Fix assay and contact role mappings to use JSON strings for study_ref and roles

Author: Zalfsten

middleware/sql_to_arc/tests/unit/test_mapper.py

@@ -107,7 +107,7 @@ def test_map_assay() -> None:
     """Test mapping of assay data."""
     row = AssayRow(
         identifier="1",
-        study_ref=["sty1"],
+        study_ref='["sty1"]',  # type: ignore[arg-type]
         investigation_ref="inv1",
         measurement_type_term="Proteomics",
         measurement_type_uri="http://example.org/prot",
@@ -132,7 +132,7 @@ def test_map_assay_with_platform() -> None:
     """Test mapping of assay data including technology platform."""
     row = AssayRow(
         identifier="2",
-        study_ref=["sty1"],
+        study_ref='["sty1"]',  # type: ignore[arg-type]
         investigation_ref="inv1",
         technology_platform="Orbitrap",
     )
@@ -173,7 +173,7 @@ def test_map_contact() -> None:
         last_name="Doe",
         first_name="John",
         email="john@example.com",
-        roles=[{"term": "Principal Investigator", "uri": "http://roles", "version": "1.0"}],
+        roles='[{"term": "Principal Investigator", "uri": "http://roles", "version": "1.0"}]',  # type: ignore[arg-type]
     )
 
     person = map_contact(row)
@@ -195,7 +195,7 @@ def test_map_contact_invalid_roles() -> None:
             investigation_ref="inv1",
             target_type="investigation",
             last_name="Smith",
-            roles=None,
+            roles="{invalid-json}",  # type: ignore[arg-type]
         )