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cidgoh / DataHarmonizer

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
MIT License
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WIP Linkml data structure version #228

Closed ddooley closed 2 years ago

ddooley commented 3 years ago

This is a version of DataHarmonizer that works directly off of LinkML schema files. Test file is in root folder called linkml.html (rather than usual main.html)

cmungall commented 2 years ago

@ddooley - is the intent to keep this PR in perpetuity, or can we have a strategy / rough timeline for merging

of course, you need to maintain compatibility with existing installations that use the tsv as Source of Truth, but isn't the approach here to add an adapter to be able to still read in the tsv?

ddooley commented 2 years ago

Yes, I'm just getting to the point where I can write an adaptor to convert the data.tsv into schema.js , and as well convert the existing customization scripts in export.js for a few of the templates, and then the linkml datastructure branch will be merged into master, to become master.

Earlier I was thinking maybe we'd have to fork this branch into a new github repo, but I think its better to face the challenge of adapting any existing DH installation use to work with the linkml branch so that our code dev is always focused on one repo.

ddooley commented 2 years ago

Just about to merge WIP validation into this, and this into master, likely today!