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Update to using current CI/CD image #41

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merged 4 commits into from
Sep 19, 2023
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Description

This just updates the CI/CD action to use the current version of the image (docker://ghcr.io/uclahs-cds/cicd-base:latest) rather than the one available from the old image store (docker://blcdsdockerregistry/cicd-base:latest).

Checklist

  • This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
    Disclosing PHI is a major problem1 - Even a small leak can be costly2.

  • This PR does NOT contain germline genetic data3, RNA-Seq, DNA methylation, microbiome or other molecular data4.

  • This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

  • I have read the code review guidelines and the code review best practice on GitHub check-list.

  • I have set up or verified the main branch protection rule following the github standards before opening this pull request.

  • The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

  • I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Footnotes

  1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records

  2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records.

  3. Genetic information is considered PHI.
    Forensic assays can identify patients with as few as 21 SNPs

  4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity.

@nwiltsie nwiltsie requested a review from a team September 11, 2023 18:27
@nwiltsie
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The only substantive changes here are:

  • Copying over the .pylintrc from the new CI/CD image and modifying a single line in that file (4e7e720)
  • Changing a for-loop to a join-statement:
    if self.nf_configs:
    config_arg = '-c ' + ' -c '.join(self.nf_configs)

@nwiltsie nwiltsie merged commit beb8dfa into main Sep 19, 2023
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@nwiltsie nwiltsie deleted the nwiltsie_upgrade_image branch September 19, 2023 15:52
This pull request was closed.
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2 participants