weaver.processes.wps_workflow

Module Contents

weaver.processes.wps_workflow.LOGGER[source]
weaver.processes.wps_workflow.DEFAULT_TMP_PREFIX = tmp[source]
weaver.processes.wps_workflow.default_make_tool(toolpath_object: Ellipsis, loading_context: cwltool.context.LoadingContext, get_job_process_definition: weaver.typedefs.GetJobProcessDefinitionFunction)cwltool.process.Process[source]
class weaver.processes.wps_workflow.CallbackJob(job: Callable[[Any, Any], Any], output_callback: cwltool.builder.Builder, cachebuilder: Text, jobcache)[source]
run(self: cwltool.context.RuntimeContext, loading_context)None[source]
class weaver.processes.wps_workflow.WpsWorkflow(toolpath_object: cwltool.context.LoadingContext, loading_context: weaver.typedefs.GetJobProcessDefinitionFunction, get_job_process_definition)[source]

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(self: Ellipsis, joborder: Dict[Text, weaver.typedefs.AnyValue], output_callbacks: Callable[[Any, Any], Any], runtime_context: cwltool.context.RuntimeContext)Generator[Union[cwltool.job.JobBase, CallbackJob], None, None][source]

Workflow job generator.

Parameters
  • joborder – 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(self: Ellipsis, ports: Set[Dict[Text, Any]], builder: cwltool.builder.Builder, outdir: Text, compute_checksum: bool = True, jobname: Text = '', readers: Dict[Text, Any] = None)cwltool.command_line_tool.OutputPorts[source]
collect_output(self: Ellipsis, schema: Dict[Text, Any], 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]]]][source]
class weaver.processes.wps_workflow.WpsWorkflowJob(builder: cwltool.builder.Builder, joborder: 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.ExpectedOutputType])[source]

Initialize the job object.

run(self: Ellipsis, runtimeContext: cwltool.context.RuntimeContext, tmpdir_lock: Optional[threading.Lock] = None)None[source]
execute(self: List[Text], runtime: MutableMapping[Text, Text], env: cwltool.context.RuntimeContext, runtime_context)None[source]