commit/galaxy-central: greg: Handle tool panel locations appropriately for tool shed repositories and repository dependencies being installed or reinstalled into Galaxy.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f93f509ca0c2/ changeset: f93f509ca0c2 user: greg date: 2013-01-04 22:10:26 summary: Handle tool panel locations appropriately for tool shed repositories and repository dependencies being installed or reinstalled into Galaxy. affected #: 2 files
diff -r 8fe64f73835cd19274dcac65c935187d426b18ba -r f93f509ca0c2a21acdf0ed17615d1caf839dcb98 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -5,6 +5,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.webapps.community.util import container_util import shed_util_common as suc +import galaxy.tools from galaxy.tools.search import ToolBoxSearch from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package, set_environment from galaxy.tool_shed import encoding_util @@ -175,14 +176,17 @@ # Attempt to ensure we're copying an appropriate file. if is_data_index_sample_file( filename ): suc.copy_sample_file( app, filename, dest_path=dest_path ) -def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, install_repository_dependencies=False ): +def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, install_repository_dependencies=False, + no_changes_checked=False, tool_panel_section=None, new_tool_panel_section=None ): """ Discover all repository dependencies and make sure all tool_shed_repository and associated repository_dependency records exist as well as the dependency relationships between installed repositories. This method is called when new repositories are being installed into a Galaxy instance and when uninstalled repositories are being reinstalled. """ message = '' + # There will be a one-to-one mapping between items in created_or_updated_tool_shed_repositories and tool_panel_section_keys. created_or_updated_tool_shed_repositories = [] + tool_panel_section_keys = [] # Repositories will be filtered (e.g., if already installed, etc), so filter the associated repo_info_dicts accordingly. filtered_repo_info_dicts = [] if install_repository_dependencies: @@ -204,6 +208,11 @@ installed_tool_shed_repository, installed_changeset_revision = \ repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, clone_dir ) if installed_tool_shed_repository: + tool_section, new_tool_panel_section, tool_panel_section_key = handle_tool_panel_selection( trans=trans, + metadata=installed_tool_shed_repository.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if reinstalling or install_repository_dependencies: if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR, trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: @@ -217,22 +226,23 @@ # There is a repository already installed which is a dependency of the repository being reinstalled. can_update = False else: - # An attempt is being made to install a tool shed repository into a Galaxy instance when the same repository was previously installed. - message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner ) - if installed_changeset_revision != changeset_revision: - message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision - else: - message += "was previously installed. " - if installed_tool_shed_repository.uninstalled: - message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. " - elif installed_tool_shed_repository.deleted: - message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. " - if installed_changeset_revision != changeset_revision: - message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " - message += "<b>Repository Actions</b> pop-up menu. " if len( all_repo_info_dicts ) == 1: + # An attempt is being made to install a tool shed repository into a Galaxy instance when the same repository was previously installed. + message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner ) + if installed_changeset_revision != changeset_revision: + message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision + else: + message += "was previously installed. " + if installed_tool_shed_repository.uninstalled: + message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. " + elif installed_tool_shed_repository.deleted: + message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. " + if installed_changeset_revision != changeset_revision: + message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " + message += "<b>Repository Actions</b> pop-up menu. " created_or_updated_tool_shed_repositories.append( installed_tool_shed_repository ) - return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message + tool_panel_section_keys.append( tool_panel_section_key ) + return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message else: can_update = True else: @@ -243,6 +253,36 @@ metadata_dict={} dist_to_shed = False if can_update: + if reinstalling or install_repository_dependencies: + # Get the repository metadata to see where it was previously located in the tool panel. + installed_tool_shed_repository = suc.get_repository_for_dependency_relationship( app=trans.app, + tool_shed=tool_shed_url, + name=name, + owner=repository_owner, + changeset_revision=changeset_revision ) + if installed_tool_shed_repository: + tool_section, new_tool_panel_section, tool_panel_section_key = \ + handle_tool_panel_selection( trans=trans, + metadata=installed_tool_shed_repository.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) + else: + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + elif tool_panel_section: + tool_panel_section_key = 'section_%s' % tool_panel_section + else: + tool_panel_section_key = None + else: + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + elif tool_panel_section: + tool_panel_section_key = 'section_%s' % tool_panel_section + else: + tool_panel_section_key = None tool_shed_repository = suc.create_or_update_tool_shed_repository( app=trans.app, name=name, description=description, @@ -255,8 +295,9 @@ owner=repository_owner, dist_to_shed=False ) created_or_updated_tool_shed_repositories.append( tool_shed_repository ) + tool_panel_section_keys.append( tool_panel_section_key ) filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) - return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message + return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message def create_repository_dict_for_proprietary_datatypes( tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None ): return dict( tool_shed=tool_shed, repository_name=name, @@ -836,6 +877,60 @@ app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) return installed_tool_dependencies +def handle_tool_panel_selection( trans, metadata, no_changes_checked, tool_panel_section, new_tool_panel_section ): + """Handle the selected tool panel location for loading tools included in tool shed repositories when installing or reinstalling them.""" + # Get the location in the tool panel in which each tool was originally loaded. + tool_section = None + tool_panel_section_key = None + if 'tools' in metadata: + if 'tool_panel_section' in metadata: + tool_panel_dict = metadata[ 'tool_panel_section' ] + if not tool_panel_dict: + tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + else: + tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + # This forces everything to be loaded into the same section (or no section) in the tool panel. + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] + original_section_id = tool_section_dict[ 'id' ] + original_section_name = tool_section_dict[ 'name' ] + if no_changes_checked: + if original_section_id: + tool_panel_section_key = 'section_%s' % str( original_section_id ) + if tool_panel_section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. + elem = Element( 'section' ) + elem.attrib[ 'name' ] = original_section_name + elem.attrib[ 'id' ] = original_section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section + else: + # The user elected to change the tool panel section to contain the tools. + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + if tool_panel_section_key in trans.app.toolbox.tool_panel: + # Appending a tool to an existing section in trans.app.toolbox.tool_panel + log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + # Appending a new section to trans.app.toolbox.tool_panel + log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) + elem = Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section + elem.attrib[ 'id' ] = section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section + elif tool_panel_section: + tool_panel_section_key = 'section_%s' % tool_panel_section + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + tool_section = None + return tool_section, new_tool_panel_section, tool_panel_section_key def handle_tool_versions( app, tool_version_dicts, tool_shed_repository ): """ Using the list of tool_version_dicts retrieved from the tool shed (one per changeset revison up to the currently installed changeset revision),
diff -r 8fe64f73835cd19274dcac65c935187d426b18ba -r f93f509ca0c2a21acdf0ed17615d1caf839dcb98 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 @@ -396,7 +396,7 @@ if operation == "activate or reinstall": repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: - if repository.includes_tools: + if repository.includes_tools or repository.has_repository_dependencies: # Only allow selecting a different section in the tool panel if the repository was uninstalled. return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reselect_tool_panel_section', @@ -835,17 +835,19 @@ @web.require_admin def install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ): """Install specified tool shed repositories.""" - repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] ) tool_path = kwd[ 'tool_path' ] includes_tool_dependencies = util.string_as_bool( kwd[ 'includes_tool_dependencies' ] ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) - tool_panel_section_key = kwd.get( 'tool_panel_section_key', None ) - if tool_panel_section_key: - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - tool_section = None - for tup in zip( tool_shed_repositories, repo_info_dicts ): - tool_shed_repository, repo_info_dict = tup + # There must be a one-to-one mapping between items in the 3 lists:tool_shed_repositories, tool_panel_section_keys, repo_info_dicts. + tool_panel_section_keys = util.listify( kwd[ 'tool_panel_section_keys' ] ) + repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] ) + for index, tool_shed_repository in enumerate( tool_shed_repositories ): + repo_info_dict = repo_info_dicts[ index ] + tool_panel_section_key = tool_panel_section_keys[ index ] + if tool_panel_section_key: + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + tool_section = None if isinstance( repo_info_dict, basestring ): repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) # Clone each repository to the configured location. @@ -1021,13 +1023,17 @@ encoded_kwd = kwd[ 'encoded_kwd' ] decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd ) tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ] + tool_panel_section_keys = decoded_kwd[ 'tool_panel_section_keys' ] + filtered_tool_panel_section_keys = [] repositories_for_installation = [] - for tsr_id in tsr_ids: + for index, tsr_id in enumerate( tsr_ids ): repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) if repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: repositories_for_installation.append( repository ) + filtered_tool_panel_section_keys.append( tool_panel_section_keys[ index ] ) if repositories_for_installation: + decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd ) else: kwd[ 'message' ] = 'All selected tool shed repositories are already installed.' @@ -1154,6 +1160,7 @@ # Every repository will be installed into the same tool panel section or all will be installed outside of any sections. new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section = kwd.get( 'tool_panel_section', '' ) + tool_panel_section_keys = [] # One or more repositories may include tools, but not necessarily all of them. includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) ) includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) ) @@ -1191,13 +1198,16 @@ else: install_tool_dependencies = False tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) - created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, - install_repository_dependencies=install_repository_dependencies ) + install_repository_dependencies=install_repository_dependencies, + no_changes_checked=False, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if message and len( repo_info_dicts ) == 1: installed_tool_shed_repository = created_or_updated_tool_shed_repositories[ 0 ] message+= 'Click <a href="%s">here</a> to manage the repository. ' % \ @@ -1235,6 +1245,10 @@ tool_panel_section_key = None tool_section = None tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] + # Create a one-to-one mapping of tool shed repository id and tool panel section key. All tools contained in the repositories + # being installed will be loaded into the same section in the tool panel. + for tsr in created_or_updated_tool_shed_repositories: + tool_panel_section_keys.append( tool_panel_section_key ) new_kwd = dict( includes_tools=includes_tools, includes_repository_dependencies=includes_repository_dependencies, install_repository_dependencies=install_repository_dependencies, @@ -1245,7 +1259,8 @@ shed_tool_conf=shed_tool_conf, status=status, tool_path=tool_path, - tool_panel_section_key=tool_panel_section_key, + + tool_panel_section_keys=tool_panel_section_keys, tool_shed_repository_ids=tsrids_list, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) @@ -1369,66 +1384,25 @@ no_changes_checked = CheckboxField.is_checked( no_changes ) install_repository_dependencies = CheckboxField.is_checked( kwd.get( 'install_repository_dependencies', '' ) ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) - new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) - tool_panel_section = kwd.get( 'tool_panel_section', '' ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) clone_dir = os.path.join( tool_path, shed_util.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) tool_section = None + tool_panel_section = kwd.get( 'tool_panel_section', '' ) + new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section_key = None + tool_panel_section_keys = [] metadata = tool_shed_repository.metadata if tool_shed_repository.includes_tools: - # Get the location in the tool panel in which each tool was originally loaded. - if 'tool_panel_section' in metadata: - tool_panel_dict = metadata[ 'tool_panel_section' ] - if not tool_panel_dict: - tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - else: - tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - # Fix this to handle the case where the tools are distributed across in more than 1 ToolSection - this assumes everything was loaded into 1 - # section (or no section) in the tool panel. - tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] - tool_section_dict = tool_section_dicts[ 0 ] - original_section_id = tool_section_dict[ 'id' ] - original_section_name = tool_section_dict[ 'name' ] - if no_changes_checked: - if original_section_id: - tool_panel_section_key = 'section_%s' % str( original_section_id ) - if tool_panel_section_key in trans.app.toolbox.tool_panel: - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. - elem = Element( 'section' ) - elem.attrib[ 'name' ] = original_section_name - elem.attrib[ 'id' ] = original_section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section - else: - # The user elected to change the tool panel section to contain the tools. - if new_tool_panel_section: - section_id = new_tool_panel_section.lower().replace( ' ', '_' ) - tool_panel_section_key = 'section_%s' % str( section_id ) - if tool_panel_section_key in trans.app.toolbox.tool_panel: - # Appending a tool to an existing section in trans.app.toolbox.tool_panel - log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - # Appending a new section to trans.app.toolbox.tool_panel - log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) - elem = Element( 'section' ) - elem.attrib[ 'name' ] = new_tool_panel_section - elem.attrib[ 'id' ] = section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section - elif tool_panel_section: - tool_panel_section_key = 'section_%s' % tool_panel_section - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - tool_section = None + # Handle the selected tool panel location for loading tools included in the tool shed repository. + tool_section, new_tool_panel_section, tool_panel_section_key = \ + shed_util.handle_tool_panel_selection( trans=trans, + metadata=metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) # The repository's status must be updated from 'Uninstall' to 'New' when initiating reinstall so the repository_installation_updater will function. tool_shed_repository = suc.create_or_update_tool_shed_repository( trans.app, tool_shed_repository.name, @@ -1471,22 +1445,31 @@ repo_info_dict = encoding_util.tool_shed_encode( repo_info_dict ) repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. - created_or_updated_tool_shed_repositories = [ tool_shed_repository ] if install_repository_dependencies: # This is a bit screwy because filtered_repo_info_dicts in this block is a list of tool_shed_encoded dictionaries, but # in the associated else block, it is a list of unencoded dictionaries - not sure if this should be corrected... - created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=True, - install_repository_dependencies=install_repository_dependencies ) + install_repository_dependencies=install_repository_dependencies, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if len( created_or_updated_tool_shed_repositories ) > 1: # Build repository dependency relationships. suc.build_repository_dependency_relationships( trans, repo_info_dicts, created_or_updated_tool_shed_repositories ) else: filtered_repo_info_dicts = [ repo_info_dict for repo_info_dict in repo_info_dicts ] + created_or_updated_tool_shed_repositories = [ tool_shed_repository ] + tool_panel_section_keys.append( tool_panel_section_key ) + # Defaulot the selected tool panel location for loading tools included in each newly installed required tool shed repository to the location + # selected for the repository selected for reinstallation. + for index, tps_key in enumerate( tool_panel_section_keys ): + if tps_key is None: + tool_panel_section_keys[ index ] = tool_panel_section_key encoded_repository_ids = [ trans.security.encode_id( r.id ) for r in created_or_updated_tool_shed_repositories ] new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, @@ -1498,7 +1481,7 @@ status=status, tool_panel_section=tool_panel_section, tool_path=tool_path, - tool_panel_section_key=tool_panel_section_key, + tool_panel_section_keys=tool_panel_section_keys, tool_shed_repository_ids=encoded_repository_ids, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) @@ -1530,6 +1513,7 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): + """Select or change the tool panel section to contain the tools included in the tool shed repositories being reinstalled.""" message = '' repository_id = kwd[ 'id' ] tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id )
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