Scout user meeting agenda 23/3 -22

[henrikstranneheim]

Welcome to the Scout user meeting @9:00-10:30 am!

Location: On zoom: https://ki-se.zoom.us/j/61414401020?pwd=WitWeThraU16NzdXekRaRE1BWEhKUT09

Please help us fill the agenda with topics that may interest you.

Agenda

• PatientMatcher MME publication
• Changes
• Roadmap
• User survey

[northwestwitch]

Meeting moved to next week --> 23/3 -22. I'm going to send an email to the users now!

[dnil]

Changes to demo

General

• Keeping it alive; libraries, system, other services, hg38, speed up things that get complex and slow, interoperability with legacy and upcoming pipelines...

  Site specific

• Solna server move
• Docker-based prod server - usable by other facilities

  Pages

  Case level

• OMIM and HPO terms can be assigned on the individual level
• OMIM terms displayed on case report now

  VariantS

• Hide by default variants only present in unaffected individuals
• Cancer SV variants filter AD, AF (tumor and normal)

  Variant

• Selectable IGV tracks
• SpliceAI
• STR links

  Gene panels

• Delete/restore

  Sharing

• SVs in PatientMatcher

Here's the changelog from last meeting. 😅

[4.50.1]

Fixed

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

[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 onhttp://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

[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

[4.48.1]

Fixed

• General case PDF report for recent cases with no pedigree

[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

[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

  [4.46.1]

  Fixed

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

[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

[4.45]

Added

Changed

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

  Fixed

• Gene panel crashing on edit action

[4.44]

Added

Changed

• Display Gene track beneath each sample track when displaying splice junctions in igv browser
• Check outdated gene symbols and update with aliases for both RD and cancer variantS

  Fixed

• Added query input check and fixed the Genes API endpoint to return a json formatted error when request is malformed
• Typo in ACMG BP6 tooltip

[4.43.1]

Added

• Added database index for OMIM disease term genes

  Changed

  Fixed

• Do not drop HPO terms collection when updating HPO terms via the command line
• Do not drop disease (OMIM) terms collection when updating diseases via the command line

[4.43]

Added

• Specify which collection(s) update/build indexes for

  Fixed

• Do not drop genes and transcripts collections when updating genes via the command line

[4.42.1]

Added

Changed

Fixed

• Freeze PyMongo lib to version<4.0 to keep supporting previous MongoDB versions
• Speed up gene panels creation and update by collecting only light gene info from database
• Avoid case page crash on Phenomizer queries timeout

[4.42]

Added

• Choose custom pinned variants to submit to MatchMaker Exchange
• Submit structural variant as genes to the MatchMaker Exchange
• Added function for maintainers and admins to remove gene panels
• Admins can restore deleted gene panels
• A development docker-compose file illustrating the scout/chanjo-report integration
• Show AD on variants view for cancer SV (tumor and normal)
• Cancer SV variants filter AD, AF (tumor and normal)
• Hiding the variants score column also from cancer SVs, as for the SNVs

  Changed

• Enforce same case _id and display_name when updating a case
• Enforce same individual ids, display names and affected status when updating a case
• Improved documentation for connecting to loqusdb instances (including loqusdbapi)
• Display and download HPO gene panels' gene symbols in italics
• A faster-built and lighter Docker image
• Reduce complexity of panels endpoint moving some code to the panels controllers
• Update requirements to use flask-ldap3-login>=0.9.17 instead of freezing WTForm

  Fixed

• Use of deprecated TextField after the upgrade of WTF to v3.0
• Freeze to WTForms to version < 3
• Remove the extra files (bed files and madeline.svg) introduced by mistake
• Cli command loading demo data in docker-compose when case custom images exist and is None
• Increased MongoDB connection serverSelectionTimeoutMS parameter to 30K (default value according to MongoDB documentation)
• Better differentiate old obs counts 0 vs N/A
• Broken cancer variants page when default gene panel was deleted
• Typo in tx_overview function in variant controllers file
• Fixed loqusdbapi SV search URL
• SV variants filtering using Decipher criterion
• Removing old gene panels that don't contain the maintainer key.

[4.41.1]

Fixed

• General reports crash for variant annotations with same variant on other cases

[4.41]

Added

• Extended the instructions for running the Scout Docker image (web app and cli).
• Enabled inclusion of custom images to STR variant view

  Fixed

• General case report sorting comments for variants with None genetic models
• Do not crash but redirect to variants page with error when a variant is not found for a case
• UCSC links coordinates for SV variants with start chromosome different than end chromosome
• Human readable variants name in case page for variants having start chromosome different from end chromosome
• Avoid always loading all transcripts when checking gene symbol: introduce gene captions
• Slow queries for evaluated variants on e.g. case page - use events instead

  Changed

• Rearrange variant page again, moving severity predictions down.
• More reactive layout width steps on variant page

[4.40.1]

Added

Fixed

• Variants dismissed with inconsistent inheritance pattern can again be shown in general case report
• General report page for variants with genes=None
• General report crashing when variants have no panels
• Added other missing keys to case and variant dictionaries passed to general report

  Changed

[4.40]

Added

• A .cff citation file
• Phenotype search API endpoint
• Added pagination to phenotype API
• Extend case search to include internal MongoDB id
• Support for connecting to a MongoDB replica set (.py config files)
• Support for connecting to a MongoDB replica set (.yaml config files)

  Fixed

• Command to load the OMIM gene panel (scout load panel --omim)
• Unify style of pinned and causative variants' badges on case page
• Removed automatic spaces after punctuation in comments
• Remove the hardcoded number of total individuals from the variant's old observations panel
• Send delete requests to a connected Beacon using the DELETE method
• Layout of the SNV and SV variant page - move frequency up

  Changed

• Stop updating database indexes after loading exons via command line
• Display validation status badge also for not Sanger-sequenced variants
• Moved Frequencies, Severity and Local observations panels up in RD variants page
• Enabled Flask CORS to communicate CORS status to js apps
• Moved the code preparing the transcripts overview to the backend
• Refactored and filtered json data used in general case report
• Changed the database used in docker-compose file to use the official MongoDB v4.4 image
• Modified the Python (3.6, 3.8) and MongoDB (3.2, 4.4, 5.0) versions used in testing matrices (GitHub actions)
• Capitalize case search terms on institute and dashboard pages

[4.39]

Added

• COSMIC IDs collected from CSQ field named COSMIC

  Fixed

• Link to other causative variants on variant page
• Allow multiple COSMIC links for a cancer variant
• Fix floating text in severity box #2808
• Fixed MitoMap and HmtVar links for hg38 cases
• Do not open new browser tabs when downloading files
• Selectable IGV tracks on variant page
• Missing splice junctions button on variant page
• Refactor variantS representative gene selection, and use it also for cancer variant summary

  Changed

• Improve Javascript performance for displaying Chromograph images
• Make ClinVar classification more evident in cancer variant page

[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

[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

[dnil]

• Tutorial on a couple of questions from the user survey?

[dnil]

Roadmap

Upcoming features

• Rank score ranges
• User event log
• Compound variants hiding

Pending integration

• ExHu ReViewer
• GENS (done Lund, pending Solna)
• vcf2cytosure Balsamic

Integration development efforts

• Beacon
• Multisource fusion reports
• Chanjo2 (can update genome/gene sets, allow detailed balsamic coverage reports, ...)
• Loqusdb for cancer
• Melter
• Reruns via Orderportalen (Solna, Rerunner Lund)

Pipeline updates

• RD: MIP 11 - (DeepVariant, totals on archive counts, ...)
• RD: nf-core/raredisease
• Following development on ExHu / non-reference loci

[dnil]

Thank you for today!