feature: enable pickling for research objects

Author: psafont

cwltool/main.py

@@ -583,7 +583,7 @@ def main(argsl=None,                   # type: List[str]
             if not args.compute_checksum:
                 _logger.error("--provenance incompatible with --no-compute-checksum")
                 return 1
-            ro = ResearchObject(runtimeContext.make_fs_access,
+            ro = ResearchObject(
                 temp_prefix_ro=args.tmpdir_prefix, orcid=args.orcid,
                 full_name=args.cwl_full_name)
             runtimeContext.research_obj = ro

cwltool/provenance.py

@@ -514,8 +514,7 @@ def declare_file(self, value):
         if not entity and 'location' in value:
             location = str(value['location'])
             # If we made it here, we'll have to add it to the RO
-            assert self.research_object.make_fs_access
-            fsaccess = self.research_object.make_fs_access("")
+            fsaccess = StdFsAccess("")
             with fsaccess.open(location, "rb") as fhandle:
                 relative_path = self.research_object.add_data_file(fhandle)
                 # FIXME: This naively relies on add_data_file setting hash as filename
@@ -605,8 +604,7 @@ def declare_directory(self, value):  # type: (MutableMapping) -> ProvEntity
         is_empty = True
 
         if not "listing" in value:
-            assert self.research_object.make_fs_access
-            fsaccess = self.research_object.make_fs_access("")
+            fsaccess = StdFsAccess("")
             get_listing(fsaccess, value)
         for entry in value.get("listing", []):
             is_empty = False
@@ -943,10 +941,9 @@ def finalize_prov_profile(self, name):
 class ResearchObject():
     """CWLProv Research Object."""
 
-    def __init__(self, make_fs_access, temp_prefix_ro="tmp", orcid='', full_name=''):
-        # type: (Callable[[Text], StdFsAccess], str, Text, Text) -> None
+    def __init__(self, temp_prefix_ro="tmp", orcid='', full_name=''):
+        # type: (str, Text, Text) -> None
 
-        self.make_fs_access = make_fs_access
         self.temp_prefix = temp_prefix_ro
         self.orcid = '' if not orcid else _valid_orcid(orcid)
         self.full_name = full_name
@@ -1553,7 +1550,7 @@ def _relativise_files(self, structure):
                     # Register in RO; but why was this not picked
                     # up by used_artefacts?
                     _logger.info("[provenance] Adding to RO %s", structure["location"])
-                    fsaccess = self.make_fs_access("")
+                    fsaccess = StdFsAccess("")
                     with fsaccess.open(structure["location"], "rb") as fp:
                         relative_path = self.add_data_file(fp)
                         checksum = posixpath.basename(relative_path)

cwltool/workflow.py

@@ -572,8 +572,6 @@ def job(self,
         builder = self._init_job(job_order, runtimeContext)
         #relativeJob=copy.deepcopy(builder.job)
         if runtimeContext.research_obj is not None:
-            if not runtimeContext.research_obj.make_fs_access:
-                runtimeContext.research_obj.make_fs_access = runtimeContext.make_fs_access
             if runtimeContext.toplevel:
                 # Record primary-job.json
                 runtimeContext.research_obj.create_job(builder.job, self.job)

tests/test_provenance.py

@@ -533,7 +533,7 @@ def test_failing_path_conversion(path, from_type, to_type):
 
 @pytest.fixture
 def research_object():
-    re_ob = provenance.ResearchObject(RuntimeContext().make_fs_access)
+    re_ob = provenance.ResearchObject()
     yield re_ob
     re_ob.close()