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chore: move curated lists to ontology-assets #48

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merged 5 commits into from
Feb 26, 2024
Merged

chore: move curated lists to ontology-assets #48

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c03c8e3
chore: moving the generated artifacts
Bento007 Feb 23, 2024
2b780c8
Merge branch 'main' into tsmtih/move-artifacts
Bento007 Feb 24, 2024
939e62b
suggestions
Bento007 Feb 26, 2024
1d86f30
suggestions
Bento007 Feb 26, 2024
66476d4
Merge branch 'main' into tsmtih/move-artifacts
Bento007 Feb 26, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/validate_curated_lists.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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0 .../ontology-references/cell_class_list.json → ontology-assets/cell_class_list.json
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0 ...tology-references/cell_subclass_list.json → ontology-assets/cell_subclass_list.json
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0 ...r/src/ontology-references/organ_list.json → ontology-assets/organ_list.json
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0 .../src/ontology-references/system_list.json → ontology-assets/system_list.json
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0 ...ology-references/tissue_general_list.json → ontology-assets/tissue_general_list.json
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4 changes: 3 additions & 1 deletion tools/ontology-builder/src/env.py
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Expand Up @@ -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")
2 changes: 1 addition & 1 deletion tools/ontology-builder/src/validate_curated_lists.py
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Expand Up @@ -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
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