more tweaking order of annotation production

biolink · Feb 22, 2024 · 9d8c131 · 9d8c131
1 parent d298942
commit 9d8c131
Showing 1 changed file with 9 additions and 3 deletions.
diff --git a/bin/validate.py b/bin/validate.py
@@ -669,16 +669,22 @@ def produce(ctx, group, metadata_dir, gpad, ttl, target, ontology, exclude, base
                                                           base_download_url=base_download_url,
                                                           replace_existing_files=not skip_existing_files)
 
-        end_gaf = mixin_a_dataset(valid_gaf, mixin_metadata_list, group_metadata["id"], dataset, absolute_target,
+        sans_noctua_gaf = mixin_a_dataset(valid_gaf, mixin_metadata_list, group_metadata["id"], dataset, absolute_target,
                                   ontology_graph, gpipaths=gpi_list, base_download_url=base_download_url,
                                   rule_metadata=rule_metadata, replace_existing_files=not skip_existing_files,
                                   gaf_output_version=gaf_output_version)
 
-        make_ttls(dataset, end_gaf, products, ontology_graph)
+        make_gpads(dataset, sans_noctua_gaf, products, ontology_graph, noctua_gpad_src)
 
-        make_gpads(dataset, end_gaf, products, ontology_graph, noctua_gpad_src)
+        # add noctua gpad to the mix _after_ grabbing its extra extension metadata for the GPAD representation above.
+        mixin_metadata_list.append(noctua_metadata)
 
+        end_gaf = mixin_a_dataset(valid_gaf, mixin_metadata_list, group_metadata["id"], dataset, absolute_target,
+                                  ontology_graph, gpipaths=gpi_list, base_download_url=base_download_url,
+                                  rule_metadata=rule_metadata, replace_existing_files=not skip_existing_files,
+                                  gaf_output_version=gaf_output_version)
 
+        make_ttls(dataset, end_gaf, products, ontology_graph)
 
 
 @cli.command()