def create_tool_dependency_objects(app, tool_shed_repository, relative_install_dir, set_status=True): """Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when installing a new tool_shed_repository.""" tool_dependency_objects = [] shed_config_dict = tool_shed_repository.get_shed_config_dict(app) if shed_config_dict.get('tool_path'): relative_install_dir = os.path.join(shed_config_dict.get('tool_path'), relative_install_dir) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', relative_install_dir) tree, error_message = xml_util.parse_xml(tool_dependencies_config) if tree is None: return tool_dependency_objects root = tree.getroot() fabric_version_checked = False for elem in root: tool_dependency_type = elem.tag if tool_dependency_type == 'package': name = elem.get('name', None) version = elem.get('version', None) if name and version: tool_dependency = create_or_update_tool_dependency( app, tool_shed_repository, name=name, version=version, type=tool_dependency_type, status=app.model.ToolDependency.installation_status. NEVER_INSTALLED, set_status=set_status) tool_dependency_objects.append(tool_dependency) elif tool_dependency_type == 'set_environment': for env_elem in elem: # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> name = env_elem.get('name', None) action = env_elem.get('action', None) if name and action: tool_dependency = create_or_update_tool_dependency( app, tool_shed_repository, name=name, version=None, type=tool_dependency_type, status=app.model.ToolDependency.installation_status. NEVER_INSTALLED, set_status=set_status) tool_dependency_objects.append(tool_dependency) return tool_dependency_objects
def create_tool_dependency_objects( app, tool_shed_repository, relative_install_dir, set_status=True ): """ Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when installing a new tool_shed_repository. """ tool_dependency_objects = [] shed_config_dict = tool_shed_repository.get_shed_config_dict( app ) if shed_config_dict.get( 'tool_path' ): relative_install_dir = os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) tree, error_message = xml_util.parse_xml( tool_dependencies_config ) if tree is None: return tool_dependency_objects root = tree.getroot() fabric_version_checked = False for elem in root: tool_dependency_type = elem.tag if tool_dependency_type == 'package': name = elem.get( 'name', None ) version = elem.get( 'version', None ) if name and version: status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED tool_dependency = create_or_update_tool_dependency( app, tool_shed_repository, name=name, version=version, type=tool_dependency_type, status=status, set_status=set_status ) tool_dependency_objects.append( tool_dependency ) elif tool_dependency_type == 'set_environment': for env_elem in elem: # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> name = env_elem.get( 'name', None ) action = env_elem.get( 'action', None ) if name and action: status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED tool_dependency = create_or_update_tool_dependency( app, tool_shed_repository, name=name, version=None, type=tool_dependency_type, status=status, set_status=set_status ) tool_dependency_objects.append( tool_dependency ) return tool_dependency_objects
def load_installed_datatypes( app, repository, relative_install_dir, deactivate=False ): # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later. metadata = repository.metadata repository_dict = None datatypes_config = suc.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, relative_install_dir ) if datatypes_config: converter_path, display_path = alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=deactivate ) if converter_path or display_path: # Create a dictionary of tool shed repository related information. repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=repository.tool_shed, name=repository.name, owner=repository.owner, installed_changeset_revision=repository.installed_changeset_revision, tool_dicts=metadata.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) return repository_dict
def load_installed_datatypes(app, repository, relative_install_dir, deactivate=False): # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later. metadata = repository.metadata repository_dict = None datatypes_config = suc.get_config_from_disk(suc.DATATYPES_CONFIG_FILENAME, relative_install_dir) if datatypes_config: converter_path, display_path = alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=deactivate) if converter_path or display_path: # Create a dictionary of tool shed repository related information. repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=repository.tool_shed, name=repository.name, owner=repository.owner, installed_changeset_revision=repository. installed_changeset_revision, tool_dicts=metadata.get('tools', []), converter_path=converter_path, display_path=display_path) return repository_dict
tool_util.add_to_tool_panel( self.app, tool_shed_repository.name, repository_clone_url, tool_shed_repository.installed_changeset_revision, repository_tools_tups, self.repository_owner, self.migrated_tools_config, tool_panel_dict=tool_panel_dict_for_display, new_install=True ) if install_dependencies and tool_dependencies and has_tool_dependencies: # Install tool dependencies. suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from disk. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=self.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, tool_dependencies=tool_dependencies, from_install_manager=True ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe following error occurred from the InstallManager while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' if 'datatypes' in metadata_dict: tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: tool_shed_repository.includes_datatypes = True self.app.install_model.context.add( tool_shed_repository ) self.app.install_model.context.flush()
def handle_repository_contents( self, tool_shed_repository, repository_clone_url, relative_install_dir, repository_elem, install_dependencies ): """Generate the metadata for the installed tool shed repository, among other things.""" tool_panel_dict_for_display = odict() if self.tool_path: repo_install_dir = os.path.join( self.tool_path, relative_install_dir ) else: repo_install_dir = relative_install_dir for tool_elem in repository_elem: # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems. is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) if is_displayed: tool_panel_dict_for_tool_config = tool_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v else: print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=self.app, repository=tool_shed_repository, changeset_revision=tool_shed_repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = self.shed_config_dict, relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=True ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() if 'tool_dependencies' in metadata_dict: # All tool_dependency objects must be created before the tools are processed even if no tool dependencies will be installed. tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) else: tool_dependencies = None if 'tools' in metadata_dict: sample_files = metadata_dict.get( 'sample_files', [] ) sample_files = [ str( s ) for s in sample_files ] tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata_dict ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. repository_tools_tups = tool_util.handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups ) # Handle missing index files for tool parameters that are dynamically generated select lists. repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( self.app, self.tool_path, sample_files, repository_tools_tups, sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. tool_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied ) if install_dependencies and tool_dependencies and 'tool_dependencies' in metadata_dict: # Install tool dependencies. suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from disk. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=self.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, tool_dependencies=tool_dependencies ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == self.app.model.ToolDependency.installation_status.ERROR: print '\nThe following error occurred from the InstallManager while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' tool_util.add_to_tool_panel( self.app, tool_shed_repository.name, repository_clone_url, tool_shed_repository.installed_changeset_revision, repository_tools_tups, self.repository_owner, self.migrated_tools_config, tool_panel_dict=tool_panel_dict_for_display, new_install=True ) if 'datatypes' in metadata_dict: tool_shed_repository.status = self.app.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: tool_shed_repository.includes_datatypes = True self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-hrc" ) datatypes_config = suc.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, repo_install_dir ) # Load proprietary data types required by tools. The value of override is not important here since the Galaxy server will be started # after this installation completes. converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir if converter_path or display_path: # Create a dictionary of tool shed repository related information. repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed, name=tool_shed_repository.name, owner=self.repository_owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, tool_dicts=metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: # Load proprietary datatype converters self.app.datatypes_registry.load_datatype_converters( self.toolbox, installed_repository_dict=repository_dict ) if display_path: # Load proprietary datatype display applications self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) try: shutil.rmtree( work_dir ) except: pass