FHIR Feature

- Add: _test_to_fhir_json()
- Update: test_write_sssom_fhir(): More assertions

src/sssom/writers.py

@@ -318,8 +318,10 @@ def to_fhir_json(msdf: MappingSetDataFrame) -> Dict:
     json_obj = {
         "resourceType": "ConceptMap",
         "url": mapping_set_id,
+        # Assumes mapping_set_id is a URI w/ artefact name at end. System becomes URI stem, value becomes artefact name
         "identifier": [
             {
+
                 "system": "/".join(mapping_set_id.split("/")[:-1]) + "/",
                 "value": mapping_set_id,
             }

tests/test_conversion.py

@@ -15,6 +15,7 @@
 from sssom.sssom_document import MappingSetDocument
 from sssom.util import MappingSetDataFrame, to_mapping_set_dataframe
 from sssom.writers import (
+    to_fhir_json,
     to_json,
     to_ontoportal_json,
     to_owl_graph,
@@ -62,6 +63,8 @@ def test_conversion(self):
                 self._test_to_json(mdoc, test)
                 logging.info("Testing ontoportal JSON export")
                 self._test_to_ontoportal_json(mdoc, test)
+                logging.info("Testing fhir_json JSON export")
+                self._test_to_fhir_json(mdoc, test)
 
     def _test_to_owl_graph(self, mdoc, test):
         msdf = to_mapping_set_dataframe(mdoc)
@@ -85,6 +88,13 @@ def _test_to_json(self, mdoc, test: SSSOMTestCase):
         with open(test.get_out_file("json"), "w") as file:
             write_json(msdf, file, serialisation="json")
 
+    def _test_to_fhir_json(self, mdoc, test: SSSOMTestCase):
+        msdf = to_mapping_set_dataframe(mdoc)
+        d = to_fhir_json(msdf)
+        self.assertEqual(
+            len(d["group"][0]["element"]), test.ct_data_frame_rows, "wrong number of mappings."
+        )
+
     def _test_to_ontoportal_json(self, mdoc, test: SSSOMTestCase):
         msdf = to_mapping_set_dataframe(mdoc)
         jsonob = to_ontoportal_json(msdf)

tests/test_writers.py

@@ -3,6 +3,7 @@
 import json
 import os
 import unittest
+from typing import Any, Dict
 
 import pandas as pd
 from curies import Converter
@@ -128,18 +129,30 @@ def test_update_sssom_context_with_prefixmap(self):
 
     def test_write_sssom_fhir(self):
         """Test writing as FHIR ConceptMap JSON."""
+        # Vars
         path = os.path.join(test_out_dir, "test_write_sssom_fhir.json")
+        msdf: MappingSetDataFrame = self.msdf
+        metadata: Dict[str, Any] = msdf.metadata
+        mapping_set_id: str = metadata["mapping_set_id"]
+        # Write
         with open(path, "w") as file:
             write_json(self.msdf, file, "fhir_json")
+        # Read
         # todo: @Joe: after implementing reader/importer, change this to `msdf = parse_sssom_fhir_json()`
         with open(path, "r") as file:
             d = json.load(file)
-        # todo: @Joe: What else is worth checking?
+        # Test
         self.assertEqual(
             len(d["group"][0]["element"]),
             self.mapping_count,
             f"{path} has the wrong number of mappings.",
         )
+        self.assertEqual(d["resourceType"], "ConceptMap")
+        self.assertEqual(d["url"], mapping_set_id)
+        self.assertIn(d["identifier"][0]["system"], mapping_set_id)
+        self.assertEqual(d["identifier"][0]["value"], mapping_set_id)
+        self.assertEqual(d["identifier"][0]["value"], d["url"])
+
         print()  # TODO: temp
 
     def test_write_sssom_owl(self):