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Sage-Bionetworks / cleanAD

Tools for cleaning and organizing study data for the AD Knowledge Portal.
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cleanAD package + specimen table script and functions #7

Closed Aryllen closed 3 years ago

Aryllen commented 3 years ago

Here it is, @avanlinden! It's a bit messy still. Not everything is tested, but I did add tests for some of the most important parts.

The script for generating the specimen table is in inst/scripts. I still need to test it on the server from the CLI; I've only tested by running each piece myself. Will update when I do.

I have updated the specimen table with the latest version of what I got from this script, as well. This gets rid of the missing IDs on ROSMAP methylationArray specimens.

Aryllen commented 3 years ago

Update: Currently creating a docker image and testing the script for automation. There's been a couple bugs so far that were missed when testing this in the RStudio instance.

Aryllen commented 3 years ago

Thank you for checking it out, @avanlinden! I appreciate it!

I just finally got a docker for it working, as well. Just need to get the details worked out for starting it on a CRON, then I'll add it here and merge (unless other errors are found in the meantime).

Aryllen commented 3 years ago

More updates have been done to improve running from command line, such as adding a config file. It's been tested, again. Merging so that I can create a docker image to run the job in.