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For #2210 #678

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merged 1 commit into from
Jul 15, 2024
Merged

For #2210 #678

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9 changes: 8 additions & 1 deletion bin/validate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]:
Expand All @@ -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,
Expand Down Expand Up @@ -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:
Expand All @@ -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,
Expand Down Expand Up @@ -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)
Expand All @@ -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,
Expand Down
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