository.get_shed_config_dict( self.app ) shed_tool_conf = shed_conf_dict[ 'config_filename' ] tool_path = shed_conf_dict[ 'tool_path' ] - tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = self.get_repository_tools_tups( repository.metadata ) - clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) - tool_shed = self.tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) - owner = repository.owner + tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( self.repository ) + repository_tools_tups = self.get_repository_tools_tups() + clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + tool_shed = self.tool_shed_from_repository_clone_url() + owner = self.repository.owner if not owner: + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) owner = suc.get_repository_owner( cleaned_repository_clone_url ) guid_to_tool_elem_dict = {} for tool_config_filename, guid, tool in repository_tools_tups: guid_to_tool_elem_dict[ guid ] = self.tpm.generate_tool_elem( tool_shed, - repository.name, - repository.changeset_revision, - repository.owner or '', + self.repository.name, + self.repository.changeset_revision, + self.repository.owner or '', tool_config_filename, tool, None ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -416,21 +416,23 @@ log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) ) finally: lock.release() - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = self.shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = self.shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict self.app.install_model.context.add( tool_shed_repository ) self.app.install_model.context.flush() - has_tool_dependencies = self.__has_tool_dependencies( metadata_dict ) + has_tool_dependencies = self.__has_tool_dependencies( irmm_metadata_dict ) if has_tool_dependencies: # All tool_dependency objects must be created before the tools are processed even if no # tool dependencies will be installed. @@ -440,14 +442,14 @@ set_status=True ) else: tool_dependencies = None - if 'tools' in metadata_dict: + if 'tools' in irmm_metadata_dict: tdtm = data_table_manager.ToolDataTableManager( self.app ) - sample_files = metadata_dict.get( 'sample_files', [] ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) sample_files = [ str( s ) for s in sample_files ] tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically # generated select lists. @@ -491,7 +493,7 @@ if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: @@ -514,7 +516,7 @@ name=tool_shed_repository.name, owner=self.repository_owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -27,31 +27,89 @@ class MetadataGenerator( object ): - def __init__( self, app ): + def __init__( self, app, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None, user=None ): self.app = app + self.user = user + self.repository = repository + if self.app.name == 'galaxy': + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.changeset_revision + else: + self.changeset_revision = changeset_revision + + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + if self.repository is not None: + self.shed_config_dict = self.repository.get_shed_config_dict( self.app ) + else: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_files_directory( self.app ) + if metadata_dict is None: + # Shed related tool panel configs are only relevant to Galaxy. + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + self.metadata_dict = metadata_dict + else: + # We're in the Tool Shed. + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.tip( self.app ) + else: + self.changeset_revision = changeset_revision + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = \ + common_util.generate_clone_url_for_repository_in_tool_shed( self.user, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + relative_install_dir = self.repository.repo_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_path( self.app ) + if metadata_dict is None: + self.metadata_dict = {} + else: + self.metadata_dict = metadata_dict + self.relative_install_dir = relative_install_dir + self.repository_files_dir = repository_files_dir + self.resetting_all_metadata_on_repository = resetting_all_metadata_on_repository + self.updating_installed_repository = updating_installed_repository + self.persist = persist + self.invalid_file_tups = [] self.sa_session = app.model.context.current self.NOT_TOOL_CONFIGS = [ suc.DATATYPES_CONFIG_FILENAME, - rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, - rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, - suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] + rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, + rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, + suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] - def generate_data_manager_metadata( self, repository, repo_dir, data_manager_config_filename, metadata_dict, + def generate_data_manager_metadata( self, repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None ): """ Update the received metadata_dict with information from the parsed data_manager_config_filename. """ if data_manager_config_filename is None: return metadata_dict - repo_path = repository.repo_path( self.app ) + repo_path = self.repository.repo_path( self.app ) try: # Galaxy Side. - repo_files_directory = repository.repo_files_directory( self.app ) + repo_files_directory = self.repository.repo_files_directory( self.app ) repo_dir = repo_files_directory - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) except AttributeError: # Tool Shed side. repo_files_directory = repo_path - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( None, repository ) relative_data_manager_dir = util.relpath( os.path.split( data_manager_config_filename )[0], repo_dir ) rel_data_manager_config_filename = os.path.join( relative_data_manager_dir, os.path.split( data_manager_config_filename )[1] ) @@ -91,7 +149,7 @@ # FIXME: default behavior is to fall back to tool.name. data_manager_name = data_manager_elem.get( 'name', data_manager_id ) version = data_manager_elem.get( 'version', DataManager.DEFAULT_VERSION ) - guid = self.generate_guid_for_object( repository_clone_url, DataManager.GUID_TYPE, data_manager_id, version ) + guid = self.generate_guid_for_object( DataManager.GUID_TYPE, data_manager_id, version ) data_tables = [] if tool_file is None: log.error( 'Data Manager entry is missing tool_file attribute in "%s".' % ( data_manager_config_filename ) ) @@ -130,8 +188,7 @@ log.debug( 'Loaded Data Manager tool_files: %s' % ( tool_file ) ) return metadata_dict - def generate_datatypes_metadata( self, tv, repository, repository_clone_url, repository_files_dir, datatypes_config, - metadata_dict ): + def generate_datatypes_metadata( self, tv, repository_files_dir, datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree, error_message = xml_util.parse_xml( datatypes_config ) if tree is None: @@ -180,11 +237,11 @@ tool_config_path = hg_util.get_config_from_disk( tool_config, repository_files_dir ) full_path = os.path.abspath( tool_config_path ) tool, valid, error_message = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), full_path ) + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: guid = None else: - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) converter_dict = dict( tool_config=tool_config, guid=guid, target_datatype=target_datatype ) @@ -226,76 +283,70 @@ valid_tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return valid_tool_dependencies_dict - def generate_guid_for_object( self, repository_clone_url, guid_type, obj_id, version ): - tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) + def generate_guid_for_object( self, guid_type, obj_id, version ): + tmp_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) return '%s/%s/%s/%s' % ( tmp_url, guid_type, obj_id, version ) - def generate_metadata_for_changeset_revision( self, repository, changeset_revision, repository_clone_url, - shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, - persist=False ): + def generate_metadata_for_changeset_revision( self ): """ Generate metadata for a repository using its files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access - that changeset revision's disk files, so the value of repository_files_dir will not - always be repository.repo_path( self.app ) (it could be an absolute path to a temporary - directory containing a clone). If it is an absolute path, the value of relative_install_dir + that changeset revision's disk files, so the value of self.repository_files_dir will not + always be self.repository.repo_path( self.app ) (it could be an absolute path to a temporary + directory containing a clone). If it is an absolute path, the value of self.relative_install_dir must contain repository.repo_path( self.app ). - The value of persist will be True when the installed repository contains a valid + The value of self.persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by self.app.config.shed_tool_data_table_config. """ tv = tool_validator.ToolValidator( self.app ) - if shed_config_dict is None: - shed_config_dict = {} - if updating_installed_repository: + if self.shed_config_dict is None: + self.shed_config_dict = {} + if self.updating_installed_repository: # Keep the original tool shed repository metadata if setting metadata on a repository # installed into a local Galaxy instance for which we have pulled updates. - original_repository_metadata = repository.metadata + original_repository_metadata = self.repository.metadata else: original_repository_metadata = None - readme_file_names = readme_util.get_readme_file_names( str( repository.name ) ) + readme_file_names = readme_util.get_readme_file_names( str( self.repository.name ) ) if self.app.name == 'galaxy': # Shed related tool panel configs are only relevant to Galaxy. - metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } + metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename' ) } else: metadata_dict = {} readme_files = [] - invalid_file_tups = [] invalid_tool_configs = [] tool_dependencies_config = None original_tool_data_path = self.app.config.tool_data_path original_tool_data_table_config_path = self.app.config.tool_data_table_config_path - if resetting_all_metadata_on_repository: - if not relative_install_dir: - raise Exception( "The value of repository.repo_path must be sent when resetting all metadata on a repository." ) + if self.resetting_all_metadata_on_repository: + if not self.relative_install_dir: + raise Exception( "The value of self.repository.repo_path must be set when resetting all metadata on a repository." ) # Keep track of the location where the repository is temporarily cloned so that we can - # strip the path when setting metadata. The value of repository_files_dir is the full - # path to the temporary directory to which the repository was cloned. - work_dir = repository_files_dir - files_dir = repository_files_dir + # strip the path when setting metadata. The value of self.repository_files_dir is the + # full path to the temporary directory to which self.repository was cloned. + work_dir = self.repository_files_dir + files_dir = self.repository_files_dir # Since we're working from a temporary directory, we can safely copy sample files included # in the repository to the repository root. - self.app.config.tool_data_path = repository_files_dir - self.app.config.tool_data_table_config_path = repository_files_dir + self.app.config.tool_data_path = self.repository_files_dir + self.app.config.tool_data_table_config_path = self.repository_files_dir else: # Use a temporary working directory to copy all sample files. work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-gmfcr" ) # All other files are on disk in the repository's repo_path, which is the value of - # relative_install_dir. - files_dir = relative_install_dir - if shed_config_dict.get( 'tool_path' ): - files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) + # self.relative_install_dir. + files_dir = self.relative_install_dir + if self.shed_config_dict.get( 'tool_path' ): + files_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], files_dir ) self.app.config.tool_data_path = work_dir #FIXME: Thread safe? self.app.config.tool_data_table_config_path = work_dir # Handle proprietary datatypes, if any. datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) if datatypes_config: metadata_dict = self.generate_datatypes_metadata( tv, - repository, - repository_clone_url, files_dir, datatypes_config, metadata_dict ) @@ -303,9 +354,8 @@ # the repository's metadata. sample_file_metadata_paths, sample_file_copy_paths = \ self.get_sample_files_from_disk( repository_files_dir=files_dir, - tool_path=shed_config_dict.get( 'tool_path' ), - relative_install_dir=relative_install_dir, - resetting_all_metadata_on_repository=resetting_all_metadata_on_repository ) + tool_path=self.shed_config_dict.get( 'tool_path' ), + relative_install_dir=self.relative_install_dir ) if sample_file_metadata_paths: metadata_dict[ 'sample_files' ] = sample_file_metadata_paths # Copy all sample files included in the repository to a single directory location so we @@ -322,7 +372,7 @@ shed_tool_data_table_config=self.app.config.shed_tool_data_table_config, persist=False ) if error_message: - invalid_file_tups.append( ( filename, error_message ) ) + self.invalid_file_tups.append( ( filename, error_message ) ) for root, dirs, files in os.walk( files_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: @@ -333,18 +383,16 @@ path_to_repository_dependencies_config = os.path.join( root, name ) metadata_dict, error_message = \ self.generate_repository_dependency_metadata( path_to_repository_dependencies_config, - metadata_dict, - updating_installed_repository=updating_installed_repository ) + metadata_dict ) if error_message: - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) # See if we have one or more READ_ME files. elif name.lower() in readme_file_names: relative_path_to_readme = self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) readme_files.append( relative_path_to_readme ) # See if we have a tool config. elif name not in self.NOT_TOOL_CONFIGS and name.endswith( '.xml' ): @@ -365,12 +413,12 @@ is_tool = element_tree_root.tag == 'tool' if is_tool: tool, valid, error_message = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: if not valid: invalid_tool_configs.append( name ) - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) else: invalid_files_and_errors_tups = \ tv.check_tool_input_params( files_dir, @@ -387,17 +435,15 @@ relative_path_to_tool_config = \ self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) metadata_dict = self.generate_tool_metadata( relative_path_to_tool_config, tool, - repository_clone_url, metadata_dict ) else: for tup in invalid_files_and_errors_tups: - invalid_file_tups.append( tup ) + self.invalid_file_tups.append( tup ) # Find all exported workflows. elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) @@ -421,11 +467,10 @@ metadata_dict ) # Handle any data manager entries data_manager_config = hg_util.get_config_from_disk( suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir ) - metadata_dict = self.generate_data_manager_metadata( repository, - files_dir, + metadata_dict = self.generate_data_manager_metadata( files_dir, data_manager_config, metadata_dict, - shed_config_dict=shed_config_dict ) + shed_config_dict=self.shed_config_dict ) if readme_files: metadata_dict[ 'readme_files' ] = readme_files @@ -433,21 +478,18 @@ tool_dependencies_config = hg_util.get_config_from_disk( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, files_dir ) if tool_dependencies_config: metadata_dict, error_message = \ - self.generate_tool_dependency_metadata( repository, - changeset_revision, - repository_clone_url, - tool_dependencies_config, + self.generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict, original_repository_metadata=original_repository_metadata ) if error_message: - invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) + self.invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs + self.metadata_dict = metadata_dict # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. self.app.config.tool_data_path = original_tool_data_path self.app.config.tool_data_table_config_path = original_tool_data_table_config_path basic_util.remove_dir( work_dir ) - return metadata_dict, invalid_file_tups def generate_package_dependency_metadata( self, elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict ): """ @@ -475,8 +517,7 @@ # where a tool dependency definition is considered invalid. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=False ) + only_if_compiling_contained_td=False ) elif sub_elem.tag == 'install': package_install_version = sub_elem.get( 'version', '1.0' ) if package_install_version == '1.0': @@ -509,8 +550,7 @@ # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) elif action_elem.tag == 'action': # <action type="set_environment_for_install"> # <repository changeset_revision="b107b91b3574" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://localhost:9009"> @@ -522,8 +562,7 @@ # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) if requirements_dict: dependency_key = '%s/%s' % ( package_name, package_version ) if repository_dependency_is_valid: @@ -538,8 +577,7 @@ repository_dependency_is_valid, \ error_message - def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict, - updating_installed_repository=False ): + def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict ): """ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method is called from the tool shed as well as from Galaxy. @@ -560,8 +598,7 @@ for repository_elem in root.findall( 'repository' ): repository_dependency_tup, repository_dependency_is_valid, err_msg = \ self.handle_repository_elem( repository_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=updating_installed_repository ) + only_if_compiling_contained_td=False ) if repository_dependency_is_valid: valid_repository_dependency_tups.append( repository_dependency_tup ) else: @@ -585,10 +622,10 @@ metadata_dict[ 'repository_dependencies' ] = valid_repository_dependencies_dict return metadata_dict, error_message - def generate_tool_metadata( self, tool_config, tool, repository_clone_url, metadata_dict ): + def generate_tool_metadata( self, tool_config, tool, metadata_dict ): """Update the received metadata_dict with changes that have been applied to the received tool.""" # Generate the guid. - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) # Handle tool.requirements. tool_requirements = [] for tool_requirement in tool.requirements: @@ -667,11 +704,10 @@ metadata_dict[ 'tools' ] = [ tool_dict ] return metadata_dict - def generate_tool_dependency_metadata( self, repository, changeset_revision, repository_clone_url, tool_dependencies_config, - metadata_dict, original_repository_metadata=None ): + def generate_tool_dependency_metadata( self, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for - at least one tool in the repository, then update the received metadata_dict with information from the + at least one tool in self.repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ error_message = '' @@ -738,7 +774,7 @@ # into a Galaxy instance, so handle changes to tool dependencies appropriately. irm = self.app.installed_repository_manager updated_tool_dependency_names, deleted_tool_dependency_names = \ - irm.handle_existing_tool_dependencies_that_changed_in_update( repository, + irm.handle_existing_tool_dependencies_that_changed_in_update( self.repository, original_valid_tool_dependencies_dict, valid_tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = valid_tool_dependencies_dict @@ -769,9 +805,14 @@ metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ] return metadata_dict - def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict, - resetting_all_metadata_on_repository ): - if resetting_all_metadata_on_repository: + def get_invalid_file_tups( self ): + return self.invalid_file_tups + + def get_metadata_dict( self ): + return self.metadata_dict + + def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict ): + if self.resetting_all_metadata_on_repository: full_path_to_file = os.path.join( root, name ) stripped_path_to_file = full_path_to_file.replace( work_dir, '' ) if stripped_path_to_file.startswith( '/' ): @@ -785,9 +826,8 @@ relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] return relative_path_to_file - def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None, - resetting_all_metadata_on_repository=False ): - if resetting_all_metadata_on_repository: + def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None ): + if self.resetting_all_metadata_on_repository: # Keep track of the location where the repository is temporarily cloned so that we can strip # it when setting metadata. work_dir = repository_files_dir @@ -797,7 +837,7 @@ if root.find( '.hg' ) < 0: for name in files: if name.endswith( '.sample' ): - if resetting_all_metadata_on_repository: + if self.resetting_all_metadata_on_repository: full_path_to_sample_file = os.path.join( root, name ) stripped_path_to_sample_file = full_path_to_sample_file.replace( work_dir, '' ) if stripped_path_to_sample_file.startswith( '/' ): @@ -816,7 +856,7 @@ sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths - def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False, updating_installed_repository=False ): + def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False ): """ Process the received repository_elem which is a <repository> tag either from a repository_dependencies.xml file or a tool_dependencies.xml file. If the former, @@ -832,7 +872,7 @@ changeset_revision = repository_elem.get( 'changeset_revision', None ) prior_installation_required = str( repository_elem.get( 'prior_installation_required', False ) ) if self.app.name == 'galaxy': - if updating_installed_repository: + if self.updating_installed_repository: pass else: # We're installing a repository into Galaxy, so make sure its contained repository @@ -889,12 +929,12 @@ updated_changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed # repository, so it will not yet be installed. Return the tuple for later # installation. return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed repository, # so it will not yet be installed. Return the tuple for later installation. return repository_dependency_tup, is_valid, error_message @@ -1006,6 +1046,46 @@ return False return True + def set_changeset_revision( self, changeset_revision ): + self.changeset_revision = changeset_revision + + def set_relative_install_dir( self, relative_install_dir ): + self.relative_install_dir = relative_install_dir + + def set_repository( self, repository, relative_install_dir=None, changeset_revision=None ): + self.repository = repository + # Shed related tool panel configs are only relevant to Galaxy. + if self.app.name == 'galaxy': + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.changeset_revision ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = repository.get_shed_config_dict( self.app ) + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + if relative_install_dir is None and self.repository is not None: + relative_install_dir = repository.repo_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.tip( self.app ) ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = {} + self.metadata_dict = {} + self.set_relative_install_dir( relative_install_dir ) + self.set_repository_files_dir() + self.resetting_all_metadata_on_repository = False + self.updating_installed_repository = False + self.persist = False + self.invalid_file_tups = [] + + def set_repository_clone_url( self, repository_clone_url ): + self.repository_clone_url = repository_clone_url + + def set_repository_files_dir( self, repository_files_dir=None ): + self.repository_files_dir = repository_files_dir + def update_repository_dependencies_metadata( self, metadata, repository_dependency_tups, is_valid, description ): if is_valid: repository_dependencies_dict = metadata.get( 'repository_dependencies', None ) diff -r 9b8d3dae67427121793b2390baca699f2887d600 -r cb6dffff27973cff0afd22d9907e675fea948113 lib/tool_shed/metadata/repository_metadata_manager.py --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -22,8 +22,16 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, user ): - super( RepositoryMetadataManager, self ).__init__( app ) + def __init__( self, app, user, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( RepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=user ) self.app = app self.user = user # Repository metadata comparisons for changeset revisions. @@ -62,7 +70,7 @@ repositories_select_field.add_option( option_label, option_value ) return repositories_select_field - def clean_repository_metadata( self, id, changeset_revisions ): + def clean_repository_metadata( self, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have # a changeset_revision that is not in changeset_revisions. We sometimes see multiple # records with the same changeset revision value - no idea how this happens. We'll @@ -71,7 +79,7 @@ changeset_revisions_checked = [] for repository_metadata in \ self.sa_session.query( self.app.model.RepositoryMetadata ) \ - .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.app.security.decode_id( id ) ) \ + .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.repository.id ) \ .order_by( self.app.model.RepositoryMetadata.table.c.changeset_revision, self.app.model.RepositoryMetadata.table.c.update_time.desc() ): changeset_revision = repository_metadata.changeset_revision @@ -79,15 +87,14 @@ self.sa_session.delete( repository_metadata ) self.sa_session.flush() - def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, - current_changeset_revision, current_metadata_dict ): + def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict ): """ Compare the contents of two changeset revisions to determine if a new repository metadata revision should be created. """ # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. - # This changeset_revision is an ancestor of current_changeset_revision which is associated - # with current_metadata_dict. A new repository_metadata record will be created only + # This changeset_revision is an ancestor of self.changeset_revision which is associated + # with self.metadata_dict. A new repository_metadata record will be created only # when this method returns the constant value self.NOT_EQUAL_AND_NOT_SUBSET. ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] ) ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) @@ -99,16 +106,16 @@ ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', {} ) ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] ) ancestor_data_manager = ancestor_metadata_dict.get( 'data_manager', {} ) - current_datatypes = current_metadata_dict.get( 'datatypes', [] ) - current_tools = current_metadata_dict.get( 'tools', [] ) + current_datatypes = self.metadata_dict.get( 'datatypes', [] ) + current_tools = self.metadata_dict.get( 'tools', [] ) current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ] current_guids.sort() - current_readme_files = current_metadata_dict.get( 'readme_files', [] ) - current_repository_dependencies_dict = current_metadata_dict.get( 'repository_dependencies', {} ) + current_readme_files = self.metadata_dict.get( 'readme_files', [] ) + current_repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) current_repository_dependencies = current_repository_dependencies_dict.get( 'repository_dependencies', [] ) - current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', {} ) - current_workflows = current_metadata_dict.get( 'workflows', [] ) - current_data_manager = current_metadata_dict.get( 'data_manager', {} ) + current_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', {} ) + current_workflows = self.metadata_dict.get( 'workflows', [] ) + current_data_manager = self.metadata_dict.get( 'data_manager', {} ) # Handle case where no metadata exists for either changeset. no_datatypes = not ancestor_datatypes and not current_datatypes no_readme_files = not ancestor_readme_files and not current_readme_files @@ -334,7 +341,7 @@ return self.SUBSET return self.NOT_EQUAL_AND_NOT_SUBSET - def create_or_update_repository_metadata( self, id, repository, changeset_revision, metadata_dict ): + def create_or_update_repository_metadata( self, changeset_revision, metadata_dict ): """Create or update a repository_metadatqa record in the tool shed.""" has_repository_dependencies = False has_repository_dependencies_only_if_compiling_contained_td = False @@ -364,7 +371,9 @@ downloadable = True else: downloadable = False - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.app.security.encode_id( self.repository.id ), + changeset_revision ) if repository_metadata: # A repository metadata record already exists with the received changeset_revision, # so we don't need to check the skip_tool_test table. @@ -381,7 +390,7 @@ # need to update the skip_tool_test table. check_skip_tool_test = True repository_metadata = \ - self.app.model.RepositoryMetadata( repository_id=repository.id, + self.app.model.RepositoryMetadata( repository_id=self.repository.id, changeset_revision=changeset_revision, metadata=metadata_dict, downloadable=downloadable, @@ -407,7 +416,7 @@ # if it is contained in the skip_tool_test table. If it is, but is not associated # with a repository_metadata record, reset that skip_tool_test record to the newly # created repository_metadata record. - repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) + repo = hg_util.get_repo_for_repository( self.app, repository=self.repository, repo_path=None, create=False ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) skip_tool_test = self.get_skip_tool_test_by_changeset_revision( changeset_hash ) @@ -531,16 +540,16 @@ .filter( self.app.model.SkipToolTest.table.c.initial_changeset_revision == changeset_revision ) \ .first() - def new_datatypes_metadata_required( self, repository_metadata, metadata_dict ): + def new_datatypes_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each datatype in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if - the last saved metadata record can be updated for datatypes instead. + in self.metadata_dict to determine if a new repository_metadata table record is required + or if the last saved metadata record can be updated for datatypes instead. """ # Datatypes are stored in metadata as a list of dictionaries that looks like: # [{'dtype': 'galaxy.datatypes.data:Text', 'subclass': 'True', 'extension': 'acedb'}] - if 'datatypes' in metadata_dict: - current_datatypes = metadata_dict[ 'datatypes' ] + if 'datatypes' in self.metadata_dict: + current_datatypes = self.metadata_dict[ 'datatypes' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -564,37 +573,31 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for datatypes, so a new repository_metadata + # self.metadata_dict includes no metadata for datatypes, so a new repository_metadata # table record is not needed. return False - def new_metadata_required_for_utilities( self, repository, new_tip_metadata_dict ): + def new_metadata_required_for_utilities( self ): """ - Galaxy utilities currently consist of datatypes, repository_dependency definitions, - tools, tool_dependency definitions and exported Galaxy workflows. This method compares - the last stored repository_metadata record associated with the received repository against - the contents of the received new_tip_metadata_dict and returns True or False for the union - set of Galaxy utilities contained in both metadata dictionaries. The metadata contained - in new_tip_metadata_dict may not be a subset of that contained in the last stored - repository_metadata record associated with the received repository because one or more - Galaxy utilities may have been deleted from the repository in the new tip. + This method compares the last stored repository_metadata record associated with self.repository + against the contents of self.metadata_dict and returns True or False for the union set of Galaxy + utilities contained in both metadata dictionaries. The metadata contained in self.metadata_dict + may not be a subset of that contained in the last stored repository_metadata record associated with + self.repository because one or more Galaxy utilities may have been deleted from self.repository in + the new tip. """ repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) - datatypes_required = self.new_datatypes_metadata_required( repository_metadata, - new_tip_metadata_dict ) + datatypes_required = self.new_datatypes_metadata_required( repository_metadata ) # Uncomment the following if we decide that README files should affect how installable # repository revisions are defined. See the NOTE in the compare_readme_files() method. - # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata, - # new_tip_metadata_dict ) + # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata ) repository_dependencies_required = \ - self.new_repository_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - tools_required = self.new_tool_metadata_required( repository_metadata, new_tip_metadata_dict ) - tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - workflows_required = self.new_workflow_metadata_required( repository_metadata, new_tip_metadata_dict ) + self.new_repository_dependency_metadata_required( repository_metadata ) + tools_required = self.new_tool_metadata_required( repository_metadata ) + tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata ) + workflows_required = self.new_workflow_metadata_required( repository_metadata ) if datatypes_required or \ repository_dependencies_required or \ tools_required or \ @@ -603,17 +606,17 @@ return True return False - def new_readme_files_metadata_required( self, repository_metadata, metadata_dict ): + def new_readme_files_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each readme file in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if the - last saved metadata record can be updated for readme files instead. + in self.metadata_dict to determine if a new repository_metadata table record is required or + if the last saved metadata record can be updated for readme files instead. """ # Repository README files are kind of a special case because they have no effect on reproducibility. # We'll simply inspect the file names to determine if any that exist in the saved metadata are - # eliminated from the new metadata in the received metadata_dict. - if 'readme_files' in metadata_dict: - current_readme_files = metadata_dict[ 'readme_files' ] + # eliminated from the new metadata in self.metadata_dict. + if 'readme_files' in self.metadata_dict: + current_readme_files = self.metadata_dict[ 'readme_files' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -638,14 +641,14 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for readme_files, so a new repository_metadata + # self.metadata_dict includes no metadata for readme_files, so a new repository_metadata # table record is not needed. return False - def new_repository_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_repository_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each repository dependency in the repository - with the new metadata in metadata_dict to determine if a new repository_metadata + with the new metadata in self.metadata_dict to determine if a new repository_metadata table record is required or if the last saved metadata record can be updated for repository_dependencies instead. """ @@ -653,9 +656,9 @@ metadata = repository_metadata.metadata if 'repository_dependencies' in metadata: saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] - new_repository_dependencies_metadata = metadata_dict.get( 'repository_dependencies', None ) + new_repository_dependencies_metadata = self.metadata_dict.get( 'repository_dependencies', None ) if new_repository_dependencies_metadata: - new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] + new_repository_dependencies = self.metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] # TODO: We used to include the following here to handle the case where repository # dependency definitions were deleted. However this erroneously returned True in # cases where is should not have done so. This usually occurred where multiple single @@ -682,21 +685,21 @@ else: return False else: - if 'repository_dependencies' in metadata_dict: + if 'repository_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata record. return True else: - # The received metadata_dict includes no metadata for repository dependencies, so - # a new repository_metadata record is not needed. + # self.metadata_dict includes no metadata for repository dependencies, so a new repository_metadata + # record is not needed. return False - def new_tool_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool in the repository with the new metadata in - metadata_dict to determine if a new repository_metadata table record is required, or if + self.metadata_dict to determine if a new repository_metadata table record is required, or if the last saved metadata record can be updated instead. """ - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -704,9 +707,9 @@ saved_tool_ids = [] # The metadata for one or more tools was successfully generated in the past # for this repository, so we first compare the version string for each tool id - # in metadata_dict with what was previously saved to see if we need to create + # in self.metadata_dict with what was previously saved to see if we need to create # a new table record or if we can simply update the existing record. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: for saved_tool_metadata_dict in metadata[ 'tools' ]: if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids: saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] ) @@ -714,10 +717,10 @@ if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: return True # So far, a new metadata record is not required, but we still have to check to see if - # any new tool ids exist in metadata_dict that are not in the saved metadata. We do + # any new tool ids exist in self.metadata_dict that are not in the saved metadata. We do # this because if a new tarball was uploaded to a repository that included tools, it # may have removed existing tool files if they were not included in the uploaded tarball. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: return True return False @@ -733,22 +736,22 @@ # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for tools, so a new repository_metadata table + # self.metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False - def new_tool_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool dependency in the repository with the new - metadata in metadata_dict to determine if a new repository_metadata table record is required - or if the last saved metadata record can be updated for tool_dependencies instead. + metadata in self.metadata_dict to determine if a new repository_metadata table record is + required or if the last saved metadata record can be updated for tool_dependencies instead. """ if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tool_dependencies' in metadata: saved_tool_dependencies = metadata[ 'tool_dependencies' ] - new_tool_dependencies = metadata_dict.get( 'tool_dependencies', None ) + new_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', None ) if new_tool_dependencies: # TODO: We used to include the following here to handle the case where # tool dependency definitions were deleted. However, this erroneously @@ -777,22 +780,22 @@ # in the repository, so we can update the existing repository metadata. return False else: - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata # record. return True else: - # The received metadata_dict includes no metadata for tool dependencies, so a new - # repository_metadata record is not needed. + # self.metadata_dict includes no metadata for tool dependencies, so a new repository_metadata + # record is not needed. return False - def new_workflow_metadata_required( self, repository_metadata, metadata_dict ): + def new_workflow_metadata_required( self, repository_metadata ): """ Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of exported workflows. If this changes at some future time, this method should be enhanced accordingly. """ - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: if repository_metadata: # The repository has metadata, so update the workflows value - # no new record is needed. @@ -801,17 +804,17 @@ # There is no saved repository metadata, so we need to create a # new repository_metadata table record. return True - # The received metadata_dict includes no metadata for workflows, so a new + # self.metadata_dict includes no metadata for workflows, so a new # repository_metadata table record is not needed. return False - def reset_all_metadata_on_repository_in_tool_shed( self, id ): + def reset_all_metadata_on_repository_in_tool_shed( self ): """Reset all metadata on a single repository in a tool shed.""" - repository = suc.get_repository_in_tool_shed( self.app, id ) - log.debug( "Resetting all metadata on repository: %s" % repository.name ) - repo_dir = repository.repo_path( self.app ) - repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) + log.debug( "Resetting all metadata on repository: %s" % self.repository.name ) + repo = hg_util.get_repo_for_repository( self.app, + repository=None, + repo_path=self.repository.repo_path( self.app ), + create=False ) # The list of changeset_revisions refers to repository_metadata records that have been created # or updated. When the following loop completes, we'll delete all repository_metadata records # for this repository that do not have a changeset_revision value in this list. @@ -822,33 +825,22 @@ metadata_dict = None ancestor_changeset_revision = None ancestor_metadata_dict = None - invalid_file_tups = [] - for changeset in repository.get_changesets_for_setting_metadata( self.app ): + for changeset in self.repository.get_changesets_for_setting_metadata( self.app ): work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ramorits" ) - current_changeset_revision = str( repo.changectx( changeset ) ) ctx = repo.changectx( changeset ) log.debug( "Cloning repository changeset revision: %s", str( ctx.rev() ) ) - cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) + cloned_ok, error_message = hg_util.clone_repository( self.repository_clone_url, work_dir, str( ctx.rev() ) ) if cloned_ok: log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) - current_metadata_dict, invalid_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=current_changeset_revision, - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=work_dir, - resetting_all_metadata_on_repository=True, - updating_installed_repository=False, - persist=False ) - # We'll only display error messages for the repository tip (it may be better to display error - # messages for each installable changeset revision). - if current_changeset_revision == repository.tip( self.app ): - invalid_file_tups.extend( invalid_tups ) - if current_metadata_dict: + self.set_changeset_revision( str( repo.changectx( changeset ) ) ) + self.set_relative_install_dir( work_dir ) + self.set_repository_files_dir( work_dir ) + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: if metadata_changeset_revision is None and metadata_dict is None: # We're at the first change set in the change log. - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict if ancestor_changeset_revision: # Compare metadata from ancestor and current. The value of comparison will be one of: # self.NO_METADATA - no metadata for either ancestor or current, so continue from current @@ -856,66 +848,56 @@ # self.SUBSET - ancestor metadata is a subset of current metadata, so continue from current # self.NOT_EQUAL_AND_NOT_SUBSET - ancestor metadata is neither equal to nor a subset of current # metadata, so persist ancestor metadata. - comparison = self.compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) + comparison = self.compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict ) if comparison in [ self.NO_METADATA, self.EQUAL, self.SUBSET ]: - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict elif comparison == self.NOT_EQUAL_AND_NOT_SUBSET: metadata_changeset_revision = ancestor_changeset_revision metadata_dict = ancestor_metadata_dict - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict else: # We're at the beginning of the change log. - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict if not ctx.children(): - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None elif ancestor_metadata_dict: - # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + # We reach here only if self.metadata_dict is empty and ancestor_metadata_dict is not. if not ctx.children(): # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None basic_util.remove_dir( work_dir ) # Delete all repository_metadata records for this repository that do not have a changeset_revision # value in changeset_revisions. - self.clean_repository_metadata( id, changeset_revisions ) + self.clean_repository_metadata( changeset_revisions ) # Set tool version information for all downloadable changeset revisions. Get the list of changeset # revisions from the changelog. - self.reset_all_tool_versions( id, repo ) + self.reset_all_tool_versions( repo ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} - return invalid_file_tups, metadata_dict - def reset_all_tool_versions( self, id, repo ): + def reset_all_tool_versions( self, repo ): """Reset tool version lineage for those changeset revisions that include valid tools.""" + encoded_repository_id = self.app.security.encode_id( self.repository.id ) changeset_revisions_that_contain_tools = [] for changeset in repo.changelog: changeset_revision = str( repo.changectx( changeset ) ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -926,7 +908,9 @@ # { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. for index, changeset_revision in enumerate( changeset_revisions_that_contain_tools ): tool_versions_dict = {} - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) metadata = repository_metadata.metadata tool_dicts = metadata[ 'tools' ] if index == 0: @@ -937,7 +921,7 @@ tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] else: for tool_dict in tool_dicts: - parent_id = self.get_parent_id( id, + parent_id = self.get_parent_id( encoded_repository_id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], @@ -962,11 +946,11 @@ for repository_id in repository_ids: try: repository = suc.get_repository_in_tool_shed( self.app, repository_id ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_repository_in_tool_shed() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) @@ -974,7 +958,7 @@ unsuccessful_count += 1 else: log.debug( "Successfully reset metadata on repository %s owned by %s" % \ - ( str( repository.name ), str( repository.user.username ) ) ) + ( str( repository.name ), str( repository.user.username ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s" % str( repository.name ) ) @@ -989,75 +973,68 @@ status = 'error' return message, status - def set_repository_metadata( self, host, repository, content_alert_str='', **kwd ): + def set_repository( self, repository ): + super( RepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) + + def set_repository_metadata( self, host, content_alert_str='', **kwd ): """ - Set metadata using the repository's current disk files, returning specific error + Set metadata using the self.repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. """ message = '' status = 'done' - encoded_id = self.app.security.encode_id( repository.id ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) - repo_dir = repository.repo_path( self.app ) + encoded_id = self.app.security.encode_id( self.repository.id ) + repo_dir = self.repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.tip( self.app ), - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - if metadata_dict: + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: repository_metadata = None - repository_type_class = self.app.repository_types_registry.get_class_by_label( repository.type ) + repository_type_class = self.app.repository_types_registry.get_class_by_label( self.repository.type ) tip_only = isinstance( repository_type_class, TipOnly ) - if not tip_only and self.new_metadata_required_for_utilities( repository, metadata_dict ): + if not tip_only and self.new_metadata_required_for_utilities(): # Create a new repository_metadata table row. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: + if len( self.repository.downloadable_revisions ) == 1: suc.handle_email_alerts( self.app, host, - repository, + self.repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: - # Update the latest stored repository metadata with the contents and attributes of metadata_dict. + # Update the latest stored repository metadata with the contents and attributes of self.metadata_dict. repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) if repository_metadata: - downloadable = metadata_util.is_downloadable( metadata_dict ) + downloadable = metadata_util.is_downloadable( self.metadata_dict ) # Update the last saved repository_metadata table row. - repository_metadata.changeset_revision = repository.tip( self.app ) - repository_metadata.metadata = metadata_dict + repository_metadata.changeset_revision = self.repository.tip( self.app ) + repository_metadata.metadata = self.metadata_dict repository_metadata.downloadable = downloadable - if 'datatypes' in metadata_dict: + if 'datatypes' in self.metadata_dict: repository_metadata.includes_datatypes = True else: repository_metadata.includes_datatypes = False # We don't store information about the special type of repository dependency that is needed only for # compiling a tool dependency defined for the dependent repository. - repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ suc.get_repository_dependency_types( repository_dependencies ) repository_metadata.has_repository_dependencies = has_repository_dependencies - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: repository_metadata.includes_tool_dependencies = True else: repository_metadata.includes_tool_dependencies = False - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: repository_metadata.includes_tools = True else: repository_metadata.includes_tools = False - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: repository_metadata.includes_workflows = True else: repository_metadata.includes_workflows = False @@ -1070,11 +1047,9 @@ self.sa_session.flush() else: # There are no metadata records associated with the repository. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) - if 'tools' in metadata_dict and repository_metadata and status != 'error': + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) + if 'tools' in self.metadata_dict and repository_metadata and status != 'error': # Set tool versions on the new downloadable change set. The order of the list of changesets is # critical, so we use the repo's changelog. changeset_revisions = [] @@ -1083,25 +1058,22 @@ if suc.get_repository_metadata_by_changeset_revision( self.app, encoded_id, changeset_revision ): changeset_revisions.append( changeset_revision ) self.add_tool_versions( encoded_id, repository_metadata, changeset_revisions ) - elif len( repo ) == 1 and not invalid_file_tups: + elif len( repo ) == 1 and not self.invalid_file_tups: message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % \ - str( repository.tip( self.app ) ) + str( self.repository.tip( self.app ) ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" - if invalid_file_tups: + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, - repository, - metadata_dict ) + self.invalid_file_tups, + self.repository, + self.metadata_dict ) status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} return message, status - def set_repository_metadata_due_to_new_tip( self, host, repository, content_alert_str=None, **kwd ): - """Set metadata on the repository tip in the tool shed.""" - error_message, status = self.set_repository_metadata( host, - repository, - content_alert_str=content_alert_str, - **kwd ) + def set_repository_metadata_due_to_new_tip( self, host, content_alert_str=None, **kwd ): + """Set metadata on the tip of self.repository in the tool shed.""" + error_message, status = self.set_repository_metadata( host, content_alert_str=content_alert_str, **kwd ) return status, error_message Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Remove old messaging code.
by commits-noreply＠bitbucket.org 15 Sep '14

15 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b8d3dae6742/ Changeset: 9b8d3dae6742 User: natefoo Date: 2014-09-15 21:53:39 Summary: Remove old messaging code. Affected #: 14 files diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 run_galaxy_listener.sh --- a/run_galaxy_listener.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0` -python scripts/galaxy_messaging/server/amqp_consumer.py --config-file=universe_wsgi.ini --http-server-section=server:main 2>&1 \ No newline at end of file diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/client/amqp_publisher.py --- a/scripts/galaxy_messaging/client/amqp_publisher.py +++ /dev/null @@ -1,100 +0,0 @@ -''' -This script gets barcode data from a barcode scanner using serial communication -and sends the state representated by the barcode scanner & the barcode string -to the Galaxy LIMS RabbitMQ server. The message is sent in XML which has 2 tags, -barcode & state. The state of the scanner should be set in the galaxy_amq.ini -file as a configuration variable. -''' - -import array -import ConfigParser -import optparse -import os -import serial -import sys -import time - -from galaxy import eggs -eggs.require("amqp") - -import amqp - - -xml = \ -''' <sample> - <barcode>%(BARCODE)s</barcode> - <state>%(STATE)s</state> - <api_key>%(API_KEY)s</api_key> - </sample>''' - - -def handle_scan(states, amqp_config, barcode): - if states.get(barcode[:2], None): - values = dict( BARCODE=barcode[2:], - STATE=states.get(barcode[:2]), - API_KEY=amqp_config['api_key'] ) - print values - data = xml % values - print data - conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], - userid=amqp_config['userid'], - password=amqp_config['password'], - virtual_host=amqp_config['virtual_host'],) - - chan = conn.channel() - msg = amqp.Message(data, - content_type='text/plain', - application_headers={'msg_type': 'sample_state_update'}) - msg.properties["delivery_mode"] = 2 - chan.basic_publish(msg, - exchange=amqp_config['exchange'], - routing_key=amqp_config['routing_key']) - chan.close() - conn.close() - -def recv_data(states, amqp_config, s): - while True: - bytes = s.inWaiting() - if bytes: - print '%i bytes recvd' % bytes - msg = s.read(bytes) - print msg - handle_scan(states, amqp_config, msg.strip()) - - -def main(): - parser = optparse.OptionParser() - parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', - dest='config_file', action='store') - parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', - dest='port', action='store') - (opts, args) = parser.parse_args() - config = ConfigParser.ConfigParser() - config.read(opts.config_file) - amqp_config = {} - states = {} - for option in config.options("galaxy:amqp"): - amqp_config[option] = config.get("galaxy:amqp", option) - # abort if api_key is not set in the config file - if not amqp_config['api_key']: - print 'Error: Set the api_key config variable in the config file before starting the amqp_publisher script.' - sys.exit( 1 ) - count = 1 - while True: - section = 'scanner%i' % count - if config.has_section(section): - states[config.get(section, 'prefix')] = config.get(section, 'state') - count = count + 1 - else: - break - print amqp_config - print states - s = serial.Serial(int(opts.port)) - print 'Port %s is open: %s' %( opts.port, s.isOpen()) - recv_data(states, amqp_config, s) - s.close() - print 'Port %s is open: %s' %( opts.port, s.isOpen()) - - -if __name__ == '__main__': - main() diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/client/galaxy_amq.ini.sample --- a/scripts/galaxy_messaging/client/galaxy_amq.ini.sample +++ /dev/null @@ -1,33 +0,0 @@ -# Galaxy Message Queue -# Galaxy uses AMQ protocol to receive messages from external sources like -# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -# For Galaxy to receive messages from a message queue the RabbitMQ server has -# to be set up with a user account and other parameters listed below. The 'host' -# and 'port' fields should point to where the RabbitMQ server is running. - -#[galaxy:amqp] -#host = 127.0.0.1 -#port = 5672 -#userid = galaxy -#password = galaxy -#virtual_host = galaxy_messaging_engine -#queue = galaxy_queue -#exchange = galaxy_exchange -#routing_key = bar_code_scanner -#api_key = - -# The following section(s) 'scanner#' is for specifying the state of the -# sample this scanner represents. This state name should be one of the -# possible states created for this request type in Galaxy -# If there multiple scanners attached to this host the add as many "scanner#" -# sections below each with the name & prefix of the bar code scanner and -# the state it represents -#[scanner1] -#name = -#state = -#prefix = - -#[scanner2] -#name = -#state = -#prefix = \ No newline at end of file diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/client/report.bat.sample --- a/scripts/galaxy_messaging/client/report.bat.sample +++ /dev/null @@ -1,1 +0,0 @@ -python scanner.py -p 2 -c galaxy_amq.ini -r \ No newline at end of file diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/client/scan.bat.sample --- a/scripts/galaxy_messaging/client/scan.bat.sample +++ /dev/null @@ -1,1 +0,0 @@ -python amqp_publisher.py -p 2 -c galaxy_amq.ini \ No newline at end of file diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/client/scan.sh.sample --- a/scripts/galaxy_messaging/client/scan.sh.sample +++ /dev/null @@ -1,1 +0,0 @@ -python amqp_publisher.py -p 3 -c galaxy_amq.ini \ No newline at end of file diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/client/scanner.py --- a/scripts/galaxy_messaging/client/scanner.py +++ /dev/null @@ -1,92 +0,0 @@ -import sys, os -import serial -import array -import time -import optparse -import ConfigParser, logging -from scanner_interface import ScannerInterface - -logging.basicConfig(level=logging.DEBUG) -log = logging.getLogger( 'Scanner' ) - -# command prefix: SYN M CR -cmd = [22, 77, 13] -response = { 6: 'ACK', 5: 'ENQ', 21: 'NAK' } -image_scanner_report = 'RPTSCN.' -get_prefix1 = 'PREBK2?.' -get_prefix2 = ':4820:PREBK2?.' -set_prefix = 'PREBK2995859.' -clear_prefix = 'PRECA2.' - -def get_prefix_cmd(name): - return ':' + name + ':' + 'PREBK2?.' - -def set_prefix_cmd(name, prefix): - prefix_str = '' - for c in prefix: - prefix_str = prefix_str + hex(ord(c))[2:] - return ':' + name + ':' + 'PREBK299' + prefix_str + '!' - -def read_config_file(config_file): - config = ConfigParser.ConfigParser() - config.read(config_file) - count = 1 - scanners_list = [] - while True: - section = 'scanner%i' % count - if config.has_section(section): - scanner = dict(name=config.get(section, 'name'), - prefix=config.get(section, 'prefix'), - state=config.get(section, 'state')) - scanners_list.append(scanner) - count = count + 1 - else: - return scanners_list - -def main(): - usage = "python %s -p PORT -c CONFIG_FILE [ OPTION ]" % sys.argv[0] - parser = optparse.OptionParser(usage=usage) - parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', - dest='port', action='store') - parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', - dest='config_file', action='store') - parser.add_option('-r', '--report', help='scanner report', - dest='report', action='store_true', default=False) - parser.add_option('-i', '--install', help='install the scanners', - dest='install', action='store_true', default=False) - (opts, args) = parser.parse_args() - # validate - if not opts.port: - parser.print_help() - sys.exit(0) - if ( opts.report or opts.install ) and not opts.config_file: - parser.print_help() - sys.exit(0) - - # create the scanner interface - si = ScannerInterface(opts.port) - if opts.install: - scanners_list = read_config_file(opts.config_file) - for scanner in scanners_list: - msg = set_prefix_cmd(scanner['name'], scanner['prefix']) - si.send(msg) - response = si.recv() - if not response: - log.error("Scanner %s could not be installed." % scanner['name']) - elif opts.report: - si.send(image_scanner_report) - rep = si.recv() - log.info(rep) - scanners_list = read_config_file(opts.config_file) - for scanner in scanners_list: - msg = get_prefix_cmd(scanner['name']) - si.send(msg) - response = si.recv() - if response: - log.info('PREFIX for scanner %s: %s' % (scanner['name'], chr(int(response[8:12][:2], 16))+chr(int(response[8:12][2:], 16)) )) - si.close() - - - -if __name__ == "__main__": - main() diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/client/scanner_interface.py --- a/scripts/galaxy_messaging/client/scanner_interface.py +++ /dev/null @@ -1,76 +0,0 @@ -import sys, os -import serial -import array -import time -import optparse -import ConfigParser -import logging - -logging.basicConfig(level=logging.INFO) -log = logging.getLogger( 'ScannerInterface' ) - -class ScannerInterface( object ): - cmdprefix = [22, 77, 13] - response = { 6: 'ACK', 5: 'ENQ', 21: 'NAK' } - - def __init__( self, port ): - if os.name in ['posix', 'mac']: - self.port = port - elif os.name == 'nt': - self.port = int(port) - if self.port: - self.open() - - def open(self): - try: - self.serial_conn = serial.Serial(self.port) - except serial.SerialException: - log.exception('Unable to open port: %s' % str(self.port)) - sys.exit(1) - log.debug('Port %s is open: %s' %( str(self.port), self.serial_conn.isOpen() ) ) - - def is_open(self): - return self.serial_conn.isOpen() - - def close(self): - self.serial_conn.close() - log.debug('Port %s is open: %s' %( str(self.port), self.serial_conn.isOpen() ) ) - - def send(self, msg): - message = self.cmdprefix + map(ord, msg) - byte_array = array.array('B', message) - log.debug('Sending message to %s: %s' % ( str(self.port), message) ) - bytes = self.serial_conn.write( byte_array.tostring() ) - log.debug('%i bytes out of %i bytes sent to the scanner' % ( bytes, len(message) ) ) - - def recv(self): - time.sleep(1) - self.serial_conn.flush() - nbytes = self.serial_conn.inWaiting() - log.debug('%i bytes received' % nbytes) - if nbytes: - msg = self.serial_conn.read(nbytes) - byte_array = map(ord, msg) - log.debug('Message received [%s]: %s' % (self.response.get(byte_array[len(byte_array)-2], byte_array[len(byte_array)-2]), - msg)) - return msg - else: - log.error('Error!') - return None - - def setup_recv(self, callback): - self.recv_callback = callback - - def wait(self): - nbytes = self.serial_conn.inWaiting() - if nbytes: - msg = self.serial_conn.read(nbytes) - byte_array = map(ord, msg) - log.debug('Message received [%s]: %s' % (self.response.get(byte_array[len(byte_array)-2], byte_array[len(byte_array)-2], - msg))) - if self.recv_callback: - self.recv_callback(msg) - return - - - diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/server/amqp_consumer.py --- a/scripts/galaxy_messaging/server/amqp_consumer.py +++ /dev/null @@ -1,164 +0,0 @@ -''' -Galaxy Messaging with AMQP (RabbitMQ) -Galaxy uses AMQ protocol to receive messages from external sources like -bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -For Galaxy to receive messages from a message queue the RabbitMQ server has -to be set up with a user account and other parameters listed in the [galaxy_amqp] -section in the universe_wsgi.ini config file -Once the RabbitMQ server has been setup and started with the given parameters, -this script can be run to receive messages and update the Galaxy database accordingly -''' - -import ConfigParser -import sys, os -import optparse -import xml.dom.minidom -import subprocess -import urllib2 - -from xml_helper import get_value, get_value_index - -from galaxydb_interface import GalaxyDbInterface - -api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] -sys.path.extend( api_path ) -import common as api - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path - -from galaxy import eggs -from galaxy.web.api.requests import RequestsAPIController -import pkg_resources -pkg_resources.require( "amqp" ) -import amqp - -import logging -log = logging.getLogger("GalaxyAMQP") -log.setLevel(logging.DEBUG) -fh = logging.FileHandler("galaxy_listener.log") -fh.setLevel(logging.DEBUG) -formatter = logging.Formatter("%(asctime)s - %(name)s - %(message)s") -fh.setFormatter(formatter) -log.addHandler(fh) - -# data transfer script -data_transfer_script = os.path.join( os.getcwd(), - "scripts/galaxy_messaging/server/data_transfer.py" ) -global config -global config_file_name -global http_server_section - - -def start_data_transfer( message ): - # fork a new process to transfer datasets - cmd = '%s "%s" "%s" "%s"' % ( "python", - data_transfer_script, - message.body, - config_file_name ) # Galaxy config file name - pid = subprocess.Popen(cmd, shell=True).pid - log.debug('Started process (%i): %s' % (pid, str(cmd))) - -def update_sample_state( message ): - dom = xml.dom.minidom.parseString(message.body) - barcode = get_value(dom, 'barcode') - state = get_value(dom, 'state') - api_key = get_value(dom, 'api_key') - log.debug('Barcode: ' + barcode) - log.debug('State: ' + state) - log.debug('API Key: ' + api_key) - # validate - if not barcode or not state or not api_key: - log.debug( 'Incomplete sample_state_update message received. Sample barcode, desired state and user API key is required.' ) - return - # update the sample state in Galaxy db - dbconnstr = config.get("app:main", "database_connection") - galaxydb = GalaxyDbInterface( dbconnstr ) - sample_id = galaxydb.get_sample_id( field_name='bar_code', value=barcode ) - if sample_id == -1: - log.debug( 'Invalid barcode.' ) - return - galaxydb.change_state(sample_id, state) - # after updating the sample state, update request status - request_id = galaxydb.get_request_id(sample_id) - update_request( api_key, request_id ) - -def update_request( api_key, request_id ): - encoded_request_id = api.encode_id( config.get( "app:main", "id_secret" ), request_id ) - data = dict( update_type=RequestsAPIController.update_types.REQUEST ) - url = "http://%s:%s/api/requests/%s" % ( config.get(http_server_section, "host"), - config.get(http_server_section, "port"), - encoded_request_id ) - log.debug( 'Updating request %i' % request_id ) - try: - retval = api.update( api_key, url, data, return_formatted=False ) - log.debug( str( retval ) ) - except Exception, e: - log.debug( 'ERROR(update_request (%s)): %s' % ( str((self.api_key, url, data)), str(e) ) ) - -def recv_callback( message ): - # check the meesage type. - msg_type = message.properties['application_headers'].get('msg_type') - log.debug( 'MESSAGE RECVD: ' + str( msg_type ) ) - if msg_type == 'data_transfer': - log.debug( 'DATA TRANSFER' ) - start_data_transfer( message ) - elif msg_type == 'sample_state_update': - log.debug( 'SAMPLE STATE UPDATE' ) - update_sample_state( message ) - -def main(): - parser = optparse.OptionParser() - parser.add_option('-c', '--config-file', help='Galaxy configuration file', - dest='config_file', action='store') - parser.add_option('-s', '--http-server-section', help='Name of the HTTP server section in the Galaxy configuration file', - dest='http_server_section', action='store') - (opts, args) = parser.parse_args() - log.debug( "GALAXY LISTENER PID: " + str(os.getpid()) + " - " + str( opts ) ) - # read the Galaxy config file - global config_file_name - config_file_name = opts.config_file - global config - config = ConfigParser.ConfigParser() - config.read( opts.config_file ) - global http_server_section - http_server_section = opts.http_server_section - amqp_config = {} - for option in config.options("galaxy_amqp"): - amqp_config[option] = config.get("galaxy_amqp", option) - log.debug( str( amqp_config ) ) - # connect - conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], - userid=amqp_config['userid'], - password=amqp_config['password'], - virtual_host=amqp_config['virtual_host']) - chan = conn.channel() - chan.queue_declare( queue=amqp_config['queue'], - durable=True, - exclusive=True, - auto_delete=False) - chan.exchange_declare( exchange=amqp_config['exchange'], - type="direct", - durable=True, - auto_delete=False,) - chan.queue_bind( queue=amqp_config['queue'], - exchange=amqp_config['exchange'], - routing_key=amqp_config['routing_key']) - - chan.basic_consume( queue=amqp_config['queue'], - no_ack=True, - callback=recv_callback, - consumer_tag="testtag") - log.debug('Connected to rabbitmq server - '+amqp_config['host']+":"+amqp_config['port']) - while True: - chan.wait() - chan.basic_cancel("testtag") - chan.close() - conn.close() - -if __name__ == '__main__': - main() - - diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/server/data_transfer.py --- a/scripts/galaxy_messaging/server/data_transfer.py +++ /dev/null @@ -1,239 +0,0 @@ -#!/usr/bin/env python -""" - -Data Transfer Script: Sequencer to Galaxy - -This script is called from Galaxy RabbitMQ listener ( amqp_consumer.py ) once -the lab admin starts the data transfer process using the user interface. - -Usage: - -python data_transfer.py <config_file> - - -""" -import ConfigParser -import cookielib -import datetime -import logging -import optparse -import os -import shutil -import sys -import time -import time -import traceback -import urllib -import urllib2 -import xml.dom.minidom - - -from xml_helper import get_value, get_value_index - -log = logging.getLogger( "datatx_" + str( os.getpid() ) ) -log.setLevel( logging.DEBUG ) -fh = logging.FileHandler( "data_transfer.log" ) -fh.setLevel( logging.DEBUG ) -formatter = logging.Formatter( "%(asctime)s - %(name)s - %(message)s" ) -fh.setFormatter( formatter ) -log.addHandler( fh ) - -api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] -sys.path.extend( api_path ) -import common as api - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path - -from galaxy import eggs -from galaxy.model import SampleDataset -from galaxy.web.api.samples import SamplesAPIController -import pkg_resources -pkg_resources.require( "pexpect" ) -import pexpect - -log.debug(str(dir(api))) - -class DataTransfer( object ): - - def __init__( self, msg, config_file ): - log.info( msg ) - self.dom = xml.dom.minidom.parseString( msg ) - self.galaxy_host = get_value( self.dom, 'galaxy_host' ) - self.api_key = get_value( self.dom, 'api_key' ) - self.sequencer_host = get_value( self.dom, 'data_host' ) - self.sequencer_username = get_value( self.dom, 'data_user' ) - self.sequencer_password = get_value( self.dom, 'data_password' ) - self.request_id = get_value( self.dom, 'request_id' ) - self.sample_id = get_value( self.dom, 'sample_id' ) - self.library_id = get_value( self.dom, 'library_id' ) - self.folder_id = get_value( self.dom, 'folder_id' ) - self.dataset_files = [] - count=0 - while True: - dataset_id = get_value_index( self.dom, 'dataset_id', count ) - file = get_value_index( self.dom, 'file', count ) - name = get_value_index( self.dom, 'name', count ) - if file: - self.dataset_files.append( dict( name=name, - dataset_id=int( dataset_id ), - file=file ) ) - else: - break - count=count+1 - # read config variables - config = ConfigParser.ConfigParser() - retval = config.read( config_file ) - if not retval: - error_msg = 'FATAL ERROR: Unable to open config file %s.' % config_file - log.error( error_msg ) - sys.exit(1) - try: - self.config_id_secret = config.get( "app:main", "id_secret" ) - except ConfigParser.NoOptionError,e: - self.config_id_secret = "USING THE DEFAULT IS NOT SECURE!" - try: - self.import_dir = config.get( "app:main", "library_import_dir" ) - except ConfigParser.NoOptionError,e: - log.error( 'ERROR: library_import_dir config variable is not set in %s. ' % config_file ) - sys.exit( 1 ) - # create the destination directory within the import directory - self.server_dir = os.path.join( self.import_dir, - 'datatx_' + str( os.getpid() ) + '_' + datetime.date.today( ).strftime( "%d%b%Y" ) ) - try: - os.mkdir( self.server_dir ) - except Exception, e: - self.error_and_exit( str( e ) ) - - def start( self ): - ''' - This method executes the file transfer from the sequencer, adds the dataset - to the data library & finally updates the data transfer status in the db - ''' - # datatx - self.transfer_files() - # add the dataset to the given library - self.add_to_library() - # update the data transfer status in the db - self.update_status( SampleDataset.transfer_status.COMPLETE ) - # cleanup - #self.cleanup() - sys.exit( 0 ) - - def cleanup( self ): - ''' - remove the directory created to store the dataset files temporarily - before adding the same to the data library - ''' - try: - time.sleep( 60 ) - shutil.rmtree( self.server_dir ) - except: - self.error_and_exit() - - - def error_and_exit( self, msg='' ): - ''' - This method is called any exception is raised. This prints the traceback - and terminates this script - ''' - log.error( traceback.format_exc() ) - log.error( 'FATAL ERROR.' + msg ) - self.update_status( 'Error', 'All', msg ) - sys.exit( 1 ) - - def transfer_files( self ): - ''' - This method executes a scp process using pexpect library to transfer - the dataset file from the remote sequencer to the Galaxy server - ''' - def print_ticks( d ): - pass - for i, dataset_file in enumerate( self.dataset_files ): - self.update_status( SampleDataset.transfer_status.TRANSFERRING, dataset_file[ 'dataset_id' ] ) - try: - cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.sequencer_username, - self.sequencer_host, - dataset_file[ 'file' ].replace( ' ', '\ ' ), - self.server_dir.replace( ' ', '\ ' ), - dataset_file[ 'name' ].replace( ' ', '\ ' ) ) - log.debug( cmd ) - output = pexpect.run( cmd, - events={ '.ssword:*': self.sequencer_password+'\r\n', - pexpect.TIMEOUT: print_ticks }, - timeout=10 ) - log.debug( output ) - path = os.path.join( self.server_dir, os.path.basename( dataset_file[ 'name' ] ) ) - if not os.path.exists( path ): - msg = 'Could not find the local file after transfer ( %s ).' % path - log.error( msg ) - raise Exception( msg ) - except Exception, e: - msg = traceback.format_exc() - self.update_status( 'Error', dataset_file['dataset_id'], msg) - - - def add_to_library( self ): - ''' - This method adds the dataset file to the target data library & folder - by opening the corresponding url in Galaxy server running. - ''' - self.update_status( SampleDataset.transfer_status.ADD_TO_LIBRARY ) - try: - data = {} - data[ 'folder_id' ] = 'F%s' % api.encode_id( self.config_id_secret, self.folder_id ) - data[ 'file_type' ] = 'auto' - data[ 'server_dir' ] = self.server_dir - data[ 'dbkey' ] = '' - data[ 'upload_option' ] = 'upload_directory' - data[ 'create_type' ] = 'file' - url = "http://%s/api/libraries/%s/contents" % ( self.galaxy_host, - api.encode_id( self.config_id_secret, self.library_id ) ) - log.debug( str( ( self.api_key, url, data ) ) ) - retval = api.submit( self.api_key, url, data, return_formatted=False ) - log.debug( str( retval ) ) - except Exception, e: - self.error_and_exit( str( e ) ) - - def update_status( self, status, dataset_id='All', msg='' ): - ''' - Update the data transfer status for this dataset in the database - ''' - try: - log.debug( 'Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str( dataset_id ), str( self.sample_id) ) ) - sample_dataset_ids = [] - if dataset_id == 'All': - for dataset in self.dataset_files: - sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset[ 'dataset_id' ] ) ) - else: - sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset_id ) ) - # update the transfer status - data = {} - data[ 'update_type' ] = SamplesAPIController.update_types.SAMPLE_DATASET[0] - data[ 'sample_dataset_ids' ] = sample_dataset_ids - data[ 'new_status' ] = status - data[ 'error_msg' ] = msg - url = "http://%s/api/samples/%s" % ( self.galaxy_host, - api.encode_id( self.config_id_secret, self.sample_id ) ) - log.debug( str( ( self.api_key, url, data))) - retval = api.update( self.api_key, url, data, return_formatted=False ) - log.debug( str( retval ) ) - except urllib2.URLError, e: - log.debug( 'ERROR( sample_dataset_transfer_status ( %s ) ): %s' % ( url, str( e ) ) ) - log.error( traceback.format_exc() ) - except: - log.error( traceback.format_exc() ) - log.error( 'FATAL ERROR' ) - sys.exit( 1 ) - -if __name__ == '__main__': - log.info( 'STARTING %i %s' % ( os.getpid(), str( sys.argv ) ) ) - # - # Start the daemon - # - dt = DataTransfer( sys.argv[1], sys.argv[2]) - dt.start() - sys.exit( 0 ) - diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/server/galaxydb_interface.py --- a/scripts/galaxy_messaging/server/galaxydb_interface.py +++ /dev/null @@ -1,167 +0,0 @@ -#/usr/bin/python - -from datetime import datetime -import sys -import optparse -import os -import time -import logging - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path -from galaxy import eggs -from galaxy.model.custom_types import * -import pkg_resources -pkg_resources.require( "psycopg2" ) -import psycopg2 -pkg_resources.require( "SQLAlchemy >= 0.4" ) -from sqlalchemy import * -from sqlalchemy.orm import sessionmaker - -#logging.basicConfig(level=logging.DEBUG) -#log = logging.getLogger( 'GalaxyDbInterface' ) - -class GalaxyDbInterface(object): - - def __init__(self, dbstr): - self.dbstr = dbstr - self.db_engine = create_engine(self.dbstr) - self.db_engine.echo = False - self.metadata = MetaData(self.db_engine) - self.session = sessionmaker(bind=self.db_engine) - self.event_table = Table('sample_event', self.metadata, autoload=True ) - self.sample_table = Table('sample', self.metadata, autoload=True ) - self.sample_dataset_table = Table('sample_dataset', self.metadata, autoload=True ) - self.request_table = Table('request', self.metadata, autoload=True ) - self.request_event_table = Table('request_event', self.metadata, autoload=True ) - self.state_table = Table('sample_state', self.metadata, autoload=True ) - - def get_sample_id(self, field_name='bar_code', value=None): - if not value: - return -1 - sample_id = -1 - if field_name =='name': - stmt = select(columns=[self.sample_table.c.id], - whereclause=self.sample_table.c.name==value) - result = stmt.execute() - sample_id = result.fetchone()[0] - elif field_name == 'bar_code': - stmt = select(columns=[self.sample_table.c.id], - whereclause=self.sample_table.c.bar_code==value) - result = stmt.execute() - x = result.fetchone() - if x: - sample_id = x[0] - #log.debug('Sample ID: %i' % sample_id) - return sample_id - return -1 - - def get_request_id(self, sample_id): - query = select(columns=[self.sample_table.c.request_id], - whereclause=self.sample_table.c.id==sample_id) - request_id = query.execute().fetchall()[0][0] - return request_id - - def current_state(self, sample_id): - ''' - This method returns the current state of the sample for the given sample_id - ''' - stmt = select(columns=[self.event_table.c.sample_state_id], - whereclause=self.event_table.c.sample_id==sample_id, - order_by=self.event_table.c.update_time.desc()) - result = stmt.execute() - all_states = result.fetchall() - current_state_id = all_states[0][0] - return current_state_id - - def all_possible_states(self, sample_id): - subsubquery = select(columns=[self.sample_table.c.request_id], - whereclause=self.sample_table.c.id==sample_id) - self.request_id = subsubquery.execute().fetchall()[0][0] - #log.debug('REQUESTID: %i' % self.request_id) - subquery = select(columns=[self.request_table.c.request_type_id], - whereclause=self.request_table.c.id==self.request_id) - request_type_id = subquery.execute().fetchall()[0][0] - #log.debug('REQUESTTYPEID: %i' % request_type_id) - query = select(columns=[self.state_table.c.id, self.state_table.c.name], - whereclause=self.state_table.c.request_type_id==request_type_id, - order_by=self.state_table.c.id.asc()) - states = query.execute().fetchall() - #log.debug('POSSIBLESTATES: '+ str(states)) - return states - - def change_state(self, sample_id, new_state=None): - ''' - This method changes the state of the sample to the the 'new_state' - ''' - if not new_state: - return - new_state_id = -1 - # find the state_id for this new state in the list of possible states - possible_states = self.all_possible_states(sample_id) - for state_id, state_name in possible_states: - if new_state == state_name: - new_state_id = state_id - if new_state_id == -1: - return - #log.debug('Updating sample_id %i state to %s' % (sample_id, new_state)) - i = self.event_table.insert() - i.execute(update_time=datetime.utcnow(), - create_time=datetime.utcnow(), - sample_id=sample_id, - sample_state_id=int(new_state_id), - comment='Update by barcode scan') - # if all the samples for this request are in the final state - # then change the request state to 'Complete' - result = select(columns=[self.sample_table.c.id], - whereclause=self.sample_table.c.request_id==self.request_id).execute() - sample_id_list = result.fetchall() - request_complete = True - for sid in sample_id_list: - current_state_id = self.current_state(sid[0]) - if current_state_id != possible_states[-1][0]: - request_complete = False - break - if request_complete: - request_state = 'Complete' - #log.debug('Updating request_id %i state to "%s"' % (self.request_id, request_state)) - i = self.request_event_table.insert() - i.execute(update_time=datetime.utcnow(), - create_time=datetime.utcnow(), - request_id=self.request_id, - state=request_state, - comment='All samples of this request have finished processing.') - - def set_sample_dataset_status(self, id, new_status, msg=None): - u = self.sample_dataset_table.update(whereclause=self.sample_dataset_table.c.id==int(id)) - u.execute(status=new_status) - if new_status == 'Error': - u.execute(error_msg=msg) - else: - u.execute(error_msg='') - return - - - -if __name__ == '__main__': - print '''This file should not be run directly. To start the Galaxy AMQP Listener: - %sh run_galaxy_listener.sh''' - dbstr = 'postgres://postgres:postgres@localhost/g2' - - parser = optparse.OptionParser() - parser.add_option('-n', '--name', help='name of the sample field', dest='name', \ - action='store', default='bar_code') - parser.add_option('-v', '--value', help='value of the sample field', dest='value', \ - action='store') - parser.add_option('-s', '--state', help='new state of the sample', dest='state', \ - action='store') - (opts, args) = parser.parse_args() - - gs = GalaxyDbInterface(dbstr) - sample_id = gs.get_sample_id(field_name=opts.name, value=opts.value) - gs.change_state(sample_id, opts.state) - - - diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/server/setup_rabbitmq.py --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ /dev/null @@ -1,38 +0,0 @@ -# -# Configuration script for RabbitMQ in Galaxy -# -# Requirements: -# - set the rabbitmqctl_path variable in the 'galaxy_amqp' section in Galaxy config file -# -# Usage: -# $ python setup_rabbitmq.py <Galaxy config file> -# - -import os, sys, csv, ConfigParser - -def main( config_file ): - try: - config = ConfigParser.ConfigParser() - config.read( config_file ) - rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) - username = config.get( 'galaxy_amqp', 'userid' ) - password = config.get( 'galaxy_amqp', 'password' ) - virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) - except Exception, e: - print 'Fatal error:', str(e) - sys.exit(1) - - cmd_list = [ - 'add_user %s %s' % ( username, password ), - 'add_vhost %s' % virtual_host, - 'set_permissions -p %s %s ".*" ".*" ".*"' % ( virtual_host, username ) - ] - - for cmd in cmd_list: - retval = os.system( rabbitmqctl_path + ' ' + cmd ) - if retval: - print "Failed command: %s" % cmd - sys.exit(1) - -if __name__ == '__main__': - main( sys.argv[1] ) diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 scripts/galaxy_messaging/server/xml_helper.py --- a/scripts/galaxy_messaging/server/xml_helper.py +++ /dev/null @@ -1,28 +0,0 @@ -#======= XML helper methods ==================================================== - -import xml.dom.minidom - -def get_value( dom, tag_name ): - ''' - This method extracts the tag value from the xml message - ''' - nodelist = dom.getElementsByTagName( tag_name )[ 0 ].childNodes - rc = "" - for node in nodelist: - if node.nodeType == node.TEXT_NODE: - rc = rc + node.data - return rc - -def get_value_index( dom, tag_name, dataset_id ): - ''' - This method extracts the tag value from the xml message - ''' - try: - nodelist = dom.getElementsByTagName( tag_name )[ dataset_id ].childNodes - except: - return None - rc = "" - for node in nodelist: - if node.nodeType == node.TEXT_NODE: - rc = rc + node.data - return rc diff -r b4924e433ae2df18771a7e43c23287f4b9bc23dd -r 9b8d3dae67427121793b2390baca699f2887d600 setup_rabbitmq.sh --- a/setup_rabbitmq.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0` -python scripts/galaxy_messaging/server/setup_rabbitmq.py universe_wsgi.ini \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove unused "Main" versions of cleanup convenienence wrappers.
by commits-noreply＠bitbucket.org 15 Sep '14

15 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b4924e433ae2/ Changeset: b4924e433ae2 User: natefoo Date: 2014-09-15 21:34:03 Summary: Remove unused "Main" versions of cleanup convenienence wrappers. Affected #: 6 files diff -r 819a7675a49ea44a9dd2207323635604c7fc16ec -r b4924e433ae2df18771a7e43c23287f4b9bc23dd scripts/cleanup_datasets/delete_datasets_main.sh --- a/scripts/cleanup_datasets/delete_datasets_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -6 -r $@ >> ./scripts/cleanup_datasets/delete_datasets.log diff -r 819a7675a49ea44a9dd2207323635604c7fc16ec -r b4924e433ae2df18771a7e43c23287f4b9bc23dd scripts/cleanup_datasets/delete_userless_histories_main.sh --- a/scripts/cleanup_datasets/delete_userless_histories_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log diff -r 819a7675a49ea44a9dd2207323635604c7fc16ec -r b4924e433ae2df18771a7e43c23287f4b9bc23dd scripts/cleanup_datasets/purge_datasets_main.sh --- a/scripts/cleanup_datasets/purge_datasets_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log diff -r 819a7675a49ea44a9dd2207323635604c7fc16ec -r b4924e433ae2df18771a7e43c23287f4b9bc23dd scripts/cleanup_datasets/purge_folders_main.sh --- a/scripts/cleanup_datasets/purge_folders_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log diff -r 819a7675a49ea44a9dd2207323635604c7fc16ec -r b4924e433ae2df18771a7e43c23287f4b9bc23dd scripts/cleanup_datasets/purge_histories_main.sh --- a/scripts/cleanup_datasets/purge_histories_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log diff -r 819a7675a49ea44a9dd2207323635604c7fc16ec -r b4924e433ae2df18771a7e43c23287f4b9bc23dd scripts/cleanup_datasets/purge_libraries_main.sh --- a/scripts/cleanup_datasets/purge_libraries_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in dan/galaxy-central-prs/stable (pull request #494)
by commits-noreply＠bitbucket.org 15 Sep '14

15 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2c0a15d8d6b4/ Changeset: 2c0a15d8d6b4 Branch: stable User: jmchilton Date: 2014-09-15 21:17:02 Summary: Merged in dan/galaxy-central-prs/stable (pull request #494) [STABLE] Fix for handling unvalidated values in select lists. Addresses https://trello.com/c/5DKHp4ck Affected #: 1 file diff -r db520d1547165e56b3a0a0ff01fb854c0f93e4b1 -r 2c0a15d8d6b4a98295df6f3b614bb54da452d1d9 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -783,6 +783,8 @@ if value is not None: if not isinstance( value, list ): value = [ value ] + # We could have an unvalidated value here when e.g. running a workflow. + value = [ val.value if isinstance( val, UnvalidatedValue ) else val for val in value ] field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Sep '14

15 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5abd9fc76f7a/ Changeset: 5abd9fc76f7a Branch: stable User: dan Date: 2014-09-15 20:58:14 Summary: Fix for handling unvalidated values in select lists. Addresses https://trello.com/c/5DKHp4ck Affected #: 1 file diff -r e8453771b1dbfe462974b63216e00752fb8c4097 -r 5abd9fc76f7ad2eca013a1f81a77a4d3fe28328a lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -783,6 +783,8 @@ if value is not None: if not isinstance( value, list ): value = [ value ] + # We could have an unvalidated value here when e.g. running a workflow. + value = [ val.value if isinstance( val, UnvalidatedValue ) else val for val in value ] field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: https://bitbucket.org/galaxy/galaxy-central/commits/2c0a15d8d6b4/ Changeset: 2c0a15d8d6b4 Branch: stable User: jmchilton Date: 2014-09-15 21:17:02 Summary: Merged in dan/galaxy-central-prs/stable (pull request #494) [STABLE] Fix for handling unvalidated values in select lists. Addresses https://trello.com/c/5DKHp4ck Affected #: 1 file diff -r db520d1547165e56b3a0a0ff01fb854c0f93e4b1 -r 2c0a15d8d6b4a98295df6f3b614bb54da452d1d9 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -783,6 +783,8 @@ if value is not None: if not isinstance( value, list ): value = [ value ] + # We could have an unvalidated value here when e.g. running a workflow. + value = [ val.value if isinstance( val, UnvalidatedValue ) else val for val in value ] field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for handling unvalidated values in select lists. Addresses https://trello.com/c/5DKHp4ck
by commits-noreply＠bitbucket.org 15 Sep '14

15 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/819a7675a49e/ Changeset: 819a7675a49e User: dan Date: 2014-09-15 20:58:14 Summary: Fix for handling unvalidated values in select lists. Addresses https://trello.com/c/5DKHp4ck Affected #: 1 file diff -r 344edd250cc9bd38b3370e4be932daa9085e7b6d -r 819a7675a49ea44a9dd2207323635604c7fc16ec lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -794,6 +794,8 @@ if value is not None: if not isinstance( value, list ): value = [ value ] + # We could have an unvalidated value here when e.g. running a workflow. + value = [ val.value if isinstance( val, UnvalidatedValue ) else val for val in value ] field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 12 Sep '14

12 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6f59b58d9092/ Changeset: 6f59b58d9092 User: dannon Date: 2014-09-13 01:45:06 Summary: Prevent double submission of workflow. Affected #: 2 files diff -r f8465681a19d189317fabebbc3c400c2418e8776 -r 6f59b58d90922f2f7e66e6f5a2aa5a3f02129933 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -593,6 +593,26 @@ }); }; + +// jQuery plugin to prevent double submission of forms +// Ref: http://stackoverflow.com/questions/2830542/prevent-double-submission-of-for… +jQuery.fn.preventDoubleSubmission = function() { + $(this).on('submit',function(e){ + var $form = $(this); + + if ($form.data('submitted') === true) { + // Previously submitted - don't submit again + e.preventDefault(); + } else { + // Mark it so that the next submit can be ignored + $form.data('submitted', true); + } + }); + + // Keep chainability + return this; +}; + $(document).ready( function() { // Refresh events for form fields. diff -r f8465681a19d189317fabebbc3c400c2418e8776 -r 6f59b58d90922f2f7e66e6f5a2aa5a3f02129933 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -218,7 +218,7 @@ } }); }); - $("#tool_form").submit(function(e) { + $("#tool_form").preventDoubleSubmission().submit(function(e) { var matchLength = -1; $('span.multiinput_wrap select[name*="|input"]').each(function() { var value = $(this).val(); https://bitbucket.org/galaxy/galaxy-central/commits/344edd250cc9/ Changeset: 344edd250cc9 User: dannon Date: 2014-09-13 01:47:00 Summary: Pack scripts. Affected #: 1 file diff -r 6f59b58d90922f2f7e66e6f5a2aa5a3f02129933 -r 344edd250cc9bd38b3370e4be932daa9085e7b6d static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){var l=i.action||i;g.append($("<li></li>").append($("<a>").attr("href",i.url).html(j).click(l)))}else{g.append($("<li></li>").addClass("head").append($("<a href='#'></a>").html(j)))}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>").append(g).appendTo("body");var 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