From 420dd1c0a9102e56dc85d8cb0116ac593d3aae5c Mon Sep 17 00:00:00 2001
From: Jasper Koehorst <jasper.koehorst@wur.nl>
Date: Thu, 17 Aug 2023 08:20:49 +0200
Subject: [PATCH] work in progress to fix the main merge

---
 cwltool/cwlprov/provenance_profile.py | 6 ++++--
 cwltool/cwlprov/ro.py                 | 3 +++
 2 files changed, 7 insertions(+), 2 deletions(-)

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: