Source code for tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager

import logging

from tool_shed.galaxy_install.tool_dependencies.recipe import step_handler
from tool_shed.galaxy_install.tool_dependencies.recipe import tag_handler

log = logging.getLogger(__name__)


[docs]class StepManager(object):

[docs]    def __init__(self, app):
        self.app = app
        self.step_handlers_by_type = self.load_step_handlers()

[docs]    def get_step_handler_by_type(self, type):
        return self.step_handlers_by_type.get(type, None)

[docs]    def execute_step(self, tool_dependency, package_name, actions, action_type, action_dict, filtered_actions,
                     env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False):
        if actions:
            step_handler = self.get_step_handler_by_type(action_type)
            tool_dependency, filtered_actions, dir = step_handler.execute_step(tool_dependency=tool_dependency,
                                                                               package_name=package_name,
                                                                               actions=actions,
                                                                               action_dict=action_dict,
                                                                               filtered_actions=filtered_actions,
                                                                               env_file_builder=env_file_builder,
                                                                               install_environment=install_environment,
                                                                               work_dir=work_dir,
                                                                               current_dir=current_dir,
                                                                               initial_download=initial_download)
        else:
            dir = None
        return tool_dependency, filtered_actions, dir

[docs]    def load_step_handlers(self):
        step_handlers_by_type = dict(assert_directory_executable=step_handler.AssertDirectoryExecutable(self.app),
                                     assert_directory_exists=step_handler.AssertDirectoryExists(self.app),
                                     assert_file_executable=step_handler.AssertFileExecutable(self.app),
                                     assert_file_exists=step_handler.AssertFileExists(self.app),
                                     autoconf=step_handler.Autoconf(self.app),
                                     change_directory=step_handler.ChangeDirectory(self.app),
                                     chmod=step_handler.Chmod(self.app),
                                     download_binary=step_handler.DownloadBinary(self.app),
                                     download_by_url=step_handler.DownloadByUrl(self.app),
                                     download_file=step_handler.DownloadFile(self.app),
                                     make_directory=step_handler.MakeDirectory(self.app),
                                     make_install=step_handler.MakeInstall(self.app),
                                     move_directory_files=step_handler.MoveDirectoryFiles(self.app),
                                     move_file=step_handler.MoveFile(self.app),
                                     regex_replace=step_handler.RegexReplace(self.app),
                                     set_environment=step_handler.SetEnvironment(self.app),
                                     set_environment_for_install=step_handler.SetEnvironmentForInstall(self.app),
                                     setup_perl_environment=step_handler.SetupPerlEnvironment(self.app),
                                     setup_r_environment=step_handler.SetupREnvironment(self.app),
                                     setup_ruby_environment=step_handler.SetupRubyEnvironment(self.app),
                                     setup_python_environment=step_handler.SetupPythonEnvironment(self.app),
                                     setup_virtualenv=step_handler.SetupVirtualEnv(self.app),
                                     shell_command=step_handler.ShellCommand(self.app),
                                     template_command=step_handler.TemplateCommand(self.app))
        return step_handlers_by_type

[docs]    def prepare_step(self, tool_dependency, action_type, action_elem, action_dict, install_environment, is_binary_download):
        """
        Prepare the recipe step for later execution.  This generally alters the received action_dict
        with new information needed during this step's execution.
        """
        if action_elem is not None:
            step_handler = self.get_step_handler_by_type(action_type)
            action_dict = step_handler.prepare_step(tool_dependency=tool_dependency,
                                                    action_elem=action_elem,
                                                    action_dict=action_dict,
                                                    install_environment=install_environment,
                                                    is_binary_download=is_binary_download)
        return action_dict


[docs]class TagManager(object):

[docs]    def __init__(self, app):
        self.app = app
        self.tag_handlers = self.load_tag_handlers()

[docs]    def get_tag_handler_by_tag(self, tag):
        return self.tag_handlers.get(tag, None)

[docs]    def process_tag_set(self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
                        from_tool_migration_manager=False, tool_dependency_db_records=None):
        tag_handler = self.get_tag_handler_by_tag(package_elem.tag)
        tool_dependency, proceed_with_install, action_elem_tuples = \
            tag_handler.process_tag_set(tool_shed_repository,
                                        tool_dependency,
                                        package_elem,
                                        package_name,
                                        package_version,
                                        from_tool_migration_manager=from_tool_migration_manager,
                                        tool_dependency_db_records=tool_dependency_db_records)
        return tool_dependency, proceed_with_install, action_elem_tuples

[docs]    def load_tag_handlers(self):
        tag_handlers = dict(environment_variable=tag_handler.SetEnvironment(self.app),
                            install=tag_handler.Install(self.app),
                            package=tag_handler.Package(self.app),
                            readme=tag_handler.ReadMe(self.app),
                            repository=tag_handler.Repository(self.app),
                            set_environment=tag_handler.SetEnvironment(self.app))
        return tag_handlers