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galaxy.tool_shed.galaxy_install.datatypes package

Submodules

galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager module

class galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader(app)

Bases: object

__init__(app)

alter_config_and_load_prorietary_datatypes(datatypes_config, relative_install_dir, deactivate=False, override=True)

Parse a custom datatypes config (a datatypes_conf.xml file included in an installed tool shed repository) and add information to appropriate element attributes that will enable custom datatype class modules, datatypes converters and display applications to be discovered and properly imported by the datatypes registry. The value of override will be False when a tool shed repository is being installed. Since installation is occurring after the datatypes registry has been initialized, the registry’s contents cannot be overridden by conflicting data types.

create_repository_dict_for_proprietary_datatypes(tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None)

get_converter_and_display_paths(registration_elem, relative_install_dir)

Find the relative path to data type converters and display applications included in installed tool shed repositories.

load_installed_datatype_converters(installed_repository_dict, deactivate=False)

Load or deactivate proprietary datatype converters.

load_installed_datatypes(repository, relative_install_dir, deactivate=False)

Load proprietary datatypes and return information needed for loading custom datatypes converters and display applications later.

load_installed_display_applications(installed_repository_dict, deactivate=False)

Load or deactivate custom datatype display applications.