1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8f86c3dd7f83/ changeset: 8f86c3dd7f83 user: greg date: 2011-08-05 22:22:23 summary: Fixes, code cleanup for setting tool shed repository metadata. affected #: 2 files (253 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Fri Aug 05 14:14:14 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Aug 05 16:22:23 2011 -0400 @@ -72,12 +72,127 @@ def get_repository( trans, id ): """Get a repository from the database via id""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) -def get_repository_metadata( trans, id, changeset_revision ): +def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ): """Get metadata for a specified repository change set from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ .first() +def get_latest_repository_metadata( trans, id ): + """Get last metadata defined for a specified repository from the database""" + return trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ + .order_by( trans.model.RepositoryMetadata.table.c.update_time.desc() ) \ + .first() +def set_workflowl_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ): + # We'll store everything except the workflow steps in the database. + flush_needed = False + workflow_dict = { 'a_galaxy_workflow' : exported_workflow_dict[ 'a_galaxy_workflow' ], + 'name' :exported_workflow_dict[ 'name' ], + 'annotation' : exported_workflow_dict[ 'annotation' ], + 'format-version' : exported_workflow_dict[ 'format-version' ] } + repository_metadata = get_latest_repository_metadata( trans, id ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata and 'workflows' in metadata: + metadata_workflows = metadata[ 'workflows' ] + found = False + for workflow_metadata_dict in metadata_workflows: + if 'a_galaxy_workflow' in workflow_metadata_dict and util.string_as_bool( workflow_metadata_dict[ 'a_galaxy_workflow' ] ) and \ + 'name' in workflow_metadata_dict and workflow_metadata_dict[ 'name' ] == exported_workflow_dict[ 'name' ] and \ + 'annotation' in workflow_metadata_dict and workflow_metadata_dict[ 'annotation' ] == exported_workflow_dict[ 'annotation' ] and \ + 'format-version' in workflow_metadata_dict and workflow_metadata_dict[ 'format-version' ] == exported_workflow_dict[ 'format-version' ]: + found = True + break + if not found: + metadata_workflows.append( workflow_dict ) + else: + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'workflows' ] = workflow_dict + repository_metadata.changeset_revision = change_set_revision + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + else: + if 'workflows' in metadata_dict: + metadata_dict[ 'workflows' ].append( workflow_dict ) + else: + metadata_dict[ 'workflows' ] = [ workflow_dict ] + return flush_needed, metadata_dict + +def set_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ): + tool_requirements = [] + flush_needed = False + for tr in tool.requirements: + requirement_dict = dict( name=tr.name, + type=tr.type, + version=tr.version ) + tool_requirements.append( requirement_dict ) + tool_tests = [] + if tool.tests: + for ttb in tool.tests: + test_dict = dict( name=ttb.name, + required_files=ttb.required_files, + inputs=ttb.inputs, + outputs=ttb.outputs ) + tool_tests.append( test_dict ) + tool_dict = dict( id=tool.id, + name=tool.name, + version=tool.version, + description=tool.description, + version_string_cmd = tool.version_string_cmd, + tool_config=os.path.join( root, name ), + requirements=tool_requirements, + tests=tool_tests ) + repository_metadata = get_latest_repository_metadata( trans, id ) + if repository_metadata: + # We have the last RepositoryMetadata record generated for this repository. + metadata = repository_metadata.metadata + if metadata and 'tools' in metadata: + # The metadata for 1 or more tools was successfully generated in the past for this repository.. + metadata_tools = metadata[ 'tools' ] + found = False + for tool_metadata_dict in metadata_tools: + if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ + 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: + # We've found a record for the current tool id and version, so we'll + # update the metadata associated with the record. + found = True + tool_metadata_dict[ 'name' ] = tool.name + tool_metadata_dict[ 'description' ] = tool.description + tool_metadata_dict[ 'version_string_cmd' ] = tool.version_string_cmd + tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) + tool_metadata_dict[ 'requirements' ] = tool_requirements + tool_metadata_dict[ 'tests' ] = tool_tests + if not flush_needed: + flush_needed = True + if found: + repository_metadata.changeset_revision = change_set_revision + else: + if 'tools' in metadata_dict: + metadata_dict[ 'tools' ].append( tool_dict ) + else: + metadata_dict[ 'tools' ] = [ tool_dict ] + if not flush_needed: + flush_needed = True + if not flush_needed: + flush_needed = True + else: + # Either the metadata is Null, or it does not include the key 'tools'. + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'tools' ] = [ tool_dict ] + repository_metadata.changeset_revision = change_set_revision + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + else: + if 'tools' in metadata_dict: + metadata_dict[ 'tools' ].append( tool_dict ) + else: + metadata_dict[ 'tools' ] = [ tool_dict ] + return flush_needed, metadata_dict def set_repository_metadata( trans, id, change_set_revision, **kwd ): """Set repository metadata""" message = '' @@ -105,60 +220,7 @@ try: full_path = os.path.abspath( os.path.join( root, name ) ) tool = load_tool( trans, full_path ) - if tool is not None: - tool_requirements = [] - for tr in tool.requirements: - requirement_dict = dict( name=tr.name, - type=tr.type, - version=tr.version ) - tool_requirements.append( requirement_dict ) - tool_tests = [] - if tool.tests: - for ttb in tool.tests: - test_dict = dict( name=ttb.name, - required_files=ttb.required_files, - inputs=ttb.inputs, - outputs=ttb.outputs ) - tool_tests.append( test_dict ) - tool_dict = dict( id=tool.id, - name=tool.name, - version=tool.version, - description=tool.description, - version_string_cmd = tool.version_string_cmd, - tool_config=os.path.join( root, name ), - requirements=tool_requirements, - tests=tool_tests ) - repository_metadata = get_repository_metadata( trans, id, change_set_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata and 'tools' in metadata: - metadata_tools = metadata[ 'tools' ] - found = False - for tool_metadata_dict in metadata_tools: - if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ - 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: - found = True - tool_metadata_dict[ 'name' ] = tool.name - tool_metadata_dict[ 'description' ] = tool.description - tool_metadata_dict[ 'version_string_cmd' ] = tool.version_string_cmd - tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) - tool_metadata_dict[ 'requirements' ] = tool_requirements - tool_metadata_dict[ 'tests' ] = tool_tests - flush_needed = True - if not found: - metadata_tools.append( tool_dict ) - else: - if metadata is None: - repository_metadata.metadata = {} - repository_metadata.metadata[ 'tools' ] = [ tool_dict ] - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True - else: - if 'tools' in metadata_dict: - metadata_dict[ 'tools' ].append( tool_dict ) - else: - metadata_dict[ 'tools' ] = [ tool_dict ] + flush_needed, metadata_dict = set_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) # Find all exported workflows @@ -170,48 +232,18 @@ workflow_text = fp.read() fp.close() exported_workflow_dict = from_json_string( workflow_text ) - # We'll store everything except the workflow steps in the database. - workflow_dict = { 'a_galaxy_workflow' : exported_workflow_dict[ 'a_galaxy_workflow' ], - 'name' :exported_workflow_dict[ 'name' ], - 'annotation' : exported_workflow_dict[ 'annotation' ], - 'format-version' : exported_workflow_dict[ 'format-version' ] } - repository_metadata = get_repository_metadata( trans, id, change_set_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata and 'workflows' in metadata: - metadata_workflows = metadata[ 'workflows' ] - found = False - for workflow_metadata_dict in metadata_workflows: - if 'a_galaxy_workflow' in workflow_metadata_dict and util.string_as_bool( workflow_metadata_dict[ 'a_galaxy_workflow' ] ) and \ - 'name' in workflow_metadata_dict and workflow_metadata_dict[ 'name' ] == exported_workflow_dict[ 'name' ] and \ - 'annotation' in workflow_metadata_dict and workflow_metadata_dict[ 'annotation' ] == exported_workflow_dict[ 'annotation' ] and \ - 'format-version' in workflow_metadata_dict and workflow_metadata_dict[ 'format-version' ] == exported_workflow_dict[ 'format-version' ]: - found = True - break - if not found: - metadata_workflows.append( workflow_dict ) - else: - if metadata is None: - repository_metadata.metadata = {} - repository_metadata.metadata[ 'workflows' ] = workflow_dict - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True - else: - if 'workflows' in metadata_dict: - metadata_dict[ 'workflows' ].append( workflow_dict ) - else: - metadata_dict[ 'workflows' ] = [ workflow_dict ] + flush_needed, metadata_dict = set_workflowl_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) if metadata_dict: # The metadata_dict dictionary will contain items only # if the repository did not already have metadata set. - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + repository_metadata = trans.model.RepositoryMetadata( repository.id, change_set_revision, metadata_dict ) trans.sa_session.add( repository_metadata ) if not flush_needed: flush_needed = True else: + # change_set is None message = "Repository does not include changeset revision '%s'." % str( change_set_revision ) status = 'error' if invalid_files: @@ -268,7 +300,7 @@ return None def change_set_is_malicious( trans, id, change_set_revision, **kwd ): """Check the malicious flag in repository metadata for a specified change set""" - repository_metadata = get_repository_metadata( trans, id, change_set_revision ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, change_set_revision ) if repository_metadata: return repository_metadata.malicious return False --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Aug 05 14:14:14 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Aug 05 16:22:23 2011 -0400 @@ -549,7 +549,7 @@ trans.sa_session.flush() checked = alerts_checked or ( user and user.email in email_alerts ) alerts_check_box = CheckboxField( 'alerts', checked=checked ) - repository_metadata = get_repository_metadata( trans, id, repository.tip ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, repository.tip ) if repository_metadata: metadata = repository_metadata.metadata else: @@ -678,7 +678,7 @@ allow_push_select_field = self.__build_allow_push_select_field( trans, current_allow_push_list ) checked = alerts_checked or user.email in email_alerts alerts_check_box = CheckboxField( 'alerts', checked=checked ) - repository_metadata = get_repository_metadata( trans, id, repository.tip ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, repository.tip ) if repository_metadata: metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious @@ -860,7 +860,7 @@ def set_metadata( self, trans, id, ctx_str, **kwd ): malicious = kwd.get( 'malicious', '' ) if kwd.get( 'malicious_button', False ): - repository_metadata = get_repository_metadata( trans, id, ctx_str ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, ctx_str ) malicious_checked = CheckboxField.is_checked( malicious ) repository_metadata.malicious = malicious_checked trans.sa_session.add( repository_metadata ) @@ -1018,7 +1018,7 @@ repository = get_repository( trans, repository_id ) metadata = {} tool = None - repository_metadata = get_repository_metadata( trans, repository_id, changeset_revision ).metadata + repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ).metadata if 'tools' in repository_metadata: for tool_metadata_dict in repository_metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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