Adding functionality to skip checksum validation through environment variables. The checksum generation gets long in runtime for very large files so adding the option to skip checksum validation as needed.
Test Results
Tested with pytest with added tests
Checklist
File Commits
[X] 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 problem[^1] - Even a small leak can be costly[^2].
[X] This PR does NOT contain germline genetic data[^3], RNA-Seq, DNA methylation, microbiome or other molecular data[^4].
[X] 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.
[X] I have set up or verified the main branch protection rule following the github standards before opening this pull request.
[X] 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].
[X] 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.
Testing
[X] I have added unit tests for the new feature(s).
[ ] I modified the integration test(s) to include the new feature.
[X] All new and previously existing tests passed locally and/or on the cluster.
[X] The docker image built successfully on the cluster.
Description
Adding functionality to skip checksum validation through environment variables. The checksum generation gets long in runtime for very large files so adding the option to skip checksum validation as needed.
Test Results
Tested with pytest with added tests
Checklist
File Commits
[X] 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 problem[^1] - Even a small leak can be costly[^2].
[X] This PR does NOT contain germline genetic data[^3], RNA-Seq, DNA methylation, microbiome or other molecular data[^4].
[^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.
.png, .jpeg),.pdf,.RData,.xlsx,.doc,.ppt, or other output files.To automatically exclude such files using a .gitignore file, see here for example.
Code Review Best Practices
[X] I have read the code review guidelines and the code review best practice on GitHub check-list.
[X] I have set up or verified the
mainbranch protection rule following the github standards before opening this pull request.[X] 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].
[X] I have added the major changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.Testing
[X] I have added unit tests for the new feature(s).
[ ] I modified the integration test(s) to include the new feature.
[X] All new and previously existing tests passed locally and/or on the cluster.
[X] The docker image built successfully on the cluster.