Make output_prefix and output_postfix optional

pipeline.Makefile

@@ -362,8 +362,8 @@ $(MAPPING_SUCCESS_SENTINEL): $(SCHEMA_FILE) $(VALIDATION_SUCCESS_SENTINEL)
 		--data_dir $(DM_INPUT_DIR) \
 		--var_dir $(DM_TRANS_SPEC_DIR) \
 		--output_dir $(MAPPING_OUTPUT_DIR) \
-		--output_prefix $(DM_MAPPING_PREFIX) \
-		--output_postfix "$(DM_MAPPING_POSTFIX)" \
+		$(if $(DM_MAPPING_PREFIX),--output_prefix $(DM_MAPPING_PREFIX)) \
+		$(if $(DM_MAPPING_POSTFIX),--output_postfix "$(DM_MAPPING_POSTFIX)") \
 		--output_type $(DM_MAP_OUTPUT_TYPE) \
 		--chunk_size $(DM_MAP_CHUNK_SIZE)
 	@echo "✓ Data mapping complete. Output written to $(MAPPING_OUTPUT_DIR)"

src/dm_bip/map_data/map_data.py

@@ -207,11 +207,11 @@ def main(
     output_prefix: Annotated[
         str,
         typer.Option(),
-    ],
+    ] = "",
     output_postfix: Annotated[
         str,
         typer.Option(),
-    ],
+    ] = "",
     output_type: Annotated[
         StreamFormat,
         typer.Option(),

tests/unit/test_map_data.py

@@ -486,6 +486,63 @@ def test_process_entities_creates_output_files(linkml_test_setup, temp_dir):
     assert first_record["id"] == "SUBJ001"
 
 
+def test_process_entities_no_prefix_no_postfix(linkml_test_setup, temp_dir):
+    """Test that process_entities works with empty prefix and postfix."""
+    entities = ["Person"]
+    process_entities(
+        entities=entities,
+        data_loader=linkml_test_setup["data_loader"],
+        var_dir=linkml_test_setup["spec_dir"],
+        source_schemaview=linkml_test_setup["source_sv"],
+        target_schemaview=linkml_test_setup["target_sv"],
+        output_dir=temp_dir,
+        output_prefix="",
+        output_postfix="",
+        output_type="jsonl",
+        chunk_size=10,
+    )
+    output_file = Path(temp_dir) / "Person.jsonl"
+    assert output_file.exists()
+
+
+def test_process_entities_prefix_only(linkml_test_setup, temp_dir):
+    """Test that process_entities works with only prefix set."""
+    entities = ["Person"]
+    process_entities(
+        entities=entities,
+        data_loader=linkml_test_setup["data_loader"],
+        var_dir=linkml_test_setup["spec_dir"],
+        source_schemaview=linkml_test_setup["source_sv"],
+        target_schemaview=linkml_test_setup["target_sv"],
+        output_dir=temp_dir,
+        output_prefix="test",
+        output_postfix="",
+        output_type="jsonl",
+        chunk_size=10,
+    )
+    output_file = Path(temp_dir) / "test-Person.jsonl"
+    assert output_file.exists()
+
+
+def test_process_entities_postfix_only(linkml_test_setup, temp_dir):
+    """Test that process_entities works with only postfix set."""
+    entities = ["Person"]
+    process_entities(
+        entities=entities,
+        data_loader=linkml_test_setup["data_loader"],
+        var_dir=linkml_test_setup["spec_dir"],
+        source_schemaview=linkml_test_setup["source_sv"],
+        target_schemaview=linkml_test_setup["target_sv"],
+        output_dir=temp_dir,
+        output_prefix="",
+        output_postfix="v1",
+        output_type="jsonl",
+        chunk_size=10,
+    )
+    output_file = Path(temp_dir) / "Person-v1.jsonl"
+    assert output_file.exists()
+
+
 def test_process_entities_skips_missing_specs(linkml_test_setup, temp_dir):
     """Test that process_entities skips entities without spec files."""
     # NonexistentEntity has no specs