changed @context backto what it was

src/sssom/constants.py

@@ -105,8 +105,6 @@
 OTHER = "other"
 COMMENT = "comment"
 
-JSON_CONTEXT_KEY = "@context"
-
 CURIE_MAP = "curie_map"
 SUBJECT_SOURCE_ID = "subject_source_id"
 OBJECT_SOURCE_ID = "object_source_id"

src/sssom/context.py

@@ -9,7 +9,7 @@
 from curies import Converter
 from rdflib.namespace import is_ncname
 
-from .constants import EXTENDED_PREFIX_MAP, JSON_CONTEXT_KEY
+from .constants import EXTENDED_PREFIX_MAP
 
 __all__ = [
     "SSSOM_BUILT_IN_PREFIXES",
@@ -53,7 +53,7 @@ def _get_built_in_prefix_map() -> Converter:
     context = _load_sssom_context()
     prefix_map = {
         prefix: uri_prefix
-        for prefix, uri_prefix in context[JSON_CONTEXT_KEY].items()
+        for prefix, uri_prefix in context["@context"].items()
         if prefix in SSSOM_BUILT_IN_PREFIXES and isinstance(uri_prefix, str)
     }
     return Converter.from_prefix_map(prefix_map)

src/sssom/parsers.py

@@ -27,7 +27,6 @@
     CONFIDENCE,
     CURIE_MAP,
     DEFAULT_MAPPING_PROPERTIES,
-    JSON_CONTEXT_KEY,
     LICENSE,
     MAPPING_JUSTIFICATION,
     MAPPING_JUSTIFICATION_UNSPECIFIED,
@@ -257,7 +256,6 @@ def parse_sssom_json(
 
     with open(file_path) as json_file:
         jsondoc = json.load(json_file)
-    context_from_jsondoc = jsondoc.get(JSON_CONTEXT_KEY)
 
     # Initialize meta if it's None
     if meta is None:
@@ -267,16 +265,9 @@ def parse_sssom_json(
     meta_keys_to_update = [MAPPING_SET_ID, LICENSE]
     meta.update({key: jsondoc[key] for key in meta_keys_to_update if key in jsondoc})
 
-    # Update CURIE_MAP if context_from_jsondoc exists
-    if context_from_jsondoc:
-        prefixes_from_json = {
-            key: value
-            for key, value in context_from_jsondoc.items()
-            if isinstance(value, str) and not key.startswith("@")
-        }
-        meta[CURIE_MAP] = prefixes_from_json
-
-    converter, meta = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
+    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)
     return msdf

src/sssom/writers.py

@@ -17,7 +17,7 @@
 
 from sssom.validators import check_all_prefixes_in_curie_map
 
-from .constants import CURIE_MAP, JSON_CONTEXT_KEY, SCHEMA_YAML, SSSOM_URI_PREFIX
+from .constants import CURIE_MAP, SCHEMA_YAML, SSSOM_URI_PREFIX
 from .context import _load_sssom_context
 from .parsers import to_mapping_set_document
 from .util import (
@@ -439,12 +439,12 @@ def _update_sssom_context_with_prefixmap(converter: Converter):
     """Prepare a JSON-LD context and dump to a string."""
     context = _load_sssom_context()
     for k, v in converter.bimap.items():
-        if k in context[JSON_CONTEXT_KEY] and context[JSON_CONTEXT_KEY][k] != v:
+        if k in context["@context"] and context["@context"][k] != v:
             logging.info(
                 f"{k} namespace is already in the context, ({context['@context'][k]}, "
                 f"but with a different value than {v}. Overwriting!"
             )
-        context[JSON_CONTEXT_KEY][k] = v
+        context["@context"][k] = v
     return context
 
 

tests/test_writers.py

@@ -10,7 +10,6 @@
 from sssom import MappingSetDataFrame
 from sssom.constants import (
     CREATOR_ID,
-    JSON_CONTEXT_KEY,
     OBJECT_ID,
     OBJECT_LABEL,
     PREDICATE_ID,
@@ -109,9 +108,9 @@ def test_write_sssom_json_context(self):
         msdf = MappingSetDataFrame(df)
         msdf.clean_prefix_map()
         json_object = to_json(msdf)
-        self.assertIn(JSON_CONTEXT_KEY, json_object)
-        self.assertIn("DOID", json_object[JSON_CONTEXT_KEY])
-        self.assertIn("mapping_set_id", json_object[JSON_CONTEXT_KEY])
+        self.assertIn("@context", json_object)
+        self.assertIn("DOID", json_object["@context"])
+        self.assertIn("mapping_set_id", json_object["@context"])
 
     def test_update_sssom_context_with_prefixmap(self):
         """Test when writing to JSON, the context is correctly written as well."""
@@ -124,10 +123,10 @@ def test_update_sssom_context_with_prefixmap(self):
         ]
         converter = Converter.from_extended_prefix_map(records)
         context = _update_sssom_context_with_prefixmap(converter)
-        self.assertIn(JSON_CONTEXT_KEY, context)
-        self.assertIn("SCTID", context[JSON_CONTEXT_KEY])
-        self.assertNotIn("snomed", context[JSON_CONTEXT_KEY])
-        self.assertIn("mapping_set_id", context[JSON_CONTEXT_KEY])
+        self.assertIn("@context", context)
+        self.assertIn("SCTID", context["@context"])
+        self.assertNotIn("snomed", context["@context"])
+        self.assertIn("mapping_set_id", context["@context"])
 
     def test_write_sssom_fhir(self):
         """Test writing as FHIR ConceptMap JSON."""