def non_shed_tool_panel_configs(self): return common_util.get_non_shed_tool_panel_configs(self.app)
def verify_tools(app, url, galaxy_config_file=None, engine_options={}): # Check the value in the migrate_tools.version database table column to verify that the number is in # sync with the number of version scripts in ~/lib/galaxy/tools/migrate/versions. # Create engine and metadata engine = create_engine(url, **engine_options) meta = MetaData(bind=engine) # The migrate_tools table was created in database version script 0092_add_migrate_tools_table.py. Table("migrate_tools", meta, autoload=True) # Verify that the code and the database are in sync. db_schema = schema.ControlledSchema(engine, migrate_repository) latest_tool_migration_script_number = migrate_repository.versions.latest if latest_tool_migration_script_number != db_schema.version: # The default behavior is that the tool shed is down. tool_shed_accessible = False if app.new_installation: # New installations will not be missing tools, so we don't need to worry about them. missing_tool_configs_dict = OrderedDict() else: tool_panel_configs = common_util.get_non_shed_tool_panel_configs(app) if tool_panel_configs: # The missing_tool_configs_dict contents are something like: # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number) else: # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in # the database. tool_shed_accessible = True missing_tool_configs_dict = OrderedDict() have_tool_dependencies = False for k, v in missing_tool_configs_dict.items(): if v: have_tool_dependencies = True break if not app.config.running_functional_tests: if tool_shed_accessible: # Automatically update the value of the migrate_tools.version database table column. manage_tools = os.path.abspath(os.path.join(os.path.dirname(__file__), 'scripts', 'manage_tools.py')) cmd = [get_executable(), manage_tools, 'upgrade', 'tools'] if galaxy_config_file: cmd[2:2] = ['-c', galaxy_config_file] proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) return_code = proc.wait() output = proc.stdout.read(32768) if return_code != 0: raise Exception("Error attempting to update the value of migrate_tools.version: %s" % output) elif missing_tool_configs_dict: if len(tool_panel_configs) == 1: plural = '' tool_panel_config_file_names = tool_panel_configs[0] else: plural = 's' tool_panel_config_file_names = ', '.join(tool_panel_configs) msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be\n" msg += "automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" msg += "be removed from your file{} named {}.\n\n".format(plural, tool_panel_config_file_names) msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="database/shed_tools">). The default location\n' msg += "setting is 'database/shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n" msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n" msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n" msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n" msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n" msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n" msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n" msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n" if have_tool_dependencies: msg += "The following tool dependencies can also optionally be installed (see the option flag in the command below). If you\n" msg += "choose to install them (recommended), they will be installed within the location specified by the 'tool_dependency_dir'\n" msg += "setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).\n" processed_tool_dependencies = [] for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): for tool_dependencies_tup in missing_tool_configs_dict[missing_tool_config]['tool_dependencies']: if tool_dependencies_tup not in processed_tool_dependencies: msg += "------------------------------------\n" msg += "Tool Dependency\n" msg += "------------------------------------\n" msg += "Name: {}, Version: {}, Type: {}\n".format(tool_dependencies_tup[0], tool_dependencies_tup[1], tool_dependencies_tup[2]) if len(tool_dependencies_tup) >= 4: msg += "Requirements and installation information:\n" msg += "%s\n" % tool_dependencies_tup[3] else: msg += "\n" msg += "------------------------------------\n" processed_tool_dependencies.append(tool_dependencies_tup) msg += "\n" msg += "%s" % output.replace('done', '') msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" msg += "sh ./scripts/migrate_tools/%04d_tools.sh\n" % latest_tool_migration_script_number msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" if have_tool_dependencies: msg += "The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies'\n" msg += "option to the above command like this:\n\n" msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" msg += "sh ./scripts/migrate_tools/%04d_tools.sh install_dependencies\n" % latest_tool_migration_script_number msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" msg += "Tool dependencies can be installed after the repositories have been installed as well.\n\n" msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been\n" msg += "removed from your file{} named {}.\n\n".format(plural, tool_panel_config_file_names) for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): msg += "%s\n" % missing_tool_config msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" raise Exception(msg) else: log.debug("The main Galaxy tool shed is not currently available, so skipped tool migration %s until next server startup" % db_schema.version) else: log.info("At migrate_tools version %d" % db_schema.version)
def __init__(self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies): """ Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. """ self.app = app self.toolbox = self.app.toolbox self.migrated_tools_config = migrated_tools_config # Initialize the ToolPanelManager. self.tpm = tool_panel_manager.ToolPanelManager(self.app) # If install_dependencies is True but tool_dependency_dir is not set, do not attempt # to install but print informative error message. if install_dependencies and app.tool_dependency_dir is None: message = 'You are attempting to install tool dependencies but do not have a value ' message += 'for "tool_dependency_dir" set in your galaxy.ini file. Set this ' message += 'location value to the path where you want tool dependencies installed and ' message += 'rerun the migration script.' raise Exception(message) # Get the local non-shed related tool panel configs (there can be more than one, and the # default name is tool_conf.xml). self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number) # Set the location where the repositories will be installed by retrieving the tool_path # setting from migrated_tools_config. try: tree, error_message = parse_xml(migrated_tools_config) except OSError as exc: if exc.errno == errno.ENOENT: with open(migrated_tools_config, 'w') as fh: fh.write( MIGRATED_TOOLS_CONF_XML.format( shed_tools_dir=self.app.config.shed_tools_dir)) tree, error_message = parse_xml(migrated_tools_config) else: raise if tree is None: log.error(error_message) else: root = tree.getroot() self.tool_path = root.get('tool_path') log.debug( "Repositories will be installed into configured tool_path location ", str(self.tool_path)) # Parse tool_shed_install_config to check each of the tools. self.tool_shed_install_config = tool_shed_install_config tree, error_message = parse_xml(tool_shed_install_config) if tree is None: log.error(error_message) else: root = tree.getroot() defined_tool_shed_url = root.get('name') self.tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, defined_tool_shed_url) self.tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( self.tool_shed_url) self.repository_owner = common_util.REPOSITORY_OWNER self.shed_config_dict = self.tpm.get_shed_tool_conf_dict( self.migrated_tools_config) # Since tool migration scripts can be executed any number of times, we need to # make sure the appropriate tools are defined in tool_conf.xml. If no tools # associated with the migration stage are defined, no repositories will be installed # on disk. The default behavior is that the tool shed is down. tool_shed_accessible = False tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app) if tool_panel_configs: # The missing_tool_configs_dict contents are something like: # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} tool_shed_accessible, missing_tool_configs_dict = \ common_util.check_for_missing_tools(app, tool_panel_configs, latest_migration_script_number) else: # It doesn't matter if the tool shed is accessible since there are no migrated # tools defined in the local Galaxy instance, but we have to set the value of # tool_shed_accessible to True so that the value of migrate_tools.version can # be correctly set in the database. tool_shed_accessible = True missing_tool_configs_dict = {} if tool_shed_accessible: if len(self.proprietary_tool_confs) == 1: plural = '' file_names = self.proprietary_tool_confs[0] else: plural = 's' file_names = ', '.join(self.proprietary_tool_confs) if missing_tool_configs_dict: for proprietary_tool_conf in self.proprietary_tool_confs: # Create a backup of the tool configuration in the un-migrated state. shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % (proprietary_tool_conf, latest_migration_script_number)) for repository_elem in root: # Make sure we have a valid repository tag. if self.__is_valid_repository_tag(repository_elem): # Get all repository dependencies for the repository defined by the # current repository_elem. Repository dependency definitions contained # in tool shed repositories with migrated tools must never define a # relationship to a repository dependency that contains a tool. The # repository dependency can only contain items that are not loaded into # the Galaxy tool panel (e.g., tool dependency definitions, custom datatypes, # etc). This restriction must be followed down the entire dependency hierarchy. name = repository_elem.get('name') changeset_revision = repository_elem.get( 'changeset_revision') tool_shed_accessible, repository_dependencies_dict = \ common_util.get_repository_dependencies(app, self.tool_shed_url, name, self.repository_owner, changeset_revision) # Make sure all repository dependency records exist (as tool_shed_repository # table rows) in the Galaxy database. created_tool_shed_repositories = \ self.create_or_update_tool_shed_repository_records(name=name, changeset_revision=changeset_revision, repository_dependencies_dict=repository_dependencies_dict) # Order the repositories for proper installation. This process is similar to the # process used when installing tool shed repositories, but does not handle managing # tool panel sections and other components since repository dependency definitions # contained in tool shed repositories with migrated tools must never define a relationship # to a repository dependency that contains a tool. ordered_tool_shed_repositories = \ self.order_repositories_for_installation(created_tool_shed_repositories, repository_dependencies_dict) for tool_shed_repository in ordered_tool_shed_repositories: is_repository_dependency = self.__is_repository_dependency( name, changeset_revision, tool_shed_repository) self.install_repository( repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency= is_repository_dependency) else: message = "\nNo tools associated with migration stage %s are defined in your " % \ str(latest_migration_script_number) message += "file%s named %s,\nso no repositories will be installed on disk.\n" % \ (plural, file_names) log.info(message) else: message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % \ str(latest_migration_script_number) message += "Try again later.\n" log.error(message)