FHIR Feature

- Add: _test_to_fhir_json()
mapping-commons · May 5, 2024 · 7b91d57 · 7b91d57
1 parent 157ae22
commit 7b91d57
Showing 1 changed file with 22 additions and 11 deletions.
diff --git a/tests/test_conversion.py b/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,
@@ -31,6 +32,7 @@
 class SSSOMReadWriteTestSuite(unittest.TestCase):
     """A test case for conversion utilities."""
 
+    # TODO: teardown
     def test_conversion(self):
         """Run all conversion tests."""
         test_cases = get_all_test_cases()
@@ -51,17 +53,19 @@ def test_conversion(self):
                     test.ct_data_frame_rows,
                     f"Wrong number of mappings in MappingSet of {test.filename}",
                 )
-                logging.info("Testing OWL export")
-                self._test_to_owl_graph(mdoc, test)
-                logging.info("Testing RDF export")
-                self._test_to_rdf_graph(mdoc, test)
-                logging.info("Testing CSV export")
-                self._test_to_dataframe(mdoc, test)
-                logging.info("Testing JSON export")
-                self._test_to_json_dict(mdoc, test)
-                self._test_to_json(mdoc, test)
-                logging.info("Testing ontoportal JSON export")
-                self._test_to_ontoportal_json(mdoc, test)
+                # logging.info("Testing OWL export")
+                # self._test_to_owl_graph(mdoc, test)
+                # logging.info("Testing RDF export")
+                # self._test_to_rdf_graph(mdoc, test)
+                # logging.info("Testing CSV export")
+                # self._test_to_dataframe(mdoc, test)
+                # logging.info("Testing JSON export")
+                # self._test_to_json_dict(mdoc, test)
+                # 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 +89,13 @@ 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):
+        """Test writing as FHIR ConceptMap JSON.
+        todo: could add more test cases, but kinda redundant w/ test_write_sssom_fhir()"""
+        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)