fix conflicts with master/main

bin/ontobio-parse-assocs.py

@@ -81,7 +81,9 @@ def main():
     parser.add_argument("-g", "--gpi", type=str, required=False, default=None,
                         help="GPI file")
     parser.add_argument("-m", "--metadata_dir", type=dir_path, required=False,
-                        help="Path to metadata directory")
+                        help="Path to metadata directory") 
+    parser.add_argument("--retracted_pub_set", type=argparse.FileType('r'), required=False,
+                        help="Path to retracted publications file") 
     parser.add_argument("-l", "--rule", action="append", required=None, default=[], dest="rule_set",
                         help="Set of rules to be run. Default is no rules to be run, with the exception \
                             of gorule-0000027 and gorule-0000020. See command line documentation in the \
@@ -144,11 +146,17 @@ def main():
         rule_set = assocparser.RuleSet.ALL
 
     goref_metadata = None
-    ref_species_metadata = None
+    ref_species_metadata = None  
     if args.metadata_dir:
         absolute_metadata = os.path.abspath(args.metadata_dir)
         goref_metadata = metadata.yamldown_lookup(os.path.join(absolute_metadata, "gorefs"))
         ref_species_metadata = metadata.yaml_set(absolute_metadata, "go-reference-species.yaml", "taxon_id")
+
+    retracted_pub_set = None
+    if args.retracted_pub_set:
+        retracted_pub_set = metadata.retracted_pub_set(args.retracted_pub_set.name)
+    elif args.metadata_dir:
+       retracted_pub_set = metadata.retracted_pub_set_from_meta(absolute_metadata)     
 
     # set configuration
     filtered_evidence_file = open(args.filtered_file, "w") if args.filtered_file else None
@@ -165,6 +173,7 @@ def main():
         gpi_authority_path=args.gpi,
         goref_metadata=goref_metadata,
         ref_species_metadata=ref_species_metadata,
+        retracted_pub_set=retracted_pub_set,
         rule_set=rule_set
     )
     p = None

bin/validate.py

@@ -34,6 +34,7 @@
 from ontobio.validation import tools
 from ontobio.validation import rules
 
+
 from typing import Dict, Set
 
 # logging.basicConfig(format="%(asctime)s - %(name)s - %(levelname)s: %(message)s", level=logging.WARNING)
@@ -223,7 +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, db_entities=None, group_idspace=None,
+                goref_metadata=None, ref_species_metadata=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]:
@@ -237,6 +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,
+        retracted_pub_set=retracted_pub_set,
         entity_idspaces=db_entities,
         group_idspace=group_idspace,
         suppress_rule_reporting_tags=suppress_rule_reporting_tags,
@@ -610,9 +612,32 @@ def cli(ctx, verbose):
 @click.option("--only-dataset", default=None)
 @click.option("--gaf-output-version", default="2.2", type=click.Choice(["2.1", "2.2"]))
 @click.option("--rule-set", "-l", "rule_set", default=[assocparser.RuleSet.ALL], multiple=True)
+@click.option("--retracted_pub_set", type=click.Path(exists=True), default=None, required=False, help="Path to retracted publications file")
 def produce(ctx, group, metadata_dir, gpad, gpad_gpi_output_version, ttl, target, ontology, exclude, base_download_url,
             suppress_rule_reporting_tag, skip_existing_files, gaferencer_file, only_dataset, gaf_output_version,
-            rule_set):
+            rule_set, retracted_pub_set):
+    """
+    Produce GAF, GPI, and TTL files for a group.
+
+    This command will download the GAF files for a group, validate them, and then produce GPI and TTL files.
+    :param ctx: Click context
+    :param group: The group to produce files for
+    :param metadata_dir: The directory containing the metadata files
+    :param gpad: Produce GPAD files
+    :param gpad_gpi_output_version: The version of the GPAD and GPI files to produce
+    :param ttl: Produce TTL files
+    :param target: The directory to put the files in
+    :param ontology: The ontology to use for validation
+    :param exclude: Datasets to exclude
+    :param base_download_url: The base URL to download files from
+    :param suppress_rule_reporting_tag: Tags to suppress in the rule reporting
+    :param skip_existing_files: Skip downloading files that already exist
+    :param gaferencer_file: The path to the Gaferencer output file
+    :param only_dataset: Only process a single dataset
+    :param gaf_output_version: The version of the GAF files to produce
+    :param rule_set: The rule set to use
+    :param retracted_pub_set: The path to the retracted publications file
+    """
     logger.info("Logging is verbose")
     products = {
         "gaf": True,
@@ -650,7 +675,7 @@ def produce(ctx, group, metadata_dir, gpad, gpad_gpi_output_version, ttl, target
 
     db_entities = metadata.database_entities(absolute_metadata)
     group_ids = metadata.groups(absolute_metadata)
-    extensions_constraints = metadata.extensions_constraints_file(absolute_metadata)
+    extensions_constraints = metadata.extensions_constraints_file(absolute_metadata)    
 
     gaferences = None
     if gaferencer_file:
@@ -660,6 +685,12 @@ def produce(ctx, group, metadata_dir, gpad, gpad_gpi_output_version, ttl, target
     if rule_set == (assocparser.RuleSet.ALL,):
         rule_set = assocparser.RuleSet.ALL
 
+    retracted_pubs = None
+    if retracted_pub_set:
+        retracted_pubs = metadata.retracted_pub_set(retracted_pub_set)
+    else:
+       retracted_pubs = metadata.retracted_pub_set_from_meta(absolute_metadata)  
+
     for dataset_metadata, source_gaf in downloaded_gaf_sources:
         dataset = dataset_metadata["dataset"]
         # Set paint to True when the group is "paint".
@@ -772,13 +803,14 @@ def paint(group, dataset, metadata, target, ontology):
     absolute_target = os.path.abspath(target)
     os.makedirs(os.path.join(absolute_target, "groups"), exist_ok=True)
     paint_metadata = metadata.dataset_metadata_file(absolute_metadata, "paint")
+
     paint_src_gaf = check_and_download_mixin_source(paint_metadata, dataset, absolute_target)
 
     click.echo("Loading ontology: {}...".format(ontology))
     ontology_graph = OntologyFactory().create(ontology)
 
     gpi_path = os.path.join(absolute_target, "groups", dataset, "{}.gpi".format(dataset))
-    click.echo("Using GPI at {}".format(gpi_path))
+    click.echo("Using GPI at {}".format(gpi_path))  
     paint_gaf = produce_gaf("paint_{}".format(dataset), paint_src_gaf, ontology_graph, gpipath=gpi_path)
 
 
@@ -788,7 +820,8 @@ def paint(group, dataset, metadata, target, ontology):
 @click.option("--ontology", type=click.Path(), required=True)
 @click.option("--gaferencer-file", "-I", type=click.Path(exists=True), default=None, required=False,
               help="Path to Gaferencer output to be used for inferences")
-def rule(metadata_dir, out, ontology, gaferencer_file):
+@click.option("--retracted_pub_set", type=click.Path(exists=True), default=None, required=False, help="Path to retracted publications file")
+def rule(metadata_dir, out, ontology, gaferencer_file, retracted_pub_set):
     absolute_metadata = os.path.abspath(metadata_dir)
 
     click.echo("Loading ontology: {}...".format(ontology))
@@ -797,6 +830,12 @@ def rule(metadata_dir, out, ontology, gaferencer_file):
     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")
+    retracted_pubs = None
+    if retracted_pub_set:
+        retracted_pubs = metadata.retracted_pub_set(retracted_pub_set)
+    else:
+       retracted_pubs = metadata.retracted_pub_set_from_meta(absolute_metadata)     
+
 
     click.echo("Found {} GO Rules".format(len(gorule_metadata.keys())))
 
@@ -811,6 +850,7 @@ def rule(metadata_dir, out, ontology, gaferencer_file):
         ontology=ontology_graph,
         goref_metadata=goref_metadata,
         ref_species_metadata=ref_species_metadata,
+        retracted_pub_set=retracted_pubs,
         entity_idspaces=db_entities,
         group_idspace=group_ids,
         annotation_inferences=gaferences,

ontobio/__init__.py

@@ -1,6 +1,6 @@
 from __future__ import absolute_import
 
-__version__ = '2.8.24'
+__version__ = '2.8.25'
 
 
 from .ontol_factory import OntologyFactory

ontobio/io/assocparser.py

@@ -234,6 +234,7 @@ def __init__(self,
                  ref_species_metadata=None,
                  group_metadata=None,
                  dbxrefs=None,
+                 retracted_pub_set=None,
                  suppress_rule_reporting_tags=[],
                  annotation_inferences=None,
                  extensions_constraints=None,
@@ -258,6 +259,7 @@ def __init__(self,
         self.goref_metadata = goref_metadata
         self.ref_species_metadata = ref_species_metadata
         self.group_metadata = group_metadata
+        self.retracted_pub_set = retracted_pub_set
         self.suppress_rule_reporting_tags = suppress_rule_reporting_tags
         self.annotation_inferences = annotation_inferences
         self.entity_idspaces = entity_idspaces

ontobio/io/qc.py

@@ -421,6 +421,20 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
             return self._result(bool(withfrom))
         else:
             return self._result(True)
+
+class GoRule22(GoRule):
+
+    def __init__(self):
+        super().__init__("GORULE:0000022", "Check for, and filter, annotations made to retracted publications", FailMode.HARD)
+
+    def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult:
+        if config.retracted_pub_set is not None:
+            references = annotation.evidence.has_supporting_reference
+            for ref in references:
+                ref = str(ref)
+                if ref in config.retracted_pub_set:
+                    return self._result(False)
+        return self._result(True)        
 
 
 class GoRule26(GoRule):
@@ -952,6 +966,7 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
     "GoRule16": GoRule16(),
     "GoRule17": GoRule17(),
     "GoRule18": GoRule18(),
+    "GoRule22": GoRule22(),
     "GoRule26": GoRule26(),
     "GoRule28": GoRule28(),
     "GoRule29": GoRule29(),

ontobio/validation/metadata.py

@@ -182,7 +182,32 @@ def yaml_set(metadata, yaml_file_name, field) -> Set[str]:
     except Exception as e:
         raise click.ClickException("Could not find or read {}: {}".format(yaml_path, str(e)))
 
-    return set([yaml[field] for yaml in yaml_list])   
+    return set([yaml[field] for yaml in yaml_list])
+
+def retracted_pub_set_from_meta(metadata) -> Set:
+    retracted_path = os.path.join(metadata, "retracted-publications.txt")
+    if os.access(retracted_path, os.R_OK):
+        return retracted_pub_set_use_abspath(retracted_path)
+    else:
+        return set()     
+
+def retracted_pub_set(abspath_retracted_file) -> Set:
+   return retracted_pub_set_use_abspath(os.path.abspath(abspath_retracted_file)) 
+
+def retracted_pub_set_use_abspath(abspath_retracted_file) -> Set:
+    try:
+        retracted_pubs = None   
+        with open(abspath_retracted_file, "r") as f:
+            retracted_pubs = set()
+            for line in f:
+                li=line.strip()
+                if not li.startswith("!"):
+                    if "," in li:
+                        li = li.partition(',')[0]
+                    retracted_pubs.add(li)
+        return retracted_pubs                
+    except Exception as e:
+        raise click.ClickException("Could not find or read {}: {}".format(abspath_retracted_file, str(e)))    
 
 
 

tests/test_qc.py

@@ -354,6 +354,20 @@ def test_go_rule_18():
     test_result = qc.GoRule18().test(assoc, all_rules_config())
     assert test_result.result_type == qc.ResultType.PASS
 
+def test_go_rule22():
+    config = assocparser.AssocParserConfig(
+        ontology=ontology,
+        retracted_pub_set={"RETRACTED:1234","PMID:37772366"},
+        rule_set=assocparser.RuleSet.ALL
+    )
+    assoc = make_annotation(goid="GO:1234567", evidence="IBA", references="PMID:12345").associations[0]   
+    test_result = qc.GoRule22().test(assoc, config)
+    assert test_result.result_type == qc.ResultType.PASS
+
+    assoc = make_annotation(goid="GO:1234567", evidence="IBA", references="PMID:37772366").associations[0]   
+    test_result = qc.GoRule22().test(assoc, config)
+    assert test_result.result_type == qc.ResultType.ERROR    
+
 def test_go_rule26():
 
     config = assocparser.AssocParserConfig(
@@ -819,7 +833,7 @@ def test_all_rules():
     assoc = gafparser.to_association(a).associations[0]
 
     test_results = qc.test_go_rules(assoc, config).all_results
-    assert len(test_results.keys()) == 26
+    assert len(test_results.keys()) == 27
     assert test_results[qc.GoRules.GoRule26.value].result_type == qc.ResultType.PASS
     assert test_results[qc.GoRules.GoRule29.value].result_type == qc.ResultType.PASS