diff --git a/bin/validate.py b/bin/validate.py index 89657d20..ad489e83 100755 --- a/bin/validate.py +++ b/bin/validate.py @@ -227,7 +227,6 @@ def produce_gaf(dataset, source_gaf, ontology_graph, gpipaths=None, paint=False, format="gaf", suppress_rule_reporting_tags=[], annotation_inferences=None, group_metadata=None, extensions_constraints=None, rule_contexts=[], gaf_output_version="2.2", rule_set=assocparser.RuleSet.ALL) -> list[str]: - filtered_associations = open(os.path.join(os.path.split(source_gaf)[0], "{}_noiea.gaf".format(dataset)), "w") config = assocparser.AssocParserConfig( ontology=ontology_graph, @@ -667,21 +666,21 @@ def produce(ctx, group, metadata_dir, gpad, ttl, target, ontology, exclude, base # like for paint_other. click.echo("source_gaf: {}".format(source_gaf)) valid_gaf = produce_gaf(dataset, source_gaf, ontology_graph, - paint=(group=="paint"), - group=group, - rule_metadata=rule_metadata, - goref_metadata=goref_metadata, - ref_species_metadata=ref_species_metadata, - db_entities=db_entities, - group_idspace=group_ids, - suppress_rule_reporting_tags=suppress_rule_reporting_tag, - annotation_inferences=gaferences, - group_metadata=group_metadata, - extensions_constraints=extensions_constraints, - rule_contexts=["import"] if dataset_metadata.get("import", False) else [], - gaf_output_version=gaf_output_version, - rule_set=rule_set - )[0] + paint=(group == "paint"), + group=group, + rule_metadata=rule_metadata, + goref_metadata=goref_metadata, + ref_species_metadata=ref_species_metadata, + db_entities=db_entities, + group_idspace=group_ids, + suppress_rule_reporting_tags=suppress_rule_reporting_tag, + annotation_inferences=gaferences, + group_metadata=group_metadata, + extensions_constraints=extensions_constraints, + rule_contexts=["import"] if dataset_metadata.get("import", False) else [], + gaf_output_version=gaf_output_version, + rule_set=rule_set + )[0] gpi = produce_gpi(dataset, absolute_target, valid_gaf, ontology_graph)