gen3_validator 2.0.1

Comprehensive toolkit for resolving Gen3 JSON schemas, validating JSON metadata against schemas, and verifying linkage integrity between data nodes. Includes utilities for parsing Excel metadata templates, generating linkage configuration maps, orchestrating schema validation, and producing detailed validation reports and statistics

Gen3 Validator

Gen3 Validator is a Python toolkit designed to make working with Gen3 metadata schemas and data validation straightforward for developers.

Installation

pip install gen3_validator
pip show gen3_validator

Docs

• example usage

Quickstart

import gen3_validator

resolver = gen3_validator.ResolveSchema(schema_path = "../tests/schema/gen3_test_schema.json")
resolver.resolve_schema()
schema = resolver.schema_resolved

data = [
    {
        "baseline_timepoint": True, # variable not in data dictionary
        "freeze_thaw_cycles": "10", # should be an integer
        "sample_collection_method": "2fddbe7d09",
        "sample_id": "d4f31f7bb6",
        "sample_in_preservation": "snap Frozen",
        "sample_in_storage": "yes",
        "sample_provider": "USYD",
        "sample_source": "UBERON:3781554",
        "sample_storage_method": "not stored",
        "sample_type": "59a8fd8005",
        "storage_location": "UMELB",
        "subjects": {
            "submitter_id": "subject_e5616257f8"
        },
        "submitter_id": "sample_efdbe56d20",
        "type": "sample"
    },
    {
        "baseline_timepoint": True, 
        "freeze_thaw_cycles": 76,
        "sample_collection_method": "e2a6403b51",
        "sample_id": 3324635, # should be a string
        "sample_in_preservation": "not allowed to collect",
        "sample_in_storage": "unknown",
        "sample_provider": "USYD",
        "sample_source": "UBERON:9332357",
        "sample_storage_method": "frozen, liquid nitrogen",
        "sample_type": "8fd28ec2f3",
        "storage_location": "Baker",
        "subjects": {
            "submitter_id": "subject_071bc3e81a"
        },
        "submitter_id": "sample_f7645c1221",
        "type": "sample"
    }
]
results = gen3_validator.validate.validate_list_dict(data, schema)

print(results)

Example output:

[
    {
        'node': 'sample',
        'index': 0,
        'validation_result': 'FAIL',
        'invalid_key': 'freeze_thaw_cycles',
        'schema_path': 'properties.freeze_thaw_cycles.type',
        'validator': 'type',
        'validator_value': 'integer',
        'validation_error': "'10' is not of type 'integer'"
    },
    {
        'node': 'sample',
        'index': 0,
        'validation_result': 'FAIL',
        'invalid_key': 'root',
        'schema_path': 'additionalProperties',
        'validator': 'additionalProperties',
        'validator_value': False,
        'validation_error': "Additional properties are not allowed ('baseline_timepoint', 'subjects' were unexpected)"
    },
    {
        'node': 'sample',
        'index': 1,
        'validation_result': 'FAIL',
        'invalid_key': 'sample_id',
        'schema_path': 'properties.sample_id.type',
        'validator': 'type',
        'validator_value': 'string',
        'validation_error': "3324635 is not of type 'string'"
    },
    {
        'node': 'sample',
        'index': 1,
        'validation_result': 'FAIL',
        'invalid_key': 'root',
        'schema_path': 'additionalProperties',
        'validator': 'additionalProperties',
        'validator_value': False,
        'validation_error': "Additional properties are not allowed ('baseline_timepoint', 'subjects' were unexpected)"
    }
]

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Dev Setup

1. Make sure you have poetry installed.
2. Clone the repository.
3. Run the following command to activate the virtual environment.

eval $(poetry env activate)

4. Run the following command to install the dependencies.

poetry install

5. Run the following command to run the tests.

pytest -vv tests/

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License

See the license page for more information.