Add synonyms in practice

src/bioregistry/record_accumulator.py

@@ -226,6 +226,8 @@ def _add_prefix_prefixes(
         primary_prefix = _add_primary_prefix(resource.prefix)
         if primary_prefix is None:
             continue
+        # TODO fix next line, since it seems to delete PUBMED from the OBO EPM
+        _add_synonym(synonym=resource.prefix, prefix=resource.prefix)
         for synonym in resource.get_synonyms():
             _add_synonym(synonym=synonym, prefix=resource.prefix)
         for uri_prefix in resource.get_uri_prefixes():

tests/test_contexts.py

@@ -57,14 +57,17 @@ def test_obo_context(self):
             msg="When overriding, this means that bioregistry prefix isn't properly added to the synonyms list",
         )
 
-    def get_obo_converter(self):
+    def test_get_obo_converter(self):
         """Test getting a converter from a context."""
         converter = manager.get_converter_from_context("obo")
-        self.assertEqual("GO", converter.standardize_prefix("GO"))
-        self.assertEqual("GO", converter.standardize_prefix("gomf"))
-        # FIXME later, handle adding canonical bioregistry prefix
-        #  as synonym when non-default prefix priority ordering is given
-        # self.assertEqual("GO", converter.standardize_prefix("go"))
+        self.assertEqual("GO", converter.standardize_prefix("GO", strict=True))
+        self.assertEqual("GO", converter.standardize_prefix("gomf", strict=True))
+        self.assertEqual("GO", converter.standardize_prefix("go", strict=True))
+        self.assertEqual("PMID", converter.standardize_prefix("pmid", strict=True))
+        self.assertEqual("PMID", converter.standardize_prefix("pubmed", strict=True))
+        self.assertEqual("PMID", converter.standardize_prefix("PubMed", strict=True))
+        # self.assertEqual("PMID", converter.standardize_prefix("PUBMED"))
+        # self.assertEqual("PMID", converter.standardize_prefix("PMID"))
 
     def test_data(self):
         """Test the data integrity."""