def get_or_create_tool_shed_repository(self, tool_shed, name, owner, changeset_revision): """ Return a tool shed repository database record defined by the combination of tool shed, repository name, repository owner and changeset_revision or installed_changeset_revision. A new tool shed repository record will be created if one is not located. """ install_model = self.app.install_model # We store the port in the database. tool_shed = common_util.remove_protocol_from_tool_shed_url(tool_shed) # This method is used only in Galaxy, not the tool shed. repository = repository_util.get_repository_for_dependency_relationship(self.app, tool_shed, name, owner, changeset_revision) if not repository: tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed) repository_clone_url = os.path.join(tool_shed_url, 'repos', owner, name) ctx_rev = suc.get_ctx_rev(self.app, tool_shed_url, name, owner, changeset_revision) repository = repository_util.create_or_update_tool_shed_repository(app=self.app, name=name, description=None, installed_changeset_revision=changeset_revision, ctx_rev=ctx_rev, repository_clone_url=repository_clone_url, metadata_dict={}, status=install_model.ToolShedRepository.installation_status.NEW, current_changeset_revision=None, owner=owner, dist_to_shed=False) return repository
def get_or_create_tool_shed_repository( self, tool_shed, name, owner, changeset_revision ): """ Return a tool shed repository database record defined by the combination of tool shed, repository name, repository owner and changeset_revision or installed_changeset_revision. A new tool shed repository record will be created if one is not located. """ install_model = self.app.install_model # We store the port in the database. tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed ) # This method is used only in Galaxy, not the tool shed. repository = repository_util.get_repository_for_dependency_relationship( self.app, tool_shed, name, owner, changeset_revision ) if not repository: tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) ctx_rev = suc.get_ctx_rev( self.app, tool_shed_url, name, owner, changeset_revision ) repository = repository_util.create_or_update_tool_shed_repository( app=self.app, name=name, description=None, installed_changeset_revision=changeset_revision, ctx_rev=ctx_rev, repository_clone_url=repository_clone_url, metadata_dict={}, status=install_model.ToolShedRepository.installation_status.NEW, current_changeset_revision=None, owner=owner, dist_to_shed=False ) return repository
def handle_complex_repository_dependency_for_package( self, elem, package_name, package_version, tool_shed_repository, from_tool_migration_manager=False ): """ Inspect the repository defined by a complex repository dependency definition and take certain steps to enable installation of the received package name and version to proceed. The received elem is the <repository> tag set which defines the complex repository dependency. The received tool_shed_repository is the installed tool shed repository for which the tool dependency defined by the received package_name and package_version is being installed. """ handled_tool_dependencies = [] tool_shed_url = elem.attrib[ 'toolshed' ] required_repository_name = elem.attrib[ 'name' ] required_repository_owner = elem.attrib[ 'owner' ] default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ] required_repository = repository_util.get_repository_for_dependency_relationship( self.app, tool_shed_url, required_repository_name, required_repository_owner, default_required_repository_changeset_revision ) tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url ) tmp_filename = None if required_repository: required_repository_changeset_revision = required_repository.installed_changeset_revision # Define the installation directory for the required tool dependency package in the required repository. required_repository_package_install_dir = \ tool_dependency_util.get_tool_dependency_install_dir( app=self.app, repository_name=required_repository_name, repository_owner=required_repository_owner, repository_changeset_revision=required_repository_changeset_revision, tool_dependency_type='package', tool_dependency_name=package_name, tool_dependency_version=package_version ) # Define this dependent repository's tool dependency installation directory that will contain # the env.sh file with a path to the required repository's installed tool dependency package. dependent_install_dir = \ tool_dependency_util.get_tool_dependency_install_dir( app=self.app, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, repository_changeset_revision=tool_shed_repository.installed_changeset_revision, tool_dependency_type='package', tool_dependency_name=package_name, tool_dependency_version=package_version ) if os.path.exists( dependent_install_dir ): # The install manager handles tool migration stages and the sync_database_with_file_system() # method handles two scenarios: (1) where a Galaxy file system environment related to installed # Tool Shed repositories and tool dependencies has somehow gotten out of sync with the Galaxy # database tables associated with these installed items, and (2) the Tool Shed's install and test # framework which installs repositories in 2 stages, those of type tool_dependency_definition # followed by those containing valid tools and tool functional test components. Neither of these # scenarios apply when the install manager is running. if from_tool_migration_manager: can_install_tool_dependency = True else: # Notice that we'll throw away the following tool_dependency if it can be installed. tool_dependency, can_install_tool_dependency = self.sync_database_with_file_system( self.app, tool_shed_repository, package_name, package_version, dependent_install_dir, tool_dependency_type='package' ) if not can_install_tool_dependency: log.debug( "Tool dependency %s version %s cannot be installed (it was probably previously installed), " "so appending it to the list of handled tool dependencies.", str( tool_dependency.name), str( tool_dependency.version ) ) handled_tool_dependencies.append( tool_dependency ) else: can_install_tool_dependency = True if can_install_tool_dependency: # Set this dependent repository's tool dependency env.sh file with a path to the required repository's # installed tool dependency package. We can get everything we need from the discovered installed # required_repository. if required_repository.is_deactivated_or_installed: if not os.path.exists( required_repository_package_install_dir ): log.error( 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) ) repo_files_dir = required_repository.repo_files_directory( self.app ) if not repo_files_dir: message = "Unable to locate the repository directory for revision %s of installed repository %s owned by %s." % \ ( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) ) raise Exception( message ) tool_dependencies_config = repository_util.get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) if tool_dependencies_config: config_to_use = tool_dependencies_config else: message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \ ( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) ) raise Exception( message ) else: # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision # should be updated if it's not current. text = metadata_util.get_updated_changeset_revisions_from_tool_shed( app=self.app, tool_shed_url=tool_shed, name=required_repository_name, owner=required_repository_owner, changeset_revision=required_repository_changeset_revision ) if text: updated_changeset_revisions = listify( text ) # The list of changeset revisions is in reverse order, so the newest will be first. required_repository_changeset_revision = updated_changeset_revisions[ 0 ] # Make a call to the tool shed to get the required repository's tool_dependencies.xml file. tmp_filename = self.create_temporary_tool_dependencies_config( tool_shed, required_repository_name, required_repository_owner, required_repository_changeset_revision ) config_to_use = tmp_filename handled_tool_dependencies = \ self.create_tool_dependency_with_initialized_env_sh_file( dependent_install_dir=dependent_install_dir, tool_shed_repository=tool_shed_repository, required_repository=required_repository, package_name=package_name, package_version=package_version, tool_dependencies_config=config_to_use ) self.remove_file( tmp_filename ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ ( str( required_repository_name ), str( required_repository_owner ), str( default_required_repository_changeset_revision ) ) raise Exception( message ) return handled_tool_dependencies
def get_env_shell_file_paths(self, elem): # Currently only the following tag set is supported. # <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056"> # <package name="numpy" version="1.7.1" /> # </repository> env_shell_file_paths = [] toolshed = elem.get('toolshed', None) repository_name = elem.get('name', None) repository_owner = elem.get('owner', None) changeset_revision = elem.get('changeset_revision', None) if toolshed and repository_name and repository_owner and changeset_revision: # The protocol is not stored, but the port is if it exists. toolshed = common_util.remove_protocol_from_tool_shed_url(toolshed) repository = repository_util.get_repository_for_dependency_relationship(self.app, toolshed, repository_name, repository_owner, changeset_revision) if repository: for sub_elem in elem: tool_dependency_type = sub_elem.tag tool_dependency_name = sub_elem.get('name') tool_dependency_version = sub_elem.get('version') if tool_dependency_type and tool_dependency_name and tool_dependency_version: # Get the tool_dependency so we can get its installation directory. tool_dependency = None for tool_dependency in repository.tool_dependencies: if tool_dependency.type == tool_dependency_type and \ tool_dependency.name == tool_dependency_name and \ tool_dependency.version == tool_dependency_version: break if tool_dependency: installation_directory = tool_dependency.installation_directory(self.app) env_shell_file_path = self.get_env_shell_file_path(installation_directory) if env_shell_file_path: env_shell_file_paths.append(env_shell_file_path) else: error_message = "Skipping tool dependency definition because unable to locate env.sh file for tool dependency " error_message += "type %s, name %s, version %s for repository %s" % \ (str(tool_dependency_type), str(tool_dependency_name), str(tool_dependency_version), str(repository.name)) log.debug(error_message) continue else: error_message = "Skipping tool dependency definition because unable to locate tool dependency " error_message += "type %s, name %s, version %s for repository %s" % \ (str(tool_dependency_type), str(tool_dependency_name), str(tool_dependency_version), str(repository.name)) log.debug(error_message) continue else: error_message = "Skipping invalid tool dependency definition: type %s, name %s, version %s." % \ (str(tool_dependency_type), str(tool_dependency_name), str(tool_dependency_version)) log.debug(error_message) continue else: error_message = "Skipping set_environment_for_install definition because unable to locate required installed tool shed repository: " error_message += "toolshed %s, name %s, owner %s, changeset_revision %s." % \ (str(toolshed), str(repository_name), str(repository_owner), str(changeset_revision)) log.debug(error_message) else: error_message = "Skipping invalid set_environment_for_install definition: toolshed %s, name %s, owner %s, changeset_revision %s." % \ (str(toolshed), str(repository_name), str(repository_owner), str(changeset_revision)) log.debug(error_message) return env_shell_file_paths
def get_env_shell_file_paths(self, elem): # Currently only the following tag set is supported. # <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056"> # <package name="numpy" version="1.7.1" /> # </repository> env_shell_file_paths = [] toolshed = elem.get('toolshed', None) repository_name = elem.get('name', None) repository_owner = elem.get('owner', None) changeset_revision = elem.get('changeset_revision', None) if toolshed and repository_name and repository_owner and changeset_revision: # The protocol is not stored, but the port is if it exists. toolshed = common_util.remove_protocol_from_tool_shed_url(toolshed) repository = repository_util.get_repository_for_dependency_relationship( self.app, toolshed, repository_name, repository_owner, changeset_revision) if repository: for sub_elem in elem: tool_dependency_type = sub_elem.tag tool_dependency_name = sub_elem.get('name') tool_dependency_version = sub_elem.get('version') if tool_dependency_type and tool_dependency_name and tool_dependency_version: # Get the tool_dependency so we can get its installation directory. tool_dependency = None for tool_dependency in repository.tool_dependencies: if tool_dependency.type == tool_dependency_type and \ tool_dependency.name == tool_dependency_name and \ tool_dependency.version == tool_dependency_version: break if tool_dependency: installation_directory = tool_dependency.installation_directory( self.app) env_shell_file_path = self.get_env_shell_file_path( installation_directory) if env_shell_file_path: env_shell_file_paths.append( env_shell_file_path) else: error_message = "Skipping tool dependency definition because unable to locate env.sh file for tool dependency " error_message += "type %s, name %s, version %s for repository %s" % \ (str(tool_dependency_type), str(tool_dependency_name), str(tool_dependency_version), str(repository.name)) log.debug(error_message) continue else: error_message = "Skipping tool dependency definition because unable to locate tool dependency " error_message += "type %s, name %s, version %s for repository %s" % \ (str(tool_dependency_type), str(tool_dependency_name), str(tool_dependency_version), str(repository.name)) log.debug(error_message) continue else: error_message = "Skipping invalid tool dependency definition: type %s, name %s, version %s." % \ (str(tool_dependency_type), str(tool_dependency_name), str(tool_dependency_version)) log.debug(error_message) continue else: error_message = "Skipping set_environment_for_install definition because unable to locate required installed tool shed repository: " error_message += "toolshed %s, name %s, owner %s, changeset_revision %s." % \ (str(toolshed), str(repository_name), str(repository_owner), str(changeset_revision)) log.debug(error_message) else: error_message = "Skipping invalid set_environment_for_install definition: toolshed %s, name %s, owner %s, changeset_revision %s." % \ (str(toolshed), str(repository_name), str(repository_owner), str(changeset_revision)) log.debug(error_message) return env_shell_file_paths