Changelog.md

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: Alexis.Lucattini@umccr.org

Hotfix

• Debug authentication issues (#229)

2024-05-06

Author: Alexis Lucattini Email: Alexis.Lucattini@umccr.org

Documentation

• Updated contribution guide (#218)

2024-02-24

Author: Alexis Lucattini Email: Alexis.Lucattini@umccr.org

Hotfixes

• Fix Run info xml regex, run info may also be named RunInfo.abc.xml (#211)
  • Resolves #210

2023-11-27

Author: Alexis Lucattini Email: Alexis.Lucattini@umccr.org

Hotfixes

• Fix Run info xml regex, run info may also come from production/raw_data (#205)
  • Resolves #204

2023-11-22

Author: Alexis Lucattini Email: Alexis.Lucattini@umccr.org

Hotfixes

• Fix deidentified samples where NAT instead of NaT null value was used (#198)
  • Resolves #197

2023-11-08

Author: Alexis Lucattini Email: Alexis.Lucattini@umccr.org

Enhancements

• Build containers with ghcr.io (yet to move)
• Dont build containers concurrently (#181)
  • Resolves #180

Hotfixes

• Quote label input when no disease id (#179)
  • Resolves #176

2023-11-07

Author: Alexis Lucattini Email: Alexis.Lucattini@umccr.org

Hotfixes

• Update how is_identified column is processed as it can both be a string and a boolean value (#163)
  • Resolves #162

2023-10-18

Author: Alexis Lucattini Email: Alexis.Lucattini@umccr.org

Bugfixes

• Update sample type trimming of _sample suffix (#150)
  • Resolves #149
• Update patient_care naming to patientcare (#156)
  • Resolves #155

2023-10-18

Author: Alexis Lucattini Email: Alexis.Lucattini@ummcr.org

Enhancement

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

  • Resolves #130

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

  • Resolves #139

2023-07-10

Author: Alexis Lucattini Email: Alexis.Lucattini@ummcr.org

Bugfix

• Re-raise ValueError after catching ValueError in .item() (#108)
  • Resolves #97
  • Resolves #98

2023-05-07

Author: Alexis Lucattini Email: Alexis.Lucattini@ummcr.org

Hotfix

Force pandas downgrade (#55)

• Fixes #54

2023-02-15

Author: Alexis Lucattini Email: Alexis.Lucattini@ummcr.org

Updates

• Upgraded Docker container base image (#35)
  • Fixes (#33)

2023-01-23

Author: Alexis Lucattini Email: Alexis.Lucattini@ummcr.org

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: Alexis.Lucattini@umccr.org

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