Merge pull request #667 from biolink/go-site-1553-gorule-0000057-has-…

…been-deprecated For #1553
biolink · Feb 22, 2024 · 95707dd · 95707dd
2 parents 57adf9c + 5d332fa
commit 95707dd
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Showing 2 changed files with 2 additions and 71 deletions.
diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py
@@ -687,35 +687,6 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
         return self._result(True)
 
 
-class GoRule57(GoRule):
-
-    def __init__(self):
-        super().__init__("GORULE:0000057", "Group specific filter rules should be applied to annotations", FailMode.HARD, tags=["context-import"])
-
-    def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult:
-        # Check group_metadata is present
-        if config.group_metadata is None:
-            return self._result(True)
-
-        evidence_codes = config.group_metadata.get("filter_out", {}).get("evidence", [])
-        if str(annotation.evidence.type) in evidence_codes:
-            return self._result(False)
-
-        evidences_references = config.group_metadata.get("filter_out", {}).get("evidence_reference", [])
-        for er in evidences_references:
-            evidence_code = er["evidence"]
-            reference = er["reference"]
-            if str(annotation.evidence.type) == evidence_code and [str(ref) for ref in annotation.evidence.has_supporting_reference] == [reference]:
-                return self._result(False)
-
-        properties = config.group_metadata.get("filter_out", {}).get("annotation_properties", [])
-        for p in properties:
-            if p in annotation.properties.keys():
-                return self._result(False)
-
-        return self._result(True)
-
-
 class GoRule58(RepairRule):
 
     def __init__(self):
@@ -947,7 +918,6 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
     "GoRule50": GoRule50(),
     #"GoRule51": GoRule51(), Do not run test
     "GoRule55": GoRule55(),
-    "GoRule57": GoRule57(),
     "GoRule58": GoRule58(),
     "GoRule61": GoRule61(),
     # GoRule13 at the bottom in order to make all other rules clean up an annotation before reaching 13

diff --git a/tests/test_qc.py b/tests/test_qc.py
@@ -1,7 +1,6 @@
 import pytest
 import datetime
 import yaml
-import json
 
 from ontobio.model import association
 from ontobio.model.association import Curie
@@ -12,7 +11,7 @@
 from ontobio.io import gafparser
 from ontobio.io.gafparser import GafParser
 from ontobio.io import gpadparser
-from ontobio import ontol, ontol_factory, ecomap
+from ontobio import ontol_factory, ecomap
 
 import copy
 
@@ -629,44 +628,6 @@ def test_gorule55():
     assert test_result.result_type == qc.ResultType.WARNING
 
 
-def test_gorule57():
-    assoc = make_annotation(db="HELLO", db_id="123", qualifier="contributes_to", goid="GO:0003674", evidence=iea_eco, taxon="taxon:2", from_gaf=False).associations[0]
-    # Look at evidence_code, reference, annotation_properties
-    config = assocparser.AssocParserConfig(
-        group_metadata={
-            "id": "mgi",
-            "label": "Mouse Genome Informatics",
-            "filter_out": {
-                "evidence": [iea_eco],
-                "evidence_reference": [
-                    {
-                        "evidence": ikr_eco,
-                        "reference": "PMID:21873635"
-                    }
-                ],
-                "annotation_properties": ["noctua-model-id"]
-            }
-        },
-        rule_set=assocparser.RuleSet.ALL
-    )
-    test_result = qc.GoRule57().test(assoc, config)
-    assert test_result.result_type == qc.ResultType.ERROR
-
-    assoc.evidence.type = Curie.from_str(ikr_eco)
-    assoc.evidence.has_supporting_reference = [Curie.from_str("PMID:21873635")]
-    test_result = qc.GoRule57().test(assoc, config)
-    assert test_result.result_type == qc.ResultType.ERROR
-
-    assoc.evidence.type = Curie.from_str("ECO:some_garbage")
-    assoc.evidence.has_supporting_reference = [Curie.from_str("PMID:some_garbage")]
-    assoc.properties = {"noctua-model-id": "some_garbage"}
-    test_result = qc.GoRule57().test(assoc, config)
-    assert test_result.result_type == qc.ResultType.ERROR
-
-    assoc.properties = {}
-    test_result = qc.GoRule57().test(assoc, config)
-    assert test_result.result_type == qc.ResultType.PASS
-
 def test_gorule58():
 
     with open("tests/resources/extensions-constraints.yaml") as exs_cons:
@@ -778,7 +739,7 @@ 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()) == 23
     assert test_results[qc.GoRules.GoRule26.value].result_type == qc.ResultType.PASS
     assert test_results[qc.GoRules.GoRule29.value].result_type == qc.ResultType.PASS