Case speed-up, load full RNA alignments, load previous causatives and upgrade pydantic

[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

BioNano FSHD reports added, fix some issues and prepare for Balsamic v13 annotations and filtering

[4.71]

Added

• Added Balsamic keys for SweGen and loqusdb local archive frequecies, SNV and SV
• New filter option for Cancer variantS: local archive RD loqusdb
• Show annotated observations on SV variantS view, also for cancer somatic SVs
• Revel filter for variantS
• Show case default panel on caseS page
• CADD filter for Cancer Somatic SNV variantS - show score
• SpliceAI-lookup link (BROAD, shows SpliceAI and Pangolin) from variant page
• BioNano Access server API - check projects, samples and fetch FSHD reports

Fixed

• Name of reference genome build for RNA for compatibility with IGV locus search change
• Howto to run the Docker image on Mac computers in admin-guide/containers/container-deploy.md
• Link to Weasyprint installation howto in README file
• Avoid filling up disk by creating a reduced VCF file for every variant that is visualized
• Remove legacy incorrectly formatted CODEOWNERS file
• Restrain variant_type requests to variantS views to "clinical" or "research"
• Visualization of cancer variants where cancer case has no affected individual
• ProteinPaint gene link (small StJude API change)
• Causative MEI variant link on causatives page
• Bionano access api settings commented out by default in Scout demo config file.
• Do not show FSHD button on freshly loaded cases without bionano_access individuals

Changed

• Remove function call that tracks users' browser version
• Include three more splice variant SO terms in clinical filter severe SO terms
• Drop old HPO term collection only after parsing and validation of new terms completes
• Move score to own column on Cancer Somatic SNV variantS page
• Refactored a few complex case operations, breaking out sub functionalities

Download gene variants, PubMed gene symbol link and bugfixes

[4.70]

Added

• Download a list of Gene Variants (max 500) resulting from SNVs and Indels search
• Variant PubMed link to search for gene symbol and any aliases

Changed

• Clearer gnomAD values in Variants page

Fixed

• CaseS page uniform column widths
• Include ClinVar variants into a scrollable div element on Case page
• canonical_transcript variable not initialized in get_hgvs function (server.blueprints.institutes.controllers.py)
• Catch and display any error while importing Phenopacket info
• Modified Docker files to use python:3.8-slim-bullseye to prevent gunicorn workers booting error

Somatic SV filter update, ClinVar submitter role, IGV and MEI fixes

[4.69]

Added

• ClinVar submission howto available also on Case page
• Somatic score and filtering for somatic SV callers, if available
• Show caller as a tooltip on variantS list

Fixed

• Crash when attempting to export phenotype from a case that had never had phenotypes
• Aesthetic fix to Causative and Pinned Variants on Case page
• Structural inconsistency for ClinVar Blueprint templates
• Updated igv.js to 2.15.8 to fix track default color bug
• Fixed release versions for actions.
• Freeze tornado below 6.3.0 for compatibility with livereload 2.6.3
• Force update variants count on case re-upload
• IGV locus search not working - add genome reference id
• Pin links to MEI variants should end up on MEI not SV variant view
• Load also matching MEI variants on forced region load
• Allow excluding MEI from case variant deletion
• Fixed the name of the assigned user when the internal user ID is different from the user email address
• Gene variantS should display gene function, region and full hgvs

Changed

• FontAwesome integrity check fail (updated resource)
• Removed ClinVar API validation buttons in favour of direct API submission
• Improved layout of Institute settings page
• ClinVar API key and allowed submitters are set in the Institute settings page

Rare Disease Mobile Element Insertions view & fixes

[4.68]

Added

• Rare Disease Mobile Element Insertion variants view

Changed

• Updated igv.js to 2.15.6

Fixed

• Docker stage build pycairo.
• Restore SNV and SV rank models versions on Causatives and Verified pages
• Saving REVEL_RANKSCORE value in a field named revel in variants database documents

Speedups and Clinical SV filter change

[4.67]

Added

• Prepare to filter local SV frequency

Changed

• Speed up instituteS page loading by refactoring cases/institutes query
• Clinical Filter for SVs includes splice_polypyrimidine_tract_variant as a severe consequence
• Clinical Filter for SVs includes local variant frequency freeze ("old") for filtering, starting at 30 counts
• Speed up caseS page loading by adding status to index and refactoring totals count
• HPO file parsing is updated to reflect that HPO have changed a few downloadable file formats with their 230405 release.

Fixed

• Page crashing when a user tries to edit a comment that was removed
• Warning instead of crashed page when attempting to retrieve a non-existent Phenopacket
• Fixed StJude ProteinPaint gene link (URL change)
• Freeze of werkzeug library to version<2.3 to avoid problems resulting from the consequential upgrade of the Flask lib
• Huge list of genes in case report for megabases-long structural variants.
• Fix displaying institutes without associated cases on institutes page
• Fix default panel selection on SVs in cancer case report

Somatic general report pin table, default panel filter matching variants and Phenomodels refactor

[4.66]

Changed

• Moved Phenomodels code under a dedicated blueprint
• Updated the instructions to load custom case report under admin guide

Added

• A summary table of pinned variants on the cancer case general report
• New openable matching causatives and managed variants lists for default gene panels only for convenience

Fixed

• Gens structural variant page link individual id typo

Fixed creating case reports with str variants containing comments

[4.65.2]

Fixed

• Generating general case report with str variants containing comments

Patch 4.65.1

[4.65.1]

Fixed

• Visibility of Gene(s) badges on SV VariantS page
• Hide dismiss bar on SV page not working well
• Delivery report PDF download
• Saving Pipeline version file when loading a case
• Backport compatible import of importlib metadata for old python versions (<3.8)

Download gene panels, panel gene comments, ClinVar submission, dismiss bar and other UI fixes

[4.65]

Added

• Option to mark a ClinVar submission as submitted
• Docs on how to create/update the PanelApp green genes as a system admin
• individual_id-parameter to both Gens links
• Download a gene panel in TXT format from gene panel page
• Panel gene comments on variant page: genes in panels can have comments that describe the gene in a panel context

Changed

• Always show each case category on caseS page, even if 0 cases in total or after current query
• Improved sorting of ClinVar submissions
• Pre-populate SV type select in ClinVar submission form, when possible
• Show comment badges in related comments tables on general report
• Updated version of several GitHub actions
• Migrate from deprecated pkg_resources lib to importlib_resources
• Dismiss bar on variantS pages is thinner.
• Dismiss bar on variantS pages can be toggled open or closed for the duration of a login session.

Fixed

• Fixed Sanger order / Cancel order modal close buttons
• Visibility of SV type in ClinVar submission form
• Fixed a couple of creations where now was called twice, so updated_at and created_at could differ
• Deprecated Ubuntu version 18.04 in one GitHub action
• Panels that have been removed (hidden) should not be visible in views where overlapping gene panels for genes are shown
• Gene panel test pointing to the right function