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Implementation of JSONata for secondary validation #51

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kdp-cloud opened this issue Oct 10, 2024 · 1 comment
Open

Implementation of JSONata for secondary validation #51

kdp-cloud opened this issue Oct 10, 2024 · 1 comment
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enhancement New feature or request mars-cli

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@kdp-cloud
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Implement JSONata in CLI. This will provide a secondary validation mechanism for the user to validate the ISA-JSON and possibly patch simple mistakes.

@kdp-cloud kdp-cloud added enhancement New feature or request mars-cli labels Oct 10, 2024
@xiaoranzhou
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I have added a prototype at branch jsonata
https://github.com/elixir-europe/MARS/blob/jsonata/mars-cli/jsonata_validate.py
One improvement could be done related to the result format.

Currently it only export lines of plain text such as:

Validation failed at row 304:
Sample ID: studies/assays/processSequence/parameterValues/unit/REFERENCE to an @id at unitCategories
Expression: @id' in $.investigation.studies.assays.processSequence.parameterValues.unit.$keys()
Result: False

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Labels
enhancement New feature or request mars-cli
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