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AlexsLemonade / refinebio

Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.
https://www.refine.bio/
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Follow redirect when downloading gene_indexes #3444

Closed davidsmejia closed 8 months ago

davidsmejia commented 8 months ago

Issue Number

3436

Purpose/Implementation Notes

NOTE: This PR encountered an error with isort that I could not reproduce locally. I saw that the repo we were using has recently changed so I am now targeting the branch that contains that fix. https://github.com/AlexsLemonade/refinebio/tree/davidsmejia/isort-upgrade-5.11.5

Running docker run -it ccdlstaging/dr_no_op ls -l /home/user/gene_indexes. Would give the correct output but rebuilding the container failed.

While testing out the code locally I noticed that curling the ID_REFINERY_URL was not downloading the indexes and the subsequent unzip command exit code 9.

This change tells curl to follow the redirect. Which then allows the no_op to build correctly.

This change invalidates the cache layer and makes the files available that were missing during the no_op tests.

Methods

n/a

Types of changes

Functional tests

List out the functional tests you've completed to verify your changes work locally.

Checklist

Screenshots

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davidsmejia commented 8 months ago

closing in favor of #3446