Add SSSOM rewire to rewire method

src/sssom/cli.py

@@ -44,7 +44,7 @@
     split_file,
     validate_file,
 )
-from .parsers import PARSING_FUNCTIONS, parse_sssom_table
+from .parsers import PARSING_FUNCTIONS, from_sssom_dataframe, parse_sssom_table
 from .rdf_util import rewire_graph
 from .sparql_util import EndpointConfig, query_mappings
 from .util import (
@@ -58,6 +58,7 @@
     remove_unmatched,
     sort_df_rows_columns,
     to_mapping_set_dataframe,
+    rewire_sssom_table,
 )
 from .writers import WRITER_FUNCTIONS, write_table
 
@@ -545,11 +546,26 @@ def rewire(
     # noqa: DAR101
     """
     msdf = parse_sssom_table(mapping_file)
-    g = Graph()
-    g.parse(input, format=input_format)
-    rewire_graph(g, msdf, precedence=precedence)
-    rdfstr = g.serialize(format=output_format)
-    print(rdfstr, file=output)
+
+    if input_format == "sssom-tsv" or input.endswith("sssom.tsv"):
+        msdf_mapping = parse_sssom_table(input)
+        df_rewired = rewire_sssom_table()  # This is the method you need to implement
+
+        # updating the metadata of the rewired df so you can recognise it was rewired?
+        metadata = msdf.metadata
+        metadata["mapping_set_id"] = msdf["mapping_set_id"] + "rewired.sssom.tsv"
+
+        # This maybe has to be revisited as the rewiring can change the SSSOM mapping
+        prefix_map = msdf.prefix_map
+
+        msdf_rewired = from_sssom_dataframe(df_rewired, prefix_map=prefix_map, meta=metadata)
+        write_table(msdf_rewired, output)
+    else:
+        g = Graph()
+        g.parse(input, format=input_format)
+        rewire_graph(g, msdf, precedence=precedence)
+        outstring = g.serialize(format=output_format)
+        print(outstring, file=output)
 
 
 @main.command()

src/sssom/util.py

@@ -109,6 +109,23 @@ def clean_context(self) -> None:
         """Clean up the context."""
         self.converter = curies.chain([_get_built_in_prefix_map(), self.converter])
 
+    def _standardize_curie_or_iri(self, curie_or_iri: str) -> str:
+        """Standardize a CURIE or IRI, returning the original if not possible."""
+        if is_iri(curie_or_iri):
+            return self.converter.standardize_uri(curie_or_iri) or curie_or_iri
+        if is_curie(curie_or_iri):
+            return self.converter.standardize_curie(curie_or_iri) or curie_or_iri
+        return curie_or_iri
+
+    def standardize(self) -> None:
+        """Standardize this MSDF."""
+        for column, values in _get_sssom_schema_object().dict["slots"].items():
+            if values["range"] != "EntityReference":
+                continue
+            if column not in self.df.columns:
+                continue
+            self.df[column] = self.df[column].map(self._standardize_curie_or_iri)
+
     def merge(self, *msdfs: "MappingSetDataFrame", inplace: bool = True) -> "MappingSetDataFrame":
         """Merge two MappingSetDataframes.
 
@@ -372,6 +389,16 @@ def get_row_based_on_hierarchy(df: pd.DataFrame):
             return hierarchical_df
 
 
+def rewire_sssom_table(df_rewire: pd.DataFrame, df_mapping: pd.DataFrame):
+    # 1. Standardise subject and object id columns using
+    # https://curies.readthedocs.io/en/latest/api/curies.Converter.html#curies.Converter.pd_standardize_curie
+    # 2. Perform the rewiring
+    # 3. Store some metadata in the "other" field?
+    # 4. Return back out
+    result_df = ...
+    return result_df
+
+
 def assign_default_confidence(
     df: pd.DataFrame,
 ) -> Tuple[pd.DataFrame, pd.DataFrame]:
@@ -1116,22 +1143,8 @@ def reconcile_prefix_and_data(
     converter = msdf.converter
     converter = curies.remap_curie_prefixes(converter, prefix_reconciliation["prefix_synonyms"])
     converter = curies.rewire(converter, prefix_reconciliation["prefix_expansion_reconciliation"])
-
-    # TODO make this standardization code directly part of msdf after
-    #  switching to native converter
-    def _upgrade(curie_or_iri: str) -> str:
-        if not is_iri(curie_or_iri) and is_curie(curie_or_iri):
-            return converter.standardize_curie(curie_or_iri) or curie_or_iri
-        return curie_or_iri
-
-    for column, values in _get_sssom_schema_object().dict["slots"].items():
-        if values["range"] != "EntityReference":
-            continue
-        if column not in msdf.df.columns:
-            continue
-        msdf.df[column] = msdf.df[column].map(_upgrade)
-
     msdf.converter = converter
+    msdf.standardize()
     return msdf