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"f3fd7c541043bd24fea6b711ddb7c43f5f724b37d405d4cd3a72803018b4a12e" diff --git a/pyproject.toml b/pyproject.toml index f4c3c239..87d956b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,7 +13,7 @@ readme = "README.md" [tool.poetry.dependencies] python = "^3.8" click = ">=8.1.6" -curies = ">=0.7.3" +curies = ">=0.7.6" linkml-runtime = ">=1.5.5" pandas = ">1.0.3" pansql = { version = ">=0.0.1", extras = ["pansql"] } diff --git a/src/sssom/util.py b/src/sssom/util.py index 64db60ed..59fbb0c6 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -246,7 +246,7 @@ def clean_prefix_map(self, strict: bool = True) -> None: if self.metadata: prefixes_in_table.update(get_prefixes_used_in_metadata(self.metadata)) - missing_prefixes = prefixes_in_table - self.converter.get_prefixes() + missing_prefixes = prefixes_in_table - self.converter.get_prefixes(include_synonyms=True) if missing_prefixes and strict: raise ValueError( f"{missing_prefixes} are used in the SSSOM mapping set but it does not exist in the prefix map" diff --git a/tests/test_utils.py b/tests/test_utils.py index e8e518e9..a296434f 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -431,6 +431,29 @@ def test_get_dict_from_mapping(self): self.assertEqual(value, result_with_mapping_object[key]) self.assertEqual(value, result_with_dict[key]) + def test_converter_get_prefixes_including_synonyms_and_get_subconverter(self): + """Test if get_subconverter() works with prefix synonyms.""" + EPM = [ + { + "prefix": "SCTID", + "prefix_synonyms": ["snomed"], + "uri_prefix": "http://snomed.info/id/", + }, + ] + + converter = Converter.from_extended_prefix_map(EPM) + self.assertNotIn("snomed", converter.get_prefixes(include_synonyms=False)) + self.assertIn("snomed", converter.get_prefixes(include_synonyms=True)) + subconverter = converter.get_subconverter(["snomed"]) + self.assertIn( + "snomed", + subconverter.bimap.keys(), + "The subconverter which is used to generate " + "the prefixmap for the serialisation does not " + "contain the 'snomed' prefix, but it is used in " + "the raw data", + ) + def test_curiechain_with_conflicts(self): """Test curie map with CURIE/URI clashes.""" PREFIXMAP_BOTH = {