weaver.processes.wps_workflow

Module Contents

weaver.processes.wps_workflow.LOGGER

weaver.processes.wps_workflow.DEFAULT_TMP_PREFIX = tmp

weaver.processes.wps_workflow.default_make_tool(toolpath_object: Ellipsis, loading_context: cwltool.context.LoadingContext, get_job_process_definition: weaver.typedefs.JobProcessDefinitionCallback) → cwltool.process.Process

class weaver.processes.wps_workflow.CallbackJob(job: WpsWorkflow, output_callback: Callable[[Any, Any], Any], cachebuilder: cwltool.builder.Builder, jobcache: Text)

run(loading_context: cwltool.context.RuntimeContext) → None

class weaver.processes.wps_workflow.WpsWorkflow(toolpath_object: Dict[Text, Any], loading_context: cwltool.context.LoadingContext, get_job_process_definition: weaver.typedefs.JobProcessDefinitionCallback)

Definition of a CWL workflow that can execute WPS application packages as intermediate job steps.

Steps are expected to be defined as individual weaver.processes.wps_package.WpsPackage references.

Build a Process object from the provided dictionary.

job(job_order: Ellipsis, output_callbacks: Callable[[Any, Any], Any], runtime_context: cwltool.context.RuntimeContext) → Generator[Union[cwltool.job.JobBase, CallbackJob], None, None]

Workflow job generator.

Parameters

• job_order – inputs of the job submission

• output_callbacks – method to fetch step outputs and corresponding step details

• runtime_context – configs about execution environment

Returns

collect_output_ports(ports: Ellipsis, builder: cwltool.builder.Builder, outdir: Text, compute_checksum: bool = True, job_name: Text = '', readers: Dict[Text, Any] = None) → cwltool.command_line_tool.OutputPorts

collect_output(schema: Ellipsis, builder: cwltool.builder.Builder, outdir: Text, fs_access: cwltool.stdfsaccess.StdFsAccess, compute_checksum: bool = True) → Optional[Union[Dict[Text, Any], List[Union[Dict[Text, Any], Text]]]]

Collect outputs from the step Process following its execution.

class weaver.processes.wps_workflow.WpsWorkflowJob(builder: Ellipsis, job_order: Dict[Text, Union[Dict[Text, Any], List, Text, None]], requirements: List[Dict[Text, Text]], hints: List[Dict[Text, Text]], name: Text, wps_process: weaver.processes.wps_process_base.WpsProcessInterface, expected_outputs: List[weaver.typedefs.CWL_Output_Type])

Initialize the job object.

run(runtimeContext: Ellipsis, tmpdir_lock: Optional[threading.Lock] = None) → None

execute(runtime: List[Text], env: MutableMapping[Text, Text], runtime_context: cwltool.context.RuntimeContext) → None

Execute the WPS Process defined as Workflow step and chains their intermediate results.