Clinical-Genomics / statina

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• add-filtering-on-dataset-for-plots
• add-link-to-new-ui
• add-middleware
• add-ratio-warnings
• analysis-archive
• auth
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• colors
• content-header-allowed
• coverage-fix
• datasets
• edit-warning-message-about-new-ui
• email-exception
• enable-deployments
• feat-dataset-collection
• ffy-plot
• filter
• filter-ffx-datasets
• filter-with-dataset-on-ratio-plot
• fix-batch-delete
• fix-bump2version
• fix-crid
• fix-filenames-download
• fix-pydantic-imports
• hard-thresholds
• include-multiple-batch-zip
• included-fix
• integration-branch-novaseqx
• lower-pf-threshold
• master
• nr_batches
• parse-data-set
• patch-ratio-chr-1-22-plot
• patch-signing-in
• patch-sort-in-samples-endpoint
• plot-bug
• ratio-plot
• reduce-number-of-decimals
• refactor-load
• remove-trailing-slash
• report-bug
• revert-unversiond-endpoints
• round
• sample-query-batch-id
• sample-status
• scope-exception
• sex-threshold
• sort-direction
• text-search
• token-verbose
• treshold
• uncorrected-ratio-plots
• update-sample-endpoint-return-ratio-13-18-21
• update_codeowners
• v2
• v2-migration
• validate-email-move

Build # 24555280404

Build Type

push

github

Committed by web-flow

Commit Message

Integration branch for NovaSeqX changes (#250) (major)

### Added

  - Dataset-based filtering for fetal fraction XY and ratio plots — control samples and abnormal classifications are now scoped to the same dataset as the batch being viewed
  - New ratio plot endpoint (/v2/batch/{batch_id}/ratio) with box plots of uncorrected ratios
  - FFY plot endpoint
  - Ratio warnings in plot responses
  - Chr13_Ratio, Chr18_Ratio, and Chr21_Ratio fields in the /v2/sample/ response body
  - Dataset field parsed and stored from the batch request

### Changed

  - Locked passlib and bcrypt versions — bcrypt 4.1.0 removed the about submodule that passlib relies on to detect the backend, causing a runtime error

### Fixed

  - Reduced number of decimals in plot responses
  - Patched Ratio (Chromosomes 1–22) calculation
  - Patched login issue

---------

Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@users.noreply.github.com>
Co-authored-by: islean <isak.ohlsson.angnell@gmail.com>

Coverage Stats

49 of 77 new or added lines in 13 files covered. (63.64%)

160 existing lines in 8 files now uncovered.

1083 of 1741 relevant lines covered (62.21%)

0.62 hits per line