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Patch that fixes several bugs in metadata validation and submission #244

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merged 8 commits into from
Jan 6, 2025

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jessicarowell
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Description

  1. Fix typo in nf-schema (to a liftoff param name)
  2. Fill in vadr_models param in nextflow.config/test config (this needs to be addressed later)
  3. Fix metadata validation to accept any valid string for populate_fields() function
  4. Make Title optional in BioSample submission xml
  5. Make fasta-file optional in update_submission module (if not gb, not required)
  6. Fix submission python script to check for GB flag in update_submission fx

Checklist

Go Through Checklist Below and Place A ✔️ (X Inside the Box) if Completed

General Checks

  • [] Have you run appropriate tests (unit/integration/end-to-end) to check logic across run environments (Conda/Docker/Singularity on Scicomp/AWS/NF Tower/Local)?

Only tested on SciComp

  • Have you conducted proper linting procedures?

    • Numpy formatted docstrings for functions
    • Comments explaining lines of code
    • Consistent and intuitive naming conventions for variables, functions, classes, methods, attributes, and scripts
    • Single empty line between class functions, two lines between non-class functions, and two lines between imports and code body
    • Camel case formatting for class names
  • Have you updated existing documentation (README.md, etc.) or created new ones within docs?

No updates needed

CDC Checks

  • Did you check for sensitive data, and remove any?
  • If you added or modified HTML, did you check that it was 508 compliant?

Are additional approvals needed for this change? If so, please mention them below:

Are there potential vulnerabilities or licensing issues with any new dependencies introduced? If so, please mention them below:

@jessicarowell jessicarowell self-assigned this Jan 6, 2025
@jessicarowell jessicarowell linked an issue Jan 6, 2025 that may be closed by this pull request
@kyleoconnell kyleoconnell merged commit 3fc1971 into dev Jan 6, 2025
1 check failed
@kyleoconnell kyleoconnell deleted the ick4-dev-patch branch January 6, 2025 17:25
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