def import_workflows(self, trans, **kwd): """ POST /api/tool_shed_repositories/import_workflows Import all of the exported workflows contained in the specified installed tool shed repository into Galaxy. :param key: the API key of the Galaxy user with which the imported workflows will be associated. :param id: the encoded id of the ToolShedRepository object """ api_key = kwd.get('key', None) if api_key is None: raise HTTPBadRequest( detail= "Missing required parameter 'key' whose value is the API key for the Galaxy user importing the specified workflow." ) tool_shed_repository_id = kwd.get('id', '') if not tool_shed_repository_id: raise HTTPBadRequest(detail="Missing required parameter 'id'.") repository = repository_util.get_tool_shed_repository_by_id( self.app, tool_shed_repository_id) exported_workflows = json.loads( self.exported_workflows(trans, tool_shed_repository_id)) imported_workflow_dicts = [] for exported_workflow_dict in exported_workflows: workflow_name = exported_workflow_dict['workflow_name'] workflow, status, error_message = workflow_util.import_workflow( trans, repository, workflow_name) if status == 'error': log.debug(error_message) else: imported_workflow_dicts.append( workflow.to_dict(view='element')) return imported_workflow_dicts
def status(self, trans, id, **kwd): """ GET /api/tool_shed_repositories/{id}/status Display a dictionary containing information about a specified repository's installation status and a list of its dependencies and the status of each. :param id: the repository's encoded id """ tool_shed_repository = repository_util.get_tool_shed_repository_by_id( self.app, id) if tool_shed_repository is None: log.debug( "Unable to locate tool_shed_repository record for id %s." % (str(id))) return {} tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper(trans, tool_shed_repository)) tool_shed_repository_dict['url'] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id(tool_shed_repository.id)) tool_shed_repository_dict[ 'repository_dependencies'] = self.__flatten_repository_dependency_list( trans, tool_shed_repository) return tool_shed_repository_dict
def import_workflow( self, trans, payload, **kwd ): """ POST /api/tool_shed_repositories/import_workflow Import the specified exported workflow contained in the specified installed tool shed repository into Galaxy. :param key: the API key of the Galaxy user with which the imported workflow will be associated. :param id: the encoded id of the ToolShedRepository object The following parameters are included in the payload. :param index: the index location of the workflow tuple in the list of exported workflows stored in the metadata for the specified repository """ api_key = kwd.get( 'key', None ) if api_key is None: raise HTTPBadRequest( detail="Missing required parameter 'key' whose value is the API key for the Galaxy user importing the specified workflow." ) tool_shed_repository_id = kwd.get( 'id', '' ) if not tool_shed_repository_id: raise HTTPBadRequest( detail="Missing required parameter 'id'." ) index = payload.get( 'index', None ) if index is None: raise HTTPBadRequest( detail="Missing required parameter 'index'." ) repository = repository_util.get_tool_shed_repository_by_id( self.app, tool_shed_repository_id ) exported_workflows = json.loads( 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 ) ] workflow_name = exported_workflow[ 'workflow_name' ] workflow, status, error_message = workflow_util.import_workflow( trans, repository, workflow_name ) if status == 'error': log.debug( error_message ) return {} return workflow.to_dict( view='element' )
def exported_workflows(self, trans, id, **kwd): """ GET /api/tool_shed_repositories/{encoded_tool_shed_repository_id}/exported_workflows Display a list of dictionaries containing information about this tool shed repository's exported workflows. :param id: the encoded id of the ToolShedRepository object """ # Example URL: http://localhost:8763/api/tool_shed_repositories/f2db41e1fa331b3e/exported_workflows # 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 = repository_util.get_tool_shed_repository_by_id( self.app, id) metadata = repository.metadata if metadata: exported_workflow_tups = metadata.get('workflows', []) else: exported_workflow_tups = [] for index, exported_workflow_tup in enumerate(exported_workflow_tups): # The exported_workflow_tup looks like ( relative_path, exported_workflow_dict ), where the value of # relative_path is the location on disk (relative to the root of the installed repository) where the # exported_workflow_dict file (.ga file) is located. exported_workflow_dict = exported_workflow_tup[1] annotation = exported_workflow_dict.get('annotation', '') format_version = exported_workflow_dict.get('format-version', '') workflow_name = exported_workflow_dict.get('name', '') # 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. display_dict = dict(index=index, annotation=annotation, format_version=format_version, workflow_name=workflow_name) exported_workflows.append(display_dict) return exported_workflows
def import_workflows( self, trans, **kwd ): """ POST /api/tool_shed_repositories/import_workflows Import all of the exported workflows contained in the specified installed tool shed repository into Galaxy. :param key: the API key of the Galaxy user with which the imported workflows will be associated. :param id: the encoded id of the ToolShedRepository object """ api_key = kwd.get( 'key', None ) if api_key is None: raise HTTPBadRequest( detail="Missing required parameter 'key' whose value is the API key for the Galaxy user importing the specified workflow." ) tool_shed_repository_id = kwd.get( 'id', '' ) if not tool_shed_repository_id: raise HTTPBadRequest( detail="Missing required parameter 'id'." ) repository = repository_util.get_tool_shed_repository_by_id( self.app, tool_shed_repository_id ) exported_workflows = json.loads( self.exported_workflows( trans, tool_shed_repository_id ) ) imported_workflow_dicts = [] for exported_workflow_dict in exported_workflows: workflow_name = exported_workflow_dict[ 'workflow_name' ] workflow, status, error_message = workflow_util.import_workflow( trans, repository, workflow_name ) if status == 'error': log.debug( error_message ) else: imported_workflow_dicts.append( workflow.to_dict( view='element' ) ) return imported_workflow_dicts
def exported_workflows( self, trans, id, **kwd ): """ GET /api/tool_shed_repositories/{encoded_tool_shed_repository_id}/exported_workflows Display a list of dictionaries containing information about this tool shed repository's exported workflows. :param id: the encoded id of the ToolShedRepository object """ # Example URL: http://localhost:8763/api/tool_shed_repositories/f2db41e1fa331b3e/exported_workflows # 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 = repository_util.get_tool_shed_repository_by_id( self.app, id ) metadata = repository.metadata if metadata: exported_workflow_tups = metadata.get( 'workflows', [] ) else: exported_workflow_tups = [] for index, exported_workflow_tup in enumerate( exported_workflow_tups ): # The exported_workflow_tup looks like ( relative_path, exported_workflow_dict ), where the value of # relative_path is the location on disk (relative to the root of the installed repository) where the # exported_workflow_dict file (.ga file) is located. exported_workflow_dict = exported_workflow_tup[ 1 ] annotation = exported_workflow_dict.get( 'annotation', '' ) format_version = exported_workflow_dict.get( 'format-version', '' ) workflow_name = exported_workflow_dict.get( 'name', '' ) # 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. display_dict = dict( index=index, annotation=annotation, format_version=format_version, workflow_name=workflow_name ) exported_workflows.append( display_dict ) return exported_workflows
def import_workflow( self, trans, payload, **kwd ): """ POST /api/tool_shed_repositories/import_workflow Import the specified exported workflow contained in the specified installed tool shed repository into Galaxy. :param key: the API key of the Galaxy user with which the imported workflow will be associated. :param id: the encoded id of the ToolShedRepository object The following parameters are included in the payload. :param index: the index location of the workflow tuple in the list of exported workflows stored in the metadata for the specified repository """ api_key = kwd.get( 'key', None ) if api_key is None: raise HTTPBadRequest( detail="Missing required parameter 'key' whose value is the API key for the Galaxy user importing the specified workflow." ) tool_shed_repository_id = kwd.get( 'id', '' ) if not tool_shed_repository_id: raise HTTPBadRequest( detail="Missing required parameter 'id'." ) index = payload.get( 'index', None ) if index is None: raise HTTPBadRequest( detail="Missing required parameter 'index'." ) repository = repository_util.get_tool_shed_repository_by_id( self.app, tool_shed_repository_id ) exported_workflows = json.loads( 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 ) ] workflow_name = exported_workflow[ 'workflow_name' ] workflow, status, error_message = workflow_util.import_workflow( trans, repository, workflow_name ) if status == 'error': log.debug( error_message ) return {} return workflow.to_dict( view='element' )
def generate_workflow_image(trans, workflow_name, repository_metadata_id=None, repository_id=None): """ Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value. """ 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.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 = repository_util.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 # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] for workflow_tup in metadata['workflows']: workflow_dict = workflow_tup[1] if workflow_dict['name'] == workflow_name: break if 'tools' in metadata: tools_metadata = metadata['tools'] else: tools_metadata = [] workflow, missing_tool_tups = get_workflow_from_dict(trans=trans, workflow_dict=workflow_dict, tools_metadata=tools_metadata, repository_id=repository_id, changeset_revision=changeset_revision) workflow_canvas = WorkflowCanvas() canvas = workflow_canvas.canvas # Store px width for boxes of each step. for step in workflow.steps: step.upgrade_messages = {} module = module_factory.from_workflow_step(trans, repository_id, changeset_revision, tools_metadata, step) tool_errors = module.type == 'tool' and not module.tool module_data_inputs = get_workflow_data_inputs(step, module) module_data_outputs = get_workflow_data_outputs(step, module, workflow.steps) module_name = get_workflow_module_name(module, missing_tool_tups) workflow_canvas.populate_data_for_step( step, module_name, module_data_inputs, module_data_outputs, tool_errors=tool_errors ) workflow_canvas.add_steps(highlight_errors=True) workflow_canvas.finish() trans.response.set_content_type("image/svg+xml") return canvas.tostring()
def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ): """ Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value. """ 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.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 = repository_util.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 # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] for workflow_tup in metadata[ 'workflows' ]: workflow_dict = workflow_tup[1] if workflow_dict[ 'name' ] == workflow_name: break if 'tools' in metadata: tools_metadata = metadata[ 'tools' ] else: tools_metadata = [] workflow, missing_tool_tups = get_workflow_from_dict( trans=trans, workflow_dict=workflow_dict, tools_metadata=tools_metadata, repository_id=repository_id, changeset_revision=changeset_revision ) workflow_canvas = WorkflowCanvas() canvas = workflow_canvas.canvas # Store px width for boxes of each step. for step in workflow.steps: step.upgrade_messages = {} module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) tool_errors = module.type == 'tool' and not module.tool module_data_inputs = get_workflow_data_inputs( step, module ) module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps ) module_name = get_workflow_module_name( module, missing_tool_tups ) workflow_canvas.populate_data_for_step( step, module_name, module_data_inputs, module_data_outputs, tool_errors=tool_errors ) workflow_canvas.add_steps( highlight_errors=True ) workflow_canvas.finish( ) trans.response.set_content_type( "image/svg+xml" ) return canvas.tostring()
def __get_repo_dict_by_id(self, id): tool_shed_repository = repository_util.get_tool_shed_repository_by_id(self.app, id) if tool_shed_repository is None: log.debug("Unable to locate tool_shed_repository record for id %s." % (str(id))) return {} tool_shed_repository_dict = tool_shed_repository.as_dict(value_mapper=self.__get_value_mapper(tool_shed_repository)) tool_shed_repository_dict['url'] = web.url_for(controller='tool_shed_repositories', action='show', id=self.app.security.encode_id(tool_shed_repository.id)) tool_shed_repository_dict['repository_dependencies'] = self.__flatten_repository_dependency_list(tool_shed_repository) return tool_shed_repository_dict
def uninstall_repository(self, trans, id=None, **kwd): """ DELETE /api/tool_shed_repositories/id DELETE /api/tool_shed_repositories/ :param id: encoded repository id. Either id or name, owner, changeset_revision and tool_shed_url need to be supplied :param kwd: 'remove_from_disk' : Remove repository from disk or deactivate repository. Defaults to `True` (= remove repository from disk). 'name' : Repository name 'owner' : Repository owner 'changeset_revision': Changeset revision to uninstall 'tool_shed_url' : Tool Shed URL """ if id: try: repository = repository_util.get_tool_shed_repository_by_id( self.app, id) except ValueError: raise HTTPBadRequest( detail="No repository with id '%s' found" % id) else: tsr_arguments = [ 'name', 'owner', 'changeset_revision', 'tool_shed_url' ] try: tsr_arguments = {key: kwd[key] for key in tsr_arguments} except KeyError as e: raise HTTPBadRequest(detail="Missing required parameter '%s'" % e.args[0]) repository = repository_util.get_installed_repository( app=self.app, tool_shed=tsr_arguments['tool_shed_url'], name=tsr_arguments['name'], owner=tsr_arguments['owner'], changeset_revision=tsr_arguments['changeset_revision']) if not repository: raise HTTPBadRequest(detail="Repository not found") irm = InstalledRepositoryManager(app=self.app) errors = irm.uninstall_repository(repository=repository, remove_from_disk=kwd.get( 'remove_from_disk', True)) if not errors: action = 'removed' if kwd.get('remove_from_disk', True) else 'deactivated' return { 'message': 'The repository named %s has been %s.' % (repository.name, action) } else: raise Exception( 'Attempting to uninstall tool dependencies for repository named %s resulted in errors: %s' % (repository.name, errors))
def show( self, trans, id, **kwd ): """ GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id} Display a dictionary containing information about a specified tool_shed_repository. :param id: the encoded id of the ToolShedRepository object """ # Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e tool_shed_repository = repository_util.get_tool_shed_repository_by_id( self.app, id ) if tool_shed_repository is None: log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) ) return {} tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) return tool_shed_repository_dict
def show( self, trans, id, **kwd ): """ GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id} Display a dictionary containing information about a specified tool_shed_repository. :param id: the encoded id of the ToolShedRepository object """ # Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e tool_shed_repository = repository_util.get_tool_shed_repository_by_id( self.app, id ) if tool_shed_repository is None: log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) ) return {} tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) return tool_shed_repository_dict
def get_components_from_repository_dependency_for_installed_repository( self, repository_dependency): """ Parse a repository dependency and return components necessary for proper display in Galaxy on the Manage repository page. """ # Default prior_installation_required and only_if_compiling_contained_td to False. prior_installation_required = 'False' only_if_compiling_contained_td = 'False' if len(repository_dependency) == 6: # Metadata should have been reset on this installed repository, but it wasn't. tool_shed_repository_id = repository_dependency[4] installation_status = repository_dependency[5] tool_shed, name, owner, changeset_revision = repository_dependency[ 0:4] repository_dependency = [ tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ] elif len(repository_dependency) == 7: # We have a repository dependency tuple that includes a prior_installation_required value but not a only_if_compiling_contained_td value. tool_shed_repository_id = repository_dependency[5] installation_status = repository_dependency[6] tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency[ 0:5] repository_dependency = \ [ tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ] elif len(repository_dependency) == 8: # We have a repository dependency tuple that includes both a prior_installation_required value # and a only_if_compiling_contained_td value. tool_shed_repository_id = repository_dependency[6] installation_status = repository_dependency[7] repository_dependency = repository_dependency[0:6] else: tool_shed_repository_id = None installation_status = 'unknown' if tool_shed_repository_id: tool_shed_repository = repository_util.get_tool_shed_repository_by_id( self.app, self.app.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 elif tool_shed_repository.missing_tool_dependencies: installation_status = '%s, missing tool dependencies' % installation_status return tool_shed_repository_id, installation_status, repository_dependency
def status( self, trans, id, **kwd ): """ GET /api/tool_shed_repositories/{id}/status Display a dictionary containing information about a specified repository's installation status and a list of its dependencies and the status of each. :param id: the repository's encoded id """ tool_shed_repository = repository_util.get_tool_shed_repository_by_id( self.app, id ) if tool_shed_repository is None: log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) ) return {} tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) tool_shed_repository_dict[ 'repository_dependencies' ] = self.__flatten_repository_dependency_list( trans, tool_shed_repository ) return tool_shed_repository_dict
def get_components_from_repository_dependency_for_installed_repository(self, repository_dependency): """ Parse a repository dependency and return components necessary for proper display in Galaxy on the Manage repository page. """ # Default prior_installation_required and only_if_compiling_contained_td to False. prior_installation_required = 'False' only_if_compiling_contained_td = 'False' if len(repository_dependency) == 6: # Metadata should have been reset on this installed repository, but it wasn't. tool_shed_repository_id = repository_dependency[4] installation_status = repository_dependency[5] tool_shed, name, owner, changeset_revision = repository_dependency[0:4] repository_dependency = [tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td] elif len(repository_dependency) == 7: # We have a repository dependency tuple that includes a prior_installation_required value but not a only_if_compiling_contained_td value. tool_shed_repository_id = repository_dependency[5] installation_status = repository_dependency[6] tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency[0:5] repository_dependency = \ [tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td] elif len(repository_dependency) == 8: # We have a repository dependency tuple that includes both a prior_installation_required value # and a only_if_compiling_contained_td value. tool_shed_repository_id = repository_dependency[6] installation_status = repository_dependency[7] repository_dependency = repository_dependency[0:6] else: tool_shed_repository_id = None installation_status = 'unknown' if tool_shed_repository_id: tool_shed_repository = repository_util.get_tool_shed_repository_by_id(self.app, self.app.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 elif tool_shed_repository.missing_tool_dependencies: installation_status = '%s, missing tool dependencies' % installation_status return tool_shed_repository_id, installation_status, repository_dependency
def uninstall_repository(self, trans, id=None, **kwd): """ DELETE /api/tool_shed_repositories/id DELETE /api/tool_shed_repositories/ :param id: encoded repository id. Either id or name, owner, changeset_revision and tool_shed_url need to be supplied :param kwd: 'remove_from_disk' : Remove repository from disk or deactivate repository. Defaults to `True` (= remove repository from disk). 'name' : Repository name 'owner' : Repository owner 'changeset_revision': Changeset revision to uninstall 'tool_shed_url' : Tool Shed URL """ if id: try: repository = repository_util.get_tool_shed_repository_by_id(self.app, id) except ValueError: raise HTTPBadRequest(detail="No repository with id '%s' found" % id) else: tsr_arguments = ['name', 'owner', 'changeset_revision', 'tool_shed_url'] try: tsr_arguments = {key: kwd[key] for key in tsr_arguments} except KeyError as e: raise HTTPBadRequest(detail="Missing required parameter '%s'" % e.args[0]) repository = repository_util.get_installed_repository(app=self.app, tool_shed=tsr_arguments['tool_shed_url'], name=tsr_arguments['name'], owner=tsr_arguments['owner'], changeset_revision=tsr_arguments['changeset_revision']) if not repository: raise HTTPBadRequest(detail="Repository not found") irm = InstalledRepositoryManager(app=self.app) errors = irm.uninstall_repository(repository=repository, remove_from_disk=kwd.get('remove_from_disk', True)) if not errors: action = 'removed' if kwd.get('remove_from_disk', True) else 'deactivated' return {'message': 'The repository named %s has been %s.' % (repository.name, action)} else: raise Exception('Attempting to uninstall tool dependencies for repository named %s resulted in errors: %s' % (repository.name, errors))