Convert SSSOM TSV => JSON => TSV and confirm the MappingSetDataFrame …

…remains consistent.

src/sssom/parsers.py

@@ -212,21 +212,28 @@ def parse_sssom_table(
                     logging.info(f"Externally provided metadata {k}:{v} is added to metadata set.")
                     sssom_metadata[k] = v
         meta = sssom_metadata
-
-        if "curie_map" in sssom_metadata:
+        if CURIE_MAP in sssom_metadata:
             if prefix_map:
+                # Convert sssom_metadata[CURIE_MAP] keys to lowercase for case-insensitive comparison
+                curie_map_lower = {k.lower(): k for k in sssom_metadata[CURIE_MAP].keys()}
+
                 for k, v in prefix_map.items():
-                    if k in sssom_metadata[CURIE_MAP]:
-                        if sssom_metadata[CURIE_MAP][k] != v:
+                    k_lower = k.lower()
+
+                    if k_lower in curie_map_lower:
+                        original_key = curie_map_lower[k_lower]
+                        if sssom_metadata[CURIE_MAP][original_key] != v:
                             logging.warning(
-                                f"SSSOM prefix map {k} ({sssom_metadata[CURIE_MAP][k]}) "
-                                f"conflicts with provided ({prefix_map[k]})."
+                                f"SSSOM prefix map {original_key} ({sssom_metadata[CURIE_MAP][original_key]}) "
+                                f"conflicts with provided ({v})."
                             )
+                            sssom_metadata[CURIE_MAP][original_key] = v
                     else:
                         logging.info(
                             f"Externally provided metadata {k}:{v} is added to metadata set."
                         )
                         sssom_metadata[CURIE_MAP][k] = v
+
             prefix_map = sssom_metadata[CURIE_MAP]
 
     meta_all = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
@@ -264,10 +271,32 @@ def parse_sssom_json(
 ) -> MappingSetDataFrame:
     """Parse a TSV to a :class:`MappingSetDocument` to a  :class`MappingSetDataFrame`."""
     raise_for_bad_path(file_path)
-    metadata = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
 
     with open(file_path) as json_file:
         jsondoc = json.load(json_file)
+
+    # Get prefix map from jsondoc and update metadata.
+    # This takes priority over default prefix_map in case of a tie.
+    jsondoc_prefix_map = jsondoc["@context"]
+
+    # Convert keys in both maps to lower case for comparison
+    if prefix_map:
+        lowercase_prefix_map = {k.lower(): v for k, v in prefix_map.items()}
+
+        # Iterate over jsondoc_prefix_map
+        for key, value in jsondoc_prefix_map.items():
+            # If lowercase key exists in lowercase_prefix_map, update the value and key
+            if key.lower() in lowercase_prefix_map:
+                # Remove the old key-value pair
+                if key in prefix_map:
+                    del prefix_map[key]
+                elif key.lower() in prefix_map:
+                    del prefix_map[key.lower()]
+                # Add the new key-value pair
+                prefix_map[key] = value
+
+    metadata = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
+
     msdf = from_sssom_json(jsondoc=jsondoc, prefix_map=metadata.prefix_map, meta=metadata.metadata)
     # df: pd.DataFrame = msdf.df
     # if mapping_predicates and not df.empty():

src/sssom/util.py

@@ -155,7 +155,13 @@ 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()
+        # Convert prefixes_in_table to lowercase
+        prefixes_in_table_lower = {prefix.lower() for prefix in prefixes_in_table}
+        # Convert self.converter.get_prefixes() to lowercase
+        converter_prefixes_lower = {prefix.lower() for prefix in self.converter.get_prefixes()}
+        missing_prefixes = prefixes_in_table_lower - converter_prefixes_lower
+        # missing_prefixes = prefixes_in_table - self.converter.get_prefixes()
+
         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"

tests/data/sample1.sssom.tsv

@@ -0,0 +1,8 @@
+#curie_map:
+#  FBbt: "http://purl.obolibrary.org/obo/FBbt_"
+#  ORCID: "https://orcid.org/"
+#  UBERON: "http://purl.obolibrary.org/obo/UBERON_"
+#creator_id:
+#  - "ORCID:0000-0002-6095-8718"
+subject_id	subject_label	predicate_id	object_id	mapping_justification
+FBbt:00000001	organism	semapv:crossSpeciesExactMatch	UBERON:0000468	semapv:ManualMappingCuration

tests/test_parsers.py

@@ -19,11 +19,12 @@
     from_sssom_dataframe,
     from_sssom_json,
     from_sssom_rdf,
+    parse_sssom_json,
     parse_sssom_table,
 )
 from sssom.typehints import Metadata
 from sssom.util import PREFIX_MAP_KEY, sort_df_rows_columns
-from sssom.writers import write_table
+from sssom.writers import to_json, write_json, write_table
 from tests.test_data import data_dir as test_data_dir
 from tests.test_data import test_out_dir
 
@@ -245,3 +246,20 @@ def test_parse_obographs_merged(self):
             )
         msdf = parse_sssom_table(outfile)
         self.assertTrue(custom_curie_map.items() <= msdf.prefix_map.items())
+
+    def test_tsv_to_json_and_back(self):
+        """Test converting SSSOM TSV => JSON => SSSOM TSV such that it is reproducible."""
+        sample_tsv = f"{test_data_dir}/sample1.sssom.tsv"
+        json_outfile = f"{test_out_dir}/sample1.json"
+        msdf1 = parse_sssom_table(sample_tsv)
+        msdf1.clean_prefix_map()
+        json_doc = to_json(msdf1)
+
+        self.assertEqual(msdf1.prefix_map, json_doc["@context"])
+
+        with open(json_outfile, "w") as file:
+            write_json(msdf1, file)
+
+        msdf2 = parse_sssom_json(json_outfile)
+        msdf2.clean_prefix_map()
+        self.assertEqual(msdf1.prefix_map, msdf2.prefix_map)