Fix support for literal mappings. (#624)

Since the LinkML-generated Mapping class does not, in itself, validates
the post-conditions specified in the schema, it cannot validate that a
Mapping object is created with either a subject_id or (if subject_type
is `rdfs literal`) a subject_label (likewise for the object side).

Instead, that validation is performed by custom code executed as part of
the parsing code.

However, the present validation is bogus because the check on the value
of `subject_type` and `object_type` is trying to compare the value of
the slot to a literal string, instead of a EntityTypeEnum object. We fix
that comparison here.

Author: gouttegd

src/sssom/parsers.py

@@ -42,7 +42,7 @@
 from linkml_runtime.loaders.rdflib_loader import RDFLibLoader
 from pandas.errors import EmptyDataError
 from rdflib import Graph
-from sssom_schema import Mapping, MappingSet
+from sssom_schema import EntityTypeEnum, Mapping, MappingSet
 from typing_extensions import Literal, TypeAlias
 
 from sssom.constants import (
@@ -1187,12 +1187,12 @@ def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]) -> Optional[Mapping]:
 
     try:
         m = Mapping(**mdict)
-        if m.subject_type == "rdfs literal":
+        if m.subject_type == EntityTypeEnum(EntityTypeEnum["rdfs literal"]):
             if m.subject_label is None:
                 raise ValueError("Missing subject_label")
         elif m.subject_id is None:
             raise ValueError("Missing subject_id")
-        if m.object_type == "rdfs literal":
+        if m.object_type == EntityTypeEnum(EntityTypeEnum["rdfs literal"]):
             if m.object_label is None:
                 raise ValueError("Missing object_label")
         elif m.object_id is None:

tests/data/literals.sssom.tsv

@@ -0,0 +1,19 @@
+#curie_map:
+#  FBcv: http://purl.obolibrary.org/obo/FBcv_
+#  ORCID: https://orcid.org/
+#  obo: http://purl.obolibrary.org/obo/
+#mapping_set_id: http://purl.obolibrary.org/obo/fbcv/agr-vocabs.sssom.tsv
+#mapping_set_description: Mappings between the FlyBase Controlled Vocabulary (FBcv) and vocabulary terms from the Alliance of Genome Resources.
+#creator_id:
+#  - ORCID:0000-0002-6095-8718
+#license: https://creativecommons.org/licenses/by/4.0/
+subject_id	subject_label	predicate_id	object_label	object_category	mapping_justification	subject_source	object_type
+FBcv:0000222	male	skos:exactMatch	male	Genetic Sex	semapv:ManualMappingCuration	obo:fbcv.owl	rdfs literal
+FBcv:0000334	female	skos:exactMatch	female	Genetic Sex	semapv:ManualMappingCuration	obo:fbcv.owl	rdfs literal
+FBcv:0003124	species study	skos:exactMatch	species	Data Set Category Tags	semapv:ManualMappingCuration	obo:fbcv.owl	rdfs literal
+FBcv:0003125	strain study	skos:exactMatch	genome variation	Data Set Category Tags	semapv:ManualMappingCuration	obo:fbcv.owl	rdfs literal
+FBcv:0003127	developmental stage study	skos:exactMatch	developmental stage	Data Set Category Tags	semapv:ManualMappingCuration	obo:fbcv.owl	rdfs literal
+FBcv:0003128	circadian rhythm study	skos:narrowMatch	time of day	Data Set Category Tags	semapv:ManualMappingCuration	obo:fbcv.owl	rdfs literal
+FBcv:0003129	cell cycle study	skos:exactMatch	cell cycle	Data Set Category Tags	semapv:ManualMappingCuration	obo:fbcv.owl	rdfs literal
+FBcv:0003130	tissue type study	skos:narrowMatch	anatomical structure	Data Set Category Tags	semapv:ManualMappingCuration	obo:fbcv.owl	rdfs literal
+FBcv:0003131	cell type study	skos:exactMatch	cell type	Data Set Category Tags	semapv:ManualMappingCuration	obo:fbcv.owl	rdfs literal

tests/test_parsers.py

@@ -147,6 +147,11 @@ def test_parse_tsv(self) -> None:
             f"{self.df_file} has the wrong number of mappings.",
         )
 
+    def test_parse_tsv_with_literal_mappings(self) -> None:
+        """Test parsing a SSSOM/TSV file containing literal mappings."""
+        msdf = parse_sssom_table(f"{test_data_dir}/literals.sssom.tsv")
+        self.assertEqual(len(msdf.df), 9, "literals.sssom.tsv has the wrong number of mappings.")
+
     def test_parse_alignment_minidom(self) -> None:
         """Test parsing an alignment XML."""
         msdf = from_alignment_minidom(