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commit/galaxy-central: jmchilton: Small clarification in previous doc addition.
by commits-noreply＠bitbucket.org 13 Jun '14

13 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8a608db6cf83/ Changeset: 8a608db6cf83 User: jmchilton Date: 2014-06-13 16:14:38 Summary: Small clarification in previous doc addition. Affected #: 1 file diff -r c9c07643e04ece14e27c07c4aa73b3578202c47b -r 8a608db6cf83b653a433f43b501f4047f63d248b 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 @@ -240,7 +240,8 @@ 'content' = [the encoded id from the HDCA] create new history dataset collection (for type 'dataset_collection') - 'source' = 'new_collection' + 'source' = 'new_collection' (default 'source' if type is + 'dataset_collection' - no need to specify this) 'collection_type' = For example, "list", "paired", "list:paired". 'name' = Name of new dataset collection. 'element_identifiers' = Recursive list structure defining collection. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Add some quick docs for creating dataset collections through API.
by commits-noreply＠bitbucket.org 13 Jun '14

13 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c9c07643e04e/ Changeset: c9c07643e04e User: jmchilton Date: 2014-06-13 16:08:56 Summary: Add some quick docs for creating dataset collections through API. For full worked examples see bioblend and API tests. Affected #: 1 file diff -r 05500f5c6710816865536335a42eb9e00caf6f03 -r c9c07643e04ece14e27c07c4aa73b3578202c47b 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 @@ -217,27 +217,54 @@ def create( self, trans, history_id, payload, **kwd ): """ create( self, trans, history_id, payload, **kwd ) - * POST /api/histories/{history_id}/contents + * POST /api/histories/{history_id}/contents/{type} create a new HDA by copying an accessible LibraryDataset :type history_id: str :param history_id: encoded id string of the new HDA's History + :type type: str + :param type: Type of history content - 'dataset' (default) or + 'dataset_collection'. :type payload: dict :param payload: dictionary structure containing:: - copy from library: + copy from library (for type 'dataset'): 'source' = 'library' 'content' = [the encoded id from the library dataset] - copy from HDA: + copy from history dataset (for type 'dataset'): 'source' = 'hda' 'content' = [the encoded id from the HDA] + copy from history dataset collection (for type 'dataset_collection') + 'source' = 'hdca' + 'content' = [the encoded id from the HDCA] + + create new history dataset collection (for type 'dataset_collection') + 'source' = 'new_collection' + 'collection_type' = For example, "list", "paired", "list:paired". + 'name' = Name of new dataset collection. + 'element_identifiers' = Recursive list structure defining collection. + Each element must have 'src' which can be + 'hda', 'ldda', 'hdca', or 'new_collection', + as well as a 'name' which is the name of + element (e.g. "forward" or "reverse" for + paired datasets, or arbitrary sample names + for instance for lists). For all src's except + 'new_collection' - a encoded 'id' attribute + must be included wiht element as well. + 'new_collection' sources must defined a + 'collection_type' and their own list of + (potentially) nested 'element_identifiers'. + ..note: Currently, a user can only copy an HDA from a history that the user owns. :rtype: dict :returns: dictionary containing detailed information for the new HDA """ + # TODO: Flush out create new collection documentation above, need some + # examples. See also bioblend and API tests for specific examples. + # get the history, if anon user and requesting current history - allow it if( ( trans.user == None ) and ( history_id == trans.security.encode_id( trans.history.id ) ) ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fix spelling error in API test.
by commits-noreply＠bitbucket.org 13 Jun '14

13 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/05500f5c6710/ Changeset: 05500f5c6710 User: jmchilton Date: 2014-06-13 15:46:01 Summary: Fix spelling error in API test. Affected #: 1 file diff -r 588559638acc7ed88542f8e77987698f2fa0b2fb -r 05500f5c6710816865536335a42eb9e00caf6f03 test/api/test_dataset_collections.py --- a/test/api/test_dataset_collections.py +++ b/test/api/test_dataset_collections.py @@ -73,12 +73,13 @@ collection_type="list:paired", instance_type="history", history_id=self.history_id, - name="nested_collecion", + name="a nested collection", element_identifiers=json.dumps( element_identifiers ), ) create_response = self._post( "dataset_collections", payload ) dataset_collection = self._check_create_response( create_response ) assert dataset_collection[ "collection_type" ] == "list:paired" + assert dataset_collection[ "name" ] == "a nested collection" returned_collections = dataset_collection[ "elements" ] assert len( returned_collections ) == 1, dataset_collection pair_1_element = returned_collections[ 0 ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fixup XML formatting in job_conf.xml.sample_advanced.
by commits-noreply＠bitbucket.org 13 Jun '14

13 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/588559638acc/ Changeset: 588559638acc User: jmchilton Date: 2014-06-13 08:02:13 Summary: Fixup XML formatting in job_conf.xml.sample_advanced. Should fix the remaining failing unit tests. Affected #: 1 file diff -r 365e1cef25a5ef79ed64934e0b1c483ae73a7445 -r 588559638acc7ed88542f8e77987698f2fa0b2fb job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -162,7 +162,7 @@  Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fix failing unit tests for 60d8de4.
by commits-noreply＠bitbucket.org 13 Jun '14

13 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/365e1cef25a5/ Changeset: 365e1cef25a5 User: jmchilton Date: 2014-06-13 07:58:23 Summary: Fix failing unit tests for 60d8de4. Affected #: 4 files diff -r 972bd6fbd63f372cc80096e0c099c5e17d33dfe7 -r 365e1cef25a5ef79ed64934e0b1c483ae73a7445 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -153,7 +153,7 @@  -  + <!-- By default, docker container will not have any networking enabled. host networking can be bridged by uncommenting next option http://docs.docker.io/reference/run/#network-settings diff -r 972bd6fbd63f372cc80096e0c099c5e17d33dfe7 -r 365e1cef25a5ef79ed64934e0b1c483ae73a7445 lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -99,6 +99,12 @@ return asbool(destination_info.get("%s_enabled" % container_type, False)) +class NullContainerFinder(object): + + def find_container(self, tool_info, destination_info, job_info): + return [] + + class ContainerRegistry(): def __init__(self): diff -r 972bd6fbd63f372cc80096e0c099c5e17d33dfe7 -r 365e1cef25a5ef79ed64934e0b1c483ae73a7445 lib/galaxy/tools/deps/requirements.py --- a/lib/galaxy/tools/deps/requirements.py +++ b/lib/galaxy/tools/deps/requirements.py @@ -53,14 +53,14 @@ ... contents_document = '''<tool><requirements>%s</requirements></tool>''' ... root = ElementTree.fromstring( contents_document % contents ) ... return parse_requirements_from_xml( root ) - >>> reqs = load_requirements('''<requirement>bwa</requirement>''') + >>> reqs, containers = load_requirements('''<requirement>bwa</requirement>''') >>> reqs[0].name 'bwa' >>> reqs[0].version is None True >>> reqs[0].type 'package' - >>> reqs = load_requirements('''<requirement type="binary" version="1.3.3">cufflinks</requirement>''') + >>> reqs, containers = load_requirements('''<requirement type="binary" version="1.3.3">cufflinks</requirement>''') >>> reqs[0].name 'cufflinks' >>> reqs[0].version diff -r 972bd6fbd63f372cc80096e0c099c5e17d33dfe7 -r 365e1cef25a5ef79ed64934e0b1c483ae73a7445 test/unit/tools_support.py --- a/test/unit/tools_support.py +++ b/test/unit/tools_support.py @@ -16,6 +16,7 @@ from galaxy.util import parse_xml from galaxy.util.dbkeys import GenomeBuilds from galaxy.jobs import NoopQueue +from galaxy.tools.deps.containers import NullContainerFinder class UsesApp( object ): @@ -126,6 +127,7 @@ self.security_agent = GalaxyRBACAgent( self.model ) self.tool_data_tables = {} self.dataset_collections_service = None + self.container_finder = NullContainerFinder() class MockContext(object): 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: dannon: Re-enable flexible default_bucket for cloudlaunch.
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/972bd6fbd63f/ Changeset: 972bd6fbd63f User: dannon Date: 2014-06-13 00:26:24 Summary: Re-enable flexible default_bucket for cloudlaunch. Affected #: 1 file diff -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c -r 972bd6fbd63f372cc80096e0c099c5e17d33dfe7 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -72,7 +72,8 @@ cml = cloudman.launch.CloudManLauncher(key_id, secret) result = cml.launch(cluster_name, ami, instance_type, password, cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, - cfg.security_groups, cfg.placement) + cfg.security_groups, cfg.placement, + bucket_default=bucket_default) # result is a dict with sg_names, kp_name, kp_material, rs, and instance_id if not result['rs']: trans.response.status = 400 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: Eliminate the use of trans in most functions in the Tool Shed's shed_util_common utility module.
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9a69f032d6d9/ Changeset: 9a69f032d6d9 User: greg Date: 2014-06-12 21:43:38 Summary: Eliminate the use of trans in most functions in the Tool Shed's shed_util_common utility module. Affected #: 24 files diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -7,6 +7,8 @@ from string import punctuation as PUNCTUATION import galaxy.queue_worker +from tool_shed.util import shed_util_common as suc + log = logging.getLogger( __name__ ) @@ -29,7 +31,7 @@ status = kwd.get( 'status', 'done' ) if trans.webapp.name == 'galaxy': installed_repositories = trans.install_model.context.query( trans.install_model.ToolShedRepository ).first() - installing_repository_ids = get_ids_of_tool_shed_repositories_being_installed( trans, as_string=True ) + installing_repository_ids = suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=True ) return trans.fill_template( '/webapps/galaxy/admin/index.mako', installed_repositories=installed_repositories, installing_repository_ids=installing_repository_ids, @@ -1091,24 +1093,6 @@ ## ---- Utility methods ------------------------------------------------------- -def get_ids_of_tool_shed_repositories_being_installed( trans, as_string=False ): - installing_repository_ids = [] - new_status = trans.install_model.ToolShedRepository.installation_status.NEW - cloning_status = trans.install_model.ToolShedRepository.installation_status.CLONING - setting_tool_versions_status = trans.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS - installing_dependencies_status = trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES - loading_datatypes_status = trans.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES - for tool_shed_repository in trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ - .filter( or_( trans.install_model.ToolShedRepository.status == new_status, - trans.install_model.ToolShedRepository.status == cloning_status, - trans.install_model.ToolShedRepository.status == setting_tool_versions_status, - trans.install_model.ToolShedRepository.status == installing_dependencies_status, - trans.install_model.ToolShedRepository.status == loading_datatypes_status ) ): - installing_repository_ids.append( trans.security.encode_id( tool_shed_repository.id ) ) - if as_string: - return ','.join( installing_repository_ids ) - return installing_repository_ids - def get_user( trans, user_id ): """Get a User from the database by id.""" user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -59,7 +59,7 @@ # Since exported workflows are dictionaries with very few attributes that differentiate them from each # other, we'll build the list based on the following dictionary of those few attributes. exported_workflows = [] - repository = suc.get_tool_shed_repository_by_id( trans, id ) + repository = suc.get_tool_shed_repository_by_id( trans.app, id ) metadata = repository.metadata if metadata: exported_workflow_tups = metadata.get( 'workflows', [] ) @@ -142,7 +142,7 @@ index = payload.get( 'index', None ) if index is None: raise HTTPBadRequest( detail="Missing required parameter 'index'." ) - repository = suc.get_tool_shed_repository_by_id( trans, tool_shed_repository_id ) + repository = suc.get_tool_shed_repository_by_id( trans.app, tool_shed_repository_id ) exported_workflows = json.from_json_string( self.exported_workflows( trans, tool_shed_repository_id ) ) # Since we don't have an in-memory object with an id, we'll identify the exported workflow via its location (i.e., index) in the list. exported_workflow = exported_workflows[ int( index ) ] @@ -169,7 +169,7 @@ tool_shed_repository_id = kwd.get( 'id', '' ) if not tool_shed_repository_id: raise HTTPBadRequest( detail="Missing required parameter 'id'." ) - repository = suc.get_tool_shed_repository_by_id( trans, tool_shed_repository_id ) + repository = suc.get_tool_shed_repository_by_id( trans.app, tool_shed_repository_id ) exported_workflows = json.from_json_string( self.exported_workflows( trans, tool_shed_repository_id ) ) imported_workflow_dicts = [] for exported_workflow_dict in exported_workflows: @@ -406,7 +406,7 @@ for repository in query: repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = metadata_util.reset_all_metadata_on_installed_repository( trans, repository_id ) + invalid_file_tups, metadata_dict = metadata_util.reset_all_metadata_on_installed_repository( trans.app, repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, @@ -436,7 +436,7 @@ :param id: the encoded id of the ToolShedRepository object """ # Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e - tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, id ) + tool_shed_repository = suc.get_tool_shed_repository_by_id( trans.app, id ) if tool_shed_repository is None: log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) ) return {} diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -326,7 +326,7 @@ repository_id = kwd.get( 'repository_id', None ) relative_path_to_image_file = kwd.get( 'image_file', None ) if repository_id and relative_path_to_image_file: - repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id ) if repository: repo_files_dir = repository.repo_files_directory( trans.app ) path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file ) @@ -433,7 +433,7 @@ status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) - repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id ) if repository: workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) if workflow: @@ -808,7 +808,7 @@ # The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a # tool dependency, but they didn't check any of the available tool dependencies on which to perform the action. repository_id = kwd.get( 'repository_id', None ) - tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + tool_shed_repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if not tool_dependency_ids: @@ -858,12 +858,12 @@ message += ' and restart your Galaxy server to install tool dependencies.' status = 'error' installed_tool_dependencies_select_field = \ - suc.build_tool_dependencies_select_field( trans, + suc.build_tool_dependencies_select_field( trans.app, tool_shed_repository=tool_shed_repository, name='inst_td_ids', uninstalled_only=False ) uninstalled_tool_dependencies_select_field = \ - suc.build_tool_dependencies_select_field( trans, + suc.build_tool_dependencies_select_field( trans.app, tool_shed_repository=tool_shed_repository, name='uninstalled_tool_dependency_ids', uninstalled_only=True ) @@ -890,7 +890,7 @@ else: # The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a # tool dependency, but they didn't check any of the available tool dependencies on which to perform the action. - tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + tool_shed_repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id ) self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies" % tool_shed_repository.name if 'operation' in kwd: operation = kwd[ 'operation' ].lower() @@ -942,7 +942,7 @@ def monitor_repository_installation( self, trans, **kwd ): tsridslist = repository_util.get_tool_shed_repository_ids( **kwd ) if not tsridslist: - tsridslist = suc.get_ids_of_tool_shed_repositories_being_installed( trans, as_string=False ) + tsridslist = suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=False ) kwd[ 'tool_shed_repository_ids' ] = tsridslist return self.repository_installation_grid( trans, **kwd ) @@ -952,7 +952,7 @@ # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - return suc.open_repository_files_folder( trans, folder_path ) + return suc.open_repository_files_folder( folder_path ) @web.expose @web.require_admin @@ -1008,7 +1008,7 @@ # but the received repository id is from the Galaxy side (the caller is this controller's # update_to_changeset_revision() method. We need to get the id of the same repository from the # Tool Shed side. - repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id ) + repository = suc.get_tool_shed_repository_by_id( trans.app, updating_repository_id ) # For backward compatibility to the 12/20/12 Galaxy release. try: params = '?name=%s&owner=%s' % ( str( repository.name ), str( repository.owner ) ) @@ -1056,7 +1056,7 @@ encoded_updated_metadata_dict = kwd.get( 'encoded_updated_metadata_dict', None ) updated_changeset_revision = kwd.get( 'updated_changeset_revision', None ) updated_ctx_rev = kwd.get( 'updated_ctx_rev', None ) - repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id ) + repository = suc.get_tool_shed_repository_by_id( trans.app, updating_repository_id ) decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) # Now that the user has decided whether they will handle dependencies, we can update # the repository to the latest revision. @@ -1070,7 +1070,7 @@ install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) else: install_tool_dependencies = False - tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) + tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans.app, shed_tool_conf ) installation_dict = dict( install_repository_dependencies=install_repository_dependencies, new_tool_panel_section_label=new_tool_panel_section_label, no_changes_checked=False, @@ -1112,7 +1112,7 @@ action='manage_repositories', **kwd ) ) shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans ) - tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) + tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans.app, shed_tool_conf ) tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans ) if len( repo_info_dicts ) == 1: # If we're installing or updating a single repository, see if it contains a readme or @@ -2053,7 +2053,7 @@ updated_count = 0 for repository in trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ .filter( trans.install_model.ToolShedRepository.table.c.deleted == False ): - ok, updated = suc.check_or_update_tool_shed_status_for_installed_repository( trans, repository ) + ok, updated = suc.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository ) if ok: success_count += 1 else: @@ -2067,8 +2067,8 @@ message += ", ".join( repository_names_not_updated ) else: repository_id = kwd.get( 'id', None ) - repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) - ok, updated = suc.check_or_update_tool_shed_status_for_installed_repository( trans, repository ) + repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id ) + ok, updated = suc.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository ) if ok: if updated: message = "The tool shed status for repository %s has been updated." % str( repository.name ) @@ -2122,7 +2122,7 @@ status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) - repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id ) changeset_revision = repository.changeset_revision metadata = repository.metadata return trans.fill_template( "/admin/tool_shed_repository/view_workflow.mako", diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/galaxy/webapps/tool_shed/api/categories.py --- a/lib/galaxy/webapps/tool_shed/api/categories.py +++ b/lib/galaxy/webapps/tool_shed/api/categories.py @@ -39,7 +39,7 @@ if not description: # Default the description to the name. description = name - if suc.get_category_by_name( trans, name ): + if suc.get_category_by_name( trans.app, name ): category_dict[ 'message' ] = 'A category with that name already exists' category_dict[ 'status' ] = 'error' else: @@ -90,7 +90,7 @@ :param id: the encoded id of the Repository object """ # Example URL: http://localhost:9009/api/categories/f9cad7b01a472135 - category = suc.get_category( trans, id ) + category = suc.get_category( trans.app, id ) if category is None: category_dict = dict( message = 'Unable to locate category record for id %s.' % ( str( id ) ), status = 'error' ) diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -498,7 +498,7 @@ repository_id = payload.get( 'repository_id', None ) if repository_id is not None: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) log.debug( "%s...resetting metadata on repository %s" % ( start_time, str( repository.name ) ) ) results = handle_repository( trans, start_time, repository ) @@ -515,7 +515,7 @@ :param id: the encoded id of the Repository object """ # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135 - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) if repository is None: log.debug( "Unable to locate repository record for id %s." % ( str( id ) ) ) return {} diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -141,7 +141,7 @@ """ # Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb12… repository_dependencies_dicts = [] - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, id ) if repository_metadata is None: log.debug( 'Invalid repository_metadata id received: %s' % str( id ) ) return repository_dependencies_dicts @@ -214,12 +214,12 @@ :param id: the encoded id of the `RepositoryMetadata` object """ # Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620 - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, id ) if repository_metadata is None: log.debug( 'Cannot locate repository_metadata with id %s' % str( id ) ) return {} encoded_repository_id = trans.security.encode_id( repository_metadata.repository_id ) - repository = suc.get_repository_by_id( trans, encoded_repository_id ) + repository = suc.get_repository_by_id( trans.app, encoded_repository_id ) repository_metadata_dict = repository_metadata.to_dict( view='element', value_mapper=self.__get_value_mapper( trans ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repositories', @@ -238,7 +238,7 @@ repository_metadata_id = kwd.get( 'id', None ) if repository_metadata_id is None: raise HTTPBadRequest( detail="Missing required parameter 'id'." ) - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id ) if repository_metadata is None: decoded_repository_metadata_id = trans.security.decode_id( repository_metadata_id ) log.debug( 'Cannot locate repository_metadata with id %s' % str( decoded_repository_metadata_id ) ) diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/galaxy/webapps/tool_shed/api/users.py --- a/lib/galaxy/webapps/tool_shed/api/users.py +++ b/lib/galaxy/webapps/tool_shed/api/users.py @@ -105,7 +105,7 @@ :param id: the encoded id of the User object. """ # Example URL: http://localhost:9009/api/users/f9cad7b01a472135 - user = suc.get_user( trans, id ) + user = suc.get_user( trans.app, id ) if user is None: user_dict = dict( message = 'Unable to locate user record for id %s.' % ( str( id ) ), status = 'error' ) diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c 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 @@ -43,14 +43,14 @@ if k.startswith( 'f-' ): del kwd[ k ] if 'user_id' in kwd: - user = suc.get_user( trans, kwd[ 'user_id' ] ) + user = suc.get_user( trans.app, kwd[ 'user_id' ] ) kwd[ 'f-email' ] = user.email del kwd[ 'user_id' ] else: # The received id is the repository id, so we need to get the id of the user # that uploaded the repository. repository_id = kwd.get( 'id', None ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) kwd[ 'f-email' ] = repository.user.email elif operation == "repositories_by_category": # Eliminate the current filters if any exist. @@ -58,7 +58,7 @@ if k.startswith( 'f-' ): del kwd[ k ] category_id = kwd.get( 'id', None ) - category = suc.get_category( trans, category_id ) + category = suc.get_category( trans.app, category_id ) kwd[ 'f-Category.name' ] = category.name elif operation == "receive email alerts": if kwd[ 'id' ]: @@ -82,7 +82,7 @@ changeset_revision_str = 'changeset_revision_' if k.startswith( changeset_revision_str ): repository_id = trans.security.encode_id( int( k.lstrip( changeset_revision_str ) ) ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( tran.apps, repository_id ) if repository.tip( trans.app ) != v: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -103,7 +103,7 @@ # The received id is a RepositoryMetadata object id, so we need to get the # associated Repository and redirect to view_or_manage_repository with the # changeset_revision. - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, kwd[ 'id' ] ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, kwd[ 'id' ] ) repository = repository_metadata.repository kwd[ 'id' ] = trans.security.encode_id( repository.id ) kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision @@ -124,7 +124,7 @@ if not name or not description: message = 'Enter a valid name and a description' status = 'error' - elif suc.get_category_by_name( trans, name ): + elif suc.get_category_by_name( trans.app, name ): message = 'A category with that name already exists' status = 'error' else: @@ -158,7 +158,7 @@ count = 0 deleted_repositories = "" for repository_id in ids: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) if repository: if not repository.deleted: # Mark all installable repository_metadata records as not installable. @@ -199,7 +199,7 @@ ids = util.listify( id ) count = 0 for repository_metadata_id in ids: - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id ) trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() count += 1 @@ -225,7 +225,7 @@ action='manage_categories', message=message, status='error' ) ) - category = suc.get_category( trans, id ) + category = suc.get_category( trans.app, id ) original_category_name = str( category.name ) original_category_description = str( category.description ) if kwd.get( 'edit_category_button', False ): @@ -236,7 +236,7 @@ if not new_name: message = 'Enter a valid name' status = 'error' - elif original_category_name != new_name and suc.get_category_by_name( trans, new_name ): + elif original_category_name != new_name and suc.get_category_by_name( trans.app, new_name ): message = 'A category with that name already exists' status = 'error' else: @@ -363,7 +363,7 @@ count = 0 undeleted_repositories = "" for repository_id in ids: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) if repository: if repository.deleted: # Inspect all repository_metadata records to determine those that are installable, and mark @@ -412,7 +412,7 @@ ids = util.listify( id ) message = "Deleted %d categories: " % len( ids ) for category_id in ids: - category = suc.get_category( trans, category_id ) + category = suc.get_category( trans.app, category_id ) category.deleted = True trans.sa_session.add( category ) trans.sa_session.flush() @@ -442,7 +442,7 @@ purged_categories = "" message = "Purged %d categories: " % len( ids ) for category_id in ids: - category = suc.get_category( trans, category_id ) + category = suc.get_category( trans.app, category_id ) if category.deleted: # Delete RepositoryCategoryAssociations for rca in category.repositories: @@ -469,7 +469,7 @@ count = 0 undeleted_categories = "" for category_id in ids: - category = suc.get_category( trans, category_id ) + category = suc.get_category( trans.app, category_id ) if category.deleted: category.deleted = False trans.sa_session.add( category ) diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c 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 @@ -127,7 +127,7 @@ operation = kwd[ 'operation' ].lower() # The received id is a RepositoryMetadata id. repository_metadata_id = kwd[ 'id' ] - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, 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, @@ -146,7 +146,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', **kwd ) ) - selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans.app, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -172,7 +172,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='deprecate', **kwd ) ) - selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans.app, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -397,7 +397,7 @@ kwd[ 'message' ] = 'You must be logged in to set email alerts.' kwd[ 'status' ] = 'error' del kwd[ 'operation' ] - selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans.app, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -428,19 +428,19 @@ # The received id is the repository id, so we need to get the id of the user that owns the repository. repository_id = kwd.get( 'id', None ) if repository_id: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) user_id = trans.security.encode_id( repository.user.id ) kwd[ 'user_id' ] = user_id else: # The user selected a repository revision which results in a refresh_on_change. - selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans.app, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=selected_changeset_revision ) ) if user_id: - user = suc.get_user( trans, user_id ) + user = suc.get_user( trans.app, user_id ) trailing_string = 'Owned by %s' % str( user.username ) default = 'Repositories Owned by %s' % str( user.username ) else: @@ -469,7 +469,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='deprecate', **kwd ) ) - selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans.app, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -495,7 +495,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='deprecate', **kwd ) ) - selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans.app, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -518,13 +518,13 @@ # The received id is the repository id, so we need to get the id of the user that owns the repository. repository_id = kwd.get( 'id', None ) if repository_id: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) user_id = trans.security.encode_id( repository.user.id ) - user = suc.get_user( trans, user_id ) + user = suc.get_user( trans.app, user_id ) self.repositories_by_user_grid.title = "Repositories owned by %s" % user.username kwd[ 'user_id' ] = user_id return self.repositories_by_user_grid( trans, **kwd ) - selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans.app, **kwd ) if repository: # The user selected a repository revision which results in a refresh_on_change. return trans.response.send_redirect( web.url_for( controller='repository', @@ -533,7 +533,7 @@ changeset_revision=selected_changeset_revision ) ) category_id = kwd.get( 'id', None ) if category_id: - category = suc.get_category( trans, category_id ) + category = suc.get_category( trans.app, category_id ) if category: trailing_string = 'in Category %s' % str( category.name ) else: @@ -718,7 +718,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) # Update repository files for browsing. hg_util.update_repository( repo ) @@ -740,7 +740,7 @@ operation = kwd[ 'operation' ].lower() # The received id is a RepositoryMetadata id. repository_metadata_id = kwd[ 'id' ] - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, 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, @@ -761,7 +761,7 @@ operation = kwd[ 'operation' ].lower() # The received id is a RepositoryMetadata id. repository_metadata_id = kwd['id' ] - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, 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, @@ -778,7 +778,7 @@ operation = kwd[ 'operation' ].lower() # The received id is a RepositoryMetadata id. repository_metadata_id = kwd[ 'id' ] - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, 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, @@ -839,13 +839,13 @@ if 'f-Category.name' in kwd: # The user browsed to a category and then entered a search string, so get the category associated with its value. category_name = kwd[ 'f-Category.name' ] - category = suc.get_category_by_name( trans, category_name ) + category = suc.get_category_by_name( trans.app, category_name ) # Set the id value in kwd since it is required by the ValidRepositoryGrid.build_initial_query method. kwd[ 'id' ] = trans.security.encode_id( category.id ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "preview_tools_in_changeset": - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repository_metadata = metadata_util.get_latest_repository_metadata( trans, repository.id, downloadable=True ) latest_installable_changeset_revision = repository_metadata.changeset_revision return trans.response.send_redirect( web.url_for( controller='repository', @@ -858,9 +858,9 @@ if k.startswith( 'f-' ): del kwd[ k ] category_id = kwd.get( 'id', None ) - category = suc.get_category( trans, category_id ) + category = suc.get_category( trans.app, category_id ) kwd[ 'f-Category.name' ] = category.name - selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans.app, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', @@ -969,7 +969,7 @@ def contact_owner( self, trans, id, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, repository.tip( trans.app ), @@ -1046,7 +1046,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) mark_deprecated = util.string_as_bool( kwd.get( 'mark_deprecated', False ) ) repository.deprecated = mark_deprecated trans.sa_session.add( repository ) @@ -1080,7 +1080,7 @@ repository_id = kwd.get( 'repository_id', None ) relative_path_to_image_file = kwd.get( 'image_file', None ) if repository_id and relative_path_to_image_file: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) if repository: repo_files_dir = repository.repo_path( trans.app ) path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file ) @@ -1142,7 +1142,7 @@ """Download an archive of the repository files compressed as zip, gz or bz2.""" # FIXME: thgis will currently only download the repository tip, no matter which installable changeset_revision is being viewed. # This should be enhanced to use the export method below, which accounts for the currently viewed changeset_revision. - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) # Allow hgweb to handle the download. This requires the tool shed # server account's .hgrc file to include the following setting: # [web] @@ -1164,7 +1164,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) export_repository_dependencies = kwd.get( 'export_repository_dependencies', '' ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) if kwd.get( 'export_repository_button', False ): # We'll currently support only gzip-compressed tar archives. file_type = 'gz' @@ -1252,9 +1252,9 @@ is_admin = trans.user_is_admin() if operation == "view_or_manage_repository": # The received id is a RepositoryMetadata id, so we have to get the repository id. - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, item_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, item_id ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision if trans.webapp.name == 'tool_shed' and ( is_admin or repository.user == trans.user ): @@ -1269,7 +1269,7 @@ encoded_repository_ids = [] changeset_revisions = [] for repository_metadata_id in util.listify( item_id ): - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id ) encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) ) changeset_revisions.append( repository_metadata.changeset_revision ) new_kwd = {} @@ -1343,9 +1343,9 @@ is_admin = trans.user_is_admin() if operation == "view_or_manage_repository": # The received id is a RepositoryMetadata id, so we have to get the repository id. - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, item_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, item_id ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision if trans.webapp.name == 'tool_shed' and ( is_admin or repository.user == trans.user ): @@ -1360,7 +1360,7 @@ encoded_repository_ids = [] changeset_revisions = [] for repository_metadata_id in util.listify( item_id ): - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, item_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, item_id ) encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) ) changeset_revisions.append( repository_metadata.changeset_revision ) new_kwd = {} @@ -2161,7 +2161,7 @@ def manage_repository( self, trans, id, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) repository_type = kwd.get( 'repository_type', str( repository.type ) ) repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) @@ -2387,7 +2387,7 @@ repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) malicious_check_box = CheckboxField( 'malicious', checked=is_malicious ) skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) - categories = suc.get_categories( trans ) + categories = suc.get_categories( trans.app ) selected_categories = [ rca.category_id for rca in repository.categories ] containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, @@ -2433,7 +2433,7 @@ def manage_repository_admins( self, trans, id, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) metadata = None if changeset_revision != hg_util.INITIAL_CHANGELOG_HASH: @@ -2531,13 +2531,13 @@ # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - return suc.open_repository_files_folder( trans, folder_path ) + return suc.open_repository_files_folder( folder_path ) @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) @@ -2646,7 +2646,7 @@ action='browse_repositories', message='Select a repository to rate', status='error' ) ) - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) changeset_revision = repository.tip( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) if repository.user == trans.user: @@ -2685,7 +2685,7 @@ # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. invalid_file_tups, metadata_dict = metadata_util.reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd ) if invalid_file_tups: - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict ) status = 'error' else: @@ -2715,7 +2715,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) selected_files_to_delete = kwd.get( 'selected_files_to_delete', '' ) @@ -2786,7 +2786,7 @@ @web.expose def send_to_owner( self, trans, id, message='' ): - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) if not message: message = 'Enter a message' status = 'error' @@ -2836,7 +2836,7 @@ total_alerts_removed = 0 flush_needed = False for repository_id in repository_ids: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) if repository.email_alerts: email_alerts = json.from_json_string( repository.email_alerts ) else: @@ -3045,7 +3045,7 @@ owner = kwd.get( 'owner', None ) changeset_revision = kwd.get( 'changeset_revision', None ) if name and owner and changeset_revision: - return suc.get_updated_changeset_revisions( trans, name, owner, changeset_revision ) + return suc.get_updated_changeset_revisions( trans.app, name, owner, changeset_revision ) return '' @web.expose @@ -3078,7 +3078,7 @@ def view_changelog( self, trans, id, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) changesets = [] for changeset in repo.changelog: @@ -3113,7 +3113,7 @@ def view_changeset( self, trans, id, ctx_str, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) ctx = hg_util.get_changectx_for_changeset( repo, ctx_str ) if ctx is None: @@ -3183,7 +3183,7 @@ def view_or_manage_repository( self, trans, **kwd ): repository_id = kwd.get( 'id', None ) if repository_id: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) user = trans.user if repository: if user is not None and ( trans.user_is_admin() or \ @@ -3202,7 +3202,7 @@ def view_repository( self, trans, id, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) @@ -3295,7 +3295,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repo_files_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_files_dir, create=False ) tool_metadata_dict = {} @@ -3345,7 +3345,10 @@ basic_util.remove_dir( work_dir ) break if guid: - tool_lineage = tool_util.get_version_lineage_for_tool( trans, repository_id, repository_metadata, guid ) + tool_lineage = tool_util.get_version_lineage_for_tool( trans.app, + repository_id, + repository_metadata, + guid ) else: repository_metadata_id = None metadata = None @@ -3377,8 +3380,8 @@ render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) - repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id ) + repository = suc.get_repository_in_tool_shed( trans.app, trans.security.encode_id( repository_metadata.repository_id ) ) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata return trans.fill_template( "/webapps/tool_shed/repository/view_workflow.mako", diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c 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 @@ -136,7 +136,7 @@ if repository_id: if changeset_revision: # Make sure there is not already a review of the revision by the user. - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) if review_util.get_review_by_repository_id_changeset_revision_user_id( trans=trans, repository_id=repository_id, changeset_revision=changeset_revision, @@ -465,7 +465,7 @@ status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) if repository_id: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] @@ -511,7 +511,7 @@ status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) changeset_revision = kwd.get( 'changeset_revision', None ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) @@ -547,7 +547,7 @@ action='view_or_manage_repository', **kwd ) ) # The user may not be the current user. The value of the received id is the encoded user id. - user = suc.get_user( trans, kwd[ 'id' ] ) + user = suc.get_user( trans.app, kwd[ 'id' ] ) self.repository_reviews_by_user_grid.title = "All repository revision reviews for user '%s'" % user.username return self.repository_reviews_by_user_grid( trans, **kwd ) @@ -575,7 +575,7 @@ # The value of the received id is the encoded repository id. message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] ) + repository = suc.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] ) changeset_revision = kwd.get( 'changeset_revision', None ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) previous_reviews_dict = review_util.get_previous_repository_reviews( trans, repository, changeset_revision ) @@ -591,7 +591,7 @@ @web.expose @web.require_login( "view or manage repository" ) def view_or_manage_repository( self, trans, **kwd ): - repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] ) + repository = suc.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] ) if trans.user_is_admin() or repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -35,9 +35,9 @@ status = kwd.get( 'status', 'done' ) commit_message = kwd.get( 'commit_message', 'Uploaded' ) category_ids = util.listify( kwd.get( 'category_id', '' ) ) - categories = suc.get_categories( trans ) + categories = suc.get_categories( trans.app ) repository_id = kwd.get( 'repository_id', '' ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) ) diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -103,7 +103,7 @@ class StatusColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): - return suc.get_tool_shed_repository_status_label( trans, tool_shed_repository ) + return suc.get_tool_shed_repository_status_label( trans.app, tool_shed_repository ) class ToolShedColumn( grids.TextColumn ): diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -185,7 +185,7 @@ return repair_dict def get_repo_info_dict( trans, repository_id, changeset_revision ): - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -579,7 +579,7 @@ filter = trans.app.repository_grid_filter_manager.get_filter( trans ) if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE: if category_id: - category = suc.get_category( trans, category_id ) + category = suc.get_category( trans.app, category_id ) if category: return trans.sa_session.query( model.Repository ) \ .join( model.RepositoryMetadata.table ) \ @@ -596,7 +596,7 @@ .outerjoin( model.Category.table ) if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES: if category_id: - category = suc.get_category( trans, category_id ) + category = suc.get_category( trans.app, category_id ) if category: return trans.sa_session.query( model.Repository ) \ .filter( model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION ) \ @@ -616,7 +616,7 @@ else: # The value of filter is None. if category_id: - category = suc.get_category( trans, category_id ) + category = suc.get_category( trans.app, category_id ) if category: return trans.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1580,7 +1580,8 @@ tool_shed_repository_id = None installation_status = 'unknown' if tool_shed_repository_id: - tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, trans.security.encode_id( tool_shed_repository_id ) ) + tool_shed_repository = suc.get_tool_shed_repository_by_id( trans.app, + trans.security.encode_id( tool_shed_repository_id ) ) if tool_shed_repository: if tool_shed_repository.missing_repository_dependencies: installation_status = '%s, missing repository dependencies' % installation_status diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -52,7 +52,7 @@ def export_repository( trans, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, export_repository_dependencies, api=False ): - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repositories_archive_filename = generate_repository_archive_filename( tool_shed_url, str( repository.name ), str( repository.user.username ), @@ -239,7 +239,7 @@ Return a list of dictionaries defining repositories that are required by the repository associated with the received repository_id. """ - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -38,7 +38,7 @@ flush = True # Do not allow dependent repository revisions to be automatically installed if population # resulted in errors. - dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( trans, repository_metadata ) + dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( trans.app, repository_metadata ) for dependent_downloadable_revision in dependent_downloadable_revisions: if dependent_downloadable_revision.downloadable: dependent_downloadable_revision.downloadable = False diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -352,10 +352,10 @@ repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) - skip_tool_test = suc.get_skip_tool_test_by_changeset_revision( trans, changeset_hash ) + skip_tool_test = suc.get_skip_tool_test_by_changeset_revision( trans.app, changeset_hash ) if skip_tool_test: # We found a skip_tool_test record associated with the changeset_revision, so see if it has a valid repository_revision. - repository_revision = suc.get_repository_metadata_by_id( trans, trans.security.encode_id( repository_metadata.id ) ) + repository_revision = get_repository_metadata_by_id( trans.app, trans.security.encode_id( repository_metadata.id ) ) if repository_revision: # The skip_tool_test record is associated with a valid repository_metadata record, so proceed. continue @@ -1117,9 +1117,10 @@ relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] return relative_path_to_file -def get_repository_metadata_by_id( trans, id ): +def get_repository_metadata_by_id( app, id ): """Get repository metadata from the database""" - return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) + sa_session = app.model.context.current + return sa_session.query( app.model.RepositoryMetadata ).get( app.security.decode_id( id ) ) def get_repository_metadata_by_repository_id_changeset_revision( trans, id, changeset_revision, metadata_only=False ): """Get a specified metadata record for a specified repository in the tool shed.""" @@ -1692,30 +1693,31 @@ workflows=None ) return containers_dict -def reset_all_metadata_on_installed_repository( trans, id ): +def reset_all_metadata_on_installed_repository( app, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" invalid_file_tups = [] metadata_dict = {} - repository = suc.get_installed_tool_shed_repository( trans.app, id ) - repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository ) - tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) + repository = suc.get_installed_tool_shed_repository( app, id ) + repository_clone_url = common_util.generate_clone_url_for_installed_repository( app, repository ) + tool_path, relative_install_dir = repository.get_tool_relative_path( app ) if relative_install_dir: original_metadata_dict = repository.metadata - metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, - repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) + metadata_dict, invalid_file_tups = \ + generate_metadata_for_changeset_revision( app=app, + repository=repository, + changeset_revision=repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: - suc.update_in_shed_tool_config( trans.app, repository ) - trans.install_model.context.add( repository ) - trans.install_model.context.flush() + suc.update_in_shed_tool_config( app, repository ) + app.install_model.context.add( repository ) + app.install_model.context.flush() log.debug( 'Metadata has been reset on repository %s.' % repository.name ) else: log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) @@ -1761,7 +1763,7 @@ repository_metadata.tool_versions = tool_versions_dict trans.sa_session.add( repository_metadata ) trans.sa_session.flush() - repository = suc.get_repository_in_tool_shed( trans, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) log.debug( "Resetting all metadata on repository: %s" % repository.name ) repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) @@ -1881,14 +1883,14 @@ try: if trans.webapp.name == 'tool_shed': # We're in the tool shed. - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) owner = str( repository.user.username ) invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, repository_id ) else: # We're in Galaxy. repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) owner = str( repository.owner ) - invalid_file_tups, metadata_dict = reset_all_metadata_on_installed_repository( trans, repository_id ) + invalid_file_tups, metadata_dict = reset_all_metadata_on_installed_repository( trans.app, repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) log.debug( message ) diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -269,10 +269,10 @@ message += '</table>' return message -def get_key_for_repository_changeset_revision( trans, toolshed_base_url, repository, repository_metadata, all_repository_dependencies ): +def get_key_for_repository_changeset_revision( app, toolshed_base_url, repository, repository_metadata, all_repository_dependencies ): # The received toolshed_base_url must include the port, but doesn't have to include the protocol. prior_installation_required, only_if_compiling_contained_td = \ - get_prior_installation_required_and_only_if_compiling_contained_td( trans, + get_prior_installation_required_and_only_if_compiling_contained_td( app, toolshed_base_url, repository, repository_metadata, @@ -286,7 +286,7 @@ only_if_compiling_contained_td=only_if_compiling_contained_td ) return key -def get_prior_installation_required_and_only_if_compiling_contained_td( trans, toolshed_base_url, repository, repository_metadata, +def get_prior_installation_required_and_only_if_compiling_contained_td( app, toolshed_base_url, repository, repository_metadata, all_repository_dependencies ): """ This method is called from the tool shed and never Galaxy. If all_repository_dependencies contains @@ -312,7 +312,7 @@ metadata = repository_metadata.metadata current_changeset_revision = str( repository_metadata.changeset_revision ) # Get the changeset revision to which the current value of required_repository_changeset_revision should be updated if it's not current. - text = suc.get_updated_changeset_revisions( trans, + text = suc.get_updated_changeset_revisions( app, name=str( repository.name ), owner=str( repository.user.username ), changeset_revision=current_changeset_revision ) @@ -401,7 +401,7 @@ # The value of the received toolshed_base_url must include the port, but doesn't have # to include the protocol. if 'repository_dependencies' in metadata: - current_repository_key = get_key_for_repository_changeset_revision( trans, + current_repository_key = get_key_for_repository_changeset_revision( trans.app, toolshed_base_url, repository, repository_metadata, diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -152,7 +152,7 @@ category_ids = [] category_names = repository_archive_dict.get( 'category_names', [] ) for category_name in category_names: - category = suc.get_category_by_name( trans, category_name ) + category = suc.get_category_by_name( trans.app, category_name ) if category is None: results_message += 'This Tool Shed does not have the category %s so it ' % str( category_name ) results_message += 'will not be associated with this repository.' diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -97,32 +97,32 @@ repositories_select_field.add_option( option_label, option_value ) return repositories_select_field -def build_tool_dependencies_select_field( trans, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled_only=False ): +def build_tool_dependencies_select_field( app, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled_only=False ): """Method called from Galaxy to generate the current list of tool dependency ids for an installed tool shed repository.""" tool_dependencies_select_field = SelectField( name=name, multiple=multiple, display=display ) for tool_dependency in tool_shed_repository.tool_dependencies: if uninstalled_only: - if tool_dependency.status not in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED, - trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: + if tool_dependency.status not in [ app.install_model.ToolDependency.installation_status.NEVER_INSTALLED, + app.install_model.ToolDependency.installation_status.UNINSTALLED ]: continue else: - if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED, - trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: + if tool_dependency.status in [ app.install_model.ToolDependency.installation_status.NEVER_INSTALLED, + app.install_model.ToolDependency.installation_status.UNINSTALLED ]: continue option_label = '%s version %s' % ( str( tool_dependency.name ), str( tool_dependency.version ) ) - option_value = trans.security.encode_id( tool_dependency.id ) + option_value = app.security.encode_id( tool_dependency.id ) tool_dependencies_select_field.add_option( option_label, option_value ) return tool_dependencies_select_field -def check_or_update_tool_shed_status_for_installed_repository( trans, repository ): +def check_or_update_tool_shed_status_for_installed_repository( app, repository ): updated = False - tool_shed_status_dict = get_tool_shed_status_for_installed_repository( trans.app, repository ) + tool_shed_status_dict = get_tool_shed_status_for_installed_repository( app, repository ) if tool_shed_status_dict: ok = True if tool_shed_status_dict != repository.tool_shed_status: repository.tool_shed_status = tool_shed_status_dict - trans.install_model.context.add( repository ) - trans.install_model.context.flush() + app.install_model.context.add( repository ) + app.install_model.context.flush() updated = True else: ok = False @@ -368,21 +368,24 @@ return os.path.abspath( os.path.join( root, name ) ) return file_path -def get_categories( trans ): +def get_categories( app ): """Get all categories from the database.""" - return trans.sa_session.query( trans.model.Category ) \ - .filter( trans.model.Category.table.c.deleted==False ) \ - .order_by( trans.model.Category.table.c.name ) \ - .all() + sa_session = app.model.context.current + return sa_session.query( app.model.Category ) \ + .filter( app.model.Category.table.c.deleted==False ) \ + .order_by( app.model.Category.table.c.name ) \ + .all() -def get_category( trans, id ): +def get_category( app, id ): """Get a category from the database.""" - return trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( id ) ) + sa_session = app.model.context.current + return sa_session.query( app.model.Category ).get( app.security.decode_id( id ) ) -def get_category_by_name( trans, name ): +def get_category_by_name( app, name ): """Get a category from the database via name.""" + sa_session = app.model.context.current try: - return trans.sa_session.query( trans.model.Category ).filter_by( name=name ).one() + return sa_session.query( app.model.Category ).filter_by( name=name ).one() except sqlalchemy.orm.exc.NoResultFound: return None @@ -419,21 +422,22 @@ return repository_metadata return None -def get_dependent_downloadable_revisions( trans, repository_metadata ): +def get_dependent_downloadable_revisions( app, repository_metadata ): """ Return all repository_metadata records that are downloadable and that depend upon the received repository_metadata record. """ # This method is called only from the tool shed. + sa_session = app.model.context.current rm_changeset_revision = repository_metadata.changeset_revision rm_repository = repository_metadata.repository rm_repository_name = str( rm_repository.name ) rm_repository_owner = str( rm_repository.user.username ) dependent_downloadable_revisions = [] - for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.id != rm_repository.id, - trans.model.Repository.table.c.deleted == False, - trans.model.Repository.table.c.deprecated == False ) ): + for repository in sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.id != rm_repository.id, + app.model.Repository.table.c.deleted == False, + app.model.Repository.table.c.deprecated == False ) ): downloadable_revisions = repository.downloadable_revisions if downloadable_revisions: for downloadable_revision in downloadable_revisions: @@ -454,14 +458,14 @@ else: # Make sure the defined changeset_revision is current. defined_repository_metadata = \ - trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) \ - .first() + sa_session.query( app.model.RepositoryMetadata ) \ + .filter( app.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) \ + .first() if defined_repository_metadata is None: # The defined changeset_revision is not associated with a repository_metadata # record, so updates must be necessary. - defined_repository = get_repository_by_name_and_owner( trans.app, name, owner ) - defined_repo = hg_util.get_repo_for_repository( trans.app, + defined_repository = get_repository_by_name_and_owner( app, name, owner ) + defined_repo = hg_util.get_repo_for_repository( app, repository=defined_repository, repo_path=None, create=False ) @@ -473,20 +477,21 @@ dependent_downloadable_revisions.append( downloadable_revision ) return dependent_downloadable_revisions -def get_ids_of_tool_shed_repositories_being_installed( trans, as_string=False ): +def get_ids_of_tool_shed_repositories_being_installed( app, as_string=False ): installing_repository_ids = [] - new_status = trans.install_model.ToolShedRepository.installation_status.NEW - cloning_status = trans.install_model.ToolShedRepository.installation_status.CLONING - setting_tool_versions_status = trans.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS - installing_dependencies_status = trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES - loading_datatypes_status = trans.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES - for tool_shed_repository in trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ - .filter( or_( trans.install_model.ToolShedRepository.status == new_status, - trans.install_model.ToolShedRepository.status == cloning_status, - trans.install_model.ToolShedRepository.status == setting_tool_versions_status, - trans.install_model.ToolShedRepository.status == installing_dependencies_status, - trans.install_model.ToolShedRepository.status == loading_datatypes_status ) ): - installing_repository_ids.append( trans.security.encode_id( tool_shed_repository.id ) ) + new_status = app.install_model.ToolShedRepository.installation_status.NEW + cloning_status = app.install_model.ToolShedRepository.installation_status.CLONING + setting_tool_versions_status = app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS + installing_dependencies_status = app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES + loading_datatypes_status = app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES + for tool_shed_repository in \ + app.install_model.context.query( app.install_model.ToolShedRepository ) \ + .filter( or_( app.install_model.ToolShedRepository.status == new_status, + app.install_model.ToolShedRepository.status == cloning_status, + app.install_model.ToolShedRepository.status == setting_tool_versions_status, + app.install_model.ToolShedRepository.status == installing_dependencies_status, + app.install_model.ToolShedRepository.status == loading_datatypes_status ) ): + installing_repository_ids.append( app.security.encode_id( tool_shed_repository.id ) ) if as_string: return ','.join( installing_repository_ids ) return installing_repository_ids @@ -723,12 +728,13 @@ repository = get_repository_by_name_and_owner( app, repository_name, repository_owner ) return repository, repository_dependencies -def get_repository_by_id( trans, id ): +def get_repository_by_id( app, id ): """Get a repository from the database via id.""" - if is_tool_shed_client( trans.app ): - return trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( id ) ) + if is_tool_shed_client( app ): + return app.install_model.context.query( app.install_model.ToolShedRepository ).get( app.security.decode_id( id ) ) else: - return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) + sa_session = app.model.context.current + return sa_session.query( app.model.Repository ).get( app.security.decode_id( id ) ) def get_repository_by_name( app, name ): """Get a repository from the database via name.""" @@ -851,7 +857,7 @@ beginning_on_size_error=True ) return safe_str -def get_repository_files( trans, folder_path ): +def get_repository_files( folder_path ): """Return the file hierarchy of a tool shed repository.""" contents = [] for item in os.listdir( folder_path ): @@ -866,7 +872,7 @@ contents.sort() return contents -def get_repository_from_refresh_on_change( trans, **kwd ): +def get_repository_from_refresh_on_change( app, **kwd ): # The changeset_revision_select_field in several grids performs a refresh_on_change which sends in request parameters like # changeset_revison_1, changeset_revision_2, etc. One of the many select fields on the grid performed the refresh_on_change, # so we loop through all of the received values to see which value is not the repository tip. If we find it, we know the @@ -876,9 +882,9 @@ for k, v in kwd.items(): changeset_revision_str = 'changeset_revision_' if k.startswith( changeset_revision_str ): - repository_id = trans.security.encode_id( int( k.lstrip( changeset_revision_str ) ) ) - repository = get_repository_in_tool_shed( trans, repository_id ) - if repository.tip( trans.app ) != v: + repository_id = app.security.encode_id( int( k.lstrip( changeset_revision_str ) ) ) + repository = get_repository_in_tool_shed( app, repository_id ) + if repository.tip( app ) != v: return v, repository # This should never be reached - raise an exception? return v, None @@ -919,9 +925,10 @@ prior_tsr_ids.append( encoded_repository_id ) return prior_tsr_ids -def get_repository_in_tool_shed( trans, id ): +def get_repository_in_tool_shed( app, id ): """Get a repository on the tool shed side from the database via id.""" - return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) + sa_session = app.model.context.current + return sa_session.query( app.model.Repository ).get( app.security.decode_id( id ) ) def get_repository_metadata_by_changeset_revision( app, id, changeset_revision ): """Get metadata for a specified repository change set from the database.""" @@ -944,9 +951,6 @@ return all_metadata_records[ 0 ] return None -def get_repository_metadata_by_id( trans, id ): - return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) - def get_repository_owner( cleaned_repository_url ): """Gvien a "cleaned" repository clone URL, return the owner of the repository.""" items = cleaned_repository_url.split( '/repos/' ) @@ -996,12 +1000,13 @@ if shed_tool_conf == file_name: return index, shed_tool_conf_dict -def get_skip_tool_test_by_changeset_revision( trans, changeset_revision ): +def get_skip_tool_test_by_changeset_revision( app, changeset_revision ): """Return a skip_tool_test record whose initial_changeset_revision is the received changeset_revision.""" # There should only be one, but we'll use first() so callers won't have to handle exceptions. - return trans.sa_session.query( trans.model.SkipToolTest ) \ - .filter( trans.model.SkipToolTest.table.c.initial_changeset_revision == changeset_revision ) \ - .first() + sa_session = app.model.context.current + return sa_session.query( app.model.SkipToolTest ) \ + .filter( app.model.SkipToolTest.table.c.initial_changeset_revision == changeset_revision ) \ + .first() def get_tool_panel_config_tool_path_install_dir( app, repository ): """ @@ -1026,12 +1031,12 @@ tool_path = shed_config_dict[ 'tool_path' ] return shed_tool_conf, tool_path, relative_install_dir -def get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ): +def get_tool_path_by_shed_tool_conf_filename( app, shed_tool_conf ): """ Return the tool_path config setting for the received shed_tool_conf file by searching the tool box's in-memory list of shed_tool_confs for the dictionary whose config_filename key has a value matching the received shed_tool_conf. """ - for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: + for shed_tool_conf_dict in app.toolbox.shed_tool_confs: config_filename = shed_tool_conf_dict[ 'config_filename' ] if config_filename == shed_tool_conf: return shed_tool_conf_dict[ 'tool_path' ] @@ -1045,12 +1050,12 @@ tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) return tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' ) -def get_tool_shed_repository_by_id( trans, repository_id ): +def get_tool_shed_repository_by_id( app, repository_id ): """Return a tool shed repository database record defined by the id.""" # This method is used only in Galaxy, not the tool shed. - return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ - .filter( trans.install_model.ToolShedRepository.table.c.id == trans.security.decode_id( repository_id ) ) \ - .first() + return app.install_model.context.query( app.install_model.ToolShedRepository ) \ + .filter( app.install_model.ToolShedRepository.table.c.id == app.security.decode_id( repository_id ) ) \ + .first() def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): """ @@ -1123,60 +1128,62 @@ log.exception( "Error attempting to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) ) return {} -def get_tool_shed_repository_status_label( trans, tool_shed_repository=None, name=None, owner=None, changeset_revision=None, repository_clone_url=None ): +def get_tool_shed_repository_status_label( app, tool_shed_repository=None, name=None, owner=None, changeset_revision=None, repository_clone_url=None ): """Return a color-coded label for the status of the received tool-shed_repository installed into Galaxy.""" if tool_shed_repository is None: if name is not None and owner is not None and repository_clone_url is not None: tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) - tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app, + tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, tool_shed, name, owner, changeset_revision ) if tool_shed_repository: status_label = tool_shed_repository.status - if tool_shed_repository.status in [ trans.install_model.ToolShedRepository.installation_status.CLONING, - trans.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS, - trans.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, - trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, - trans.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]: - bgcolor = trans.install_model.ToolShedRepository.states.INSTALLING - elif tool_shed_repository.status in [ trans.install_model.ToolShedRepository.installation_status.NEW, - trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]: - bgcolor = trans.install_model.ToolShedRepository.states.UNINSTALLED - elif tool_shed_repository.status in [ trans.install_model.ToolShedRepository.installation_status.ERROR ]: - bgcolor = trans.install_model.ToolShedRepository.states.ERROR - elif tool_shed_repository.status in [ trans.install_model.ToolShedRepository.installation_status.DEACTIVATED ]: - bgcolor = trans.install_model.ToolShedRepository.states.WARNING - elif tool_shed_repository.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLED ]: + if tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.CLONING, + app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS, + app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, + app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, + app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]: + bgcolor = app.install_model.ToolShedRepository.states.INSTALLING + elif tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.NEW, + app.install_model.ToolShedRepository.installation_status.UNINSTALLED ]: + bgcolor = app.install_model.ToolShedRepository.states.UNINSTALLED + elif tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.ERROR ]: + bgcolor = app.install_model.ToolShedRepository.states.ERROR + elif tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]: + bgcolor = app.install_model.ToolShedRepository.states.WARNING + elif tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.INSTALLED ]: if tool_shed_repository.repository_dependencies_being_installed: - bgcolor = trans.install_model.ToolShedRepository.states.WARNING - status_label = '%s, %s' % ( status_label, trans.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES ) + bgcolor = app.install_model.ToolShedRepository.states.WARNING + status_label = '%s, %s' % ( status_label, + app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES ) elif tool_shed_repository.missing_repository_dependencies: - bgcolor = trans.install_model.ToolShedRepository.states.WARNING + bgcolor = app.install_model.ToolShedRepository.states.WARNING status_label = '%s, missing repository dependencies' % status_label elif tool_shed_repository.tool_dependencies_being_installed: - bgcolor = trans.install_model.ToolShedRepository.states.WARNING - status_label = '%s, %s' % (status_label, trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + bgcolor = app.install_model.ToolShedRepository.states.WARNING + status_label = '%s, %s' % ( status_label, + app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) elif tool_shed_repository.missing_tool_dependencies: - bgcolor = trans.install_model.ToolShedRepository.states.WARNING + bgcolor = app.install_model.ToolShedRepository.states.WARNING status_label = '%s, missing tool dependencies' % status_label else: - bgcolor = trans.install_model.ToolShedRepository.states.OK + bgcolor = app.install_model.ToolShedRepository.states.OK else: - bgcolor = trans.install_model.ToolShedRepository.states.ERROR + bgcolor = app.install_model.ToolShedRepository.states.ERROR else: - bgcolor = trans.install_model.ToolShedRepository.states.WARNING + bgcolor = app.install_model.ToolShedRepository.states.WARNING status_label = 'unknown status' return '<div class="count-box state-color-%s">%s</div>' % ( bgcolor, status_label ) -def get_updated_changeset_revisions( trans, name, owner, changeset_revision ): +def get_updated_changeset_revisions( app, name, owner, changeset_revision ): """ Return a string of comma-separated changeset revision hashes for all available updates to the received changeset revision for the repository defined by the received name and owner. """ - repository = get_repository_by_name_and_owner( trans.app, name, owner ) - repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) + repository = get_repository_by_name_and_owner( app, name, owner ) + repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) # Get the upper bound changeset revision. upper_bound_changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) # Build the list of changeset revision hashes defining each available update up to, but excluding @@ -1208,9 +1215,10 @@ text = common_util.tool_shed_get( app, tool_shed_url, url ) return text -def get_user( trans, id ): +def get_user( app, id ): """Get a user from the database by id.""" - return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) + sa_session = app.model.context.current + return sa_session.query( app.model.User ).get( app.security.decode_id( id ) ) def get_user_by_username( app, username ): """Get a user from the database by username.""" @@ -1325,7 +1333,6 @@ return True return False - def is_tool_shed_client( app ): """ The tool shed and clients to the tool (i.e. Galaxy) require a lot of similar functionality in this file but with small differences. This @@ -1334,14 +1341,13 @@ """ return hasattr( app, "install_model" ) - -def open_repository_files_folder( trans, folder_path ): +def open_repository_files_folder( folder_path ): """ Return a list of dictionaries, each of which contains information for a file or directory contained within a directory in a repository file hierarchy. """ try: - files_list = get_repository_files( trans, folder_path ) + files_list = get_repository_files( folder_path ) except OSError, e: if str( e ).find( 'No such file or directory' ) >= 0: # We have a repository with no contents. diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -526,20 +526,20 @@ app.install_model.ToolVersionAssociation.table.c.tool_id == tool_version.id ) ) \ .first() -def get_version_lineage_for_tool( trans, repository_id, repository_metadata, guid ): +def get_version_lineage_for_tool( app, repository_id, repository_metadata, guid ): """ Return the tool version lineage chain in descendant order for the received guid contained in the received repsitory_metadata.tool_versions. """ - repository = suc.get_repository_by_id( trans, repository_id ) - repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) + repository = suc.get_repository_by_id( app, repository_id ) + repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) # Initialize the tool lineage version_lineage = [ guid ] # Get all ancestor guids of the received guid. current_child_guid = guid for changeset in hg_util.reversed_upper_bounded_changelog( repo, repository_metadata.changeset_revision ): ctx = repo.changectx( changeset ) - rm = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, str( ctx ) ) + rm = suc.get_repository_metadata_by_changeset_revision( app, repository_id, str( ctx ) ) if rm: parent_guid = rm.tool_versions.get( current_child_guid, None ) if parent_guid: @@ -549,9 +549,9 @@ current_parent_guid = guid for changeset in hg_util.reversed_lower_upper_bounded_changelog( repo, repository_metadata.changeset_revision, - repository.tip( trans.app ) ): + repository.tip( app ) ): ctx = repo.changectx( changeset ) - rm = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, str( ctx ) ) + rm = suc.get_repository_metadata_by_changeset_revision( app, repository_id, str( ctx ) ) if rm: tool_versions = rm.tool_versions for child_guid, parent_guid in tool_versions.items(): @@ -853,12 +853,14 @@ def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ): """ - Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename. The value of changeset_revision - is a valid (downloadable) changset revision. The tool config will be located in the repository manifest between the received valid changeset - revision and the first changeset revision in the repository, searching backwards. + Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value + of tool_config_filename. The value of changeset_revision is a valid (downloadable) + changset revision. The tool config will be located in the repository manifest between + the received valid changeset revision and the first changeset revision in the repository, + searching backwards. """ original_tool_data_path = trans.app.config.tool_data_path - repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) repo_files_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_files_dir, create=False ) message = '' @@ -869,7 +871,11 @@ can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision ) if can_use_disk_file: trans.app.config.tool_data_path = work_dir - tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, repository_id, tool_config_filepath, work_dir ) + tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans, + repo_files_dir, + repository_id, + tool_config_filepath, + work_dir ) if tool is not None: invalid_files_and_errors_tups = check_tool_input_params( trans.app, repo_files_dir, @@ -885,7 +891,12 @@ displaying_invalid_tool=True ) message = concat_messages( message, message2 ) else: - tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, repository_id, changeset_revision, tool_config_filename, work_dir ) + tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, + repo, + repository_id, + changeset_revision, + tool_config_filename, + work_dir ) basic_util.remove_dir( work_dir ) trans.app.config.tool_data_path = original_tool_data_path # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -176,13 +176,13 @@ workflow_name = encoding_util.tool_shed_decode( workflow_name ) if trans.webapp.name == 'tool_shed': # We're in the tool shed. - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata else: # We're in Galaxy. - repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id ) changeset_revision = repository.changeset_revision metadata = repository.metadata # metadata[ 'workflows' ] is a list of tuples where each contained tuple is diff -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc -r 9a69f032d6d9a0d5ece25332db78a81b3a18d91c templates/admin/tool_shed_repository/repair_repository.mako --- a/templates/admin/tool_shed_repository/repair_repository.mako +++ b/templates/admin/tool_shed_repository/repair_repository.mako @@ -56,7 +56,7 @@ for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple break - status_label = get_tool_shed_repository_status_label( trans, + status_label = get_tool_shed_repository_status_label( trans.app, tool_shed_repository=None, name=name, owner=repository_owner, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add the ability to purge a "white ghost" tool shed repository from Galaxy.
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7d6f8afcac4d/ Changeset: 7d6f8afcac4d User: greg Date: 2014-06-12 20:16:00 Summary: Add the ability to purge a "white ghost" tool shed repository from Galaxy. Affected #: 6 files diff -r 08fe9352836ee4d18ac3d446c45d84e5a7db9611 -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -238,7 +238,7 @@ def is_deactivated_or_installed( self ): return self.status in [ self.installation_status.DEACTIVATED, self.installation_status.INSTALLED ] - + @property def is_installed( self ): return self.status == self.installation_status.INSTALLED @@ -250,6 +250,10 @@ return False @property + def is_new( self ): + return self.status == self.installation_status.NEW + + @property def missing_repository_dependencies( self ): """Return the repository's repository dependencies that are not currently installed, and may not ever have been installed.""" missing_required_repositories = [] @@ -629,11 +633,11 @@ def to_dict( self, view='element' ): rval = super( ToolVersion, self ).to_dict( view=view ) - rval['tool_name'] = self.tool_id + rval[ 'tool_name' ] = self.tool_id for a in self.parent_tool_association: - rval['parent_tool_id'] = a.parent_id + rval[ 'parent_tool_id' ] = a.parent_id for a in self.child_tool_association: - rval['child_tool_id'] = a.tool_id + rval[ 'child_tool_id' ] = a.tool_id return rval diff -r 08fe9352836ee4d18ac3d446c45d84e5a7db9611 -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -45,7 +45,7 @@ def activate_repository( self, trans, **kwd ): """Activate a repository that was deactivated but not uninstalled.""" repository_id = kwd[ 'id' ] - repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) try: common_install_util.activate_repository( trans.app, repository ) except Exception, e: @@ -71,7 +71,7 @@ def browse_repository( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako', repository=repository, message=message, @@ -99,8 +99,13 @@ return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reset_to_install', **kwd ) ) + if operation == "purge": + kwd[ 'purge_repository' ] = True + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='purge_repository', + **kwd ) ) if operation == "activate or reinstall": - repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) if repository.uninstalled: # Since we're reinstalling the repository we need to find the latest changeset revision to which it can # be updated so that we can reset the metadata if necessary. This will ensure that information about @@ -134,7 +139,7 @@ **kwd ) ) else: message = "Unable to get latest revision for repository %s from " % str( repository.name ) - message += "the Tool Shed, so repository reinstallation is not possible at this time." + message += "the Tool Shed, so repository re-installation is not possible at this time." status = "error" return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', @@ -152,6 +157,10 @@ return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='install_latest_repository_revision', **kwd ) ) + if operation == 'install': + # The user is attempting to install a white ghost. + kwd[ 'status' ] = 'error' + kwd[ 'message' ] = 'It seems you are attempting to install a "white ghost", which should instead be purged.' return self.installed_repository_grid( trans, **kwd ) @web.expose @@ -196,7 +205,7 @@ def check_for_updates( self, trans, **kwd ): """Send a request to the relevant tool shed to see if there are any updates.""" repository_id = kwd.get( 'id', None ) - repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) params = '?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( web.url_for( '/', qualified=True ), @@ -220,7 +229,7 @@ status = kwd.get( 'status', 'done' ) remove_from_disk = kwd.get( 'remove_from_disk', '' ) remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) - tool_shed_repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) if relative_install_dir: if tool_path: @@ -375,7 +384,7 @@ of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which it was installed. """ - repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None: message = "Unable to retrieve tool dependencies from the Tool Shed because one or more of the following required " @@ -400,7 +409,7 @@ Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an uninstalled tool shed repository. """ - repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None: message = "Unable to retrieve updated repository information from the Tool Shed because one or more of the following " @@ -495,7 +504,7 @@ status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) if repository_id is not None: - repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) if repository is not None: tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) name = str( repository.name ) @@ -553,7 +562,7 @@ dependencies are included in the updated revision. """ updating_repository_id = kwd.get( 'updating_repository_id', None ) - repository = suc.get_installed_tool_shed_repository( trans, updating_repository_id ) + repository = suc.get_installed_tool_shed_repository( trans.app, updating_repository_id ) # All received dependencies need to be installed - confirmed by the caller. encoded_tool_dependencies_dict = kwd.get( 'encoded_tool_dependencies_dict', None ) if encoded_tool_dependencies_dict is not None: @@ -730,7 +739,7 @@ if repository_id is None: return trans.show_error_message( 'Missing required encoded repository id.' ) operation = kwd.get( 'operation', None ) - repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) if repository is None: return trans.show_error_message( 'Invalid repository specified.' ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) @@ -1254,6 +1263,32 @@ @web.expose @web.require_admin + def purge_repository( self, trans, **kwd ): + """Purge a "white ghost" repository from the database.""" + repository_id = kwd.get( 'id', None ) + new_kwd = {} + if repository_id is not None: + repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + if repository: + if kwd.get( 'purge_repository', False ): + purge_status, purge_message = repository_util.purge_repository( trans.app, repository ) + if purge_status == 'ok': + new_kwd[ 'status' ] = "done" + else: + new_kwd[ 'status' ] = 'error' + new_kwd[ 'message' ] = purge_message + else: + new_kwd[ 'status' ] = 'error' + new_kwd[ 'message' ] = 'Cannot locate the database record for the repository with encoded id %s.' % str( repository_id ) + else: + new_kwd[ 'status' ] = 'error' + new_kwd[ 'message' ] = 'Invalid repository id value "None" received for repository to be purged.' + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + **new_kwd ) ) + + @web.expose + @web.require_admin def reinstall_repository( self, trans, **kwd ): """ Reinstall a tool shed repository that has been previously uninstalled, making sure to handle all repository @@ -1262,7 +1297,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd[ 'id' ] - tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) no_changes = kwd.get( 'no_changes', '' ) no_changes_checked = CheckboxField.is_checked( no_changes ) install_repository_dependencies = CheckboxField.is_checked( kwd.get( 'install_repository_dependencies', '' ) ) @@ -1407,7 +1442,7 @@ action='browse_repositories', message=message, status=status ) ) - tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) if kwd.get( 'repair_repository_button', False ): encoded_repair_dict = kwd.get( 'repair_dict', None ) if encoded_repair_dict: @@ -1424,7 +1459,7 @@ repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) repositories_for_repair.append( repository ) return self.repair_tool_shed_repositories( trans, repositories_for_repair, ordered_repo_info_dicts ) - tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) encoded_repair_dict = encoding_util.tool_shed_encode( repair_dict ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) @@ -1486,7 +1521,7 @@ repository_id = kwd.get( 'id', None ) latest_changeset_revision = kwd.get( 'latest_changeset_revision', None ) latest_ctx_rev = kwd.get( 'latest_ctx_rev', None ) - tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) metadata = tool_shed_repository.metadata tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( tool_shed_repository.tool_shed ) ) @@ -1672,7 +1707,7 @@ @web.require_admin def reset_repository_metadata( self, trans, id ): """Reset all metadata on a single installed tool shed repository.""" - repository = suc.get_installed_tool_shed_repository( trans, id ) + repository = suc.get_installed_tool_shed_repository( trans.app, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: @@ -1711,7 +1746,7 @@ @web.require_admin def reset_to_install( self, trans, **kwd ): """An error occurred while cloning the repository, so reset everything necessary to enable another attempt.""" - repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) if kwd.get( 'reset_repository', False ): repository_util.set_repository_attributes( trans.app, repository, @@ -1721,7 +1756,7 @@ uninstalled=False, remove_from_disk=True ) new_kwd = {} - new_kwd[ 'message' ] = "You can now attempt to install the repository named %s again." % repository.name + new_kwd[ 'message' ] = "You can now attempt to install the repository named %s again." % str( repository.name ) new_kwd[ 'status' ] = "done" return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', @@ -1737,7 +1772,7 @@ Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed repository and update the metadata for the repository's revision in the Galaxy database. """ - repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ), str( repository.owner ), @@ -2052,7 +2087,7 @@ def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) repository_metadata = repository.metadata shed_config_dict = repository.get_shed_config_dict( trans.app ) tool_metadata = {} diff -r 08fe9352836ee4d18ac3d446c45d84e5a7db9611 -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -214,7 +214,14 @@ target=None, url_args=dict( controller='admin_toolshed', action='browse_repositories', - operation='activate or reinstall' ) ) ] + operation='activate or reinstall' ) ), + grids.GridOperation( label="Purge", + condition=( lambda item: item.is_new ), + allow_multiple=False, + target=None, + url_args=dict( controller='admin_toolshed', + action='browse_repositories', + operation='purge' ) ) ] standard_filters = [] default_filter = dict( deleted="False" ) num_rows_per_page = 50 diff -r 08fe9352836ee4d18ac3d446c45d84e5a7db9611 -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -976,6 +976,117 @@ """Pull changes from a remote repository to a local one.""" commands.pull( hg_util.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] ) +def purge_repository( app, repository ): + """Purge a repository with status New (a white ghost) from the database.""" + sa_session = app.model.context.current + status = 'ok' + message = '' + purged_tool_versions = 0 + purged_tool_dependencies = 0 + purged_required_repositories = 0 + purged_orphan_repository_repository_dependency_association_records = 0 + purged_orphan_repository_dependency_records = 0 + if repository.is_new: + # Purge this repository's associated tool versions. + if repository.tool_versions: + for tool_version in repository.tool_versions: + try: + tool_version_association = tool_version.parent_tool_association + sa_session.delete( tool_version_association ) + sa_session.flush() + except Exception, e: + status = 'error' + message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + try: + tool_version_association = tool_version.child_tool_association + sa_session.delete( tool_version_association ) + sa_session.flush() + except Exception, e: + status = 'error' + message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + try: + sa_session.delete( tool_version ) + sa_session.flush() + purged_tool_versions += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + # Purge this repository's associated tool dependencies. + if repository.tool_dependencies: + for tool_dependency in repository.tool_dependencies: + try: + sa_session.delete( tool_dependency ) + sa_session.flush() + purged_tool_dependencies += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge tool_dependencies for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + # Purge this repository's associated required repositories. + if repository.required_repositories: + for rrda in repository.required_repositories: + try: + sa_session.delete( rrda ) + sa_session.flush() + purged_required_repositories += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge required_repositories for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + # Purge any "orphan" repository_dependency records associated with the repository, but not with any + # repository_repository_dependency_association records. + for orphan_repository_dependency in \ + sa_session.query( app.install_model.RepositoryDependency ) \ + .filter( app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id ): + # Purge any repository_repository_dependency_association records whose repository_dependency_id is + # the id of the orphan repository_dependency record. + for orphan_rrda in \ + sa_session.query( app.install_model.RepositoryRepositoryDependencyAssociation ) \ + .filter( app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == orphan_repository_dependency.id ): + try: + sa_session.delete( orphan_rrda ) + sa_session.flush() + purged_orphan_repository_repository_dependency_association_records += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge repository_repository_dependency_association records associated with ' + message += 'an orphan repository_dependency record for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + try: + sa_session.delete( orphan_repository_dependency ) + sa_session.flush() + purged_orphan_repository_dependency_records += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge orphan repository_dependency records for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + # Purge the repository. + sa_session.delete( repository ) + sa_session.flush() + message = 'The repository named %s with status %s has been purged. ' % \ + ( str( repository.name ), str( repository.status ) ) + message += 'Total associated tool_version records purged: %d ' % purged_tool_versions + message += 'Total associated tool_dependency records purged: %d ' % purged_tool_dependencies + message += 'Total associated repository_repository_dependency_association records purged: %d ' % purged_required_repositories + message += 'Total associated orphan repository_repository_dependency_association records purged: %d ' % \ + purged_orphan_repository_repository_dependency_association_records + message += 'Total associated orphan repository_dependency records purged: %d ' % purged_orphan_repository_dependency_records + else: + status = 'error' + message = 'A repository must have the status New in order to be purged. This repository has ' + message += ' the status %s.' % str( repository.status ) + return status, message + def repair_tool_shed_repository( trans, repository, repo_info_dict ): def add_repair_dict_entry( repository_name, error_message ): diff -r 08fe9352836ee4d18ac3d446c45d84e5a7db9611 -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1696,7 +1696,7 @@ """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" invalid_file_tups = [] metadata_dict = {} - repository = suc.get_installed_tool_shed_repository( trans, id ) + repository = suc.get_installed_tool_shed_repository( trans.app, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: @@ -1886,7 +1886,7 @@ invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, repository_id ) else: # We're in Galaxy. - repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) owner = str( repository.owner ) invalid_file_tups, metadata_dict = reset_all_metadata_on_installed_repository( trans, repository_id ) if invalid_file_tups: diff -r 08fe9352836ee4d18ac3d446c45d84e5a7db9611 -r 7d6f8afcac4d6c208e864c9b8eb35d14d98725cc lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -491,9 +491,9 @@ return ','.join( installing_repository_ids ) return installing_repository_ids -def get_installed_tool_shed_repository( trans, id ): +def get_installed_tool_shed_repository( app, id ): """Get a tool shed repository record from the Galaxy database defined by the id.""" - return trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( id ) ) + return app.install_model.context.query( app.install_model.ToolShedRepository ).get( app.security.decode_id( id ) ) def get_latest_changeset_revision( app, repository, repo ): repository_tip = repository.tip( app ) 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: davebgx: Merge fix for dataset stdio.
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/08fe9352836e/ Changeset: 08fe9352836e User: davebgx Date: 2014-06-12 19:59:49 Summary: Merge fix for dataset stdio. Affected #: 1 file diff -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 -r 08fe9352836ee4d18ac3d446c45d84e5a7db9611 test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -386,8 +386,7 @@ self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) def get_job_stream( self, history_id, output_data, stream ): - encoded_id = self.twill_test_case.security.encode_id( output_data.get( 'id' ) ) - return self.twill_test_case._get_job_stream_output( encoded_id, stream=stream, format=False ) + return self.twill_test_case._get_job_stream_output( output_data.get( 'id' ), stream=stream, format=False ) def stage_data_async( self, test_data, history, shed_tool_id, async=True ): name = test_data.get( 'name', None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Revert change that ended up breaking display of job stdio in functional tests.
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b78595ec114/ Changeset: 9b78595ec114 Branch: stable User: davebgx Date: 2014-06-12 19:40:04 Summary: Revert change that ended up breaking display of job stdio in functional tests. Affected #: 1 file diff -r d6b1ea3a6a9ed2e7c3fa41518c5a690ed49c1265 -r 9b78595ec1142d75930dbfffd8baeaa689cb4c6c test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -386,8 +386,7 @@ self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) def get_job_stream( self, history_id, output_data, stream ): - encoded_id = self.twill_test_case.security.encode_id( output_data.get( 'id' ) ) - return self.twill_test_case._get_job_stream_output( encoded_id, stream=stream, format=False ) + return self.twill_test_case._get_job_stream_output( output_data.get( 'id' ), stream=stream, format=False ) def stage_data_async( self, test_data, history, shed_tool_id, async=True ): name = test_data.get( 'name', None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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