Merge pull request #692 from biolink/go-site-2360-gorule-0000027-hand…

…le-db-without-syntax-pattern

For #2360 - Updated to handle DBs without id syntax pattern

ontobio/io/assocparser.py

@@ -811,7 +811,7 @@ def _validate_id(self, id, line: SplitLine, allowed_ids=None, context=None):
 
         if allowed_ids is not None and id_prefix not in allowed_ids:
             # For now we will just issue a warning here, and we won't filter out the annotation here
-            self.report.warning(line.line, Report.INVALID_ID_DBXREF, id_prefix, "allowed: {}".format(allowed_ids), rule=27)
+            self.report.warning(line.line, Report.INVALID_ID_DBXREF, id_prefix, "{} is not present in DB xrefs file".format(id_prefix), rule=27)
 
         # ensure that the ID space of the annotation class (e.g. GO)
         # conforms to what is expected
@@ -824,14 +824,15 @@ def _validate_id(self, id, line: SplitLine, allowed_ids=None, context=None):
         if self.config.db_type_name_regex_id_syntax is not None:
             if id_prefix in self.config.db_type_name_regex_id_syntax:
                 type_name_regex_patterns = self.config.db_type_name_regex_id_syntax[id_prefix]
-                identity_matches_pattern = False
-                for regex in type_name_regex_patterns.values():
-                    if regex.fullmatch(right):
-                        identity_matches_pattern = True
-                        break
-                if identity_matches_pattern == False:
-                    self.report.warning(line.line, Report.INVALID_ID, id,
-                    "GORULE:0000027: {} does not match any id_syntax patterns for {} in dbxrefs".format(right, id_prefix), taxon=line.taxon, rule=27)
+                if type_name_regex_patterns is not None and len(type_name_regex_patterns) > 0:
+                    identity_matches_pattern = False
+                    for regex in type_name_regex_patterns.values():
+                        if regex.fullmatch(right):
+                            identity_matches_pattern = True
+                            break
+                    if identity_matches_pattern == False:
+                        self.report.warning(line.line, Report.INVALID_ID, id,
+                        "GORULE:0000027: {} does not match any id_syntax patterns for {} in dbxrefs".format(right, id_prefix), taxon=line.taxon, rule=27)
             else:
                 self.report.warning(line.line, Report.INVALID_ID, id,
                     "GORULE:0000027: {} not found in list of database names in dbxrefs".format(id_prefix), taxon=line.taxon, rule=27)  

ontobio/validation/metadata.py

@@ -165,9 +165,8 @@ def database_type_name_regex_id_syntax(metadata):
         entity_types = entity.get("entity_types", {})
         for et in entity_types:
             if "id_syntax" in et and "type_name" in et:
-                type_names[et["type_name"]] = re.compile(et["id_syntax"])
-        if len(type_names) > 0:        
-            d[entity["database"]] = type_names
+                type_names[et["type_name"]] = re.compile(et["id_syntax"])      
+        d[entity["database"]] = type_names
 
     return d    
 

tests/test_gafparser.py

@@ -620,7 +620,11 @@ def test_id_syntax():
 
     pombase_types = {}
     pombase_types['entity'] = re.compile('S\\w+(\\.)?\\w+(\\.)?')
-    database_id_syntax_lookups['PomBase'] = pombase_types    
+    database_id_syntax_lookups['PomBase'] = pombase_types
+
+    wb_ref_types = {}
+    database_id_syntax_lookups['WB_REF'] = wb_ref_types 
+
     p = GafParser(config=assocparser.AssocParserConfig(
         ontology=OntologyFactory().create(ONT), db_type_name_regex_id_syntax=database_id_syntax_lookups))
 
@@ -629,6 +633,12 @@ def test_id_syntax():
     assert assoc_result.skipped == False
     messages = p.report.to_report_json()["messages"]
     assert "gorule-0000027" not in messages
+
+    assoc_result = p.parse_line("PomBase\tSPBC1289.03c\tspi1\t\tGO:0005515\tWB_REF:WBPaper00006408|PMID:18422602\tIPI\tPomBase:SPAC25A8.01c\tF\tRan GTPase Spi1\t\tprotein\ttaxon:4896\t20080718\tPomBase\t")
+    assert len(assoc_result.associations) == 1
+    assert assoc_result.skipped == False
+    messages = p.report.to_report_json()["messages"]
+    assert "gorule-0000027" not in messages    
 
     p = GafParser(config=assocparser.AssocParserConfig(
         ontology=OntologyFactory().create(ONT), db_type_name_regex_id_syntax=database_id_syntax_lookups))

tests/test_gpad_parser.py

@@ -339,6 +339,9 @@ def test_id_syntax():
     eco_types['entity'] = re.compile(pattern)
     database_id_syntax_lookups['ECO'] = eco_types
 
+    wb_ref_types = {}
+    database_id_syntax_lookups['WB_REF'] = wb_ref_types     
+
     vals = ["PomBase",
             "SPAC25A8.01c",
             "acts_upstream_of_or_within",
@@ -362,6 +365,29 @@ def test_id_syntax():
     messages = p.report.to_report_json()["messages"]
     assert "gorule-0000027" not in messages       
 
+    vals = ["PomBase",
+            "SPAC25A8.01c",
+            "acts_upstream_of_or_within",
+            "GO:0007155",
+            "WB_REF:WBPaper00006408|PMID:15494018",
+            "ECO:0000305",
+            "GO:0005913",
+            "",
+            "20041026",
+            "ZFIN",
+            "",
+            "PomBase"
+            ]
+
+    config = assocparser.AssocParserConfig(
+        ontology=OntologyFactory().create(ALT_ID_ONT), db_type_name_regex_id_syntax=database_id_syntax_lookups)
+    p = GpadParser(config=config)
+    result = p.parse_line("\t".join(vals))
+    assert len(result.associations) == 1
+    assert result.skipped == False  
+    messages = p.report.to_report_json()["messages"]
+    assert "gorule-0000027" not in messages     
+
     vals = ["PomBase",
             "SPAC25A8.01c",
             "acts_upstream_of_or_within",