Handle preferred curies

biopragmatics · Jan 4, 2024 · f5d6779 · f5d6779
1 parent d1f435e
commit f5d6779
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Showing 2 changed files with 17 additions and 0 deletions.
diff --git a/src/pyobo/reader.py b/src/pyobo/reader.py
@@ -454,6 +454,10 @@ def _extract_synonym(
                 rest = rest[len(_stype.curie) :].strip()
                 stype = _stype
                 break
+            elif rest.startswith(_stype.preferred_curie):
+                rest = rest[len(_stype.preferred_curie) :].strip()
+                stype = _stype
+                break
             elif rest.startswith(_stype.identifier):
                 rest = rest[len(_stype.identifier) :].strip()
                 stype = _stype

diff --git a/tests/test_get.py b/tests/test_get.py
@@ -106,6 +106,7 @@ def test_extract_synonym(self):
         iupac_name = SynonymTypeDef.from_text("IUPAC NAME", lower=False)
         synoynym_typedefs = {
             "IUPAC_NAME": iupac_name,
+            acronym.curie: acronym,
         }
 
         for expected_synonym, text in [
@@ -142,6 +143,18 @@ def test_extract_synonym(self):
                 Synonym(name="HAdV-A", specificity="BROAD", type=acronym),
                 '"HAdV-A" BROAD OMO:0003012 []',
             ),
+            (
+                Synonym(name="HAdV-A", specificity="BROAD", type=acronym),
+                '"HAdV-A" BROAD omo:0003012 []',
+            ),
+            (
+                Synonym(name="HAdV-A", specificity="EXACT", type=acronym),
+                '"HAdV-A" OMO:0003012 []',
+            ),
+            (
+                Synonym(name="HAdV-A", specificity="EXACT", type=acronym),
+                '"HAdV-A" omo:0003012 []',
+            ),
         ]:
             with self.subTest(s=text):
                 actual_synonym = _extract_synonym(