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Changelog.md

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CtTSO-ICA-To-PierianDx Changelog

Changes in this log refer only to changes that make it to the 'main' branch. and

For changes in deployment, please see the deployment changelog

2024-05-27

Author: Alexis Lucattini Email: [email protected]

Hotfix

  • Debug authentication issues (#229)

2024-05-06

Author: Alexis Lucattini Email: [email protected]

Documentation

  • Updated contribution guide (#218)

2024-02-24

Author: Alexis Lucattini Email: [email protected]

Hotfixes

  • Fix Run info xml regex, run info may also be named RunInfo.abc.xml (#211)

2023-11-27

Author: Alexis Lucattini Email: [email protected]

Hotfixes

  • Fix Run info xml regex, run info may also come from production/raw_data (#205)

2023-11-22

Author: Alexis Lucattini Email: [email protected]

Hotfixes

  • Fix deidentified samples where NAT instead of NaT null value was used (#198)

2023-11-08

Author: Alexis Lucattini Email: [email protected]

Enhancements

  • Build containers with ghcr.io (yet to move)
  • Dont build containers concurrently (#181)

Hotfixes

  • Quote label input when no disease id (#179)

2023-11-07

Author: Alexis Lucattini Email: [email protected]

Hotfixes

  • Update how is_identified column is processed as it can both be a string and a boolean value (#163)

2023-10-18

Author: Alexis Lucattini Email: [email protected]

Bugfixes

  • Update sample type trimming of _sample suffix (#150)
  • Update patient_care naming to patientcare (#156)

2023-10-18

Author: Alexis Lucattini Email: [email protected]

Enhancement

  • Add portal run id to sequencer run attribute of PierianDx Case Accession (#142)

  • Allow both sub_panel and subpanel as valid panel types (#143)

2023-07-10

Author: Alexis Lucattini Email: [email protected]

Bugfix

  • Re-raise ValueError after catching ValueError in .item() (#108)

2023-05-07

Author: Alexis Lucattini Email: [email protected]

Hotfix

Force pandas downgrade (#55)

2023-02-15

Author: Alexis Lucattini Email: [email protected]

Updates

  • Upgraded Docker container base image (#35)

2023-01-23

Author: Alexis Lucattini Email: [email protected]

Updates

  • Updated panel from VALIDATION, PATIENTCARE names to MAIN, SUBPANEL respectively (#19)
    • This change better reflects the flexibility between panel and sample types.
    • Some clinical samples or research samples may need to go through the main panel
    • We may also wish to test the subpanel with validation samples

2022-08-30

Author: Alexis Lucattini Email: [email protected]

Summary

  • Wrapped portal Run ID name collector in try-exception clause

    • Don't want workflow to break if we can't collect the run name
  • Added date handlers to be better accessible to times that aren't utc times

  • Use PIERIANDX_USER_AUTH_TOKEN env var instead of PIERIANDX_USER_PASSWORD

    • See deployment changes for more information
  • Added PanelType as an enum

    • Validation samples continue to go through "tso500_ctDNA_vcf_workflow_university_of_melbourne"
    • While clinical samples now go through "tso500_ctDNA_vcf_subpanel_workflow_university_of_melbourne"
  • Conda env

    • Updated to pyriandx 0.3.0 to allow for token usage
  • Readme

    • Swapped out password for auth_token in environment variables