fix generation

.github/workflows/generate_curated_lists.yml

@@ -36,7 +36,11 @@ jobs:
       - name: ontology-processing
         run: |
           python3 ./tools/ontology-builder/src/curated_lists.py
-          git add --all
+          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"

tools/ontology-builder/src/curated_lists.py

@@ -1,6 +1,6 @@
-# #### Hand-Curation of Systems and Organs
-# #### Tissue Constants
-# Hand-curated systems.
+# # Hand-Curation of Systems and Organs
+# ## Tissue Constants
+# ### Hand-curated systems.
 SYSTEM_TISSUES = [
     "UBERON_0001017",
     "UBERON_0004535",
@@ -21,7 +21,7 @@
     "UBERON_0001434",
 ]
 
-# Hand-curated organs.
+# ### Hand-curated organs.
 ORGAN_TISSUES = [
     "UBERON_0000992",
     "UBERON_0000029",
@@ -167,9 +167,9 @@
     "UBERON_0000916",  # abdomen
 ]
 
-# ### Cell Type Constants
-# Hand-Curation of Cell Classes and Cell Subclasses
-# Hand-curated cell classes.
+# # Cell Type Constants
+# ## Hand-Curation of Cell Classes and Cell Subclasses
+# ### Hand-curated cell classes.
 CELL_CLASSES = [
     "CL_0002494",  # cardiocyte
     "CL_0002320",  # connective tissue cell
@@ -196,7 +196,7 @@
     "CL_4033054",  # perivascular cell
 ]
 
-# Hand-curated cell subclasses.
+# ### Hand-curated cell subclasses.
 CELL_SUBCLASSES = [
     "CL_0000624",  # CD4-positive, alpha-beta T cell
     "CL_0000625",  # CD8-positive, alpha-beta T cell

tools/ontology-builder/src/curation_list_generator.py

@@ -2,6 +2,7 @@
 import os.path
 from typing import List
 
+import env
 from curated_lists import CELL_CLASSES, CELL_SUBCLASSES, ORGAN_TISSUES, SYSTEM_TISSUES, TISSUE_GENERAL
 
 
@@ -17,20 +18,20 @@ def main(path: str = "ontology-references") -> None:
     :return:
     """
     # Create a dictionary that matches the JSON schema in artifact-schemas
-    with open(os.path.join(path, "system_list.json"), "w") as f:
-        json.dump(reformat_ontology_term_ids(SYSTEM_TISSUES), f)
+    with open(os.path.join(env.ONTOLOGY_REF_DIR, "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:
-        json.dump(reformat_ontology_term_ids(ORGAN_TISSUES), f)
+        json.dump(reformat_ontology_term_ids(ORGAN_TISSUES), f, indent=0)
 
     with open(os.path.join(path, "tissue_general_list.json"), "w") as f:
-        json.dump(reformat_ontology_term_ids(TISSUE_GENERAL), f)
+        json.dump(reformat_ontology_term_ids(TISSUE_GENERAL), f, indent=0)
 
     with open(os.path.join(path, "cell_class_list.json"), "w") as f:
-        json.dump(reformat_ontology_term_ids(CELL_CLASSES), f)
+        json.dump(reformat_ontology_term_ids(CELL_CLASSES), f, indent=0)
 
     with open(os.path.join(path, "cell_subclass_list.json"), "w") as f:
-        json.dump(reformat_ontology_term_ids(CELL_SUBCLASSES), f)
+        json.dump(reformat_ontology_term_ids(CELL_SUBCLASSES), f, indent=0)
 
 
 if __name__ == "__main__":