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elixir-europe / MARS

Multi-Repository Data Submission using ISA-JSON
MIT License
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Implementation of JSONata for secondary validation #51

Open kdp-cloud opened 1 month ago

kdp-cloud commented 1 month ago

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

xiaoranzhou commented 1 month ago

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