galaxy.tool_shed.galaxy_install.tools package

Submodules

galaxy.tool_shed.galaxy_install.tools.data_manager module

class galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler(app: InstallationTarget)[source]

Bases: object

root: Element | None = None

__init__(app: InstallationTarget)[source]

app: InstallationTarget

property data_managers_path: str | None

install_data_managers(shed_data_manager_conf_filename: str | PathLike, metadata_dict: Dict[str, Any], shed_config_dict: Dict[str, Any], relative_install_dir: str | PathLike, repository, repository_tools_tups) → List[DataManagerInterface][source]

remove_from_data_manager(repository)[source]

galaxy.tool_shed.galaxy_install.tools.tool_panel_manager module

class galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager(app: InstallationTarget)[source]

Bases: object

__init__(app: InstallationTarget)[source]

app: InstallationTarget

add_to_shed_tool_config(shed_tool_conf_dict: Dict[str, Any], elem_list: list) → None[source]: “A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have been deactivated.

add_to_tool_panel(repository_name, repository_clone_url, changeset_revision, repository_tools_tups, owner, shed_tool_conf, tool_panel_dict, new_install=True, tool_panel_section_mapping=None)[source]: A tool shed repository is being installed or updated so handle tool panel alterations accordingly.

config_elems_to_xml_file(config_elems, config_filename, tool_path, tool_cache_data_dir=None) → None[source]: Persist the current in-memory list of config_elems to a file named by the value of config_filename.

generate_tool_elem(tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section) → Element[source]: Create and return an ElementTree tool Element.

generate_tool_panel_dict_for_new_install(tool_dicts, tool_section=None)[source]: When installing a repository that contains tools, all tools must currently be defined within the same tool section in the tool panel or outside of any sections.

generate_tool_panel_dict_for_tool_config(guid, tool_config, tool_sections=None) → Dict[str, List[Dict[str, Any]]][source]

Create a dictionary of the following type for a single tool config file name. The intent is to call this method for every tool config in a repository and append each of these as entries to a tool panel dictionary for the repository. This enables each tool to be loaded into a different section in the tool panel.

{<Tool guid> :
    [{ tool_config : <tool_config_file>,
        id: <ToolSection id>,
        version : <ToolSection version>,
        name : <TooSection name>}]}

generate_tool_panel_dict_from_shed_tool_conf_entries(repository) → Dict[str, List[Dict[str, Any]]][source]: Keep track of the section in the tool panel in which this repository’s tools will be contained by parsing the shed_tool_conf in which the repository’s tools are defined and storing the tool panel definition of each tool in the repository. This method is called only when the repository is being deactivated or un-installed and allows for activation or re-installation using the original layout.

generate_tool_panel_elem_list(repository_name: str, repository_clone_url: str, changeset_revision: str, tool_panel_dict: dict, repository_tools_tups: List[tuple], owner='')[source]: Generate a list of ElementTree Element objects for each section or tool.

generate_tool_section_dicts(tool_config=None, tool_sections=None) → List[Dict[str, Any]][source]

generate_tool_section_element_from_dict(tool_section_dict: Dict[str, str]) → Element[source]

get_or_create_tool_section(toolbox, tool_panel_section_id, new_tool_panel_section_label=None)[source]

get_shed_tool_conf_dict(shed_tool_conf)[source]: Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry in the shed_tool_conf_dict associated with the file.

handle_tool_panel_section(toolbox, tool_panel_section_id=None, new_tool_panel_section_label=None)[source]: Return a ToolSection object retrieved from the current in-memory tool_panel.

handle_tool_panel_selection(toolbox, metadata, no_changes_checked, tool_panel_section_id, new_tool_panel_section_label)[source]: Handle the selected tool panel location for loading tools included in tool shed repositories when installing or reinstalling them.

remove_from_shed_tool_config(shed_tool_conf_dict, metadata)[source]: A tool shed repository is being uninstalled so change the shed_tool_conf file. Parse the config file to generate the entire list of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have been deactivated.

remove_repository_contents(repository, shed_tool_conf, uninstall)[source]: A tool shed repository is being deactivated or uninstalled, so handle tool panel alterations accordingly.

update_tool_panel_dict(tool_panel_dict, tool_panel_section_mapping, repository_tools_tups)[source]