weaver.processes.wps_workflow
Module Contents
- 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 [source]
- class weaver.processes.wps_workflow.CallbackJob(job: Callable[[Any, Any], Any], output_callback: cwltool.builder.Builder, cachebuilder: Text, jobcache)[source]
- class weaver.processes.wps_workflow.WpsWorkflow(toolpath_object: cwltool.context.LoadingContext, loading_context: weaver.typedefs.JobProcessDefinitionCallback, get_job_process_definition)[source]
Definition of a CWL
workflow
that can executeWPS
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.AnyValueType], 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]
Collect outputs from the step Process following its execution.
- 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.CWL_ExpectedOutputs])[source]
Initialize the job object.
- run(self: Ellipsis, runtimeContext: cwltool.context.RuntimeContext, tmpdir_lock: Optional[threading.Lock] = None) None [source]