Shade compounds, improved general report SVs

[4.51]

Added

• Config file containing codecov settings for pull requests
• Add an IGV.js direct link button from case page
• Security policy file
• Hide/shade compound variants based on rank score on variantS from filter
• Chromograph legend documentation direct link

Changed

• Updated deprecated Codecov GitHub action to v.2
• Simplified code of scout/adapter/mongo/variant
• Update IGV.js to v2.11.2
• Show summary number of variant gene panels on general report if more than 3

Fixed

• Marrvel link for variants in genome build 38 (using liftover to build 37)
• Remove flags from codecov config file
• Fixed filter bug with high negative SPIDEX scores
• Renamed IARC TP53 button to to TP53 Database, modified also link since IARC has been moved to the US NCI: https://tp53.isb-cgc.org/
• Parsing new format of OMIM case info when exporting patients to Matchmaker
• Remove flask-debugtoolbar lib dependency that is using deprecated code and causes app to crash after new release of Jinja2 (3.1)
• Variant page crashing for cases with old OMIM terms structure (a list of integers instead of dictionary)
• Variant page crashing when creating MARRVEL link for cases with no genome build
• SpliceAI documentation link
• Fix deprecated safe_str_cmp import from werkzeug.security by freezing Werkzeug lib to v2.0 until Flask_login v.0.6 with bugfix is released
• List gene names densely in general report for SVs that contain more than 3 genes
• Show transcript ids on refseq genes on hg19 in IGV.js, using refgene source
• Display correct number of genes in general report for SVs that contain more than 32 genes
• Broken Google login after new major release of lepture/authlib
• Fix frequency and callers display on case general report

Fixed missing links to matching STR causatives

[4.50.1]

Fixed

• Show matching causative STR_repid for legacy str variants (pre Stranger hgnc_id)

v4.50 - individual OMIM, more links, fixes and refactoring

[4.50]

Added

• Individual-specific OMIM terms
• OMIM disease descriptions in ClinVar submission form
• Add a toggle for melter rerun monitoring of cases
• Add a config option to show the rerun monitoring toggle
• Add a cli option to export cases with rerun monitoring enabled
• Add a link to STRipy for STR variants; shallow for ARX and HOXA13
• Hide by default variants only present in unaffected individuals in variants filters
• OMIM terms in general case report
• Individual-level info on OMIM and HPO terms in general case report
• PanelApp gene link among the external links on variant page
• Dashboard case filters fields help
• Filter cases by OMIM terms in cases and dashboard pages

Fixed

• A malformed panel id request would crash with exception: now gives user warning flash with redirect
• Link to HPO resource file hosted on http://purl.obolibrary.org
• Gene search form when gene exists only in build 38
• Fixed odd redirect error and poor error message on missing column for gene panel csv upload
• Typo in parse variant transcripts function
• Modified keys name used to parse local observations (archived) frequencies to reflect change in MIP keys naming
• Better error handling for partly broken/timed out chanjo reports
• Broken javascript code when case Chromograph data is malformed
• Broader space for case synopsis in general report
• Show partial causatives on causatives and matching causatives panels
• Partial causative assignment in cases with no OMIM or HPO terms
• Partial causative OMIM select options in variant page

Changed

• Slightly smaller and improved layout of content in case PDF report
• Relabel more cancer variant pages somatic for navigation
• Unify caseS nav links
• Removed unused add_compounds param from variant controllers function
• Changed default hg19 genome for IGV.js to legacy hg19_1kg_decoy to fix a few problematic loci
• Reduce code complexity (parse/ensembl.py)
• Silence certain fields in ClinVar export if prioritised ones exist (chrom-start-end if hgvs exist)
• Made phenotype non-mandatory when marking a variant as partial causative
• Only one phenotype condition type (OMIM or HPO) per variant is used in ClinVar submissions
• ClinVar submission variant condition prefers OMIM over HPO if available
• Use lighter version of gene objects in Omim MongoDB adapter, panels controllers, panels views and institute controllers
• Gene-variants table size is now adaptive
• Remove unused file upload on gene-variants page

Report PDF export improvements and other fixes

[4.49]

Fixed

• Pydantic model types for genome_build, madeline_info, peddy_ped_check and peddy_sex_check, rank_model_version and sv_rank_model_version
• Replace MatchMaker with Matchmaker in all places visible by a user
• Save diagnosis labels along with OMIM terms in Matchmaker Exchange submission objects
• libegl-mesa0_21.0.3-0ubuntu0.3~20.04.5_amd64.deb lib not found by GitHub actions Docker build
• Remove unused chromograph_image_files and chromograph_prefixes keys saved when creating or updating an RD case
• Search managed variants by description and with ignore case

Changed

• Introduced page margins on exported PDF reports
• Smaller gene fonts in downloaded HPO genes PDF reports
• Reintroduced gene coverage data in the PDF-exported general report of rare-disease cases
• Check for existence of case report files before creating sidebar links
• Better description of HPO and OMIM terms for patients submitted to Matchmaker Exchange
• Remove null non-mandatory key/values when updating a case
• Freeze WTForms<3 due to several form input rendering changes

Fix general report PDF export for cases with no pedigree

[4.48.1]

Fixed

• General case PDF report for recent cases with no pedigree

Improved PDF generation with PDFKit, new IGV.js and cyvcf2

[4.48]

Added

• Option to cancel a request for research variants in case page

Changed

• Update igv.js to v2.10.5
• Updated example of a case delivery report
• Unfreeze cyvcf2
• Builder images used in Scout Dockerfiles
• Crash report email subject gives host name
• Export general case report to PDF using PDFKit instead of WeasyPrint
• Do not include coverage report in PDF case report since they might have different orientation
• Export cancer cases's "Coverage and QC report" to PDF using PDFKit instead of Weasyprint
• Updated cancer "Coverage and QC report" example
• Keep portrait orientation in PDF delivery report
• Export delivery report to PDF using PDFKit instead of Weasyprint
• PDF export of clinical and research HPO panels using PDFKit instead of Weasyprint
• Export gene panel report to PDF using PDFKit
• Removed WeasyPrint lib dependency

Fixed

• Reintroduced missing links to Swegen and Beacon and dbSNP in RD variant page, summary section
• Demo delivery report orientation to fit new columns
• Missing delivery report in demo case
• Cast MNVs to SNV for test
• Export verified variants from all institutes when user is admin
• Cancer coverage and QC report not found for demo cancer case
• Pull request template instructions on how to deploy to test server
• PDF Delivery report not showing Swedac logo
• Fix code typos
• Disable codefactor raised by ESLint for javascript functions located on another file
• Loading spinner stuck after downloading a PDF gene panel report
• IGV browser crashing when file system with alignment files is not mounted

Improved variants export file and Docker image with fixed chanjo-report version

[4.47]

Added

• Added CADD, GnomAD and genotype calls to variantS export

Changed

• Pull request template, to illustrate how to deploy pull request branches on cg-vm1 stage server

fixed

• Compiled Docker image contains a patched version (v4.9) of chanjo-report

Fixed download of reports and files generated within the app container

[4.46.1]

Fixed

• Downloading of files generated within the app container (MT-report, verified variants, pedigrees, ..)

Dockerfiles, pydantic case parsing and gene variants fixes

[4.46]

Added

• Created a Dockefile to be used to serve the dockerized app in production
• Modified the code to collect database params specified as env vars
• Created a GitHub action that pushes the Dockerfile-server image to Docker Hub (scout-server-stage) every time a PR is opened
• Created a GitHub action that pushes the Dockerfile-server image to Docker Hub (scout-server) every time a new release is created
• Reassign MatchMaker Exchange submission to another user when a Scout user is deleted
• Expose public API JSON gene panels endpoint, primarily to enable automated rerun checking for updates
• Add utils for dictionary type
• Filter institute cases using multiple HPO terms
• Vulture GitHub action to identify and remove unused variables and imports

Changed

• Updated the python config file documentation in admin guide
• Case configuration parsing now uses Pydantic for improved typechecking and config handling
• Removed test matrices to speed up automatic testing of PRs
• Switch from Coveralls to Codecov to handle CI test coverage
• Speed-up CI tests by caching installation of libs and splitting tests into randomized groups using pytest-test-groups
• Improved LDAP login documentation
• Use lib flask-ldapconn instead of flask_ldap3_login> to handle ldap authentication
• Updated Managed variant documentation in user guide
• Fix and simplify creating and editing of gene panels
• Simplified gene variants search code
• Increased the height of the genes track in the IGV viewer

Fixed

• Validate uploaded managed variant file lines, warning the user.
• Exporting validated variants with missing "genes" database key
• No results returned when searching for gene variants using a phenotype term
• Variants filtering by gene symbols file
• Make gene HGNC symbols field mandatory in gene variants page and run search only on form submit
• Make sure collaborator gene variants are still visible, even if HPO filter is used

Fix gene panel edit and clarify custom inheritance models

[4.45]

Added

Changed

• Start Scout also when loqusdbapi is not reachable
• Clearer definition of manual standard and custom inheritance models in gene panels

Fixed

• Gene panel crashing on edit action