Optionally hide Alamut button and fixes

[4.38]

Added

• Option to hide Alamut button in the app config file

Fixed

• Library deprecation warning fixed (insert is deprecated. Use insert_one or insert_many instead)
• Update genes command will not trigger an update of database indices any more
• Missing resources in temporary downloading directory when updating genes using the command line
• Restore previous variant ACMG classification in a scrollable div
• Loading spinner not stopping after downloading PDF case reports and variant list export
• Add extra Alamut links higher up on variant pages
• Improve UX for phenotypes in case page
• Filter and export of STR variants
• Update look of variants page navigation buttons

Changed

Improved cancer case pages, new features and bugfixes

[4.37]

Added

• Highlight and show version number for RefSeq MANE transcripts.
• Added integration to a rerunner service for toggling reanalysis with updated pedigree information
• SpliceAI display and parsing from VEP CSQ
• Display matching tiered variants for cancer variants
• Display a loading icon (spinner) until the page loads completely
• Display filter badges in cancer variants list
• Update genes from pre-downloaded file resources
• On login, OS, browser version and screen size are saved anonymously to understand how users are using Scout
• API returning institutes data for a given user: /api/v1/institutes
• API returning case data for a given institute: /api/v1/institutes/<institute_id>/cases
• Added GMS and Lund university hospital logos to login page
• Made display of Swedac logo configurable
• Support for displaying custom images in case view
• Individual-specific HPO terms
• Optional alamut_key in institute settings for Alamut Plus software
• Case report API endpoint
• Tooltip in case explaining that genes with genome build different than case genome build will not be added to dynamic HPO panel.
• Add DeepVariant as a caller

Fixed

• Updated IGV to v2.8.5 to solve missing gene labels on some zoom levels
• Demo cancer case config file to load somatic SNVs and SVs only.
• Expand list of refseq trancripts in ClinVar submission form
• Renamed All SNVs and INDELs institute sidebar element to Search SNVs and INDELs and fixed its style.
• Add missing parameters to case load-config documentation
• Allow creating/editing gene panels and dynamic gene panels with genes present in genome build 38
• Bugfix broken Pytests
• Bulk dismissing variants error due to key conversion from string to integer
• Fix typo in index documentation
• Fixed crash in institute settings page if "collaborators" key is not set in database
• Don't stop Scout execution if LoqusDB call fails and print stacktrace to log
• Bug when case contains custom images with value None
• Bug introduced when fixing another bug in Scout-LoqusDB interaction
• Loading of OMIM diagnoses in Scout demo instance
• Remove the docker-compose with chanjo integration because it doesn't work yet.
• Fixed standard docker-compose with scout demo data and database
• Clinical variant assessments not present for pinned and causative variants on case page.
• MatchMaker matching one node at the time only
• Remove link from previously tiered variants badge in cancer variants page
• Typo in gene cell on cancer variants page
• Managed variants filter form

Changed

• Better naming for variants buttons on cancer track (somatic, germline). Also show cancer research button if available.
• Load case with missing panels in config files, but show warning.
• Changing the (Female, Male) symbols to (F/M) letters in individuals_table and case-sma.
• Print stacktrace if case load command fails
• Added sort icon and a pointer to the cursor to all tables with sortable fields
• Moved variant, gene and panel info from the basic pane to summary panel for all variants.
• Renamed Basics panel to Classify on variant page.
• Revamped Basics panel to a panel dedicated to classify variants
• Revamped the summary panel to be more compact.
• Added dedicated template for cancer variants
• Removed Gene models, Gene annotations and Conservation panels for cancer variants
• Reorganized the orders of panels for variant and cancer variant views
• Added dedicated variant quality panel and removed relevant panes
• A more compact case page
• Removed OMIM genes panel
• Make genes panel, pinned variants panel, causative variants panel and ClinVar panel scrollable on case page
• Update to Scilifelab's 2020 logo
• Update Gens URL to support Gens v2.0 format
• Refactor tests for parsing case configurations
• Updated links to HPO downloadable resources
• Managed variants filtering defaults to all variant categories
• Changing the (Kind) drop-down according to (Category) drop-down in Managed variant add variant
• Moved Gens button to individuals table
• Check resource files availability before starting updating OMIM diagnoses
• Fix typo in SHOW_OBSERVED_VARIANT_ARCHIVE config param

Splice junction track, menu size and research variant count fixes

[4.36]

Added

• Parse and save splice junction tracks from case config file
• Tooltip in observations panel, explaining that case variants with no link might be old variants, not uploaded after a case rerun

Fixed

• Warning on overwriting variants with same position was no longer shown
• Increase the height of the dropdowns to 425px
• More indices for the case table as it grows, specifically for causatives queries
• Splice junction tracks not centered over variant genes
• Total number of research variants count
• Update variants stats in case documents every time new variants are loaded
• Bug in flashing warning messages when filtering variants

Changed

• Clearer warning messages for genes and gene/gene-panels searches in variants filters

Cancer case page, STR formatting improved - and some fixes after previous release

[4.35]

Added

• A new index for hgnc_symbol in the hgnc_gene collection
• A Pedigree panel in STR page
• Display Tier I and II variants in case view causatives card for cancer cases

Fixed

• Send partial file data to igv.js when visualizing sashimi plots with splice junction tracks
• Research variants filtering by gene
• Do not attempt to populate annotations for not loaded pinned/causatives
• Add max-height to all dropdowns in filters

Changed

• Switch off non-clinical gene warnings when filtering research variants
• Don't display OMIM disease card in case view for cancer cases
• Refactored Individuals and Causative card in case view for cancer cases
• Update and style STR case report

Support for Flask2 and LoqusDB REST API. Fix HGNC symbol search bug and other fixes

[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

Standard inheritance models in Clinvar and other causatives crash fix

[4.33.1]

Fixed

• Include markdown for release autodeploy docs
• Use standard inheritance model in ClinVar (https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Mode_of_inheritance.txt)
• Fix issue crash with variants that have been unflagged causative not being available in other causatives

Filter cases and dashboard by track, IGV update

[4.33]

Fixed

• Command line crashing when updating an individual not found in database
• Dashboard page crashing when filters return no data
• Cancer variants filter by chromosome
• /api/v1/genes now searches for genes in all genome builds by default
• Upgraded igv.js to version 2.8.1 (Fixed Unparsable bed record error)

Added

• Autodeploy docs on release
• Documentation for updating case individuals tracks
• Filter cases and dashboard stats by analysis track

Changed

• Changed from deprecated db update method
• Pre-selected fields to run queries with in dashboard page
• Do not filter by any institute when first accessing the dashboard

Fix institute cases page crashing when a case has track:Null

[4.32.1]

Fixed

• iSort lint check only
• Institute cases page crashing when a case has track:Null

MITOMAP annotations support, Splice Junction Tracks and maintenance

[4.32]

Added

• Load and show MITOMAP associated diseases from VCF (INFO field: MitomapAssociatedDiseases, via HmtNote)
• Show variant allele frequencies for mitochondrial variants (GRCh38 cases)
• Extend "public" json API with diseases (OMIM) and phenotypes (HPO)
• HPO gene list download now has option for clinical and non-clinical genes
• Display gene splice junctions data in sashimi plots
• Update case individuals with splice junctions tracks
• Simple Docker compose for development with local build
• Make Phenomodels subpanels collapsible
• User side documentation of cytogenomics features (Gens, Chromograph, vcf2cytosure, rhocall)
• iSort GitHub Action

Fixed

• Show other causative once, even if several events point to it
• Filtering variants by mitochondrial chromosome for cases with genome build=38
• HPO gene search button triggers any warnings for clinical / non-existing genes also on first search
• Fixed a bug in variants pages caused by MT variants without alt_frequency
• Tests for CADD score parsing function
• Fixed the look of IGV settings on SNV variant page
• Cases analyzed once shown as rerun
• Missing case track on case re-upload
• Fixed severity rank for SO term "regulatory region ablation"

Changed

• Refactor according to CodeFactor - mostly reuse of duplicated code
• Phenomodels language adjustment
• Open variants in a new window (from variants page)
• Open overlapping and compound variants in a new window (from variant page)
• gnomAD link points to gnomAD v.3 (build GRCh38) for mitochondrial variants.
• Display only number of affected genes for dismissed SVs in general report
• Chromosome build check when populating the variants filter chromosome selection
• Display mitochondrial and rare diseases coverage report in cases with missing 'rare' track

Cancer-specific case reports and ClinVar form fix

[4.31.1]

Added

Changed

• Remove mitochondrial and coverage report from cancer cases sidebar

Fixed

• ClinVar page when dbSNP id is None