:py:mod:`wfexs_backend.workflow_engines` ======================================== .. py:module:: wfexs_backend.workflow_engines .. autodoc2-docstring:: wfexs_backend.workflow_engines :allowtitles: Submodules ---------- .. toctree:: :titlesonly: :maxdepth: 1 wfexs_backend.workflow_engines.nextflow_engine wfexs_backend.workflow_engines.cwl_engine Package Contents ---------------- Classes ~~~~~~~ .. list-table:: :class: autosummary longtable :align: left * - :py:obj:`WorkflowType ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType :summary: * - :py:obj:`MaterializedWorkflowEngine ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine :summary: * - :py:obj:`StagedExecution ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution :summary: * - :py:obj:`AbstractWorkflowEngineType ` - * - :py:obj:`WorkflowEngine ` - Data ~~~~ .. list-table:: :class: autosummary longtable :align: left * - :py:obj:`WORKDIR_INPUTS_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_INPUTS_RELDIR :summary: * - :py:obj:`WORKDIR_EXTRAPOLATED_INPUTS_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_EXTRAPOLATED_INPUTS_RELDIR :summary: * - :py:obj:`WORKDIR_INTERMEDIATE_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_INTERMEDIATE_RELDIR :summary: * - :py:obj:`WORKDIR_META_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_META_RELDIR :summary: * - :py:obj:`WORKDIR_STATS_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_STATS_RELDIR :summary: * - :py:obj:`WORKDIR_OUTPUTS_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_OUTPUTS_RELDIR :summary: * - :py:obj:`WORKDIR_ENGINE_TWEAKS_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_ENGINE_TWEAKS_RELDIR :summary: * - :py:obj:`WORKDIR_WORKFLOW_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_WORKFLOW_RELDIR :summary: * - :py:obj:`WORKDIR_CONSOLIDATED_WORKFLOW_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_CONSOLIDATED_WORKFLOW_RELDIR :summary: * - :py:obj:`WORKDIR_CONTAINERS_RELDIR ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_CONTAINERS_RELDIR :summary: * - :py:obj:`WORKDIR_STDOUT_FILE ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_STDOUT_FILE :summary: * - :py:obj:`WORKDIR_STDERR_FILE ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_STDERR_FILE :summary: * - :py:obj:`WORKDIR_WORKFLOW_META_FILE ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_WORKFLOW_META_FILE :summary: * - :py:obj:`WORKDIR_MARSHALLED_STAGE_FILE ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_MARSHALLED_STAGE_FILE :summary: * - :py:obj:`WORKDIR_MARSHALLED_EXECUTE_FILE ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_MARSHALLED_EXECUTE_FILE :summary: * - :py:obj:`WORKDIR_MARSHALLED_EXPORT_FILE ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_MARSHALLED_EXPORT_FILE :summary: * - :py:obj:`WORKDIR_PASSPHRASE_FILE ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_PASSPHRASE_FILE :summary: * - :py:obj:`STATS_DAG_DOT_FILE ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.STATS_DAG_DOT_FILE :summary: * - :py:obj:`DEFAULT_PRIORITY ` - .. autodoc2-docstring:: wfexs_backend.workflow_engines.DEFAULT_PRIORITY :summary: API ~~~ .. py:data:: WORKDIR_INPUTS_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_INPUTS_RELDIR :value: 'inputs' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_INPUTS_RELDIR .. py:data:: WORKDIR_EXTRAPOLATED_INPUTS_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_EXTRAPOLATED_INPUTS_RELDIR :value: 'extrapolated-inputs' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_EXTRAPOLATED_INPUTS_RELDIR .. py:data:: WORKDIR_INTERMEDIATE_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_INTERMEDIATE_RELDIR :value: 'intermediate' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_INTERMEDIATE_RELDIR .. py:data:: WORKDIR_META_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_META_RELDIR :value: 'meta' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_META_RELDIR .. py:data:: WORKDIR_STATS_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_STATS_RELDIR :value: 'stats' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_STATS_RELDIR .. py:data:: WORKDIR_OUTPUTS_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_OUTPUTS_RELDIR :value: 'outputs' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_OUTPUTS_RELDIR .. py:data:: WORKDIR_ENGINE_TWEAKS_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_ENGINE_TWEAKS_RELDIR :value: 'engineTweaks' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_ENGINE_TWEAKS_RELDIR .. py:data:: WORKDIR_WORKFLOW_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_WORKFLOW_RELDIR :value: 'workflow' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_WORKFLOW_RELDIR .. py:data:: WORKDIR_CONSOLIDATED_WORKFLOW_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_CONSOLIDATED_WORKFLOW_RELDIR :value: 'consolidated-workflow' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_CONSOLIDATED_WORKFLOW_RELDIR .. py:data:: WORKDIR_CONTAINERS_RELDIR :canonical: wfexs_backend.workflow_engines.WORKDIR_CONTAINERS_RELDIR :value: 'containers' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_CONTAINERS_RELDIR .. py:data:: WORKDIR_STDOUT_FILE :canonical: wfexs_backend.workflow_engines.WORKDIR_STDOUT_FILE :value: 'cast(...)' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_STDOUT_FILE .. py:data:: WORKDIR_STDERR_FILE :canonical: wfexs_backend.workflow_engines.WORKDIR_STDERR_FILE :value: 'cast(...)' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_STDERR_FILE .. py:data:: WORKDIR_WORKFLOW_META_FILE :canonical: wfexs_backend.workflow_engines.WORKDIR_WORKFLOW_META_FILE :value: 'cast(...)' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_WORKFLOW_META_FILE .. py:data:: WORKDIR_MARSHALLED_STAGE_FILE :canonical: wfexs_backend.workflow_engines.WORKDIR_MARSHALLED_STAGE_FILE :value: 'cast(...)' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_MARSHALLED_STAGE_FILE .. py:data:: WORKDIR_MARSHALLED_EXECUTE_FILE :canonical: wfexs_backend.workflow_engines.WORKDIR_MARSHALLED_EXECUTE_FILE :value: 'cast(...)' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_MARSHALLED_EXECUTE_FILE .. py:data:: WORKDIR_MARSHALLED_EXPORT_FILE :canonical: wfexs_backend.workflow_engines.WORKDIR_MARSHALLED_EXPORT_FILE :value: 'cast(...)' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_MARSHALLED_EXPORT_FILE .. py:data:: WORKDIR_PASSPHRASE_FILE :canonical: wfexs_backend.workflow_engines.WORKDIR_PASSPHRASE_FILE :value: 'cast(...)' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WORKDIR_PASSPHRASE_FILE .. py:data:: STATS_DAG_DOT_FILE :canonical: wfexs_backend.workflow_engines.STATS_DAG_DOT_FILE :value: 'cast(...)' .. autodoc2-docstring:: wfexs_backend.workflow_engines.STATS_DAG_DOT_FILE .. py:data:: DEFAULT_PRIORITY :canonical: wfexs_backend.workflow_engines.DEFAULT_PRIORITY :type: Final[int] :value: 0 .. autodoc2-docstring:: wfexs_backend.workflow_engines.DEFAULT_PRIORITY .. py:class:: WorkflowType :canonical: wfexs_backend.workflow_engines.WorkflowType Bases: :py:obj:`typing.NamedTuple` .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType .. py:attribute:: engineName :canonical: wfexs_backend.workflow_engines.WorkflowType.engineName :type: str :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.engineName .. py:attribute:: shortname :canonical: wfexs_backend.workflow_engines.WorkflowType.shortname :type: str :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.shortname .. py:attribute:: name :canonical: wfexs_backend.workflow_engines.WorkflowType.name :type: str :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.name .. py:attribute:: clazz :canonical: wfexs_backend.workflow_engines.WorkflowType.clazz :type: Type[AbstractWorkflowEngineType] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.clazz .. py:attribute:: uriMatch :canonical: wfexs_backend.workflow_engines.WorkflowType.uriMatch :type: Sequence[Union[Pattern[str], URIType]] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.uriMatch .. py:attribute:: uriTemplate :canonical: wfexs_backend.workflow_engines.WorkflowType.uriTemplate :type: wfexs_backend.common.URIType :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.uriTemplate .. py:attribute:: url :canonical: wfexs_backend.workflow_engines.WorkflowType.url :type: wfexs_backend.common.URIType :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.url .. py:attribute:: trs_descriptor :canonical: wfexs_backend.workflow_engines.WorkflowType.trs_descriptor :type: wfexs_backend.common.TRS_Workflow_Descriptor :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.trs_descriptor .. py:attribute:: rocrate_programming_language :canonical: wfexs_backend.workflow_engines.WorkflowType.rocrate_programming_language :type: str :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.rocrate_programming_language .. py:attribute:: priority :canonical: wfexs_backend.workflow_engines.WorkflowType.priority :type: int :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.priority .. py:attribute:: enabled :canonical: wfexs_backend.workflow_engines.WorkflowType.enabled :type: bool :value: True .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.enabled .. py:method:: _value_fixes() -> Mapping[str, Optional[str]] :canonical: wfexs_backend.workflow_engines.WorkflowType._value_fixes :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType._value_fixes .. py:property:: has_explicit_outputs :canonical: wfexs_backend.workflow_engines.WorkflowType.has_explicit_outputs :type: bool .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowType.has_explicit_outputs .. py:class:: MaterializedWorkflowEngine :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine Bases: :py:obj:`typing.NamedTuple` .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine .. py:attribute:: instance :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.instance :type: AbstractWorkflowEngineType :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.instance .. py:attribute:: version :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.version :type: wfexs_backend.common.EngineVersion :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.version .. py:attribute:: fingerprint :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.fingerprint :type: Union[Fingerprint, str] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.fingerprint .. py:attribute:: engine_path :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.engine_path :type: pathlib.Path :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.engine_path .. py:attribute:: workflow :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.workflow :type: wfexs_backend.common.LocalWorkflow :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.workflow .. py:attribute:: containers_path :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.containers_path :type: Optional[pathlib.Path] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.containers_path .. py:attribute:: containers :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.containers :type: Optional[Sequence[Container]] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.containers .. py:attribute:: operational_containers :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.operational_containers :type: Optional[Sequence[Container]] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine.operational_containers .. py:method:: _mapping_fixes(orig: Mapping[str, Any], workdir: Optional[pathlib.Path]) -> Mapping[str, Any] :canonical: wfexs_backend.workflow_engines.MaterializedWorkflowEngine._mapping_fixes :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.MaterializedWorkflowEngine._mapping_fixes .. py:class:: StagedExecution :canonical: wfexs_backend.workflow_engines.StagedExecution Bases: :py:obj:`typing.NamedTuple` .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution .. py:attribute:: exitVal :canonical: wfexs_backend.workflow_engines.StagedExecution.exitVal :type: wfexs_backend.common.ExitVal :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.exitVal .. py:attribute:: augmentedInputs :canonical: wfexs_backend.workflow_engines.StagedExecution.augmentedInputs :type: Sequence[MaterializedInput] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.augmentedInputs .. py:attribute:: matCheckOutputs :canonical: wfexs_backend.workflow_engines.StagedExecution.matCheckOutputs :type: Sequence[MaterializedOutput] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.matCheckOutputs .. py:attribute:: outputsDir :canonical: wfexs_backend.workflow_engines.StagedExecution.outputsDir :type: pathlib.Path :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.outputsDir .. py:attribute:: started :canonical: wfexs_backend.workflow_engines.StagedExecution.started :type: datetime.datetime :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.started .. py:attribute:: ended :canonical: wfexs_backend.workflow_engines.StagedExecution.ended :type: datetime.datetime :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.ended .. py:attribute:: environment :canonical: wfexs_backend.workflow_engines.StagedExecution.environment :type: Sequence[MaterializedInput] :value: [] .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.environment .. py:attribute:: outputMetaDir :canonical: wfexs_backend.workflow_engines.StagedExecution.outputMetaDir :type: Optional[pathlib.Path] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.outputMetaDir .. py:attribute:: diagram :canonical: wfexs_backend.workflow_engines.StagedExecution.diagram :type: Optional[pathlib.Path] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.diagram .. py:attribute:: logfile :canonical: wfexs_backend.workflow_engines.StagedExecution.logfile :type: Sequence[pathlib.Path] :value: [] .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.logfile .. py:attribute:: profiles :canonical: wfexs_backend.workflow_engines.StagedExecution.profiles :type: Optional[Sequence[str]] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.profiles .. py:attribute:: queued :canonical: wfexs_backend.workflow_engines.StagedExecution.queued :type: Optional[datetime.datetime] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.queued .. py:attribute:: status :canonical: wfexs_backend.workflow_engines.StagedExecution.status :type: wfexs_backend.common.ExecutionStatus :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.status .. py:attribute:: job_id :canonical: wfexs_backend.workflow_engines.StagedExecution.job_id :type: Optional[str] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution.job_id .. py:method:: _mapping_fixes(orig: Mapping[str, Any], workdir: Optional[pathlib.Path]) -> Mapping[str, Any] :canonical: wfexs_backend.workflow_engines.StagedExecution._mapping_fixes :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.StagedExecution._mapping_fixes .. py:class:: AbstractWorkflowEngineType :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType Bases: :py:obj:`abc.ABC` .. py:method:: MyWorkflowType() -> wfexs_backend.workflow_engines.WorkflowType :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.MyWorkflowType :abstractmethod: :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.MyWorkflowType .. py:method:: HasExplicitOutputs() -> bool :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.HasExplicitOutputs :abstractmethod: :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.HasExplicitOutputs .. py:property:: workflowType :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.workflowType :type: wfexs_backend.workflow_engines.WorkflowType .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.workflowType .. py:method:: getConfiguredContainerType() -> wfexs_backend.common.ContainerType :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.getConfiguredContainerType :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.getConfiguredContainerType .. py:property:: configuredContainerType :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.configuredContainerType :type: wfexs_backend.common.ContainerType .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.configuredContainerType .. py:property:: engine_url :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.engine_url :abstractmethod: :type: wfexs_backend.common.URIType .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.engine_url .. py:method:: _get_engine_version_str(matWfEng: wfexs_backend.workflow_engines.MaterializedWorkflowEngine) -> wfexs_backend.workflow_engines.WorkflowEngineVersionStr :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType._get_engine_version_str :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType._get_engine_version_str .. py:method:: sideContainers() -> Sequence[ContainerTaggedName] :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.sideContainers :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.sideContainers .. py:method:: materialize_containers(listOfContainerTags: Sequence[ContainerTaggedName], containersDir: pathlib.Path, offline: bool = False, force: bool = False, injectable_containers: Sequence[Container] = []) -> Tuple[ContainerEngineVersionStr, Sequence[Container], ContainerOperatingSystem, ProcessorArchitecture] :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.materialize_containers :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.materialize_containers .. py:method:: deploy_containers(containers_list: Sequence[Container], containersDir: Optional[pathlib.Path] = None, force: bool = False) -> Sequence[Container] :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.deploy_containers :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.deploy_containers .. py:property:: staged_containers_dir :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.staged_containers_dir :abstractmethod: :type: pathlib.Path .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.staged_containers_dir .. py:method:: materializeEngine(localWf: wfexs_backend.common.LocalWorkflow, engineVersion: Optional[EngineVersion] = None, do_identify: bool = False) -> Optional[MaterializedWorkflowEngine] :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.materializeEngine :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.materializeEngine .. py:method:: identifyWorkflow(localWf: wfexs_backend.common.LocalWorkflow, engineVer: Optional[EngineVersion] = None) -> Union[Tuple[EngineVersion, LocalWorkflow], Tuple[None, None]] :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.identifyWorkflow :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.identifyWorkflow .. py:method:: materializeWorkflow(matWorfklowEngine: wfexs_backend.workflow_engines.MaterializedWorkflowEngine, consolidatedWorkflowDir: pathlib.Path, offline: bool = False, profiles: Optional[Sequence[str]] = None) -> Tuple[MaterializedWorkflowEngine, Sequence[ContainerTaggedName]] :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.materializeWorkflow :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.materializeWorkflow .. py:method:: launchWorkflow(matWfEng: wfexs_backend.workflow_engines.MaterializedWorkflowEngine, inputs: Sequence[MaterializedInput], environment: Sequence[MaterializedInput], outputs: Sequence[ExpectedOutput], profiles: Optional[Sequence[str]] = None) -> Iterator[StagedExecution] :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.launchWorkflow :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.launchWorkflow .. py:method:: FromStagedSetup(staged_setup: wfexs_backend.common.StagedSetup, container_factory_classes: Sequence[Type[ContainerFactory]] = [NoContainerFactory], progs_mapping: Optional[ProgsMapping] = None, cache_dir: Optional[pathlib.Path] = None, cache_workflow_dir: Optional[pathlib.Path] = None, cache_workflow_inputs_dir: Optional[pathlib.Path] = None, local_config: Optional[EngineLocalConfig] = None, config_directory: Optional[pathlib.Path] = None) -> wfexs_backend.workflow_engines.AbstractWorkflowEngineType :canonical: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.FromStagedSetup :abstractmethod: :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.AbstractWorkflowEngineType.FromStagedSetup .. py:exception:: WorkflowEngineException() :canonical: wfexs_backend.workflow_engines.WorkflowEngineException Bases: :py:obj:`wfexs_backend.common.AbstractWfExSException` .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngineException .. rubric:: Initialization .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngineException.__init__ .. py:exception:: WorkflowEngineInstallException() :canonical: wfexs_backend.workflow_engines.WorkflowEngineInstallException Bases: :py:obj:`wfexs_backend.workflow_engines.WorkflowEngineException` .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngineInstallException .. rubric:: Initialization .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngineInstallException.__init__ .. py:class:: WorkflowEngine(container_factory_clazz: Type[ContainerFactory] = NoContainerFactory, cacheDir: Optional[pathlib.Path] = None, engine_config: Optional[EngineLocalConfig] = None, progs_mapping: Optional[ProgsMapping] = None, engineTweaksDir: Optional[pathlib.Path] = None, cacheWorkflowDir: Optional[pathlib.Path] = None, cacheWorkflowInputsDir: Optional[pathlib.Path] = None, workDir: Optional[pathlib.Path] = None, outputsDir: Optional[pathlib.Path] = None, outputMetaDir: Optional[pathlib.Path] = None, intermediateDir: Optional[pathlib.Path] = None, tempDir: Optional[pathlib.Path] = None, stagedContainersDir: Optional[pathlib.Path] = None, secure_exec: bool = False, allowOther: bool = False, config_directory: Optional[pathlib.Path] = None, engine_mode: wfexs_backend.common.EngineMode = DEFAULT_ENGINE_MODE, writable_containers: bool = False) :canonical: wfexs_backend.workflow_engines.WorkflowEngine Bases: :py:obj:`wfexs_backend.workflow_engines.AbstractWorkflowEngineType` .. py:attribute:: ENGINE_NAME :canonical: wfexs_backend.workflow_engines.WorkflowEngine.ENGINE_NAME :value: 'abstract' .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.ENGINE_NAME .. py:method:: FromStagedSetup(staged_setup: wfexs_backend.common.StagedSetup, container_factory_classes: Sequence[Type[ContainerFactory]] = [NoContainerFactory], progs_mapping: Optional[ProgsMapping] = None, cache_dir: Optional[pathlib.Path] = None, cache_workflow_dir: Optional[pathlib.Path] = None, cache_workflow_inputs_dir: Optional[pathlib.Path] = None, local_config: Optional[EngineLocalConfig] = None, config_directory: Optional[pathlib.Path] = None) -> wfexs_backend.workflow_engines.AbstractWorkflowEngineType :canonical: wfexs_backend.workflow_engines.WorkflowEngine.FromStagedSetup :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.FromStagedSetup .. py:method:: getConfiguredContainerType() -> wfexs_backend.common.ContainerType :canonical: wfexs_backend.workflow_engines.WorkflowEngine.getConfiguredContainerType .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.getConfiguredContainerType .. py:method:: SupportedContainerTypes() -> Set[ContainerType] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.SupportedContainerTypes :abstractmethod: :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.SupportedContainerTypes .. py:method:: SupportedSecureExecContainerTypes() -> Set[ContainerType] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.SupportedSecureExecContainerTypes :abstractmethod: :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.SupportedSecureExecContainerTypes .. py:method:: SupportsContainerType(container_type: wfexs_backend.common.ContainerType) -> bool :canonical: wfexs_backend.workflow_engines.WorkflowEngine.SupportsContainerType :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.SupportsContainerType .. py:method:: SupportsContainerFactory(container_factory_clazz: Type[ContainerFactory]) -> bool :canonical: wfexs_backend.workflow_engines.WorkflowEngine.SupportsContainerFactory :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.SupportsContainerFactory .. py:method:: SupportsSecureExecContainerType(container_type: wfexs_backend.common.ContainerType) -> bool :canonical: wfexs_backend.workflow_engines.WorkflowEngine.SupportsSecureExecContainerType :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.SupportsSecureExecContainerType .. py:method:: SupportsSecureExecContainerFactory(container_factory_clazz: Type[ContainerFactory]) -> bool :canonical: wfexs_backend.workflow_engines.WorkflowEngine.SupportsSecureExecContainerFactory :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.SupportsSecureExecContainerFactory .. py:method:: identifyWorkflow(localWf: wfexs_backend.common.LocalWorkflow, engineVer: Optional[EngineVersion] = None) -> Union[Tuple[EngineVersion, LocalWorkflow], Tuple[None, None]] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.identifyWorkflow :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.identifyWorkflow .. py:method:: materializeEngineVersion(engineVersion: wfexs_backend.common.EngineVersion) -> Tuple[EngineVersion, pathlib.Path, Fingerprint] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.materializeEngineVersion :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.materializeEngineVersion .. py:method:: GetEngineVersion(matWfEng: wfexs_backend.workflow_engines.MaterializedWorkflowEngine) -> wfexs_backend.workflow_engines.WorkflowEngineVersionStr :canonical: wfexs_backend.workflow_engines.WorkflowEngine.GetEngineVersion :staticmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.GetEngineVersion .. py:method:: materializeEngine(localWf: wfexs_backend.common.LocalWorkflow, engineVersion: Optional[EngineVersion] = None, do_identify: bool = False) -> Optional[MaterializedWorkflowEngine] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.materializeEngine .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.materializeEngine .. py:method:: materializeWorkflow(matWorfklowEngine: wfexs_backend.workflow_engines.MaterializedWorkflowEngine, consolidatedWorkflowDir: pathlib.Path, offline: bool = False, profiles: Optional[Sequence[str]] = None) -> Tuple[MaterializedWorkflowEngine, Sequence[ContainerTaggedName]] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.materializeWorkflow :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.materializeWorkflow .. py:method:: sideContainers() -> Sequence[ContainerTaggedName] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.sideContainers .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.sideContainers .. py:method:: simpleContainerFileName(imageUrl: wfexs_backend.common.URIType) -> Sequence[RelPath] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.simpleContainerFileName :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.simpleContainerFileName .. py:method:: materialize_containers(listOfContainerTags: Sequence[ContainerTaggedName], containersDir: Optional[pathlib.Path] = None, offline: bool = False, force: bool = False, injectable_containers: Sequence[Container] = []) -> Tuple[ContainerEngineVersionStr, Sequence[Container], ContainerOperatingSystem, ProcessorArchitecture] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.materialize_containers .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.materialize_containers .. py:method:: deploy_containers(containers_list: Sequence[Container], containersDir: Optional[pathlib.Path] = None, force: bool = False) -> Sequence[Container] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.deploy_containers .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.deploy_containers .. py:property:: staged_containers_dir :canonical: wfexs_backend.workflow_engines.WorkflowEngine.staged_containers_dir :type: pathlib.Path .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.staged_containers_dir .. py:method:: create_job_directories() -> Tuple[str, pathlib.Path, pathlib.Path, pathlib.Path] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.create_job_directories .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.create_job_directories .. py:method:: launchWorkflow(matWfEng: wfexs_backend.workflow_engines.MaterializedWorkflowEngine, inputs: Sequence[MaterializedInput], environment: Sequence[MaterializedInput], outputs: Sequence[ExpectedOutput], profiles: Optional[Sequence[str]] = None) -> Iterator[StagedExecution] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.launchWorkflow :abstractmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.launchWorkflow .. py:method:: ExecuteWorkflow(matWfEng: wfexs_backend.workflow_engines.MaterializedWorkflowEngine, inputs: Sequence[MaterializedInput], environment: Sequence[MaterializedInput], outputs: Sequence[ExpectedOutput], profiles: Optional[Sequence[str]] = None) -> Iterator[StagedExecution] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.ExecuteWorkflow :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.ExecuteWorkflow .. py:method:: MaterializeWorkflowAndContainers(matWfEng: wfexs_backend.workflow_engines.MaterializedWorkflowEngine, containersDir: pathlib.Path, consolidatedWorkflowDir: pathlib.Path, offline: bool = False, injectable_containers: Sequence[Container] = [], injectable_operational_containers: Sequence[Container] = [], profiles: Optional[Sequence[str]] = None) -> Tuple[MaterializedWorkflowEngine, ContainerEngineVersionStr, ContainerOperatingSystem, ProcessorArchitecture] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.MaterializeWorkflowAndContainers :classmethod: .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.MaterializeWorkflowAndContainers .. py:attribute:: GuessedCardinalityMapping :canonical: wfexs_backend.workflow_engines.WorkflowEngine.GuessedCardinalityMapping :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.GuessedCardinalityMapping .. py:attribute:: GuessedOutputKindMapping :canonical: wfexs_backend.workflow_engines.WorkflowEngine.GuessedOutputKindMapping :type: Mapping[str, ContentKind] :value: None .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.GuessedOutputKindMapping .. py:method:: identifyMaterializedOutputs(matInputs: Sequence[MaterializedInput], expectedOutputs: Sequence[ExpectedOutput], outputsDir: pathlib.Path, outputsMapping: Optional[Mapping[SymbolicOutputName, Any]] = None) -> Sequence[MaterializedOutput] :canonical: wfexs_backend.workflow_engines.WorkflowEngine.identifyMaterializedOutputs .. autodoc2-docstring:: wfexs_backend.workflow_engines.WorkflowEngine.identifyMaterializedOutputs