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Published May 19, 2021 | Version v4.34
Software Open

Clinical-Genomics/scout: Support Flask2 and LoqusDB REST API. Fix HGNC symbol search bug and other fixes

Authors/Creators

  • 1. Clinical Genomics, Science for Life Laboratory,
  • 2. Science for Life Labs
  • 3. @hedviginsurance
  • 4. @Clinical-Genomics
  • 5. Karolinska Institutet, Genomic Medicine Sweden
  • 6. Unemployed for the moment
  • 7. SciLifeLab, @Clinical-Genomics

Description

[4.34] Added
  • Saved filter lock and unlock
  • Filters can optionally be marked audited, logging the filter name, user and date on the case events and general report.
  • Added ClinVar hits and Cosmic hits in cancer SNVs filters
  • Added ClinVar hits to variants filter (rare disease track)
  • Load cancer demo case in docker-compose files (default and demo file)
  • Inclusive-language check using woke github action
  • Add link to HmtVar for mitochondrial variants (if VCF is annotated with HmtNote)
  • Grey background for dismissed compounds in variants list and variant page
  • Pin badge for pinned compounds in variants list and variant page
  • Support LoqusDB REST API queries
  • Add a docker-compose-matchmaker under scout/containers/development to test matchmaker locally
  • Script to investigate consequences of symbol search bug
  • Added GATK to list of SV and cancer SV callers ### Fixed
  • Make MitoMap link work for hg38 again
  • Export Variants feature crashing when one of the variants has no primary transcripts
  • Redirect to last visited variantS page when dismissing variants from variants list
  • Improved matching of SVs Loqus occurrences in other cases
  • Remove padding from the list inside (Matching causatives from other cases) panel
  • Pass None to get_app function in CLI base since passing script_info to app factory functions was deprecated in Flask 2.0
  • Fixed failing tests due to Flask update to version 2.0
  • Speed up user events view
  • Causative view sort out of memory error
  • Use hgnc_id for gene filter query
  • Typo in case controllers displaying an error every time a patient is matched against external MatchMaker nodes
  • Do not crash while attempting an update for variant documents that are too big (> 16 MB)
  • Old STR causatives (and other variants) may not have HGNC symbols - fix sort lambda
  • Check if gene_obj has primary_transcript before trying to access it
  • Warn if a gene manually searched is in a clinical panel with an outdated name when filtering variants
  • ChrPos split js not needed on STR page yet ### Changed
  • Remove parsing of case genome_version, since it's not used anywhere downstream
  • Introduce deprecation warning for Loqus configs that are not dictionaries
  • SV clinical filter no longer filters out sub 100 nt variants
  • Count cases in LoqusDB by variant type
  • Commit pulse repo badge temporarily set to weekly
  • Sort ClinVar submissions objects by ascending "Last evaluated" date
  • Refactored the MatchMaker integration as an extension
  • Replaced some sensitive words as suggested by woke linter
  • Documentation for load-configuration rewritten.
  • Add styles to MatchMaker matches table
  • More detailed info on the data shared in MatchMaker submission form

Files

Clinical-Genomics/scout-v4.34.zip

Files (15.2 MB)

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md5:5eeffe186024f7e6f5bbd82528a5737a
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Additional details

Related works

Is supplement to
https://github.com/Clinical-Genomics/scout/tree/v4.34 (URL)