galaxy-commits December 2013

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commit/galaxy-central: 9 new changesets
by commits-noreply＠bitbucket.org 31 Dec '13

31 Dec '13

9 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0e9a8f32b5a9/ Changeset: 0e9a8f32b5a9 Branch: page-api User: kellrott Date: 2013-12-06 09:17:29 Summary: Starting to add the elements of API based page access Affected #: 2 files diff -r d50335029705d4e587a7a6428b9da6e4fc4890cf -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 lib/galaxy/webapps/galaxy/api/pages.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -0,0 +1,32 @@ +""" +API for searching Galaxy Datasets +""" +import logging +from galaxy import web +from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController +from galaxy.model.search import GalaxySearchEngine +from galaxy.exceptions import ItemAccessibilityException + +log = logging.getLogger( __name__ ) + +class PagesController( BaseAPIController, SharableItemSecurityMixin ): + + @web.expose_api + def index( self, trans, deleted='False', **kwd ): + r = trans.sa_session.query( trans.app.model.Page ) + out = [] + for row in r: + out.append( self.encode_all_ids( trans, row.to_dict(), True) ) + return out + + + @web.expose_api + def create( self, trans, payload, **kwd ): + return {} + + @web.expose_api + def show( self, trans, id, deleted='False', **kwd ): + page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id( id ) ) + rval = self.encode_all_ids( trans, page.to_dict(), True) + rval['content'] = page.latest_revision.content + return rval \ No newline at end of file diff -r d50335029705d4e587a7a6428b9da6e4fc4890cf -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -166,6 +166,7 @@ webapp.mapper.resource( 'datatype', 'datatypes', path_prefix='/api' ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) + webapp.mapper.resource( 'page', 'pages', path_prefix="/api") # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", https://bitbucket.org/galaxy/galaxy-central/commits/0e7881a4d1cf/ Changeset: 0e7881a4d1cf Branch: page-api User: Kyle Ellrott Date: 2013-12-17 20:22:45 Summary: Default Merge Affected #: 389 files diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf config/plugins/visualizations/scatterplot/templates/scatterplot.mako --- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako +++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako @@ -15,7 +15,6 @@ <script type="text/javascript" src="/static/scripts/libs/jquery/jquery.migrate.js"></script><script type="text/javascript" src="/static/scripts/libs/underscore.js"></script><script type="text/javascript" src="/static/scripts/libs/backbone/backbone.js"></script> -<script type="text/javascript" src="/static/scripts/libs/backbone/backbone-relational.js"></script><script type="text/javascript" src="/static/scripts/libs/handlebars.runtime.js"></script><script type="text/javascript" src="/static/scripts/libs/d3.js"></script><script type="text/javascript" src="/static/scripts/libs/bootstrap.js"></script> diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf 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 @@ -205,6 +205,11 @@ The request and response format should be considered alpha and are subject to change. +API Return Codes and Formats +================== + +A set of error codes for API requests is being established and will be +documented here. This is a long-term project however so stayed tuned. API Controllers =============== @@ -393,3 +398,67 @@ :undoc-members: :show-inheritance: + +API Design Guidelines +===================== + +The following section outlines guidelines related to extending and/or modifing +the Galaxy API. The Galaxy API has grown in an ad-hoc fashion over time by +many contributors and so clients SHOULD NOT expect the API will conform to +these guidelines - but developers contributing to the Galaxy API SHOULD follow +these guidelines. + + - API functionality should include docstring documentation for consumption + by readthedocs.org. + - Developers should familarize themselves with the HTTP status code definitions + http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html. The API responses + should properly set the status code according to the result - in particular + 2XX responses should be used for successful requests, 4XX for various + kinds of client errors, and 5XX for errors on the server side. + - If there is an error processing some part of request (one item in a list + for instance), the status code should be set to reflect the error and the + partial result may or may not be returned depending on the controller - + this behavior should be documented. + - (TODO) API methods should throw a finite number of exceptions (defined in) + `galaxy.exceptions` and these should subclass `MessageException` and not + paste/wsgi HTTP exceptions. When possible, the framework itself should be + responsible catching these exceptions, setting the status code, and + building an error response. + - Error responses should not consist of plain text strings - they should be + dictionaries describing the error and containing the following keys (TODO: + spell out nature of this.) Various error conditions (once a format has + been chosen and framework to enforce it in place) should be spelled out + in this document. + - Backward compatibility is important and should maintained when possible. + If changing behavior in a non-backward compatibile way please ensure one + of the following holds - there is a strong reason to believe no consumers + depend on a behavior, the behavior is effectively broken, or the API + method being modified has not been part of a tagged dist release. + +The following bullet points represent good practices more than guidelines, please +consider them when modifying the API. + + - Functionality should not be copied and pasted between controllers - + consider refactoring functionality into associated classes or short of + that into Mixins (http://en.wikipedia.org/wiki/Composition_over_inheritance). + - API additions are more permanent changes to Galaxy than many other potential + changes and so a second opinion on API changes should be sought. (Consider a + pull request!) + - New API functionality should include functional tests. These functional + tests should be implemented in Python and placed in + `test/functional/api`. (Once such a framework is in place - it is not + right now). + - Changes to reflect modifications to the API should be pushed upstream to + the BioBlend project possible. + +Longer term goals/notes. + + - It would be advantageous to have a clearer separation of anonymous and + admin handling functionality. + - If at some point in the future, functionality needs to be added that + breaks backward compatibility in a significant way to a compontent used by + the community should be alerted - a "dev" variant of the API will be + established and the community should be alerted and given a timeframe + for when the old behavior will be replaced with the new behavior. + - Consistent standards for range-based requests, batch requests, filtered + requests, etc... should be established and documented here. diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -52,15 +52,44 @@ <param id="private_token">123456789changeme</param> + server). Alternatively action can be set to 'copy' - to replace + http transfers with file system copies. --> +  +  +  +  +  +  +  +  +  +  + </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_Execution_Time">24:00:00</param> + <param id="job_Resource_List">walltime=24:00:00,ncpus=4</param></destination><destination id="condor" runner="condor"><!-- With no params, jobs are submitted to the 'vanilla' universe with: diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -1,16 +1,10 @@ from __future__ import absolute_import -import sys, os, atexit +import sys +import os -from galaxy import config, jobs, util, tools, web -import galaxy.tools.search -import galaxy.tools.data -import tool_shed.galaxy_install -import tool_shed.tool_shed_registry -from galaxy.web import security +from galaxy import config, jobs import galaxy.model -import galaxy.datatypes.registry import galaxy.security -from galaxy.objectstore import build_object_store_from_config import galaxy.quota from galaxy.tags.tag_handler import GalaxyTagHandler from galaxy.visualization.genomes import Genomes @@ -27,7 +21,8 @@ import logging log = logging.getLogger( __name__ ) -class UniverseApplication( object ): + +class UniverseApplication( object, config.ConfiguresGalaxyMixin ): """Encapsulates the state of a Universe application""" def __init__( self, **kwargs ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) @@ -38,72 +33,38 @@ self.config.check() config.configure_logging( self.config ) self.configure_fluent_log() - # Determine the database url - if self.config.database_connection: - db_url = self.config.database_connection - else: - db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database - # 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 ) - else: - self.tool_shed_registry = None - # Initialize database / check for appropriate schema version. # If this - # is a new installation, we'll restrict the tool migration messaging. - from galaxy.model.migrate.check import create_or_verify_database - create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) - # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. - from tool_shed.galaxy_install.migrate.check import verify_tools - verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) - # Object store manager - self.object_store = build_object_store_from_config(self.config, fsmon=True) + + self._configure_tool_shed_registry() + + self._configure_object_store( fsmon=True ) + # Setup the database engine and ORM - from galaxy.model import mapping - self.model = mapping.init( self.config.file_path, - db_url, - self.config.database_engine_options, - database_query_profiling_proxy = self.config.database_query_profiling_proxy, - object_store = self.object_store, - trace_logger=self.trace_logger, - use_pbkdf2=self.config.get_bool( 'use_pbkdf2', True ) ) + config_file = kwargs.get( 'global_conf', {} ).get( '__file__', None ) + self._configure_models( check_migrate_databases=True, check_migrate_tools=True, config_file=config_file ) + # Manage installed tool shed repositories. - self.installed_repository_manager = tool_shed.galaxy_install.InstalledRepositoryManager( self ) - # Create an empty datatypes registry. - self.datatypes_registry = galaxy.datatypes.registry.Registry() - # Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We - # load proprietary datatypes before datatypes in the distribution because Galaxy's default sniffers include some - # generic sniffers (eg text,xml) which catch anything, so it's impossible for proprietary sniffers to be used. - # However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype - # in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict - # between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence. - self.installed_repository_manager.load_proprietary_datatypes() - # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. - self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) + from tool_shed.galaxy_install import installed_repository_manager + self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager( self ) + + self._configure_datatypes_registry( self.installed_repository_manager ) galaxy.model.set_datatypes_registry( self.datatypes_registry ) + # Security helper - self.security = security.SecurityHelper( id_secret=self.config.id_secret ) + self._configure_security() # Tag handler self.tag_handler = GalaxyTagHandler() # Genomes self.genomes = Genomes( self ) # Data providers registry. self.data_provider_registry = DataProviderRegistry() - # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( tool_data_path=self.config.tool_data_path, - config_filename=self.config.tool_data_table_config_path ) - # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. - self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, - tool_data_path=self.tool_data_tables.tool_data_path, - from_shed_config=False ) + + self._configure_tool_data_tables( from_shed_config=False ) + # Initialize the job management configuration self.job_config = jobs.JobConfiguration(self) - # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. - tool_configs = self.config.tool_configs - if self.config.migrated_tools_config not in tool_configs: - tool_configs.append( self.config.migrated_tools_config ) - self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) - # Search support for tools - self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) + + self._configure_toolbox() + # Load Data Manager self.data_managers = DataManagers( self ) # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories. diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -1,6 +1,8 @@ """ Universe configuration builder. """ +# absolute_import needed for tool_shed package. +from __future__ import absolute_import import sys, os, tempfile, re import logging, logging.config @@ -33,15 +35,22 @@ self.umask = os.umask( 077 ) # get the current umask os.umask( self.umask ) # can't get w/o set, so set it back self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster + # Database related configuration self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) self.database_engine_options = get_database_engine_options( kwargs ) self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) ) self.database_query_profiling_proxy = string_as_bool( kwargs.get( "database_query_profiling_proxy", "False" ) ) + # Don't set this to true for production databases, but probably should # default to True for sqlite databases. self.database_auto_migrate = string_as_bool( kwargs.get( "database_auto_migrate", "False" ) ) + + # Install database related configuration (if different). + self.install_database_connection = kwargs.get( "install_database_connection", None ) + self.install_database_engine_options = get_database_engine_options( kwargs, model_prefix="install_" ) + # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) @@ -439,7 +448,7 @@ admin_users = [ x.strip() for x in self.get( "admin_users", "" ).split( "," ) ] return ( user is not None and user.email in admin_users ) -def get_database_engine_options( kwargs ): +def get_database_engine_options( kwargs, model_prefix='' ): """ Allow options for the SQLAlchemy database engine to be passed by using the prefix "database_engine_option". @@ -455,7 +464,7 @@ 'pool_threadlocal': string_as_bool, 'server_side_cursors': string_as_bool } - prefix = "database_engine_option_" + prefix = "%sdatabase_engine_option_" % model_prefix prefix_len = len( prefix ) rval = {} for key, value in kwargs.iteritems(): @@ -466,6 +475,7 @@ rval[ key ] = value return rval + def configure_logging( config ): """ Allow some basic logging configuration to be read from ini file. @@ -506,3 +516,110 @@ sentry_handler.setLevel( logging.WARN ) root.addHandler( sentry_handler ) + +class ConfiguresGalaxyMixin: + """ Shared code for configuring Galaxy-like app objects. + """ + + def _configure_toolbox( self ): + # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. + tool_configs = self.config.tool_configs + if self.config.migrated_tools_config not in tool_configs: + tool_configs.append( self.config.migrated_tools_config ) + from galaxy import tools + self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) + # Search support for tools + import galaxy.tools.search + self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) + + def _configure_tool_data_tables( self, from_shed_config ): + from galaxy.tools.data import ToolDataTableManager + + # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. + self.tool_data_tables = ToolDataTableManager( tool_data_path=self.config.tool_data_path, + config_filename=self.config.tool_data_table_config_path ) + # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. + self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, + tool_data_path=self.tool_data_tables.tool_data_path, + from_shed_config=from_shed_config ) + + def _configure_datatypes_registry( self, installed_repository_manager=None ): + from galaxy.datatypes import registry + # Create an empty datatypes registry. + self.datatypes_registry = registry.Registry() + if installed_repository_manager: + # Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We + # load proprietary datatypes before datatypes in the distribution because Galaxy's default sniffers include some + # generic sniffers (eg text,xml) which catch anything, so it's impossible for proprietary sniffers to be used. + # However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype + # in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict + # between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence. + installed_repository_manager.load_proprietary_datatypes() + # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. + self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) + + def _configure_object_store( self, **kwds ): + from galaxy.objectstore import build_object_store_from_config + self.object_store = build_object_store_from_config( self.config, **kwds ) + + def _configure_security( self ): + from galaxy.web import security + self.security = security.SecurityHelper( id_secret=self.config.id_secret ) + + def _configure_tool_shed_registry( self ): + 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 ) + else: + self.tool_shed_registry = None + + def _configure_models( self, check_migrate_databases=False, check_migrate_tools=False, config_file=None ): + """ + Preconditions: object_store must be set on self. + """ + if self.config.database_connection: + db_url = self.config.database_connection + else: + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database + install_db_url = self.config.install_database_connection + # TODO: Consider more aggressive check here that this is not the same + # database file under the hood. + combined_install_database = not( install_db_url and install_db_url != db_url ) + install_db_url = install_db_url or db_url + + if check_migrate_databases: + # Initialize database / check for appropriate schema version. # If this + # is a new installation, we'll restrict the tool migration messaging. + from galaxy.model.migrate.check import create_or_verify_database + create_or_verify_database( db_url, config_file, self.config.database_engine_options, app=self ) + if not combined_install_database: + from galaxy.model.tool_shed_install.migrate.check import create_or_verify_database as tsi_create_or_verify_database + tsi_create_or_verify_database( install_db_url, self.config.install_database_engine_options, app=self ) + + if check_migrate_tools: + # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. + from tool_shed.galaxy_install.migrate.check import verify_tools + verify_tools( self, install_db_url, config_file, self.config.database_engine_options ) + + from galaxy.model import mapping + self.model = mapping.init( self.config.file_path, + db_url, + self.config.database_engine_options, + map_install_models=combined_install_database, + database_query_profiling_proxy=self.config.database_query_profiling_proxy, + object_store=self.object_store, + trace_logger=getattr(self, "trace_logger", None), + use_pbkdf2=self.config.get_bool( 'use_pbkdf2', True ) ) + + if combined_install_database: + log.info("Install database targetting Galaxy's database configuration.") + self.install_model = self.model + else: + from galaxy.model.tool_shed_install import mapping as install_mapping + install_db_url = self.config.install_database_connection + log.info("Install database using its own connection %s" % install_db_url) + install_db_engine_options = self.config.install_database_engine_options + self.install_model = install_mapping.init( install_db_url, + install_db_engine_options ) diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/datatypes/checkers.py --- a/lib/galaxy/datatypes/checkers.py +++ b/lib/galaxy/datatypes/checkers.py @@ -2,6 +2,8 @@ from galaxy import util from StringIO import StringIO +HTML_CHECK_LINES = 100 + try: import Image as PIL except ImportError: @@ -32,9 +34,11 @@ regexp1 = re.compile( "<A\s+[^>]*HREF[^>]+>", re.I ) regexp2 = re.compile( "<IFRAME[^>]*>", re.I ) regexp3 = re.compile( "<FRAMESET[^>]*>", re.I ) - regexp4 = re.compile( "<META[^>]*>", re.I ) + regexp4 = re.compile( "<META[\W][^>]*>", re.I ) regexp5 = re.compile( "<SCRIPT[^>]*>", re.I ) lineno = 0 + # TODO: Potentially reading huge lines into string here, this should be + # reworked. for line in temp: lineno += 1 matches = regexp1.search( line ) or regexp2.search( line ) or regexp3.search( line ) or regexp4.search( line ) or regexp5.search( line ) @@ -42,7 +46,7 @@ if chunk is None: temp.close() return True - if lineno > 100: + if HTML_CHECK_LINES and (lineno > HTML_CHECK_LINES): break if chunk is None: temp.close() diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -199,6 +199,26 @@ out = "Can't create peek %s" % str( exc ) return out + def _archive_main_file(self, archive, display_name, data_filename): + """Called from _archive_composite_dataset to add central file to archive. + + Unless subclassed, this will add the main dataset file (argument data_filename) + to the archive, as an HTML file with its filename derived from the dataset name + (argument outfname). + + Returns a tuple of boolean, string, string: (error, msg, messagetype) + """ + error, msg, messagetype = False, "", "" + archname = '%s.html' % display_name # fake the real nature of the html file + try: + archive.add(data_filename, archname) + except IOError: + error = True + log.exception("Unable to add composite parent %s to temporary library download archive" % data_filename) + msg = "Unable to create archive for download, please report this error" + messagetype = "error" + return error, msg, messagetype + def _archive_composite_dataset( self, trans, data=None, **kwd ): # save a composite object into a compressed archive for downloading params = util.Params( kwd ) @@ -237,29 +257,27 @@ path = data.file_name fname = os.path.split(path)[-1] efp = data.extra_files_path - htmlname = os.path.splitext(outfname)[0] - if not htmlname.endswith(ext): - htmlname = '%s_%s' % (htmlname,ext) - archname = '%s.html' % htmlname # fake the real nature of the html file - try: - archive.add(data.file_name,archname) - except IOError: - error = True - log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - for root, dirs, files in os.walk(efp): - for fname in files: - fpath = os.path.join(root,fname) - rpath = os.path.relpath(fpath,efp) - try: - archive.add( fpath,rpath ) - except IOError: - error = True - log.exception( "Unable to add %s to temporary library download archive" % rpath) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - continue + #Add any central file to the archive, + + display_name = os.path.splitext(outfname)[0] + if not display_name.endswith(ext): + display_name = '%s_%s' % (display_name, ext) + + error, msg, messagetype = self._archive_main_file(archive, display_name, path) + if not error: + #Add any child files to the archive, + for root, dirs, files in os.walk(efp): + for fname in files: + fpath = os.path.join(root,fname) + rpath = os.path.relpath(fpath,efp) + try: + archive.add( fpath,rpath ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive" % rpath) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' + continue if not error: if params.do_action == 'zip': archive.close() @@ -288,7 +306,14 @@ return open( dataset.file_name ) def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd): - """ Old display method, for transition """ + """ Old display method, for transition - though still used by API and + test framework. Datatypes should be very careful if overridding this + method and this interface between datatypes and Galaxy will likely + change. + + TOOD: Document alternatives to overridding this method (data + providers?). + """ #Relocate all composite datatype display to a common location. composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) composite_extensions.append('html') # for archiving composite datatypes diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -348,7 +348,7 @@ try: aclass = getattr( module, datatype_class_name )() except Exception, e: - self.log.exception( 'Error calling method %s from class %s: %s' ( str( datatype_class_name ), str( module ), str( e ) ) ) + self.log.exception( 'Error calling method %s from class %s: %s', str( datatype_class_name ), str( module ), str( e ) ) ok = False if ok: if deactivate: @@ -598,6 +598,9 @@ tool_xml_text = """ <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.1" tool_type="set_metadata"><type class="SetMetadataTool" module="galaxy.tools"/> + <requirements> + <requirement type="package">samtools</requirement> + </requirements><action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/><command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command><inputs> diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -1,6 +1,10 @@ """ Custom exceptions for Galaxy """ + +from galaxy import eggs +eggs.require( "Paste" ) + from paste import httpexceptions class MessageException( Exception ): diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -14,7 +14,6 @@ import shutil import subprocess import sys -import threading import traceback from galaxy import model, util from galaxy.datatypes import metadata @@ -39,21 +38,6 @@ # and should eventually become API'd TOOL_PROVIDED_JOB_METADATA_FILE = 'galaxy.json' -class Sleeper( object ): - """ - Provides a 'sleep' method that sleeps for a number of seconds *unless* - the notify method is called (from a different thread). - """ - def __init__( self ): - self.condition = threading.Condition() - def sleep( self, seconds ): - self.condition.acquire() - self.condition.wait( seconds ) - self.condition.release() - def wake( self ): - self.condition.acquire() - self.condition.notify() - self.condition.release() class JobDestination( Bunch ): """ @@ -704,10 +688,7 @@ if self.command_line and self.command_line.startswith( 'python' ): self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root # Shell fragment to inject dependencies - if self.app.config.use_tool_dependencies: - self.dependency_shell_commands = self.tool.build_dependency_shell_commands() - else: - self.dependency_shell_commands = None + self.dependency_shell_commands = self.tool.build_dependency_shell_commands() # We need command_line persisted to the db in order for Galaxy to re-queue the job # if the server was stopped and restarted before the job finished job.command_line = self.command_line @@ -1451,10 +1432,7 @@ if self.command_line and self.command_line.startswith( 'python' ): self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root # Shell fragment to inject dependencies - if self.app.config.use_tool_dependencies: - self.dependency_shell_commands = self.tool.build_dependency_shell_commands() - else: - self.dependency_shell_commands = None + self.dependency_shell_commands = self.tool.build_dependency_shell_commands() # We need command_line persisted to the db in order for Galaxy to re-queue the job # if the server was stopped and restarted before the job finished task.command_line = self.command_line diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -12,7 +12,7 @@ form = """ if (pja.action_type == "%s"){ p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'> %s <br/> on " + pja.output_name + "\ - <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; + <div style='float: right;' class='buttons'><img src='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; %s p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) @@ -20,7 +20,7 @@ form = """ if (pja.action_type == "%s"){ p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + "</span><div class='toolFormTitle'> %s \ - <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; + <div style='float: right;' class='buttons'><img src='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; %s p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/command_factory.py --- a/lib/galaxy/jobs/command_factory.py +++ b/lib/galaxy/jobs/command_factory.py @@ -1,8 +1,11 @@ from os import getcwd from os.path import abspath +CAPTURE_RETURN_CODE = "return_code=$?" +YIELD_CAPTURED_CODE = 'sh -c "exit $return_code"' -def build_command( job, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): + +def build_command( runner, job_wrapper, include_metadata=False, include_work_dir_outputs=True, remote_command_params={} ): """ Compose the sequence of commands necessary to execute a job. This will currently include: @@ -13,64 +16,125 @@ - commands to set metadata (if include_metadata is True) """ - commands = job_wrapper.get_command_line() + commands_builder = CommandsBuilder(job_wrapper.get_command_line()) # All job runners currently handle this case which should never occur - if not commands: + if not commands_builder.commands: return None - # Remove trailing semi-colon so we can start hacking up this command. - # TODO: Refactor to compose a list and join with ';', would be more clean. - commands = commands.rstrip("; ") + __handle_version_command(commands_builder, job_wrapper) + __handle_task_splitting(commands_builder, job_wrapper) + __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params) + if include_work_dir_outputs: + __handle_work_dir_outputs(commands_builder, job_wrapper, runner, remote_command_params) + + if include_metadata and job_wrapper.requires_setting_metadata: + __handle_metadata(commands_builder, job_wrapper, runner, remote_command_params) + + return commands_builder.build() + + +def __handle_version_command(commands_builder, job_wrapper): # Prepend version string if job_wrapper.version_string_cmd: - commands = "%s &> %s; " % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands + version_command = "%s &> %s" % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands_builder.prepend_command(version_command) + +def __handle_task_splitting(commands_builder, job_wrapper): # prepend getting input files (if defined) - if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: - commands = "; ".join( job_wrapper.prepare_input_files_cmds + [ commands ] ) + if getattr(job_wrapper, 'prepare_input_files_cmds', None): + commands_builder.prepend_commands(job_wrapper.prepare_input_files_cmds) + + +def __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params): + local_dependency_resolution = remote_command_params.get("dependency_resolution", "local") == "local" # Prepend dependency injection - if job_wrapper.dependency_shell_commands: - commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) + if job_wrapper.dependency_shell_commands and local_dependency_resolution: + commands_builder.prepend_commands(job_wrapper.dependency_shell_commands) - # Coping work dir outputs or setting metadata will mask return code of - # tool command. If these are used capture the return code and ensure - # the last thing that happens is an exit with return code. - capture_return_code_command = "; return_code=$?" - captured_return_code = False +def __handle_work_dir_outputs(commands_builder, job_wrapper, runner, remote_command_params): # Append commands to copy job outputs based on from_work_dir attribute. - if include_work_dir_outputs: - work_dir_outputs = job.get_work_dir_outputs( job_wrapper ) - if work_dir_outputs: - if not captured_return_code: - commands += capture_return_code_command - captured_return_code = True + work_dir_outputs_kwds = {} + if 'working_directory' in remote_command_params: + work_dir_outputs_kwds['job_working_directory'] = remote_command_params['working_directory'] + work_dir_outputs = runner.get_work_dir_outputs( job_wrapper, **work_dir_outputs_kwds ) + if work_dir_outputs: + commands_builder.capture_return_code() + copy_commands = map(__copy_if_exists_command, work_dir_outputs) + commands_builder.append_commands(copy_commands) - commands += "; " + "; ".join( [ "if [ -f %s ] ; then cp %s %s ; fi" % - ( source_file, source_file, destination ) for ( source_file, destination ) in work_dir_outputs ] ) +def __handle_metadata(commands_builder, job_wrapper, runner, remote_command_params): # Append metadata setting commands, we don't want to overwrite metadata # that was copied over in init_meta(), as per established behavior - if include_metadata and job_wrapper.requires_setting_metadata: - metadata_command = job_wrapper.setup_external_metadata( - exec_dir=abspath( getcwd() ), - tmp_dir=job_wrapper.working_directory, - dataset_files_path=job.app.model.Dataset.file_path, - output_fnames=job_wrapper.get_output_fnames(), - set_extension=False, - kwds={ 'overwrite' : False } - ) or '' - metadata_command = metadata_command.strip() - if metadata_command: - if not captured_return_code: - commands += capture_return_code_command - captured_return_code = True - commands += "; cd %s; %s" % (abspath( getcwd() ), metadata_command) + metadata_kwds = remote_command_params.get('metadata_kwds', {}) + exec_dir = metadata_kwds.get( 'exec_dir', abspath( getcwd() ) ) + tmp_dir = metadata_kwds.get( 'tmp_dir', job_wrapper.working_directory ) + dataset_files_path = metadata_kwds.get( 'dataset_files_path', runner.app.model.Dataset.file_path ) + output_fnames = metadata_kwds.get( 'output_fnames', job_wrapper.get_output_fnames() ) + config_root = metadata_kwds.get( 'config_root', None ) + config_file = metadata_kwds.get( 'config_file', None ) + datatypes_config = metadata_kwds.get( 'datatypes_config', None ) + metadata_command = job_wrapper.setup_external_metadata( + exec_dir=exec_dir, + tmp_dir=tmp_dir, + dataset_files_path=dataset_files_path, + output_fnames=output_fnames, + set_extension=False, + config_root=config_root, + config_file=config_file, + datatypes_config=datatypes_config, + kwds={ 'overwrite' : False } + ) or '' + metadata_command = metadata_command.strip() + if metadata_command: + commands_builder.capture_return_code() + commands_builder.append_command("cd %s; %s" % (exec_dir, metadata_command)) - if captured_return_code: - commands += '; sh -c "exit $return_code"' - return commands +def __copy_if_exists_command(work_dir_output): + source_file, destination = work_dir_output + return "if [ -f %s ] ; then cp %s %s ; fi" % ( source_file, source_file, destination ) + + +class CommandsBuilder(object): + + def __init__(self, initial_command): + # Remove trailing semi-colon so we can start hacking up this command. + # TODO: Refactor to compose a list and join with ';', would be more clean. + commands = initial_command.rstrip("; ") + self.commands = commands + + # Coping work dir outputs or setting metadata will mask return code of + # tool command. If these are used capture the return code and ensure + # the last thing that happens is an exit with return code. + self.return_code_captured = False + + def prepend_command(self, command): + self.commands = "%s; %s" % (command, self.commands) + return self + + def prepend_commands(self, commands): + return self.prepend_command("; ".join(commands)) + + def append_command(self, command): + self.commands = "%s; %s" % (self.commands, command) + + def append_commands(self, commands): + self.append_command("; ".join(commands)) + + def capture_return_code(self): + if not self.return_code_captured: + self.return_code_captured = True + self.append_command(CAPTURE_RETURN_CODE) + + def build(self): + if self.return_code_captured: + self.append_command(YIELD_CAPTURED_CODE) + return self.commands + +__all__ = [build_command] diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -11,7 +11,8 @@ from sqlalchemy.sql.expression import and_, or_, select, func from galaxy import model -from galaxy.jobs import Sleeper, JobWrapper, TaskWrapper, JobDestination +from galaxy.util.sleeper import Sleeper +from galaxy.jobs import JobWrapper, TaskWrapper, JobDestination log = logging.getLogger( __name__ ) diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -11,7 +11,8 @@ from Queue import Empty, Queue from galaxy import model -from galaxy.jobs import handler, JobWrapper, NoopQueue, Sleeper +from galaxy.util.sleeper import Sleeper +from galaxy.jobs import handler, JobWrapper, NoopQueue from galaxy.util.json import from_json_string log = logging.getLogger( __name__ ) diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -146,11 +146,13 @@ def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) - def get_work_dir_outputs( self, job_wrapper ): + def get_work_dir_outputs( self, job_wrapper, job_working_directory=None ): """ Returns list of pairs (source_file, destination) describing path to work_dir output file and ultimate destination. """ + if not job_working_directory: + job_working_directory = os.path.abspath( job_wrapper.working_directory ) def in_directory( file, directory ): """ @@ -186,7 +188,7 @@ if hda_tool_output and hda_tool_output.from_work_dir: # Copy from working dir to HDA. # TODO: move instead of copy to save time? - source_file = os.path.join( os.path.abspath( job_wrapper.working_directory ), hda_tool_output.from_work_dir ) + source_file = os.path.join( job_working_directory, hda_tool_output.from_work_dir ) destination = job_wrapper.get_output_destination( output_paths[ dataset.dataset_id ] ) if in_directory( source_file, job_wrapper.working_directory ): output_pairs.append( ( source_file, destination ) ) @@ -196,7 +198,7 @@ log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) return output_pairs - def _handle_metadata_externally(self, job_wrapper): + def _handle_metadata_externally( self, job_wrapper, resolve_requirements=False ): """ Set metadata externally. Used by the local and lwr job runners where this shouldn't be attached to command-line to execute. @@ -210,6 +212,12 @@ tmp_dir=job_wrapper.working_directory, #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior kwds={ 'overwrite' : False } ) + if resolve_requirements: + dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands() + if dependency_shell_commands: + if isinstance( dependency_shell_commands, list ): + dependency_shell_commands = "&&".join( dependency_shell_commands ) + external_metadata_script = "%s&&%s" % ( dependency_shell_commands, external_metadata_script ) log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) external_metadata_proc = subprocess.Popen( args=external_metadata_script, shell=True, diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/cli_job/torque.py --- a/lib/galaxy/jobs/runners/cli_job/torque.py +++ b/lib/galaxy/jobs/runners/cli_job/torque.py @@ -35,7 +35,8 @@ echo $? > %s """ -argmap = { 'Execution_Time' : '-a', +argmap = { 'destination' : '-q', + 'Execution_Time' : '-a', 'Account_Name' : '-A', 'Checkpoint' : '-c', 'Error_Path' : '-e', diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -302,7 +302,15 @@ The external script will be run with sudo, and will setuid() to the specified user. Effectively, will QSUB as a different user (then the one used by Galaxy). """ - p = subprocess.Popen([ '/usr/bin/sudo', '-E', self.external_runJob_script, str(username), jobtemplate_filename ], + script_parts = self.external_runJob_script.split() + script = script_parts[0] + command = [ '/usr/bin/sudo', '-E', script] + for script_argument in script_parts[1:]: + command.append(script_argument) + + command.extend( [ str(username), jobtemplate_filename ] ) + log.info("Running command %s" % command) + p = subprocess.Popen(command, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) (stdoutdata, stderrdata) = p.communicate() exitcode = p.returncode diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -110,7 +110,7 @@ job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - self._handle_metadata_externally( job_wrapper ) + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job! try: job_wrapper.finish( stdout, stderr, exit_code ) diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -3,7 +3,9 @@ from galaxy import model from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner from galaxy.jobs import JobDestination +from galaxy.jobs.command_factory import build_command from galaxy.util import string_as_bool_or_none +from galaxy.util.bunch import Bunch import errno from time import sleep @@ -12,11 +14,15 @@ from .lwr_client import ClientManager, url_to_destination_params from .lwr_client import finish_job as lwr_finish_job from .lwr_client import submit_job as lwr_submit_job +from .lwr_client import ClientJobDescription log = logging.getLogger( __name__ ) __all__ = [ 'LwrJobRunner' ] +NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "LWR misconfiguration - LWR client configured to set metadata remotely, but remote LWR isn't properly configured with a galaxy_home directory." +NO_REMOTE_DATATYPES_CONFIG = "LWR client is configured to use remote datatypes configuration when setting metadata externally, but LWR is not configured with this information. Defaulting to datatypes_conf.xml." + class LwrJobRunner( AsynchronousJobRunner ): """ @@ -54,40 +60,31 @@ return job_state def queue_job(self, job_wrapper): - command_line = '' job_destination = job_wrapper.job_destination - try: - job_wrapper.prepare() - if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: - for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files - #log.debug( 'executing: %s' % cmd ) - if 0 != os.system(cmd): - raise Exception('Error running file staging command: %s' % cmd) - job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line - command_line = self.build_command_line( job_wrapper, include_metadata=False, include_work_dir_outputs=False ) - except: - job_wrapper.fail( "failure preparing job", exception=True ) - log.exception("failure running job %d" % job_wrapper.job_id) - return + command_line, client, remote_job_config = self.__prepare_job( job_wrapper, job_destination ) - # If we were able to get a command line, run the job if not command_line: - job_wrapper.finish( '', '' ) return try: - client = self.get_client_from_wrapper(job_wrapper) - output_files = self.get_output_files(job_wrapper) - input_files = job_wrapper.get_input_fnames() - working_directory = job_wrapper.working_directory - tool = job_wrapper.tool - config_files = job_wrapper.extra_filenames - job_id = lwr_submit_job(client, tool, command_line, config_files, input_files, output_files, working_directory) + dependency_resolution = LwrJobRunner.__dependency_resolution( client ) + remote_dependency_resolution = dependency_resolution == "remote" + requirements = job_wrapper.tool.requirements if remote_dependency_resolution else [] + client_job_description = ClientJobDescription( + command_line=command_line, + output_files=self.get_output_files(job_wrapper), + input_files=job_wrapper.get_input_fnames(), + working_directory=job_wrapper.working_directory, + tool=job_wrapper.tool, + config_files=job_wrapper.extra_filenames, + requirements=requirements, + ) + job_id = lwr_submit_job(client, client_job_description, remote_job_config) log.info("lwr job submitted with job_id %s" % job_id) job_wrapper.set_job_destination( job_destination, job_id ) job_wrapper.change_state( model.Job.states.QUEUED ) - except: + except Exception: job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return @@ -100,6 +97,52 @@ lwr_job_state.job_destination = job_destination self.monitor_job(lwr_job_state) + def __prepare_job(self, job_wrapper, job_destination): + """ Build command-line and LWR client for this job. """ + command_line = None + client = None + remote_job_config = None + try: + job_wrapper.prepare() + self.__prepare_input_files_locally(job_wrapper) + client = self.get_client_from_wrapper(job_wrapper) + tool = job_wrapper.tool + remote_job_config = client.setup(tool.id, tool.version) + remote_metadata = LwrJobRunner.__remote_metadata( client ) + remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client ) + dependency_resolution = LwrJobRunner.__dependency_resolution( client ) + metadata_kwds = self.__build_metadata_configuration(client, job_wrapper, remote_metadata, remote_job_config) + remote_command_params = dict( + working_directory=remote_job_config['working_directory'], + metadata_kwds=metadata_kwds, + dependency_resolution=dependency_resolution, + ) + command_line = build_command( + self, + job_wrapper=job_wrapper, + include_metadata=remote_metadata, + include_work_dir_outputs=remote_work_dir_copy, + remote_command_params=remote_command_params, + ) + except Exception: + job_wrapper.fail( "failure preparing job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + + # If we were able to get a command line, run the job + if not command_line: + job_wrapper.finish( '', '' ) + + return command_line, client, remote_job_config + + def __prepare_input_files_locally(self, job_wrapper): + """Run task splitting commands locally.""" + prepare_input_files_cmds = getattr(job_wrapper, 'prepare_input_files_cmds', None) + if prepare_input_files_cmds is not None: + for cmd in prepare_input_files_cmds: # run the commands to stage the input files + if 0 != os.system(cmd): + raise Exception('Error running file staging command: %s' % cmd) + job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line + def get_output_files(self, job_wrapper): output_fnames = job_wrapper.get_output_fnames() return [ str( o ) for o in output_fnames ] @@ -130,34 +173,42 @@ run_results = client.raw_check_complete() stdout = run_results.get('stdout', '') stderr = run_results.get('stderr', '') - + working_directory_contents = run_results.get('working_directory_contents', []) # Use LWR client code to transfer/copy files back # and cleanup job if needed. completed_normally = \ job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] cleanup_job = self.app.config.cleanup_job - work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) + remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client ) + if not remote_work_dir_copy: + work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) + else: + # They have already been copied over to look like regular outputs remotely, + # no need to handle them differently here. + work_dir_outputs = [] output_files = self.get_output_files( job_wrapper ) finish_args = dict( client=client, working_directory=job_wrapper.working_directory, job_completed_normally=completed_normally, cleanup_job=cleanup_job, work_dir_outputs=work_dir_outputs, - output_files=output_files ) + output_files=output_files, + working_directory_contents=working_directory_contents ) failed = lwr_finish_job( **finish_args ) if failed: job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True) - except: + except Exception: message = "Failed to communicate with remote job server." job_wrapper.fail( message, exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - self._handle_metadata_externally( job_wrapper ) + if not LwrJobRunner.__remote_metadata( client ): + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job try: job_wrapper.finish( stdout, stderr ) - except: + except Exception: log.exception("Job wrapper finish method failed") job_wrapper.fail("Unable to finish job", exception=True) @@ -225,3 +276,71 @@ job_state.old_state = True job_state.running = state == model.Job.states.RUNNING self.monitor_queue.put( job_state ) + + @staticmethod + def __dependency_resolution( lwr_client ): + dependency_resolution = lwr_client.destination_params.get( "dependency_resolution", "local" ) + if dependency_resolution not in ["none", "local", "remote"]: + raise Exception("Unknown dependency_resolution value encountered %s" % dependency_resolution) + return dependency_resolution + + @staticmethod + def __remote_metadata( lwr_client ): + remote_metadata = string_as_bool_or_none( lwr_client.destination_params.get( "remote_metadata", False ) ) + return remote_metadata + + @staticmethod + def __remote_work_dir_copy( lwr_client ): + # Right now remote metadata handling assumes from_work_dir outputs + # have been copied over before it runs. So do that remotely. This is + # not the default though because adding it to the command line is not + # cross-platform (no cp on Windows) and its un-needed work outside + # the context of metadata settting (just as easy to download from + # either place.) + return LwrJobRunner.__remote_metadata( lwr_client ) + + @staticmethod + def __use_remote_datatypes_conf( lwr_client ): + """ When setting remote metadata, use integrated datatypes from this + Galaxy instance or use the datatypes config configured via the remote + LWR. + + Both options are broken in different ways for same reason - datatypes + may not match. One can push the local datatypes config to the remote + server - but there is no guarentee these datatypes will be defined + there. Alternatively, one can use the remote datatype config - but + there is no guarentee that it will contain all the datatypes available + to this Galaxy. + """ + use_remote_datatypes = string_as_bool_or_none( lwr_client.destination_params.get( "use_remote_datatypes", False ) ) + return use_remote_datatypes + + def __build_metadata_configuration(self, client, job_wrapper, remote_metadata, remote_job_config): + metadata_kwds = {} + if remote_metadata: + remote_system_properties = remote_job_config.get("system_properties", {}) + remote_galaxy_home = remote_system_properties.get("galaxy_home", None) + if not remote_galaxy_home: + raise Exception(NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE) + metadata_kwds['exec_dir'] = remote_galaxy_home + outputs_directory = remote_job_config['outputs_directory'] + configs_directory = remote_job_config['configs_directory'] + outputs = [Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper)] + metadata_kwds['output_fnames'] = outputs + metadata_kwds['config_root'] = remote_galaxy_home + default_config_file = os.path.join(remote_galaxy_home, 'universe_wsgi.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 ): + remote_datatypes_config = remote_system_properties.get('galaxy_datatypes_config_file', None) + if not remote_datatypes_config: + log.warn(NO_REMOTE_DATATYPES_CONFIG) + remote_datatypes_config = os.path.join(remote_galaxy_home, 'datatypes_conf.xml') + metadata_kwds['datatypes_config'] = remote_datatypes_config + else: + integrates_datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs + # Ensure this file gets pushed out to the remote config dir. + job_wrapper.extra_filenames.append(integrates_datatypes_config) + + metadata_kwds['datatypes_config'] = os.path.join(configs_directory, os.path.basename(integrates_datatypes_config)) + return metadata_kwds diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf 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 @@ -6,9 +6,9 @@ """ -from .stager import submit_job, finish_job +from .stager import submit_job, finish_job, ClientJobDescription from .client import OutputNotFoundException from .manager import ClientManager from .destination import url_to_destination_params -__all__ = [ClientManager, OutputNotFoundException, url_to_destination_params, finish_job, submit_job] +__all__ = [ClientManager, OutputNotFoundException, url_to_destination_params, finish_job, submit_job, ClientJobDescription] diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/lwr_client/action_mapper.py --- a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py +++ b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py @@ -21,7 +21,7 @@ >>> from tempfile import NamedTemporaryFile >>> from os import unlink >>> f = NamedTemporaryFile(delete=False) - >>> f.write(json_string) + >>> write_result = f.write(json_string.encode('UTF-8')) >>> f.close() >>> class MockClient(): ... default_file_action = 'none' @@ -30,23 +30,23 @@ >>> mapper = FileActionMapper(MockClient()) >>> unlink(f.name) >>> # Test first config line above, implicit path prefix mapper - >>> mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input') - ('none',) + >>> mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input')[0] == u'none' + True >>> # Test another (2nd) mapper, this one with a different action - >>> mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input') - ('transfer',) + >>> mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input')[0] == u'transfer' + True >>> # Always at least copy work_dir outputs. - >>> mapper.action('/opt/galaxy/database/working_directory/45.sh', 'work_dir') - ('copy',) + >>> mapper.action('/opt/galaxy/database/working_directory/45.sh', 'work_dir')[0] == u'copy' + True >>> # Test glob mapper (matching test) - >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input') - ('copy',) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input')[0] == u'copy' + True >>> # Test glob mapper (non-matching test) - >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input') - ('none',) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input')[0] == u'none' + True >>> # Regex mapper test. - >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input') - ('copy',) + >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input')[0] == u'copy' + True """ def __init__(self, client): diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -50,7 +50,7 @@ return "No remote output found for path %s" % self.path -class Client(object): +class JobClient(object): """ Objects of this client class perform low-level communication with a remote LWR server. @@ -161,25 +161,23 @@ raise Exception("Unknown output_type returned from LWR server %s" % output_type) return output_path - def fetch_work_dir_output(self, source, working_directory, output_path, action='transfer'): + def fetch_work_dir_output(self, name, working_directory, output_path, action='transfer'): """ Download an output dataset specified with from_work_dir from the remote server. **Parameters** - source : str + name : str Path in job's working_directory to find output in. working_directory : str Local working_directory for the job. output_path : str Full path to output dataset. """ - output = open(output_path, "wb") - name = os.path.basename(source) if action == 'transfer': - self.__raw_download_output(name, self.job_id, "work_dir", output) - elif action == 'copy': + self.__raw_download_output(name, self.job_id, "work_dir", output_path) + else: # Even if action is none - LWR has a different work_dir so this needs to be copied. lwr_path = self._output_path(name, self.job_id, 'work_dir')['path'] self._copy(lwr_path, output_path) @@ -199,7 +197,7 @@ } self._raw_execute("download_output", output_params, output_path=output_path) - def launch(self, command_line): + def launch(self, command_line, requirements=[]): """ Run or queue up the execution of the supplied `command_line` on the remote server. @@ -213,6 +211,8 @@ submit_params = self._submit_params if submit_params: launch_params['params'] = dumps(submit_params) + if requirements: + launch_params['requirements'] = dumps([requirement.to_dict() for requirement in requirements]) return self._raw_execute("launch", launch_params) def kill(self): @@ -285,13 +285,13 @@ shutil.copyfile(source, destination) -class InputCachingClient(Client): +class InputCachingJobClient(JobClient): """ Beta client that cache's staged files to prevent duplication. """ def __init__(self, destination_params, job_id, job_manager_interface, client_cacher): - super(InputCachingClient, self).__init__(destination_params, job_id, job_manager_interface) + super(InputCachingJobClient, self).__init__(destination_params, job_id, job_manager_interface) self.client_cacher = client_cacher @parseJson() @@ -326,3 +326,55 @@ @parseJson() def file_available(self, path): return self._raw_execute("file_available", {"path": path}) + + +class ObjectStoreClient(object): + + def __init__(self, lwr_interface): + self.lwr_interface = lwr_interface + + @parseJson() + def exists(self, **kwds): + return self._raw_execute("object_store_exists", args=self.__data(**kwds)) + + @parseJson() + def file_ready(self, **kwds): + return self._raw_execute("object_store_file_ready", args=self.__data(**kwds)) + + @parseJson() + def create(self, **kwds): + return self._raw_execute("object_store_create", args=self.__data(**kwds)) + + @parseJson() + def empty(self, **kwds): + return self._raw_execute("object_store_empty", args=self.__data(**kwds)) + + @parseJson() + def size(self, **kwds): + return self._raw_execute("object_store_size", args=self.__data(**kwds)) + + @parseJson() + def delete(self, **kwds): + return self._raw_execute("object_store_delete", args=self.__data(**kwds)) + + @parseJson() + def get_data(self, **kwds): + return self._raw_execute("object_store_get_data", args=self.__data(**kwds)) + + @parseJson() + def get_filename(self, **kwds): + return self._raw_execute("object_store_get_filename", args=self.__data(**kwds)) + + @parseJson() + def update_from_file(self, **kwds): + return self._raw_execute("object_store_update_from_file", args=self.__data(**kwds)) + + @parseJson() + def get_store_usage_percent(self): + return self._raw_execute("object_store_get_store_usage_percent", args={}) + + def __data(self, **kwds): + return kwds + + def _raw_execute(self, command, args={}): + return self.lwr_interface.execute(command, args, data=None, input_path=None, output_path=None) diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/lwr_client/destination.py --- a/lib/galaxy/jobs/runners/lwr_client/destination.py +++ b/lib/galaxy/jobs/runners/lwr_client/destination.py @@ -51,9 +51,10 @@ >>> destination_params = {"private_token": "12345", "submit_native_specification": "-q batch"} >>> result = submit_params(destination_params) - >>> result.items() - [('native_specification', '-q batch')] + >>> result + {'native_specification': '-q batch'} """ - return dict([(key[len(SUBMIT_PREFIX):], value) - for key, value in (destination_params or {}).iteritems() + destination_params = destination_params or {} + return dict([(key[len(SUBMIT_PREFIX):], destination_params[key]) + for key in destination_params if key.startswith(SUBMIT_PREFIX)]) diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -5,10 +5,22 @@ from queue import Queue from threading import Thread from os import getenv -from urllib import urlencode -from StringIO import StringIO +try: + from urllib import urlencode +except ImportError: + from urllib.parse import urlencode +try: + from StringIO import StringIO as BytesIO +except ImportError: + from io import BytesIO +try: + from six import text_type +except ImportError: + from galaxy.util import unicodify as text_type -from .client import Client, InputCachingClient +from .client import JobClient +from .client import InputCachingJobClient +from .client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager from .destination import url_to_destination_params @@ -27,10 +39,10 @@ """ def __init__(self, **kwds): if 'job_manager' in kwds: - self.job_manager_interface_class = LocalJobManagerInterface + self.job_manager_interface_class = LocalLwrInterface self.job_manager_interface_args = dict(job_manager=kwds['job_manager'], file_cache=kwds['file_cache']) else: - self.job_manager_interface_class = HttpJobManagerInterface + self.job_manager_interface_class = HttpLwrInterface transport_type = kwds.get('transport_type', None) transport = get_transport(transport_type) self.job_manager_interface_args = dict(transport=transport) @@ -40,11 +52,11 @@ if cache: log.info("Setting LWR client class to caching variant.") self.client_cacher = ClientCacher(**kwds) - self.client_class = InputCachingClient + self.client_class = InputCachingJobClient self.extra_client_kwds = {"client_cacher": self.client_cacher} else: log.info("Setting LWR client class to standard, non-caching variant.") - self.client_class = Client + self.client_class = JobClient self.extra_client_kwds = {} def get_client(self, destination_params, job_id): @@ -55,11 +67,35 @@ return self.client_class(destination_params, job_id, job_manager_interface, **self.extra_client_kwds) def __parse_destination_params(self, destination_params): - if isinstance(destination_params, str) or isinstance(destination_params, unicode): + try: + unicode_type = unicode + except NameError: + unicode_type = str + if isinstance(destination_params, str) or isinstance(destination_params, unicode_type): destination_params = url_to_destination_params(destination_params) return destination_params +class ObjectStoreClientManager(object): + + def __init__(self, **kwds): + if 'object_store' in kwds: + self.interface_class = LocalLwrInterface + self.interface_args = dict(object_store=kwds['object_store']) + else: + self.interface_class = HttpLwrInterface + transport_type = kwds.get('transport_type', None) + transport = get_transport(transport_type) + self.interface_args = dict(transport=transport) + self.extra_client_kwds = {} + + def get_client(self, client_params): + interface_class = self.interface_class + interface_args = dict(destination_params=client_params, **self.interface_args) + interface = interface_class(**interface_args) + return ObjectStoreClient(interface) + + class JobManagerInteface(object): """ Abstract base class describes how client communicates with remote job @@ -76,7 +112,7 @@ """ -class HttpJobManagerInterface(object): +class HttpLwrInterface(object): def __init__(self, destination_params, transport): self.transport = transport @@ -92,16 +128,18 @@ def __build_url(self, command, args): if self.private_key: args["private_key"] = self.private_key - data = urlencode(args) + arg_bytes = dict([(k, text_type(args[k]).encode('utf-8')) for k in args]) + data = urlencode(arg_bytes) url = self.remote_host + command + "?" + data return url -class LocalJobManagerInterface(object): +class LocalLwrInterface(object): - def __init__(self, destination_params, job_manager, file_cache): + def __init__(self, destination_params, job_manager=None, file_cache=None, object_store=None): self.job_manager = job_manager self.file_cache = file_cache + self.object_store = object_store def __app_args(self): ## Arguments that would be specified from LwrApp if running @@ -109,10 +147,12 @@ return { 'manager': self.job_manager, 'file_cache': self.file_cache, + 'object_store': self.object_store, 'ip': None } def execute(self, command, args={}, data=None, input_path=None, output_path=None): + # If data set, should be unicode (on Python 2) or str (on Python 3). from lwr import routes from lwr.framework import build_func_args controller = getattr(routes, command) @@ -129,9 +169,9 @@ def __build_body(self, data, input_path): if data is not None: - return StringIO(data) + return BytesIO(data.encode('utf-8')) elif input_path is not None: - return open(input_path, 'r') + return open(input_path, 'rb') else: return None @@ -188,4 +228,4 @@ int_val = int(val) return int_val -__all__ = [ClientManager, HttpJobManagerInterface] +__all__ = [ClientManager, ObjectStoreClientManager, HttpLwrInterface] diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/lwr_client/stager.py --- a/lib/galaxy/jobs/runners/lwr_client/stager.py +++ b/lib/galaxy/jobs/runners/lwr_client/stager.py @@ -1,12 +1,21 @@ from os.path import abspath, basename, join, exists from os import listdir, sep from re import findall +from re import compile +from io import open +from contextlib import contextmanager from .action_mapper import FileActionMapper from logging import getLogger log = getLogger(__name__) +# All output files marked with from_work_dir attributes will copied or downloaded +# this pattern picks up attiditional files to copy back - such as those +# associated with multiple outputs and metadata configuration. Set to .* to just +# copy everything +COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*") + class JobInputs(object): """ @@ -24,22 +33,24 @@ >>> import tempfile >>> tf = tempfile.NamedTemporaryFile() >>> def setup_inputs(tf): - ... open(tf.name, "w").write("world /path/to/input the rest") - ... inputs = JobInputs("hello /path/to/input", [tf.name]) + ... open(tf.name, "w").write(u"world /path/to/input the rest") + ... inputs = JobInputs(u"hello /path/to/input", [tf.name]) ... return inputs >>> inputs = setup_inputs(tf) - >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') - >>> inputs.rewritten_command_line - 'hello C:\\\\input' - >>> inputs.rewritten_config_files[tf.name] - 'world C:\\\\input the rest' + >>> inputs.rewrite_paths(u"/path/to/input", u'C:\\input') + >>> inputs.rewritten_command_line == u'hello C:\\\\input' + True + >>> inputs.rewritten_config_files[tf.name] == u'world C:\\\\input the rest' + True >>> tf.close() >>> tf = tempfile.NamedTemporaryFile() >>> inputs = setup_inputs(tf) - >>> inputs.find_referenced_subfiles('/path/to') - ['/path/to/input'] + >>> inputs.find_referenced_subfiles('/path/to') == [u'/path/to/input'] + True >>> inputs.path_referenced('/path/to') True + >>> inputs.path_referenced(u'/path/to') + True >>> inputs.path_referenced('/path/to/input') True >>> inputs.path_referenced('/path/to/notinput') @@ -92,7 +103,7 @@ self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) def __rewrite_config_files(self, local_path, remote_path): - for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): + for config_file, rewritten_contents in self.rewritten_config_files.items(): self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) def __items(self): @@ -140,7 +151,7 @@ For each file that has been transferred and renamed, updated command_line and configfiles to reflect that rewrite. """ - for local_path, remote_path in self.file_renames.iteritems(): + for local_path, remote_path in self.file_renames.items(): self.job_inputs.rewrite_paths(local_path, remote_path) def __action(self, path, type): @@ -154,35 +165,24 @@ **Parameters** - client : Client + client : JobClient LWR client object. - command_line : str - The local command line to execute, this will be rewritten for the remote server. - config_files : list - List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. - input_files : list - List of input files used by job. These will be transferred and references rewritten. - output_files : list - List of output_files produced by job. - tool_dir : str - Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). - working_directory : str - Local path created by Galaxy for running this job. - + client_job_description : client_job_description + Description of client view of job to stage and execute remotely. """ - def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): + def __init__(self, client, client_job_description, job_config): """ """ self.client = client - self.command_line = command_line - self.config_files = config_files - self.input_files = input_files - self.output_files = output_files - self.tool_id = tool.id - self.tool_version = tool.version - self.tool_dir = abspath(tool.tool_dir) - self.working_directory = working_directory + self.command_line = client_job_description.command_line + self.config_files = client_job_description.config_files + self.input_files = client_job_description.input_files + self.output_files = client_job_description.output_files + self.tool_id = client_job_description.tool.id + self.tool_version = client_job_description.tool.version + self.tool_dir = abspath(client_job_description.tool.tool_dir) + self.working_directory = client_job_description.working_directory # Setup job inputs, these will need to be rewritten before # shipping off to remote LWR server. @@ -190,7 +190,7 @@ self.transfer_tracker = TransferTracker(client, self.job_inputs) - self.__handle_setup() + self.__handle_setup(job_config) self.__initialize_referenced_tool_files() self.__upload_tool_files() self.__upload_input_files() @@ -201,8 +201,9 @@ self.__handle_rewrites() self.__upload_rewritten_config_files() - def __handle_setup(self): - job_config = self.client.setup(self.tool_id, self.tool_version) + def __handle_setup(self, job_config): + if not job_config: + job_config = self.client.setup(self.tool_id, self.tool_version) self.new_working_directory = job_config['working_directory'] self.new_outputs_directory = job_config['outputs_directory'] @@ -283,7 +284,7 @@ self.transfer_tracker.rewrite_input_paths() def __upload_rewritten_config_files(self): - for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): + for config_file, new_config_contents in self.job_inputs.rewritten_config_files.items(): self.client.put_file(config_file, input_type='config', contents=new_config_contents) def get_rewritten_command_line(self): @@ -294,32 +295,66 @@ return self.job_inputs.rewritten_command_line -def finish_job(client, cleanup_job, job_completed_normally, working_directory, work_dir_outputs, output_files): +def finish_job(client, cleanup_job, job_completed_normally, working_directory, work_dir_outputs, output_files, working_directory_contents=[]): """ """ - action_mapper = FileActionMapper(client) download_failure_exceptions = [] if job_completed_normally: - for source_file, output_file in work_dir_outputs: - try: + download_failure_exceptions = __download_results(client, working_directory, work_dir_outputs, output_files, working_directory_contents) + return __clean(download_failure_exceptions, cleanup_job, client) + + +def __download_results(client, working_directory, work_dir_outputs, output_files, working_directory_contents): + action_mapper = FileActionMapper(client) + downloaded_working_directory_files = [] + exception_tracker = DownloadExceptionTracker() + + # Fetch explicit working directory outputs. + for source_file, output_file in work_dir_outputs: + name = basename(source_file) + with exception_tracker(): + action = action_mapper.action(output_file, 'output') + client.fetch_work_dir_output(name, working_directory, output_file, action[0]) + downloaded_working_directory_files.append(name) + # Remove from full output_files list so don't try to download directly. + output_files.remove(output_file) + + # Fetch output files. + for output_file in output_files: + with exception_tracker(): + action = action_mapper.action(output_file, 'output') + client.fetch_output(output_file, working_directory=working_directory, action=action[0]) + + # Fetch remaining working directory outputs of interest. + for name in working_directory_contents: + if name in downloaded_working_directory_files: + continue + if COPY_FROM_WORKING_DIRECTORY_PATTERN.match(name): + with exception_tracker(): + output_file = join(working_directory, name) action = action_mapper.action(output_file, 'output') - client.fetch_work_dir_output(source_file, working_directory, output_file, action[0]) - except Exception, e: - download_failure_exceptions.append(e) - # Remove from full output_files list so don't try to download directly. - output_files.remove(output_file) - for output_file in output_files: - try: - action = action_mapper.action(output_file, 'output') - client.fetch_output(output_file, working_directory=working_directory, action=action[0]) - except Exception, e: - download_failure_exceptions.append(e) - return __clean(download_failure_exceptions, cleanup_job, client) + client.fetch_work_dir_output(name, working_directory, output_file, action=action[0]) + downloaded_working_directory_files.append(name) + + return exception_tracker.download_failure_exceptions + + +class DownloadExceptionTracker(object): + + def __init__(self): + self.download_failure_exceptions = [] + + @contextmanager + def __call__(self): + try: + yield + except Exception as e: + self.download_failure_exceptions.append(e) def __clean(download_failure_exceptions, cleanup_job, client): failed = (len(download_failure_exceptions) > 0) - if not failed or cleanup_job == "always": + if (not failed and cleanup_job != "never") or cleanup_job == "always": try: client.clean() except: @@ -327,25 +362,56 @@ return failed -def submit_job(client, tool, command_line, config_files, input_files, output_files, working_directory): +def submit_job(client, client_job_description, job_config=None): """ """ - file_stager = FileStager(client, tool, command_line, config_files, input_files, output_files, working_directory) + file_stager = FileStager(client, client_job_description, job_config) rebuilt_command_line = file_stager.get_rewritten_command_line() job_id = file_stager.job_id - client.launch(rebuilt_command_line) + client.launch(rebuilt_command_line, requirements=client_job_description.requirements) return job_id def _read(path): """ Utility method to quickly read small files (config files and tool - wrappers) into memory as strings. + wrappers) into memory as bytes. """ - input = open(path, "r") + input = open(path, "r", encoding="utf-8") try: return input.read() finally: input.close() -__all__ = [submit_job, finish_job] + +class ClientJobDescription(object): + """ A description of how client views job - command_line, inputs, etc.. + + **Parameters** + + command_line : str + The local command line to execute, this will be rewritten for the remote server. + config_files : list + List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. + input_files : list + List of input files used by job. These will be transferred and references rewritten. + output_files : list + List of output_files produced by job. + tool_dir : str + Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). + working_directory : str + Local path created by Galaxy for running this job. + requirements : list + List of requirements for tool execution. + """ + + def __init__(self, tool, command_line, config_files, input_files, output_files, working_directory, requirements): + self.tool = tool + self.command_line = command_line + self.config_files = config_files + self.input_files = input_files + self.output_files = output_files + self.working_directory = working_directory + self.requirements = requirements + +__all__ = [submit_job, ClientJobDescription, finish_job] diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/lwr_client/transport/curl.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/curl.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/curl.py @@ -1,4 +1,7 @@ -from cStringIO import StringIO +try: + from cStringIO import StringIO +except ImportError: + from io import StringIO try: from pycurl import Curl except: @@ -25,6 +28,8 @@ c.setopt(c.INFILESIZE, filesize) if data: c.setopt(c.POST, 1) + if type(data).__name__ == 'unicode': + data = data.encode('UTF-8') c.setopt(c.POSTFIELDS, data) c.perform() if not output_path: diff -r 0e9a8f32b5a9c54a91f2af08b49c944b679937c7 -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf lib/galaxy/jobs/runners/lwr_client/transport/standard.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/standard.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/standard.py @@ -2,22 +2,33 @@ LWR HTTP Client layer based on Python Standard Library (urllib2) """ from __future__ import with_statement +from os.path import getsize import mmap -import urllib2 +try: + from urllib2 import urlopen +except ImportError: + from urllib.request import urlopen +try: + from urllib2 import Request +except ImportError: + from urllib.request import Request class Urllib2Transport(object): def _url_open(self, request, data): - return urllib2.urlopen(request, data) + return urlopen(request, data) def execute(self, url, data=None, input_path=None, output_path=None): - request = urllib2.Request(url=url, data=data) + request = Request(url=url, data=data) input = None try: if input_path: - input = open(input_path, 'rb') - data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) + if getsize(input_path): + input = open(input_path, 'rb') + data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) + else: + data = b"" response = self._url_open(request, data) finally: if input: @@ -26,7 +37,7 @@ with open(output_path, 'wb') as output: while True: buffer = response.read(1024) - if buffer == "": + if not buffer: break output.write(buffer) return response This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/c28eeb2c4324/ Changeset: c28eeb2c4324 Branch: page-api User: Kyle Ellrott Date: 2013-12-18 01:36:08 Summary: Filling out the page and page revision portions of the api. Affected #: 5 files diff -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf -r c28eeb2c4324639c38db4ca5f371d48e1d3084d8 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3178,7 +3178,7 @@ self.openid = openid class Page( object, Dictifiable ): - dict_element_visible_keys = [ 'id', 'title', 'latest_revision_id', 'slug' ] + dict_element_visible_keys = [ 'id', 'title', 'latest_revision_id', 'slug', 'published', 'importable' ] def __init__( self ): self.id = None self.user = None diff -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf -r c28eeb2c4324639c38db4ca5f371d48e1d3084d8 lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -476,6 +476,7 @@ DOMAIN = "page" FIELDS = { 'id': ViewField('id', sqlalchemy_field=(Page, "id"), id_decode=True), + 'slug': ViewField('slug', sqlalchemy_field=(Page, "slug")), 'title': ViewField('title', sqlalchemy_field=(Page, "title")), } diff -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf -r c28eeb2c4324639c38db4ca5f371d48e1d3084d8 lib/galaxy/webapps/galaxy/api/page_revisions.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py @@ -0,0 +1,66 @@ +""" +API for updating Galaxy Pages +""" +import logging +from galaxy import web +from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin +from galaxy.model.search import GalaxySearchEngine +from galaxy.model.item_attrs import UsesAnnotations +from galaxy.exceptions import ItemAccessibilityException +from galaxy.util.sanitize_html import sanitize_html + +log = logging.getLogger( __name__ ) + +class PageRevisionsController( BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin ): + + @web.expose_api + def index( self, trans, page_id, **kwd ): + r = trans.sa_session.query( trans.app.model.PageRevision ).filter_by( page_id=trans.security.decode_id(page_id) ) + out = [] + for page in r: + if self.security_check( trans, page, True, True ): + out.append( self.encode_all_ids( trans, page.to_dict(), True) ) + return out + + + @web.expose_api + def create( self, trans, page_id, payload, **kwd ): + """ + payload keys: + page_id + content + """ + user = trans.get_user() + error_str = "" + + if not page_id: + error_str = "page_id is required" + elif not payload.get("content", None): + error_str = "content is required" + else: + + # Create the new stored page + page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id(page_id) ) + if page is None: + return { "error" : "page not found"} + + if not self.security_check( trans, page, True, True ): + return { "error" : "page not found"} + + if 'title' in payload: + title = payload['title'] + else: + title = page.title + + page_revision = trans.app.model.PageRevision() + page_revision.title = title + page_revision.page = page + page.latest_revision = page_revision + page_revision.content = payload.get("content", "") + # Persist + session = trans.sa_session + session.flush() + + return {"success" : "revision posted"} + + return { "error" : error_str } diff -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf -r c28eeb2c4324639c38db4ca5f371d48e1d3084d8 lib/galaxy/webapps/galaxy/api/pages.py --- a/lib/galaxy/webapps/galaxy/api/pages.py +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -1,15 +1,17 @@ """ -API for searching Galaxy Datasets +API for updating Galaxy Pages """ import logging from galaxy import web -from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController +from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin from galaxy.model.search import GalaxySearchEngine +from galaxy.model.item_attrs import UsesAnnotations from galaxy.exceptions import ItemAccessibilityException +from galaxy.util.sanitize_html import sanitize_html log = logging.getLogger( __name__ ) -class PagesController( BaseAPIController, SharableItemSecurityMixin ): +class PagesController( BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin ): @web.expose_api def index( self, trans, deleted='False', **kwd ): @@ -22,7 +24,65 @@ @web.expose_api def create( self, trans, payload, **kwd ): - return {} + """ + payload keys: + slug + title + content + annotation + """ + user = trans.get_user() + error_str = "" + + if not payload.get("title", None): + error_str = "Page name is required" + elif not payload.get("slug", None): + error_str = "Page id is required" + elif not self._is_valid_slug( payload["slug"] ): + error_str = "Page identifier must consist of only lowercase letters, numbers, and the '-' character" + elif trans.sa_session.query( trans.app.model.Page ).filter_by( user=user, slug=payload["slug"], deleted=False ).first(): + error_str = "Page id must be unique" + else: + # Create the new stored page + page = trans.app.model.Page() + page.title = payload['title'] + page.slug = payload['slug'] + page_annotation = sanitize_html( payload.get("annotation",""), 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation ) + page.user = user + # And the first (empty) page revision + page_revision = trans.app.model.PageRevision() + page_revision.title = payload['title'] + page_revision.page = page + page.latest_revision = page_revision + page_revision.content = payload.get("content", "") + # Persist + session = trans.sa_session + session.add( page ) + session.flush() + + rval = self.encode_all_ids( trans, page.to_dict(), True) + return rval + + return { "error" : error_str } + + + @web.expose_api + def delete( self, trans, id, **kwd ): + page_id = id; + try: + page = trans.sa_session.query(self.app.model.Page).get(trans.security.decode_id(page_id)) + except Exception, e: + return { "error" : "Page with ID='%s' can not be found\n Exception: %s" % (page_id, str( e )) } + + # check to see if user has permissions to selected workflow + if page.user != trans.user and not trans.user_is_admin(): + return { "error" : "Workflow is not owned by or shared with current user" } + + #Mark a workflow as deleted + page.deleted = True + trans.sa_session.flush() + return {"success" : "Deleted", "id" : page_id} @web.expose_api def show( self, trans, id, deleted='False', **kwd ): diff -r 0e7881a4d1cf8dee171a46c60088cfe82df1c9cf -r c28eeb2c4324639c38db4ca5f371d48e1d3084d8 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -171,6 +171,10 @@ #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) webapp.mapper.resource( 'page', 'pages', path_prefix="/api") + webapp.mapper.resource( 'revision', 'revisions', + path_prefix='/api/pages/:page_id', + controller='page_revisions', + parent_resources=dict( member_name='page', collection_name='pages' ) ) # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", https://bitbucket.org/galaxy/galaxy-central/commits/aa016b917225/ Changeset: aa016b917225 Branch: page-api User: Kyle Ellrott Date: 2013-12-18 23:27:20 Summary: Adding more documentation to newly added API calls Affected #: 2 files diff -r c28eeb2c4324639c38db4ca5f371d48e1d3084d8 -r aa016b91722549d96e2b2a7d5bfc855cb20b1a6e lib/galaxy/webapps/galaxy/api/page_revisions.py --- a/lib/galaxy/webapps/galaxy/api/page_revisions.py +++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py @@ -15,6 +15,16 @@ @web.expose_api def index( self, trans, page_id, **kwd ): + """ + index( self, trans, page_id, **kwd ) + * GET /api/pages/{page_id}/revisions + return a list of Page revisions + + :param page_id: Display the revisions of Page with ID=page_id + + :rtype: list + :returns: dictionaries containing different revisions of the page + """ r = trans.sa_session.query( trans.app.model.PageRevision ).filter_by( page_id=trans.security.decode_id(page_id) ) out = [] for page in r: @@ -26,9 +36,17 @@ @web.expose_api def create( self, trans, page_id, payload, **kwd ): """ - payload keys: - page_id - content + create( self, trans, page_id, payload **kwd ) + * POST /api/pages/{page_id}/revisions + Create a new revision for a page + + :param page_id: Add revision to Page with ID=page_id + :param payload: A dictionary containing:: + 'title' = New title of the page + 'content' = New content of the page + + :rtype: dictionary + :returns: Dictionary with 'success' or 'error' element to indicate the result of the request """ user = trans.get_user() error_str = "" diff -r c28eeb2c4324639c38db4ca5f371d48e1d3084d8 -r aa016b91722549d96e2b2a7d5bfc855cb20b1a6e lib/galaxy/webapps/galaxy/api/pages.py --- a/lib/galaxy/webapps/galaxy/api/pages.py +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -15,7 +15,19 @@ @web.expose_api def index( self, trans, deleted='False', **kwd ): + """ + index( self, trans, deleted='False', **kwd ) + * GET /api/pages + return a list of Pages viewable by the user + + :param deleted: Display deleted pages + + :rtype: list + :returns: dictionaries containing summary or detailed Page information + """ r = trans.sa_session.query( trans.app.model.Page ) + if not deleted: + r = r.filter_by(deleted=False) out = [] for row in r: out.append( self.encode_all_ids( trans, row.to_dict(), True) ) @@ -25,11 +37,18 @@ @web.expose_api def create( self, trans, payload, **kwd ): """ - payload keys: - slug - title - content - annotation + create( self, trans, payload, **kwd ) + * POST /api/pages + Create a page and return dictionary containing Page summary + + :param payload: dictionary structure containing:: + 'slug' = The title slug for the page URL, must be unique + 'title' = Title of the page + 'content' = HTML contents of the page + 'annotation' = Annotation that will be attached to the page + + :rtype: dict + :returns: Dictionary return of the Page.to_dict call """ user = trans.get_user() error_str = "" @@ -69,6 +88,16 @@ @web.expose_api def delete( self, trans, id, **kwd ): + """ + delete( self, trans, id, **kwd ) + * DELETE /api/pages/{id} + Create a page and return dictionary containing Page summary + + :param id: ID of page to be deleted + + :rtype: dict + :returns: Dictionary with 'success' or 'error' element to indicate the result of the request + """ page_id = id; try: page = trans.sa_session.query(self.app.model.Page).get(trans.security.decode_id(page_id)) @@ -85,7 +114,17 @@ return {"success" : "Deleted", "id" : page_id} @web.expose_api - def show( self, trans, id, deleted='False', **kwd ): + def show( self, trans, id, **kwd ): + """ + show( self, trans, id, **kwd ) + * GET /api/pages/{id} + View a page summary and the content of the latest revision + + :param id: ID of page to be displayed + + :rtype: dict + :returns: Dictionary return of the Page.to_dict call with the 'content' field populated by the most recent revision + """ page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id( id ) ) rval = self.encode_all_ids( trans, page.to_dict(), True) rval['content'] = page.latest_revision.content https://bitbucket.org/galaxy/galaxy-central/commits/05ff06be8f05/ Changeset: 05ff06be8f05 Branch: page-api User: Kyle Ellrott Date: 2013-12-18 23:31:42 Summary: Adding ability to select Pages using the 'deleted' field Affected #: 1 file diff -r aa016b91722549d96e2b2a7d5bfc855cb20b1a6e -r 05ff06be8f055d4d52b798615df007e5f0094ecb lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -478,6 +478,7 @@ 'id': ViewField('id', sqlalchemy_field=(Page, "id"), id_decode=True), 'slug': ViewField('slug', sqlalchemy_field=(Page, "slug")), 'title': ViewField('title', sqlalchemy_field=(Page, "title")), + 'deleted': ViewField('deleted', sqlalchemy_field=(Page, "deleted")) } def search(self, trans): https://bitbucket.org/galaxy/galaxy-central/commits/65a083eee933/ Changeset: 65a083eee933 Branch: page-api User: Kyle Ellrott Date: 2013-12-20 20:31:11 Summary: Default merge Affected #: 84 files diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f 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 @@ -302,6 +302,14 @@ :undoc-members: :show-inheritance: +:mod:`lda_datasets` Module +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.lda_datasets + :members: + :undoc-members: + :show-inheritance: + :mod:`libraries` Module ----------------------- diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -2,14 +2,20 @@ # A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/ -# The test/install_and_test_tool_shed_repositories/functional_tests.py can not be executed directly, because it must have certain functional test definitions -# in sys.argv. Running it through this shell script is the best way to ensure that it has the required definitions. +# The test/install_and_test_tool_shed_repositories/functional_tests.py cannot be executed directly because it must +# have certain functional test definitions in sys.argv. Running it through this shell script is the best way to +# ensure that it has the required definitions. -# This script requires the following environment variables: +# This script requires setting of the following environment variables: # GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY - must be set to the API key for the tool shed that is being checked. # GALAXY_INSTALL_TEST_TOOL_SHED_URL - must be set to a URL that the tool shed is listening on. -# If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to a tool sheds configuration file -# that does specify that url, otherwise repository installation will fail. + +# If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to +# a tool sheds configuration file that does specify that url or repository installation will fail. + +# This script accepts the command line option -w to select which set of tests to run. The default behavior is to test +# first tool_dependency_definition repositories and then repositories with tools. Provide the value 'dependencies' +# to test only tool_dependency_definition repositories or 'tools' to test only repositories with tools. if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY ] ; then echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty." @@ -37,7 +43,45 @@ fi fi -python test/install_and_test_tool_shed_repositories/functional_tests.py $* -v --with-nosehtml --html-report-file \ - test/install_and_test_tool_shed_repositories/run_functional_tests.html \ - test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ - test/functional/test_toolbox.py +test_tool_dependency_definitions () { + # Test installation of repositories of type tool_dependency_definition. + python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py +} + +test_repositories_with_tools () { + # Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. + python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py +} + +which='both' + +while getopts "w:" arg; do + case $arg in + w) + which=$OPTARG + ;; + esac +done + +case $which in + # Use "-w tool_dependency_definitions" when you want to test repositories of type tool_dependency_definition. + tool_dependency_definitions) + test_tool_dependency_definitions + ;; + # Use "-w repositories_with_tools" parameter when you want to test repositories that contain tools. + repositories_with_tools) + test_repositories_with_tools + ;; + # No received parameters or any received parameter not in [ tool_dependency_definitions, repositories_with_tools ] + # will execute both scripts. + *) + test_tool_dependency_definitions + test_repositories_with_tools + ;; +esac diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -19,7 +19,6 @@ import socket import time from string import Template -from itertools import ifilter import galaxy.datatypes import galaxy.datatypes.registry @@ -44,11 +43,6 @@ # Default Value Required for unit tests datatypes_registry.load_datatypes() -# When constructing filters with in for a fixed set of ids, maximum -# number of items to place in the IN statement. Different databases -# are going to have different limits so it is likely best to not let -# this be unlimited - filter in Python if over this limit. -MAX_IN_FILTER_LENGTH = 100 class NoConverterException(Exception): def __init__(self, value): @@ -899,32 +893,6 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval - def contents_iter( self, **kwds ): - """ - Fetch filtered list of contents of history. - """ - python_filter = None - db_session = object_session( self ) - assert db_session != None - query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ) - deleted = galaxy.util.string_as_bool_or_none( kwds.get( 'deleted', None ) ) - if deleted is not None: - query = query.filter( HistoryDatasetAssociation.deleted == bool( kwds['deleted'] ) ) - visible = galaxy.util.string_as_bool_or_none( kwds.get( 'visible', None ) ) - if visible is not None: - query = query.filter( HistoryDatasetAssociation.visible == bool( kwds['visible'] ) ) - if 'ids' in kwds: - ids = kwds['ids'] - max_in_filter_length = kwds.get('max_in_filter_length', MAX_IN_FILTER_LENGTH) - if len(ids) < max_in_filter_length: - query = query.filter( HistoryDatasetAssociation.id.in_(ids) ) - else: - python_filter = lambda hda: hda.id in ids - if python_filter: - return ifilter(python_filter, query) - else: - return query - def copy_tags_from(self,target_user,source_history): for src_shta in source_history.tags: new_shta = src_shta.copy() @@ -1859,7 +1827,7 @@ class Library( object, Dictifiable ): permitted_actions = get_permitted_actions( filter='LIBRARY' ) dict_collection_visible_keys = ( 'id', 'name' ) - dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis' ) + dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id' ) def __init__( self, name=None, description=None, synopsis=None, root_folder=None ): self.name = name or "Unnamed library" self.description = description @@ -1926,7 +1894,7 @@ return name class LibraryFolder( object, Dictifiable ): - dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' ) + dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time' ) def __init__( self, name=None, description=None, item_count=0, order_id=None ): self.name = name or "Unnamed folder" self.description = description @@ -2092,6 +2060,7 @@ genome_build = ldda.dbkey, misc_info = ldda.info, misc_blurb = ldda.blurb, + peek = ( lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None )( ldda ), template_data = template_data ) if ldda.dataset.uuid is None: rval['uuid'] = None diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1852,8 +1852,9 @@ table = self.table trans = conn.begin() try: - next_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() - table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) ) + current_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() + next_hid = current_hid + 1 + table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid ) ) trans.commit() return next_hid except: diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -265,8 +265,7 @@ """Return the repository's tool dependencies that are currently installed, but possibly in an error state.""" installed_dependencies = [] for tool_dependency in self.tool_dependencies: - if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, - ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED ]: installed_dependencies.append( tool_dependency ) return installed_dependencies @@ -442,6 +441,16 @@ return dependencies_being_installed @property + def tool_dependencies_installed_or_in_error( self ): + """Return the repository's tool dependencies that are currently installed, but possibly in an error state.""" + installed_dependencies = [] + for tool_dependency in self.tool_dependencies: + if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, + ToolDependency.installation_status.ERROR ]: + installed_dependencies.append( tool_dependency ) + return installed_dependencies + + @property def tool_dependencies_missing_or_being_installed( self ): dependencies_missing_or_being_installed = [] for tool_dependency in self.tool_dependencies: diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2733,7 +2733,7 @@ def build_dependency_shell_commands( self ): """Return a list of commands to be run to populate the current environment to include this tools requirements.""" if self.tool_shed_repository: - installed_tool_dependencies = self.tool_shed_repository.installed_tool_dependencies + installed_tool_dependencies = self.tool_shed_repository.tool_dependencies_installed_or_in_error else: installed_tool_dependencies = None return self.app.toolbox.dependency_manager.dependency_shell_commands( self.requirements, diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/util/streamball.py --- a/lib/galaxy/util/streamball.py +++ b/lib/galaxy/util/streamball.py @@ -3,6 +3,7 @@ """ import os import logging, tarfile +from galaxy.exceptions import ObjectNotFound log = logging.getLogger( __name__ ) @@ -14,8 +15,12 @@ self.mode = mode self.wsgi_status = None self.wsgi_headeritems = None - def add( self, file, relpath ): - self.members[file] = relpath + def add( self, file, relpath, check_file=False): + if check_file and len(file)>0: + if not os.path.isfile(file): + raise ObjectNotFound + else: + self.members[file] = relpath def stream( self, environ, start_response ): response_write = start_response( self.wsgi_status, self.wsgi_headeritems ) class tarfileobj: diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -3,6 +3,8 @@ """ import logging, sys, os, time + +from operator import itemgetter from cgi import escape from galaxy.util import restore_text, relpath, nice_size, unicodify from galaxy.web import url_for @@ -212,6 +214,7 @@ ctime=time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) if not uploads: rval += '<tr><td colspan="4"><em>Your FTP upload directory contains no files.</em></td></tr>' + uploads = sorted(uploads, key=itemgetter("path")) for upload in uploads: rval += FTPFileField.trow % ( prefix, self.name, upload['path'], upload['path'], upload['size'], upload['ctime'] ) rval += FTPFileField.tfoot diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a dataset. +API operations on the contents of a history dataset. """ from galaxy import web from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a library. +API operations on the contents of a folder. """ import logging, os, string, shutil, urllib, re, socket from cgi import escape, FieldStorage @@ -11,67 +11,122 @@ log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): + """ + Class controls retrieval, creation and updating of folder contents. + """ + + def load_folder_contents( self, trans, folder ): + """ + Loads all contents of the folder (folders and data sets) but only in the first level. + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + content_items = [] + for subfolder in folder.active_folders: + if not is_admin: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) + if (is_admin or can_access) and not subfolder.deleted: + subfolder.api_type = 'folder' + content_items.append( subfolder ) + for dataset in folder.datasets: + if not is_admin: + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) + if (is_admin or can_access) and not dataset.deleted: + dataset.api_type = 'file' + content_items.append( dataset ) + return content_items @web.expose_api def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents Displays a collection (list) of a folder's contents (files and folders). - The /api/library_contents/{encoded_library_id}/contents - lists everything in a library recursively, which is not what - we want here. We could add a parameter to use the recursive - style, but this is meant to act similar to an "ls" directory listing. + Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. + Full path is provided as a separate object in response providing data for breadcrumb path building. """ - rval = [] + folder_container = [] current_user_roles = trans.get_current_user_roles() - def traverse( folder ): - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_type = 'folder' - rval.append( subfolder ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_type = 'file' - rval.append( ld ) - return rval - - try: - decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) - except TypeError: - trans.response.status = 400 - return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) + if ( folder_id.startswith( 'F' ) ): + try: + decoded_folder_id = trans.security.decode_id( folder_id[1:] ) + except TypeError: + trans.response.status = 400 + return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) - parent_library = folder.parent_library except: folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder %s" - % folder_id ) + log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) - # TODO: Find the API's path to this folder if necessary. - # This was needed in recursive descent, but it's not needed - # for "ls"-style content checking: - if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + # We didn't find the folder or user does not have an access to it. + if not folder: trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) + + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) + trans.response.status = 400 + return "Invalid folder id ( %s ) specified." % str( folder_id ) + + path_to_root = [] + def build_path ( folder ): + """ + Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. + """ + path_to_root = [] + # We are almost in root + if folder.parent_id is None: + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + else: + # We add the current folder and traverse up one folder. + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( build_path( upper_folder ) ) + return path_to_root + + # Return the reversed path so it starts with the library node. + full_path = build_path( folder )[::-1] + folder_container.append( dict( full_path = full_path ) ) + + folder_contents = [] + time_updated = '' + time_created = '' + # Go through every item in the folder and include its meta-data. + for content_item in self.load_folder_contents( trans, folder ): +# rval = content_item.to_dict() + return_item = {} + encoded_id = trans.security.encode_id( content_item.id ) + time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) + + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_id = 'F' + encoded_id +# time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + return_item.update ( dict ( item_count = content_item.item_count ) ) - for content in traverse( folder ): - encoded_id = trans.security.encode_id( content.id ) - if content.api_type == 'folder': - encoded_id = 'F' + encoded_id - rval.append( dict( id = encoded_id, - type = content.api_type, - name = content.name, - url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) - return rval + if content_item.api_type == 'file': + library_dataset_dict = content_item.to_dict() + library_dataset_dict['data_type'] + library_dataset_dict['file_size'] + library_dataset_dict['date_uploaded'] + return_item.update ( dict ( data_type = library_dataset_dict['data_type'], + file_size = library_dataset_dict['file_size'], + date_uploaded = library_dataset_dict['date_uploaded'] ) ) + + # For every item return also the default meta-data + return_item.update( dict( id = encoded_id, + type = content_item.api_type, + name = content_item.name, + time_updated = time_updated, + time_created = time_created + ) ) + folder_contents.append( return_item ) + # Put the data in the container + folder_container.append( dict( folder_contents = folder_contents ) ) + return folder_container @web.expose_api def show( self, trans, id, library_id, **kwd ): diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -51,28 +51,47 @@ else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) - contents_kwds = {} + # if ids, return _FULL_ data (as show) for each id passed if ids: - ids = map( lambda id: trans.security.decode_id( id ), ids.split( ',' ) ) - contents_kwds[ 'ids' ] = ids - # If explicit ids given, always used detailed result. - details = 'all' + ids = ids.split( ',' ) + for index, hda in enumerate( history.datasets ): + encoded_hda_id = trans.security.encode_id( hda.id ) + if encoded_hda_id in ids: + #TODO: share code with show + rval.append( self._detailed_hda_dict( trans, hda ) ) + + # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history else: - contents_kwds[ 'deleted' ] = kwd.get( 'deleted', None ) - contents_kwds[ 'visible' ] = kwd.get( 'visible', None ) # details param allows a mixed set of summary and detailed hdas #TODO: this is getting convoluted due to backwards compat details = kwd.get( 'details', None ) or [] if details and details != 'all': details = util.listify( details ) - for hda in history.contents_iter( **contents_kwds ): - encoded_hda_id = trans.security.encode_id( hda.id ) - detailed = details == 'all' or ( encoded_hda_id in details ) - if detailed: - rval.append( self._detailed_hda_dict( trans, hda ) ) - else: - rval.append( self._summary_hda_dict( trans, history_id, hda ) ) + # by default return all datasets - even if deleted or hidden (defaulting the next switches to None) + # if specified return those datasets that match the setting + # backwards compat + return_deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) ) + return_visible = util.string_as_bool_or_none( kwd.get( 'visible', None ) ) + + for hda in history.datasets: + # if either return_ setting has been requested (!= None), skip hdas that don't match the request + if return_deleted is not None: + if( ( return_deleted and not hda.deleted ) + or ( not return_deleted and hda.deleted ) ): + continue + if return_visible is not None: + if( ( return_visible and not hda.visible ) + or ( not return_visible and hda.visible ) ): + continue + + encoded_hda_id = trans.security.encode_id( hda.id ) + if( ( encoded_hda_id in details ) + or ( details == 'all' ) ): + rval.append( self._detailed_hda_dict( trans, hda ) ) + else: + rval.append( self._summary_hda_dict( trans, history_id, hda ) ) + except Exception, e: # for errors that are not specific to one hda (history lookup or summary list) rval = "Error in history API at listing contents: " + str( e ) diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/api/lda_datasets.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -0,0 +1,261 @@ +""" +API operations on the datasets from library. +""" +import glob +import logging +import operator +import os +import os.path +import string +import sys +import tarfile +import tempfile +import urllib +import urllib2 +import zipfile +from paste.httpexceptions import HTTPBadRequest +from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound +from galaxy.security import Action +from galaxy import util, web +from galaxy.util.streamball import StreamBall +from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin + +import logging +log = logging.getLogger( __name__ ) + +class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + show( self, trans, id, **kwd ) + * GET /api/libraries/datasets/{encoded_dataset_id}: + Displays information about the dataset identified by the encoded id. + + + :type id: an encoded id string + :param id: the encoded id of the dataset to query + + :rtype: dictionary + :returns: detailed dataset information from + :func:`galaxy.web.base.controller.UsesVisualizationMixin.get_library_dataset.to_dict()` + """ + # Get dataset. + try: + dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True ) + except Exception, e: + trans.response.status = 500 + return str( e ) + try: + # Default: return dataset as dict. + rval = dataset.to_dict() + except Exception, e: + rval = "Error in dataset API at listing contents: " + str( e ) + log.error( rval + ": %s" % str(e), exc_info=True ) + trans.response.status = 500 + return "Error in dataset API at listing contents: " + str( e ) + + rval['id'] = trans.security.encode_id(rval['id']); + rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); + rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) + trans.response.status = 200 + return rval + + @web.expose + def download( self, trans, format, **kwd ): + """ + download( self, trans, format, **kwd ) + * GET /api/libraries/datasets/download/{format} + + .. code-block:: + example: + GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828 + + :type format: string + :param format: string representing requested archive format + + .. note:: supported formats are: zip, tgz, tbz, uncompressed + + :type lddas[]: an array + :param lddas[]: an array of encoded ids + + :rtype: file + :returns: either archive with the requested datasets packed inside or a single uncompressed dataset + + :raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound + """ + lddas = [] + datasets_to_download = kwd['ldda_ids%5B%5D'] + + if ( datasets_to_download != None ): + datasets_to_download = util.listify( datasets_to_download ) + for dataset_id in datasets_to_download: + try: + ldda = self.get_hda_or_ldda( trans, hda_ldda='ldda', dataset_id=dataset_id ) + lddas.append( ldda ) + except ItemAccessibilityException: + trans.response.status = 403 + return 'Insufficient rights to access library dataset with id: (%s)' % str( dataset_id ) + except MessageException: + trans.response.status = 400 + return 'Wrong library dataset id: (%s)' % str( dataset_id ) + except ItemDeletionException: + trans.response.status = 400 + return 'The item with library dataset id: (%s) is deleted' % str( dataset_id ) + except HTTPBadRequest, e: + return 'http bad request' + str( e.err_msg ) + except Exception, e: + trans.response.status = 500 + return 'error of unknown kind' + str( e ) + + if format in [ 'zip','tgz','tbz' ]: + # error = False + killme = string.punctuation + string.whitespace + trantab = string.maketrans(killme,'_'*len(killme)) + try: + outext = 'zip' + if format == 'zip': + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, self.app.config.gid ) + tmpf = os.path.join( tmpd, 'library_download.' + format ) + if trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif format == 'tgz': + if trans.app.config.upstream_gzip: + archive = StreamBall( 'w|' ) + outext = 'tar' + else: + archive = StreamBall( 'w|gz' ) + outext = 'tgz' + elif format == 'tbz': + archive = StreamBall( 'w|bz2' ) + outext = 'tbz2' + except ( OSError, zipfile.BadZipfile ): + log.exception( "Unable to create archive for download" ) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except: + log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) + trans.response.status = 500 + return "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + composite_extensions = trans.app.datatypes_registry.get_composite_extensions() + seen = [] + for ldda in lddas: + ext = ldda.extension + is_composite = ext in composite_extensions + path = "" + parent_folder = ldda.library_dataset.folder + while parent_folder is not None: + # Exclude the now-hidden "root folder" + if parent_folder.parent is None: + path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) + parent_folder = parent_folder.parent + path += ldda.name + while path in seen: + path += '_' + seen.append( path ) + zpath = os.path.split(path)[-1] # comes as base_name/fname + outfname,zpathext = os.path.splitext(zpath) + if is_composite: # need to add all the components from the extra_files_path to the zip + if zpathext == '': + zpath = '%s.html' % zpath # fake the real nature of the html file + try: + if format=='zip': + archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set + else: + archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set + except IOError: + log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" + flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths + for fpath in flist: + efp,fname = os.path.split(fpath) + if fname > '': + fname = fname.translate(trantab) + try: + if format=='zip': + archive.add( fpath,fname ) + else: + archive.add( fpath,fname, check_file=True ) + except IOError: + log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % fpath ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" + else: # simple case + try: + if format=='zip': + archive.add( ldda.dataset.file_name, path ) + else: + archive.add( ldda.dataset.file_name, path, check_file=True ) + except IOError: + log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" + lname = 'selected_dataset' + fname = lname.replace( ' ', '_' ) + '_files' + if format == 'zip': + archive.close() + trans.response.set_content_type( "application/octet-stream" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive = util.streamball.ZipBall(tmpf, tmpd) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + trans.response.status = 200 + return archive.stream + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + trans.response.status = 200 + return archive.stream + elif format == 'uncompressed': + if len(lddas) != 1: + trans.response.status = 400 + return 'Wrong request' + else: + single_dataset = lddas[0] + trans.response.set_content_type( single_dataset.get_mime() ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname + try: + trans.response.status = 200 + return open( single_dataset.file_name ) + except: + trans.response.status = 500 + return 'This dataset contains no content' + else: + trans.response.status = 400 + return 'Wrong format parameter specified'; diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -49,9 +49,10 @@ trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) rval = [] for library in query: - item = library.to_dict() + item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) - item['id'] = trans.security.encode_id( item['id'] ) + item['id'] = 'F' + trans.security.encode_id( item['id'] ) + item['root_folder_id'] = 'F' + trans.security.encode_id( item['root_folder_id'] ) rval.append( item ) return rval @@ -131,6 +132,9 @@ rval['name'] = name rval['id'] = encoded_id return rval + + def edit( self, trans, payload, **kwd ): + return "Not implemented yet" @web.expose_api def delete( self, trans, id, **kwd ): diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,7 +1,7 @@ import urllib from galaxy import web, util -from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin +from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, UsesHistoryMixin from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import to_json_string, from_json_string from galaxy.visualization.data_providers.genome import * @@ -10,7 +10,7 @@ log = logging.getLogger( __name__ ) -class ToolsController( BaseAPIController, UsesVisualizationMixin ): +class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMixin ): """ RESTful controller for interactions with tools. """ @@ -86,8 +86,7 @@ # dataset upload. history_id = payload.get("history_id", None) if history_id: - target_history = trans.sa_session.query(trans.app.model.History).get( - trans.security.decode_id(history_id)) + target_history = self.get_history( trans, history_id ) else: target_history = None diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -112,8 +112,6 @@ # ------------------------------------------------------------------------------- # - - if 'workflow_id' not in payload: # create new if 'installed_repository_file' in payload: @@ -241,11 +239,15 @@ visit_input_values( tool.inputs, step.state.inputs, callback ) job, out_data = tool.execute( trans, step.state.inputs, history=history) outputs[ step.id ] = out_data + + # Do post-job actions. + replacement_params = payload.get('replacement_params', {}) for pja in step.post_job_actions: if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(self.app, trans.sa_session, pja, job, replacement_dict=None) + ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict=replacement_params) else: job.add_post_job_action(pja) + for v in out_data.itervalues(): rval['outputs'].append(trans.security.encode_id(v.id)) else: @@ -278,6 +280,10 @@ return("Workflow is not owned by or shared with current user") ret_dict = self._workflow_to_dict( trans, stored_workflow ); + if not ret_dict: + #This workflow has a tool that's missing from the distribution + trans.response.status = 400 + return "Workflow cannot be exported due to missing tools." return ret_dict @web.expose_api @@ -453,6 +459,8 @@ for step in workflow.steps: # Load from database representation module = module_factory.from_workflow_step( trans, step ) + if not module: + return None ### ----------------------------------- ### ## RPARK EDIT ## diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,12 +46,6 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) - # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', - controller='admin_toolshed', - action='display_image_in_repository', - repository_id=None, - image_file=None ) webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) @@ -75,22 +69,12 @@ webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' ) webapp.add_route( '/search', controller='search', action='index' ) - # Add the web API + # ================ + # ===== API ===== + # ================ + webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) - # The /folders section is experimental at this point: - log.debug( "app.config.api_folders: %s" % app.config.api_folders ) - webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) - webapp.mapper.resource( 'content', 'contents', - controller='folder_contents', - name_prefix='folder_', - path_prefix='/api/folders/:folder_id', - parent_resources=dict( member_name='folder', collection_name='folders' ) ) - webapp.mapper.resource( 'content', - 'contents', - controller='library_contents', - name_prefix='library_', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'content', 'contents', controller='history_contents', @@ -102,10 +86,6 @@ controller="datasets", action="display", conditions=dict(method=["GET"])) - webapp.mapper.resource( 'permission', - 'permissions', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.mapper.resource( 'user', 'users', controller='group_users', @@ -127,11 +107,6 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - - _add_item_extended_metadata_controller( webapp, - name_prefix="library_dataset_", - path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) - _add_item_annotation_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -141,7 +116,6 @@ _add_item_annotation_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - _add_item_provenance_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -193,6 +167,64 @@ webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + + # ======================= + # ===== LIBRARY API ===== + # ======================= + + webapp.mapper.connect( 'show_lda_item', + '/api/libraries/datasets/:id', + controller='lda_datasets', + action='show', + conditions=dict( method=[ "GET" ] ) ) + + webapp.mapper.connect( 'download_lda_items', + '/api/libraries/datasets/download/:format', + controller='lda_datasets', + action='download', + conditions=dict( method=[ "POST", "GET" ] ) ) + + webapp.mapper.resource_with_deleted( 'library', + 'libraries', + path_prefix='/api' ) + webapp.mapper.resource( 'folder', + 'folders', + path_prefix='/api' ) + + webapp.mapper.resource( 'content', + 'contents', + controller='folder_contents', + name_prefix='folder_', + path_prefix='/api/folders/:folder_id', + parent_resources=dict( member_name='folder', collection_name='folders' ) ) + + webapp.mapper.resource( 'content', + 'contents', + controller='library_contents', + name_prefix='library_', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + + webapp.mapper.resource( 'permission', + 'permissions', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + + _add_item_extended_metadata_controller( webapp, + name_prefix="library_dataset_", + path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) + + # ==================== + # ===== TOOLSHED ===== + # ==================== + + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. + webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + controller='admin_toolshed', + action='display_image_in_repository', + repository_id=None, + image_file=None ) + # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', @@ -206,6 +238,7 @@ path_prefix='/api', new={ 'install_repository_revision' : 'POST' }, parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) ) + # Connect logger from app if app.trace_logger: webapp.trace_logger = app.trace_logger @@ -226,7 +259,7 @@ galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() except: pass - # Close any pooled database connections before forking + # Close any pooled database connections before forking try: galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() except: diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f 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 @@ -255,7 +255,7 @@ tool_shed_repository.uninstalled = True # Remove all installed tool dependencies and tool dependencies stuck in the INSTALLING state, but don't touch any # repository dependencies. - tool_dependencies_to_uninstall = tool_shed_repository.installed_tool_dependencies + tool_dependencies_to_uninstall = tool_shed_repository.tool_dependencies_installed_or_in_error tool_dependencies_to_uninstall.extend( tool_shed_repository.tool_dependencies_being_installed ) for tool_dependency in tool_dependencies_to_uninstall: uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans.app, tool_dependency ) diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -76,6 +76,17 @@ library_list_grid = LibraryListGrid() + + @web.expose + def list( self, trans, **kwd ): + params = util.Params( kwd ) + # define app configuration for generic mako template + app = { + 'jscript' : "galaxy.library" + } + # fill template + return trans.fill_template('galaxy.panels.mako', config = {'app' : app}) + @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -18,7 +18,7 @@ from galaxy.util import inflector from galaxy.util.json import to_json_string, from_json_string from galaxy.util.streamball import StreamBall -from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin +from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, build_select_field from galaxy.model.orm import and_, eagerload_all @@ -65,7 +65,7 @@ except: pass -class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin ): +class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems ): @web.json def library_item_updates( self, trans, ids=None, states=None ): # Avoid caching @@ -1750,7 +1750,8 @@ ldda_ids = util.listify( ldda_ids ) for ldda_id in ldda_ids: try: - ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) + # Load the ldda requested and check whether the user has access to them + ldda = self.get_library_dataset_dataset_association( trans, ldda_id ) assert not ldda.dataset.purged lddas.append( ldda ) except: diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -826,19 +826,22 @@ if email is None or activation_token is None: # We don't have the email or activation_token, show error. - return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email.<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) + return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) else: # Find the user user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() + # If the user is active already don't try to activate + if user.active == True: + return trans.show_ok_message( "Your account is already active. Nothing has changed. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) if user.activation_token == activation_token: user.activation_token = None user.active = True trans.sa_session.add(user) trans.sa_session.flush() - return trans.show_ok_message( "Your account has been successfully activated!<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_ok_message( "Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) else: # Tokens don't match. Activation is denied. - return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email.<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) return def __get_user_type_form_definition( self, trans, user=None, **kwd ): diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -9,6 +9,11 @@ from tool_shed.util import export_util import tool_shed.util.shed_util_common as suc +from galaxy import eggs +eggs.require( 'mercurial' ) + +from mercurial import hg + log = logging.getLogger( __name__ ) @@ -66,6 +71,40 @@ return message @web.expose_api_anonymous + def repository_dependencies( self, trans, id, **kwd ): + """ + GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies + Displays information about a repository_metadata record in the Tool Shed. + + :param id: the encoded id of the `RepositoryMetadata` object + """ + # Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb12… + value_mapper = { 'id' : trans.security.encode_id, + 'user_id' : trans.security.encode_id } + repository_dependencies_dicts = [] + try: + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) + metadata = repository_metadata.metadata + if metadata and 'repository_dependencies' in metadata: + rd_tups = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] + for rd_tup in rd_tups: + tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] + repository_dependency = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + repository_dependency_dict = repository_dependency.to_dict( view='element', value_mapper=value_mapper ) + # We have to add the changeset_revision of of the repository dependency. + repository_dependency_dict[ 'changeset_revision' ] = changeset_revision + repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', + action='show', + id=trans.security.encode_id( repository_dependency.id ) ) + repository_dependencies_dicts.append( repository_dependency_dict ) + return repository_dependencies_dicts + except Exception, e: + message = "Error in the Tool Shed repository_revisions API in repository_dependencies: %s" % str( e ) + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + + @web.expose_api_anonymous def index( self, trans, **kwd ): """ GET /api/repository_revisions @@ -116,7 +155,7 @@ try: query = trans.sa_session.query( trans.app.model.RepositoryMetadata ) \ .filter( and_( *clause_list ) ) \ - .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \ + .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id.desc() ) \ .all() for repository_metadata in query: repository_metadata_dict = repository_metadata.to_dict( view='collection', diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -94,7 +94,8 @@ parent_resources=dict( member_name='repository', collection_name='repositories' ) ) webapp.mapper.resource( 'repository_revision', 'repository_revisions', - member={ 'export' : 'POST' }, + member={ 'repository_dependencies' : 'GET', + 'export' : 'POST' }, controller='repository_revisions', name_prefix='repository_revision_', path_prefix='/api', diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f 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 @@ -244,21 +244,20 @@ def get_guid( self, repository_clone_url, relative_install_dir, tool_config ): if self.shed_config_dict.get( 'tool_path' ): - relative_install_dir = os.path.join( self.shed_config_dict['tool_path'], relative_install_dir ) - found = False + relative_install_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], relative_install_dir ) + tool_config_filename = suc.strip_path( tool_config ) for root, dirs, files in os.walk( relative_install_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: dirs.remove( '.hg' ) for name in files: - if name == tool_config: - found = True - break - if found: - break - full_path = str( os.path.abspath( os.path.join( root, name ) ) ) - tool = self.toolbox.load_tool( full_path ) - return suc.generate_tool_guid( repository_clone_url, tool ) + filename = suc.strip_path( name ) + if filename == tool_config_filename: + full_path = str( os.path.abspath( os.path.join( root, name ) ) ) + tool = self.toolbox.load_tool( full_path ) + return suc.generate_tool_guid( repository_clone_url, tool ) + # Not quite sure what should happen here, throw an exception or what? + return None def get_prior_install_required_dict( self, tool_shed_repositories, repository_dependencies_dict ): """ diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py --- a/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py +++ b/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py @@ -89,8 +89,9 @@ now = strftime( "%Y-%m-%d %H:%M:%S" ) print "#############################################################################" - print "# %s - Validating repositories of type %s on %s..." % ( now, TOOL_DEPENDENCY_DEFINITION, config_parser.get( config_section, 'host' ) ) - print "# This tool shed is configured to listen on %s:%s" % ( config_parser.get( config_section, 'host' ), config_parser.get( config_section, 'port' ) ) + print "# %s - Validating repositories of type %s" % ( now, TOOL_DEPENDENCY_DEFINITION ) + print "# This tool shed is configured to listen on %s:%s" % ( config_parser.get( config_section, 'host' ), + config_parser.get( config_section, 'port' ) ) app = RepositoriesApplication( config ) @@ -196,7 +197,16 @@ test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) tool_test_results_dict[ 'test_environment' ] = test_environment_dict - repository_metadata.tool_test_results = tool_test_results_dict + # Store only the configured number of test runs. + num_tool_test_results_saved = int( app.config.num_tool_test_results_saved ) + if len( tool_test_results_dicts ) >= num_tool_test_results_saved: + test_results_index = num_tool_test_results_saved - 1 + new_tool_test_results_dicts = tool_test_results_dicts[ :test_results_index ] + else: + new_tool_test_results_dicts = [ d for d in tool_test_results_dicts ] + # Insert the new element into the first position in the list. + new_tool_test_results_dicts.insert( 0, tool_test_results_dict ) + repository_metadata.tool_test_results = new_tool_test_results_dicts app.sa_session.add( repository_metadata ) app.sa_session.flush() stop = time.time() diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/tool_shed/scripts/clean_up_tool_dependency_directory.py --- a/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py +++ b/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py @@ -4,55 +4,27 @@ import shutil def main( args ): - if not os.path.exists( args.basepath ): - print 'Tool dependency path %s does not exist.' % str( args.basepath ) - return 1 - if args.delete: - print 'Deleting contents of tool dependency path %s.' % args.basepath - for node in os.listdir( args.basepath ): - path = os.path.join( args.basepath, node ) - if os.path.isdir( path ): - try: - shutil.rmtree( path ) - print 'Deleted directory %s and all its contents.' % path - except Exception, e: - print 'Error deleting directory %s: %s' % ( path, str( e ) ) - pass - elif os.path.isfile( path ): - try: - os.remove( path ) - print 'Deleted file %s.' % path - except Exception, e: - print 'Error deleting file %s: %s' % ( path, str( e ) ) - pass - elif os.path.islink( path ): - print 'Deleting symlink %s with target %s.' % ( path, os.path.realpath( path ) ) - try: - os.remove( path ) - except Exception, e: - print 'Error deleting symlink %s: %s' % ( path, str( e ) ) - pass + if not os.path.exists( args.tool_dependency_dir ): + print 'Tool dependency base path %s does not exist, creating.' % str( args.tool_dependency_dir ) + os.mkdir( args.tool_dependency_dir ) + return 0 else: - print 'Tool dependency path %s contains the following files and directories:' % args.basepath - for element in os.listdir( args.basepath ): - print element - return 0 + for content in os.listdir( args.tool_dependency_dir ): + print 'Deleting directory %s from %s.' % ( content, args.tool_dependency_dir ) + full_path = os.path.join( args.tool_dependency_dir, content ) + if os.path.isdir( full_path ): + shutil.rmtree( full_path ) + else: + os.remove( full_path ) if __name__ == '__main__': - description = 'Clean out or list the contents of the provided tool dependency path. Remove if ' - description += 'the --delete command line argument is provided.' + description = 'Clean out the configured tool dependency path, creating it if it does not exist.' parser = argparse.ArgumentParser( description=description ) - parser.add_argument( '--delete', - dest='delete', - required=False, - action='store_true', - default=False, - help='Whether to delete all folders and files or list them on exit.' ) - parser.add_argument( '--basepath', - dest='basepath', + parser.add_argument( '--tool_dependency_dir', + dest='tool_dependency_dir', required=True, action='store', metavar='name', - help='The base path where tool dependencies are installed.' ) + help='The base path where tool dependencies will be installed.' ) args = parser.parse_args() sys.exit( main( args ) ) diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py --- /dev/null +++ b/lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py @@ -0,0 +1,75 @@ +import argparse +import os +import sys + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[ 1: ] ) +sys.path = new_path + +from galaxy import eggs +eggs.require( "SQLAlchemy >= 0.4" ) + +import galaxy.model +import galaxy.model.tool_shed_install.mapping as install_mapper +import galaxy.config as galaxy_config + + +class CleanUpDependencyApplication( object ): + """Application that enables querying the database using the tool_shed_install model.""" + + def __init__( self, config ): + self.config = config + # Setup the database engine and ORM + self.model = install_mapper.init( self.config.database_connection, engine_options={}, create_tables=False ) + + @property + def sa_session( self ): + """Returns a SQLAlchemy session.""" + return self.model.context.current + + def shutdown( self ): + pass + +def main( args, app ): + if not os.path.exists( args.basepath ): + print 'Tool dependency base path %s does not exist.' % str( args.basepath ) + return + print 'Checking tool dependency path %s' % args.basepath + tool_dependency_dirs = get_tool_dependency_dirs( app ) + for tool_dependency_dir in tool_dependency_dirs: + path = os.path.join( args.basepath, tool_dependency_dir ) + if os.path.exists( path ): + path_contents = os.listdir( path ) + if len( path_contents ) > 0: + print 'Found non-empty tool dependency installation directory %s.' % path + print 'Directory has the following contents: \n %s' % '\n '.join( path_contents ) + +def get_tool_dependency_dirs( app ): + dependency_paths = [] + for tool_dependency in app.sa_session.query( galaxy.model.tool_shed_install.ToolDependency ).all(): + dependency_paths.append( tool_dependency.installation_directory( app ) ) + return dependency_paths + +if __name__ == '__main__': + description = 'Clean out or list the contents any tool dependency directory under the provided' + description += 'tool dependency path. Remove any non-empty directories found if the ' + description += '--delete command line argument is provided.' + parser = argparse.ArgumentParser( description=description ) + parser.add_argument( '--basepath', + dest='basepath', + required=True, + action='store', + metavar='name', + help='The base path where tool dependencies are installed.' ) + parser.add_argument( '--dburi', + dest='dburi', + required=True, + action='store', + metavar='dburi', + help='The database URI to connect to.' ) + args = parser.parse_args() + database_connection = args.dburi + config_dict = dict( database_connection=database_connection, tool_dependency_dir=args.basepath ) + config = galaxy_config.Configuration( **config_dict ) + app = CleanUpDependencyApplication( config ) + sys.exit( main( args, app ) ) diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -21,26 +21,29 @@ self.key = key self.label = label self.parent = parent + self.current_repository_installation_errors = [] + self.current_repository_successful_installations = [] self.description = None self.datatypes = [] + self.failed_tests = [] self.folders = [] + self.invalid_data_managers = [] self.invalid_repository_dependencies = [] self.invalid_tool_dependencies = [] self.invalid_tools = [] - self.current_repository_installation_errors = [] - self.repository_installation_errors = [] - self.tool_dependency_installation_errors = [] - self.valid_tools = [] - self.valid_data_managers = [] - self.invalid_data_managers = [] - self.tool_dependencies = [] - self.failed_tests = [] self.missing_test_components = [] self.not_tested = [] self.passed_tests = [] + self.readme_files = [] + self.repository_dependencies = [] + self.repository_installation_errors = [] + self.repository_successful_installations = [] self.test_environments = [] - self.repository_dependencies = [] - self.readme_files = [] + self.tool_dependencies = [] + self.tool_dependency_installation_errors = [] + self.tool_dependency_successful_installations = [] + self.valid_tools = [] + self.valid_data_managers = [] self.workflows = [] def contains_folder( self, folder ): @@ -230,6 +233,17 @@ self.error_message = error_message +class RepositorySuccessfulInstallation( object ): + """Repository installation object""" + + def __init__( self, id=None, tool_shed=None, name=None, owner=None, changeset_revision=None ): + self.id = id + self.tool_shed = tool_shed + self.name = name + self.owner = owner + self.changeset_revision = changeset_revision + + class TestEnvironment( object ): """Tool test environment object""" @@ -294,6 +308,16 @@ self.error_message = error_message +class ToolDependencySuccessfulInstallation( object ): + """Tool dependency installation object""" + + def __init__( self, id=None, type=None, name=None, version=None, installation_directory=None ): + self.id = id + self.type = type + self.name = name + self.version = version + self.installation_directory = installation_directory + class Workflow( object ): """Workflow object.""" @@ -1097,7 +1121,8 @@ # {'python_version': '2.7.4', 'tool_shed_mercurial_version': '2.2.3', 'system': 'Linux 3.8.0-30-generic', # 'tool_shed_database_version': 21, 'architecture': 'x86_64', 'galaxy_revision': '11573:a62c54ddbe2a', # 'galaxy_database_version': 117, 'time_tested': '2013-12-03 09:11:48', 'tool_shed_revision': '11556:228156daa575'}, - # 'installation_errors': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []} + # 'installation_errors': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []}, + # 'successful_installations': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []} # } test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) if test_environment_dict is None: @@ -1335,6 +1360,82 @@ version=td_version, error_message=td_error_message ) tool_dependencies_folder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) + successful_installation_dict = tool_test_results_dict.get( 'successful_installations', {} ) + if len( successful_installation_dict ) > 0: + # 'successful_installation': + # {'current_repository': [], + # 'repository_dependencies': [], + # 'tool_dependencies': + # [{'installation_directory': 'some path' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}] + # } + current_repository_successful_installation_dicts = successful_installation_dict.get( 'current_repository', [] ) + repository_dependency_successful_installation_dicts = successful_installation_dict.get( 'repository_dependencies', [] ) + tool_dependency_successful_installation_dicts = successful_installation_dict.get( 'tool_dependencies', [] ) + if len( current_repository_successful_installation_dicts ) > 0 or \ + len( repository_dependency_successful_installation_dicts ) > 0 or \ + len( tool_dependency_successful_installation_dicts ) > 0: + repository_installation_success_id = 0 + folder_id += 1 + successful_installation_base_folder = Folder( id=folder_id, + key='successful_installations', + label='Successful installations', + parent=containing_folder ) + containing_folder.folders.append( successful_installation_base_folder ) + # Displaying the successful installation of the current repository is not really necessary, so we'll skip it. + if len( repository_dependency_successful_installation_dicts ) > 0: + folder_id += 1 + repository_dependencies_folder = Folder( id=folder_id, + key='repository_dependency_successful_installations', + label='Repository dependencies', + parent=successful_installation_base_folder ) + successful_installation_base_folder.folders.append( repository_dependencies_folder ) + for repository_dependency_successful_installation_dict in repository_dependency_successful_installation_dicts: + repository_installation_success_id += 1 + try: + rd_tool_shed = str( repository_dependency_successful_installation_dict.get( 'tool_shed', '' ) ) + rd_name = str( repository_dependency_successful_installation_dict.get( 'name', '' ) ) + rd_owner = str( repository_dependency_successful_installation_dict.get( 'owner', '' ) ) + rd_changeset_revision = str( repository_dependency_successful_installation_dict.get( 'changeset_revision', '' ) ) + except Exception, e: + rd_tool_shed = 'unknown' + rd_name = 'unknown' + rd_owner = 'unknown' + rd_changeset_revision = 'unknown' + repository_installation_success = \ + RepositoryInstallationSuccess( id=repository_installation_success_id, + tool_shed=rd_tool_shed, + name=rd_name, + owner=rd_owner, + changeset_revision=rd_changeset_revision ) + repository_dependencies_folder.repository_successful_installations.append( repository_installation_success ) + if len( tool_dependency_successful_installation_dicts ) > 0: + # [{'installation_directory': 'some path' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}] + folder_id += 1 + tool_dependencies_folder = Folder( id=folder_id, + key='tool_dependency_successful_installations', + label='Tool dependencies', + parent=successful_installation_base_folder ) + successful_installation_base_folder.folders.append( tool_dependencies_folder ) + tool_dependency_error_id = 0 + for tool_dependency_successful_installation_dict in tool_dependency_successful_installation_dicts: + tool_dependency_error_id += 1 + try: + td_type = str( tool_dependency_successful_installation_dict.get( 'type', '' ) ) + td_name = str( tool_dependency_successful_installation_dict.get( 'name', '' ) ) + td_version = str( tool_dependency_successful_installation_dict.get( 'version', '' ) ) + td_installation_directory = tool_dependency_successful_installation_dict.get( 'installation_directory', '' ) + except Exception, e: + td_type = 'unknown' + td_name = 'unknown' + td_version = 'unknown' + td_installation_directory = str( e ) + tool_dependency_successful_installation = \ + ToolDependencySuccessfulInstallation( id=tool_dependency_error_id, + type=td_type, + name=td_name, + version=td_version, + installation_directory=td_installation_directory ) + tool_dependencies_folder.tool_dependency_successful_installations.append( tool_dependency_successful_installation ) else: tool_test_results_root_folder = None return folder_id, tool_test_results_root_folder diff -r 05ff06be8f055d4d52b798615df007e5f0094ecb -r 65a083eee9332b2d178126588d536ee4c66fd66f lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -247,12 +247,16 @@ bold_start = '' bold_end = '' message = '' + if trans.webapp.name == 'galaxy': + tip_rev = str( repository.changeset_revision ) + else: + tip_rev = str( repository.tip( trans.app ) ) if not displaying_invalid_tool: if metadata_dict: - message += "Metadata may have been defined for some items in revision '%s'. " % str( repository.tip( trans.app ) ) + message += "Metadata may have been defined for some items in revision '%s'. " % tip_rev message += "Correct the following problems if necessary and reset metadata.%s" % new_line else: - message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip( trans.app ) ) + message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % tip_rev message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.%s" % new_line for itc_tup in invalid_file_tups: tool_file, exception_msg = itc_tup This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/fe71eca6e5b1/ Changeset: fe71eca6e5b1 Branch: page-api User: Kyle Ellrott Date: 2013-12-20 21:02:33 Summary: Adding some more page api security checks and fixing deletion filtering Affected #: 2 files diff -r 65a083eee9332b2d178126588d536ee4c66fd66f -r fe71eca6e5b19ecbe0be362c9ec84d72ab06e658 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3147,7 +3147,7 @@ self.openid = openid class Page( object, Dictifiable ): - dict_element_visible_keys = [ 'id', 'title', 'latest_revision_id', 'slug', 'published', 'importable' ] + dict_element_visible_keys = [ 'id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted' ] def __init__( self ): self.id = None self.user = None diff -r 65a083eee9332b2d178126588d536ee4c66fd66f -r fe71eca6e5b19ecbe0be362c9ec84d72ab06e658 lib/galaxy/webapps/galaxy/api/pages.py --- a/lib/galaxy/webapps/galaxy/api/pages.py +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -14,9 +14,9 @@ class PagesController( BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin ): @web.expose_api - def index( self, trans, deleted='False', **kwd ): + def index( self, trans, deleted=False, **kwd ): """ - index( self, trans, deleted='False', **kwd ) + index( self, trans, deleted=False, **kwd ) * GET /api/pages return a list of Pages viewable by the user @@ -25,12 +25,27 @@ :rtype: list :returns: dictionaries containing summary or detailed Page information """ - r = trans.sa_session.query( trans.app.model.Page ) - if not deleted: - r = r.filter_by(deleted=False) out = [] - for row in r: - out.append( self.encode_all_ids( trans, row.to_dict(), True) ) + + if trans.user_is_admin(): + r = trans.sa_session.query( trans.app.model.Page ) + if not deleted: + r = r.filter_by(deleted=False) + for row in r: + out.append( self.encode_all_ids( trans, row.to_dict(), True) ) + else: + user = trans.get_user() + r = trans.sa_session.query( trans.app.model.Page ).filter_by( user=user ) + if not deleted: + r = r.filter_by(deleted=False) + for row in r: + out.append( self.encode_all_ids( trans, row.to_dict(), True) ) + r = trans.sa_session.query( trans.app.model.Page ).filter( trans.app.model.Page.user != user ).filter_by(published=True) + if not deleted: + r = r.filter_by(deleted=False) + for row in r: + out.append( self.encode_all_ids( trans, row.to_dict(), True) ) + return out @@ -126,6 +141,7 @@ :returns: Dictionary return of the Page.to_dict call with the 'content' field populated by the most recent revision """ page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id( id ) ) + self.security_check( trans, page, check_ownership=False, check_accessible=True) rval = self.encode_all_ids( trans, page.to_dict(), True) rval['content'] = page.latest_revision.content return rval \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/6a42cefbe721/ Changeset: 6a42cefbe721 Branch: page-api User: kellrott Date: 2013-12-27 06:59:40 Summary: Sanitizing incoming page content. Affected #: 2 files diff -r fe71eca6e5b19ecbe0be362c9ec84d72ab06e658 -r 6a42cefbe7211bf5fcc0eab68f5c858fb88f3658 lib/galaxy/webapps/galaxy/api/page_revisions.py --- a/lib/galaxy/webapps/galaxy/api/page_revisions.py +++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py @@ -70,11 +70,14 @@ else: title = page.title + content = payload.get("content", "") + content = sanitize_html( content, 'utf-8', 'text/html' ) + page_revision = trans.app.model.PageRevision() page_revision.title = title page_revision.page = page page.latest_revision = page_revision - page_revision.content = payload.get("content", "") + page_revision.content = content # Persist session = trans.sa_session session.flush() diff -r fe71eca6e5b19ecbe0be362c9ec84d72ab06e658 -r 6a42cefbe7211bf5fcc0eab68f5c858fb88f3658 lib/galaxy/webapps/galaxy/api/pages.py --- a/lib/galaxy/webapps/galaxy/api/pages.py +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -77,6 +77,10 @@ elif trans.sa_session.query( trans.app.model.Page ).filter_by( user=user, slug=payload["slug"], deleted=False ).first(): error_str = "Page id must be unique" else: + + content = payload.get("content", "") + content = sanitize_html( content, 'utf-8', 'text/html' ) + # Create the new stored page page = trans.app.model.Page() page.title = payload['title'] @@ -89,7 +93,7 @@ page_revision.title = payload['title'] page_revision.page = page page.latest_revision = page_revision - page_revision.content = payload.get("content", "") + page_revision.content = content # Persist session = trans.sa_session session.add( page ) https://bitbucket.org/galaxy/galaxy-central/commits/8e1a2e81499c/ Changeset: 8e1a2e81499c User: dannon Date: 2013-12-31 16:04:06 Summary: Merged in kellrott/galaxy-central/page-api (pull request #277) Page API Affected #: 5 files diff -r 84478d0ec6c426180a286a410f733eff63d2f28b -r 8e1a2e81499c780acf08c3f195717a3523f4e55d lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3150,7 +3150,7 @@ self.openid = openid class Page( object, Dictifiable ): - dict_element_visible_keys = [ 'id', 'title', 'latest_revision_id', 'slug' ] + dict_element_visible_keys = [ 'id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted' ] def __init__( self ): self.id = None self.user = None diff -r 84478d0ec6c426180a286a410f733eff63d2f28b -r 8e1a2e81499c780acf08c3f195717a3523f4e55d lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -495,7 +495,9 @@ DOMAIN = "page" FIELDS = { 'id': ViewField('id', sqlalchemy_field=(Page, "id"), id_decode=True), + 'slug': ViewField('slug', sqlalchemy_field=(Page, "slug")), 'title': ViewField('title', sqlalchemy_field=(Page, "title")), + 'deleted': ViewField('deleted', sqlalchemy_field=(Page, "deleted")) } def search(self, trans): diff -r 84478d0ec6c426180a286a410f733eff63d2f28b -r 8e1a2e81499c780acf08c3f195717a3523f4e55d lib/galaxy/webapps/galaxy/api/page_revisions.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py @@ -0,0 +1,87 @@ +""" +API for updating Galaxy Pages +""" +import logging +from galaxy import web +from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin +from galaxy.model.search import GalaxySearchEngine +from galaxy.model.item_attrs import UsesAnnotations +from galaxy.exceptions import ItemAccessibilityException +from galaxy.util.sanitize_html import sanitize_html + +log = logging.getLogger( __name__ ) + +class PageRevisionsController( BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin ): + + @web.expose_api + def index( self, trans, page_id, **kwd ): + """ + index( self, trans, page_id, **kwd ) + * GET /api/pages/{page_id}/revisions + return a list of Page revisions + + :param page_id: Display the revisions of Page with ID=page_id + + :rtype: list + :returns: dictionaries containing different revisions of the page + """ + r = trans.sa_session.query( trans.app.model.PageRevision ).filter_by( page_id=trans.security.decode_id(page_id) ) + out = [] + for page in r: + if self.security_check( trans, page, True, True ): + out.append( self.encode_all_ids( trans, page.to_dict(), True) ) + return out + + + @web.expose_api + def create( self, trans, page_id, payload, **kwd ): + """ + create( self, trans, page_id, payload **kwd ) + * POST /api/pages/{page_id}/revisions + Create a new revision for a page + + :param page_id: Add revision to Page with ID=page_id + :param payload: A dictionary containing:: + 'title' = New title of the page + 'content' = New content of the page + + :rtype: dictionary + :returns: Dictionary with 'success' or 'error' element to indicate the result of the request + """ + user = trans.get_user() + error_str = "" + + if not page_id: + error_str = "page_id is required" + elif not payload.get("content", None): + error_str = "content is required" + else: + + # Create the new stored page + page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id(page_id) ) + if page is None: + return { "error" : "page not found"} + + if not self.security_check( trans, page, True, True ): + return { "error" : "page not found"} + + if 'title' in payload: + title = payload['title'] + else: + title = page.title + + content = payload.get("content", "") + content = sanitize_html( content, 'utf-8', 'text/html' ) + + page_revision = trans.app.model.PageRevision() + page_revision.title = title + page_revision.page = page + page.latest_revision = page_revision + page_revision.content = content + # Persist + session = trans.sa_session + session.flush() + + return {"success" : "revision posted"} + + return { "error" : error_str } diff -r 84478d0ec6c426180a286a410f733eff63d2f28b -r 8e1a2e81499c780acf08c3f195717a3523f4e55d lib/galaxy/webapps/galaxy/api/pages.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -0,0 +1,151 @@ +""" +API for updating Galaxy Pages +""" +import logging +from galaxy import web +from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin +from galaxy.model.search import GalaxySearchEngine +from galaxy.model.item_attrs import UsesAnnotations +from galaxy.exceptions import ItemAccessibilityException +from galaxy.util.sanitize_html import sanitize_html + +log = logging.getLogger( __name__ ) + +class PagesController( BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin ): + + @web.expose_api + def index( self, trans, deleted=False, **kwd ): + """ + index( self, trans, deleted=False, **kwd ) + * GET /api/pages + return a list of Pages viewable by the user + + :param deleted: Display deleted pages + + :rtype: list + :returns: dictionaries containing summary or detailed Page information + """ + out = [] + + if trans.user_is_admin(): + r = trans.sa_session.query( trans.app.model.Page ) + if not deleted: + r = r.filter_by(deleted=False) + for row in r: + out.append( self.encode_all_ids( trans, row.to_dict(), True) ) + else: + user = trans.get_user() + r = trans.sa_session.query( trans.app.model.Page ).filter_by( user=user ) + if not deleted: + r = r.filter_by(deleted=False) + for row in r: + out.append( self.encode_all_ids( trans, row.to_dict(), True) ) + r = trans.sa_session.query( trans.app.model.Page ).filter( trans.app.model.Page.user != user ).filter_by(published=True) + if not deleted: + r = r.filter_by(deleted=False) + for row in r: + out.append( self.encode_all_ids( trans, row.to_dict(), True) ) + + return out + + + @web.expose_api + def create( self, trans, payload, **kwd ): + """ + create( self, trans, payload, **kwd ) + * POST /api/pages + Create a page and return dictionary containing Page summary + + :param payload: dictionary structure containing:: + 'slug' = The title slug for the page URL, must be unique + 'title' = Title of the page + 'content' = HTML contents of the page + 'annotation' = Annotation that will be attached to the page + + :rtype: dict + :returns: Dictionary return of the Page.to_dict call + """ + user = trans.get_user() + error_str = "" + + if not payload.get("title", None): + error_str = "Page name is required" + elif not payload.get("slug", None): + error_str = "Page id is required" + elif not self._is_valid_slug( payload["slug"] ): + error_str = "Page identifier must consist of only lowercase letters, numbers, and the '-' character" + elif trans.sa_session.query( trans.app.model.Page ).filter_by( user=user, slug=payload["slug"], deleted=False ).first(): + error_str = "Page id must be unique" + else: + + content = payload.get("content", "") + content = sanitize_html( content, 'utf-8', 'text/html' ) + + # Create the new stored page + page = trans.app.model.Page() + page.title = payload['title'] + page.slug = payload['slug'] + page_annotation = sanitize_html( payload.get("annotation",""), 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation ) + page.user = user + # And the first (empty) page revision + page_revision = trans.app.model.PageRevision() + page_revision.title = payload['title'] + page_revision.page = page + page.latest_revision = page_revision + page_revision.content = content + # Persist + session = trans.sa_session + session.add( page ) + session.flush() + + rval = self.encode_all_ids( trans, page.to_dict(), True) + return rval + + return { "error" : error_str } + + + @web.expose_api + def delete( self, trans, id, **kwd ): + """ + delete( self, trans, id, **kwd ) + * DELETE /api/pages/{id} + Create a page and return dictionary containing Page summary + + :param id: ID of page to be deleted + + :rtype: dict + :returns: Dictionary with 'success' or 'error' element to indicate the result of the request + """ + page_id = id; + try: + page = trans.sa_session.query(self.app.model.Page).get(trans.security.decode_id(page_id)) + except Exception, e: + return { "error" : "Page with ID='%s' can not be found\n Exception: %s" % (page_id, str( e )) } + + # check to see if user has permissions to selected workflow + if page.user != trans.user and not trans.user_is_admin(): + return { "error" : "Workflow is not owned by or shared with current user" } + + #Mark a workflow as deleted + page.deleted = True + trans.sa_session.flush() + return {"success" : "Deleted", "id" : page_id} + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + show( self, trans, id, **kwd ) + * GET /api/pages/{id} + View a page summary and the content of the latest revision + + :param id: ID of page to be displayed + + :rtype: dict + :returns: Dictionary return of the Page.to_dict call with the 'content' field populated by the most recent revision + """ + page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id( id ) ) + self.security_check( trans, page, check_ownership=False, check_accessible=True) + rval = self.encode_all_ids( trans, page.to_dict(), True) + rval['content'] = page.latest_revision.content + return rval \ No newline at end of file diff -r 84478d0ec6c426180a286a410f733eff63d2f28b -r 8e1a2e81499c780acf08c3f195717a3523f4e55d lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -144,7 +144,11 @@ parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) - + webapp.mapper.resource( 'page', 'pages', path_prefix="/api") + webapp.mapper.resource( 'revision', 'revisions', + path_prefix='/api/pages/:page_id', + controller='page_revisions', + parent_resources=dict( member_name='page', collection_name='pages' ) ) # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", 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 31 Dec '13

31 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0befff261a71/ Changeset: 0befff261a71 User: nsoranzo Date: 2013-12-20 17:48:04 Summary: Log a failed chmod action when installing tool dependencies. Affected #: 1 file diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r 0befff261a714eccb452821c8bf7463a0a8d3fc9 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -698,6 +698,8 @@ for target_file, mode in action_dict[ 'change_modes' ]: if os.path.exists( target_file ): os.chmod( target_file, mode ) + else: + log.error( 'Invalid file %s specified, ignoring %s action.', target_file, action_type ) elif action_type == 'download_binary': url = action_dict[ 'url' ] target_directory = action_dict.get( 'target_directory', None ) https://bitbucket.org/galaxy/galaxy-central/commits/fa0531f4ee00/ Changeset: fa0531f4ee00 User: dannon Date: 2013-12-31 15:56:46 Summary: Merged in nsoranzo/galaxy-central (pull request #284) Log a failed chmod action when installing tool dependencies. Affected #: 1 file diff -r c304bf90e8cffa8c39eba2d14d940ac24a67457a -r fa0531f4ee00ed81f9229e02ae847d84b7e0bdf0 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -698,6 +698,8 @@ for target_file, mode in action_dict[ 'change_modes' ]: if os.path.exists( target_file ): os.chmod( target_file, mode ) + else: + log.error( 'Invalid file %s specified, ignoring %s action.', target_file, action_type ) elif action_type == 'download_binary': url = action_dict[ 'url' ] target_directory = action_dict.get( 'target_directory', None ) 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: 2 new changesets
by commits-noreply＠bitbucket.org 26 Dec '13

26 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5a264a194528/ Changeset: 5a264a194528 User: Gian...(a)crs4.it Date: 2013-12-20 10:58:08 Summary: Add <version_command>. Affected #: 2 files diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r 5a264a194528efdffd6aec050b96a38701a7563e tools/sr_assembly/velvetg.xml --- a/tools/sr_assembly/velvetg.xml +++ b/tools/sr_assembly/velvetg.xml @@ -1,5 +1,6 @@ <tool id="velvetg" name="velvetg" version="1.0.0"><description>Velvet sequence assembler for very short reads</description> + <version_command>velvetg 2>&1 | grep "Version" | sed -e 's/Version //'</version_command><command interpreter="python"> velvetg_wrapper.py '$input.extra_files_path' diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r 5a264a194528efdffd6aec050b96a38701a7563e tools/sr_assembly/velveth.xml --- a/tools/sr_assembly/velveth.xml +++ b/tools/sr_assembly/velveth.xml @@ -1,5 +1,6 @@ <tool id="velveth" name="velveth" version="1.0.0"><description>Prepare a dataset for the Velvet velvetg Assembler</description> + <version_command>velveth 2>&1 | grep "Version" | sed -e 's/Version //'</version_command><command interpreter="python"> velveth_wrapper.py '$out_file1' '$out_file1.extra_files_path' https://bitbucket.org/galaxy/galaxy-central/commits/c304bf90e8cf/ Changeset: c304bf90e8cf User: jmchilton Date: 2013-12-26 15:41:39 Summary: Merged in gmauro/galaxy-central (pull request #283) Add <version_command>. Affected #: 2 files diff -r 2c64d7fe6a7827b8d2b870c557ffc4d7acc24eca -r c304bf90e8cffa8c39eba2d14d940ac24a67457a tools/sr_assembly/velvetg.xml --- a/tools/sr_assembly/velvetg.xml +++ b/tools/sr_assembly/velvetg.xml @@ -1,5 +1,6 @@ <tool id="velvetg" name="velvetg" version="1.0.0"><description>Velvet sequence assembler for very short reads</description> + <version_command>velvetg 2>&1 | grep "Version" | sed -e 's/Version //'</version_command><command interpreter="python"> velvetg_wrapper.py '$input.extra_files_path' diff -r 2c64d7fe6a7827b8d2b870c557ffc4d7acc24eca -r c304bf90e8cffa8c39eba2d14d940ac24a67457a tools/sr_assembly/velveth.xml --- a/tools/sr_assembly/velveth.xml +++ b/tools/sr_assembly/velveth.xml @@ -1,5 +1,6 @@ <tool id="velveth" name="velveth" version="1.0.0"><description>Prepare a dataset for the Velvet velvetg Assembler</description> + <version_command>velveth 2>&1 | grep "Version" | sed -e 's/Version //'</version_command><command interpreter="python"> velveth_wrapper.py '$out_file1' '$out_file1.extra_files_path' 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: 2 new changesets
by commits-noreply＠bitbucket.org 24 Dec '13

24 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4961f4e87947/ Changeset: 4961f4e87947 User: jgoecks Date: 2013-12-23 17:54:46 Summary: Workflows API, run workflow: enable multiple parameter values to be set for a single step. Affected #: 1 file diff -r 31f4f354b66105d5c2bedc36d7fd80b37327b75e -r 4961f4e8794729f899a2901caf613201c7bb9f7a lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -207,15 +207,18 @@ # Update step parameters as directed by payload's parameter mapping. if step.tool_id in param_map: - # Get parameter settings. - change_param = param_map[step.tool_id]['param']; - change_value = param_map[step.tool_id]['value']; - step_id = param_map[step.tool_id].get('step_id', '') + param_dict = param_map[ step.tool_id ] + step_id = param_dict.get( 'step_id', '' ) + + # Backward compatibility: convert param/value dict to new 'name': 'value' format. + if 'param' in param_dict and 'value' in param_dict: + param_dict[ param_dict['param'] ] = param_dict['value'] # Update step if there's no step id (i.e. all steps with tool are # updated) or update if step ids match. if not step_id or ( step_id and int( step_id ) == step.id ): - step.state.inputs[change_param] = change_value + for name, value in param_dict.items(): + step.state.inputs[ name ] = value if step.tool_errors: trans.response.status = 400 https://bitbucket.org/galaxy/galaxy-central/commits/2c64d7fe6a78/ Changeset: 2c64d7fe6a78 User: jgoecks Date: 2013-12-24 02:26:25 Summary: Automated merge. Affected #: 2 files diff -r 4961f4e8794729f899a2901caf613201c7bb9f7a -r 2c64d7fe6a7827b8d2b870c557ffc4d7acc24eca lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1368,11 +1368,11 @@ # 'tool_dependencies': # [{'installation_directory': 'some path' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}] # } - current_repository_successful_installation_dicts = successful_installation_dict.get( 'current_repository', [] ) + # We won't display the current repository in this container. I fit is not displaying installation errors, + # then it must be a successful installation. repository_dependency_successful_installation_dicts = successful_installation_dict.get( 'repository_dependencies', [] ) tool_dependency_successful_installation_dicts = successful_installation_dict.get( 'tool_dependencies', [] ) - if len( current_repository_successful_installation_dicts ) > 0 or \ - len( repository_dependency_successful_installation_dicts ) > 0 or \ + if len( repository_dependency_successful_installation_dicts ) > 0 or \ len( tool_dependency_successful_installation_dicts ) > 0: repository_installation_success_id = 0 folder_id += 1 diff -r 4961f4e8794729f899a2901caf613201c7bb9f7a -r 2c64d7fe6a7827b8d2b870c557ffc4d7acc24eca lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -56,7 +56,7 @@ if str( tool_dependency.status ) != str( status ): debug_msg = 'Updating an existing record for version %s of tool dependency %s for revision %s of repository %s ' % \ ( str( version ), str( name ), str( tool_shed_repository.changeset_revision ), str( tool_shed_repository.name ) ) - debug_msg += 'by updating the status from %s to %s.' % str( tool_dependency.status ), str( status ) + debug_msg += 'by updating the status from %s to %s.' % ( str( tool_dependency.status ), str( status ) ) log.debug( debug_msg ) tool_dependency.status = status context.add( tool_dependency ) @@ -65,7 +65,7 @@ # Create a new tool_dependency record for the tool_shed_repository. debug_msg = 'Creating a new record for version %s of tool dependency %s for revision %s of repository %s. ' % \ ( str( version ), str( name ), str( tool_shed_repository.changeset_revision ), str( tool_shed_repository.name ) ) - debug_msg += 'The statis is being set to %s.' % str( status ) + debug_msg += 'The status is being set to %s.' % str( status ) log.debug( debug_msg ) tool_dependency = app.install_model.ToolDependency( tool_shed_repository.id, name, version, type, status ) context.add( tool_dependency ) 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: greg: Minor fixes for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 23 Dec '13

23 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ee86b02e26ab/ Changeset: ee86b02e26ab User: greg Date: 2013-12-23 13:15:57 Summary: Minor fixes for the tool shed's install and test framework. Affected #: 2 files diff -r 31f4f354b66105d5c2bedc36d7fd80b37327b75e -r ee86b02e26ab788122ec940f1f28c51208385cc2 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1368,11 +1368,11 @@ # 'tool_dependencies': # [{'installation_directory': 'some path' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}] # } - current_repository_successful_installation_dicts = successful_installation_dict.get( 'current_repository', [] ) + # We won't display the current repository in this container. I fit is not displaying installation errors, + # then it must be a successful installation. repository_dependency_successful_installation_dicts = successful_installation_dict.get( 'repository_dependencies', [] ) tool_dependency_successful_installation_dicts = successful_installation_dict.get( 'tool_dependencies', [] ) - if len( current_repository_successful_installation_dicts ) > 0 or \ - len( repository_dependency_successful_installation_dicts ) > 0 or \ + if len( repository_dependency_successful_installation_dicts ) > 0 or \ len( tool_dependency_successful_installation_dicts ) > 0: repository_installation_success_id = 0 folder_id += 1 diff -r 31f4f354b66105d5c2bedc36d7fd80b37327b75e -r ee86b02e26ab788122ec940f1f28c51208385cc2 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -56,7 +56,7 @@ if str( tool_dependency.status ) != str( status ): debug_msg = 'Updating an existing record for version %s of tool dependency %s for revision %s of repository %s ' % \ ( str( version ), str( name ), str( tool_shed_repository.changeset_revision ), str( tool_shed_repository.name ) ) - debug_msg += 'by updating the status from %s to %s.' % str( tool_dependency.status ), str( status ) + debug_msg += 'by updating the status from %s to %s.' % ( str( tool_dependency.status ), str( status ) ) log.debug( debug_msg ) tool_dependency.status = status context.add( tool_dependency ) @@ -65,7 +65,7 @@ # Create a new tool_dependency record for the tool_shed_repository. debug_msg = 'Creating a new record for version %s of tool dependency %s for revision %s of repository %s. ' % \ ( str( version ), str( name ), str( tool_shed_repository.changeset_revision ), str( tool_shed_repository.name ) ) - debug_msg += 'The statis is being set to %s.' % str( status ) + debug_msg += 'The status is being set to %s.' % str( status ) log.debug( debug_msg ) tool_dependency = app.install_model.ToolDependency( tool_shed_repository.id, name, version, type, status ) context.add( tool_dependency ) 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: jgoecks: Workflows API, running workflows: (a) improve code documentation and (b) add option to specify step_id when setting parameters so that parameters are set for a single step rather than all steps with a given tool id.
by commits-noreply＠bitbucket.org 23 Dec '13

23 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31f4f354b661/ Changeset: 31f4f354b661 User: jgoecks Date: 2013-12-23 01:24:37 Summary: Workflows API, running workflows: (a) improve code documentation and (b) add option to specify step_id when setting parameters so that parameters are set for a single step rather than all steps with a given tool id. Affected #: 1 file diff -r 9264df2bd5f015e7d8c011683b4f89e6beeacb4a -r 31f4f354b66105d5c2bedc36d7fd80b37327b75e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -104,15 +104,15 @@ However, we will import them if installed_repository_file is specified """ - # ------------------------------------------------------------------------------- # - ### RPARK: dictionary containing which workflows to change and edit ### - param_map = {}; - if (payload.has_key('parameters') ): - param_map = payload['parameters']; - # ------------------------------------------------------------------------------- # + # Pull parameters out of payload. + workflow_id = payload['workflow_id'] + param_map = payload.get('parameters', {}) + ds_map = payload['ds_map'] + add_to_history = 'no_add_to_history' not in payload + history_param = payload['history'] - - if 'workflow_id' not in payload: + # Get/create workflow. + if not workflow_id: # create new if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] @@ -125,26 +125,31 @@ if 'installed_repository_file' in payload: trans.response.status = 403 return "installed_repository_file may not be specified with workflow_id" + + # Get workflow + accessibility check. stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get( - trans.security.decode_id(payload['workflow_id'])) + trans.security.decode_id(workflow_id)) if stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: trans.response.status = 400 return("Workflow is not owned by or shared with current user") workflow = stored_workflow.latest_workflow - if payload['history'].startswith('hist_id='): + + # Get target history. + if history_param.startswith('hist_id='): #Passing an existing history to use. history = trans.sa_session.query(self.app.model.History).get( - trans.security.decode_id(payload['history'][8:])) + trans.security.decode_id(history_param[8:])) if history.user != trans.user and not trans.user_is_admin(): trans.response.status = 400 return "Invalid History specified." else: - history = self.app.model.History(name=payload['history'], user=trans.user) + # Send workflow outputs to new history. + history = self.app.model.History(name=history_param, user=trans.user) trans.sa_session.add(history) trans.sa_session.flush() - ds_map = payload['ds_map'] - add_to_history = 'no_add_to_history' not in payload + + # Set workflow inputs. for k in ds_map: try: if ds_map[k]['src'] == 'ldda': @@ -172,6 +177,8 @@ except AssertionError: trans.response.status = 400 return "Invalid Dataset '%s' Specified" % ds_map[k]['id'] + + # Sanity checks. if not workflow: trans.response.status = 400 return "Workflow not found." @@ -184,6 +191,7 @@ if workflow.has_errors: trans.response.status = 400 return "Workflow cannot be run because of validation errors in some steps" + # Build the state for each step rval = {} for step in workflow.steps: @@ -197,16 +205,18 @@ step.module.add_dummy_datasets( connections=step.input_connections ) step.state = step.module.state - #################################################### - #################################################### - # RPARK: IF TOOL_NAME IN PARAMETER MAP # + # Update step parameters as directed by payload's parameter mapping. if step.tool_id in param_map: + # Get parameter settings. change_param = param_map[step.tool_id]['param']; change_value = param_map[step.tool_id]['value']; - step.state.inputs[change_param] = change_value; - #################################################### - #################################################### + step_id = param_map[step.tool_id].get('step_id', '') + # Update step if there's no step id (i.e. all steps with tool are + # updated) or update if step ids match. + if not step_id or ( step_id and int( step_id ) == step.id ): + step.state.inputs[change_param] = change_value + if step.tool_errors: trans.response.status = 400 return "Workflow cannot be run because of validation errors in some steps: %s" % step_errors @@ -221,6 +231,7 @@ step.module = module_factory.from_workflow_step( trans, step ) step.state = step.module.get_runtime_state() step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) + # Run each step, connecting outputs to inputs workflow_invocation = self.app.model.WorkflowInvocation() workflow_invocation.workflow = workflow Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Improve logging when creating or updating tool dependency records installed into Galaxy.
by commits-noreply＠bitbucket.org 22 Dec '13

22 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9264df2bd5f0/ Changeset: 9264df2bd5f0 User: greg Date: 2013-12-22 14:13:19 Summary: Improve logging when creating or updating tool dependency records installed into Galaxy. Affected #: 2 files diff -r 37ddaa4b6a112c776b5ac011464b680c9cb50545 -r 9264df2bd5f015e7d8c011683b4f89e6beeacb4a lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -88,23 +88,29 @@ # the path defined by required_tool_dependency_env_file_path. It doesn't matter if the required env.sh # file currently exists.. required_tool_dependency_env_file_path = \ - tool_dependency_util.get_required_repository_package_env_sh_path( app, package_name, package_version, required_repository ) + tool_dependency_util.get_required_repository_package_env_sh_path( app, + package_name, + package_version, + required_repository ) env_file_builder = fabric_util.EnvFileBuilder( tool_dependency.installation_directory( app ) ) env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path ) return_code = env_file_builder.return_code if return_code: - error_message = 'Error defining env.sh file for package %s, return_code: %s' % ( str( package_name ), str( return_code ) ) - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, - tool_dependency, - error_message, - remove_installation_path=False ) + error_message = 'Error defining env.sh file for package %s, return_code: %s' % \ + ( str( package_name ), str( return_code ) ) + tool_dependency = \ + tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) elif required_tool_dependency is not None and required_tool_dependency.in_error_state: error_message = "This tool dependency's required tool dependency %s version %s has status %s." % \ ( str( required_tool_dependency.name ), str( required_tool_dependency.version ), str( required_tool_dependency.status ) ) - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, - tool_dependency, - error_message, - remove_installation_path=False ) + tool_dependency = \ + tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) else: tool_dependency = \ tool_dependency_util.set_tool_dependency_attributes( app, diff -r 37ddaa4b6a112c776b5ac011464b680c9cb50545 -r 9264df2bd5f015e7d8c011683b4f89e6beeacb4a lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -51,18 +51,25 @@ else: tool_dependency = get_tool_dependency_by_name_type_repository( app, tool_shed_repository, name, type ) if tool_dependency: - log.debug( 'Updating an existing record for tool dependency %s version %s for tool shed repository %s with changeset revision %s.' % - ( str( name ), str( version ), str( tool_shed_repository.name ), str( tool_shed_repository.changeset_revision ) ) ) # In some cases we should not override the current status of an existing tool_dependency, so do so only if set_status is True. if set_status: + if str( tool_dependency.status ) != str( status ): + debug_msg = 'Updating an existing record for version %s of tool dependency %s for revision %s of repository %s ' % \ + ( str( version ), str( name ), str( tool_shed_repository.changeset_revision ), str( tool_shed_repository.name ) ) + debug_msg += 'by updating the status from %s to %s.' % str( tool_dependency.status ), str( status ) + log.debug( debug_msg ) tool_dependency.status = status + context.add( tool_dependency ) + context.flush() else: # Create a new tool_dependency record for the tool_shed_repository. - log.debug( 'Creating a new record for tool dependency %s version %s for tool shed repository %s with changeset revision %s.' % - ( str( name ), str( version ), str( tool_shed_repository.name ), str( tool_shed_repository.changeset_revision ) ) ) + debug_msg = 'Creating a new record for version %s of tool dependency %s for revision %s of repository %s. ' % \ + ( str( version ), str( name ), str( tool_shed_repository.changeset_revision ), str( tool_shed_repository.name ) ) + debug_msg += 'The statis is being set to %s.' % str( status ) + log.debug( debug_msg ) tool_dependency = app.install_model.ToolDependency( tool_shed_repository.id, name, version, type, status ) - context.add( tool_dependency ) - context.flush() + context.add( tool_dependency ) + context.flush() return tool_dependency def create_tool_dependency_objects( app, tool_shed_repository, relative_install_dir, set_status=True ): 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: greg: Log the location of the exclude list file for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 22 Dec '13

22 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/37ddaa4b6a11/ Changeset: 37ddaa4b6a11 User: greg Date: 2013-12-22 05:01:55 Summary: Log the location of the exclude list file for the tool shed's install and test framework. Affected #: 2 files diff -r 12cbce6f1a20d8eecabc4ef50ca4d44c89eea505 -r 37ddaa4b6a112c776b5ac011464b680c9cb50545 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 @@ -64,7 +64,7 @@ # the database, new repositories, etc. galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' ) # File containing information about problematic repositories to exclude from test runs. -exclude_list_file = os.path.join( test_home_directory, 'exclude.xml' ) +exclude_list_file = os.path.abspath( os.path.join( test_home_directory, 'exclude.xml' ) ) default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir @@ -145,6 +145,7 @@ if error_message: return None, error_message # Handle repositories not to be tested. + log.debug( 'The exclude list file is defined as %s' % str( exclude_list_file ) ) if os.path.exists( exclude_list_file ): log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % str( exclude_list_file ) ) # The following exclude_list will look something like this: @@ -153,6 +154,7 @@ # ( name, owner, changeset_revision if changeset_revision else None )]}] exclude_list_dicts = install_and_test_base_util.parse_exclude_list( exclude_list_file ) else: + log.debug( 'The exclude list file %s does not exist, so no repositories will be excluded from testing.' % str( exclude_list_file ) ) exclude_list_dicts = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was # started up, installing repository and tool dependencies. Upon successful installation, generate a test case for each diff -r 12cbce6f1a20d8eecabc4ef50ca4d44c89eea505 -r 37ddaa4b6a112c776b5ac011464b680c9cb50545 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 @@ -62,7 +62,7 @@ # the database, new repositories, etc. galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' ) # File containing information about problematic repositories to exclude from test runs. -exclude_list_file = os.path.join( test_home_directory, 'exclude.xml' ) +exclude_list_file = os.path.abspath( os.path.join( test_home_directory, 'exclude.xml' ) ) default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir @@ -83,6 +83,7 @@ install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework ) if error_message: return None, error_message + log.debug( 'The exclude list file is defined as %s' % str( exclude_list_file ) ) if os.path.exists( exclude_list_file ): log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % str( exclude_list_file ) ) # The following exclude_list will look something like this: @@ -91,6 +92,7 @@ # ( name, owner, changeset_revision if changeset_revision else None )]}] exclude_list_dicts = install_and_test_base_util.parse_exclude_list( exclude_list_file ) else: + log.debug( 'The exclude list file %s does not exist, so no repositories will be excluded from testing.' % str( exclude_list_file ) ) exclude_list_dicts = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was # started up, installing repository and tool dependencies. Upon successful installation, generate a test case for each 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: greg: Fix for my last commit.
by commits-noreply＠bitbucket.org 22 Dec '13

22 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/12cbce6f1a20/ Changeset: 12cbce6f1a20 User: greg Date: 2013-12-22 02:39:36 Summary: Fix for my last commit. Affected #: 1 file diff -r 23d547cfc2d1007e7c82e8f018d087c18642dc49 -r 12cbce6f1a20d8eecabc4ef50ca4d44c89eea505 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 @@ -197,7 +197,7 @@ ( changeset_revision, name, owner ) ) else: # See if the repository was installed in a previous test. - repository = install_and_test_base_utilget_repository( name, owner, changeset_revision ) + repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) if repository is None: # The repository was not previously installed, so install it now. tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_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: greg: Fix prep scripts for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 22 Dec '13

22 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/23d547cfc2d1/ Changeset: 23d547cfc2d1 User: greg Date: 2013-12-22 02:31:18 Summary: Fix prep scripts for the tool shed's install and test framework. Affected #: 2 files diff -r 0f70f0b461678cd8224861857055f3eaf7646b05 -r 23d547cfc2d1007e7c82e8f018d087c18642dc49 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 @@ -197,7 +197,7 @@ ( changeset_revision, name, owner ) ) else: # See if the repository was installed in a previous test. - repository = get_repository( name, owner, changeset_revision ) + repository = install_and_test_base_utilget_repository( name, owner, changeset_revision ) if repository is None: # The repository was not previously installed, so install it now. tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) diff -r 0f70f0b461678cd8224861857055f3eaf7646b05 -r 23d547cfc2d1007e7c82e8f018d087c18642dc49 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 @@ -135,7 +135,7 @@ ( changeset_revision, name, owner ) ) else: # See if the repository was installed in a previous test. - repository = get_repository( name, owner, changeset_revision ) + repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) if repository is None: # The repository was not previously installed, so install it now. tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_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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galaxy-commits December 2013