Fix output result metadata (#65)

* bugfix: refactored variable name for associated works in task_output_results was not propogated to task_maintenance_metadata.

* Updated github action.

* dependabot version bump. Updated postgres in github action.

* bumped postgres in docker-compose.

* fixed erroneous correction of update_citation_target_metadata.

.github/workflows/python_actions.yml

@@ -1,6 +1,10 @@
 name: Python CI actions
 
-on: [pull_request]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
 env:
   PGDATABASE: citation_capture_pipeline_test
   PGPASSWORD: postgres
@@ -15,7 +19,7 @@ jobs:
 
     services:
       postgres:
-        image: postgres:9.6
+        image: postgres:14.0
         env:
           POSTGRES_DB: citation_capture_pipeline_test
           POSTGRES_PASSWORD: postgres

.gitignore

@@ -24,6 +24,7 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+.DS_Store
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

ADSCitationCapture/doi.py

@@ -211,13 +211,7 @@ def _parse_metadata_zenodo_doi(raw_metadata):
             parsed_metadata['bibcode'] = bibcode
     return parsed_metadata
 
-def fetch_all_versions_doi(base_doi_url, base_datacite_url, parsed_metadata):  
-    """
-    Takes zenodo parsed metadata and fetches DOI for all versions of zenodo repository
-    """
-    return _fetch_all_versions_doi(base_doi_url, base_datacite_url, parsed_metadata)
-
-def _fetch_all_versions_doi(base_doi_url, base_datacite_url, parsed_metadata):
+def fetch_all_versions_doi(base_doi_url, base_datacite_url, parsed_metadata):
     """
     Takes zenodo parsed metadata and fetches DOI for base repository as well as DOI for all versions.
     """

ADSCitationCapture/tasks.py

@@ -215,7 +215,7 @@ def task_process_updated_citation(citation_change, force=False):
             original_citations = db.get_citations_by_bibcode(app, citation_target_bibcode)
             citations = api.get_canonical_bibcodes(app, original_citations)
             logger.debug("Calling 'task_output_results' with '%s'", citation_change)
-            task_output_results.delay(citation_change, parsed_metadata, citations, db_versions = no_self_ref_versions, readers=readers)
+            task_output_results.delay(citation_change, parsed_metadata, citations, db_versions=no_self_ref_versions, readers=readers)
         logger.debug("Calling '_emit_citation_change' with '%s'", citation_change)
         _emit_citation_change(citation_change, parsed_metadata)
 
@@ -659,7 +659,7 @@ def task_maintenance_metadata(dois, bibcodes, reset=False):
                 citations = api.get_canonical_bibcodes(app, original_citations)
                 readers = db.get_citation_target_readers(app, registered_record['bibcode'], parsed_metadata.get('alternate_bibcode', []))
                 logger.debug("Calling 'task_output_results' with '%s'", citation_change)
-                task_output_results.delay(citation_change, modified_metadata, citations, bibcode_replaced=bibcode_replaced, associated=registered_record.get('associated_works', {"":""}), readers=readers)     
+                task_output_results.delay(citation_change, modified_metadata, citations, bibcode_replaced=bibcode_replaced, db_versions=registered_record.get('associated_works', {"":""}), readers=readers)     
 
 @app.task(queue='maintenance_metadata')
 def task_maintenance_curation(dois, bibcodes, curated_entries, reset=False):
@@ -821,7 +821,7 @@ def task_maintenance_curation(dois, bibcodes, curated_entries, reset=False):
                         citations = api.get_canonical_bibcodes(app, original_citations)
                         readers = db.get_citation_target_readers(app, registered_record['bibcode'], parsed_metadata.get('alternate_bibcode', []))
                         logger.debug("Calling 'task_output_results' with '%s'", citation_change)
-                        task_output_results.delay(citation_change, modified_metadata, citations, bibcode_replaced=bibcode_replaced, associated=registered_record.get('associated_works', {"":""}), readers=readers)    
+                        task_output_results.delay(citation_change, modified_metadata, citations, bibcode_replaced=bibcode_replaced, db_versions=registered_record.get('associated_works', {"":""}), readers=readers)    
                 else:
                     logger.warn("Curated metadata did not result in a change to recorded metadata for {}.".format(registered_record.get('content')))
             except Exception as e:
@@ -940,7 +940,7 @@ def task_maintenance_resend(dois, bibcodes, broker, only_nonbib=False):
                 # Only update master
                 readers = db.get_citation_target_readers(app, parsed_metadata.get('bibcode',''), parsed_metadata.get('alternate_bibcode', []))
                 logger.debug("Calling 'task_output_results' with '%s'", custom_citation_change)
-                task_output_results.delay(custom_citation_change, parsed_metadata, citations, db_versions = registered_record.get('associated_works',{"":""}), readers=readers, only_nonbib=only_nonbib)
+                task_output_results.delay(custom_citation_change, parsed_metadata, citations, db_versions=registered_record.get('associated_works',{"":""}), readers=readers, only_nonbib=only_nonbib)
 
             else:
                 # Only re-emit to the broker