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Create subset CI files for v18 -- edition 2 #888

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Jan 5, 2021

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@cansavvy cansavvy commented Jan 5, 2021

Purpose/implementation Section

This PR is for creating the subset files for circle CI testing for v18 release.

This is the second edition of this PR due to some v18 changes that it turned out we didn't want in here quite yet. See #873 for more details on this.

I cherry picked the two commits noted on that PR discussion to this branch which was created from master.

This in addition to adding the updated pbta-histologies.tsv file from #879 will close #871

After I have the updated pbta-histologies.tsv file from 879 's changes I will re-run the create_subset_files.sh but use the SKIP_SUBSETTING=1 option so I can upload an updated md5sum.txt and pbta-histologies.tsv file to CI.

What was your approach?

This PR,

  • Adds copy over step for pbta-histologies-base.tsv file and changes the create-subset.sh to use v18
  • With those changes I ran this on AWS as described by v18 CI files #871 and then in I added biospecimen_ids_for_subset.RDS file here

What GitHub issue does your pull request address?

Closes #871

@cansavvy cansavvy changed the title Create subset CI files -- edition 2 Create subset CI files for v18 -- edition 2 Jan 5, 2021
@cansavvy cansavvy marked this pull request as ready for review January 5, 2021 15:22
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Changes LGTM

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cansavvy commented Jan 5, 2021

Testing files have been updated by me doing these steps: In a docker container for ccdlopenpbta/open-pbta:latest:

  1. I checked out jharenza:v18-files, downloaded the updated v18 data (with updated pbta-histologies.tsv).
  2. I checked out this branch.
  3. Ran create-subset-files.sh with SKIP_SUBSETTING=1
  4. I uploaded the new pbta-histologies.tsv and md5sum.txt that was placed in data/testing/release-v18-20201123 to the S3 openpbta/testing bucket. (deleted the old versions).

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I was waiting for CI to pass to merge to make sure there were no issues with the testing files. When #889 is resolved before v18, we'll need to update the testing files again but the code here will not change. I'm going to go ahead and merge this.

@jaclyn-taroni jaclyn-taroni merged commit be5e09f into AlexsLemonade:master Jan 5, 2021
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v18 CI files
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