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galaxy.tool_shed.metadata package

Submodules

galaxy.tool_shed.metadata.metadata_generator module

class galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator(app, repository=None, changeset_revision=None, repository_clone_url=None, shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False, metadata_dict=None, user=None)[source]

Bases: object

__init__(app, repository=None, changeset_revision=None, repository_clone_url=None, shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False, metadata_dict=None, user=None)[source]

Initialize self. See help(type(self)) for accurate signature.

generate_data_manager_metadata(repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None)[source]

Update the received metadata_dict with information from the parsed data_manager_config_filename.

generate_datatypes_metadata(tv, repository_files_dir, datatypes_config, metadata_dict)[source]

Update the received metadata_dict with information from the parsed datatypes_config.

generate_environment_dependency_metadata(elem, valid_tool_dependencies_dict)[source]

The value of env_var_name must match the value of the “set_environment” type in the tool config’s <requirements> tag set, or the tool dependency will be considered an orphan.

generate_guid_for_object(guid_type, obj_id, version)[source]
generate_metadata_for_changeset_revision()[source]

Generate metadata for a repository using its files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision’s disk files, so the value of self.repository_files_dir will not always be self.repository.repo_path( self.app ) (it could be an absolute path to a temporary directory containing a clone). If it is an absolute path, the value of self.relative_install_dir must contain repository.repo_path( self.app ).

The value of self.persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by self.app.config.shed_tool_data_table_config.

generate_package_dependency_metadata(elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict)[source]

Generate the metadata for a tool dependencies package defined for a repository. The value of package_name must match the value of the “package” type in the tool config’s <requirements> tag set.

generate_repository_dependency_metadata(repository_dependencies_config, metadata_dict)[source]

Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method is called from the tool shed as well as from Galaxy.

generate_tool_metadata(tool_config, tool, metadata_dict)[source]

Update the received metadata_dict with changes that have been applied to the received tool.

generate_tool_dependency_metadata(tool_dependencies_config, metadata_dict, original_repository_metadata=None)[source]

If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in self.repository, then update the received metadata_dict with information from the parsed tool_dependencies_config.

generate_workflow_metadata(relative_path, exported_workflow_dict, metadata_dict)[source]

Update the received metadata_dict with changes that have been applied to the received exported_workflow_dict.

get_invalid_file_tups()[source]
get_metadata_dict()[source]
get_relative_path_to_repository_file(root, name, relative_install_dir, work_dir, shed_config_dict)[source]
get_sample_files_from_disk(repository_files_dir, tool_path=None, relative_install_dir=None)[source]
handle_repository_elem(repository_elem, only_if_compiling_contained_td=False)[source]

Process the received repository_elem which is a <repository> tag either from a repository_dependencies.xml file or a tool_dependencies.xml file. If the former, we’re generating repository dependencies metadata for a repository in the Tool Shed. If the latter, we’re generating package dependency metadata within Galaxy or the Tool Shed.

set_add_to_tool_panel_attribute_for_tool(tool, guid, datatypes)[source]

Determine if a tool should be loaded into the Galaxy tool panel. Examples of valid tools that should not be displayed in the tool panel are datatypes converters and DataManager tools.

set_changeset_revision(changeset_revision)[source]
set_relative_install_dir(relative_install_dir)[source]
set_repository(repository, relative_install_dir=None, changeset_revision=None)[source]
set_repository_clone_url(repository_clone_url)[source]
set_repository_files_dir(repository_files_dir=None)[source]
update_repository_dependencies_metadata(metadata, repository_dependency_tups, is_valid, description)[source]