Merge branch 'master' into gopreprocess-gpad20

biolink · Jan 29, 2024 · df4b831 · df4b831
2 parents 1b8df3a + 7e4ca73
commit df4b831
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Showing 6 changed files with 10 additions and 10 deletions.
diff --git a/ontobio/__init__.py b/ontobio/__init__.py
@@ -1,6 +1,6 @@
 from __future__ import absolute_import
 
-__version__ = '2.8.20'
+__version__ = '2.8.22'
 
 
 from .ontol_factory import OntologyFactory

diff --git a/ontobio/config.yaml b/ontobio/config.yaml
@@ -2,7 +2,7 @@ solr_assocs:
   url: "https://solr.monarchinitiative.org/solr/golr"
   timeout: 60
 amigo_solr_assocs:
-  url: "http://golr-aux.geneontology.io/solr"
+  url: "http://golr.geneontology.org/solr"
   timeout: 15
 solr_search:
   url: "https://solr.monarchinitiative.org/solr/search"
@@ -11,7 +11,7 @@ lay_person_search:
   url: "https://solr.monarchinitiative.org/solr/hpo-pl"
   timeout: 15
 amigo_solr_search:
-  url: "http://golr-aux.geneontology.io/solr"
+  url: "http://golr.geneontology.org/solr"
   timeout: 15
 sparql:
   url: "http://sparql.hegroup.org/sparql"

diff --git a/ontobio/golr/golr_query.py b/ontobio/golr/golr_query.py
@@ -1852,7 +1852,7 @@ def map_id(self,id, prefix, closure_list):
 
 ## Should take those URLs from config.yaml
 class ESOLR(Enum):
-    GOLR = "http://golr-aux.geneontology.io/solr/"
+    GOLR = "http://golr.geneontology.org/solr/"
     MOLR = "https://solr.monarchinitiative.org/solr/search"
 
 class ESOLRDoc(Enum):

diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py
@@ -517,7 +517,7 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
 class GoRule37(GoRule):
 
     def __init__(self):
-        super().__init__("GORULE:0000037", "IBA annotations should ONLY be assigned_by GO_Central and have GOREF:0000033 as a reference", FailMode.HARD)
+        super().__init__("GORULE:0000037", "IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference", FailMode.HARD)
 
     def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult:
         # If the evidence code is IBA, then (1) the assigned_by field must be GO_Central and (2) the reference field must be PMID:21873635
@@ -527,7 +527,7 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
 
         result = self._result(True) # By default we pass
         if evidence == iba_eco:
-            result = self._result(assigned_by == "GO_Central" and "GOREF:0000033" in references)
+            result = self._result(assigned_by == "GO_Central" and "GO_REF:0000033" in references)
 
         return result
 

diff --git a/tests/resources/test-config.yaml b/tests/resources/test-config.yaml
@@ -2,13 +2,13 @@ solr_assocs:
   url: "https://example.org"
   timeout: 999
 amigo_solr_assocs:
-  url: "http://golr-aux.geneontology.io/solr"
+  url: "http://golr.geneontology.org/solr"
   timeout: 2
 solr_search:
   url: "https://solr-dev.monarchinitiative.org/solr/search"
   timeout: 2
 amigo_solr_search:
-  url: "http://golr-aux.geneontology.io/solr"
+  url: "http://golr.geneontology.org/solr"
   timeout: 2
 sparql:
   url: "http://sparql.hegroup.org/sparql"

diff --git a/tests/test_qc.py b/tests/test_qc.py
@@ -462,7 +462,7 @@ def test_gorule30():
     assert test_result.result_type == qc.ResultType.PASS
 
 def test_gorule37():
-    assoc = make_annotation(evidence="IBA", references="GOREF:0000033", assigned_by="GO_Central").associations[0]
+    assoc = make_annotation(evidence="IBA", references="GO_REF:0000033", assigned_by="GO_Central").associations[0]
 
     test_result = qc.GoRule37().test(assoc, all_rules_config())
     assert test_result.result_type == qc.ResultType.PASS
@@ -476,7 +476,7 @@ def test_gorule37():
     test_result = qc.GoRule37().test(assoc, all_rules_config())
     assert test_result.result_type == qc.ResultType.ERROR
 
-    assoc.evidence.has_supporting_reference = [Curie.from_str("GOREF:0000033")]
+    assoc.evidence.has_supporting_reference = [Curie.from_str("GO_REF:0000033")]
     assoc.provided_by = "Pascale"  # IBA, but wrong assigned_by
     test_result = qc.GoRule37().test(assoc, all_rules_config())
     assert test_result.result_type == qc.ResultType.ERROR