Merge pull request #654 from biolink/go-site-2081-gorule-0000006-iep-…

…and-hep--restricted-usage

For #2081 repair goid, with/from and extension before running gorule …

ontobio/io/gafparser.py

@@ -201,6 +201,46 @@ def parse_line(self, line):
         if self.gaf_version() == "2.1" and (vals[3] == "" or vals[3] == "NOT") and self.config.ontology:
             assoc = self.upgrade_empty_qualifier(assoc)
 
+        # Check for valid GO id and repair if necessary
+        split_line = assocparser.SplitLine(line=line, values=vals, taxon=str(assoc.object.taxon))        
+        if not self._validate_id(str(assoc.object.id), split_line, context=ANNOTATION):
+            print("skipping because {} not validated!".format(assoc.object.id))
+            return assocparser.ParseResult(line, [], True)
+
+        valid_goid = self._validate_ontology_class_id(str(assoc.object.id), split_line)
+        if valid_goid is None:
+            return assocparser.ParseResult(line, [], True)
+        assoc.object.id = association.Curie.from_str(valid_goid)
+
+        references = self.validate_curie_ids(assoc.evidence.has_supporting_reference, split_line)
+        if references is None:
+            # Reporting occurs in above function call
+            return assocparser.ParseResult(line, [], True)
+
+        # With/From
+        for wf in assoc.evidence.with_support_from:
+            validated = self.validate_curie_ids(wf.elements, split_line)
+            if validated is None:
+                return assocparser.ParseResult(line, [], True)
+        with_support_from = self._unroll_withfrom_and_replair_obsoletes(split_line, 'gaf')
+        if with_support_from is None:
+            return assocparser.ParseResult(line, [], True)
+        assoc.evidence.with_support_from = with_support_from
+
+        # Extension
+        # repair, if possible any GO terms in the extensions that may be obsolete
+        if (0 < len(assoc.object_extensions)):
+            for ext in assoc.object_extensions:
+                validated = self.validate_curie_ids([e.term for e in ext.elements], split_line)
+                if validated is None:
+                    return assocparser.ParseResult(line, [], True)
+            repaired = self._repair_extensions(assoc.object_extensions, split_line)
+            if repaired is None:
+                    assoc.object_extensions = []        
+                    return assocparser.ParseResult(line, [], True)
+            assoc.object_extensions = repaired   
+
+
         ## Run GO Rules, save split values into individual variables
         # print("Config is {}".format(self.config.__dict__.keys()))
         go_rule_results = qc.test_go_rules(assoc, self.config, group=self.group)
@@ -220,7 +260,7 @@ def parse_line(self, line):
                                     msg="Passing Rule", rule=int(rule.id.split(":")[1]))
 
         assoc = go_rule_results.annotation  # type: association.GoAssociation
-        split_line = assocparser.SplitLine(line=line, values=vals, taxon=str(assoc.object.taxon))
+        #split_line = assocparser.SplitLine(line=line, values=vals, taxon=str(assoc.object.taxon))
 
         if self.config.group_idspace is not None and assoc.provided_by not in self.config.group_idspace:
             self.report.warning(line, Report.INVALID_ID, assoc.provided_by,
@@ -240,53 +280,7 @@ def parse_line(self, line):
         ## --assigned_by
         if not self._validate_id(str(assoc.subject.id), split_line, allowed_ids=self.config.entity_idspaces):
             return assocparser.ParseResult(line, [], True)
-
-        # Using a given gpi file to validate the gene object
-        # if self.gpi is not None:
-        #     entity = self.gpi.get(str(assoc.subject.id), None)
-        #     if entity is not None:
-        #         assoc.subject.label = entity["symbol"]
-        #         assoc.subject.fullname = entity["name"]
-        #         assoc.subject.synonyms = entity["synonyms"].split("|")
-        #         assoc.subject.type = entity["type"]
-
-        if not self._validate_id(str(assoc.object.id), split_line, context=ANNOTATION):
-            print("skipping because {} not validated!".format(assoc.object.id))
-            return assocparser.ParseResult(line, [], True)
-
-        valid_goid = self._validate_ontology_class_id(str(assoc.object.id), split_line)
-        if valid_goid is None:
-            return assocparser.ParseResult(line, [], True)
-        assoc.object.id = association.Curie.from_str(valid_goid)
-
-        references = self.validate_curie_ids(assoc.evidence.has_supporting_reference, split_line)
-        if references is None:
-            # Reporting occurs in above function call
-            return assocparser.ParseResult(line, [], True)
-
-        # With/From
-        for wf in assoc.evidence.with_support_from:
-            validated = self.validate_curie_ids(wf.elements, split_line)
-            if validated is None:
-                return assocparser.ParseResult(line, [], True)
-        with_support_from = self._unroll_withfrom_and_replair_obsoletes(split_line, 'gaf')
-        if with_support_from is None:
-            return assocparser.ParseResult(line, [], True)
-        assoc.evidence.with_support_from = with_support_from
-
-        # Extension
-        # repair, if possible any GO terms in the extensions that may be obsolete
-        if (0 < len(assoc.object_extensions)):
-            for ext in assoc.object_extensions:
-                validated = self.validate_curie_ids([e.term for e in ext.elements], split_line)
-                if validated is None:
-                    return assocparser.ParseResult(line, [], True)
-            repaired = self._repair_extensions(assoc.object_extensions, split_line)
-            if repaired is None:
-                    assoc.object_extensions = []        
-                    return assocparser.ParseResult(line, [], True)
-            assoc.object_extensions = repaired    
-
+
         # validation
         self._validate_symbol(assoc.subject.label, split_line)
 

tests/resources/obsolete.json

@@ -115,6 +115,60 @@
       "type" : "CLASS",
       "lbl" : "ferric iron import across cell outer membrane"
     }, {
+      "id" : "http://purl.obolibrary.org/obo/GO_0006758",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/GO_0006754"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/GO_0006754",
+      "meta" : {
+        "definition" : {
+          "val" : "The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.",
+          "xrefs" : [ "GOC:go_curators", "ISBN:0198506732" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "ATP anabolism",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasNarrowSynonym",
+          "val" : "ATP regeneration",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ATP synthesis",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ATP biosynthesis",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ATP formation",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "GO:0006759"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "GO:0006758"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "biological_process"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "ATP biosynthetic process"
+    },  {
       "id" : "http://purl.obolibrary.org/obo/GO_0016458",
       "meta" : {
         "definition" : {

tests/test_local_json.py

@@ -256,4 +256,5 @@ def test_obsolete():
     assert ont.replaced_by('GO:1') == ['GO:2']
     assert ont.replaced_by('GO:4') == ['GO:3']
     assert ont.replaced_by('GO:0005913') == ['GO:0005912']
-    assert n_obs == 4
+    assert ont.replaced_by('GO:0006758') == ['GO:0006754']
+    assert n_obs == 5

tests/test_qc.py

@@ -9,6 +9,7 @@
 from ontobio.io import gaference
 from ontobio.io import assocparser
 from ontobio.io import gafparser
+from ontobio.io.gafparser import GafParser
 from ontobio.io import gpadparser
 from ontobio import ontol, ontol_factory, ecomap
 
@@ -117,6 +118,17 @@ def test_go_rule_06():
     test_result = qc.GoRule06().test(assoc, all_rules_config(ontology=ontology))
     assert test_result.result_type == qc.ResultType.ERROR
 
+    #Ensure obsoleted GO id is repaired with alternate id first before Gorule06
+    line = ["GeneDB", "PF3D7_0507500", "SUB1", "enables", "GO:0006758", "PMID:12764150", "IEP", "PANTHER:PTN000623979|TAIR:locus:2099478", "C", "GORULE:0000006-6", "protease 1", "gene", "NCBITaxon:36329", "20090624", "GeneDB", "", ""]
+    obs_ontology = ontol_factory.OntologyFactory().create("tests/resources/obsolete.json")
+    p = GafParser(config=assocparser.AssocParserConfig(ontology=obs_ontology, rule_set = assocparser.RuleSet.ALL))
+    p.version = "2.2"
+    parsed = p.parse_line("\t".join(line))
+    assoc = parsed.associations[0]
+    assert assoc.object.id == Curie.from_str("GO:0006754")
+    test_result = qc.GoRule06().test(assoc, all_rules_config(ontology=obs_ontology))
+    assert test_result.result_type == qc.ResultType.PASS
+
 def test_go_rule_07():
 
     assoc = make_annotation(goid="GO:0003824", evidence="IPI").associations[0]