Directly unpack metadata tuple (#453)

This PR makes it much more direct how the Metadata tuple object is
unpacked. Additionally, the need to expose a "prefix_map" is no longer
there, so this is removed.

src/sssom/io.py

@@ -80,27 +80,27 @@ def parse_file(
     :param mapping_predicate_filter: Optional list of mapping predicates or filepath containing the same.
     """
     raise_for_bad_path(input_path)
-    metadata = get_metadata_and_prefix_map(
+    converter, meta = get_metadata_and_prefix_map(
         metadata_path=metadata_path, prefix_map_mode=prefix_map_mode
     )
     parse_func = get_parsing_function(input_format, input_path)
     mapping_predicates = None
     # Get list of predicates of interest.
     if mapping_predicate_filter:
-        mapping_predicates = get_list_of_predicate_iri(mapping_predicate_filter, metadata.converter)
+        mapping_predicates = get_list_of_predicate_iri(mapping_predicate_filter, converter)
 
     # if mapping_predicates:
     doc = parse_func(
         input_path,
-        prefix_map=metadata.prefix_map,
-        meta=metadata.metadata,
+        prefix_map=converter,
+        meta=meta,
         mapping_predicates=mapping_predicates,
     )
     # else:
     #     doc = parse_func(
     #         input_path,
-    #         prefix_map=metadata.prefix_map,
-    #         meta=metadata.metadata,
+    #         prefix_map=converter,
+    #         meta=meta,
     #     )
     if clean_prefixes:
         # We do this because we got a lot of prefixes from the default SSSOM prefixes!

src/sssom/parsers.py

@@ -233,11 +233,11 @@ def parse_sssom_rdf(
 ) -> 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)
+    converter, meta = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
 
     g = Graph()
     g.parse(file_path, format=serialisation)
-    msdf = from_sssom_rdf(g, prefix_map=metadata.prefix_map, meta=metadata.metadata)
+    msdf = from_sssom_rdf(g, prefix_map=converter, meta=meta)
     # df: pd.DataFrame = msdf.df
     # if mapping_predicates and not df.empty():
     #     msdf.df = df[df["predicate_id"].isin(mapping_predicates)]
@@ -253,11 +253,11 @@ 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)
+    converter, meta = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
 
     with open(file_path) as json_file:
         jsondoc = json.load(json_file)
-    msdf = from_sssom_json(jsondoc=jsondoc, prefix_map=metadata.prefix_map, meta=metadata.metadata)
+    msdf = from_sssom_json(jsondoc=jsondoc, prefix_map=converter, meta=meta)
     # df: pd.DataFrame = msdf.df
     # if mapping_predicates and not df.empty():
     #     msdf.df = df[df["predicate_id"].isin(mapping_predicates)]
@@ -283,15 +283,15 @@ def parse_obographs_json(
     """
     raise_for_bad_path(file_path)
 
-    _xmetadata = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
+    converter, meta = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
 
     with open(file_path) as json_file:
         jsondoc = json.load(json_file)
 
     return from_obographs(
         jsondoc,
-        prefix_map=_xmetadata.prefix_map,
-        meta=_xmetadata.metadata,
+        prefix_map=converter,
+        meta=meta,
         mapping_predicates=mapping_predicates,
     )
 
@@ -354,13 +354,13 @@ def parse_alignment_xml(
     """Parse a TSV -> MappingSetDocument -> MappingSetDataFrame."""
     raise_for_bad_path(file_path)
 
-    metadata = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
+    converter, meta = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
     logging.info("Loading from alignment API")
     xmldoc = minidom.parse(file_path)
     msdf = from_alignment_minidom(
         xmldoc,
-        prefix_map=metadata.prefix_map,
-        meta=metadata.metadata,
+        prefix_map=converter,
+        meta=meta,
         mapping_predicates=mapping_predicates,
     )
     return msdf

src/sssom/typehints.py

@@ -27,11 +27,6 @@ class Metadata(NamedTuple):
     converter: Converter
     metadata: MetadataType
 
-    @property
-    def prefix_map(self):
-        """Get the bimap."""
-        return self.converter.bimap
-
     @classmethod
     def default(cls):
         """Get default metadata."""

tests/test_parsers.py

@@ -13,10 +13,11 @@
 import numpy as np
 import pandas as pd
 import yaml
+from curies import Converter
 from rdflib import Graph
 
 from sssom.constants import CURIE_MAP, DEFAULT_LICENSE, SSSOM_URI_PREFIX
-from sssom.context import SSSOM_BUILT_IN_PREFIXES, ensure_converter
+from sssom.context import SSSOM_BUILT_IN_PREFIXES, ensure_converter, get_converter
 from sssom.io import parse_file
 from sssom.parsers import (
     _open_input,
@@ -28,7 +29,7 @@
     from_sssom_rdf,
     parse_sssom_table,
 )
-from sssom.typehints import Metadata
+from sssom.typehints import get_default_metadata
 from sssom.util import MappingSetDataFrame, sort_df_rows_columns
 from sssom.writers import write_table
 from tests.test_data import data_dir as test_data_dir
@@ -65,12 +66,13 @@ def setUp(self) -> None:
 
         with open(f"{test_data_dir}/basic-meta-external.yml") as file:
             df_meta = yaml.safe_load(file)
-            self.df_prefix_map = df_meta.pop(CURIE_MAP)
+            self.df_converter = Converter.from_prefix_map(df_meta.pop(CURIE_MAP))
             self.df_meta = df_meta
 
         self.alignmentxml_file = f"{test_data_dir}/oaei-ordo-hp.rdf"
         self.alignmentxml = minidom.parse(self.alignmentxml_file)
-        self.metadata = Metadata.default()
+        self.metadata = get_default_metadata()
+        self.converter = get_converter()
 
     def test_parse_sssom_dataframe_from_file(self):
         """Test parsing a TSV."""
@@ -117,21 +119,23 @@ def test_parse_obographs(self):
         """Test parsing OBO Graph JSON."""
         msdf = from_obographs(
             jsondoc=self.obographs,
-            prefix_map=self.metadata.prefix_map,
-            meta=self.metadata.metadata,
+            prefix_map=self.converter,
+            meta=self.metadata,
         )
         path = os.path.join(test_out_dir, "test_parse_obographs.tsv")
         with open(path, "w") as file:
             write_table(msdf, file)
         self.assertEqual(
+            # this number went up from 8099 when the curies.Converter was introduced
+            # since it was able to handle CURIE prefix and URI prefix synonyms
+            8488,
             len(msdf.df),
-            8099,
             f"{self.obographs_file} has the wrong number of mappings.",
         )
 
     def test_parse_tsv(self):
         """Test parsing TSV."""
-        msdf = from_sssom_dataframe(df=self.df, prefix_map=self.df_prefix_map, meta=self.df_meta)
+        msdf = from_sssom_dataframe(df=self.df, prefix_map=self.df_converter, meta=self.df_meta)
         path = os.path.join(test_out_dir, "test_parse_tsv.tsv")
         with open(path, "w") as file:
             write_table(msdf, file)
@@ -145,8 +149,8 @@ def test_parse_alignment_minidom(self):
         """Test parsing an alignment XML."""
         msdf = from_alignment_minidom(
             dom=self.alignmentxml,
-            prefix_map=self.metadata.prefix_map,
-            meta=self.metadata.metadata,
+            prefix_map=self.converter,
+            meta=self.metadata,
         )
         path = os.path.join(test_out_dir, "test_parse_alignment_minidom.tsv")
         with open(path, "w") as file:
@@ -244,9 +248,7 @@ def test_parse_alignment_xml(self):
 
     def test_parse_sssom_rdf(self):
         """Test parsing RDF."""
-        msdf = from_sssom_rdf(
-            g=self.rdf_graph, prefix_map=self.df_prefix_map, meta=self.metadata.metadata
-        )
+        msdf = from_sssom_rdf(g=self.rdf_graph, prefix_map=self.df_converter, meta=self.metadata)
         path = os.path.join(test_out_dir, "test_parse_sssom_rdf.tsv")
         with open(path, "w") as file:
             write_table(msdf, file)
@@ -260,8 +262,8 @@ def test_parse_sssom_json(self):
         """Test parsing JSON."""
         msdf = from_sssom_json(
             jsondoc=self.json,
-            prefix_map=self.df_prefix_map,
-            meta=self.metadata.metadata,
+            prefix_map=self.df_converter,
+            meta=self.metadata,
         )
         path = os.path.join(test_out_dir, "test_parse_sssom_json.tsv")
         with open(path, "w") as file: