March 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Add links for set_environment tool dependency type in the Tool dependency definitions Galaxy Utilities grid.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9af8161548a/ changeset: b9af8161548a user: greg date: 2013-03-05 01:47:23 summary: Add links for set_environment tool dependency type in the Tool dependency definitions Galaxy Utilities grid. affected #: 1 file diff -r 26315fa894cefb9192a38ee596f3cb93d8c33e3f -r b9af8161548a17653704304a72d392d2a328cc4b lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -843,12 +843,14 @@ # Example: "set_environment": [{"name": "JAVA_JAR_FILE", "type": "set_environment"}] env_dicts = tds_dict[ 'set_environment' ] num_env_dicts = len( env_dicts ) - td_str += 'environment: ' - for index, env_dict in enumerate( env_dicts ): - td_str += '%s' % escape_html( env_dict[ 'name' ] ) - if index < num_env_dicts - 1: - td_str += ', ' - td_str += ' ' + if num_env_dicts > 0: + td_str += '<a href="browse_datatypes?operation=view_or_manage_repository&id=%s">' % trans.security.encode_id( repository_metadata.id ) + td_str += 'environment: ' + for index, env_dict in enumerate( env_dicts ): + td_str += '%s' % escape_html( env_dict[ 'name' ] ) + if index < num_env_dicts - 1: + td_str += ', ' + td_str += '</a> ' for index, key in enumerate( sorted_keys ): if key == 'set_environment': continue Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Better aggangement of Galaxy utility grid columns in the tool shed, and fix for the Repository Dependency link in the Valid repository dependency definitions Galaxy Utilities grid.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26315fa894ce/ changeset: 26315fa894ce user: greg date: 2013-03-05 01:39:23 summary: Better aggangement of Galaxy utility grid columns in the tool shed, and fix for the Repository Dependency link in the Valid repository dependency definitions Galaxy Utilities grid. affected #: 1 file diff -r 3254331483381a1f9d4be24a81cc4d88a703f8bb -r 26315fa894cefb9192a38ee596f3cb93d8c33e3f lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -9,6 +9,8 @@ from galaxy import eggs eggs.require('markupsafe') from markupsafe import escape as escape_html +eggs.require('mercurial') +from mercurial import hg, ui, patch, commands log = logging.getLogger( __name__ ) @@ -774,7 +776,14 @@ required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if required_repository: required_repository_id = trans.security.encode_id( required_repository.id ) - rd_str += '<a href="browse_repository_dependencies?operation=view_or_manage_repository&id=%s&changeset_revision=%s">' % ( required_repository_id, changeset_revision ) + required_repository_metadata = suc.get_repository_metadata_by_repository_id_changeset_revision( trans, required_repository_id, changeset_revision ) + if not required_repository_metadata: + repo_dir = required_repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + updated_changeset_revision = suc.get_next_downloadable_changeset_revision( required_repository, repo, changeset_revision ) + required_repository_metadata = suc.get_repository_metadata_by_repository_id_changeset_revision( trans, required_repository_id, updated_changeset_revision ) + required_repository_metadata_id = trans.security.encode_id( required_repository_metadata.id ) + rd_str += '<a href="browse_repository_dependencies?operation=view_or_manage_repository&id=%s">' % ( required_repository_metadata_id ) rd_str += 'Repository %s revision %s owned by %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 3 ] ), escape_html( rd_tup[ 2 ] ) ) if required_repository: rd_str += '</a>' @@ -785,6 +794,8 @@ title = "Valid repository dependency definitions in this tool shed" default_sort_key = "Repository.name" columns = [ + RequiredRepositoryColumn( "Repository dependency", + attach_popup=False ), RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -795,12 +806,10 @@ attach_popup=False, key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - RequiredRepositoryColumn( "Repository dependency", - attach_popup=False ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -848,7 +857,9 @@ name = td_dict[ 'name' ] type = td_dict[ 'type' ] version = td_dict[ 'version' ] + td_str += '<a href="browse_datatypes?operation=view_or_manage_repository&id=%s">' % trans.security.encode_id( repository_metadata.id ) td_str += '%s version %s' % ( escape_html( name ), escape_html( version ) ) + td_str += '</a>' if index < num_keys - 1: td_str += ' ' return td_str @@ -856,6 +867,8 @@ title = "Tool dependency definitions in this tool shed" default_sort_key = "Repository.name" columns = [ + ToolDependencyColumn( "Tool dependency", + attach_popup=False ), RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -866,12 +879,10 @@ attach_popup=False, key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - ToolDependencyColumn( "Tool dependency", - attach_popup=False ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -910,7 +921,9 @@ for index, tool_tup in enumerate( sorted_tool_tups ): tool_id = tool_tup[ 0 ] version = tool_tup[ 1 ] + tool_str += '<a href="browse_datatypes?operation=view_or_manage_repository&id=%s">' % trans.security.encode_id( repository_metadata.id ) tool_str += '%s: %s' % ( escape_html( tool_id ), escape_html( version ) ) + tool_str += '</a>' if index < num_tool_tups - 1: tool_str += ' ' return tool_str @@ -918,6 +931,8 @@ title = "Valid tools in this tool shed" default_sort_key = "Repository.name" columns = [ + ToolsColumn( "Tool id and version", + attach_popup=False ), RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -928,12 +943,10 @@ attach_popup=False, key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - ToolsColumn( "Tool id and version", - attach_popup=False ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -975,7 +988,9 @@ for index, datatype_tup in enumerate( sorted_datatype_tups ): extension = datatype_tup[ 0 ] dtype = datatype_tup[ 1 ] + datatype_str += '<a href="browse_datatypes?operation=view_or_manage_repository&id=%s">' % trans.security.encode_id( repository_metadata.id ) datatype_str += '%s: %s' % ( escape_html( extension ), escape_html( dtype ) ) + datatype_str += '</a>' if index < num_datatype_tups - 1: datatype_str += ' ' return datatype_str @@ -983,6 +998,8 @@ title = "Custom datatypes in this tool shed" default_sort_key = "Repository.name" columns = [ + DatatypesColumn( "Datatype extension and class", + attach_popup=False ), RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -993,12 +1010,10 @@ attach_popup=False, key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - DatatypesColumn( "Datatype extension and class", - attach_popup=False ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Speed up the searches for tools and workflows contained in repositories in the tool shed.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/325433148338/ changeset: 325433148338 user: greg date: 2013-03-04 23:21:46 summary: Speed up the searches for tools and workflows contained in repositories in the tool shed. affected #: 1 file diff -r 5705e0578adfb202d1bba0c4b12a9f6344fdd6b7 -r 3254331483381a1f9d4be24a81cc4d88a703f8bb lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1927,73 +1927,80 @@ def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): match_tuples = [] ok = True - for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): - metadata = repository_metadata.metadata - if tool_ids or tool_names or tool_versions: - if 'tools' in metadata: - tools = metadata[ 'tools' ] - else: - tools = [] - for tool_dict in tools: - if tool_ids and not tool_names and not tool_versions: - for tool_id in tool_ids: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_names and not tool_ids and not tool_versions: - for tool_name in tool_names: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_versions and not tool_ids and not tool_names: - for tool_version in tool_versions: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_ids and tool_names and not tool_versions: - if len( tool_ids ) == len( tool_names ): - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - elif len( tool_ids ) == 1 or len( tool_names ) == 1: - tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - else: - ok = False - elif tool_ids and tool_versions and not tool_names: - if len( tool_ids ) == len( tool_versions ): - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - elif len( tool_ids ) == 1 or len( tool_versions ) == 1: - tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and not tool_ids: - if len( tool_versions ) == len( tool_names ): - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - elif len( tool_versions ) == 1 or len( tool_names ) == 1: - tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and tool_ids: - if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): - for i, tool_version in enumerate( tool_versions ): - tool_name = tool_names[ i ] - tool_id = tool_ids[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + if tool_ids or tool_names or tool_versions: + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.includes_tools == True ) \ + .join( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): + metadata = repository_metadata.metadata + if metadata: + tools = metadata.get( 'tools', [] ) + for tool_dict in tools: + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - ok = False - elif workflow_names: - if 'workflows' in metadata: + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + elif len( tool_ids ) == 1 or len( tool_names ) == 1: + tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + else: + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + elif len( tool_ids ) == 1 or len( tool_versions ) == 1: + tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + elif len( tool_versions ) == 1 or len( tool_names ) == 1: + tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and tool_ids: + if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + tool_id = tool_ids[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + ok = False + elif workflow_names or all_workflows: + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.includes_workflows == True ) \ + .join( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): + metadata = repository_metadata.metadata + if metadata: # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - workflow_tups = metadata[ 'workflows' ] - workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] - else: - workflows = [] - for workflow_dict in workflows: - for workflow_name in workflow_names: - if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif all_workflows and 'workflows' in metadata: - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + if workflow_names: + workflow_tups = metadata.get( 'workflows', [] ) + workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] + for workflow_dict in workflows: + for workflow_name in workflow_names: + if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif all_workflows: + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return ok, match_tuples @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Update migrate_tools to the correct path.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5705e0578adf/ changeset: 5705e0578adf user: dannon date: 2013-03-04 20:43:41 summary: Update migrate_tools to the correct path. affected #: 1 file diff -r 7010204f7ccda05f806cfe7f30a6a3bc03a5e2d7 -r 5705e0578adfb202d1bba0c4b12a9f6344fdd6b7 lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py @@ -0,0 +1,44 @@ +""" +Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + # Create the table. + try: + cmd = "UPDATE migrate_tools set repository_path='lib/tool_shed/galaxy_install/migrate';" + db_session.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';" + db_session.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed: %s" % str( e ) ) + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix links in the tool shed's Galaxy utilities grids.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7010204f7ccd/ changeset: 7010204f7ccd user: greg date: 2013-03-04 20:29:23 summary: Fix links in the tool shed's Galaxy utilities grids. affected #: 2 files diff -r 93f0c6867e3427d582f6fba6ca2877ecf472b6d5 -r 7010204f7ccda05f806cfe7f30a6a3bc03a5e2d7 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -82,10 +82,17 @@ def browse_datatypes( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() + # The received id is a RepositoryMetadata id. + repository_metadata_id = kwd[ 'id' ] + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision + new_kwd = dict( id=repository_id, + changeset_revision=changeset_revision ) if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', - **kwd ) ) + **new_kwd ) ) return self.datatypes_grid( trans, **kwd ) @web.expose @@ -256,34 +263,55 @@ def browse_repository_dependencies( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() + # The received id is a RepositoryMetadata id. + repository_metadata_id = kwd[ 'id' ] + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision + new_kwd = dict( id=repository_id, + changeset_revision=changeset_revision ) if operation == "browse_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', - **kwd ) ) + **new_kwd ) ) if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', - **kwd ) ) + **new_kwd ) ) return self.repository_dependencies_grid( trans, **kwd ) @web.expose def browse_tools( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() + # The received id is a RepositoryMetadata id. + repository_metadata_id = kwd['id' ] + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision + new_kwd = dict( id=repository_id, + changeset_revision=changeset_revision ) if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', - **kwd ) ) + **new_kwd ) ) return self.tools_grid( trans, **kwd ) @web.expose def browse_tool_dependencies( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() + # The received id is a RepositoryMetadata id. + repository_metadata_id = kwd[ 'id' ] + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision + new_kwd = dict( id=repository_id, + changeset_revision=changeset_revision ) if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', - **kwd ) ) + **new_kwd ) ) return self.tool_dependencies_grid( trans, **kwd ) @web.expose diff -r 93f0c6867e3427d582f6fba6ca2877ecf472b6d5 -r 7010204f7ccda05f806cfe7f30a6a3bc03a5e2d7 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -787,7 +787,7 @@ columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -858,7 +858,7 @@ columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -920,7 +920,7 @@ columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -985,7 +985,7 @@ columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: call_hook: Fix to handle exception.args more gracefully when modifying
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/93f0c6867e34/ changeset: 93f0c6867e34 user: carlfeberhard date: 2013-03-04 19:51:52 summary: call_hook: Fix to handle exception.args more gracefully when modifying affected #: 1 file diff -r 141c99107f8d2a11a1b91c80ad0ce8e264ee806c -r 93f0c6867e3427d582f6fba6ca2877ecf472b6d5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2715,7 +2715,10 @@ if code: return code( *args, **kwargs ) except Exception, e: - e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ), ) + original_message = '' + if len( e.args ): + original_message = e.args[0] + e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, original_message ), ) raise def exec_before_job( self, app, inp_data, out_data, param_dict={} ): pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Clean up recently introduced tool shed repository Galaxy utilities grids.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/141c99107f8d/ changeset: 141c99107f8d user: greg date: 2013-03-04 19:01:33 summary: Clean up recently introduced tool shed repository Galaxy utilities grids. affected #: 2 files diff -r 8236c09e92011aa2c8c4d4bcd63f0b91de773488 -r 141c99107f8d2a11a1b91c80ad0ce8e264ee806c lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -280,9 +280,9 @@ def browse_tool_dependencies( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() - if operation == "browse_repository": + if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', + action='view_or_manage_repository', **kwd ) ) return self.tool_dependencies_grid( trans, **kwd ) diff -r 8236c09e92011aa2c8c4d4bcd63f0b91de773488 -r 141c99107f8d2a11a1b91c80ad0ce8e264ee806c lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -643,7 +643,10 @@ class ChangesetRevisionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.changeset_revision ) + repository = repository_metadata.repository + changeset_revision = repository_metadata.changeset_revision + changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision ) + return escape_html( changeset_revision_label ) class MaliciousColumn( grids.BooleanColumn ): @@ -719,6 +722,7 @@ default_sort_key = "Repository.name" columns = [ RepositoryNameColumn( "Repository name", + key="Repository.name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ), RepositoryOwnerColumn( "Owner", @@ -743,8 +747,7 @@ .join( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class RepositoryDependenciesGrid( RepositoryMetadataGrid ): @@ -767,22 +770,24 @@ for index, rd_tup in enumerate( sorted_rd_tups ): name = rd_tup[ 1 ] owner = rd_tup[ 2 ] + changeset_revision = rd_tup[ 3 ] required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if required_repository: required_repository_id = trans.security.encode_id( required_repository.id ) - rd_str += '<a href="browse_repository_dependencies?operation=browse_repository&id=%s">' % required_repository_id - rd_str += 'name: %s | owner: %s | revision: %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) ) + rd_str += '<a href="browse_repository_dependencies?operation=view_or_manage_repository&id=%s&changeset_revision=%s">' % ( required_repository_id, changeset_revision ) + rd_str += 'Repository %s revision %s owned by %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 3 ] ), escape_html( rd_tup[ 2 ] ) ) if required_repository: rd_str += '</a>' if index < num_tups - 1: rd_str += ' ' return rd_str - title = "Repository dependency definitions in this tool shed" + title = "Valid repository dependency definitions in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -806,8 +811,7 @@ .filter( and_( model.RepositoryMetadata.table.c.has_repository_dependencies == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class ToolDependenciesGrid( RepositoryMetadataGrid ): @@ -850,10 +854,11 @@ return td_str title = "Tool dependency definitions in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -877,8 +882,7 @@ .filter( and_( model.RepositoryMetadata.table.c.includes_tool_dependencies == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class ToolsGrid( RepositoryMetadataGrid ): @@ -893,21 +897,30 @@ if metadata: tool_dicts = metadata.get( 'tools', [] ) if tool_dicts: - num_tool_dicts = len( tool_dicts ) - for index, tool_dict in enumerate( tool_dicts ): - tool_id = tool_dict[ 'id' ] - name = tool_dict[ 'name' ] - version = tool_dict[ 'version' ] - tool_str += '%s | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) ) - if index < num_tool_dicts - 1: + # Create tuples of the attributes we want so we can sort them by extension. + tool_tups = [] + for tool_dict in tool_dicts: + tool_id = tool_dict.get( 'id', '' ) + version = tool_dict.get( 'version', '' ) + # For now we'll just display tool id and version. + if tool_id and version: + tool_tups.append( ( tool_id, version ) ) + sorted_tool_tups = sorted( tool_tups, key=lambda tool_tup: tool_tup[ 0 ] ) + num_tool_tups = len( sorted_tool_tups ) + for index, tool_tup in enumerate( sorted_tool_tups ): + tool_id = tool_tup[ 0 ] + version = tool_tup[ 1 ] + tool_str += '%s: %s' % ( escape_html( tool_id ), escape_html( version ) ) + if index < num_tool_tups - 1: tool_str += ' ' return tool_str title = "Valid tools in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -916,7 +929,7 @@ key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", attach_popup=False ), - ToolsColumn( "Tool id | name | version", + ToolsColumn( "Tool id and version", attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", @@ -931,8 +944,7 @@ .filter( and_( model.RepositoryMetadata.table.c.includes_tools == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class DatatypesGrid( RepositoryMetadataGrid ): @@ -947,23 +959,33 @@ if metadata: datatype_dicts = metadata.get( 'datatypes', [] ) if datatype_dicts: - num_datatype_dicts = len( datatype_dicts ) - for index, datatype_dict in enumerate( datatype_dicts ): + # Create tuples of the attributes we want so we can sort them by extension. + datatype_tups = [] + for datatype_dict in datatype_dicts: # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} extension = datatype_dict.get( 'extension', '' ) dtype = datatype_dict.get( 'dtype', '' ) mimetype = datatype_dict.get( 'mimetype', '' ) display_in_upload = datatype_dict.get( 'display_in_upload', False ) - datatype_str += '%s | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) - if index < num_datatype_dicts - 1: + # For now we'll just display extension and dtype. + if extension and dtype: + datatype_tups.append( ( extension, dtype ) ) + sorted_datatype_tups = sorted( datatype_tups, key=lambda datatype_tup: datatype_tup[ 0 ] ) + num_datatype_tups = len( sorted_datatype_tups ) + for index, datatype_tup in enumerate( sorted_datatype_tups ): + extension = datatype_tup[ 0 ] + dtype = datatype_tup[ 1 ] + datatype_str += '%s: %s' % ( escape_html( extension ), escape_html( dtype ) ) + if index < num_datatype_tups - 1: datatype_str += ' ' return datatype_str title = "Custom datatypes in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -972,7 +994,7 @@ key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", attach_popup=False ), - DatatypesColumn( "Datatype extension | Type | Mimetype", + DatatypesColumn( "Datatype extension and class", attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", @@ -987,5 +1009,4 @@ .filter( and_( model.RepositoryMetadata.table.c.includes_datatypes == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/32c6537bef27/ changeset: 32c6537bef27 user: jmchilton date: 2013-02-26 06:09:22 summary: Implement equivalent of dataset display through the API. affected #: 4 files diff -r 993c232d34cda550a5605f87d7416467d4e2c33f -r 32c6537bef27b7d481aed08a7189f11c5161a3ee lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py +++ b/lib/galaxy/web/__init__.py @@ -2,6 +2,6 @@ The Galaxy web application framework """ -from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder, expose_api +from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder, expose_api, expose_api_raw from framework.base import httpexceptions diff -r 993c232d34cda550a5605f87d7416467d4e2c33f -r 32c6537bef27b7d481aed08a7189f11c5161a3ee lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -99,7 +99,14 @@ return decorator return argcatcher -def expose_api( func ): +def expose_api_raw( func ): + """ + Expose this function via the API but don't dump the results + to JSON. + """ + return expose_api( func, to_json=False ) + +def expose_api( func, to_json=True ): @wraps(func) def decorator( self, trans, *args, **kwargs ): def error( environ, start_response ): @@ -183,10 +190,12 @@ trans.response.status = 400 return "That user does not exist." try: - if trans.debug: - return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) - else: - return simplejson.dumps( func( self, trans, *args, **kwargs ) ) + rval = func( self, trans, *args, **kwargs) + if to_json and trans.debug: + rval = simplejson.dumps( rval, indent=4, sort_keys=True ) + elif to_json: + rval = simplejson.dumps( rval ) + return rval except paste.httpexceptions.HTTPException: raise # handled except: diff -r 993c232d34cda550a5605f87d7416467d4e2c33f -r 32c6537bef27b7d481aed08a7189f11c5161a3ee lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -125,6 +125,33 @@ 'error' : str( exception ) } + @web.expose_api_raw + def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): + """ + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} + Displays history content (dataset). + """ + hda_dict = {} + try: + # for anon users: + #TODO: check login_required? + #TODO: this isn't actually most_recently_used (as defined in histories) + if( ( trans.user == None ) + and ( history_id == trans.security.encode_id( trans.history.id ) ) ): + history = trans.history + #TODO: dataset/hda by id (from history) OR check_ownership for anon user + hda = self.get_history_dataset_association( trans, history, history_content_id, + check_ownership=False, check_accessible=True ) + + else: + history = self.get_history( trans, history_id, + check_ownership=True, check_accessible=True, deleted=False ) + hda = self.get_history_dataset_association( trans, history, history_content_id, + check_ownership=True, check_accessible=True ) + except: + raise + return hda.datatype.display_data(trans, hda, preview, filename, to_ext, chunk, **kwd) + @web.expose_api def show( self, trans, id, history_id, **kwd ): """ diff -r 993c232d34cda550a5605f87d7416467d4e2c33f -r 32c6537bef27b7d481aed08a7189f11c5161a3ee lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -83,6 +83,11 @@ name_prefix='history_', path_prefix='/api/histories/:history_id', parent_resources=dict( member_name='history', collection_name='histories' ) ) + webapp.api_mapper.connect("history_contents_display", + "/api/histories/:history_id/contents/:history_content_id/display", + controller="history_contents", + action="display", + conditions=dict(method=["GET"])) webapp.api_mapper.resource( 'permission', 'permissions', path_prefix='/api/libraries/:library_id', https://bitbucket.org/galaxy/galaxy-central/commits/3284b58ae9fd/ changeset: 3284b58ae9fd user: jmchilton date: 2013-02-26 16:56:15 summary: Update HDA API return value to reflect new API-based path for downloads. affected #: 1 file diff -r 32c6537bef27b7d481aed08a7189f11c5161a3ee -r 3284b58ae9fd65dd276d0faa2ed930f245c9df5d lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -155,7 +155,7 @@ @web.expose_api def show( self, trans, id, history_id, **kwd ): """ - GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display Displays information about a history content (dataset). """ hda_dict = {} @@ -230,14 +230,7 @@ hda_dict[ 'file_name' ] = hda.file_name if not hda_dict[ 'deleted' ]: - # Problem: Method url_for cannot use the dataset controller - # Get the environment from DefaultWebTransaction - # and use default webapp mapper instead of webapp API mapper - web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ ) - # http://routes.groovie.org/generating.html - # url_for is being phased out, so new applications should use url - hda_dict[ 'download_url' ] = web_url_for( controller='dataset', action='display', - dataset_id=trans.security.encode_id( hda.id ), to_ext=hda.ext ) + hda_dict[ 'download_url' ] = url_for( 'history_contents_display', history_id = trans.security.encode_id( history.id ), history_content_id = trans.security.encode_id( hda.id ) ) can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda ) https://bitbucket.org/galaxy/galaxy-central/commits/440cad876d23/ changeset: 440cad876d23 user: jmchilton date: 2013-02-26 16:59:40 summary: In previous commit, I modified documentation in the wrong place. affected #: 1 file diff -r 3284b58ae9fd65dd276d0faa2ed930f245c9df5d -r 440cad876d23f467bf4ad63ac26a9fe7c4c5eeed lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -128,7 +128,7 @@ @web.expose_api_raw def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): """ - GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display Displays history content (dataset). """ hda_dict = {} @@ -155,7 +155,7 @@ @web.expose_api def show( self, trans, id, history_id, **kwd ): """ - GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} Displays information about a history content (dataset). """ hda_dict = {} https://bitbucket.org/galaxy/galaxy-central/commits/a2424331a3f9/ changeset: a2424331a3f9 user: jmchilton date: 2013-03-04 17:32:32 summary: Per Jeremy's request I have moved the API history contents dataset display functionality to the dataset controller - https://bitbucket.org/galaxy/galaxy-central/pull-request/131/implement-equi…. affected #: 3 files diff -r 440cad876d23f467bf4ad63ac26a9fe7c4c5eeed -r a2424331a3f929bfadafea1dedbab5fb4b651472 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -4,12 +4,12 @@ import logging, os, string, shutil, urllib, re, socket from galaxy import util, datatypes, jobs, web, util from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider -from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin +from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin from galaxy.web.framework.helpers import is_true log = logging.getLogger( __name__ ) -class DatasetsController( BaseAPIController, UsesVisualizationMixin ): +class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin ): @web.expose_api def index( self, trans, **kwd ): @@ -191,3 +191,31 @@ data = data_provider.get_data( **kwargs ) return data + + @web.expose_api_raw + def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): + """ + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display + Displays history content (dataset). + """ + # Huge amount of code overlap with lib/galaxy/webapps/galaxy/api/history_content:show here. + hda_dict = {} + try: + # for anon users: + #TODO: check login_required? + #TODO: this isn't actually most_recently_used (as defined in histories) + if( ( trans.user == None ) + and ( history_id == trans.security.encode_id( trans.history.id ) ) ): + history = trans.history + #TODO: dataset/hda by id (from history) OR check_ownership for anon user + hda = self.get_history_dataset_association( trans, history, history_content_id, + check_ownership=False, check_accessible=True ) + + else: + history = self.get_history( trans, history_id, + check_ownership=True, check_accessible=True, deleted=False ) + hda = self.get_history_dataset_association( trans, history, history_content_id, + check_ownership=True, check_accessible=True ) + except: + raise + return hda.datatype.display_data(trans, hda, preview, filename, to_ext, chunk, **kwd) diff -r 440cad876d23f467bf4ad63ac26a9fe7c4c5eeed -r a2424331a3f929bfadafea1dedbab5fb4b651472 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -125,33 +125,6 @@ 'error' : str( exception ) } - @web.expose_api_raw - def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): - """ - GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display - Displays history content (dataset). - """ - hda_dict = {} - try: - # for anon users: - #TODO: check login_required? - #TODO: this isn't actually most_recently_used (as defined in histories) - if( ( trans.user == None ) - and ( history_id == trans.security.encode_id( trans.history.id ) ) ): - history = trans.history - #TODO: dataset/hda by id (from history) OR check_ownership for anon user - hda = self.get_history_dataset_association( trans, history, history_content_id, - check_ownership=False, check_accessible=True ) - - else: - history = self.get_history( trans, history_id, - check_ownership=True, check_accessible=True, deleted=False ) - hda = self.get_history_dataset_association( trans, history, history_content_id, - check_ownership=True, check_accessible=True ) - except: - raise - return hda.datatype.display_data(trans, hda, preview, filename, to_ext, chunk, **kwd) - @web.expose_api def show( self, trans, id, history_id, **kwd ): """ diff -r 440cad876d23f467bf4ad63ac26a9fe7c4c5eeed -r a2424331a3f929bfadafea1dedbab5fb4b651472 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -85,7 +85,7 @@ parent_resources=dict( member_name='history', collection_name='histories' ) ) webapp.api_mapper.connect("history_contents_display", "/api/histories/:history_id/contents/:history_content_id/display", - controller="history_contents", + controller="datasets", action="display", conditions=dict(method=["GET"])) webapp.api_mapper.resource( 'permission', https://bitbucket.org/galaxy/galaxy-central/commits/8236c09e9201/ changeset: 8236c09e9201 user: dannon date: 2013-03-04 18:06:15 summary: Merged in galaxyp/galaxy-central-parallelism-refactorings (pull request #131) Implement equivalent of dataset display through the API. affected #: 5 files Diff not available. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Move the tool shed's repository review grid classes out of the repository_review controller and into ~/tool_shed/grids.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cd3270cefc61/ changeset: cd3270cefc61 user: greg date: 2013-03-04 16:07:31 summary: Move the tool shed's repository review grid classes out of the repository_review controller and into ~/tool_shed/grids. affected #: 2 files diff -r 6cd65073a397246e7b6fa8884d2c26760865ffad -r cd3270cefc612315602e43e1a41a17e0f92dec1d lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -2,15 +2,12 @@ from galaxy import web, util from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import SelectField, CheckboxField -from galaxy.webapps.tool_shed import model -from galaxy.web.framework.helpers import grids -from galaxy.model.orm import and_ from sqlalchemy.sql.expression import func from galaxy.webapps.tool_shed.util import common_util from galaxy.webapps.tool_shed.util.container_util import STRSEP -from tool_shed.grids.repository_grids import RepositoryGrid import tool_shed.util.shed_util_common as suc from galaxy.util.odict import odict +import tool_shed.grids.repository_review_grids as repository_review_grids from galaxy import eggs eggs.require('mercurial') @@ -18,259 +15,15 @@ log = logging.getLogger( __name__ ) -class ComponentGrid( grids.Grid ): - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, component ): - return component.name - class DescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, component ): - return component.description - title = "Repository review components" - model_class = model.Component - template='/webapps/tool_shed/repository_review/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - key="Component.name", - link=( lambda item: dict( operation="edit", id=item.id ) ), - attach_popup=False ), - DescriptionColumn( "Description", - key="Component.description", - attach_popup=False ) - ] - default_filter = {} - global_actions = [ - grids.GridAction( "Add new component", - dict( controller='repository_review', action='manage_components', operation='create' ) ) - ] - operations = [] - standard_filters = [] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - -class RepositoriesWithReviewsGrid( RepositoryGrid ): - # This grid filters out repositories that have been marked as either deprecated or deleted. - class WithReviewsRevisionColumn( grids.GridColumn ): - def get_value( self, trans, grid, repository ): - # Restrict to revisions that have been reviewed. - if repository.reviews: - rval = '' - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - for review in repository.reviews: - changeset_revision = review.changeset_revision - rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) - rval += '<a href="manage_repository_reviews_of_revision' - rval += '?id=%s&changeset_revision=%s">%s</a> ' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) - return rval - return '' - class WithoutReviewsRevisionColumn( grids.GridColumn ): - def get_value( self, trans, grid, repository ): - # Restrict the options to revisions that have not yet been reviewed. - repository_metadata_revisions = suc.get_repository_metadata_revisions_for_review( repository, reviewed=False ) - if repository_metadata_revisions: - rval = '' - for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) - rval += '<a href="manage_repository_reviews_of_revision' - rval += '?id=%s&changeset_revision=%s">%s</a> ' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) - return rval - return '' - class ReviewersColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository ): - rval = '' - if repository.reviewers: - for user in repository.reviewers: - rval += '<a class="view-info" href="repository_reviews_by_user?id=%s">' % trans.security.encode_id( user.id ) - rval += '%s</a> | ' % user.username - rval = rval.rstrip( ' | ' ) - return rval - title = "All reviewed repositories" - model_class = model.Repository - template='/webapps/tool_shed/repository_review/grid.mako' - default_sort_key = "Repository.name" - columns = [ - RepositoryGrid.NameColumn( "Repository name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - WithReviewsRevisionColumn( "Reviewed revisions" ), - WithoutReviewsRevisionColumn( "Revisions for review" ), - RepositoryGrid.UserColumn( "Owner", attach_popup=False ), - ReviewersColumn( "Reviewers", attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ - grids.GridOperation( "Inspect repository revisions", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) - ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ - .join( ( model.User.table, model.User.table.c.id == model.Repository.table.c.user_id ) ) \ - .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ - .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) - -class RepositoriesWithoutReviewsGrid( RepositoriesWithReviewsGrid ): - # This grid filters out repositories that have been marked as either deprecated or deleted. - title = "Repositories with no reviews" - columns = [ - RepositoriesWithReviewsGrid.NameColumn( "Repository name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoriesWithReviewsGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), - RepositoriesWithReviewsGrid.UserColumn( "Owner", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ grids.GridOperation( "Inspect repository revisions", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False, - model.Repository.reviews == None ) ) \ - .join( model.User.table ) - -class RepositoriesReviewedByMeGrid( RepositoriesWithReviewsGrid ): - # This grid filters out repositories that have been marked as either deprecated or deleted. - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ - .filter( model.RepositoryReview.table.c.user_id == trans.user.id ) \ - .join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \ - .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ - .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) - -class RepositoryReviewsByUserGrid( grids.Grid ): - # This grid filters out repositories that have been marked as deprecated. - class RepositoryNameColumn( grids.TextColumn ): - def get_value( self, trans, grid, review ): - return review.repository.name - class RepositoryDescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, review ): - return review.repository.description - class RevisionColumn( grids.TextColumn ): - def get_value( self, trans, grid, review ): - encoded_review_id = trans.security.encode_id( review.id ) - rval = '<a class="action-button" href="' - if review.user == trans.user: - rval += 'edit_review' - else: - rval +='browse_review' - rval += '?id=%s">%s</a>' % ( encoded_review_id, suc.get_revision_label( trans, review.repository, review.changeset_revision ) ) - return rval - class RatingColumn( grids.TextColumn ): - def get_value( self, trans, grid, review ): - if review.rating: - rval = '<input ' - rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) - rval += 'type="radio" ' - rval += 'class="community_rating_star star" ' - rval += 'disabled="disabled" ' - rval += 'value="%s"' % str( review.rating ) - rval += '/>' - return rval - return '' - title = "Reviews by user" - model_class = model.RepositoryReview - template='/webapps/tool_shed/repository_review/grid.mako' - default_sort_key = 'repository_id' - columns = [ - RepositoryNameColumn( "Repository Name", - model_class=model.Repository, - key="Repository.name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoryDescriptionColumn( "Description", - model_class=model.Repository, - key="Repository.description", - attach_popup=False ), - RevisionColumn( "Revision", attach_popup=False ), - RatingColumn( "Rating", attach_popup=False ), - ] - # Override these - default_filter = {} - global_actions = [] - operations = [ - grids.GridOperation( "Inspect repository revisions", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) - ] - standard_filters = [] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - def build_initial_query( self, trans, **kwd ): - user_id = trans.security.decode_id( kwd[ 'id' ] ) - return trans.sa_session.query( model.RepositoryReview ) \ - .filter( and_( model.RepositoryReview.table.c.deleted == False, \ - model.RepositoryReview.table.c.user_id == user_id ) ) \ - .join( ( model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ - .filter( model.Repository.table.c.deprecated == False ) - -class ReviewedRepositoriesIOwnGrid( RepositoriesWithReviewsGrid ): - title = "Reviewed repositories I own" - columns = [ - RepositoriesWithReviewsGrid.NameColumn( "Repository name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoriesWithReviewsGrid.WithReviewsRevisionColumn( "Reviewed revisions" ), - RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), - RepositoriesWithReviewsGrid.ReviewersColumn( "Reviewers", attach_popup=False ), - RepositoryGrid.DeprecatedColumn( "Deprecated" ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ - grids.GridOperation( "Inspect repository revisions", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) - ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ - .filter( model.Repository.table.c.user_id == trans.user.id ) \ - .join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \ - .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ - .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) class RepositoryReviewController( BaseUIController, common_util.ItemRatings ): - component_grid = ComponentGrid() - repositories_reviewed_by_me_grid = RepositoriesReviewedByMeGrid() - repositories_with_reviews_grid = RepositoriesWithReviewsGrid() - repositories_without_reviews_grid = RepositoriesWithoutReviewsGrid() - repository_reviews_by_user_grid = RepositoryReviewsByUserGrid() - reviewed_repositories_i_own_grid = ReviewedRepositoriesIOwnGrid() + component_grid = repository_review_grids.ComponentGrid() + repositories_reviewed_by_me_grid = repository_review_grids.RepositoriesReviewedByMeGrid() + repositories_with_reviews_grid = repository_review_grids.RepositoriesWithReviewsGrid() + repositories_without_reviews_grid = repository_review_grids.RepositoriesWithoutReviewsGrid() + repository_reviews_by_user_grid = repository_review_grids.RepositoryReviewsByUserGrid() + reviewed_repositories_i_own_grid = repository_review_grids.ReviewedRepositoriesIOwnGrid() @web.expose @web.require_login( "approve repository review" ) diff -r 6cd65073a397246e7b6fa8884d2c26760865ffad -r cd3270cefc612315602e43e1a41a17e0f92dec1d lib/tool_shed/grids/repository_review_grids.py --- /dev/null +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -0,0 +1,258 @@ +import os, logging +from galaxy.webapps.tool_shed import model +from galaxy.web.framework.helpers import grids +from galaxy.model.orm import and_ +from tool_shed.grids.repository_grids import RepositoryGrid +import tool_shed.util.shed_util_common as suc + +from galaxy import eggs +eggs.require('mercurial') +from mercurial import hg, ui, patch, commands + +log = logging.getLogger( __name__ ) + +class ComponentGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, component ): + return component.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, component ): + return component.description + title = "Repository review components" + model_class = model.Component + template='/webapps/tool_shed/repository_review/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="Component.name", + link=( lambda item: dict( operation="edit", id=item.id ) ), + attach_popup=False ), + DescriptionColumn( "Description", + key="Component.description", + attach_popup=False ) + ] + default_filter = {} + global_actions = [ + grids.GridAction( "Add new component", + dict( controller='repository_review', action='manage_components', operation='create' ) ) + ] + operations = [] + standard_filters = [] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + +class RepositoriesWithReviewsGrid( RepositoryGrid ): + # This grid filters out repositories that have been marked as either deprecated or deleted. + class WithReviewsRevisionColumn( grids.GridColumn ): + def get_value( self, trans, grid, repository ): + # Restrict to revisions that have been reviewed. + if repository.reviews: + rval = '' + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + for review in repository.reviews: + changeset_revision = review.changeset_revision + rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rval += '<a href="manage_repository_reviews_of_revision' + rval += '?id=%s&changeset_revision=%s">%s</a> ' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) + return rval + return '' + class WithoutReviewsRevisionColumn( grids.GridColumn ): + def get_value( self, trans, grid, repository ): + # Restrict the options to revisions that have not yet been reviewed. + repository_metadata_revisions = suc.get_repository_metadata_revisions_for_review( repository, reviewed=False ) + if repository_metadata_revisions: + rval = '' + for repository_metadata in repository_metadata_revisions: + rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository ) + rval += '<a href="manage_repository_reviews_of_revision' + rval += '?id=%s&changeset_revision=%s">%s</a> ' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) + return rval + return '' + class ReviewersColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): + rval = '' + if repository.reviewers: + for user in repository.reviewers: + rval += '<a class="view-info" href="repository_reviews_by_user?id=%s">' % trans.security.encode_id( user.id ) + rval += '%s</a> | ' % user.username + rval = rval.rstrip( ' | ' ) + return rval + title = "All reviewed repositories" + model_class = model.Repository + template='/webapps/tool_shed/repository_review/grid.mako' + default_sort_key = "Repository.name" + columns = [ + RepositoryGrid.NameColumn( "Repository name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + WithReviewsRevisionColumn( "Reviewed revisions" ), + WithoutReviewsRevisionColumn( "Revisions for review" ), + RepositoryGrid.UserColumn( "Owner", attach_popup=False ), + ReviewersColumn( "Reviewers", attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ + grids.GridOperation( "Inspect repository revisions", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) + ] + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ + .join( ( model.User.table, model.User.table.c.id == model.Repository.table.c.user_id ) ) \ + .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ + .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) + +class RepositoriesWithoutReviewsGrid( RepositoriesWithReviewsGrid ): + # This grid filters out repositories that have been marked as either deprecated or deleted. + title = "Repositories with no reviews" + columns = [ + RepositoriesWithReviewsGrid.NameColumn( "Repository name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoriesWithReviewsGrid.DescriptionColumn( "Synopsis", + key="description", + attach_popup=False ), + RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), + RepositoriesWithReviewsGrid.UserColumn( "Owner", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, description", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ grids.GridOperation( "Inspect repository revisions", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) ] + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False, + model.Repository.reviews == None ) ) \ + .join( model.User.table ) + +class RepositoriesReviewedByMeGrid( RepositoriesWithReviewsGrid ): + # This grid filters out repositories that have been marked as either deprecated or deleted. + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ + .filter( model.RepositoryReview.table.c.user_id == trans.user.id ) \ + .join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \ + .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ + .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) + +class RepositoryReviewsByUserGrid( grids.Grid ): + # This grid filters out repositories that have been marked as deprecated. + class RepositoryNameColumn( grids.TextColumn ): + def get_value( self, trans, grid, review ): + return review.repository.name + class RepositoryDescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, review ): + return review.repository.description + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, review ): + encoded_review_id = trans.security.encode_id( review.id ) + rval = '<a class="action-button" href="' + if review.user == trans.user: + rval += 'edit_review' + else: + rval +='browse_review' + rval += '?id=%s">%s</a>' % ( encoded_review_id, suc.get_revision_label( trans, review.repository, review.changeset_revision ) ) + return rval + class RatingColumn( grids.TextColumn ): + def get_value( self, trans, grid, review ): + if review.rating: + rval = '<input ' + rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) + rval += 'type="radio" ' + rval += 'class="community_rating_star star" ' + rval += 'disabled="disabled" ' + rval += 'value="%s"' % str( review.rating ) + rval += '/>' + return rval + return '' + title = "Reviews by user" + model_class = model.RepositoryReview + template='/webapps/tool_shed/repository_review/grid.mako' + default_sort_key = 'repository_id' + columns = [ + RepositoryNameColumn( "Repository Name", + model_class=model.Repository, + key="Repository.name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoryDescriptionColumn( "Description", + model_class=model.Repository, + key="Repository.description", + attach_popup=False ), + RevisionColumn( "Revision", attach_popup=False ), + RatingColumn( "Rating", attach_popup=False ), + ] + # Override these + default_filter = {} + global_actions = [] + operations = [ + grids.GridOperation( "Inspect repository revisions", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) + ] + standard_filters = [] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + user_id = trans.security.decode_id( kwd[ 'id' ] ) + return trans.sa_session.query( model.RepositoryReview ) \ + .filter( and_( model.RepositoryReview.table.c.deleted == False, \ + model.RepositoryReview.table.c.user_id == user_id ) ) \ + .join( ( model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ + .filter( model.Repository.table.c.deprecated == False ) + +class ReviewedRepositoriesIOwnGrid( RepositoriesWithReviewsGrid ): + title = "Reviewed repositories I own" + columns = [ + RepositoriesWithReviewsGrid.NameColumn( "Repository name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoriesWithReviewsGrid.WithReviewsRevisionColumn( "Reviewed revisions" ), + RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), + RepositoriesWithReviewsGrid.ReviewersColumn( "Reviewers", attach_popup=False ), + RepositoryGrid.DeprecatedColumn( "Deprecated" ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ + grids.GridOperation( "Inspect repository revisions", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) + ] + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ + .filter( model.Repository.table.c.user_id == trans.user.id ) \ + .join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \ + .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ + .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) + \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Move the tool shed's administrative grids out of the admin controller and into ~/tool_shed/grids.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6cd65073a397/ changeset: 6cd65073a397 user: greg date: 2013-03-04 15:47:37 summary: Move the tool shed's administrative grids out of the admin controller and into ~/tool_shed/grids. affected #: 3 files diff -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 -r 6cd65073a397246e7b6fa8884d2c26760865ffad lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -1,12 +1,9 @@ from galaxy.web.base.controller import BaseUIController from galaxy import web, util from galaxy.web.base.controllers.admin import Admin -from galaxy.webapps.tool_shed import model -from galaxy.model.orm import and_ -from galaxy.web.framework.helpers import time_ago, grids from galaxy.util import inflector import tool_shed.util.shed_util_common as suc -from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid +import tool_shed.grids.admin_grids as admin_grids from galaxy import eggs eggs.require( 'mercurial' ) @@ -16,440 +13,15 @@ log = logging.getLogger( __name__ ) -class UserGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. - class UserLoginColumn( grids.TextColumn ): - def get_value( self, trans, grid, user ): - return user.email - class UserNameColumn( grids.TextColumn ): - def get_value( self, trans, grid, user ): - if user.username: - return user.username - return 'not set' - class GroupsColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.groups: - return len( user.groups ) - return 0 - class RolesColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.roles: - return len( user.roles ) - return 0 - class ExternalColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.external: - return 'yes' - return 'no' - class LastLoginColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.galaxy_sessions: - return self.format( user.galaxy_sessions[ 0 ].update_time ) - return 'never' - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.purged: - return "purged" - elif user.deleted: - return "deleted" - return "" - class EmailColumn( grids.GridColumn ): - def filter( self, trans, user, query, column_filter ): - if column_filter == 'All': - return query - return query.filter( and_( model.Tool.table.c.user_id == model.User.table.c.id, - model.User.table.c.email == column_filter ) ) - title = "Users" - model_class = model.User - template='/admin/user/grid.mako' - default_sort_key = "email" - columns = [ - UserLoginColumn( "Email", - key="email", - link=( lambda item: dict( operation="information", id=item.id ) ), - attach_popup=True, - filterable="advanced" ), - UserNameColumn( "User Name", - key="username", - attach_popup=False, - filterable="advanced" ), - GroupsColumn( "Groups", attach_popup=False ), - RolesColumn( "Roles", attach_popup=False ), - ExternalColumn( "External", attach_popup=False ), - LastLoginColumn( "Last Login", format=time_ago ), - StatusColumn( "Status", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - EmailColumn( "Email", - key="email", - visible=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Create new user", - dict( controller='admin', action='users', operation='create' ) ) - ] - operations = [ - grids.GridOperation( "Manage Roles and Groups", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="manage_roles_and_groups_for_user" ) ), - grids.GridOperation( "Reset Password", - condition=( lambda item: not item.deleted ), - allow_multiple=True, - allow_popup=False, - url_args=dict( action="reset_user_password" ) ) - ] - standard_filters = [ - grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), - grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ), - grids.GridColumnFilter( "Purged", args=dict( purged=True ) ), - grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) - ] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - def get_current_item( self, trans, **kwargs ): - return trans.user - -class RoleGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, role ): - return role.name - class DescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, role ): - if role.description: - return role.description - return '' - class TypeColumn( grids.TextColumn ): - def get_value( self, trans, grid, role ): - return role.type - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, role ): - if role.deleted: - return "deleted" - return "" - class GroupsColumn( grids.GridColumn ): - def get_value( self, trans, grid, role ): - if role.groups: - return len( role.groups ) - return 0 - class UsersColumn( grids.GridColumn ): - def get_value( self, trans, grid, role ): - if role.users: - return len( role.users ) - return 0 - title = "Roles" - model_class = model.Role - template='/admin/dataset_security/role/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="Manage users and groups", id=item.id ) ), - attach_popup=True, - filterable="advanced" ), - DescriptionColumn( "Description", - key='description', - attach_popup=False, - filterable="advanced" ), - TypeColumn( "Type", - key='type', - attach_popup=False, - filterable="advanced" ), - GroupsColumn( "Groups", attach_popup=False ), - UsersColumn( "Users", attach_popup=False ), - StatusColumn( "Status", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) - ] - columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Add new role", - dict( controller='admin', action='roles', operation='create' ) ) - ] - operations = [ grids.GridOperation( "Rename", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="rename_role" ) ), - grids.GridOperation( "Delete", - condition=( lambda item: not item.deleted ), - allow_multiple=True, - url_args=dict( action="mark_role_deleted" ) ), - grids.GridOperation( "Undelete", - condition=( lambda item: item.deleted ), - allow_multiple=True, - url_args=dict( action="undelete_role" ) ), - grids.GridOperation( "Purge", - condition=( lambda item: item.deleted ), - allow_multiple=True, - url_args=dict( action="purge_role" ) ) ] - standard_filters = [ - grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), - grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), - grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) - ] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - def apply_query_filter( self, trans, query, **kwd ): - return query.filter( model.Role.type != model.Role.types.PRIVATE ) - -class GroupGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, group ): - return group.name - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, group ): - if group.deleted: - return "deleted" - return "" - class RolesColumn( grids.GridColumn ): - def get_value( self, trans, grid, group ): - if group.roles: - return len( group.roles ) - return 0 - class UsersColumn( grids.GridColumn ): - def get_value( self, trans, grid, group ): - if group.members: - return len( group.members ) - return 0 - title = "Groups" - model_class = model.Group - template='/admin/dataset_security/group/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - link=( lambda item: dict( operation="Manage users and roles", id=item.id ) ), - attach_popup=True ), - UsersColumn( "Users", attach_popup=False ), - RolesColumn( "Roles", attach_popup=False ), - StatusColumn( "Status", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) - ] - columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Add new group", - dict( controller='admin', action='groups', operation='create' ) ) - ] - operations = [ grids.GridOperation( "Rename", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="rename_group" ) ), - grids.GridOperation( "Delete", - condition=( lambda item: not item.deleted ), - allow_multiple=True, - url_args=dict( action="mark_group_deleted" ) ), - grids.GridOperation( "Undelete", - condition=( lambda item: item.deleted ), - allow_multiple=True, - url_args=dict( action="undelete_group" ) ), - grids.GridOperation( "Purge", - condition=( lambda item: item.deleted ), - allow_multiple=True, - url_args=dict( action="purge_group" ) ) ] - standard_filters = [ - grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), - grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), - grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) - ] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - -class ManageCategoryGrid( CategoryGrid ): - columns = [ col for col in CategoryGrid.columns ] - # Override the NameColumn to include an Edit link - columns[ 0 ] = CategoryGrid.NameColumn( "Name", - key="Category.name", - link=( lambda item: dict( operation="Edit", id=item.id ) ), - model_class=model.Category, - attach_popup=False ) - global_actions = [ - grids.GridAction( "Add new category", - dict( controller='admin', action='manage_categories', operation='create' ) ) - ] - -class AdminRepositoryGrid( RepositoryGrid ): - class DeletedColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository ): - if repository.deleted: - return 'yes' - return '' - columns = [ RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoryGrid.UserColumn( "Owner", - model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), - attach_popup=False, - key="User.username" ), - RepositoryGrid.DeprecatedColumn( "Deprecated", key="deprecated", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", attach_popup=False ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ operation for operation in RepositoryGrid.operations ] - operations.append( grids.GridOperation( "Delete", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ) - operations.append( grids.GridOperation( "Undelete", - allow_multiple=False, - condition=( lambda item: item.deleted ), - async_compatible=False ) ) - standard_filters = [] - default_filter = {} - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .join( model.User.table ) - -class RepositoryMetadataGrid( grids.Grid ): - class IdColumn( grids.IntegerColumn ): - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.id - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.name - class OwnerColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.user.username - class RevisionColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - repository = repository_metadata.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) - class ToolsColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - tools_str = '0' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'tools' in metadata: - # We used to display the following, but grid was too cluttered. - #for tool_metadata_dict in metadata[ 'tools' ]: - # tools_str += '%s %s ' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) - return '%d' % len( metadata[ 'tools' ] ) - return tools_str - class DatatypesColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - datatypes_str = '0' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'datatypes' in metadata: - # We used to display the following, but grid was too cluttered. - #for datatype_metadata_dict in metadata[ 'datatypes' ]: - # datatypes_str += '%s ' % datatype_metadata_dict[ 'extension' ] - return '%d' % len( metadata[ 'datatypes' ] ) - return datatypes_str - class WorkflowsColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - workflows_str = '0' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'workflows' in metadata: - # We used to display the following, but grid was too cluttered. - #workflows_str += 'Workflows: ' - # metadata[ 'workflows' ] is a list of tuples where each contained tuple is - # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - #workflow_tups = metadata[ 'workflows' ] - #workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] - #for workflow_metadata_dict in workflow_metadata_dicts: - # workflows_str += '%s ' % workflow_metadata_dict[ 'name' ] - return '%d' % len( metadata[ 'workflows' ] ) - return workflows_str - class DeletedColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.repository.deleted: - return 'yes' - return '' - class DeprecatedColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.repository.deprecated: - return 'yes' - return '' - class MaliciousColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.malicious: - return 'yes' - return '' - # Grid definition - title = "Repository Metadata" - model_class = model.RepositoryMetadata - template='/webapps/tool_shed/repository/grid.mako' - default_sort_key = "name" - columns = [ - IdColumn( "Id", - visible=False, - attach_popup=False ), - NameColumn( "Name", - key="name", - model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository_revision", id=item.id ) ), - attach_popup=True ), - OwnerColumn( "Owner", attach_popup=False ), - RevisionColumn( "Revision", attach_popup=False ), - ToolsColumn( "Tools", attach_popup=False ), - DatatypesColumn( "Datatypes", attach_popup=False ), - WorkflowsColumn( "Workflows", attach_popup=False ), - DeletedColumn( "Deleted", attach_popup=False ), - DeprecatedColumn( "Deprecated", attach_popup=False ), - MaliciousColumn( "Malicious", attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ grids.GridOperation( "Delete", - allow_multiple=False, - allow_popup=True, - async_compatible=False, - confirm="Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items." ) ] - standard_filters = [] - default_filter = {} - num_rows_per_page = 50 - preserve_state = False - use_paging = True - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository.table ) class AdminController( BaseUIController, Admin ): - user_list_grid = UserGrid() - role_list_grid = RoleGrid() - group_list_grid = GroupGrid() - manage_category_grid = ManageCategoryGrid() - repository_grid = AdminRepositoryGrid() - repository_metadata_grid = RepositoryMetadataGrid() + user_list_grid = admin_grids.UserGrid() + role_list_grid = admin_grids.RoleGrid() + group_list_grid = admin_grids.GroupGrid() + manage_category_grid = admin_grids.ManageCategoryGrid() + repository_grid = admin_grids.AdminRepositoryGrid() + repository_metadata_grid = admin_grids.RepositoryMetadataGrid() @web.expose @web.require_admin diff -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 -r 6cd65073a397246e7b6fa8884d2c26760865ffad lib/tool_shed/grids/admin_grids.py --- /dev/null +++ b/lib/tool_shed/grids/admin_grids.py @@ -0,0 +1,435 @@ +import os, logging +from galaxy.web.framework.helpers import time_ago, grids +from galaxy.webapps.tool_shed import model +from galaxy.model.orm import and_ +import tool_shed.util.shed_util_common as suc +from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid + +log = logging.getLogger( __name__ ) + + +class UserGrid( grids.Grid ): + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + class UserLoginColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): + return user.email + class UserNameColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): + if user.username: + return user.username + return 'not set' + class GroupsColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.groups: + return len( user.groups ) + return 0 + class RolesColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.roles: + return len( user.roles ) + return 0 + class ExternalColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.external: + return 'yes' + return 'no' + class LastLoginColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.galaxy_sessions: + return self.format( user.galaxy_sessions[ 0 ].update_time ) + return 'never' + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.purged: + return "purged" + elif user.deleted: + return "deleted" + return "" + class EmailColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): + if column_filter == 'All': + return query + return query.filter( and_( model.Tool.table.c.user_id == model.User.table.c.id, + model.User.table.c.email == column_filter ) ) + title = "Users" + model_class = model.User + template='/admin/user/grid.mako' + default_sort_key = "email" + columns = [ + UserLoginColumn( "Email", + key="email", + link=( lambda item: dict( operation="information", id=item.id ) ), + attach_popup=True, + filterable="advanced" ), + UserNameColumn( "User Name", + key="username", + attach_popup=False, + filterable="advanced" ), + GroupsColumn( "Groups", attach_popup=False ), + RolesColumn( "Roles", attach_popup=False ), + ExternalColumn( "External", attach_popup=False ), + LastLoginColumn( "Last Login", format=time_ago ), + StatusColumn( "Status", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + EmailColumn( "Email", + key="email", + visible=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Create new user", + dict( controller='admin', action='users', operation='create' ) ) + ] + operations = [ + grids.GridOperation( "Manage Roles and Groups", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="manage_roles_and_groups_for_user" ) ), + grids.GridOperation( "Reset Password", + condition=( lambda item: not item.deleted ), + allow_multiple=True, + allow_popup=False, + url_args=dict( action="reset_user_password" ) ) + ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ), + grids.GridColumnFilter( "Purged", args=dict( purged=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def get_current_item( self, trans, **kwargs ): + return trans.user + +class RoleGrid( grids.Grid ): + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): + return role.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): + if role.description: + return role.description + return '' + class TypeColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): + return role.type + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): + if role.deleted: + return "deleted" + return "" + class GroupsColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): + if role.groups: + return len( role.groups ) + return 0 + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): + if role.users: + return len( role.users ) + return 0 + title = "Roles" + model_class = model.Role + template='/admin/dataset_security/role/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="Manage users and groups", id=item.id ) ), + attach_popup=True, + filterable="advanced" ), + DescriptionColumn( "Description", + key='description', + attach_popup=False, + filterable="advanced" ), + TypeColumn( "Type", + key='type', + attach_popup=False, + filterable="advanced" ), + GroupsColumn( "Groups", attach_popup=False ), + UsersColumn( "Users", attach_popup=False ), + StatusColumn( "Status", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Add new role", + dict( controller='admin', action='roles', operation='create' ) ) + ] + operations = [ grids.GridOperation( "Rename", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="rename_role" ) ), + grids.GridOperation( "Delete", + condition=( lambda item: not item.deleted ), + allow_multiple=True, + url_args=dict( action="mark_role_deleted" ) ), + grids.GridOperation( "Undelete", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( action="undelete_role" ) ), + grids.GridOperation( "Purge", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( action="purge_role" ) ) ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def apply_query_filter( self, trans, query, **kwd ): + return query.filter( model.Role.type != model.Role.types.PRIVATE ) + +class GroupGrid( grids.Grid ): + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, group ): + return group.name + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): + if group.deleted: + return "deleted" + return "" + class RolesColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): + if group.roles: + return len( group.roles ) + return 0 + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): + if group.members: + return len( group.members ) + return 0 + title = "Groups" + model_class = model.Group + template='/admin/dataset_security/group/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + link=( lambda item: dict( operation="Manage users and roles", id=item.id ) ), + attach_popup=True ), + UsersColumn( "Users", attach_popup=False ), + RolesColumn( "Roles", attach_popup=False ), + StatusColumn( "Status", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Add new group", + dict( controller='admin', action='groups', operation='create' ) ) + ] + operations = [ grids.GridOperation( "Rename", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="rename_group" ) ), + grids.GridOperation( "Delete", + condition=( lambda item: not item.deleted ), + allow_multiple=True, + url_args=dict( action="mark_group_deleted" ) ), + grids.GridOperation( "Undelete", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( action="undelete_group" ) ), + grids.GridOperation( "Purge", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( action="purge_group" ) ) ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + +class ManageCategoryGrid( CategoryGrid ): + columns = [ col for col in CategoryGrid.columns ] + # Override the NameColumn to include an Edit link + columns[ 0 ] = CategoryGrid.NameColumn( "Name", + key="Category.name", + link=( lambda item: dict( operation="Edit", id=item.id ) ), + model_class=model.Category, + attach_popup=False ) + global_actions = [ + grids.GridAction( "Add new category", + dict( controller='admin', action='manage_categories', operation='create' ) ) + ] + +class AdminRepositoryGrid( RepositoryGrid ): + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository ): + if repository.deleted: + return 'yes' + return '' + columns = [ RepositoryGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoryGrid.UserColumn( "Owner", + model_class=model.User, + link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), + attach_popup=False, + key="User.username" ), + RepositoryGrid.DeprecatedColumn( "Deprecated", key="deprecated", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + DeletedColumn( "Deleted", key="deleted", attach_popup=False ) ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ operation for operation in RepositoryGrid.operations ] + operations.append( grids.GridOperation( "Delete", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) ) + operations.append( grids.GridOperation( "Undelete", + allow_multiple=False, + condition=( lambda item: item.deleted ), + async_compatible=False ) ) + standard_filters = [] + default_filter = {} + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .join( model.User.table ) + +class RepositoryMetadataGrid( grids.Grid ): + class IdColumn( grids.IntegerColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.id + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.name + class OwnerColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.user.username + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + repository = repository_metadata.repository + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) + return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + tools_str = '0' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'tools' in metadata: + # We used to display the following, but grid was too cluttered. + #for tool_metadata_dict in metadata[ 'tools' ]: + # tools_str += '%s %s ' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + return '%d' % len( metadata[ 'tools' ] ) + return tools_str + class DatatypesColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + datatypes_str = '0' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'datatypes' in metadata: + # We used to display the following, but grid was too cluttered. + #for datatype_metadata_dict in metadata[ 'datatypes' ]: + # datatypes_str += '%s ' % datatype_metadata_dict[ 'extension' ] + return '%d' % len( metadata[ 'datatypes' ] ) + return datatypes_str + class WorkflowsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + workflows_str = '0' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'workflows' in metadata: + # We used to display the following, but grid was too cluttered. + #workflows_str += 'Workflows: ' + # metadata[ 'workflows' ] is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + #workflow_tups = metadata[ 'workflows' ] + #workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] + #for workflow_metadata_dict in workflow_metadata_dicts: + # workflows_str += '%s ' % workflow_metadata_dict[ 'name' ] + return '%d' % len( metadata[ 'workflows' ] ) + return workflows_str + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.deleted: + return 'yes' + return '' + class DeprecatedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.deprecated: + return 'yes' + return '' + class MaliciousColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.malicious: + return 'yes' + return '' + # Grid definition + title = "Repository Metadata" + model_class = model.RepositoryMetadata + template='/webapps/tool_shed/repository/grid.mako' + default_sort_key = "name" + columns = [ + IdColumn( "Id", + visible=False, + attach_popup=False ), + NameColumn( "Name", + key="name", + model_class=model.Repository, + link=( lambda item: dict( operation="view_or_manage_repository_revision", id=item.id ) ), + attach_popup=True ), + OwnerColumn( "Owner", attach_popup=False ), + RevisionColumn( "Revision", attach_popup=False ), + ToolsColumn( "Tools", attach_popup=False ), + DatatypesColumn( "Datatypes", attach_popup=False ), + WorkflowsColumn( "Workflows", attach_popup=False ), + DeletedColumn( "Deleted", attach_popup=False ), + DeprecatedColumn( "Deprecated", attach_popup=False ), + MaliciousColumn( "Malicious", attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ grids.GridOperation( "Delete", + allow_multiple=False, + allow_popup=True, + async_compatible=False, + confirm="Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items." ) ] + standard_filters = [] + default_filter = {} + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository.table ) diff -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 -r 6cd65073a397246e7b6fa8884d2c26760865ffad lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -10,6 +10,8 @@ eggs.require('markupsafe') from markupsafe import escape as escape_html +log = logging.getLogger( __name__ ) + class CategoryGrid( grids.Grid ): 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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