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tool_shed.metadata package
Submodules
tool_shed.metadata.metadata_generator module
tool_shed.metadata.repository_metadata_manager module
- class tool_shed.metadata.repository_metadata_manager.ToolShedMetadataGenerator(trans: ProvidesRepositoriesContext, repository: Repository | None = None, changeset_revision: str | None = None, repository_clone_url: str | None = None, shed_config_dict: Dict[str, Any] | None = 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:
BaseMetadataGenerator
A MetadataGenerator building on ToolShed’s app and repository constructs.
- __init__(trans: ProvidesRepositoriesContext, repository: Repository | None = None, changeset_revision: str | None = None, repository_clone_url: str | None = None, shed_config_dict: Dict[str, Any] | None = 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]
- app: ToolShedApp
- repository: Repository | None
- set_repository(repository, relative_install_dir: str | None = None, changeset_revision: str | None = None)[source]
- handle_repository_elem(repository_elem, only_if_compiling_contained_td=False) Tuple[List, bool, str] [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.
- class tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager(trans: ProvidesRepositoriesContext, 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)[source]
Bases:
ToolShedMetadataGenerator
- __init__(trans: ProvidesRepositoriesContext, 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)[source]
- app: ToolShedApp
- build_repository_ids_select_field(name='repository_ids', multiple=True, display='checkboxes', my_writable=False)[source]
Generate the current list of repositories for resetting metadata.
- compare_changeset_revisions(ancestor_changeset_revision, ancestor_metadata_dict)[source]
Compare the contents of two changeset revisions to determine if a new repository metadata revision should be created.
- compare_data_manager(ancestor_metadata, current_metadata)[source]
Determine if ancestor_metadata is the same as or a subset of current_metadata for data_managers.
- compare_repository_dependencies(ancestor_repository_dependencies, current_repository_dependencies)[source]
Determine if ancestor_repository_dependencies is the same as or a subset of current_repository_dependencies.
- compare_tool_dependencies(ancestor_tool_dependencies, current_tool_dependencies)[source]
Determine if ancestor_tool_dependencies is the same as or a subset of current_tool_dependencies.
- create_or_update_repository_metadata(changeset_revision, metadata_dict)[source]
Create or update a repository_metadata record in the tool shed.
- different_revision_defines_tip_only_repository_dependency(rd_tup, repository_dependencies)[source]
Determine if the only difference between rd_tup and a dependency definition in the list of repository_dependencies is the changeset_revision value.
- get_repositories_for_setting_metadata(my_writable=False, order=True)[source]
Return a list of repositories for resetting metadata. The order parameter is used for displaying the list of repositories ordered alphabetically for display on a page. When called from the Tool Shed API, order is False.
- new_metadata_required_for_utilities()[source]
This method compares the last stored repository_metadata record associated with self.repository against the contents of self.metadata_dict and returns True or False for the union set of Galaxy utilities contained in both metadata dictionaries. The metadata contained in self.metadata_dict may not be a subset of that contained in the last stored repository_metadata record associated with self.repository because one or more Galaxy utilities may have been deleted from self.repository in the new tip.
- new_repository_dependency_metadata_required(repository_metadata)[source]
Compare the last saved metadata for each repository dependency in the repository with the new metadata in self.metadata_dict to determine if a new repository_metadata table record is required or if the last saved metadata record can be updated for repository_dependencies instead.
- new_tool_metadata_required(repository_metadata)[source]
Compare the last saved metadata for each tool in the repository with the new metadata in self.metadata_dict to determine if a new repository_metadata table record is required, or if the last saved metadata record can be updated instead.
- new_tool_dependency_metadata_required(repository_metadata)[source]
Compare the last saved metadata for each tool dependency in the repository with the new metadata in self.metadata_dict to determine if a new repository_metadata table record is required or if the last saved metadata record can be updated for tool_dependencies instead.
- reset_all_metadata_on_repository_in_tool_shed(repository_clone_url=None)[source]
Reset all metadata on a single repository in a tool shed.
- reset_metadata_on_selected_repositories(**kwd)[source]
Inspect the repository changelog to reset metadata for all appropriate changeset revisions. This method is called from both Galaxy and the Tool Shed.
- set_repository(repository, relative_install_dir: str | None = None, changeset_revision: str | None = None)[source]
- set_repository_metadata(host, content_alert_str='', **kwd)[source]
Set metadata using the self.repository’s current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems.
- repository: Repository | None
- tool_shed.metadata.repository_metadata_manager.get_repository_metadata(session, repository_id)[source]