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galaxy.tools.actions package

class galaxy.tools.actions.ToolAction

Bases: object

The actions to be taken when a tool is run (after parameters have been converted and validated).

abstract execute(tool, trans, incoming: Dict[str, Any] | None = None, history: History | None = None, job_params=None, rerun_remap_job_id: int | None = None, execution_cache: ToolExecutionCache | None = None, dataset_collection_elements: Dict[str, DatasetCollectionElement] | None = None, completed_job: Job | None = None, collection_info: MatchingCollections | None = None, job_callback: Callable | None = None, preferred_object_store_id: str | None = None, set_output_hid: bool = True, flush_job: bool = True, skip: bool = False) → Tuple[Job, Dict[str, DatasetInstance], History | None] | Tuple[Job, Dict[str, DatasetInstance]]

Perform target tool action.

abstract get_output_name(output, dataset=None, tool=None, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None) → str

Get name to assign a tool output.

class galaxy.tools.actions.DefaultToolAction

Bases: ToolAction

Default tool action is to run an external command

produces_real_jobs: bool = True

collect_input_dataset_collections(tool, param_values)

execute(tool, trans, incoming: Dict[str, Any] | None = None, history: History | None = None, job_params=None, rerun_remap_job_id: int | None = None, execution_cache: ToolExecutionCache | None = None, dataset_collection_elements=None, completed_job: Job | None = None, collection_info: MatchingCollections | None = None, job_callback: Callable | None = None, preferred_object_store_id: str | None = None, set_output_hid: bool = True, flush_job: bool = True, skip: bool = False) → Tuple[Job, Dict[str, DatasetInstance], History | None] | Tuple[Job, Dict[str, DatasetInstance]]

Executes a tool, creating job and tool outputs, associating them, and submitting the job to the job queue. If history is not specified, use trans.history as destination for tool’s output datasets.

get_output_name(output, dataset=None, tool=None, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None) → str

Get name to assign a tool output.

class galaxy.tools.actions.OutputCollections(trans, history, tool, tool_action, input_collections, dataset_collection_elements, on_text, incoming, params, job_params, tags, hdca_tags)

Bases: object

Keeps track of collections (DC or HDCA) created by actions.

Actions do fairly different things depending on whether we are creating just part of an collection or a whole output collection (mapping_over_collection parameter).

__init__(trans, history, tool, tool_action, input_collections, dataset_collection_elements, on_text, incoming, params, job_params, tags, hdca_tags)

create_collection(output, name, collection_type=None, completed_job=None, propagate_hda_tags=True, **element_kwds)

galaxy.tools.actions.get_ext_or_implicit_ext(hda)

galaxy.tools.actions.determine_output_format(output: ToolOutput, parameter_context, input_datasets, input_dataset_collections, random_input_ext, python_template_version='3', execution_cache=None)

Determines the output format for a dataset based on an abstract description of the output (galaxy.tool_util.parser.ToolOutput), the parameter wrappers, a map of the input datasets (name => HDA), and the last input extensions in the tool form.

TODO: Make the input extension used deterministic instead of random.

Submodules

galaxy.tools.actions.data_manager module

class galaxy.tools.actions.data_manager.DataManagerToolAction

Bases: DefaultToolAction

Tool action used for Data Manager Tools

execute(tool, trans, incoming: Dict[str, Any] | None = None, history: History | None = None, job_params=None, rerun_remap_job_id: int | None = None, execution_cache: ToolExecutionCache | None = None, dataset_collection_elements: Dict[str, DatasetCollectionElement] | None = None, completed_job: Job | None = None, collection_info: MatchingCollections | None = None, job_callback: Callable | None = None, preferred_object_store_id: str | None = None, set_output_hid: bool = True, flush_job: bool = True, skip: bool = False) → Tuple[Job, Dict[str, DatasetInstance], History | None] | Tuple[Job, Dict[str, DatasetInstance]]

Executes a tool, creating job and tool outputs, associating them, and submitting the job to the job queue. If history is not specified, use trans.history as destination for tool’s output datasets.

galaxy.tools.actions.data_source module

class galaxy.tools.actions.data_source.DataSourceToolAction

Bases: DefaultToolAction

Tool action used for Data Source Tools

galaxy.tools.actions.history_imp_exp module

class galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction

Bases: ToolAction

Tool action used for importing a history to an archive.

produces_real_jobs: bool = True

execute(tool, trans, incoming: Dict[str, Any] | None = None, history: History | None = None, job_params=None, rerun_remap_job_id: int | None = None, execution_cache: ToolExecutionCache | None = None, dataset_collection_elements: Dict[str, DatasetCollectionElement] | None = None, completed_job: Job | None = None, collection_info: MatchingCollections | None = None, job_callback: Callable | None = None, preferred_object_store_id: str | None = None, set_output_hid: bool = True, flush_job: bool = True, skip: bool = False) → Tuple[Job, Dict[str, DatasetInstance], History | None] | Tuple[Job, Dict[str, DatasetInstance]]

Perform target tool action.

class galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction

Bases: ToolAction

Tool action used for exporting a history to an archive.

produces_real_jobs: bool = True

execute(tool, trans, incoming: Dict[str, Any] | None = None, history: History | None = None, job_params=None, rerun_remap_job_id: int | None = None, execution_cache: ToolExecutionCache | None = None, dataset_collection_elements: Dict[str, DatasetCollectionElement] | None = None, completed_job: Job | None = None, collection_info: MatchingCollections | None = None, job_callback: Callable | None = None, preferred_object_store_id: str | None = None, set_output_hid: bool = True, flush_job: bool = True, skip: bool = False) → Tuple[Job, Dict[str, DatasetInstance], History | None] | Tuple[Job, Dict[str, DatasetInstance]]

Perform target tool action.

galaxy.tools.actions.metadata module

class galaxy.tools.actions.metadata.SetMetadataToolAction

Bases: ToolAction

Tool action used for setting external metadata on an existing dataset

produces_real_jobs: bool = False

set_output_hid: bool = False

execute(tool, trans, incoming: Dict[str, Any] | None = None, history: History | None = None, job_params=None, rerun_remap_job_id: int | None = None, execution_cache: ToolExecutionCache | None = None, dataset_collection_elements: Dict[str, DatasetCollectionElement] | None = None, completed_job: Job | None = None, collection_info: MatchingCollections | None = None, job_callback: Callable | None = None, preferred_object_store_id: str | None = None, set_output_hid: bool = True, flush_job: bool = True, skip: bool = False)

Execute using a web transaction.

execute_via_trans(tool, trans, incoming: Dict[str, Any] | None, overwrite: bool = True, history: History | None = None, job_params: Dict[str, Any] | None = None)

execute_via_app(tool, app, session_id: int | None, history_id: int | None, user: User | None = None, incoming: Dict[str, Any] | None = None, overwrite: bool = True, history: History | None = None, job_params: Dict[str, Any] | None = None)

Execute using application.

galaxy.tools.actions.model_operations module

class galaxy.tools.actions.model_operations.ModelOperationToolAction

Bases: DefaultToolAction

produces_real_jobs: bool = False

check_inputs_ready(tool, trans, incoming, history, execution_cache=None, collection_info=None)

execute(tool, trans, incoming: Dict[str, Any] | None = None, history: History | None = None, job_params=None, rerun_remap_job_id: int | None = None, execution_cache: ToolExecutionCache | None = None, dataset_collection_elements: Dict[str, DatasetCollectionElement] | None = None, completed_job: Job | None = None, collection_info: MatchingCollections | None = None, job_callback: Callable | None = None, preferred_object_store_id: str | None = None, set_output_hid: bool = True, flush_job: bool = True, skip: bool = False) → Tuple[Job, Dict[str, DatasetInstance], History | None] | Tuple[Job, Dict[str, DatasetInstance]]

Executes a tool, creating job and tool outputs, associating them, and submitting the job to the job queue. If history is not specified, use trans.history as destination for tool’s output datasets.

galaxy.tools.actions.upload module

class galaxy.tools.actions.upload.BaseUploadToolAction

Bases: ToolAction

produces_real_jobs = True

execute(tool, trans, incoming: Dict[str, Any] | None = None, history: History | None = None, job_params=None, rerun_remap_job_id: int | None = None, execution_cache: ToolExecutionCache | None = None, dataset_collection_elements: Dict[str, DatasetCollectionElement] | None = None, completed_job: Job | None = None, collection_info: MatchingCollections | None = None, job_callback: Callable | None = None, preferred_object_store_id: str | None = None, set_output_hid: bool = True, flush_job: bool = True, skip: bool = False) → Tuple[Job, Dict[str, DatasetInstance], History | None] | Tuple[Job, Dict[str, DatasetInstance]]

Perform target tool action.

class galaxy.tools.actions.upload.UploadToolAction

Bases: BaseUploadToolAction

class galaxy.tools.actions.upload.FetchUploadToolAction

Bases: BaseUploadToolAction

galaxy.tools.actions.upload_common module

galaxy.tools.actions.upload_common.validate_datatype_extension(datatypes_registry, ext)

galaxy.tools.actions.upload_common.persist_uploads(params, trans)

Turn any uploads in the submitted form to persisted files.

class galaxy.tools.actions.upload_common.LibraryParams(roles: List[galaxy.model.Role], tags: List[str] | NoneType, template: galaxy.model.FormDefinition | NoneType, template_field_contents: Dict[str, str], folder: galaxy.model.LibraryFolder, message: str, replace_dataset: galaxy.model.LibraryDataset | NoneType)

Bases: object

roles: List[Role]

tags: List[str] | None

template: FormDefinition | None

template_field_contents: Dict[str, str]

folder: LibraryFolder

message: str

replace_dataset: LibraryDataset | None

__init__(roles: List[Role], tags: List[str] | None, template: FormDefinition | None, template_field_contents: Dict[str, str], folder: LibraryFolder, message: str, replace_dataset: LibraryDataset | None) → None

galaxy.tools.actions.upload_common.handle_library_params(trans, params, folder_id: int, replace_dataset: LibraryDataset | None = None) → LibraryParams

galaxy.tools.actions.upload_common.new_upload(trans: ProvidesUserContext, cntrller, uploaded_dataset, library_bunch=None, history=None, state=None, tag_list=None)

galaxy.tools.actions.upload_common.get_uploaded_datasets(trans, cntrller, params, dataset_upload_inputs, library_bunch=None, history=None)

galaxy.tools.actions.upload_common.create_paramfile(trans, uploaded_datasets)

Create the upload tool’s JSON “param” file.

galaxy.tools.actions.upload_common.create_job(trans, params, tool, json_file_path, outputs, folder=None, history=None, job_params=None)

Create the upload job.

galaxy.tools.actions.upload_common.active_folders(trans, folder)