Merge pull request #80 from workflowhub-eu/fix-orcid-again

More defensive modifcations for ORCID enrichment

Author: elichad

Snakefile

@@ -23,12 +23,13 @@ rule source_ro_crates:
     output:
         f"{config['output-dir']}/{config['sourced-list']}"
     params: 
+        min_workflow_id = config['min-workflow-id'],
         max_workflow_id = config['max-workflow-id'],
         output_dir = config['output-dir'],
         base_url = config['base-url']
     shell:
         "source-crates "
-        "--workflow-ids 1-{params.max_workflow_id} "
+        "--workflow-ids {params.min_workflow_id}-{params.max_workflow_id} "
         "--output-dir {params.output_dir} "
         "--base-url {params.base_url} "
 
@@ -105,4 +106,4 @@ rule create_ro_crate:
         --enrichments-dir {params.enrichments_dir} \
         --workflow-file {params.workflow_file} \
         --output-dir {params.output_dir}
-        """
+        """

workflowhub_graph/workflowhub_graph/enrichment_strategies/orcid.py

@@ -60,30 +60,32 @@ def graph_for_orcid(orcid_id, orcid_data):
     person_data = orcid_data.get('person', {})
     name_data = person_data.get('name', {})
 
-    given_name = name_data.get('given-names', {}).get('value')
-    if given_name:
-        graph.add((orcid_uri, SCHEMA.givenName, Literal(given_name)))
-        logging.info(f"Added ORCID ID {orcid_id} with given name {given_name}")
-
-    family_name = name_data.get('family-name', {}).get('value')
-    if family_name:
-        graph.add((orcid_uri, SCHEMA.familyName, Literal(family_name)))
-        logging.info(f"Added ORCID ID {orcid_id} with name {given_name} {family_name}")
+    if name_data:
+        given_name = name_data.get('given-names', {}).get('value')
+        if given_name:
+            graph.add((orcid_uri, SCHEMA.givenName, Literal(given_name)))
+            logging.info(f"Added ORCID ID {orcid_id} with given name {given_name}")
+
+        family_name = name_data.get('family-name', {}).get('value')
+        if family_name:
+            graph.add((orcid_uri, SCHEMA.familyName, Literal(family_name)))
+            logging.info(f"Added ORCID ID {orcid_id} with name {given_name} {family_name}")
 
     # add employment information
     #  jq '._decoded_content["activities-summary"].employments["affiliation-group"] | .[] | .summaries[0]["employment-summary"].organization.name'
 
     activities = orcid_data.get('activities-summary', {})
-    employments = activities.get('employments', {}).get('affiliation-group', [])
-    for employment in employments:
-        summaries = employment.get('summaries', [])
-        if summaries and len(summaries) > 0:
-            employment_summary = summaries[0].get('employment-summary', {})
-            organization = employment_summary.get('organization', {})
-            org_name = organization.get('name')
-            if org_name:
-                graph.add((orcid_uri, SCHEMA.affiliation, Literal(org_name)))
-                logging.info(f"Added affiliation {org_name} for ORCID ID {orcid_id}")
+    if activities:
+        employments = activities.get('employments', {}).get('affiliation-group', [])
+        for employment in employments:
+            summaries = employment.get('summaries', [])
+            if summaries and len(summaries) > 0:
+                employment_summary = summaries[0].get('employment-summary', {})
+                organization = employment_summary.get('organization', {})
+                org_name = organization.get('name')
+                if org_name:
+                    graph.add((orcid_uri, SCHEMA.affiliation, Literal(org_name)))
+                    logging.info(f"Added affiliation {org_name} for ORCID ID {orcid_id}")
 
     return graph