Improve testing of round trip serialization

src/sssom/parsers.py

@@ -27,8 +27,10 @@
     CONFIDENCE,
     CURIE_MAP,
     DEFAULT_MAPPING_PROPERTIES,
+    LICENSE,
     MAPPING_JUSTIFICATION,
     MAPPING_JUSTIFICATION_UNSPECIFIED,
+    MAPPING_SET_ID,
     OBJECT_ID,
     OBJECT_LABEL,
     OBJECT_SOURCE,
@@ -247,22 +249,27 @@ def parse_sssom_rdf(
 
 
 def parse_sssom_json(
-    file_path: str,
-    prefix_map: ConverterHint = None,
-    meta: Optional[MetadataType] = None,
-    **kwargs
-    # mapping_predicates: Optional[List[str]] = None,
+    file_path: str, prefix_map: ConverterHint = None, meta: Optional[MetadataType] = None, **kwargs
 ) -> MappingSetDataFrame:
-    """Parse a TSV to a :class:`MappingSetDocument` to a  :class`MappingSetDataFrame`."""
+    """Parse a TSV to a :class:`MappingSetDocument` to a :class:`MappingSetDataFrame`."""
     raise_for_bad_path(file_path)
-    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)
+
+    # Initialize meta if it's None
+    if meta is None:
+        meta = {}
+
+    # Update metadata with values from JSON document
+    meta_keys_to_update = [MAPPING_SET_ID, LICENSE]
+    meta.update({key: jsondoc[key] for key in meta_keys_to_update if key in jsondoc})
+
+    converter_from_jsonld = Converter.from_jsonld(file_path)
+    converter_via_metadata, meta = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
+    converter = curies.chain([converter_from_jsonld, converter_via_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)]
     return msdf
 
 

tests/data/basic_subset.tsv

@@ -13,6 +13,7 @@
 #  b: "http://example.org/b/"
 #  c: "http://example.org/c/"
 #  d: "http://example.org/d/"
+#  orcid: "https://orcid.org/"
 subject_id	subject_label	predicate_id	predicate_modifier	object_id	object_label	mapping_justification	subject_source	object_source	mapping_tool	confidence	subject_match_field	object_match_field	subject_category	object_category	match_string	comment
 x:appendage	appendage	owl:equivalentClass		y:appendage	appendages	semapv:ManualMappingCuration	x	y	rdf_matcher	0.840714406	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	appendag	.
 x:appendage	appendage	owl:equivalentClass		z:appendage	APPENDAGE	semapv:ManualMappingCuration	x	z	rdf_matcher	0.840714406	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	appendag	.

tests/test_parsers.py

@@ -4,9 +4,9 @@
 import json
 import math
 import os
-import tempfile
 import unittest
 from pathlib import Path
+from tempfile import TemporaryDirectory
 from textwrap import dedent
 from xml.dom import minidom
 
@@ -18,7 +18,7 @@
 
 from sssom.constants import CURIE_MAP, DEFAULT_LICENSE, SSSOM_URI_PREFIX, get_default_metadata
 from sssom.context import SSSOM_BUILT_IN_PREFIXES, ensure_converter, get_converter
-from sssom.io import parse_file
+from sssom.io import convert_file, parse_file
 from sssom.parsers import (
     _open_input,
     _read_pandas_and_metadata,
@@ -378,7 +378,7 @@ def test_round_trip(self):
             set(msdf.prefix_map),
         )
 
-        with tempfile.TemporaryDirectory() as directory:
+        with TemporaryDirectory() as directory:
             directory = Path(directory)
             path = directory.joinpath("test.sssom.tsv")
             with path.open("w") as file:
@@ -410,3 +410,26 @@ def test_round_trip(self):
 
         # This checks that nothing funny gets added unexpectedly
         self.assertEqual(expected_prefix_map, reconsitited_msdf.prefix_map)
+
+    def test_round_trip_tsv_json_tsv(self):
+        """Test TSV => JSON => TSV using convert() + parse()."""
+        input_tsv = test_data_dir.joinpath("basic_subset.tsv")
+        input_msdf = parse_sssom_table(input_tsv)
+        input_msdf.clean_prefix_map()
+        with TemporaryDirectory() as directory:
+            directory = Path(directory)
+            json_path = directory.joinpath("basic_subset.json")
+            tsv_path = directory.joinpath("json_to_tsv.tsv")
+            with json_path.open("w") as jfile:
+                convert_file(input_path=input_tsv, output_format="json", output=jfile)
+            with tsv_path.open("w") as tfile:
+                parse_file(
+                    input_path=str(json_path),
+                    input_format="json",
+                    prefix_map_mode="merged",
+                    output=tfile,
+                )
+            msdf = parse_sssom_table(tsv_path)
+            pd.testing.assert_frame_equal(input_msdf.df, msdf.df)
+            self.assertEqual(input_msdf.prefix_map, msdf.prefix_map)
+            self.assertEqual(input_msdf.metadata, msdf.metadata)