diff --git a/bin/validate.py b/bin/validate.py index f604a6c3..e8ff485e 100755 --- a/bin/validate.py +++ b/bin/validate.py @@ -224,7 +224,7 @@ def create_parser(config, group, dataset, format="gaf"): @tools.gzips def produce_gaf(dataset, source_gaf, ontology_graph, gpipaths=None, paint=False, group="unknown", rule_metadata=None, - goref_metadata=None, ref_species_metadata=None, retracted_pub_set=None, db_entities=None, group_idspace=None, + goref_metadata=None, ref_species_metadata=None, db_type_name_regex_id_syntax=None, retracted_pub_set=None, db_entities=None, group_idspace=None, 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]: @@ -238,6 +238,7 @@ def produce_gaf(dataset, source_gaf, ontology_graph, gpipaths=None, paint=False, rule_metadata=rule_metadata, goref_metadata=goref_metadata, ref_species_metadata=ref_species_metadata, + db_type_name_regex_id_syntax=db_type_name_regex_id_syntax, retracted_pub_set=retracted_pub_set, entity_idspaces=db_entities, group_idspace=group_idspace, @@ -684,6 +685,8 @@ def produce(ctx, group, metadata_dir, gpad, gpad_gpi_output_version, ttl, target # Default comes through as single-element tuple if rule_set == (assocparser.RuleSet.ALL,): rule_set = assocparser.RuleSet.ALL + + db_type_name_regex_id_syntax = metadata.database_type_name_regex_id_syntax(absolute_metadata) retracted_pubs = None if retracted_pub_set: @@ -703,6 +706,8 @@ def produce(ctx, group, metadata_dir, gpad, gpad_gpi_output_version, ttl, target rule_metadata=rule_metadata, goref_metadata=goref_metadata, ref_species_metadata=ref_species_metadata, + db_type_name_regex_id_syntax=db_type_name_regex_id_syntax, + retracted_pub_set=retracted_pubs, db_entities=db_entities, group_idspace=group_ids, suppress_rule_reporting_tags=suppress_rule_reporting_tag, @@ -830,6 +835,7 @@ def rule(metadata_dir, out, ontology, gaferencer_file, retracted_pub_set): goref_metadata = metadata.yamldown_lookup(os.path.join(absolute_metadata, "gorefs")) gorule_metadata = metadata.yamldown_lookup(os.path.join(absolute_metadata, "rules")) ref_species_metadata = metadata.yaml_set(absolute_metadata, "go-reference-species.yaml", "taxon_id") + db_type_name_regex_id_syntax = metadata.database_type_name_regex_id_syntax(absolute_metadata) retracted_pubs = None if retracted_pub_set: retracted_pubs = metadata.retracted_pub_set(retracted_pub_set) @@ -850,6 +856,7 @@ def rule(metadata_dir, out, ontology, gaferencer_file, retracted_pub_set): ontology=ontology_graph, goref_metadata=goref_metadata, ref_species_metadata=ref_species_metadata, + db_type_name_regex_id_syntax=db_type_name_regex_id_syntax, retracted_pub_set=retracted_pubs, entity_idspaces=db_entities, group_idspace=group_ids,