fix generation

.github/workflows/generate_curated_lists.yml

@@ -36,12 +36,12 @@ jobs:
       - name: ontology-processing
         run: |
           python3 ./tools/ontology-builder/src/curated_lists.py
+      - name: Commit
+        run: |
           git add ./tools/ontology-builder/src/ontology-references/tissue_general_list.json
           git add ./tools/ontology-builder/src/ontology-references/organ_list.json
           git add ./tools/ontology-builder/src/ontology-references/cell_class_list.json
           git add ./tools/ontology-builder/src/ontology-references/cell_subclass_list.json
           git add ./tools/ontology-builder/src/ontology-references/system_list.json
-      - name: Commit
-        run: |
           git commit -m "AUTO: update curated_lists"
           git push

tools/ontology-builder/src/curated_lists.py

@@ -1,3 +1,4 @@
+#
 # # Hand-Curation of Systems and Organs
 # ## Tissue Constants
 # ### Hand-curated systems.

tools/ontology-builder/src/curation_list_generator.py

@@ -11,14 +11,14 @@ def reformat_ontology_term_ids(d: List[str]) -> List[str]:
     return [i.replace("_", ":") for i in d]
 
 
-def main(path: str = "ontology-references") -> None:
+def main(path: str = env.ONTOLOGY_REF_DIR) -> None:
     """
     Using the dictionarys from curated_list.py, generate a json file that matches the JSON schema in artifact-schemas
     :param path: The destination path for the json files
     :return:
     """
     # Create a dictionary that matches the JSON schema in artifact-schemas
-    with open(os.path.join(env.ONTOLOGY_REF_DIR, "system_list.json"), "w") as f:
+    with open(os.path.join(path, "system_list.json"), "w") as f:
         json.dump(reformat_ontology_term_ids(SYSTEM_TISSUES), f, indent=0)
 
     with open(os.path.join(path, "organ_list.json"), "w") as f: