diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index dd043d49e..bd1c2fc02 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -24,6 +24,8 @@ from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity from schema_salad.sourceline import SourceLine +import cwltool.workflow + from ..errors import WorkflowException from ..job import CommandLineJob, JobBase from ..loghandler import _logger @@ -55,7 +57,7 @@ from .ro import ResearchObject -def copy_job_order(job: Union[Process, JobsType], job_order_object: CWLObjectType) -> CWLObjectType: +def copy_job_order(job: Union[Process, JobsType], job_order_object: CWLObjectType, process) -> CWLObjectType: """Create copy of job object for provenance.""" if not isinstance(job, WorkflowJob): # direct command line tool execution @@ -265,7 +267,7 @@ def evaluate( if not hasattr(process, "steps"): # record provenance of independent commandline tool executions self.prospective_prov(job) - customised_job = copy_job_order(job, job_order_object) + customised_job = copy_job_order(job, job_order_object, process) self.used_artefacts(customised_job, self.workflow_run_uri) create_job(research_obj, customised_job) elif hasattr(job, "workflow"): diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 87c060cdc..62b8cd61c 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -93,6 +93,9 @@ def __init__( self._initialize() _logger.debug("[provenance] Temporary research object: %s", self.folder) + # No data option + self.no_data = False + def self_check(self) -> None: """Raise ValueError if this RO is closed.""" if self.closed: