hca-schema-validator 0.13.0

HCA schema validation for single-cell datasets

HCA Schema Validator

HCA-specific extensions for cellxgene schema validation.

Installation

From PyPI (Recommended)

pip install hca-schema-validator

From Source (Development)

# Clone the repository
git clone https://github.com/clevercanary/hca-validation-tools.git
cd hca-validation-tools/packages/hca-schema-validator

# Install Poetry if you haven't already
curl -sSL https://install.python-poetry.org | python3 -

# Install dependencies and package
poetry install

# Run tests
poetry run pytest tests/

Usage

from hca_schema_validator import HCAValidator

# Create validator instance
validator = HCAValidator()

# Validate an h5ad file
is_valid = validator.validate_adata("path/to/file.h5ad")

# Check results
if is_valid:
    print("✅ Validation passed!")
else:
    print("❌ Validation failed:")
    for error in validator.errors:
        print(f"  - {error}")

Development Status

Current Version: 0.1.0 - Minimal passthrough implementation

Currently a passthrough wrapper around cellxgene-schema Validator. HCA-specific validation rules will be added incrementally.

Testing

cd hca_schema_validator
poetry run pytest tests/

Project Structure

hca_schema_validator/
├── src/
│   └── hca_schema_validator/
│       ├── __init__.py       # Package exports
│       └── validator.py      # HCAValidator class
├── tests/
│   └── test_validator.py # Unit tests
├── pyproject.toml        # Poetry configuration & dependencies
└── README.md            # This file

Ontology Data Overlay

The validator depends on cellxgene-ontology-guide for ontology term lookups. When that package is missing terms we need (e.g., newly added CL or EFO terms), we generate updated ontology data files and overlay them at runtime.

How it works

_vendored/cellxgene_schema/ontology_parser.py monkey-patches two functions from cellxgene_ontology_guide.supported_versions:

• load_supported_versions() loads upstream version data and patches only the ontology versions listed in _ONTOLOGY_VERSION_OVERRIDES — all other ontologies and any new entries added by future package releases are preserved unchanged.
• load_ontology_file(file_name) checks ontology_data/ first for a .json.zst file, falling back to the package's bundled data.

Current overlays

Ontology	Overlay Version	Bundled Version	Why
CL	v2025-12-17	v2025-07-30	Missing salivary gland cell types (CL:4052065-4052069)

How to add/update an ontology overlay

Prerequisites: Python 3.10+, Docker, ~1GB disk for OWL files.

1. Clone CZI's ontology-guide repo (contains the build pipeline):

   cd /tmp && mkdir ontology-guide-build && cd ontology-guide-build
   git clone --depth 1 https://github.com/chanzuckerberg/cellxgene-ontology-guide.git
   

2. Set up build environment:

   python3 -m venv venv && source venv/bin/activate
   pip install owlready2==0.48 zstandard jsonschema semantic-version referencing cellxgene-ontology-guide
   docker pull obolibrary/robot:v1.9.8
   

3. Create a targeted ontology_info JSON with only the ontology to build. Save as cellxgene-ontology-guide/ontology-assets/ontology_info_custom.json:

   {
     "7.0.0": {
       "ontologies": {
         "EFO": {
           "version": "v3.86.0",
           "source": "https://github.com/EBISPOT/efo/releases/download/{version}/{filename}",
           "filename": "efo.owl"
         }
       }
     }
   }
   

   Find the latest release version on the ontology's GitHub releases page (e.g., CL releases, EFO releases).

   Copy the ontology entry from the existing ontology_info.json in ontology-assets/ and update the version field. Keep source, filename, and any other fields (like cross_ontology_mapping) the same.

4. Run the build script:

   #!/usr/bin/env python3
   import json, logging, os, sys
   logging.basicConfig(level=logging.INFO)
   
   REPO_DIR = "/tmp/ontology-guide-build/cellxgene-ontology-guide"
   sys.path.insert(0, os.path.join(REPO_DIR, "tools/ontology-builder/src"))
   import env
   env.ONTOLOGY_INFO_FILE = os.path.join(REPO_DIR, "ontology-assets/ontology_info_custom.json")
   env.ONTOLOGY_ASSETS_DIR = os.path.join(REPO_DIR, "ontology-assets")
   
   from all_ontology_generator import _download_ontologies, _parse_ontologies, get_ontology_info_file
   onto_info = get_ontology_info_file(env.ONTOLOGY_INFO_FILE)["7.0.0"]["ontologies"]
   _download_ontologies(onto_info)
   for f in _parse_ontologies(onto_info):
       logging.info(f"Generated: {f}")
   

5. Copy the .json.zst output into src/hca_schema_validator/ontology_data/.

6. Add an entry to _ONTOLOGY_VERSION_OVERRIDES in ontology_parser.py:

   _ONTOLOGY_VERSION_OVERRIDES = {
       ("7.0.0", "CL"): "v2025-12-17",
       ("7.0.0", "EFO"): "v3.86.0",  # new
   }
   

7. Verify and test:

   poetry run python -c "
   from hca_schema_validator._vendored.cellxgene_schema.ontology_parser import ONTOLOGY_PARSER
   print(ONTOLOGY_PARSER.is_valid_term_id('CL:4052065'))  # True
   "
   poetry run pytest tests/ -v
   

8. Clean up: rm -rf /tmp/ontology-guide-build

Removing the overlay

Once cellxgene-ontology-guide publishes a version that includes all the terms we need:

1. Delete the overlay files from ontology_data/ (keep only __init__.py)
2. Revert ontology_parser.py to its original form:

   from cellxgene_ontology_guide.ontology_parser import OntologyParser
   ONTOLOGY_PARSER = OntologyParser(schema_version="v7.0.0")
   

3. Bump cellxgene-ontology-guide version in pyproject.toml

License

MIT