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Case speed-up, load full RNA alignments, load previous causatives and upgrade pydantic
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@dnil dnil released this 18 Oct 16:29
· 1200 commits to main since this release
v4.72
47f0516
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Learn about vigilant mode.

[4.72]

Added

  • A GitHub action that checks for broken internal links in docs pages
  • Link validation settings in mkdocs.yml file
  • Load and display full RNA alignments on alignment viewer
  • Genome build check when loading a case
  • Extend event index to previous causative variants and always load them

Fixed

  • Documentation nav links for a few documents
  • Slightly extended the BioNano Genomics Access integration docs
  • Loading of SVs when VCF is missing the INFO.END field but has INFO.SVLEN field
  • Escape protein sequence name (if available) in case general report to render special characters correctly
  • CaseS HPO term searches for multiple terms works independent of order
  • CaseS search regexp should not allow backslash
  • CaseS cohort tags can contain whitespace and still match
  • Remove diagnoses from cases even if OMIM term is not found in the database
  • Parsing of disease-associated genes
  • Removed an annoying warning while updating database's disease terms
  • Displaying custom case images loaded with scout version <= 4.71
  • Use pydantic version >=2 in requirements.txt file

Changed

  • Column width adjustment on caseS page
  • Use Python 3.11 in tests
  • Update some github actions
  • Upgraded Pydantic to version 2
  • Case validation fails on loading when associated files (alignments, VCFs and reports) are not present on disk
  • Case validation fails on loading when custom images have format different then ["gif", "svg", "png", "jpg", "jpeg"]
  • Custom images keys case and str in case config yaml file are renamed to case_images and str_variants_images
  • Simplify and speed up case general report code
  • Speed up case retrieval in case_matching_causatives
  • Upgrade pymongo to version 4
  • When updating disease terms, check that all terms are consistent with a DiseaseTerm model before dropping the old collection
  • Better separation between modules loading HPO terms and diseases
  • Deleted unused scout.build.phenotype module
  • Stricter validation of mandatory genome build key when loading a case. Allowed values are ['37','38',37,38]
  • Improved readability of variants length and coordinates on variantS pages
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