From 9d8c1316f769d3058ef2f1216fe7c61965f6091d Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 22 Feb 2024 13:59:18 -0800 Subject: [PATCH] more tweaking order of annotation production --- bin/validate.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/bin/validate.py b/bin/validate.py index 870da38a..b206cfa6 100755 --- 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()