Propagate input annotations to primary.cwlprov files

cwltool/provenance_profile.py

@@ -76,6 +76,7 @@ def copy_job_order(
     return customised_job
 
 
+
 class ProvenanceProfile:
     """
     Provenance profile.
@@ -247,6 +248,18 @@ def evaluate(
             self.prospective_prov(job)
             customised_job = copy_job_order(job, job_order_object)
             self.used_artefacts(customised_job, self.workflow_run_uri)
+            # if CWLPROV['prov'].uri in job_order_object: # maybe move this to another place
+            #     metadata = job_order_object[CWLPROV['prov'].uri] # change uri to CWLPROV['prov'].uri
+            #     for item in metadata:
+            #         # make a new entity with id
+            #         # give it type additionalType value
+            #         # add nested annotations
+            #         # how much of this can we reuse from _add_nested_annotations?
+            #         # how do we identify the correct file to write to? self.workflow_run_uri?
+            #         # 
+            #         pass
+
+
 
     def record_process_start(
         self, process: Process, job: JobsType, process_run_id: Optional[str] = None
@@ -296,6 +309,27 @@ def record_process_end(
         self.generate_output_prov(outputs, process_run_id, process_name)
         self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when)
 
+    def _add_nested_annotations(self, annotation_key, annotation_value, e: ProvEntity) -> ProvEntity:
+        """Propagate input data annotations to provenance."""
+        # Change https:// into http:// first
+        schema2_uri = "https://schema.org/" 
+        if schema2_uri in annotation_key:
+            annotation_key = SCHEMA[annotation_key.replace(schema2_uri, '')].uri 
+
+        if not isinstance(annotation_value, (MutableSequence, MutableMapping)):            
+            e.add_attributes({annotation_key: str(annotation_value)})
+        elif isinstance(annotation_value, MutableSequence):
+            for item_value in annotation_value:
+                e = self._add_nested_annotations(annotation_key, item_value, e)
+        else:
+            nested_id = uuid.uuid4().urn
+            nested_entity = self.document.entity(nested_id)
+            e.add_attributes({annotation_key: nested_entity.identifier})
+            for nested_key in annotation_value:
+                nested_value = annotation_value[nested_key] 
+                nested_entity = self._add_nested_annotations(nested_key, nested_value, nested_entity)
+        return e
+
     def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, str]:
         if value["class"] != "File":
             raise ValueError("Must have class:File: %s" % value)
@@ -350,6 +384,21 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st
             file_entity.add_attributes({CWLPROV["nameext"]: value["nameext"]})
         self.document.specializationOf(file_entity, entity)
 
+        # Identify all schema annotations
+        schema_annotations = dict([(v, value[v]) for v in value.keys() if 'schema.org' in v])
+
+        # Transfer SCHEMA annotations to provenance
+        for s in schema_annotations:
+            if "additionalType" in s:
+                additional_type = schema_annotations[s].split(sep='/')[-1] # find better method?
+                file_entity.add_attributes( {PROV_TYPE: SCHEMA[additional_type]}) 
+            else: 
+                file_entity = self._add_nested_annotations(s, schema_annotations[s], file_entity)
+
+        # Transfer format annotations to provenance:
+        if "format" in value:
+            file_entity.add_attributes({SCHEMA["encodingFormat"]: value["format"]})
+
         # Check for secondaries
         for sec in cast(
             MutableSequence[CWLObjectType], value.get("secondaryFiles", [])
@@ -395,6 +444,7 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity:
                 (PROV_TYPE, RO["Folder"]),
             ],
         )
+
         # ORE description of ro:Folder, saved separately
         coll_b = dir_bundle.entity(
             dir_id,
@@ -454,7 +504,18 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity:
 
         coll.add_attributes(coll_attribs)
         coll_b.add_attributes(coll_b_attribs)
-
+
+        # Identify all schema annotations
+        schema_annotations = dict([(v, value[v]) for v in value.keys() if 'schema.org' in v])
+
+        # Transfer SCHEMA annotations to provenance
+        for s in schema_annotations:
+            if "additionalType" in s:
+                additional_type = schema_annotations[s].split(sep='/')[-1] # find better method?
+                coll.add_attributes( {PROV_TYPE: SCHEMA[additional_type]}) 
+            elif "hasPart" not in s:
+                coll = self._add_nested_annotations(s, schema_annotations[s], coll)
+
         # Also Save ORE Folder as annotation metadata
         ore_doc = ProvDocument()
         ore_doc.add_namespace(ORE)