Merge pull request #644 from biolink/go-site-2058-gorule-0000051-firs…

…t-implementation For #2058 gorule-0000051 first implementation
biolink · Sep 13, 2023 · 5d15999 · 5d15999
2 parents 3dd9050 + d29d031
commit 5d15999
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Showing 4 changed files with 25 additions and 3 deletions.
diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py
@@ -646,6 +646,17 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
 
         return result
 
+class GoRule51(GoRule):
+
+    def __init__(self):
+            super().__init__("GORULE:0000051", "Some GO terms require a value in the Annotation Extension field", FailMode.SOFT)
+
+    def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult:
+
+        term = str(annotation.object.id)
+        no_extensions = (annotation.object_extensions is None or len(annotation.object_extensions) == 0)
+        fails = (term == "GO:0005488" or term == "GO:0005515") and no_extensions
+        return self._result(not fails)
 
 class GoRule55(GoRule):
 
@@ -908,6 +919,7 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
     "GoRule43": GoRule43(),
     "GoRule46": GoRule46(),
     "GoRule50": GoRule50(),
+    "GoRule51": GoRule51(),   
     "GoRule55": GoRule55(),
     "GoRule57": GoRule57(),
     "GoRule58": GoRule58(),

diff --git a/tests/resources/errors.gaf b/tests/resources/errors.gaf
@@ -5,7 +5,7 @@
 !
 ! bad GO ID
 PomBase	SPAC25B8.17	ypf1		BAD_GO_ID	GO_REF:0000024	ISO	SGD:S000001583	C	intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)	ppp81	protein	taxon:4896	20150305	PomBase
-! No gene symbol
+! No gene symbol, fail since gene symbol is a required field
 PomBase	SPAC977.10			GO:1990578	PMID:19171118	IDA		C	plasma membrane sodium ion/proton antiporter Nhe1/Sod2	sod2	protein	taxon:4896	20151201	PomBase
 ! Blank lines
 

diff --git a/tests/test_gafparser.py b/tests/test_gafparser.py
@@ -365,7 +365,7 @@ def test_errors_gaf():
             n_invalid_idspace += 1
     assert len(msgs) == 13
     assert n_invalid_idspace == 1
-    assert len(assocs) == 2
+    assert len(assocs) == 1
 
     w = GafWriter()
     w.write(assocs)

diff --git a/tests/test_qc.py b/tests/test_qc.py
@@ -563,6 +563,16 @@ def test_gorule50():
     assoc.evidence.type = Curie.from_str(iea_eco)
     test_result = qc.GoRule50().test(assoc, all_rules_config())
     assert test_result.result_type == qc.ResultType.PASS
+
+def test_gorule51():
+    assoc = make_annotation(goid="GO:0005515", extension="has_input(GO:0003674),occurs_in(CL:123456)").associations[0]
+
+    test_result = qc.GoRule51().test(assoc, all_rules_config())
+    assert test_result.result_type == qc.ResultType.PASS
+
+    assoc = make_annotation(goid="GO:0005488").associations[0]
+    test_result = qc.GoRule51().test(assoc, all_rules_config())
+    assert test_result.result_type == qc.ResultType.WARNING      
 
 def test_gorule55():
     a = ["blah"] * 15
@@ -722,7 +732,7 @@ 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()) == 24
+    assert len(test_results.keys()) == 25
     assert test_results[qc.GoRules.GoRule26.value].result_type == qc.ResultType.PASS
     assert test_results[qc.GoRules.GoRule29.value].result_type == qc.ResultType.PASS