Fixed crashing MT report and missing pedigree images

[4.94.1]

Fixed

• Temporary directory generation for MT reports and pedigree files to avoid pages crashing

Case report ACMG VUS temperature, export cases list, and new build system

[4.94]

Added

• Max-level provenance and Software Bill Of Materials (SBOM) to the Docker images pushed to Docker Hub
• ACMG VUS Bayesian score / temperature on case reports
• Button to filter and download case individuals/samples from institute's caseS page

Changed

• On variant page, RefSeq transcripts panel, truncate very long protein change descriptions
• Build system changed to uv/hatchling, remove setuptools, version file, add project toml and associated files
• On variantS pages, display chromosome directly on start and end chromosome if different
• On cancer variantS pages, display allele counts and frequency the same way for SNVs and SVs (refactor macro)
• Stricter coordinate check in BND variants queries (affecting search results on SV variants page)

Fixed

• UCSC hg38 links are updated
• Variants page tooltip errors
• Cancer variantS page had poor visibility of VAF and chromosome coordinate on causatives (green background)

What's Changed

• Fix #5111 - pypi build action with explicit setuptools by @dnil in #5113
• Version 4.93.1 - patch release by @dnil in #5114
• Fix UCSC hg38 link by @dnil in #5119
• Truncate protein change descriptions on variant page, RefSeq transcripts panel by @northwestwitch in #5121
• Add max-level provenance and SBOM to the images pushed to Docker Hub by @northwestwitch in #5122
• Add ACMG VUS Bayesian score / temperature on case reports by @northwestwitch in #5120
• Fix #5053 - project toml, uv/hatchling settings by @dnil in #5124
• Fix tooltips on variants not overlapping with any gene panels by @northwestwitch in #5131
• Fix #5128 - visibility of muted vaf counts, position on cancer variantS by @dnil in #5132
• Fix #5129 - show chromosome on each BND end if diffent by @dnil in #5136
• Download institute samples by @northwestwitch in #5125
• Refactor and follow up on #5128 fix also for SVs by @dnil in #5138
• Add complexity to SV queries when SV is BND by @northwestwitch in #5137
• Remove obsolete version file by @dnil in #5141
• Minor release 4.94 by @northwestwitch in #5140

Full Changelog: v4.93...v4.94

Fix PyPi build action

[4.93.1]

Fixed

• Updated PyPi build GitHub action to explicitly include setuptools (for Python 3.12 distro)

ClinGen-CGC-VICC oncogenicity classification and updated Docker base images

Also note that chanjo and chanjo-report releases are available to support new Docker builds.

[4.93]

Added

• ClinGen-CGC-VICC oncogenicity classification for cancer SNVs
• A warning to not to post sensitive or personal info when opening an issue

Changed

• "Show more/less" button to toggle showing 50 observed cases in LoqusDB observation panel
• Show customer id on share and revoke sharing case collapsible sidebar dialog
• Switch to python v.3.12 in Dockerfiles and automatic tests

Fixed

• Limit the size of custom images displayed on case and variant page and add a link to display them in full size in a new tab
• Classified variants not showing on case report when collaborator adds classification
• On variantS page, when a variant has more than one gene, then the gene panel badge reflect the panels each gene is actually in
• Updating genes on a gene panel using a file
• Link out to Horak 2020 from CCV classify page opens in new tab

What's Changed

• Contain custom image size and add a link to show them full size in another tab by @northwestwitch in #5093
• Clingen-CGC-VICC oncogenicity classification by @molucorner in #5069
• Fix missing classifications in case report by @northwestwitch in #5096
• Expand observation number by @Jakob37 in #5092
• Add a warning to not to post sensitive info on issues by @northwestwitch in #5098
• Fix #5102 - customer id in sharing dialog by @dnil in #5103
• Fix multigene panels count by @northwestwitch in #5097
• Fix updating gene panels via file by @northwestwitch in #5105
• Switch to Python 3.12 in Dockerfiles and automatic tests by @northwestwitch in #5107
• Fix #5109 - CCV Horak link in new window by @dnil in #5110
• Minor release 4.93 by @northwestwitch in #5108

New Contributors

• @molucorner made their first contribution in #5069

Full Changelog: v4.92...v4.93

Delete command options and PanelApp links

[4.92]

Added

• PanelApp link on gene page and on gene panels description

Changed

• Add more filters to the delete variants command (institute ID and text file with list of case IDs)
• Use the clinicalgenomics/python3.11-venv:1.0 image everywhere in the Dockerfiles

Fixed

• list/List typing issue on PanelApp extension module

Variant parsing fixes and gene panels page improvements

[4.91.2]

Fixed

• Stranger TRGT parsing of . in FORMAT.MC
• Parse ClinVar low-penetrance info and display it alongside Pathogenic and likely pathogenic on SNVs pages
• Gene panel indexes to reflect the indexes used in production database
• Panel version check while editing the genes of a panel
• Display unknown filter tags as "danger" marked badges
• Open WTS variantS SNVs and SVs in new tabs
• PanelApp panels update documentation to reflect the latest changes in the command line
• Display panel IDs alongside panel display names on gene panels page
• Just one Hide removed panels checkbox for all panels on gene panels page
• Variant filters redecoration from multiple classifications crash on general case report

Structural variantS header fix and IGV.js v3.1.0

[4.91.1]

Fixed

• Update IGV.js to v3.1.0
• Columns/headings on SV variantS shifted

v4.91 - PanelApp extension, Dashboard advanced search, fixing ClinVar conflicting classifications and more

This release notably contains

• A new PanelApp extension, using the newer PanelApp API, allows more control building PanelApp "Green" aggregate panels.
• The Dashboard statistics now also uses the advanced caseS search.
• ClinVar category 8 had changed to "Conflicting classifications of pathogenicity" instead of "interpretations", causing many conflicting classifications to be presented as CLNSIG "other" on the variantS page. This is fixed for new cases.
• Some fixes related to the Balsamic 16 release, e.g. prioritising FORMAT.AF over AD for VAF and more accessible display of variant caller on variantS pages.
• Some LRS related fixes to variant export, and alignment display (IGV v3.0.9).
• Some fixes to ClinVar submission support.

A special thank you to contributors @molucorner (for Franklin links) and @Jakob37 (for WTS Outlier coordinate copy buttons)!

[4.91]

Added

• Variant link to Franklin in database buttons (different depending on rare or cancer track)
• MANE badges on list of variant's Genes/Transcripts/Proteins table, this way also SVs will display MANE annotations
• Export variant type and callers-related info fields when exporting variants from variantS pages
• Cases advanced search on the dashboard page
• Possibility to use only signed off panels when building the PanelApp GREEN panel

Changed

• On genes panel page and gene panel PDF export, it's more evident which genes were newly introduced into the panel
• WTS outlier position copy button on WTS outliers page
• Update IGV.js to v3.0.9
• Managed variants VCF export more verbose on SVs
• /api/v1/hpo-terms returns pymongo OperationFailure errors when provided query string contains problematic characters
• When parsing variants, prioritise caller AF if set in FORMAT over recalculation from AD
• Expand the submissions information section on the ClinVar submissions page to fully display long text entries
• Jarvik et al for PP1 added to ACMG modification guidelines
• Display institute _id + display name on dashboard filters
• ClinVar category 8 has changed to "Conflicting classifications of pathogenicity" instead of "interpretations"
• Simplify always loading ClinVar CLNSIG P, LP and conflicting annotations slightly
• Increased visibility of variant callers's "Pass" or "Filtered" on the following pages: SNV variants (cancer cases), SV variants (both RD and cancer cases)
• Names on IGV buttons, including an overview level IGV MT button
• Cases query no longer accepts strings for the name_query parameter, only ImmutableMultiDict (form data)
• Refactor the loading of PanelApp panels to use the maintained API - Customised PanelApp GREEN panels
• Better layout for Consequence cell on cancer SNVs page
• Merged Qual and Callers cell on cancer SNVs page

Fixed

• Empty custom_images dicts in case load config do not crash
• Tracks missing alignment files are skipped on generating IGV views
• ClinVar form to accept MedGen phenotypes
• Cancer SV variantS page spinner on variant export
• STRs variants export (do not allow null estimated variant size and repeat locus ID)
• STRs variants page when one or more variants have SweGen mean frequency but lack Short Tandem Repeat motif count
• ClinVar submission enquiry status for all submissions after the latest
• CLI scout update type hint error when running commands using Python 3.9
• Missing alignment files but present index files could crash the function creating alignment tracks for IGV display
• Fix missing "Repeat locus" info on STRs export

What's Changed

• On genes panel page, make more evident which genes are new after the panel is updated by @northwestwitch in #4957
• Fix #4970 - empty custom images dict does not crash on load by @dnil in #4971
• Fix #4974 - crash on missing aln file for one of the inds by @dnil in #4975
• WTS outlier copy to clipboard by @Jakob37 in #4981
• Fix #4977 - update IGV.js to 3.0.9 by @dnil in #4978
• Fix #4969 - adress the VCF output of given managed variants by @dnil in #4973
• /api/v1/hpo-terms handles pymongo OperationFailure errors by @northwestwitch in #4984
• Triallelic cancer VAF by @dnil in #4994
• Fix ClinVar form to accept MedGen phenotypes by @northwestwitch in #4998
• Expand ClinVar submission description section to display full info by @northwestwitch in #5000
• add form validate for cancer svs by @dnil in #5014
• Fix STRs variant export by @northwestwitch in #5015
• Fix #5001 - Jarvik for ACMG PP1 modification by @dnil in #5010
• Add MANE badges to the long list of transcripts on variant page by @northwestwitch in #5009
• Display institute _id + display name on dashboard filters by @northwestwitch in #5019
• Fix #5017 - ClinVar classifications of pathogenicity by @dnil in #5020
• Increased visibility of variant callers's "Pass" or "Filtered" on SNVs and SVs variants pages (both RD and cancer variants) by @northwestwitch in #5016
• Fix broken ClinVar submission status enquiry for all submissions after the latest by @northwestwitch in #5022
• Missing track item pt2 by @dnil in #5027
• Fix #4958 - IGV button names and IGV MT overview link by @dnil in #4976
• Advanced cases search on dashboard page by @northwestwitch in #4985
• Fix #5017 pt2 - swings and merry-go-rounds by @dnil in #5028
• Fix typing error when using python 3.9 by @northwestwitch in #5033
• Fix STRs export - part 2 by @northwestwitch in #5035
• Refactor PanelApp panels loading to use the correct PanelApp API by @northwestwitch in #5025
• Better layout for Consequence cell in cancer SNVs page by @northwestwitch in #5040
• Fix STRs variants view by @northwestwitch in #5038
• Franklin variant link by @dnil in #5041
• Fix missing track round3 by @northwestwitch in #5050
• Merge Qual and Callers cell on cancer SNVs page by @northwestwitch in #5045
• Fix missing repeat locus info on STRs export by @northwestwitch in #5052
• Minor release 4.91 by @northwestwitch in #5024

Full Changelog: v4.90.1...v4.91

Fixed parsing of Matchmaker Exchange's matches dates causing matchings page to crash

[4.90.1]

Fixed

• Parsing Matchmaker Exchange's matches dates

ACMG classification improvements, gene panels import/export fixes and more

[4.90]

Added

• Link to chanjo2 MANE coverage overview on case page and panel page
• More SVI recommendation links on the ACMG page
• IGV buttons for SMN CN page
• Warnings on ACMG classifications for potentially conflicting classification pairs
• ACMG Bayesian foundation point scale after Tavtigian for variant heat profile

Changed

• Variants query backend allows rank_score filtering
• Added script to tabulate causatives clinical filter rank
• Do not display inheritance models associated to ORPHA terms on variant page
• Moved edit and delete buttons close to gene names on gene panel page and other aesthetical fixes
• SNV VariantS page functional annotation and region annotation columns merged
• VariantS pages (not cancer) gene cells show OMIM inheritance pattern badges also without hover
• STR variantS page to show STR inheritance model without hover (fallback to OMIM for non-Stranger annotation)
• VariantS page local observation badges have counts visible also without hover
• On Matchmaker page, show number of matches together with matching attempt date
• Display all custom inheritance models, both standard and non-standard, as gathered from the gene panel information on the variant page

Fixed

• Make BA1 fully stand-alone to Benign prediction
• Modifying Benign terms to "Moderate" has no effect under Richards. Ignored completely before, will retain unmodified significance now
• Extract all fields correctly when exporting a panel to file from gene panel page
• Custom updates to a gene in a panel
• Gene panel PDF export, including gene links
• Cancer SV, Fusion, MEI and Outlier filters are shown on the Institute Filters overview
• CaseS advanced search limit
• Visibility of Matchmaker Exchange matches on dark mode
• When creating a new gene panel from file, all gene fields are saved, including comments and manual inheritance models
• Downloading on gene names from EBI
• Links to gene panels on variant page, summary panel
• Exporting gene variants when one or more variants' genes are missing HGNC symbol