chore: move curated lists to ontology-assets (#48)

## Reason for Change - preparing the repo for automated data releases. - moving the assets that will be part of ontology asset release to thier own directly make it easier to added them to a release. ## Changes - update validator to look for curated lists in ontology-assets - move curated lists to ontology-assets ## Testing steps - Check that GHA validate curated lists passes - Check that unit tests pass.
chanzuckerberg · Feb 26, 2024 · 77916df · 77916df
2 parents 3121833 + 66476d4
commit 77916df
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Showing 8 changed files with 5 additions and 3 deletions.
diff --git a/.github/workflows/validate_curated_lists.yml b/.github/workflows/validate_curated_lists.yml
@@ -3,7 +3,7 @@ name: Validate Curated List Update
 on:
   push:
     paths:
-      - "**/tools/ontology-builder/src/ontology-references/**.json"
+      - "**/ontology-assets/**.json"
       - "**/artifact-schemas/**.json"
     branches-ignore:
       - main

diff --git a/.../ontology-references/cell_class_list.json → ontology-assets/cell_class_list.json b/.../ontology-references/cell_class_list.json → ontology-assets/cell_class_list.json
diff --git a/...tology-references/cell_subclass_list.json → ontology-assets/cell_subclass_list.json b/...tology-references/cell_subclass_list.json → ontology-assets/cell_subclass_list.json
diff --git a/...r/src/ontology-references/organ_list.json → ontology-assets/organ_list.json b/...r/src/ontology-references/organ_list.json → ontology-assets/organ_list.json
diff --git a/.../src/ontology-references/system_list.json → ontology-assets/system_list.json b/.../src/ontology-references/system_list.json → ontology-assets/system_list.json
diff --git a/...ology-references/tissue_general_list.json → ontology-assets/tissue_general_list.json b/...ology-references/tissue_general_list.json → ontology-assets/tissue_general_list.json
diff --git a/tools/ontology-builder/src/env.py b/tools/ontology-builder/src/env.py
@@ -7,4 +7,6 @@
 RAW_ONTOLOGY_DIR = os.path.join(ONTOLOGY_REF_DIR, "raw-files")
 ONTO_INFO_YAML = os.path.join(FIXTURES_ROOT, "ontology_info.yml")
 PARSED_ONTOLOGIES_FILE = os.path.join(FIXTURES_ROOT, "all_ontology.json.gz")
-SCHEMA_DIR = os.path.join(os.path.realpath(__file__).rsplit("/", maxsplit=4)[0], "artifact-schemas")
+PROJECT_ROOT_DIR = os.path.realpath(__file__).rsplit("/", maxsplit=4)[0]
+SCHEMA_DIR = os.path.join(PROJECT_ROOT_DIR, "artifact-schemas")
+ONTOLOGY_ASSETS_DIR = os.path.join(PROJECT_ROOT_DIR, "ontology-assets")
diff --git a/tools/ontology-builder/src/validate_curated_lists.py b/tools/ontology-builder/src/validate_curated_lists.py
@@ -29,7 +29,7 @@ def verify_json(schema_file_name: str, json_file_name: str) -> bool:
     return True
 
 
-def main(path: str = env.ONTOLOGY_REF_DIR) -> None:
+def main(path: str = env.ONTOLOGY_ASSETS_DIR) -> None:
     """
     Verify the curated JSON lists match their respective JSON schema in artifact-schemas
     :param path: The destination path for the json files