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tableschema-to-template

Description

The HuBMAP project will incorporate dozens of different assay types, each with its own metadata requirements. While validation at ingest time can prevent bad metadata from entering the system, that still requires the data submitter to read the error, open the original TSV, find the corresponding row and column, and make the fix.

We can avoid many data entry mistakes in the first place with input validation in Excel or Google Sheets. tableschema-to-template is a small tool, installable from Pypi, which takes a Table Schema as input, and returns an Excel template with embedded documentation and some basic validations. It can be used either as a command-line tool, or as a Python library.

Examples of output can be found in the HuBMAP ingest-validation-tools documentation: Each directory includes an Excel file generated for that assay type.

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GitHub

Funding