fix makefile

Author: sierra-moxon

Makefile

@@ -14,3 +14,28 @@ integration-tests:
 
 docs:
 	cd docs && $(RUN) make html
+
+# Clean up intermediate schema files
+schema-clean:
+	@echo "Cleaning up intermediate schema files..."
+	rm -f kgx/schema/kgx_merged.yaml kgx/schema/kgx_final.yaml kgx/schema/derived_kgx_schema.yaml
+	rm -f kgx/schema/transformations/full_transform.transform.yaml
+
+# Merge imported schemas (biolink-model) into a single file
+schema-merge: schema-clean
+	@echo "Merging schemas..."
+	poetry run gen-linkml --mergeimports --format yaml kgx/schema/kgx.yaml -o kgx/schema/kgx_merged.yaml
+
+# Generate transformation specification
+schema-transform: schema-merge
+	@echo "Generating transformation specification..."
+	poetry run python kgx/schema/scripts/generate_transform.py kgx/schema/kgx_merged.yaml kgx/schema/transformations/full_transform.transform.yaml
+
+# Apply transformation to create final schema
+schema-apply: schema-transform
+	@echo "Applying transformation..."
+	poetry run linkml-map derive-schema -T kgx/schema/transformations/full_transform.transform.yaml -o kgx/schema/kgx_complete.yaml kgx/schema/kgx_merged.yaml
+
+# Complete schema build process
+schema: schema-apply
+	@echo "Schema build complete. Final schema is at kgx/schema/kgx_complete.yaml"