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commit/galaxy-central: natefoo: Stop recovering jobs that don't need to be recovered - jobs in the 'NEW' state when tracking in the database.
by commits-noreply＠bitbucket.org 17 Sep '14

17 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3d92d6f0ec74/ Changeset: 3d92d6f0ec74 User: natefoo Date: 2014-09-16 23:51:40 Summary: Stop recovering jobs that don't need to be recovered - jobs in the 'NEW' state when tracking in the database. Affected #: 1 file diff -r 77ec2da4bab3d7649aaff20edc8a8a1aa6594bdd -r 3d92d6f0ec740391c9b69c0faef1b4cd0c66e946 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -101,19 +101,22 @@ In case the activation is enforced it will filter out the jobs of inactive users. """ jobs_at_startup = [] + if self.track_jobs_in_database: + in_list = ( model.Job.states.QUEUED, + model.Job.states.RUNNING ) + else: + in_list = ( model.Job.states.NEW, + model.Job.states.QUEUED, + model.Job.states.RUNNING ) if self.app.config.user_activation_on: jobs_at_startup = self.sa_session.query( model.Job ).enable_eagerloads( False ) \ .outerjoin( model.User ) \ - .filter( ( ( model.Job.state == model.Job.states.NEW ) \ - | ( model.Job.state == model.Job.states.RUNNING ) \ - | ( model.Job.state == model.Job.states.QUEUED ) ) \ + .filter( model.Job.state.in_( in_list ) \ & ( model.Job.handler == self.app.config.server_name ) \ & or_( ( model.Job.user_id == None ), ( model.User.active == True ) ) ).all() else: jobs_at_startup = self.sa_session.query( model.Job ).enable_eagerloads( False ) \ - .filter( ( ( model.Job.state == model.Job.states.NEW ) \ - | ( model.Job.state == model.Job.states.RUNNING ) \ - | ( model.Job.state == model.Job.states.QUEUED ) ) \ + .filter( model.Job.state.in_( in_list ) \ & ( model.Job.handler == self.app.config.server_name ) ).all() for job in jobs_at_startup: 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: Handle Pulsar job stop when setting metadata remotely.
by commits-noreply＠bitbucket.org 17 Sep '14

17 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/21f2a42a06d7/ Changeset: 21f2a42a06d7 Branch: stable User: natefoo Date: 2014-09-05 17:41:05 Summary: Handle Pulsar job stop when setting metadata remotely. Affected #: 1 file diff -r 65d1a7c363e95b1af3ba81655c3965d5b8917af0 -r 21f2a42a06d7d2b8c408aed22c691f5e8b209311 lib/galaxy/jobs/runners/pulsar.py --- a/lib/galaxy/jobs/runners/pulsar.py +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -416,8 +416,9 @@ def stop_job( self, job ): #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished + client = self.get_client( job.destination_params, job.job_runner_external_id ) job_ext_output_metadata = job.get_external_output_metadata() - if job_ext_output_metadata: + if not PulsarJobRunner.__remote_metadata( client ) and job_ext_output_metadata: pid = job_ext_output_metadata[0].job_runner_external_pid # every JobExternalOutputMetadata has a pid set, we just need to take from one of them if pid in [ None, '' ]: log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) 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: Fix a bug with config/galaxy.ini in run.sh
by commits-noreply＠bitbucket.org 17 Sep '14

17 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/77ec2da4bab3/ Changeset: 77ec2da4bab3 User: natefoo Date: 2014-09-16 23:13:17 Summary: Fix a bug with config/galaxy.ini in run.sh Affected #: 1 file diff -r 9207ecb43d81853da7a58cd5634683dc87991c4f -r 77ec2da4bab3d7649aaff20edc8a8a1aa6594bdd run.sh --- a/run.sh +++ b/run.sh @@ -22,7 +22,7 @@ if [ -f universe_wsgi.ini ]; then GALAXY_CONFIG_FILE=universe_wsgi.ini elif [ -f config/galaxy.ini ]; then - GALAXY_CONFIG_FILE=universe_wsgi.ini + GALAXY_CONFIG_FILE=config/galaxy.ini else GALAXY_CONFIG_FILE=config/galaxy.ini.sample fi 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] 97a97e: New vcflib tools on Test.
by GitHub 17 Sep '14

17 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 97a97e710719da7f6fae51ca79a84ffe7865e38c https://github.com/galaxyproject/usegalaxy-playbook/commit/97a97e710719da7f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-16 (Tue, 16 Sep 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- New vcflib tools on Test. Commit: 1dc0e52d939974c426781532254254d11a82172b https://github.com/galaxyproject/usegalaxy-playbook/commit/1dc0e52d939974c4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-16 (Tue, 16 Sep 2014) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test. Commit: 8b4e8640633cbd5cc301224550c8393cf9149813 https://github.com/galaxyproject/usegalaxy-playbook/commit/8b4e8640633cbd5c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-16 (Tue, 16 Sep 2014) Changed paths: M production/group_vars/pulsarservers.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Pulsar on Test and Main. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/41a99bc0c13e...…

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[galaxyproject/usegalaxy-playbook] 41a99b: Update Main.
by GitHub 17 Sep '14

17 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 41a99bc0c13e728c4faea908c7a94597d5f58f40 https://github.com/galaxyproject/usegalaxy-playbook/commit/41a99bc0c13e728c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-16 (Tue, 16 Sep 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main.

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commit/galaxy-central: jmchilton: Update to latest Pulsar client.
by commits-noreply＠bitbucket.org 17 Sep '14

17 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 17 Sep '14

17 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 17 Sep '14

17 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. 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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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