galaxy-commits January 2014

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commit/galaxy-central: martenson: reports: addressing stringification bug
by commits-noreply＠bitbucket.org 30 Jan '14

30 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2ce1ba52c6a7/ Changeset: 2ce1ba52c6a7 User: martenson Date: 2014-01-30 22:38:04 Summary: reports: addressing stringification bug Affected #: 1 file diff -r 72a210496cda233f28769dac11c116e0e6a71f18 -r 2ce1ba52c6a7b33676ffebb73053ab3f9e9baa21 lib/galaxy/webapps/reports/controllers/jobs.py --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -29,7 +29,7 @@ return job.tool_id class CreateTimeColumn( grids.DateTimeColumn ): def get_value( self, trans, grid, job ): - return job.create_time + return job.create_time.isoformat() class UserColumn( grids.GridColumn ): def get_value( self, trans, grid, job ): if job.user: 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 30 Jan '14

30 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c77d83fe4c3e/ Changeset: c77d83fe4c3e Branch: next-stable User: jeremy goecks Date: 2014-01-30 21:54:26 Summary: Fix bug that prevented relative path from being used for len_file_path config option. Affected #: 2 files diff -r fd4936ae82193639011ed06b9552ec1a8c8166e5 -r c77d83fe4c3e37d07c241bb1f76064a3d0b7f149 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -67,7 +67,7 @@ self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) ) self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) - self.len_file_path = kwargs.get( "len_file_path", resolve_path(os.path.join(self.tool_data_path, 'shared','ucsc','chrom'), self.root) ) + self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ), self.root ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) # The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution # and moved to the tool shed. diff -r fd4936ae82193639011ed06b9552ec1a8c8166e5 -r c77d83fe4c3e37d07c241bb1f76064a3d0b7f149 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -236,7 +236,7 @@ if not chrom_info: # Default to built-in build. chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey ) - incoming[ "chromInfo" ] = chrom_info + incoming[ "chromInfo" ] = os.path.abspath( chrom_info ) inp_data.update( db_datasets ) # Determine output dataset permission/roles list https://bitbucket.org/galaxy/galaxy-central/commits/72a210496cda/ Changeset: 72a210496cda User: jeremy goecks Date: 2014-01-30 21:54:54 Summary: Automated merge of next-stable to default branch Affected #: 2 files diff -r bf7251133a037cda8ca7025a15af4ab9efb326ba -r 72a210496cda233f28769dac11c116e0e6a71f18 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -67,7 +67,7 @@ self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) ) self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) - self.len_file_path = kwargs.get( "len_file_path", resolve_path(os.path.join(self.tool_data_path, 'shared','ucsc','chrom'), self.root) ) + self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ), self.root ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) # The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution # and moved to the tool shed. diff -r bf7251133a037cda8ca7025a15af4ab9efb326ba -r 72a210496cda233f28769dac11c116e0e6a71f18 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -236,7 +236,7 @@ if not chrom_info: # Default to built-in build. chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey ) - incoming[ "chromInfo" ] = chrom_info + incoming[ "chromInfo" ] = os.path.abspath( chrom_info ) inp_data.update( db_datasets ) # Determine output dataset permission/roles list Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Visualizations Registry: small fixes
by commits-noreply＠bitbucket.org 30 Jan '14

30 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bf7251133a03/ Changeset: bf7251133a03 User: carlfeberhard Date: 2014-01-30 19:10:34 Summary: Visualizations Registry: small fixes Affected #: 4 files diff -r d9f6f3f2467195397828d452664c68e5e4c104ef -r bf7251133a037cda8ca7025a15af4ab9efb326ba lib/galaxy/datatypes/dataproviders/decorators.py --- a/lib/galaxy/datatypes/dataproviders/decorators.py +++ b/lib/galaxy/datatypes/dataproviders/decorators.py @@ -18,6 +18,7 @@ from functools import wraps #from types import MethodType +import urllib2 import copy import logging @@ -143,8 +144,9 @@ 'int' : int, 'float' : float, 'bool' : bool, - 'list:str' : lambda s: list_from_query_string( s ), - 'list:int' : lambda s: [ int( i ) for i in list_from_query_string( s ) ], + 'list:str' : lambda s: list_from_query_string( s ), + 'list:escaped' : lambda s: [ urllib2.unquote( e ) for e in list_from_query_string( s ) ], + 'list:int' : lambda s: [ int( i ) for i in list_from_query_string( s ) ], } settings = settings or {} # yay! yet another set of query string parsers! <-- sarcasm diff -r d9f6f3f2467195397828d452664c68e5e4c104ef -r bf7251133a037cda8ca7025a15af4ab9efb326ba lib/galaxy/datatypes/dataproviders/line.py --- a/lib/galaxy/datatypes/dataproviders/line.py +++ b/lib/galaxy/datatypes/dataproviders/line.py @@ -78,7 +78,7 @@ line = line.strip( '\n' ) if not self.provide_blank and line == '': return None - elif line.startswith( self.comment_char ): + elif self.comment_char and line.startswith( self.comment_char ): return None return super( FilteredLineDataProvider, self ).filter( line ) @@ -94,7 +94,7 @@ the line it is considered valid and will be provided). """ settings = { - 'regex_list' : 'list:str', + 'regex_list' : 'list:escaped', 'invert' : 'bool', } diff -r d9f6f3f2467195397828d452664c68e5e4c104ef -r bf7251133a037cda8ca7025a15af4ab9efb326ba lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -41,23 +41,18 @@ NOTE: also searches dictionaries """ - #print '\n\t getattr_recursive:', item, attr_key using_default = len( args ) >= 1 default = args[0] if using_default else None - #print '\t defaults:', using_default, default for attr_key in attr_key.split( '.' ): try: - #print '\t\t attr:', attr_key, 'item:', item if isinstance( item, dict ): item = item.__getitem__( attr_key ) else: item = getattr( item, attr_key ) except ( KeyError, AttributeError ), err: - #print '\t\t error:', err if using_default: - #print '\t\t\t default:', default return default raise @@ -77,7 +72,6 @@ attr_key = last_key try: - #print '\t\t attr:', attr_key, 'item:', item if isinstance( item, dict ): return item.__contains__( attr_key ) else: @@ -88,6 +82,7 @@ return True + # ------------------------------------------------------------------- the registry class VisualizationsRegistry( pluginframework.PageServingPluginManager ): """ @@ -118,7 +113,7 @@ super( VisualizationsRegistry, self ).__init__( app, 'visualizations', **kwargs ) # what to use to parse query strings into resources/vars for the template self.resource_parser = ResourceParser() - log.debug( '%s loaded', str( self ) ) + #log.debug( '%s loaded', str( self ) ) def is_plugin( self, plugin_path ): """ @@ -265,8 +260,6 @@ #precondition: the target_object should be usable by the visualization (accrd. to data_sources) # convert params using vis.data_source.to_params params = self.get_url_params( trans, target_object, param_data ) - #for param in params: - # print param # we want existing visualizations to work as normal but still be part of the registry (without mod'ing) # so generate their urls differently @@ -294,12 +287,8 @@ # assign takes precedence (goes last, overwrites)? #NOTE this is only one level - #print 'target_object:', target_object - #print 'target_attr:', target_attr - if target_attr and hasattr_recursive( target_object, target_attr ): params[ to_param_name ] = getattr_recursive( target_object, target_attr ) - #print 'params[ %s ]:' %( to_param_name ), params[ to_param_name ] if assign: params[ to_param_name ] = assign @@ -394,7 +383,6 @@ returned[ 'name' ] = xml_tree.attrib.get( 'name', None ) if not returned[ 'name' ]: raise ParsingException( 'visualization needs a name attribute' ) - print returned[ 'name' ] # a (for now) text description of what the visualization does description = xml_tree.find( 'description' ) @@ -532,7 +520,7 @@ raise ParsingException( 'data_source entry requires a model_class' ) if xml_tree.text not in self.ALLOWED_MODEL_CLASSES: - log.debug( 'available data_source model_classes: %s' %( str( self.ALLOWED_MODEL_CLASSES ) ) ) + #log.debug( 'available data_source model_classes: %s' %( str( self.ALLOWED_MODEL_CLASSES ) ) ) raise ParsingException( 'Invalid data_source model_class: %s' %( xml_tree.text ) ) # look up the model from the model module returning an empty data_source if not found @@ -760,6 +748,7 @@ If param is required and not present, raises a `KeyError`. """ + #log.debug( 'parse_parameter_dictionary, query_params:\n%s', query_params ) # first parse any params from any visualizations that were passed query_params = self.get_params_from_visualization_param( trans, controller, param_config_dict, query_params ) @@ -842,8 +831,8 @@ return self.parse_parameter( trans, param_config, default ) def get_params_from_visualization_param( self, trans, controller, param_config_dict, query_params ): - log.debug( 'parse_visualization_params: %s', param_config_dict ) - log.debug( ' : %s', query_params ) + #log.debug( 'parse_visualization_params: %s', param_config_dict ) + #log.debug( ' : %s', query_params ) # first, find the visualization in the parameters if any visualization = None @@ -854,25 +843,25 @@ if query_val is None: continue - log.debug( 'found visualization param: %s, %s', param_name, query_val ) + #log.debug( 'found visualization param: %s, %s', param_name, query_val ) visualization = self.parse_parameter( trans, controller, param_config, query_val ) if visualization: break # if no vis is found, can't get any new params from it: return the original query_params if not visualization: - log.debug( 'visualization not found' ) + #log.debug( 'visualization not found' ) return query_params - log.debug( 'found visualization: %s', visualization ) + #log.debug( 'found visualization: %s', visualization ) # next, attempt to copy any params from the visualizations config visualization_config = visualization.latest_revision.config - log.debug( '\t config: %s', visualization_config ) + #log.debug( '\t config: %s', visualization_config ) params_from_visualization = {} for param_name, param_config in param_config_dict.items(): if param_name in visualization_config: params_from_visualization[ param_name ] = visualization_config[ param_name ] - log.debug( 'params_from_visualization: %s', params_from_visualization ) + #log.debug( 'params_from_visualization: %s', params_from_visualization ) # layer the query_params over the params from the visualization, returning the combined params_from_visualization.update( query_params ) @@ -926,7 +915,7 @@ #TODO: subclass here? elif param_type == 'visualization': encoded_visualization_id = query_param - log.debug( 'visualization param, id : %s', encoded_visualization_id ) + #log.debug( 'visualization param, id : %s', encoded_visualization_id ) #TODO:?? some fallback if there's no get_X in controller that's passed? parsed_param = controller.get_visualization( trans, encoded_visualization_id, check_ownership=False, check_accessible=True ) @@ -948,5 +937,4 @@ dbkey = query_param parsed_param = galaxy.util.sanitize_html.sanitize_html( dbkey, 'utf-8' ) - #print ( '%s, %s -> %s, %s' %( param_type, query_param, str( type( parsed_param ) ), parsed_param ) ) return parsed_param diff -r d9f6f3f2467195397828d452664c68e5e4c104ef -r bf7251133a037cda8ca7025a15af4ab9efb326ba lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -62,7 +62,7 @@ :param skip_bad_plugins: whether to skip plugins that cause exceptions when loaded or to raise that exception """ - log.debug( 'PluginManager.init: %s, %s', directories_setting, kwargs ) + #log.debug( 'PluginManager.init: %s, %s', directories_setting, kwargs ) self.directories = [] self.skip_bad_plugins = skip_bad_plugins self.plugins = odict.odict() 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 30 Jan '14

30 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd4936ae8219/ Changeset: fd4936ae8219 Branch: next-stable User: greg Date: 2014-01-30 17:20:04 Summary: Fixes in the tool shed's install and test framework for handling repositories containing tools that install correctly but with one or more dependencies that do not. Affected #: 2 files diff -r 593be4d22c470abe6bdbbfa51f2a8e7ac035de33 -r fd4936ae82193639011ed06b9552ec1a8c8166e5 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -735,6 +735,8 @@ repository_name = str( repository.name ) repository_owner = str( repository.owner ) repository_changeset_revision = str( repository.changeset_revision ) + print 'Populating dependency install containers for revision %s of repository %s owned by %s.' % \ + ( repository_changeset_revision, repository_name, repository_owner ) processed_successful_repository_installations = install_and_test_statistics_dict.get( 'successful_repository_installations', [] ) if repository_identifier_tup not in processed_successful_repository_installations: install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_tup ) @@ -844,12 +846,17 @@ repository_name = str( repository.name ) repository_owner = str( repository.owner ) repository_changeset_revision = str( repository.changeset_revision ) + print 'Potentially populating install containers for repository dependencies of revision %s of repository %s owned by %s.' % \ + ( repository_changeset_revision, repository_name, repository_owner ) repository_dependencies_dicts, error_message = get_repository_dependencies_dicts( galaxy_tool_shed_url, repository_metadata_id ) if error_message: - print 'Cannot check or populate repository dependency install containers for version %s of repository %s owned by %s ' % \ + print 'Cannot check or populate repository dependency install containers for revision %s of repository %s owned by %s ' % \ ( repository_changeset_revision, repository_name, repository_owner ) print 'due to the following error getting repository_dependencies_dicts:\n%s' % str( error_message ) else: + if not repository_dependencies_dicts: + print 'Revision %s of repository %s owned by %s has no repository dependencies.' % \ + ( repository_changeset_revision, repository_name, repository_owner ) for repository_dependencies_dict in repository_dependencies_dicts: if not isinstance( repository_dependencies_dict, dict ): print 'Skipping invalid repository_dependencies_dict: %s' % str( repository_dependencies_dict ) @@ -951,7 +958,7 @@ can_update_tool_shed ) print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) - print'=============================================================' + print'\n=============================================================' else: # The required repository's installation failed. tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) @@ -965,7 +972,7 @@ can_update_tool_shed ) print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) - print'=============================================================' + print'\n=============================================================' else: print 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ ( changeset_revision, name, owner ) @@ -1056,7 +1063,7 @@ name = str( name ) owner = str( owner ) changeset_revision = str( changeset_revision ) - print '=============================================================' + print '\n=============================================================' print 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( tool_test_results_dict ) ) print 'Updating tool_test_results for repository_metadata id %s.' % metadata_revision_id diff -r 593be4d22c470abe6bdbbfa51f2a8e7ac035de33 -r fd4936ae82193639011ed06b9552ec1a8c8166e5 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 @@ -251,6 +251,19 @@ repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ) + if params.get( 'test_install_error', False ): + # The repository was successfully installed, but one or more dependencies had installation errors, + # so we'll populate the test result containers since we cannot execute any tests. + response_dict = \ + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) + print'\n=============================================================' # Populate the installation containers (success or error) for the repository's immediate repository # dependencies whose containers are not yet populated. install_and_test_base_util.populate_install_containers_for_repository_dependencies( app, @@ -266,6 +279,10 @@ print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ ( changeset_revision, name, owner ) print 'because one or more dependencies has installation errors.' + # The repository was installed successfully, but one or more dependencies had installation errors. Since + # we cannot test the tools due to these errors, we'll remove tests and tools were created during the repository + # installation process so nose will not discover them and attempt to execute them. + remove_tests( app ) else: print 'Revision %s of repository %s owned by %s installed successfully, so running tool tests.' % \ ( changeset_revision, name, owner ) @@ -279,6 +296,9 @@ from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) # If the repository has a test-data directory we write the generated shed_tools_dict to a temporary # file so the functional test framework can find it. + # TODO: Eliminate the need for this shed_tools_dict since it grows large over the course of each test run. + # If it cannot be eliminated altogether, reinitialize it with each new repository install so at this point + # it contains only entries for the current repository dependency hierarchy being tested. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) print 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, shed_tools_dict ) try: @@ -605,6 +625,7 @@ owner = str( repository.owner ) changeset_revision = str( repository.changeset_revision ) repository_identifier_tup = ( name, owner, changeset_revision ) + print 'Testing tools contained in revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) # Generate the test methods for this installed repository. We need to pass testing_shed_tools=True here # or twill will look in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test # files. https://bitbucket.org/galaxy/galaxy-central/commits/d9f6f3f24671/ Changeset: d9f6f3f24671 User: greg Date: 2014-01-30 17:20:33 Summary: Merged from next-stable Affected #: 2 files diff -r b67a464b8588525e17fd64910b9b9f3bcadb82ae -r d9f6f3f2467195397828d452664c68e5e4c104ef test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -735,6 +735,8 @@ repository_name = str( repository.name ) repository_owner = str( repository.owner ) repository_changeset_revision = str( repository.changeset_revision ) + print 'Populating dependency install containers for revision %s of repository %s owned by %s.' % \ + ( repository_changeset_revision, repository_name, repository_owner ) processed_successful_repository_installations = install_and_test_statistics_dict.get( 'successful_repository_installations', [] ) if repository_identifier_tup not in processed_successful_repository_installations: install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_tup ) @@ -844,12 +846,17 @@ repository_name = str( repository.name ) repository_owner = str( repository.owner ) repository_changeset_revision = str( repository.changeset_revision ) + print 'Potentially populating install containers for repository dependencies of revision %s of repository %s owned by %s.' % \ + ( repository_changeset_revision, repository_name, repository_owner ) repository_dependencies_dicts, error_message = get_repository_dependencies_dicts( galaxy_tool_shed_url, repository_metadata_id ) if error_message: - print 'Cannot check or populate repository dependency install containers for version %s of repository %s owned by %s ' % \ + print 'Cannot check or populate repository dependency install containers for revision %s of repository %s owned by %s ' % \ ( repository_changeset_revision, repository_name, repository_owner ) print 'due to the following error getting repository_dependencies_dicts:\n%s' % str( error_message ) else: + if not repository_dependencies_dicts: + print 'Revision %s of repository %s owned by %s has no repository dependencies.' % \ + ( repository_changeset_revision, repository_name, repository_owner ) for repository_dependencies_dict in repository_dependencies_dicts: if not isinstance( repository_dependencies_dict, dict ): print 'Skipping invalid repository_dependencies_dict: %s' % str( repository_dependencies_dict ) @@ -951,7 +958,7 @@ can_update_tool_shed ) print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) - print'=============================================================' + print'\n=============================================================' else: # The required repository's installation failed. tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) @@ -965,7 +972,7 @@ can_update_tool_shed ) print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) - print'=============================================================' + print'\n=============================================================' else: print 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ ( changeset_revision, name, owner ) @@ -1056,7 +1063,7 @@ name = str( name ) owner = str( owner ) changeset_revision = str( changeset_revision ) - print '=============================================================' + print '\n=============================================================' print 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( tool_test_results_dict ) ) print 'Updating tool_test_results for repository_metadata id %s.' % metadata_revision_id diff -r b67a464b8588525e17fd64910b9b9f3bcadb82ae -r d9f6f3f2467195397828d452664c68e5e4c104ef 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 @@ -251,6 +251,19 @@ repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ) + if params.get( 'test_install_error', False ): + # The repository was successfully installed, but one or more dependencies had installation errors, + # so we'll populate the test result containers since we cannot execute any tests. + response_dict = \ + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) + print'\n=============================================================' # Populate the installation containers (success or error) for the repository's immediate repository # dependencies whose containers are not yet populated. install_and_test_base_util.populate_install_containers_for_repository_dependencies( app, @@ -266,6 +279,10 @@ print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ ( changeset_revision, name, owner ) print 'because one or more dependencies has installation errors.' + # The repository was installed successfully, but one or more dependencies had installation errors. Since + # we cannot test the tools due to these errors, we'll remove tests and tools were created during the repository + # installation process so nose will not discover them and attempt to execute them. + remove_tests( app ) else: print 'Revision %s of repository %s owned by %s installed successfully, so running tool tests.' % \ ( changeset_revision, name, owner ) @@ -279,6 +296,9 @@ from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) # If the repository has a test-data directory we write the generated shed_tools_dict to a temporary # file so the functional test framework can find it. + # TODO: Eliminate the need for this shed_tools_dict since it grows large over the course of each test run. + # If it cannot be eliminated altogether, reinitialize it with each new repository install so at this point + # it contains only entries for the current repository dependency hierarchy being tested. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) print 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, shed_tools_dict ) try: @@ -605,6 +625,7 @@ owner = str( repository.owner ) changeset_revision = str( repository.changeset_revision ) repository_identifier_tup = ( name, owner, changeset_revision ) + print 'Testing tools contained in revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) # Generate the test methods for this installed repository. We need to pass testing_shed_tools=True here # or twill will look in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test # files. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fix division by zero error in quota.
by commits-noreply＠bitbucket.org 29 Jan '14

29 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b67a464b8588/ Changeset: b67a464b8588 User: jmchilton Date: 2014-01-30 01:35:54 Summary: Fix division by zero error in quota. Affected #: 1 file diff -r 286b0d3b0485cfd1e5434dda86528662549d4468 -r b67a464b8588525e17fd64910b9b9f3bcadb82ae lib/galaxy/quota/__init__.py --- a/lib/galaxy/quota/__init__.py +++ b/lib/galaxy/quota/__init__.py @@ -138,7 +138,11 @@ # get the usage, if it wasn't passed if usage is False: usage = self.get_usage( trans, user, history ) - return min( ( int( float( usage ) / quota * 100 ), 100 ) ) + try: + return min( ( int( float( usage ) / quota * 100 ), 100 ) ) + except ZeroDivisionError: + return 100 + def set_entity_quota_associations( self, quotas=[], users=[], groups=[], delete_existing_assocs=True ): for quota in quotas: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 29 Jan '14

29 Jan '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e034999e8b1a/ Changeset: e034999e8b1a User: jmchilton Date: 2014-01-29 15:36:32 Summary: Bugfix: History import when 'cleanup_job=never'. Affected #: 1 file diff -r 6a7cb977238c76359f39c8484b88cdd1daff4b1f -r e034999e8b1a2820f81e6fe64c623b7417e38148 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -789,8 +789,8 @@ # If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up if self.tool: self.tool.job_failed( self, message, exception ) - if self.app.config.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED): - self.cleanup() + delete_files = self.app.config.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED) + self.cleanup( delete_files=delete_files ) def pause( self, job=None, message=None ): if job is None: @@ -1067,22 +1067,27 @@ self.sa_session.flush() log.debug( 'job %d ended' % self.job_id ) - if self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ): - self.cleanup() + # TODO: Also fix "not stderr" below, use final_job_state. + delete_files = self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ) + self.cleanup( delete_files=delete_files ) def check_tool_output( self, stdout, stderr, tool_exit_code, job ): return check_output( self.tool, stdout, stderr, tool_exit_code, job ) - def cleanup( self ): - # remove temporary files + def cleanup( self, delete_files=True ): + # At least one of these tool cleanup actions (job import), is needed + # for thetool to work properly, that is why one might want to run + # cleanup but not delete files. try: - for fname in self.extra_filenames: - os.remove( fname ) - self.external_output_metadata.cleanup_external_metadata( self.sa_session ) + if delete_files: + for fname in self.extra_filenames: + os.remove( fname ) + self.external_output_metadata.cleanup_external_metadata( self.sa_session ) galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.app, self.job_id ).cleanup_after_job() galaxy.tools.genome_index.GenomeIndexToolWrapper( self.job_id ).postprocessing( self.sa_session, self.app ) - self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id)) + if delete_files: + self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id)) except: log.exception( "Unable to cleanup job %d" % self.job_id ) @@ -1520,8 +1525,8 @@ # if the job was deleted, don't finish it if task.state == task.states.DELETED: # Job was deleted by an administrator - if self.app.config.cleanup_job in ( 'always', 'onsuccess' ): - self.cleanup() + delete_files = self.app.config.cleanup_job in ( 'always', 'onsuccess' ) + self.cleanup( delete_files=delete_files ) return elif task.state == task.states.ERROR: self.fail( task.info ) https://bitbucket.org/galaxy/galaxy-central/commits/40d94d94900b/ Changeset: 40d94d94900b User: jmchilton Date: 2014-01-29 15:36:32 Summary: Bugfix: cleanup_job for newer job error checking logic. Affected #: 1 file diff -r e034999e8b1a2820f81e6fe64c623b7417e38148 -r 40d94d94900b82be76e11b778626d09a421e4966 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1067,8 +1067,7 @@ self.sa_session.flush() log.debug( 'job %d ended' % self.job_id ) - # TODO: Also fix "not stderr" below, use final_job_state. - delete_files = self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ) + delete_files = self.app.config.cleanup_job == 'always' or ( job.state == job.states.OK and self.app.config.cleanup_job == 'onsuccess' ) self.cleanup( delete_files=delete_files ) def check_tool_output( self, stdout, stderr, tool_exit_code, job ): https://bitbucket.org/galaxy/galaxy-central/commits/07dceba219c3/ Changeset: 07dceba219c3 User: jmchilton Date: 2014-01-29 15:36:32 Summary: Eliminate unneeded if in jobs/__init__.py. Checking if job.state is ERROR when that cannot be (method returns self.fail above this if that were the case). Even if it were somehow possible, subsequent code would fail badly with final_job_state not being set. Affected #: 1 file diff -r 40d94d94900b82be76e11b778626d09a421e4966 -r 07dceba219c315e2857f105abfdaf030efa1f16c lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -883,11 +883,10 @@ # We set final_job_state to use for dataset management, but *don't* set # job.state until after dataset collection to prevent history issues - if job.states.ERROR != job.state: - if ( self.check_tool_output( stdout, stderr, tool_exit_code, job )): - final_job_state = job.states.OK - else: - final_job_state = job.states.ERROR + if ( self.check_tool_output( stdout, stderr, tool_exit_code, job ) ): + final_job_state = job.states.OK + else: + final_job_state = job.states.ERROR if self.version_string_cmd: version_filename = self.get_version_string_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: jmchilton: Fix for a failing API test in buildbot.
by commits-noreply＠bitbucket.org 29 Jan '14

29 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6a7cb977238c/ Changeset: 6a7cb977238c User: jmchilton Date: 2014-01-29 07:27:30 Summary: Fix for a failing API test in buildbot. Just noticed these are actually running tonight, that is good news. Affected #: 1 file diff -r 60203bad003cc6b4bc054500248e5a69cbe9b8bc -r 6a7cb977238c76359f39c8484b88cdd1daff4b1f test/functional/api/test_page_revisions.py --- a/test/functional/api/test_page_revisions.py +++ b/test/functional/api/test_page_revisions.py @@ -1,5 +1,5 @@ from galaxy.exceptions import error_codes -from functional.api.pages import BasePageApiTestCase +from functional.api.test_pages import BasePageApiTestCase class PageRevisionsApiTestCase( BasePageApiTestCase ): 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: 11 new changesets
by commits-noreply＠bitbucket.org 29 Jan '14

29 Jan '14

11 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b928679cc4ac/ Changeset: b928679cc4ac User: jmchilton Date: 2014-01-28 21:35:14 Summary: PEP-8 and style fixes for various files related to history import/export. Affected #: 3 files diff -r 0ab0eb81d9828b0527d68f404a36acc64359f5f8 -r b928679cc4acd843e8a6dcfb24c89f5a0b40d3a6 lib/galaxy/tools/imp_exp/__init__.py --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -1,4 +1,8 @@ -import os, shutil, logging, tempfile, json +import os +import shutil +import logging +import tempfile +import json from galaxy import model from galaxy.tools.parameters.basic import UnvalidatedValue from galaxy.web.framework.helpers import to_unicode @@ -8,6 +12,7 @@ log = logging.getLogger(__name__) + def load_history_imp_exp_tools( toolbox ): """ Adds tools for importing/exporting histories to archives. """ # Use same process as that used in load_external_metadata_tool; see that @@ -42,6 +47,7 @@ toolbox.tools_by_id[ history_imp_tool.id ] = history_imp_tool log.debug( "Loaded history import tool: %s", history_imp_tool.id ) + class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ): """ Class provides support for performing jobs that import a history from @@ -144,23 +150,23 @@ metadata = dataset_attrs['metadata'] # Create dataset and HDA. - hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), - extension = dataset_attrs['extension'], - info = dataset_attrs['info'].encode( 'utf-8' ), - blurb = dataset_attrs['blurb'], - peek = dataset_attrs['peek'], - designation = dataset_attrs['designation'], - visible = dataset_attrs['visible'], - dbkey = metadata['dbkey'], - metadata = metadata, - history = new_history, - create_dataset = True, - sa_session = self.sa_session ) + hda = model.HistoryDatasetAssociation( name=dataset_attrs['name'].encode( 'utf-8' ), + extension=dataset_attrs['extension'], + info=dataset_attrs['info'].encode( 'utf-8' ), + blurb=dataset_attrs['blurb'], + peek=dataset_attrs['peek'], + designation=dataset_attrs['designation'], + visible=dataset_attrs['visible'], + dbkey=metadata['dbkey'], + metadata=metadata, + history=new_history, + create_dataset=True, + sa_session=self.sa_session ) hda.state = hda.states.OK self.sa_session.add( hda ) self.sa_session.flush() - new_history.add_dataset( hda, genome_build = None ) - hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. + new_history.add_dataset( hda, genome_build=None ) + hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. # TODO: Is there a way to recover permissions? Is this needed? #permissions = trans.app.security_agent.history_get_default_permissions( new_history ) #trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) @@ -273,6 +279,7 @@ jiha.job.stderr += "Error cleaning up history import job: %s" % e self.sa_session.flush() + class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ): """ Class provides support for performing jobs that export a history to an @@ -317,23 +324,23 @@ """ Encode an HDA, default encoding for everything else. """ if isinstance( obj, trans.app.model.HistoryDatasetAssociation ): return { - "__HistoryDatasetAssociation__" : True, - "create_time" : obj.create_time.__str__(), - "update_time" : obj.update_time.__str__(), - "hid" : obj.hid, - "name" : to_unicode( obj.name ), - "info" : to_unicode( obj.info ), - "blurb" : obj.blurb, - "peek" : obj.peek, - "extension" : obj.extension, - "metadata" : prepare_metadata( dict( obj.metadata.items() ) ), - "parent_id" : obj.parent_id, - "designation" : obj.designation, - "deleted" : obj.deleted, - "visible" : obj.visible, - "file_name" : obj.file_name, - "annotation" : to_unicode( getattr( obj, 'annotation', '' ) ), - "tags" : get_item_tag_dict( obj ), + "__HistoryDatasetAssociation__": True, + "create_time": obj.create_time.__str__(), + "update_time": obj.update_time.__str__(), + "hid": obj.hid, + "name": to_unicode( obj.name ), + "info": to_unicode( obj.info ), + "blurb": obj.blurb, + "peek": obj.peek, + "extension": obj.extension, + "metadata": prepare_metadata( dict( obj.metadata.items() ) ), + "parent_id": obj.parent_id, + "designation": obj.designation, + "deleted": obj.deleted, + "visible": obj.visible, + "file_name": obj.file_name, + "annotation": to_unicode( getattr( obj, 'annotation', '' ) ), + "tags": get_item_tag_dict( obj ), } if isinstance( obj, UnvalidatedValue ): return obj.__str__() @@ -347,15 +354,15 @@ # Write history attributes to file. history = jeha.history history_attrs = { - "create_time" : history.create_time.__str__(), - "update_time" : history.update_time.__str__(), - "name" : to_unicode( history.name ), - "hid_counter" : history.hid_counter, - "genome_build" : history.genome_build, - "annotation" : to_unicode( self.get_item_annotation_str( trans.sa_session, history.user, history ) ), - "tags" : get_item_tag_dict( history ), - "includes_hidden_datasets" : include_hidden, - "includes_deleted_datasets" : include_deleted + "create_time": history.create_time.__str__(), + "update_time": history.update_time.__str__(), + "name": to_unicode( history.name ), + "hid_counter": history.hid_counter, + "genome_build": history.genome_build, + "annotation": to_unicode( self.get_item_annotation_str( trans.sa_session, history.user, history ) ), + "tags": get_item_tag_dict( history ), + "includes_hidden_datasets": include_hidden, + "includes_deleted_datasets": include_deleted } history_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name history_attrs_out = open( history_attrs_filename, 'w' ) @@ -391,7 +398,7 @@ # Get the associated job, if any. If this hda was copied from another, # we need to find the job that created the origial hda job_hda = hda - while job_hda.copied_from_history_dataset_association: #should this check library datasets as well? + while job_hda.copied_from_history_dataset_association: # should this check library datasets as well? job_hda = job_hda.copied_from_history_dataset_association if not job_hda.creating_job_associations: # No viable HDA found. @@ -472,4 +479,3 @@ shutil.rmtree( temp_dir ) except Exception, e: log.debug( 'Error deleting directory containing attribute files (%s): %s' % ( temp_dir, e ) ) - diff -r 0ab0eb81d9828b0527d68f404a36acc64359f5f8 -r b928679cc4acd843e8a6dcfb24c89f5a0b40d3a6 lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py --- a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py +++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py @@ -6,19 +6,25 @@ --[url|file] source type, either a URL or a file. """ -import sys, optparse, tarfile, tempfile, urllib2, math +import sys +import optparse +import tarfile +import tempfile +import urllib2 +import math # Set max size of archive/file that will be handled to be 100 GB. This is # arbitrary and should be adjusted as needed. MAX_SIZE = 100 * math.pow( 2, 30 ) + def url_to_file( url, dest_file ): """ Transfer a file from a remote URL to a temporary file. """ try: url_reader = urllib2.urlopen( url ) - CHUNK = 10 * 1024 # 10k + CHUNK = 10 * 1024 # 10k total = 0 fp = open( dest_file, 'wb') while True: @@ -35,6 +41,7 @@ print "Exception getting file from URL: %s" % e, sys.stderr return None + def unpack_archive( archive_file, dest_dir ): """ Unpack a tar and/or gzipped archive into a destination directory. @@ -63,4 +70,4 @@ # Unpack archive. unpack_archive( archive_file, dest_dir ) except Exception, e: - print "Error unpacking tar/gz archive: %s" % e, sys.stderr \ No newline at end of file + print "Error unpacking tar/gz archive: %s" % e, sys.stderr diff -r 0ab0eb81d9828b0527d68f404a36acc64359f5f8 -r b928679cc4acd843e8a6dcfb24c89f5a0b40d3a6 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -11,15 +11,17 @@ from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous -from galaxy.util import string_as_bool, restore_text -from galaxy.util.sanitize_html import sanitize_html -from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin, UsesTagsMixin +from galaxy.util import string_as_bool +from galaxy.util import restore_text +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import UsesTagsMixin from galaxy.web import url_for -from galaxy.model.orm import desc import logging log = logging.getLogger( __name__ ) + class HistoriesController( BaseAPIController, UsesHistoryMixin, UsesTagsMixin ): @expose_api_anonymous @@ -46,14 +48,14 @@ histories = self.get_user_histories( trans, user=trans.user, only_deleted=deleted ) #for history in query: for history in histories: - item = history.to_dict(value_mapper={'id':trans.security.encode_id}) + item = history.to_dict(value_mapper={'id': trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) rval.append( item ) elif trans.galaxy_session.current_history: #No user, this must be session authentication with an anonymous user. history = trans.galaxy_session.current_history - item = history.to_dict(value_mapper={'id':trans.security.encode_id}) + item = history.to_dict(value_mapper={'id': trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) rval.append(item) @@ -257,7 +259,7 @@ log.exception( 'Histories API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', history_id, str( kwd ), str( http_server_err ) ) raise - except HTTPException, http_exc: + except HTTPException: raise except Exception, exc: log.exception( 'Histories API, delete: uncaught exception: %s, %s\n%s', https://bitbucket.org/galaxy/galaxy-central/commits/f4485c8dd5f5/ Changeset: f4485c8dd5f5 Branch: job-search User: Kyle Ellrott Date: 2014-01-22 02:30:47 Summary: Adding in /api/jobs and refining the Job.to_dict method Affected #: 4 files diff -r 54defa390a91ec1db34141f97711e673218cde13 -r f4485c8dd5f5392f1cc8a1ed296fb772064f1e10 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -209,8 +209,8 @@ class Job( object, Dictifiable ): - dict_collection_visible_keys = [ 'id', 'state', 'exit_code' ] - dict_element_visible_keys = [ 'id', 'state', 'exit_code' ] + dict_collection_visible_keys = [ 'id', 'state', 'exit_code', 'update_time', 'create_time' ] + dict_element_visible_keys = [ 'id', 'state', 'exit_code', 'update_time', 'create_time' ] """ A job represents a request to run a tool given input datasets, tool @@ -416,30 +416,31 @@ dataset.info = 'Job output deleted by user before job completed' def to_dict( self, view='collection' ): rval = super( Job, self ).to_dict( view=view ) - rval['tool_name'] = self.tool_id - param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) - rval['params'] = param_dict + if view == 'element': + rval['tool_name'] = self.tool_id + param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) + rval['params'] = param_dict - input_dict = {} - for i in self.input_datasets: - if i.dataset is not None: - input_dict[i.name] = {"hda_id" : i.dataset.id} - for i in self.input_library_datasets: - if i.dataset is not None: - input_dict[i.name] = {"ldda_id" : i.dataset.id} - for k in input_dict: - if k in param_dict: - del param_dict[k] - rval['inputs'] = input_dict + input_dict = {} + for i in self.input_datasets: + if i.dataset is not None: + input_dict[i.name] = {"id" : i.dataset.id, "src" : "hda"} + for i in self.input_library_datasets: + if i.dataset is not None: + input_dict[i.name] = {"id" : i.dataset.id, "src" : "ldda"} + for k in input_dict: + if k in param_dict: + del param_dict[k] + rval['inputs'] = input_dict - output_dict = {} - for i in self.output_datasets: - if i.dataset is not None: - output_dict[i.name] = {"hda_id" : i.dataset.id} - for i in self.output_library_datasets: - if i.dataset is not None: - output_dict[i.name] = {"ldda_id" : i.dataset.id} - rval['outputs'] = output_dict + output_dict = {} + for i in self.output_datasets: + if i.dataset is not None: + output_dict[i.name] = {"id" : i.dataset.id, "src" : "hda"} + for i in self.output_library_datasets: + if i.dataset is not None: + output_dict[i.name] = {"id" : i.dataset.id, "src" : "ldda"} + rval['outputs'] = output_dict return rval diff -r 54defa390a91ec1db34141f97711e673218cde13 -r f4485c8dd5f5392f1cc8a1ed296fb772064f1e10 lib/galaxy/webapps/galaxy/api/jobs.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -0,0 +1,84 @@ +""" +API operations on a jobs. + +.. seealso:: :class:`galaxy.model.Jobs` +""" + +import pkg_resources +pkg_resources.require( "Paste" ) +from paste.httpexceptions import HTTPBadRequest, HTTPForbidden, HTTPInternalServerError, HTTPException + +from sqlalchemy import or_ + +from galaxy import web +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy.util import string_as_bool, restore_text +from galaxy.util.sanitize_html import sanitize_html +from galaxy.web.base.controller import BaseAPIController +from galaxy.web import url_for +from galaxy.model.orm import desc + +import logging +log = logging.getLogger( __name__ ) + +class HistoriesController( BaseAPIController ): + + @web.expose_api + def index( self, trans, **kwd ): + """ + index( trans, state=None ) + * GET /api/jobs: + return jobs for current user + + :type state: string or list + :param state: limit listing of jobs to those that match one of the included states. If none, all are returned. + Valid Galaxy job states include: + 'new', 'upload', 'waiting', 'queued', 'running', 'ok', 'error', 'paused', 'deleted', 'deleted_new' + + :rtype: list + :returns: list of dictionaries containing summary job information + """ + + state = kwd.get('state', None) + query = trans.sa_session.query(trans.app.model.Job).filter( + trans.app.model.Job.user == trans.user ) + if state is not None: + if isinstance(state, basestring): + query = query.filter( trans.app.model.Job.state == state ) + elif isinstance(state, list): + t = [] + for s in state: + t.append( trans.app.model.Job.state == s ) + query = query.filter( or_( *t ) ) + + out = [] + for job in query.order_by( + trans.app.model.Job.update_time.desc() + ).all(): + out.append( self.encode_all_ids( trans, job.to_dict('collection'), True) ) + return out + + @web.expose_api + def show( self, trans, id, **kwd ): + decoded_job_id = trans.security.decode_id(id) + query = trans.sa_session.query(trans.app.model.Job).filter( + trans.app.model.Job.user == trans.user, + trans.app.model.Job.id == decoded_job_id) + job = query.first() + if job is None: + return None + return self.encode_all_ids( trans, job.to_dict('element'), True) + + @expose_api + def create( self, trans, payload, **kwd ): + error = None + if 'tool_id' not in payload: + error = "No tool ID" + + tool_id = payload.get('tool_id') + + if error is not None: + return { "error" : error } + + diff -r 54defa390a91ec1db34141f97711e673218cde13 -r f4485c8dd5f5392f1cc8a1ed296fb772064f1e10 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -78,7 +78,12 @@ # -- Execute tool. -- # Get tool. - tool = trans.app.toolbox.get_tool( payload[ 'tool_id' ] ) if 'tool_id' in payload else None + tool = None + if 'tool_id' in payload: + tool = trans.app.toolbox.get_tool( payload[ 'tool_id' ] ) + if 'tool_name' in payload: + #in job descriptions it is called 'tool_name' to avoid having the name 'crushed' + tool = trans.app.toolbox.get_tool( payload[ 'tool_name' ] ) if not tool: trans.response.status = 404 return { "message": { "type": "error", "text" : trans.app.model.Dataset.conversion_messages.NO_TOOL } } diff -r 54defa390a91ec1db34141f97711e673218cde13 -r f4485c8dd5f5392f1cc8a1ed296fb772064f1e10 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -228,6 +228,12 @@ path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'job', + 'jobs', + path_prefix='/api' ) + #webapp.mapper.connect( 'job_item', '/api/jobs/:job_id', controller='jobs', action='show', conditions=dict( method=['GET'] ) ) + + _add_item_extended_metadata_controller( webapp, name_prefix="library_dataset_", path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) https://bitbucket.org/galaxy/galaxy-central/commits/f78bab3d44f0/ Changeset: f78bab3d44f0 Branch: job-search User: Kyle Ellrott Date: 2014-01-22 23:09:36 Summary: Adding job search method that attempts to find previous tool runs with the same requested inputs and outputs. Affected #: 2 files diff -r f4485c8dd5f5392f1cc8a1ed296fb772064f1e10 -r f78bab3d44f00b245beebce45cac2a2287c8f4ce lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -416,8 +416,8 @@ dataset.info = 'Job output deleted by user before job completed' def to_dict( self, view='collection' ): rval = super( Job, self ).to_dict( view=view ) + rval['tool_name'] = self.tool_id if view == 'element': - rval['tool_name'] = self.tool_id param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) rval['params'] = param_dict diff -r f4485c8dd5f5392f1cc8a1ed296fb772064f1e10 -r f78bab3d44f00b245beebce45cac2a2287c8f4ce lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -8,21 +8,22 @@ pkg_resources.require( "Paste" ) from paste.httpexceptions import HTTPBadRequest, HTTPForbidden, HTTPInternalServerError, HTTPException -from sqlalchemy import or_ - +from sqlalchemy import or_, and_ +from sqlalchemy.orm import aliased +import json from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.util import string_as_bool, restore_text from galaxy.util.sanitize_html import sanitize_html -from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems from galaxy.web import url_for from galaxy.model.orm import desc import logging log = logging.getLogger( __name__ ) -class HistoriesController( BaseAPIController ): +class HistoriesController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems ): @web.expose_api def index( self, trans, **kwd ): @@ -61,6 +62,18 @@ @web.expose_api def show( self, trans, id, **kwd ): + """ + show( trans, id ) + * GET /api/jobs/{job_id}: + return jobs for current user + + :type id: string + :param id: Specific job id + + :rtype: dictionary + :returns: dictionary containing full description of job data + """ + decoded_job_id = trans.security.decode_id(id) query = trans.sa_session.query(trans.app.model.Job).filter( trans.app.model.Job.user == trans.user, @@ -72,13 +85,100 @@ @expose_api def create( self, trans, payload, **kwd ): + """ + show( trans, payload ) + * POST /api/jobs: + return jobs for current user + + :type payload: dict + :param payload: Dictionary containing description of requested job. This is in the same format as + a request to POST /apt/tools would take to initiate a job + + :rtype: list + :returns: list of dictionaries containing summary job information of the jobs that match the requested job run + + This method is designed to scan the list of previously run jobs and find records of jobs that had + the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply + recycle the old results. + """ + error = None - if 'tool_id' not in payload: + tool_id = None + if 'tool_id' in payload: + tool_id = payload.get('tool_id') + if 'tool_name' in payload: + tool_id = payload.get('tool_name') + + tool = trans.app.toolbox.get_tool( tool_id ) + if tool is None: + error = "Requested tool not found" + if 'inputs' not in payload: + error = "No inputs defined" + if tool_id is None: error = "No tool ID" - - tool_id = payload.get('tool_id') - if error is not None: return { "error" : error } + inputs = payload['inputs'] + input_data = {} + input_param = {} + for k, v in inputs.items(): + if isinstance(v,dict): + if 'id' in v: + try: + if 'src' not in v or v['src'] == 'hda': + dataset = self.get_dataset( trans, v['id'], check_ownership=False, check_accessible=True ) + else: + dataset = self.get_library_dataset_dataset_association( trans, v['id'] ) + except Exception, e: + return { "error" : str( e ) } + if dataset is None: + return { "error" : "Dataset %s not found" % (v['id']) } + input_data[k] = dataset.dataset_id + else: + input_param[k] = json.dumps(v) + + query = trans.sa_session.query( trans.app.model.Job ).filter( + trans.app.model.Job.tool_id == tool_id, + trans.app.model.Job.user == trans.user + ).filter( + or_( + trans.app.model.Job.state == 'running', + trans.app.model.Job.state == 'queued', + trans.app.model.Job.state == 'waiting', + trans.app.model.Job.state == 'running', + trans.app.model.Job.state == 'ok', + ) + ) + + for k,v in input_param.items(): + a = aliased(trans.app.model.JobParameter) + query = query.filter( and_( + trans.app.model.Job.id == a.job_id, + a.name == k, + a.value == v + )) + + for k,v in input_data.items(): + """ + Here we are attempting to link the inputs to the underlying dataset (not the dataset association) + This way, if the calulation was done using a copied HDA (copied from the library or another history) + the search will still find the job + """ + a = aliased(trans.app.model.JobToInputDatasetAssociation) + b = aliased(trans.app.model.HistoryDatasetAssociation) + query = query.filter( and_( + trans.app.model.Job.id == a.job_id, + a.dataset_id == b.id, + b.deleted == False, + b.dataset_id == v + )) + out = [] + for job in query.all(): + """ + check to make sure none of the output files have been deleted + """ + if all(list(a.dataset.deleted == False for a in job.output_datasets)): + out.append( self.encode_all_ids( trans, job.to_dict('element'), True) ) + return out https://bitbucket.org/galaxy/galaxy-central/commits/3284b02d842a/ Changeset: 3284b02d842a Branch: job-search User: kellrott Date: 2014-01-24 21:05:03 Summary: Modified patch behavoir to match comments to pull request Affected #: 5 files diff -r f78bab3d44f00b245beebce45cac2a2287c8f4ce -r 3284b02d842a48c92bab4669982231ab0ac3ca98 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -416,7 +416,7 @@ dataset.info = 'Job output deleted by user before job completed' def to_dict( self, view='collection' ): rval = super( Job, self ).to_dict( view=view ) - rval['tool_name'] = self.tool_id + rval['tool_id'] = self.tool_id if view == 'element': param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) rval['params'] = param_dict diff -r f78bab3d44f00b245beebce45cac2a2287c8f4ce -r 3284b02d842a48c92bab4669982231ab0ac3ca98 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -161,7 +161,7 @@ if type( rval ) != dict: return rval for k, v in rval.items(): - if (k == 'id' or k.endswith( '_id' )) and v is not None: + if (k == 'id' or k.endswith( '_id' )) and v is not None and k not in ['tool_id']: try: rval[k] = trans.security.encode_id( v ) except: diff -r f78bab3d44f00b245beebce45cac2a2287c8f4ce -r 3284b02d842a48c92bab4669982231ab0ac3ca98 lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -23,7 +23,7 @@ import logging log = logging.getLogger( __name__ ) -class HistoriesController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems ): +class JobController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems ): @web.expose_api def index( self, trans, **kwd ): @@ -85,9 +85,13 @@ @expose_api def create( self, trans, payload, **kwd ): + raise NotImplementedError() + + @expose_api + def search(self, trans, payload, **kwd): """ - show( trans, payload ) - * POST /api/jobs: + search( trans, payload ) + * POST /api/jobs/search: return jobs for current user :type payload: dict @@ -106,8 +110,6 @@ tool_id = None if 'tool_id' in payload: tool_id = payload.get('tool_id') - if 'tool_name' in payload: - tool_id = payload.get('tool_name') tool = trans.app.toolbox.get_tool( tool_id ) if tool is None: @@ -142,15 +144,28 @@ query = trans.sa_session.query( trans.app.model.Job ).filter( trans.app.model.Job.tool_id == tool_id, trans.app.model.Job.user == trans.user - ).filter( - or_( - trans.app.model.Job.state == 'running', - trans.app.model.Job.state == 'queued', - trans.app.model.Job.state == 'waiting', - trans.app.model.Job.state == 'running', - trans.app.model.Job.state == 'ok', + ) + + if 'state' not in payload: + query = query.filter( + or_( + trans.app.model.Job.state == 'running', + trans.app.model.Job.state == 'queued', + trans.app.model.Job.state == 'waiting', + trans.app.model.Job.state == 'running', + trans.app.model.Job.state == 'ok', + ) ) - ) + else: + if isinstance(payload['state'], basestring): + query = query.filter( trans.app.model.Job.state == payload['state'] ) + elif isinstance(payload['state'], list): + o = [] + for s in payload['state']: + o.append( trans.app.model.Job.state == s ) + query = query.filter( + or_(*o) + ) for k,v in input_param.items(): a = aliased(trans.app.model.JobParameter) diff -r f78bab3d44f00b245beebce45cac2a2287c8f4ce -r 3284b02d842a48c92bab4669982231ab0ac3ca98 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -78,12 +78,7 @@ # -- Execute tool. -- # Get tool. - tool = None - if 'tool_id' in payload: - tool = trans.app.toolbox.get_tool( payload[ 'tool_id' ] ) - if 'tool_name' in payload: - #in job descriptions it is called 'tool_name' to avoid having the name 'crushed' - tool = trans.app.toolbox.get_tool( payload[ 'tool_name' ] ) + tool = trans.app.toolbox.get_tool( payload[ 'tool_id' ] ) if 'tool_id' in payload else None if not tool: trans.response.status = 404 return { "message": { "type": "error", "text" : trans.app.model.Dataset.conversion_messages.NO_TOOL } } diff -r f78bab3d44f00b245beebce45cac2a2287c8f4ce -r 3284b02d842a48c92bab4669982231ab0ac3ca98 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -231,7 +231,7 @@ webapp.mapper.resource( 'job', 'jobs', path_prefix='/api' ) - #webapp.mapper.connect( 'job_item', '/api/jobs/:job_id', controller='jobs', action='show', conditions=dict( method=['GET'] ) ) + webapp.mapper.connect( 'job_search', '/api/jobs/search', controller='jobs', action='search', conditions=dict( method=['POST'] ) ) _add_item_extended_metadata_controller( webapp, https://bitbucket.org/galaxy/galaxy-central/commits/558fb7b96b49/ Changeset: 558fb7b96b49 Branch: job-search User: kellrott Date: 2014-01-24 22:59:36 Summary: Adding more standard exceptions Affected #: 1 file diff -r 3284b02d842a48c92bab4669982231ab0ac3ca98 -r 558fb7b96b49bdcec0321a0c8d50afbf37ff972b lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -19,6 +19,7 @@ from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems from galaxy.web import url_for from galaxy.model.orm import desc +from galaxy import exceptions import logging log = logging.getLogger( __name__ ) @@ -73,14 +74,16 @@ :rtype: dictionary :returns: dictionary containing full description of job data """ - - decoded_job_id = trans.security.decode_id(id) + try: + decoded_job_id = trans.security.decode_id(id) + except: + raise exceptions.ObjectAttributeInvalidException() query = trans.sa_session.query(trans.app.model.Job).filter( trans.app.model.Job.user == trans.user, trans.app.model.Job.id == decoded_job_id) job = query.first() if job is None: - return None + raise exceptions.ObjectNotFound() return self.encode_all_ids( trans, job.to_dict('element'), True) @expose_api @@ -106,20 +109,17 @@ recycle the old results. """ - error = None tool_id = None if 'tool_id' in payload: tool_id = payload.get('tool_id') + if tool_id is None: + raise exceptions.ObjectAttributeMissingException("No tool id") tool = trans.app.toolbox.get_tool( tool_id ) if tool is None: - error = "Requested tool not found" + raise exceptions.ObjectNotFound( "Requested tool not found" ) if 'inputs' not in payload: - error = "No inputs defined" - if tool_id is None: - error = "No tool ID" - if error is not None: - return { "error" : error } + raise exceptions.ObjectAttributeMissingException("No inputs defined") inputs = payload['inputs'] @@ -136,7 +136,7 @@ except Exception, e: return { "error" : str( e ) } if dataset is None: - return { "error" : "Dataset %s not found" % (v['id']) } + raise exceptions.ObjectNotFound("Dataset %s not found" % (v['id'])) input_data[k] = dataset.dataset_id else: input_param[k] = json.dumps(v) https://bitbucket.org/galaxy/galaxy-central/commits/95747eacf09c/ Changeset: 95747eacf09c Branch: job-search User: jmchilton Date: 2014-01-29 06:29:15 Summary: PEP-8 and other style adjustments for new jobs API. Affected #: 1 file diff -r 558fb7b96b49bdcec0321a0c8d50afbf37ff972b -r 95747eacf09c21335323131382de433409b86e16 lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -4,26 +4,20 @@ .. seealso:: :class:`galaxy.model.Jobs` """ -import pkg_resources -pkg_resources.require( "Paste" ) -from paste.httpexceptions import HTTPBadRequest, HTTPForbidden, HTTPInternalServerError, HTTPException - from sqlalchemy import or_, and_ from sqlalchemy.orm import aliased import json from galaxy import web from galaxy.web import _future_expose_api as expose_api -from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous -from galaxy.util import string_as_bool, restore_text -from galaxy.util.sanitize_html import sanitize_html -from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems -from galaxy.web import url_for -from galaxy.model.orm import desc +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin +from galaxy.web.base.controller import UsesLibraryMixinItems from galaxy import exceptions import logging log = logging.getLogger( __name__ ) + class JobController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems ): @web.expose_api @@ -42,13 +36,14 @@ :returns: list of dictionaries containing summary job information """ - state = kwd.get('state', None) - query = trans.sa_session.query(trans.app.model.Job).filter( - trans.app.model.Job.user == trans.user ) + state = kwd.get( 'state', None ) + query = trans.sa_session.query( trans.app.model.Job ).filter( + trans.app.model.Job.user == trans.user + ) if state is not None: - if isinstance(state, basestring): + if isinstance( state, basestring ): query = query.filter( trans.app.model.Job.state == state ) - elif isinstance(state, list): + elif isinstance( state, list ): t = [] for s in state: t.append( trans.app.model.Job.state == s ) @@ -58,7 +53,7 @@ for job in query.order_by( trans.app.model.Job.update_time.desc() ).all(): - out.append( self.encode_all_ids( trans, job.to_dict('collection'), True) ) + out.append( self.encode_all_ids( trans, job.to_dict( 'collection' ), True ) ) return out @web.expose_api @@ -78,20 +73,21 @@ decoded_job_id = trans.security.decode_id(id) except: raise exceptions.ObjectAttributeInvalidException() - query = trans.sa_session.query(trans.app.model.Job).filter( + query = trans.sa_session.query( trans.app.model.Job ).filter( trans.app.model.Job.user == trans.user, - trans.app.model.Job.id == decoded_job_id) + trans.app.model.Job.id == decoded_job_id + ) job = query.first() if job is None: raise exceptions.ObjectNotFound() - return self.encode_all_ids( trans, job.to_dict('element'), True) + return self.encode_all_ids( trans, job.to_dict( 'element' ), True ) @expose_api def create( self, trans, payload, **kwd ): raise NotImplementedError() @expose_api - def search(self, trans, payload, **kwd): + def search( self, trans, payload, **kwd ): """ search( trans, payload ) * POST /api/jobs/search: @@ -104,96 +100,97 @@ :rtype: list :returns: list of dictionaries containing summary job information of the jobs that match the requested job run - This method is designed to scan the list of previously run jobs and find records of jobs that had - the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply + This method is designed to scan the list of previously run jobs and find records of jobs that had + the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply recycle the old results. """ tool_id = None if 'tool_id' in payload: - tool_id = payload.get('tool_id') + tool_id = payload.get( 'tool_id' ) if tool_id is None: - raise exceptions.ObjectAttributeMissingException("No tool id") + raise exceptions.ObjectAttributeMissingException( "No tool id" ) tool = trans.app.toolbox.get_tool( tool_id ) if tool is None: raise exceptions.ObjectNotFound( "Requested tool not found" ) if 'inputs' not in payload: - raise exceptions.ObjectAttributeMissingException("No inputs defined") + raise exceptions.ObjectAttributeMissingException( "No inputs defined" ) - inputs = payload['inputs'] + inputs = payload[ 'inputs' ] input_data = {} input_param = {} for k, v in inputs.items(): - if isinstance(v,dict): + if isinstance( v, dict ): if 'id' in v: try: - if 'src' not in v or v['src'] == 'hda': + if 'src' not in v or v[ 'src' ] == 'hda': dataset = self.get_dataset( trans, v['id'], check_ownership=False, check_accessible=True ) else: dataset = self.get_library_dataset_dataset_association( trans, v['id'] ) except Exception, e: return { "error" : str( e ) } if dataset is None: - raise exceptions.ObjectNotFound("Dataset %s not found" % (v['id'])) + raise exceptions.ObjectNotFound( "Dataset %s not found" % ( v[ 'id' ] ) ) input_data[k] = dataset.dataset_id else: - input_param[k] = json.dumps(v) + input_param[k] = json.dumps( v ) - query = trans.sa_session.query( trans.app.model.Job ).filter( - trans.app.model.Job.tool_id == tool_id, + query = trans.sa_session.query( trans.app.model.Job ).filter( + trans.app.model.Job.tool_id == tool_id, trans.app.model.Job.user == trans.user ) if 'state' not in payload: query = query.filter( - or_( - trans.app.model.Job.state == 'running', - trans.app.model.Job.state == 'queued', - trans.app.model.Job.state == 'waiting', + or_( trans.app.model.Job.state == 'running', - trans.app.model.Job.state == 'ok', + trans.app.model.Job.state == 'queued', + trans.app.model.Job.state == 'waiting', + trans.app.model.Job.state == 'running', + trans.app.model.Job.state == 'ok', ) ) else: - if isinstance(payload['state'], basestring): - query = query.filter( trans.app.model.Job.state == payload['state'] ) - elif isinstance(payload['state'], list): + if isinstance( payload[ 'state' ], basestring ): + query = query.filter( trans.app.model.Job.state == payload[ 'state' ] ) + elif isinstance( payload[ 'state' ], list ): o = [] - for s in payload['state']: + for s in payload[ 'state' ]: o.append( trans.app.model.Job.state == s ) query = query.filter( - or_(*o) + or_( *o ) ) - for k,v in input_param.items(): - a = aliased(trans.app.model.JobParameter) + for k, v in input_param.items(): + a = aliased( trans.app.model.JobParameter ) query = query.filter( and_( trans.app.model.Job.id == a.job_id, a.name == k, a.value == v - )) + ) ) - for k,v in input_data.items(): + for k, v in input_data.items(): """ Here we are attempting to link the inputs to the underlying dataset (not the dataset association) This way, if the calulation was done using a copied HDA (copied from the library or another history) the search will still find the job """ - a = aliased(trans.app.model.JobToInputDatasetAssociation) - b = aliased(trans.app.model.HistoryDatasetAssociation) + a = aliased( trans.app.model.JobToInputDatasetAssociation ) + b = aliased( trans.app.model.HistoryDatasetAssociation ) query = query.filter( and_( trans.app.model.Job.id == a.job_id, a.dataset_id == b.id, b.deleted == False, b.dataset_id == v - )) + ) ) + out = [] for job in query.all(): """ check to make sure none of the output files have been deleted """ - if all(list(a.dataset.deleted == False for a in job.output_datasets)): - out.append( self.encode_all_ids( trans, job.to_dict('element'), True) ) + if all( list( a.dataset.deleted == False for a in job.output_datasets ) ): + out.append( self.encode_all_ids( trans, job.to_dict( 'element' ), True ) ) return out https://bitbucket.org/galaxy/galaxy-central/commits/e20e9d60eb80/ Changeset: e20e9d60eb80 Branch: job-search User: jmchilton Date: 2014-01-29 06:34:04 Summary: Tweak Jobs API to only use new style API decorator, exception handling. Affected #: 1 file diff -r 95747eacf09c21335323131382de433409b86e16 -r e20e9d60eb8017a241976912bfceb30dd316b20e lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -7,7 +7,6 @@ from sqlalchemy import or_, and_ from sqlalchemy.orm import aliased import json -from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin @@ -20,7 +19,7 @@ class JobController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems ): - @web.expose_api + @expose_api def index( self, trans, **kwd ): """ index( trans, state=None ) @@ -56,7 +55,7 @@ out.append( self.encode_all_ids( trans, job.to_dict( 'collection' ), True ) ) return out - @web.expose_api + @expose_api def show( self, trans, id, **kwd ): """ show( trans, id ) @@ -124,13 +123,10 @@ for k, v in inputs.items(): if isinstance( v, dict ): if 'id' in v: - try: - if 'src' not in v or v[ 'src' ] == 'hda': - dataset = self.get_dataset( trans, v['id'], check_ownership=False, check_accessible=True ) - else: - dataset = self.get_library_dataset_dataset_association( trans, v['id'] ) - except Exception, e: - return { "error" : str( e ) } + if 'src' not in v or v[ 'src' ] == 'hda': + dataset = self.get_dataset( trans, v['id'], check_ownership=False, check_accessible=True ) + else: + dataset = self.get_library_dataset_dataset_association( trans, v['id'] ) if dataset is None: raise exceptions.ObjectNotFound( "Dataset %s not found" % ( v[ 'id' ] ) ) input_data[k] = dataset.dataset_id https://bitbucket.org/galaxy/galaxy-central/commits/8d408c81c6c4/ Changeset: 8d408c81c6c4 Branch: job-search User: jmchilton Date: 2014-01-29 06:34:29 Summary: Add functional tests for new jobs API. Affected #: 1 file diff -r e20e9d60eb8017a241976912bfceb30dd316b20e -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 test/functional/api/test_jobs.py --- /dev/null +++ b/test/functional/api/test_jobs.py @@ -0,0 +1,118 @@ +import json +from operator import itemgetter + +from base import api + +from .helpers import TestsDatasets + + +class JobsApiTestCase( api.ApiTestCase, TestsDatasets ): + + def test_index( self ): + # Create HDA to ensure at least one job exists... + self.__history_with_new_dataset() + jobs_response = self._get( "jobs" ) + + self._assert_status_code_is( jobs_response, 200 ) + + jobs = jobs_response.json() + assert isinstance( jobs, list ) + assert "upload1" in map( itemgetter( "tool_id" ), jobs ) + + def test_index_state_filter( self ): + # Initial number of ok jobs + original_count = len( self.__uploads_with_state( "ok" ) ) + + # Run through dataset upload to ensure num uplaods at least greater + # by 1. + self.__history_with_ok_dataset() + + # Verify number of ok jobs is actually greater. + new_count = len( self.__uploads_with_state( "ok" ) ) + assert original_count < new_count + + def test_index_multiple_states_filter( self ): + # Initial number of ok jobs + original_count = len( self.__uploads_with_state( "ok", "new" ) ) + + # Run through dataset upload to ensure num uplaods at least greater + # by 1. + self.__history_with_ok_dataset() + + # Verify number of ok jobs is actually greater. + new_count = len( self.__uploads_with_state( "new", "ok" ) ) + assert original_count < new_count, new_count + + def test_show( self ): + # Create HDA to ensure at least one job exists... + self.__history_with_new_dataset() + + jobs_response = self._get( "jobs" ) + first_job = jobs_response.json()[ 0 ] + self._assert_has_key( first_job, 'id', 'state', 'exit_code', 'update_time', 'create_time' ) + + job_id = first_job[ "id" ] + show_jobs_response = self._get( "jobs/%s" % job_id ) + self._assert_status_code_is( show_jobs_response, 200 ) + + job_details = show_jobs_response.json() + self._assert_has_key( job_details, 'id', 'state', 'exit_code', 'update_time', 'create_time' ) + + def test_search( self ): + history_id, dataset_id = self.__history_with_ok_dataset() + + inputs = json.dumps( + dict( + input1=dict( + src='hda', + id=dataset_id, + ) + ) + ) + search_payload = dict( + tool_id="cat1", + inputs=inputs, + state="ok", + ) + + empty_search_response = self._post( "jobs/search", data=search_payload ) + self._assert_status_code_is( empty_search_response, 200 ) + assert len( empty_search_response.json() ) == 0 + + self.__run_cat_tool( history_id, dataset_id ) + self._wait_for_history( history_id, assert_ok=True ) + + search_response = self._post( "jobs/search", data=search_payload ) + self._assert_status_code_is( empty_search_response, 200 ) + assert len( search_response.json() ) == 1, search_response.json() + + def __run_cat_tool( self, history_id, dataset_id ): + # Code duplication with test_jobs.py, eliminate + payload = self._run_tool_payload( + tool_id='cat1', + inputs=dict( + input1=dict( + src='hda', + id=dataset_id + ), + ), + history_id=history_id, + ) + self._post( "tools", data=payload ) + + def __uploads_with_state( self, *states ): + jobs_response = self._get( "jobs", data=dict( state=states ) ) + self._assert_status_code_is( jobs_response, 200 ) + jobs = jobs_response.json() + assert not filter( lambda j: j[ "state" ] not in states, jobs ) + return filter( lambda j: j[ "tool_id" ] == "upload1", jobs ) + + def __history_with_new_dataset( self ): + history_id = self._new_history() + dataset_id = self._new_dataset( history_id )[ "id" ] + return history_id, dataset_id + + def __history_with_ok_dataset( self ): + history_id, dataset_id = self.__history_with_new_dataset() + self._wait_for_history( history_id, assert_ok=True ) + return history_id, dataset_id https://bitbucket.org/galaxy/galaxy-central/commits/6d8959c8866c/ Changeset: 6d8959c8866c User: jmchilton Date: 2014-01-29 06:57:46 Summary: Merge job-search branch. Affected #: 6 files diff -r d3bc7ea60b05f3025de3dca2684f1bce0be2c0eb -r 6d8959c8866c699ee0e9461db2a1fcc0381bfac2 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -211,8 +211,8 @@ class Job( object, Dictifiable ): - dict_collection_visible_keys = [ 'id', 'state', 'exit_code' ] - dict_element_visible_keys = [ 'id', 'state', 'exit_code' ] + dict_collection_visible_keys = [ 'id', 'state', 'exit_code', 'update_time', 'create_time' ] + dict_element_visible_keys = [ 'id', 'state', 'exit_code', 'update_time', 'create_time' ] """ A job represents a request to run a tool given input datasets, tool @@ -418,30 +418,31 @@ dataset.info = 'Job output deleted by user before job completed' def to_dict( self, view='collection' ): rval = super( Job, self ).to_dict( view=view ) - rval['tool_name'] = self.tool_id - param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) - rval['params'] = param_dict + rval['tool_id'] = self.tool_id + if view == 'element': + param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) + rval['params'] = param_dict - input_dict = {} - for i in self.input_datasets: - if i.dataset is not None: - input_dict[i.name] = {"hda_id" : i.dataset.id} - for i in self.input_library_datasets: - if i.dataset is not None: - input_dict[i.name] = {"ldda_id" : i.dataset.id} - for k in input_dict: - if k in param_dict: - del param_dict[k] - rval['inputs'] = input_dict + input_dict = {} + for i in self.input_datasets: + if i.dataset is not None: + input_dict[i.name] = {"id" : i.dataset.id, "src" : "hda"} + for i in self.input_library_datasets: + if i.dataset is not None: + input_dict[i.name] = {"id" : i.dataset.id, "src" : "ldda"} + for k in input_dict: + if k in param_dict: + del param_dict[k] + rval['inputs'] = input_dict - output_dict = {} - for i in self.output_datasets: - if i.dataset is not None: - output_dict[i.name] = {"hda_id" : i.dataset.id} - for i in self.output_library_datasets: - if i.dataset is not None: - output_dict[i.name] = {"ldda_id" : i.dataset.id} - rval['outputs'] = output_dict + output_dict = {} + for i in self.output_datasets: + if i.dataset is not None: + output_dict[i.name] = {"id" : i.dataset.id, "src" : "hda"} + for i in self.output_library_datasets: + if i.dataset is not None: + output_dict[i.name] = {"id" : i.dataset.id, "src" : "ldda"} + rval['outputs'] = output_dict return rval diff -r d3bc7ea60b05f3025de3dca2684f1bce0be2c0eb -r 6d8959c8866c699ee0e9461db2a1fcc0381bfac2 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -160,7 +160,7 @@ if type( rval ) != dict: return rval for k, v in rval.items(): - if (k == 'id' or k.endswith( '_id' )) and v is not None: + if (k == 'id' or k.endswith( '_id' )) and v is not None and k not in ['tool_id']: try: rval[k] = trans.security.encode_id( v ) except: diff -r d3bc7ea60b05f3025de3dca2684f1bce0be2c0eb -r 6d8959c8866c699ee0e9461db2a1fcc0381bfac2 lib/galaxy/webapps/galaxy/api/jobs.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -0,0 +1,192 @@ +""" +API operations on a jobs. + +.. seealso:: :class:`galaxy.model.Jobs` +""" + +from sqlalchemy import or_, and_ +from sqlalchemy.orm import aliased +import json +from galaxy.web import _future_expose_api as expose_api +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin +from galaxy.web.base.controller import UsesLibraryMixinItems +from galaxy import exceptions + +import logging +log = logging.getLogger( __name__ ) + + +class JobController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems ): + + @expose_api + def index( self, trans, **kwd ): + """ + index( trans, state=None ) + * GET /api/jobs: + return jobs for current user + + :type state: string or list + :param state: limit listing of jobs to those that match one of the included states. If none, all are returned. + Valid Galaxy job states include: + 'new', 'upload', 'waiting', 'queued', 'running', 'ok', 'error', 'paused', 'deleted', 'deleted_new' + + :rtype: list + :returns: list of dictionaries containing summary job information + """ + + state = kwd.get( 'state', None ) + query = trans.sa_session.query( trans.app.model.Job ).filter( + trans.app.model.Job.user == trans.user + ) + if state is not None: + if isinstance( state, basestring ): + query = query.filter( trans.app.model.Job.state == state ) + elif isinstance( state, list ): + t = [] + for s in state: + t.append( trans.app.model.Job.state == s ) + query = query.filter( or_( *t ) ) + + out = [] + for job in query.order_by( + trans.app.model.Job.update_time.desc() + ).all(): + out.append( self.encode_all_ids( trans, job.to_dict( 'collection' ), True ) ) + return out + + @expose_api + def show( self, trans, id, **kwd ): + """ + show( trans, id ) + * GET /api/jobs/{job_id}: + return jobs for current user + + :type id: string + :param id: Specific job id + + :rtype: dictionary + :returns: dictionary containing full description of job data + """ + try: + decoded_job_id = trans.security.decode_id(id) + except: + raise exceptions.ObjectAttributeInvalidException() + query = trans.sa_session.query( trans.app.model.Job ).filter( + trans.app.model.Job.user == trans.user, + trans.app.model.Job.id == decoded_job_id + ) + job = query.first() + if job is None: + raise exceptions.ObjectNotFound() + return self.encode_all_ids( trans, job.to_dict( 'element' ), True ) + + @expose_api + def create( self, trans, payload, **kwd ): + raise NotImplementedError() + + @expose_api + def search( self, trans, payload, **kwd ): + """ + search( trans, payload ) + * POST /api/jobs/search: + return jobs for current user + + :type payload: dict + :param payload: Dictionary containing description of requested job. This is in the same format as + a request to POST /apt/tools would take to initiate a job + + :rtype: list + :returns: list of dictionaries containing summary job information of the jobs that match the requested job run + + This method is designed to scan the list of previously run jobs and find records of jobs that had + the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply + recycle the old results. + """ + + tool_id = None + if 'tool_id' in payload: + tool_id = payload.get( 'tool_id' ) + if tool_id is None: + raise exceptions.ObjectAttributeMissingException( "No tool id" ) + + tool = trans.app.toolbox.get_tool( tool_id ) + if tool is None: + raise exceptions.ObjectNotFound( "Requested tool not found" ) + if 'inputs' not in payload: + raise exceptions.ObjectAttributeMissingException( "No inputs defined" ) + + inputs = payload[ 'inputs' ] + + input_data = {} + input_param = {} + for k, v in inputs.items(): + if isinstance( v, dict ): + if 'id' in v: + if 'src' not in v or v[ 'src' ] == 'hda': + dataset = self.get_dataset( trans, v['id'], check_ownership=False, check_accessible=True ) + else: + dataset = self.get_library_dataset_dataset_association( trans, v['id'] ) + if dataset is None: + raise exceptions.ObjectNotFound( "Dataset %s not found" % ( v[ 'id' ] ) ) + input_data[k] = dataset.dataset_id + else: + input_param[k] = json.dumps( v ) + + query = trans.sa_session.query( trans.app.model.Job ).filter( + trans.app.model.Job.tool_id == tool_id, + trans.app.model.Job.user == trans.user + ) + + if 'state' not in payload: + query = query.filter( + or_( + trans.app.model.Job.state == 'running', + trans.app.model.Job.state == 'queued', + trans.app.model.Job.state == 'waiting', + trans.app.model.Job.state == 'running', + trans.app.model.Job.state == 'ok', + ) + ) + else: + if isinstance( payload[ 'state' ], basestring ): + query = query.filter( trans.app.model.Job.state == payload[ 'state' ] ) + elif isinstance( payload[ 'state' ], list ): + o = [] + for s in payload[ 'state' ]: + o.append( trans.app.model.Job.state == s ) + query = query.filter( + or_( *o ) + ) + + for k, v in input_param.items(): + a = aliased( trans.app.model.JobParameter ) + query = query.filter( and_( + trans.app.model.Job.id == a.job_id, + a.name == k, + a.value == v + ) ) + + for k, v in input_data.items(): + """ + Here we are attempting to link the inputs to the underlying dataset (not the dataset association) + This way, if the calulation was done using a copied HDA (copied from the library or another history) + the search will still find the job + """ + a = aliased( trans.app.model.JobToInputDatasetAssociation ) + b = aliased( trans.app.model.HistoryDatasetAssociation ) + query = query.filter( and_( + trans.app.model.Job.id == a.job_id, + a.dataset_id == b.id, + b.deleted == False, + b.dataset_id == v + ) ) + + out = [] + for job in query.all(): + """ + check to make sure none of the output files have been deleted + """ + if all( list( a.dataset.deleted == False for a in job.output_datasets ) ): + out.append( self.encode_all_ids( trans, job.to_dict( 'element' ), True ) ) + return out diff -r d3bc7ea60b05f3025de3dca2684f1bce0be2c0eb -r 6d8959c8866c699ee0e9461db2a1fcc0381bfac2 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -228,6 +228,12 @@ path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'job', + 'jobs', + path_prefix='/api' ) + webapp.mapper.connect( 'job_search', '/api/jobs/search', controller='jobs', action='search', conditions=dict( method=['POST'] ) ) + + _add_item_extended_metadata_controller( webapp, name_prefix="library_dataset_", path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) diff -r d3bc7ea60b05f3025de3dca2684f1bce0be2c0eb -r 6d8959c8866c699ee0e9461db2a1fcc0381bfac2 test/functional/api/test_jobs.py --- /dev/null +++ b/test/functional/api/test_jobs.py @@ -0,0 +1,118 @@ +import json +from operator import itemgetter + +from base import api + +from .helpers import TestsDatasets + + +class JobsApiTestCase( api.ApiTestCase, TestsDatasets ): + + def test_index( self ): + # Create HDA to ensure at least one job exists... + self.__history_with_new_dataset() + jobs_response = self._get( "jobs" ) + + self._assert_status_code_is( jobs_response, 200 ) + + jobs = jobs_response.json() + assert isinstance( jobs, list ) + assert "upload1" in map( itemgetter( "tool_id" ), jobs ) + + def test_index_state_filter( self ): + # Initial number of ok jobs + original_count = len( self.__uploads_with_state( "ok" ) ) + + # Run through dataset upload to ensure num uplaods at least greater + # by 1. + self.__history_with_ok_dataset() + + # Verify number of ok jobs is actually greater. + new_count = len( self.__uploads_with_state( "ok" ) ) + assert original_count < new_count + + def test_index_multiple_states_filter( self ): + # Initial number of ok jobs + original_count = len( self.__uploads_with_state( "ok", "new" ) ) + + # Run through dataset upload to ensure num uplaods at least greater + # by 1. + self.__history_with_ok_dataset() + + # Verify number of ok jobs is actually greater. + new_count = len( self.__uploads_with_state( "new", "ok" ) ) + assert original_count < new_count, new_count + + def test_show( self ): + # Create HDA to ensure at least one job exists... + self.__history_with_new_dataset() + + jobs_response = self._get( "jobs" ) + first_job = jobs_response.json()[ 0 ] + self._assert_has_key( first_job, 'id', 'state', 'exit_code', 'update_time', 'create_time' ) + + job_id = first_job[ "id" ] + show_jobs_response = self._get( "jobs/%s" % job_id ) + self._assert_status_code_is( show_jobs_response, 200 ) + + job_details = show_jobs_response.json() + self._assert_has_key( job_details, 'id', 'state', 'exit_code', 'update_time', 'create_time' ) + + def test_search( self ): + history_id, dataset_id = self.__history_with_ok_dataset() + + inputs = json.dumps( + dict( + input1=dict( + src='hda', + id=dataset_id, + ) + ) + ) + search_payload = dict( + tool_id="cat1", + inputs=inputs, + state="ok", + ) + + empty_search_response = self._post( "jobs/search", data=search_payload ) + self._assert_status_code_is( empty_search_response, 200 ) + assert len( empty_search_response.json() ) == 0 + + self.__run_cat_tool( history_id, dataset_id ) + self._wait_for_history( history_id, assert_ok=True ) + + search_response = self._post( "jobs/search", data=search_payload ) + self._assert_status_code_is( empty_search_response, 200 ) + assert len( search_response.json() ) == 1, search_response.json() + + def __run_cat_tool( self, history_id, dataset_id ): + # Code duplication with test_jobs.py, eliminate + payload = self._run_tool_payload( + tool_id='cat1', + inputs=dict( + input1=dict( + src='hda', + id=dataset_id + ), + ), + history_id=history_id, + ) + self._post( "tools", data=payload ) + + def __uploads_with_state( self, *states ): + jobs_response = self._get( "jobs", data=dict( state=states ) ) + self._assert_status_code_is( jobs_response, 200 ) + jobs = jobs_response.json() + assert not filter( lambda j: j[ "state" ] not in states, jobs ) + return filter( lambda j: j[ "tool_id" ] == "upload1", jobs ) + + def __history_with_new_dataset( self ): + history_id = self._new_history() + dataset_id = self._new_dataset( history_id )[ "id" ] + return history_id, dataset_id + + def __history_with_ok_dataset( self ): + history_id, dataset_id = self.__history_with_new_dataset() + self._wait_for_history( history_id, assert_ok=True ) + return history_id, dataset_id https://bitbucket.org/galaxy/galaxy-central/commits/1dd912d65cfb/ Changeset: 1dd912d65cfb Branch: job-search User: jmchilton Date: 2014-01-29 06:58:04 Summary: Close branch job-search. Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/60203bad003c/ Changeset: 60203bad003c User: jmchilton Date: 2014-01-29 07:05:15 Summary: Merge. Affected #: 3 files diff -r 6d8959c8866c699ee0e9461db2a1fcc0381bfac2 -r 60203bad003cc6b4bc054500248e5a69cbe9b8bc lib/galaxy/tools/imp_exp/__init__.py --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -1,4 +1,8 @@ -import os, shutil, logging, tempfile, json +import os +import shutil +import logging +import tempfile +import json from galaxy import model from galaxy.tools.parameters.basic import UnvalidatedValue from galaxy.web.framework.helpers import to_unicode @@ -8,6 +12,7 @@ log = logging.getLogger(__name__) + def load_history_imp_exp_tools( toolbox ): """ Adds tools for importing/exporting histories to archives. """ # Use same process as that used in load_external_metadata_tool; see that @@ -42,6 +47,7 @@ toolbox.tools_by_id[ history_imp_tool.id ] = history_imp_tool log.debug( "Loaded history import tool: %s", history_imp_tool.id ) + class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ): """ Class provides support for performing jobs that import a history from @@ -144,23 +150,23 @@ metadata = dataset_attrs['metadata'] # Create dataset and HDA. - hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), - extension = dataset_attrs['extension'], - info = dataset_attrs['info'].encode( 'utf-8' ), - blurb = dataset_attrs['blurb'], - peek = dataset_attrs['peek'], - designation = dataset_attrs['designation'], - visible = dataset_attrs['visible'], - dbkey = metadata['dbkey'], - metadata = metadata, - history = new_history, - create_dataset = True, - sa_session = self.sa_session ) + hda = model.HistoryDatasetAssociation( name=dataset_attrs['name'].encode( 'utf-8' ), + extension=dataset_attrs['extension'], + info=dataset_attrs['info'].encode( 'utf-8' ), + blurb=dataset_attrs['blurb'], + peek=dataset_attrs['peek'], + designation=dataset_attrs['designation'], + visible=dataset_attrs['visible'], + dbkey=metadata['dbkey'], + metadata=metadata, + history=new_history, + create_dataset=True, + sa_session=self.sa_session ) hda.state = hda.states.OK self.sa_session.add( hda ) self.sa_session.flush() - new_history.add_dataset( hda, genome_build = None ) - hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. + new_history.add_dataset( hda, genome_build=None ) + hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. # TODO: Is there a way to recover permissions? Is this needed? #permissions = trans.app.security_agent.history_get_default_permissions( new_history ) #trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) @@ -273,6 +279,7 @@ jiha.job.stderr += "Error cleaning up history import job: %s" % e self.sa_session.flush() + class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ): """ Class provides support for performing jobs that export a history to an @@ -317,23 +324,23 @@ """ Encode an HDA, default encoding for everything else. """ if isinstance( obj, trans.app.model.HistoryDatasetAssociation ): return { - "__HistoryDatasetAssociation__" : True, - "create_time" : obj.create_time.__str__(), - "update_time" : obj.update_time.__str__(), - "hid" : obj.hid, - "name" : to_unicode( obj.name ), - "info" : to_unicode( obj.info ), - "blurb" : obj.blurb, - "peek" : obj.peek, - "extension" : obj.extension, - "metadata" : prepare_metadata( dict( obj.metadata.items() ) ), - "parent_id" : obj.parent_id, - "designation" : obj.designation, - "deleted" : obj.deleted, - "visible" : obj.visible, - "file_name" : obj.file_name, - "annotation" : to_unicode( getattr( obj, 'annotation', '' ) ), - "tags" : get_item_tag_dict( obj ), + "__HistoryDatasetAssociation__": True, + "create_time": obj.create_time.__str__(), + "update_time": obj.update_time.__str__(), + "hid": obj.hid, + "name": to_unicode( obj.name ), + "info": to_unicode( obj.info ), + "blurb": obj.blurb, + "peek": obj.peek, + "extension": obj.extension, + "metadata": prepare_metadata( dict( obj.metadata.items() ) ), + "parent_id": obj.parent_id, + "designation": obj.designation, + "deleted": obj.deleted, + "visible": obj.visible, + "file_name": obj.file_name, + "annotation": to_unicode( getattr( obj, 'annotation', '' ) ), + "tags": get_item_tag_dict( obj ), } if isinstance( obj, UnvalidatedValue ): return obj.__str__() @@ -347,15 +354,15 @@ # Write history attributes to file. history = jeha.history history_attrs = { - "create_time" : history.create_time.__str__(), - "update_time" : history.update_time.__str__(), - "name" : to_unicode( history.name ), - "hid_counter" : history.hid_counter, - "genome_build" : history.genome_build, - "annotation" : to_unicode( self.get_item_annotation_str( trans.sa_session, history.user, history ) ), - "tags" : get_item_tag_dict( history ), - "includes_hidden_datasets" : include_hidden, - "includes_deleted_datasets" : include_deleted + "create_time": history.create_time.__str__(), + "update_time": history.update_time.__str__(), + "name": to_unicode( history.name ), + "hid_counter": history.hid_counter, + "genome_build": history.genome_build, + "annotation": to_unicode( self.get_item_annotation_str( trans.sa_session, history.user, history ) ), + "tags": get_item_tag_dict( history ), + "includes_hidden_datasets": include_hidden, + "includes_deleted_datasets": include_deleted } history_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name history_attrs_out = open( history_attrs_filename, 'w' ) @@ -391,7 +398,7 @@ # Get the associated job, if any. If this hda was copied from another, # we need to find the job that created the origial hda job_hda = hda - while job_hda.copied_from_history_dataset_association: #should this check library datasets as well? + while job_hda.copied_from_history_dataset_association: # should this check library datasets as well? job_hda = job_hda.copied_from_history_dataset_association if not job_hda.creating_job_associations: # No viable HDA found. @@ -472,4 +479,3 @@ shutil.rmtree( temp_dir ) except Exception, e: log.debug( 'Error deleting directory containing attribute files (%s): %s' % ( temp_dir, e ) ) - diff -r 6d8959c8866c699ee0e9461db2a1fcc0381bfac2 -r 60203bad003cc6b4bc054500248e5a69cbe9b8bc lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py --- a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py +++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py @@ -6,19 +6,25 @@ --[url|file] source type, either a URL or a file. """ -import sys, optparse, tarfile, tempfile, urllib2, math +import sys +import optparse +import tarfile +import tempfile +import urllib2 +import math # Set max size of archive/file that will be handled to be 100 GB. This is # arbitrary and should be adjusted as needed. MAX_SIZE = 100 * math.pow( 2, 30 ) + def url_to_file( url, dest_file ): """ Transfer a file from a remote URL to a temporary file. """ try: url_reader = urllib2.urlopen( url ) - CHUNK = 10 * 1024 # 10k + CHUNK = 10 * 1024 # 10k total = 0 fp = open( dest_file, 'wb') while True: @@ -35,6 +41,7 @@ print "Exception getting file from URL: %s" % e, sys.stderr return None + def unpack_archive( archive_file, dest_dir ): """ Unpack a tar and/or gzipped archive into a destination directory. @@ -63,4 +70,4 @@ # Unpack archive. unpack_archive( archive_file, dest_dir ) except Exception, e: - print "Error unpacking tar/gz archive: %s" % e, sys.stderr \ No newline at end of file + print "Error unpacking tar/gz archive: %s" % e, sys.stderr diff -r 6d8959c8866c699ee0e9461db2a1fcc0381bfac2 -r 60203bad003cc6b4bc054500248e5a69cbe9b8bc lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -11,15 +11,17 @@ from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous -from galaxy.util import string_as_bool, restore_text -from galaxy.util.sanitize_html import sanitize_html -from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin, UsesTagsMixin +from galaxy.util import string_as_bool +from galaxy.util import restore_text +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import UsesTagsMixin from galaxy.web import url_for -from galaxy.model.orm import desc import logging log = logging.getLogger( __name__ ) + class HistoriesController( BaseAPIController, UsesHistoryMixin, UsesTagsMixin ): @expose_api_anonymous @@ -46,14 +48,14 @@ histories = self.get_user_histories( trans, user=trans.user, only_deleted=deleted ) #for history in query: for history in histories: - item = history.to_dict(value_mapper={'id':trans.security.encode_id}) + item = history.to_dict(value_mapper={'id': trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) rval.append( item ) elif trans.galaxy_session.current_history: #No user, this must be session authentication with an anonymous user. history = trans.galaxy_session.current_history - item = history.to_dict(value_mapper={'id':trans.security.encode_id}) + item = history.to_dict(value_mapper={'id': trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) rval.append(item) @@ -257,7 +259,7 @@ log.exception( 'Histories API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', history_id, str( kwd ), str( http_server_err ) ) raise - except HTTPException, http_exc: + except HTTPException: raise except Exception, exc: log.exception( 'Histories API, delete: uncaught exception: %s, %s\n%s', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Merge
by commits-noreply＠bitbucket.org 28 Jan '14

28 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d3bc7ea60b05/ Changeset: d3bc7ea60b05 User: guerler Date: 2014-01-29 00:29:23 Summary: Merge Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Grids: Option to pick between persistent and transient messages
by commits-noreply＠bitbucket.org 28 Jan '14

28 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/593be4d22c47/ Changeset: 593be4d22c47 Branch: next-stable User: guerler Date: 2014-01-28 18:26:40 Summary: Grids: Option to pick between persistent and transient messages Affected #: 7 files diff -r 44538b70d174dd36836a88123a865e1147c016b5 -r 593be4d22c470abe6bdbbfa51f2a8e7ac035de33 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -24,6 +24,7 @@ template = "grid_base.mako" async_template = "grid_base_async.mako" use_async = False + use_hide_message = True global_actions = [] columns = [] operations = [] @@ -286,6 +287,7 @@ status = status, message = message, use_panels=self.use_panels, + use_hide_message=self.use_hide_message, advanced_search=self.advanced_search, show_item_checkboxes = ( self.show_item_checkboxes or kwargs.get( 'show_item_checkboxes', '' ) in [ 'True', 'true' ] ), diff -r 44538b70d174dd36836a88123a865e1147c016b5 -r 593be4d22c470abe6bdbbfa51f2a8e7ac035de33 lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -508,6 +508,7 @@ model_class = model.RepositoryMetadata template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "name" + use_hide_message = False columns = [ IdColumn( "Id", visible=False, diff -r 44538b70d174dd36836a88123a865e1147c016b5 -r 593be4d22c470abe6bdbbfa51f2a8e7ac035de33 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -236,6 +236,7 @@ model_class = model.Repository template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "name" + use_hide_message = False columns = [ NameColumn( "Name", key="name", @@ -344,6 +345,7 @@ model_class = model.RepositoryMetadata template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "Repository.name" + use_hide_message = False columns = [ NameColumn( "Repository name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -652,7 +654,7 @@ columns = [ col for col in RepositoriesMissingToolTestComponentsGrid.columns ] operations = [] use_paging = False - + def build_initial_query( self, trans, **kwd ): # First get all repositories that the current user is authorized to update. username = trans.user.username diff -r 44538b70d174dd36836a88123a865e1147c016b5 -r 593be4d22c470abe6bdbbfa51f2a8e7ac035de33 lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -36,6 +36,7 @@ model_class = model.Component template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = "name" + use_hide_message = False columns = [ NameColumn( "Name", key="Component.name", @@ -333,6 +334,7 @@ model_class = model.RepositoryReview template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = 'repository_id' + use_hide_message = False columns = [ RepositoryNameColumn( "Repository Name", model_class=model.Repository, diff -r 44538b70d174dd36836a88123a865e1147c016b5 -r 593be4d22c470abe6bdbbfa51f2a8e7ac035de33 static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -194,7 +194,9 @@ // update message if (options.message) { $('#grid-message').html(this.template_message(options)); - setTimeout( function() { $('#grid-message').html(''); }, 5000); + if (options.use_hide_message) { + setTimeout( function() { $('#grid-message').html(''); }, 5000); + } } // configure elements diff -r 44538b70d174dd36836a88123a865e1147c016b5 -r 593be4d22c470abe6bdbbfa51f2a8e7ac035de33 static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements();init_refresh_on_change()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){c.init_grid($.parseJSON(e));$(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},template_body:function(t){var m="";var u=0;var g=t.items.length;if(g==0){m+='<tr><td colspan="100"><em>No Items</em></td></tr>';u=1}for(var h in t.items){var r=t.items[h];var c=r.encode_id;var k="grid-"+h+"-popup";m+="<tr ";if(t.current_item_id==r.id){m+='class="current"'}m+=">";if(t.show_item_checkboxes){m+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in t.columns){var f=t.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var s=r.column_config[f.label];var l=s.link;var n=s.value;var q=s.inbound;if(jQuery.type(n)==="string"){n=n.replace(/\/\//g,"/")}var d="";var p="";if(f.attach_popup){d="grid-"+h+"-popup";p="menubutton";if(l!=""){p+=" split"}p+=" popup"}m+="<td "+e+">";if(l){if(t.operations.length!=0){m+='<div id="'+d+'" class="'+p+'" style="float: left;">'}var o="";if(q){o="use-inbound"}else{o="use-outbound"}m+='<a class="label '+o+'" href="'+l+'" onclick="return false;">'+n+"</a>";if(t.operations.length!=0){m+="</div>"}}else{m+='<div id="'+d+'" class="'+p+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+n+"</label></div>"}m+="</td>"}}m+="</tr>";u++}return m},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file +jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));if(d.use_hide_message){setTimeout(function(){$("#grid-message").html("")},5000)}}this.init_grid_elements();init_refresh_on_change()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){c.init_grid($.parseJSON(e));$(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},template_body:function(t){var m="";var u=0;var g=t.items.length;if(g==0){m+='<tr><td colspan="100"><em>No Items</em></td></tr>';u=1}for(var h in t.items){var r=t.items[h];var c=r.encode_id;var k="grid-"+h+"-popup";m+="<tr ";if(t.current_item_id==r.id){m+='class="current"'}m+=">";if(t.show_item_checkboxes){m+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in t.columns){var f=t.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var s=r.column_config[f.label];var l=s.link;var n=s.value;var q=s.inbound;if(jQuery.type(n)==="string"){n=n.replace(/\/\//g,"/")}var d="";var p="";if(f.attach_popup){d="grid-"+h+"-popup";p="menubutton";if(l!=""){p+=" split"}p+=" popup"}m+="<td "+e+">";if(l){if(t.operations.length!=0){m+='<div id="'+d+'" class="'+p+'" style="float: left;">'}var o="";if(q){o="use-inbound"}else{o="use-outbound"}m+='<a class="label '+o+'" href="'+l+'" onclick="return false;">'+n+"</a>";if(t.operations.length!=0){m+="</div>"}}else{m+='<div id="'+d+'" class="'+p+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+n+"</label></div>"}m+="</td>"}}m+="</tr>";u++}return m},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file diff -r 44538b70d174dd36836a88123a865e1147c016b5 -r 593be4d22c470abe6bdbbfa51f2a8e7ac035de33 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -64,6 +64,7 @@ 'legend' : grid.legend, 'current_item_id' : False, 'use_panels' : context.get('use_panels'), + 'use_hide_message' : grid.use_hide_message, 'insert' : insert, 'default_filter_dict' : default_filter_dict, 'advanced_search' : advanced_search, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits January 2014