Merge pull request #837 from common-workflow-language/CWLProv

Research Object: don't copy input files into snapshot

Author: mr-c

cwltool/main.py

@@ -662,12 +662,6 @@ def loc_to_path(obj):
             prov_dep = prov_dependencies[1]
             assert prov_dep
             runtimeContext.research_obj.generate_snapshot(prov_dep)
-            #for input file dependencies
-            if input_for_prov:
-                runtimeContext.research_obj.generate_snapshot(input_for_prov)
-            #NOTE: keep these commented out lines to evaluate tests later
-            #if job_order_object:
-                #runtimeContext.research_obj.generate_snapshot(job_order_object)
 
             runtimeContext.research_obj.close(args.provenance)
 

cwltool/provenance.py

@@ -4,18 +4,6 @@
 """
 from __future__ import absolute_import
 
-__citation__ = "https://doi.org/10.5281/zenodo.1208477"
-
-# NOTE: Semantic versioning of the CWLProv Research Object
-# **and** the cwlprov files
-#
-# Rough guide (major.minor.patch):
-# 1. Bump minor number if adding resources or PROV statements
-# 2. Bump major number if removing/"breaking" resources or PROV statements
-# 3. Bump patch number for non-breaking non-adding changes, 
-#    e.g. fixing broken relative paths
-CWLPROV_VERSION = "https://w3id.org/cwl/prov/0.3.0"
-
 import io
 from io import open
 import json
@@ -77,7 +65,19 @@
 
 if six.PY2:
     class PermissionError(OSError):
+        "to avoid mypy3 error"
         pass
+__citation__ = "https://doi.org/10.5281/zenodo.1208477"
+
+# NOTE: Semantic versioning of the CWLProv Research Object
+# **and** the cwlprov files
+#
+# Rough guide (major.minor.patch):
+# 1. Bump minor number if adding resources or PROV statements
+# 2. Bump major number if removing/"breaking" resources or PROV statements
+# 3. Bump patch number for non-breaking non-adding changes,
+#    e.g. fixing broken relative paths
+CWLPROV_VERSION = "https://w3id.org/cwl/prov/0.3.0"
 
 relativised_input_object = {}  # type: Dict[str, Any]
 #FIXME not module global
@@ -813,6 +813,7 @@ def _finalize(self):
 
     def user_provenance(self, document):
         # type: (ProvDocument) -> None
+        "adds the user provenance"
         (username, fullname) = _whoami()
 
         if not self.full_name:
@@ -1023,7 +1024,7 @@ def _ro_annotations(self):
         # FIXME: Only primary*
         prov_files = [posixpath.relpath(p, METADATA) for p in self.tagfiles
                       if p.startswith(_posix_path(PROVENANCE))
-                         and "/primary." in p]
+                        and "/primary." in p]
         annotations.append({
             "uri": uuid.uuid4().urn,
             "about": self.workflow_run_uri,