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PNNL-CompBio / srpAnalytics

This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.
MIT License
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Update database schema to YAML/linkML (from json) and dockerize validation process #40

Open sgosline opened 2 years ago

sgosline commented 2 years ago

We should have the descriptions in the json file to describe each field. These will be populated in the excel spreadsheets.

sgosline commented 2 years ago

Added these to newer JSONs, but need to harmonize schema files. will work on this soon.

sgosline commented 2 months ago

we need to update the json files to YAML/linkML and build a docker container to validate any incoming tables - both those pre and post processing

sgosline commented 2 months ago

More detail: current DB schema is encoded in json files: https://github.com/PNNL-CompBio/srpAnalytics/tree/main/dbSchema

  1. we need to move this to a single linkML file (https://linkml.io/linkml/schemas/)
  2. we need to write a docker container that uses the linkml python package to validate any incoming files
  3. add validation docker call to github automation