scout-browser - v4.104 - WUI user edit, more WTS filters, ESCAT cancer SNV tiers, clickable rows

[4.104]

Added

• Parsing variant'slocal_obs_cancer_somatic_panel_old and local_obs_cancer_somatic_panel_old_freqfrom Cancer_Somatic_Panel_Obs and Cancer_Somatic_Panel_Frq INFO keys respectively (#5594)
• Filter cancer variants by archived number of cancer somatic panel observations (#5598)
• Export Managed Variants: CLI now supports --category to filter by one or more categories (snv, sv, cancersnv, cancersv). Defaults to all. (#5608)
• New form to create/edit users on the general users page (visible to admin users only) (#5610 and #5613)
• Scout-Reviewer-Service endpoint to visualise PacBio trgt called expansions (#5611)
• Updated the documentation with instructions on how, as an admin, to add/edit/remove users from the main users page (#5625)
• Button to remove users from the main users page (visible to admins only) (#5612)
• New "P-value, abs log₂FC and abs ΔΨ WTS filters options (#5639)
• ESCAT tiers for cancer SNVs (#5660) ### Changed
• Avoid utcnow() deprecated code by installing Flask-Login from its main branch (#5592)
• Compute chanjo2 coverage on exons only when at least case individual has analysis_type=panel (#5601)
• Display conservation scores for PHAST, GERP and phyloP alongside "Conserved" or "NotConserved" (#5593)
• Exporting managed variants from the command line with the --collaborator option will return variants from the specified institute plus those not assigned to any institute (#5607)
• Safer redirect to previous page for variants views (#5599)
• Make whole caseS row clickable link for case page (#5620)
• Make whole variantS row clickable link for variant page (#5618)
• Refined the filtering logic for Clinical WTS variants. The clinical filter now selects variants with either padjust < 0.05 or (p_adjust_gene < 0.1 and abs(delta_psi) > 0.1), for OUTRIDER expression variants and FRASER splicing variants respectively (#5630)
• Removing git installers when building Docker images (#5644)
• Refactored the parsing of the app config file so there exists only one centralized loader for both cli and web app (#5638)
• Restrict gene-overlapping variants (DNA and WTS outliers) search to variants found in affected individuals (#5623, #5659)
• Update command: scout export variants now scout export causatives (backward-compatible) (#5654)
• Show estimated VAF% also for panel and WES SNVs, much as for MT variants (#5658) ### Fixed
• Treat -1 values as None values when parsing archived LoqusDB frequencies - works retroactively on variantS page, not on variant page yet (#5591)
• Links to SNVs and SVs from SMN CN page (#5600)
• Consistent panel display on variants pages for unselected "All" panels (#5600)
• Bump tj-actions-branch-names GitHub action to v9 (#5605)
• Missing variant key tool_hits causing fusion variants page to crash (#5614)
• Add/fix conflicts between ClinGen-CGC-VICC classification criteria to fix discrepancies to Horak et al (#5629)
• Fix display of gene symbols for TRGT loci on variantS page (#5634)
• Parse and store also SpliceAI, CADD scores where all scores are 0. (#5637)
• Git missing from docker bookworm slim image (#5642)
• Matching cancer_snv managed variants failure (#5647)
• Parsing of database name when provided on a .yaml config file (#5663)
• Export causatives command crashing on variants that have been removed (#5665)
• Don't follow row link for checkboxes or other input elements (#5668)
• Parse error on REViewer.trgt case load entries (#5672)
• Fix SpliceAI 0.0 score display (#5675)

Full Changelog: https://github.com/Clinical-Genomics/scout/compare/v4.103.3...v4.104

- HTML
Published by dnil 6 months ago

scout-browser - Fixes and improvements on the "Search SNVs and SVs" and STRs pages

[4.103.3]

Changed

• Sort institute multiselect alphabetically by display name on 'Search SNVs & SVs' page (#5584)
• Always display STRs sorted by ascending gene symbol (#5580) ### Fixed
• App filter format_variant_canonical_transcripts (used on Search SNVs and SVs page) crashing when a gene has no canonical transcript (#5582)
• STRs not displaying a repeat locus (#5587)

- HTML
Published by northwestwitch 8 months ago

scout-browser - IGV update to v3.4.1

[4.103.2]

Changed

• Display number of available/displayed variants on variantS pages without having to expand search filters (#5571) with collapsing chevron (#5572)
• Update to IGV.js v3.4.1 (#5573)
• Allow autoscaling on IGV tracks, but group alignment scale (#5574) ### Fixed
• Fixed panel filename sanitization in download panel function (#5577)

- HTML
Published by dnil 8 months ago

scout-browser - Patch to SV variant VQ display

[4.103.1]

Fixed

• Rounding of SV VQ with undefined value (#5568)

- HTML
Published by dnil 8 months ago

scout-browser - ClinVar oncogenicity submission, colourful predictor scores, callers for nf-core raredisease and Nallo STR improvements

[4.103]

Added

• Add cancer SNVs to Oncogenicity ClinVar submissions (downloadable json document) (#5449)
• Fold changes values alongside Log2 fold changes values (l2fc) on WTS outliers page (#5536)
• REVEL and SpliceAI scores are now displayed as multi-colored, labeled badges on the variant and report pages (#5537, #5538)
• Filter results in Search SNVs & SVs page by one or more institutes (#5539)
• New exome CNV caller GATK CNV (#5557)
• Automatic ClinVar oncogenicity submissions via ClinVar API (#5510)
• Parse and show normalized rank scores (RankScoreNormalized) on SNVs (RD & cancer) and SVs (RD) pages (#5554)
• Add MuTect2 SNV caller (used in nf-core/raredisease MT calling) (#5558)
• Option to remove any role assigned to a user, not only the admin role (#5523) ### Changed
• Improved test that checks code collecting other categories of variants overlapping a variant (#5521)
• Enable insertion/deletion size display on IGV.js alignment tracks (#5547)
• LRS STR variant read support (TRGT SD) stored and displayed on variant as ref/alt depth (#5552)
• On Search SNVs and SVs page, display multiple HGVS descriptors when variant has more than one gene (#5513)
• Deprecated the --remove-admin flag in the update user command line (#5523) ### Fixed
• Instance badge class and config option documentation (#5500)
• Fix incorrect reference to non-existent pymongo.synchronous (#5517)
• More clearly dim cases for empty queries (#5507)
• Case search form enforces numeric input for number of results returned (Limit field) (#5519)
• Parsing of canonical transcript in variants genes when variant is outside the coding sequence (#5515)
• Download of a ClinVar submission's json file when observation data is no longer present in the database (#5520)
• Removed extra warnings for missing file types on case loading (#5525)
• Matchmaker Exchange submissions page crashing when one or more cases have no synopsis(#5534)
• Loading PathologicStruc from Stranger annotated TRGT STR files (#5542)
• Badge color for missing REVEL and SpliceAI scores (#5546)
• Truncate long STR RepeatUnit names, from loci missing formal RU just showing ref allele (#5551)
• Do not reorder Sanger sequencing for variants when case is re-uploaded. Just assign Sanger status = ordered to them. (#5504)
• Do not create new variant-associated events, when re-uploading a case. New variant inherits key/values from old evaluated variants (#5507)
• Increased bottom margin in ClinVar submission option on institute's sidebar (#5561)
• Search SNVs & SVs for cases which have been removed (#5563)
• SpliceAI label color when variant hits multiple genes (#5565)

- HTML
Published by dnil 8 months ago

scout-browser - General report updates, highlight case search results, logout fix

[4.102]

Added

• ClinVar data with link to ClinVar for variants present on the general case report (#5478)
• Customise Scout instance color and name, by adding INSTANCE_NAME and INSTANCE_COLOR parameters in the app config file (#5479)
• Display local archived frequencies on general case report (#5492) ### Changed
• Refactored and simplified code that fetches case's genome build (#5443)
• On caseS page, dim cases only included from the always display cases with status option (#5464)
• Reuse the variant frequencies table from variant page on case reports (#5478)
• Loading of outliers files (Fraser and Outrider) do not raise error when path to these files is missing or wrong, just a warning (#5486)
• Updated libraries on uv lock file (#5495) ### Fixed
• Fix long STR variant pinned display on case page (#5455)
• Variant page crashing when Loqusdb instance is chosen on institute settings but is not found at the given URL (#5447)
• Show assignees in case list when user ID is different from email (#5460)
• When removing a germline variant from a ClinVar submission, make sure to remove also its associated observations from the database (#5463)
• Chanjo2 genes full coverage check when variant has no genes (#5468)
• Full Flask user logout blocked by session clear (#5470)
• SV page UCSC link for breakpoints did not detect genome build 38 (#5489)
• HPO term deep link URL updated to a working one (#5488)
• Add str_trid as a sorting criterion when selecting STRs. This fixes the sort order problem of STRs from cases with genome build 38 (#5491)
• Always use GitHub original for igv.js genomes.json config - it is intended as official backup URL already (#5496)
• Update igv.js to v3.3.0 (#5496)
• Introduced a function that checks redirect URLs to avoid redirection to external sites (#5458)
• Loading of missing outliers files should also not raise error if key exists but is unset (#5497)
• Do not add null references to HPO-associated genes when parsing errors occur (#5472)
• Possibility to change user immediately after logging out from Google Oauth or Keycloak (#5493)
• Trust hgnc_id for unique aliases for HPO-associated genes (#5498)

- HTML
Published by dnil 10 months ago

scout-browser - Variant load order fix and user interface improvements

[4.101]

Changed

• Institutes are now sorted by ID on gene panels page (#5436)
• Simplified visualization of previous ACMG and CCV classifications for a variant on variantS page (#5439 & #5440)
• On ClinVar multistep submission form, skip fetching transcript versions for build 38 transcripts which are not MANE Select or MANE Plus Clinical (#5426) ### Fixed
• Malformatted table cell for analysis date on caseS page (#5438)
• Remove "Add to ClinVar submission" button for pinned MEI variants as submission is not supported at the moment (#5442)
• Clinical variant files could once again be read in arbitrary order on load (#5452)
• Fix testsangervalidation test to be run with a mock app instantiated (#5453)

- HTML
Published by dnil 10 months ago

scout-browser - Fix parsing and loading of Ensembl transcripts

[4.100.2]

Fixed

• Keyerror 'ensembltranscriptid' when loading transcripts from a pre-downloaded Ensembl transcripts file (#5435)

- HTML
Published by northwestwitch 10 months ago

scout-browser - Removed an extra x from compounds functional annotation cells

[4.100.1]

Fixed

• Removed an extra x from compounds functional annotation cells (#5432)

- HTML
Published by northwestwitch 10 months ago

scout-browser - ClinVar oncogenicity filter, WTS outliers matching, Matchmaker submissions page, and MAF track for LRS IGV

[4.100]

Added

• Button with link to cancerhotspots.org on variant page for cancer cases (#5359)
• Link to ClinGen ACMG CSPEC Criteria Specification Registry from ACMG classification page (#5364)
• Documentation on how to export data from the scout database using the command line (#5373)
• Filter cancer SNVs by ClinVar oncogenicity. OBS: since annotations are still sparse in ClinVar, relying solely on them could be too restrictive (#5367)
• Include eventual gene-matching WTS outliers on variantS page (Overlap column) and variant page (Gene overlapping non-SNVs table) (#5371)
• Minor Allele Frequency (HiFiCNV) IGV.js track for Nallo cases (#5401)
• A page showing all cases submitted to the Matchmaker Exchange, accessible from the institute's sidebar (#5378)
• Variants' loader progress bar (#5411) ### Changed
• Allow matching compounded subcategories from SV callers e.g. DUP:INV (#5360)
• Adjust the link to the chanjo2 gene coverage report to reflect the type of analyses used for the samples (#5368)
• Gene panels open in new tabs from case panels and display case name on the top of the page (#5369)
• When uploading research variants, use rank threshold defined in case settings, if available, otherwise use the default threshold of 8 (#5370)
• Display genome build version on case general report (#5381)
• On pull request template, fixed instructions on how to deploy a branch to the development server (#5382)
• On case general report, when a variant is classified (ACMG or CCV), tagged, commented and also dismissed, will only be displayed among the dismissed variants (#5377)
• If case is re-runned/re-uploaded with the --keep-actions tag, remember also previously assigned diseases, HPO terms, phenotype groups and HPO panels (#5365)
• Case load config alias and updated track label for TIDDIT coverage tracks to accommodate HiFiCNV dito (#5401)
• On variants page, compounds popup table, truncate the display name of compound variants with display name that exceeds 20 characters (#5404)
• Update dataTables js (#5407)
• Load variants command prints more clearly which categories of variants are being loaded (#5409)
• Tooltips instead of popovers (no click needed) for matching indicators on variantS page (#5419)
• Call chanjo2 coverage completeness indicator via API after window loading completes (#5366)
• On ClinVar multistep submission form, silence warnings coming from missing HGVS version using Entrez Eutils (#5424) ### Fixed
• Style of Alamut button on variant page (#5358)
• Scope of overlapping functions (#5385)
• Tests involving the variants controllers, which failed when not run in a specific order (#5391)
• Option to return to the previous step in each of the steps of the ClinVar submission form (#5393)
• chanjo2 MT report for cases in build 38 (#5397)
• Fixed some variantS view tests accessing database out of app context (#5415)
• Display of matching manual rank on the SV variant page (#5419)
• Broken scout setup database command (#5422)
• Collecting and removing ClinVar submission data for cases which have been removed (#5421)
• Speed up query for gene overlapping variants (#5413)

- HTML
Published by dnil 10 months ago

scout-browser - ClinVar oncogenicity, gene overlapping SV and MEI, Keycloak support and more IGV tracks

[4.99]

Added

• De novo assembly alignment file load and display (#5284)
• Paraphase bam-let alignment file load and display (#5284)
• Parsing and showing ClinVar somatic oncogenicity anontations, when available (#5304)
• Gene overlapping variants (superset of compounds) for SVs (#5332)
• Gene overlapping variants for MEIs (#5332)
• Gene overlapping variants for cancer (and cancer_sv) (#5332)
• Tests for the Google login functionality (#5335)
• Support for login using Keycloak (#5337)
• Documentation on Keycloak login system integration (#5342)
• Integrity check for genes/transcripts/exons files downloaded from Ensembl (#5353)
• Options for custom ID/display name for PanelApp Green updates (#5355)

Changed

• Allow ACMG criteria strength modification to Very strong/Stand-alone (#5297)
• Mocked the Ensembl liftover service in igv tracks tests (#5319)
• Refactored the login function into smaller functions, handling respectively: user consent, LDAP login, Google login, database login and user validation (#5331)
• Allow loading of mixed analysis type cases where some individuals are fully WTS and do not appear in DNA VCFs (#5327)
• Documentation available in dark mode, and expanded installation instructions (#5343)

Fixed

• Re-enable display of case and individual specific tracks (pre-computed coverage, UPD, zygosity) (#5300)
• Disable 2-color mode in IGV.js by default, since it obscures variant proportion of reads. Can be manually enabled (#5311)
• Institute settings reset (#5309)
• Updated color scheme for variant assessment badges that were hard to see in light mode, notably Risk Factor (#5318)
• Avoid page timeout by skipping HGVS validations in ClinVar multistep submission for non-MANE transcripts from variants in build 38 (#5302)
• Sashimi view page displaying an error message when Ensembl REST API (LiftOver) is not available (#5322)
• Refactored the liftover functionality to avoid using the old Ensembl REST API (#5326)
• Downloading of Ensembl resources by fixing the URL to the schug server, pointing to the production instance instead of the staging one (#5348)
• Missing MT genes from the IGV track (#5339)
• Paraphase and de novo assembly tracks could mismatch alignment sample labels - refactor to case specific tracks (#5357)

- HTML
Published by dnil 12 months ago

scout-browser - Old research cases patch, improved documentation and institute filters page

[4.98]

Added

• Documentation on how to delete variants for one or more cases
• Document the option to collect green genes from any panel when updating the PanelApp green genes panel
• On the institute's filters page, display also any soft filters applied to institute's variants ### Fixed
• Case page patch for research cases without WTS outliers

- HTML
Published by northwestwitch about 1 year ago

scout-browser - WTS outlier research, in_normal filter, clinvar exclude, chanjo2 coverage completeness and more

🌞☁️There are several new features in this early spring cleaning release.☁️🌞

Please see below. Note in particular that due to the ClinVar refactor, saved filters with clinsig_confident_always_returned enabled will be re-saved with the new options prioritised_clivar and clinvar_trusted_revstat enabled.

🙏 Extra thanks to @molucorner for the HRD display!

Added

• Software version and link to the relative release on GitHub on the top left dropdown menu
• Option to sort WTS outliers by p_value, Δψ, ψ value, zscore or l2fc
• Display pLI score and LOEUF on rare diseases and cancer SNV pages
• Preselect MANE SELECT transcripts in the multi-step ClinVar variant add to submission process
• Allow updating case with WTS Fraser and Outrider research files
• Load research WTS outliers using the scout load variants --outliers-research command
• Chanjo2 gene coverage completeness indicator and report from variant page, summary card
• Enhanced SNV and SV filtering for cancer and rare disease cases, now supporting size thresholds (≥ or < a specified base pair length)
• Option to exclude ClinVar significance status in SNVs filters form
• Made HRD a config parameter and display it for cancer cases.
• Preset institute-level soft filters for variants (filtering based on "filters" values on variant documents). Settings editable by admins on the institute's settings page. Allows e.g. hiding tumor in_normal and germline_risk filter status variants.
• Load pedigree and sex check from Somalier, provided by e.g. the Nallo pipeline
• Expand the command line to remove more types of variants. Now supports: cancer, cancer_sv, fusion, mei, outlier, snv, str, and sv.
• New prioritise_clinvar checkbox on rare diseases cases, SNVs page, used by clinical filter or for expanding the search to always return variants that match the selected ClinVar conditions
• ClinVar CLNSIG Exclude option on cancer variantS filters ### Changed
• Do not show overlapping gene panels badge on variants from cases runned without gene panels
• Set case as research case if it contains any type of research variants
• Update igv.js to 3.2.0
• IGV DNA alignment track defaults to group by tag:HP and color by methylation (useful for LRS), and show soft-clips
• Update gnomAD constraint to v4.1
• HG38 genes track in igv.js browser, to correctly display gene names
• Refactored code for prioritizing the order of variant loading
• Modified the web pages body style to adapt content to smaller screens
• Refactored filters to filter variants by ClinVar significance, CLINSIG Confident and ClinVar hits at the same time
• Improved tooltips for ClinVar filter in SNVs filter form
• showSoftClips parameter in igv.js is set to false by default for WES and PANEL samples ### Fixed
• Don't save any "-1", "." or "0" frequency values for SNVs - same as for SVs
• Downloading and parsing of genes from Ensembl (including MT-TP)
• Don't parse SV frequencies for SNVs even if the name matches. Also accept "." as missing value for SV frequencies.
• HPO search on WTS Outliers page
• Stop using dynamic gene panel (HPO generated list) for clinical filter when the last gene is removed from the dynamic gene panel
• Return only variants with ClinVar annotation when ClinVar hits checkbox is checked on variants search form
• Legacy variant filter option clinsig_confident_always_returned on saved filters is remapped as prioritised_clivar and clinvar_trusted_revstat
• Variants queries excluding ClinVar tags without prioritise_clinvar checkbox checked

What's Changed

• Add software version and link to the GitHub release on the top left dropdown by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5205
• Fix parse neg AF by @dnil in https://github.com/Clinical-Genomics/scout/pull/5207
• No overlapping panels badge if overlapping panels are 0 by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5210
• Sort WTS outliers by p_value, Δψ, ψ value, zscore or l2fc by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5213
• Fix parsing of entire Ensembl documents - including MT-TP gene by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5218
• pLI scores on SNV and cancer SNV pages by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5209
• Set case as research case if it contains any type of research variants by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5225
• Fix #5230 - IGV v3.1.4 and more aln track defaults by @dnil in https://github.com/Clinical-Genomics/scout/pull/5233
• Fix #5227 - update gnomAD constraint to 4.1 by @dnil in https://github.com/Clinical-Genomics/scout/pull/5228
• Fix #5214 - parse SV freq only for SVs, accept . as missing value by @dnil in https://github.com/Clinical-Genomics/scout/pull/5215
• Preselect MANE SELECT transcripts in the ClinVar multistep form by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5238
• Fix #5235 - fraser and outrider research update case by @dnil in https://github.com/Clinical-Genomics/scout/pull/5236
• Change genes 38 track in igv.js by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5240
• Refactor variants loading prio by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5234
• Fix #5237 - enable HPO searches on WTS outlier page by @dnil in https://github.com/Clinical-Genomics/scout/pull/5243
• Attempt at cases page fix for smaller screens by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5242
• Load research WTS outliers using the load variants command by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5241
• Complete coverage indicator chanjo2 by @dnil in https://github.com/Clinical-Genomics/scout/pull/5245
• Variants filter by size by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5244
• Group the 3 ClinVar filters together by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5006
• Fix #5250 - update IGV.js to 3.2.0 by @dnil in https://github.com/Clinical-Genomics/scout/pull/5251
• Ordered filters by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5257
• Better ClinVar tooltips and added exclude clinsig status for SNVs filter by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/4993
• Make HRD a config parameter and display for cancer cases. by @molucorner in https://github.com/Clinical-Genomics/scout/pull/5262
• Institute-level soft filters for variants by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5254
• Fix #5258 - stop clinical filter HPO when dynamic gene panel is emptied by @dnil in https://github.com/Clinical-Genomics/scout/pull/5259
• Fix #2177 - load somalier files by @dnil in https://github.com/Clinical-Genomics/scout/pull/5260
• Remove any variant type by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5219
• Prioritise ClinVar checkbox by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5264
• preserve saved filters by @dnil in https://github.com/Clinical-Genomics/scout/pull/5268
• Hide soft clips in IGV for wes and panel samples by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5271
• Fix exclude ClinVar + secondary filter by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5269
• Fix demo file and operator priority by @dnil in https://github.com/Clinical-Genomics/scout/pull/5273
• Fix #5274 - exclude clnsig also on cancer variantS page by @dnil in https://github.com/Clinical-Genomics/scout/pull/5275
• Version 4.97 & updated libs by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5261

Full Changelog: https://github.com/Clinical-Genomics/scout/compare/v4.96...v4.97

- HTML
Published by dnil about 1 year ago

scout-browser - Expanded annotations on report, improved case status and loading support, more ACMG warnings, fixes and updates

[4.96]

Added

• Support case status assignment upon loading (by providing case status in the case config file)
• Severity predictions on general case report for SNVs and cancer SNVs
• Variant functional annotation on general case report for SNVs and cancer SNVs
• Version of Scout used when the case was loaded is displayed on case page and general report ### Removed
• Discontinue ClinVar submissions via CSV files and support only submission via API: removed buttons for downloading ClinVar submission objects as CSV files ### Changed
• Display STR variant filter status on corresponding variantS page
• Warning and reference to Biesecker et al when using PP1/BS4 and PP4 together in ACMG classifications
• Warning to not use PP4 criterion together with PS2/PM6 in ACMG classifications with reference to the SVI Recommendation for de novo Criteria (PS2 & PM6)
• Button to directly remove accepted submissions from ClinVar
• Upgraded libs in uv.lock file ### Fixed
• Release docs to include instructions for upgrading dependencies
• Truncated long HGVS descriptions on cancer SNV and SNVs pages
• Avoid recurrent error by removing variant ranking settings in unranked demo case
• Actually re-raise exception after load aborts and has rolled back variant insertion

- HTML
Published by northwestwitch about 1 year ago

scout-browser - Case report CCV score, PanelApp loading improvements

This release addresses - CCV scores on case reports - Multiple fixes ACMG scores on case reports; bayesian temperature could miss modifiers - The SNV classification for can now also be accessed for SVs. It is intended primarily for small SVs. ACMG SV classification for larger SVs can be reached via link to clingen, and is intended to still be reported as manual rank. - Fixes and simplifications for PanelApp panel loading

Version 4.95

Added

• CCV score / temperature on case reports
• ACMG SNV classification form also accessible from SV variant page
• Simplify updating of the PanelApp Green panel from all source types in the command line interactive session ### Changed
• Clearer link to Richards 2015 on ACMG classification section on SVs and SVs variants pages
• Parse HGNC Ids directly from PanelApp when updating/downloading PanelApp panels
• Skip variant genotype matching check and just return True when matching causative is found in a case with only one individual/sample
• Reduced number of research MEI variants present in the demo case from 17K to 145 to speed up automatic tests ### Fixed
• ACMG temperature on case general report should respect term modifiers
• Missing inheritance, constraint info for genes with symbols matching other genes previous aliases with some lower case letters
• Loading of all PanelApp panels from command line
• Saving gene inheritance models when loading/updating specific/all PanelApp panels (doesn't apply to the PanelApp Green Genes panel)
• Save also complete penetrance status (in addition to incomplete) if available when loading specific/all PanelApp panels (does not apply to the PanelApp Green Genes panel)
• Variants and managed variants query by coordinates, which was returning all variants in the chromosome if start position was 0
• Compound loading matches also "chr"-containing compound variant names

- HTML
Published by dnil about 1 year ago

scout-browser - 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

- HTML
Published by northwestwitch about 1 year ago

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

Full Changelog: https://github.com/Clinical-Genomics/scout/compare/v4.93...v4.94

- HTML
Published by dnil about 1 year ago

scout-browser - Fix PyPi build action

[4.93.1]

Fixed

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

- HTML
Published by dnil about 1 year ago

scout-browser - 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 https://github.com/Clinical-Genomics/scout/pull/5093
• Clingen-CGC-VICC oncogenicity classification by @molucorner in https://github.com/Clinical-Genomics/scout/pull/5069
• Fix missing classifications in case report by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5096
• Expand observation number by @Jakob37 in https://github.com/Clinical-Genomics/scout/pull/5092
• Add a warning to not to post sensitive info on issues by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5098
• Fix #5102 - customer id in sharing dialog by @dnil in https://github.com/Clinical-Genomics/scout/pull/5103
• Fix multigene panels count by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5097
• Fix updating gene panels via file by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5105
• Switch to Python 3.12 in Dockerfiles and automatic tests by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5107
• Fix #5109 - CCV Horak link in new window by @dnil in https://github.com/Clinical-Genomics/scout/pull/5110
• Minor release 4.93 by @northwestwitch in https://github.com/Clinical-Genomics/scout/pull/5108

New Contributors

• @molucorner made their first contribution in https://github.com/Clinical-Genomics/scout/pull/5069

Full Changelog: https://github.com/Clinical-Genomics/scout/compare/v4.92...v4.93

- HTML
Published by dnil about 1 year ago

scout-browser - 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

- HTML
Published by dnil over 1 year ago

scout-browser - 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

- HTML
Published by northwestwitch over 1 year ago

scout-browser - 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

- HTML
Published by dnil over 1 year ago

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

Full Changelog: https://github.com/Clinical-Genomics/scout/compare/v4.90.1...v4.91

- HTML
Published by dnil over 1 year ago

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

[4.90.1]

Fixed

• Parsing Matchmaker Exchange's matches dates

- HTML
Published by northwestwitch over 1 year ago

scout-browser - 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

- HTML
Published by northwestwitch over 1 year ago

scout-browser - OMIM-AUTO gene panel gene symbols alias fallback

Patch release due to a current issue with in particular one gene symbol alias (POPDC1 aka BVES) on OMIM-AUTO.

[4.89.2]

Fixed

• If OMIM gene panel gene symbols are not mapping to hgnc_id, allow fallback use of a unique gene alias

- HTML
Published by dnil over 1 year ago

scout-browser - Patch general case report

[4.89.1]

Fixed

• General case report crash when encountering STR variants without source tags
• Coloring and SV inheritance patterns on general case report

- HTML
Published by dnil over 1 year ago

scout-browser - Minor version 4.89 - advanced search, more OMICS load options, chanjo2 for MT report and user level request log

[4.89]

Added

• Button on SMN CN page to search variants within SMN1 and SMN2 genes
• Options for selectively updating OMICS variants (fraser, outrider) on a case
• Log users' activity to file by specifying USERS_ACTIVITY_LOG_PATH parameter in app config
• Mean MT coverage, Mean chrom 14 coverage and Estimated mtDNA copy number on MT coverage file from chanjo2 if available
• In ClinVar multistep form, preselect ACMG criteria according to the variant's ACMG classification, if available
• Subject id search from caseS page (supporting multiple sample types e.g.) - adding indexes to speed up caseS queries
• Advanced cases search to narrow down results using more than one search parameter
• Coverage report available for any case with samples containing d4 files, even if case has no associated gene panels
• RNA delivery reports ### Changed
• Documentation for OMICS variants and updating a case
• Include both creation and deletion dates in gene panels pages
• Moved code to collect MT copy number stats for the MT report to the chanjo extension
• On the gene panelS page, show expanded gene panel version list in one column only
• IGV.js WTS loci default to zoom to a region around a variant instead of whole gene
• Refactored logging module
• Case general report no longer shows ORPHA inheritance models. OMIM models are shown colored.
• Chromosome alias tab files used in the igv.js browser, which now contain the alias for chromosome "M"
• Renamed "Comment on clinical significance" to "Comment on classification" in ClinVar multistep form
• Enable Gens CN button also for non-wgs cancer track cases ### Fixed
• Broken heading anchors in the documentation (admin-guide/login-system.md and admin-guide/setup-scout.md files)
• Avoid open login redirect attacks by always redirecting to cases page upon user login
• Stricter check of ID of gene panels to prevent file downloading vulnerability
• Removed link to the retired SPANR service. SPIDEX scores are still parsed and displayed if available from variant annotation.
• Omics variant view test coverage
• String pattern escape warnings
• Code creating Alamut links for variant genes without canonical_transcript set
• Variant delete button in ClinVar submissions page
• Broken search cases by case similarity

- HTML
Published by dnil over 1 year ago

scout-browser - Patch update igv.js to 3.0.5

[4.88.1]

Fixed

• Patch update igv.js to 3.0.5

- HTML
Published by northwestwitch over 1 year ago

scout-browser - Fixed broken database setup command, new -omics variants keys

[4.88]

Added

• Added CoLoRSdb frequency to Pop Freq column on variantS page
• Hovertip to gene panel names with associated genes in SV variant view, when variant covers more than one gene
• RNA sample ID can be provided in case load config if different from sample_id ### Fixed
• Broken scout setup database command
• Update demo VCF header, adding missing keys found on variants
• Broken upload to Codecov step in Tests & Coverage GitHub action
• Tomte DROP column names have been updated (backwards compatibility preserved for main fields)
• WTS outlierS view to display correct individual IDs for cases with multiple individuals
• WTS outlierS not displayed on WTS outlierS view

- HTML
Published by northwestwitch over 1 year ago

scout-browser - Positioning and alignment of genes cell on variantS page

Quick patch release.

[4.87.1]

Fixed

• Positioning and alignment of genes cell on variantS page

- HTML
Published by dnil over 1 year ago

scout-browser - Configure RNA build, add igv.js genome aliases

[4.87]

Added

• Option to configure RNA build on case load (default '38') ### Changed
• Tooltip on RNA alignments now shows RNA genome build version
• Updated igv.js to v3.0.4 ### Fixed
• Style of "SNVs" and "SVs" buttons on WTS Outliers page
• Chromosome alias files for igv.js
• Genes track displayed also when RNA alignments are present without splice junctions track on igv browser
• Genes track displayed again when splice junction tracks are present

- HTML
Published by dnil over 1 year ago

scout-browser - Fix loading and updating of PanelApp panels

[4.86.1]

Fixed

• Loading and updating PanelApp panels, including PanelApp green

- HTML
Published by northwestwitch over 1 year ago

scout-browser - -OMICs variants, searchable SV genes, echtvar fields parsing and more

[4.86]

Added

• Display samples' name (tooltip) and affected status directly on caseS page
• Search SVs across all cases, in given genes
• CLINVAR_API_URL param can be specified in app settings to override the URL used to send ClinVar submissions to. Intended for testing.
• Support for loading and storing OMICS data
• Parse DROP Fraser and Outrider TSVs
• Display omics variants - wts outliers (Fraser, Outrider)
• Parse GNOMAD gnomad_af and gnomad_popmax_af keys from variants annotated with echtvar
• Make removed panel optionally visible to non-admin or non maintainers
• Parse CoLoRSdb frequencies annotated in the variant INFO field with the colorsdb_af key
• Download -omics variants using the Filter and export button
• Clickable COSMIC links on IGV tracks
• Possibility to un-audit previously audited filters
• Reverted table style and removed font awesome style from IGV template
• Case status tags displayed on dashboard case overview ### Changed
• Updated igv.js to v3.0.1
• Alphabetically sort IGV track available for custom selection
• Updated wokeignore to avoid unfixable warning
• Update Chart.js to v4.4.3
• Use tornado library version >= 6.4.1
• Fewer variants in the MEI demo file
• Switch to FontAwesome v.6 instead of using icons v.5 + kit with icons v.6
• Show time (hours and minutes) additionally to date on comments and activity panel ### Fixed
• Only add expected caller keys to variant (FOUNDIN or SVDBORIGIN)
• Splice junction merged track height offset in IGV.js
• Splice junction initiation crash with empty variant obj
• Splice junction variant routing for cases with WTS but without outlier data
• Variant links to ExAC, now pointing to gnomAD, since the ExAC browser is no longer available
• Style of HPO terms assigned to a case, now one phenotype per line
• RNA sashimi view rendering should work also if the gene track is user disabled
• Respect IGV tracks chosen by user in variant IGV settings

- HTML
Published by northwestwitch over 1 year ago

scout-browser - Load IGH genes and fixes

[4.85]

Added

• Load also genes which are missing Ensembl gene ID (72 in both builds), including immunoglobulins and fragile sites ### Changed
• Unfreeze werkzeug again
• Show "(Removed)" after removed panels in dropdown
• The REVEL score is collected as the maximum REVEL score from all of the variant's transcripts
• Parse GNOMAD POPMAX values only if they are numerical when loading variants ### Fixed
• Alphabetically sort "select default panels" dropdown menu options on case page
• Show gene panel removed status on case page
• Fixed visibility of the following buttons: remove assignee, remove pinned/causative, remove comment, remove case from group

- HTML
Published by northwestwitch over 1 year ago

scout-browser - Fix load order, loqusdbapi connection and chanjo-report extension load warning

[4.84]

Changed

• Clearer error message when a loqusdb query fails for an instance that initially connected
• Do not load chanjo-report module if not needed and more visible message when it fails loading
• Converted the HgncGene class into a Pydantic class
• Swap menu open and collapse indicator chevrons - down is now displayed-open, right hidden-closed
• Linters and actions now all use python 3.11 ### Fixed
• Safer way to update variant genes and compounds that avoids saving temporary decorators into variants' database documents
• Link to HGNC gene report on gene page
• Case file load priority so that e.g. SNV get loaded before SV, or clinical before research, for consistent variant_id collisions

- HTML
Published by dnil over 1 year ago

scout-browser - Load MT VCFs, case-editing events, local IGV tracks & more

[4.83]

Added

• Edit ACMG classifications from variant page (only for classifications with criteria)
• Events for case CLI events (load case, update case, update individual)
• Support for loading and displaying local custom IGV tracks
• MANE IGV track to be used as a local track for igv.js (see scout demo config file)
• Optional separate MT VCFs, for nf-core/raredisease ### Changed
• Avoid passing verbs from CaseHandler - functions for case sample and individual in CaseEventHandler
• Hide mtDNA report and coverage report links on case sidebar for cases with WTS data only
• Modified OMIM-AUTO gene panel to include genes in both genome builds
• Moved chanjo code into a dedicated extension
• Optimise the function that collects "match-safe" genes for an institute by avoiding duplicated genes from different panels
• Users must actively select "show matching causatives/managed" on a case page to see matching numbers
• Upgraded python version from 3.8 to 3.11 in Docker images ### Fixed
• Fix several tests that relied on number of events after setup to be 0
• Removed unused load case function
• Artwork logo sync sketch with png and export svg
• Clearer exception handling on chanjo-report setup - fail early and visibly
• mtDNA report crashing when one or more samples from a case is not in the chanjo database
• Case page crashing on missing phenotype terms
• ACMG benign modifiers
• Speed up tests by caching python env correctly in Github action and adding two more test groups
• Agile issue templates were added globally to the CG-org. Adding custom issue templates to avoid exposing customers
• PanelApp panel not saving genes with empty EnsembleGeneIds list
• Speed up checking outdated gene panels
• Do not load research variants automatically when loading a case

- HTML
Published by northwestwitch over 1 year ago

scout-browser - Show STR size, red warning on sex check

[4.82.2]

Fixed

• Warning icon in case pages for individuals where confirmed_sex is false
• Show allele sizes form ExpansionHunter on STR variantS page again

- HTML
Published by dnil almost 2 years ago

scout-browser - Revert installation of flask-ldapconn

[4.82.1]

Fixed

• Revert the installation of flask-ldapconn to use the version available on PyPI to be able to push new scout releases to PyPI

- HTML
Published by northwestwitch almost 2 years ago

scout-browser - ClinVar submission updates, TRGT STR VCFs and other fixes

[4.82]

Added

• Tooltip for combined score in tables for compounds and overlapping variants
• Checkbox to filter variants by excluding genes listed in selected gene panels, files or provided as list
• STR variant information card with database links, replacing empty frequency panel
• Display paging and number of HPO terms available in the database on Phenotypes page
• On case page, typeahead hints when searching for a disease using substrings containing source ("OMIM:", "ORPHA:")
• Button to monitor the status of submissions on ClinVar Submissions page
• Option to filter cancer variants by number of observations in somatic and germline archived database
• Documentation for integrating chanjo2
• More up-to-date VEP CSQ dbNSFP frequency keys
• Parse PacBio TRGT (Tandem repeat genotyping tool) Short Tandem Repeat VCFs ### Changed
• In the case_report #panel-tables has a fixed width
• Updated IGV.js to 2.15.11
• Fusion variants in case report now contain same info as on fusion variantS page
• Block submission of somatic variants to ClinVar until we harmonise with their changed API
• Additional control on the format of conditions provided in ClinVar form
• Errors while loading managed variants from file are now displayed on the Managed Variants page
• Chanjo2 coverage button visible only when query will contain a list of HGNC gene IDs
• Use Python-Markdown directly instead of the unmaintained Flask-Markdown
• Use Markupsafe instead of long deprecated, now removed Flask Markup
• Prepare to unfreeze Werkzeug, but don't actually activate until chanjo can deal with the change ### Fixed
• Submit requests to Chanjo2 using HTML forms instead of JSON data
• Research somatic variants link name on caseS page
• Broken Install the HTML 2 PDF renderer step in a GitHub action
• Fix ClinVar form parsing to not include ":" in conditionType.id when condition conditionType.db is Orphanet
• Fix condition dropdown and pre-selection on ClinVar form for cases with associated ORPHA diagnoses
• Improved visibility of ClinVar form in dark mode
• End coordinates for indels in ClinVar form
• Diagnoses API search crashing with empty search string
• Variant's overlapping panels should show overlapping of variant genes against the latest version of the panel
• Case page crashing when case has both variants in a ClinVar submission and pinned not loaded variants
• Installation of git in second build stage of Dockerfile, allowing correct installation of libraries

- HTML
Published by dnil almost 2 years ago

scout-browser - Somatic SV IGH-DUX4 tag, case report improvements and other fixes

[4.81]

Added

• Tag for somatic SV IGH-DUX4 detection samtools script ### Changed
• Upgraded Bootstrap version in reports from 4.3.1 to 5.1.3 ### Fixed
• Buttons layout in HPO genes panel on case page
• Added back old variant rankscore index with different key order to help loading on demo instance
• Cancer case_report panel-table no longer contains inheritance information
• Case report pinned variants card now displays info text if all pinned variants are present in causatives
• Darkmode setting now applies to the comment-box accordion
• Typo in case report causing cancer_rank_options is undefined error

- HTML
Published by northwestwitch almost 2 years ago

scout-browser - chanjo2 integration, index updates, frontend and Fusion gene fixes

[4.80]

Added

• Support for .d4 files coverage using chanjo2 (Case page sidebar link) with test
• Link to chanjo2 coverage report and coverage gene overview on gene panel page
• Link to chanjo2 coverage report on Case page, HPO dynamic gene list
• Link to genes coverage overview report on Case page, HPO dynamic gene list ### Changed
• All links in disease table on diagnosis page now open in a new tab
• Dark mode settings applied to multi-selects on institute settings page
• Comments on case and variant pages can be viewed by expanding an accordion
• On case page information on pinned variants and variants submitted to ClinVar are displayed in the same table
• Demo case file paths are now stored as absolute paths
• Optimised indices to address slow queries
• On case page default panels are now found at the top of the table, and it can be sorted by this trait ### Fixed
• On variants page, search for variants in genes present only in build 38 returning no results
• Pin/unpin with API was not able to make event links
• A new field Explanation for multiple conditions is available in ClinVar for submitting variants with more than one associated condition
• Fusion genes with partners lacking gene HGNC id will still be fully loaded
• Fusion variantS export now contains fusion variant specific columns
• When Loqusdb observations count is one the table includes information on if observation was for the current or another case

- HTML
Published by dnil almost 2 years ago

scout-browser -

[4.79.1]

Fixed

• Exporting variants without rank score causing page to crash
• Display custom annotations also on cancer variant page

- HTML
Published by northwestwitch almost 2 years ago

scout-browser - More ORPHA-related refactoring, other improvements and fixes

[4.79]

Added

• Added tags for Sniffles and CNVpytor, two LRS SV callers
• Button on case page for displaying STR variants occurring in the dynamic HPO panel
• Display functional annotation relative to variant gene's MANE transcripts on variant summary, when available
• Links to ACMG structural variant pathogenicity classification guidelines
• Phenomodels checkboxes can now include orpha terms
• Add incidental finding to case tags ### Changed
• In the diagnoses page genes associated with a disease are displayed using hgnc symbol instead of hgnc id
• Refactor view route to allow navigation directly to unique variant document id, improve permissions check
• Do not show MANE and MANE Plus Clinical transcripts annotated from VEP (saved in variants) but collect this info from the transcripts database collection
• Refactor view route to allow navigation directly to unique case id (in particular for gens)
• Institutes to share cases with on institute's settings page now displays institutes names and IDs
• View route with document id selects view template based on variant category ### Fixed
• Refactored code in cases blueprints and variant_events adapter (set diseases for partial causative variants) to use "disease" instead of "omim" to encompass also ORPHA terms
• Refactored code in scout/parse/omim.py and scout/parse/disease_terms.py to use "disease" instead of "phenotype" to differentiate from HPO terms
• Be more careful about checking access to variant on API access
• Show also ACMG VUS on general report (could be missing if not e.g. pinned)

- HTML
Published by northwestwitch almost 2 years ago

scout-browser - Case status labels, ORPHA disorders, MANE and ClinVar updates

[4.78]

Added

• Case status labels can be added, giving more finegrained details on a solved status (provisional, diagnostic, carrier, UPD, SMN, ...)
• New SO terms: sequence_variant and coding_transcript_variant
• More MEI specific annotation is shown on the variant page
• Parse and save MANE transcripts info when updating genes in build 38
• Mane Select and Mane Plus Clinical badges on Gene page, when available
• ClinVar submission can now be downloaded as a json file
• API endpoint to pin variant
• Display common/uncommon/rare on summary of mei variant page ### Changed
• In the ClinVar form, database and id of assertion criteria citation are now separate inputs
• Customise institute settings to be able to display all cases with a certain status on cases page (admin users)
• Renamed Clinical Significance to Germline Classification on multistep ClinVar form
• Changed the "x" in cases.utils.remove_form button text to red for better visibility in dark mode
• Update GitHub actions
• Default loglevel up to INFO, making logs with default start easier to read
• Add XTR region to PAR region definition
• Diagnoses can be searched on diagnoses page without waiting for load first ### Fixed
• Removed log info showing hgnc IDs used in variantS search
• Maintain Matchmaker Exchange and Beacon submission status when a case is re-uploaded
• Inheritance mode from ORPHA should not be confounded with the OMIM inheritance model
• Decipher link URL changes
• Refactored code in cases blueprints to use "disease" instead of "omim" to encompass also ORPHA terms

- HTML
Published by dnil about 2 years ago

scout-browser - Updates to ClinVar submission, GnomAD constraints, ORPHA and bug fixes

[4.77]

Added

• Orpha disease terms now include information on inheritance
• Case loading via .yaml config file accepts subjectid and phenotypegroups (if previously defined as constant default or added per institute)
• Possibility to submit variants associated with Orphanet conditions to ClinVar
• Option update path to .d4 files path for individuals of an existing case using the command line
• More constraint information is displayed per gene in addition to pLi: missense and LoF OE, CI (inluding LOEUF) and Z-score. ### Changed
• Introduce validation in the ClinVar multistep form to make sure users provide at least one variant-associated condition
• CLI scout update individual accepts subject_id
• Update ClinVar inheritance models to reflect changes in ClinVar submission API
• Handle variant-associated condition ID format in background when creating ClinVar submissions
• Replace the code that downloads Ensembl genes, transcripts and exons with the Schug web app
• Add more info to error log when transcript variant frequency parsing fails.
• GnomAD v4 constraint information replaces ExAC constraints (pLi). ### Fixed
• Text input of associated condition in ClinVar form now aligns to the left
• Alignment of contents in the case report has been updated
• Missing number of phenotypes and genes from case diagnoses
• Associate OMIM and/or ORPHA diagnoses with partial causatives
• Visualization of partial causatives' diagnoses on case page: style and links
• Revert style of pinned variants window on the case page
• Rename Clinical significanc to Germline classification in ClinVar submissions exported files
• Rename Clinical significance citations to Classification citations in ClinVar submissions exported files
• Rename Comment on clinical significance to Comment on classification in ClinVar submissions exported files
• Show matching partial causatives on variant page
• Matching causatives shown on case page consisting only of variant matching the default panels of the case - bug introduced since scout v4.72 (Oct 18, 2023)
• Missing somatic variant read depth leading to report division by zero

- HTML
Published by dnil about 2 years ago

scout-browser - d4 files, ClinVar event audit, and winter bug fixes

[4.76]

Added

• Pydantic validation of image paths provided in case load config file
• Info on the user which created a ClinVar submission, when available
• Associate .d4 files to case individuals when loading a case via config file ### Changed
• In diagnoses page the load of diseases are initiated by clicking a button
• Revel score, Revel rank score and SpliceAI values are also displayed in Causatives and Validated variants tables
• Remove unused functions and tests
• Analysis type and direct link from cases list for OGM cases
• Removed unused case_obj parameter from server/blueprints/variant/controllers/observations function
• Possibility to reset ClinVar submission ID
• Allow ClinVar submissions with custom API key for users registered as ClinVar submitters or when institute doesn't have a preset list of ClinVar submitters
• Ordered event verbs alphabetically and created ClinVar-related user events
• Removed the unused "no-variants" option from the load case command line ### Fixed
• All disease_terms have gene HGNC ids as integers when added to the scout database
• Disease_term identifiers are now prefixed with the name of the coding system
• Command line crashing with error when updating a user that doesn't exist
• Thaw coloredlogs - 15.0.1 restores errorhandler issue
• Thaw crypography - current base image and library version allow Docker builds
• Missing delete icons on phenomodels page
• Missing cryptography lib error while running Scout container on an ARM processor
• Round CADD values with many decimals on causatives and validated variants pages
• Dark-mode visibility of some fields on causatives and validated variants pages
• Clinvar submitters would be cleared when unprivileged users saved institute settings page
• Added a default empty string in cases search form to avoid None default value
• Page crashing when user tries to remove the same variant from a ClinVar submission in different browser tabs
• Update more GnomAD links to GnomAD v4 (v38 SNVs, MT vars, STRs)
• Empty cells for RNA fusion variants in Causatives and Verified variants page
• Submenu icons missing from collapsible actionbar
• The collapsible actionbar had some non-collapsing overly long entries
• Cancer observations for SVs not appearing in the variant details view
• Archived local observations not visible on cancer variantS page
• Empty Population Frequency column in the Cancer SV Variants view
• Capital letters in ClinVar events description shown on case page

- HTML
Published by dnil about 2 years ago

scout-browser - Display gene panel membership on gene hovers, Fusion variant filters, Alamut link improvements, and more

[4.75]

Added

• Hovertip to gene panel names with associated genes in variant view, when variant covers more than one gene
• Tests for panel to genes
• Download of Orphadata enproduct6 and enproduct4 from CLI
• Parse and save database_found key/values for RNA fusion variants
• Added fusionscore, ffpm, splitreads, junctionreads and fusioncaller to the list of filters on RNA fusion variants page
• Renamed the function get_mei_info to set_mei_info to be consistent with the other functions
• Fixed removing None key/values from parsed variants ### Changed
• Allow use of projections when retrieving gene panels
• Do not save custom images as binary data into case and variant database documents
• Retrieve and display case and variant custom images using image's saved path
• Cases are activated by viewing FSHD and SMA reports
• Split multi-gene SNV variants into single genes when submitting to Matchmaker Exchange
• Alamut links also on the gene level, using transcript and HGVS: better for indels. Keep variant link for missing HGVS
• Thaw WTForms - explicitly coerce form decimal field entries when filters fetched from db ### Fixed
• Removed some extra characters from top of general report left over from FontAwsome fix
• Do not save fusion variants-specific key/values in other types of variants
• Alamut link for MT variants in build 38
• Convert RNA fusions variants tool_hits and fusion_score keys from string to numbers
• Fix genotype reference and alternative sequencing depths defaulting to -1 when values are 0
• DecimalFields were limited to two decimal places for several forms - lifting restrictions on AF, CADD etc.

- HTML
Published by dnil about 2 years ago

scout-browser - Fix BioNano API FSHD report requests, missing icons and load OMIM terms not associated to genes

[4.74.1]

Changed

• Parse and save into database also OMIM terms not associated to genes ### Fixed
• BioNano API FSHD report requests are GET in Access 1.8, were POST in 1.7
• Update more FontAwesome icons to avoid Pro icons
• Test if files still exist before attempting to load research variants

- HTML
Published by northwestwitch over 2 years ago

scout-browser - Loading of RNA fusion variants, missing icons fix & other

[4.74]

Added

• SNVs and Indels, MEI and str variants genes have links to Decipher
• An owner + case display name index for cases database collection
• Test and fixtures for RNA fusion case page
• Load and display fusion variants from VCF files as the other variant types
• Option to update case document with path to mei variants (clinical and research) ### Changed
• Details on variant type and category for audit filters on case general report
• Enable Gens CN profile button also in somatic case view
• Fix case of analysis type check for Gens analysis button - only show for WGS ### Fixed
• loqusdb table no longer has empty row below each loqusid
• MatchMaker submission details page crashing because of change in date format returned by PatientMatcher
• Variant external links buttons style does not change color when visited
• Hide compounds with compounds follow filter for region or function would fail for variants in multiple genes
• Updated FontAwesome version to fix missing icons

- HTML
Published by northwestwitch over 2 years ago

scout-browser - Fix loading of cases without display name and other improvements

[4.73]

Added

• Shortcut button for HPO panel MEI variants from case page
• Export managed variants from CLI ### Changed
• STRs visualization on case panel to emphasize abnormal repeat count and associated condition
• Removed cytoband column from STRs variant view on case report
• More long integers formatted with thin spaces, and copy to clipboard buttons added ### Fixed
• OMIM table is scrollable if higher than 700px on SV page
• Pinned variants validation badge is now red for false positives.
• Case display name defaulting to case ID when family_name or display_name are missing from case upload config file
• Expanded menu visible at screen sizes below 1000px now has background color
• The image in ClinVar howto-modal is now responsive
• Clicking on a case in case groups when case was already removed from group in another browser tab

- HTML
Published by northwestwitch over 2 years ago

scout-browser - GnomAD default build change

A patch release to correct links to match the new GnomAD v4 release, which changed default build to 38 in their API just in time for ASHG.

[4.72.4]

Changed

• Automatic test mongod version increased to v7 ### Fixed
• GnomAD now defaults to hg38 - change build 37 links accordingly

- HTML
Published by dnil over 2 years ago

scout-browser - Fix cancer cases general report report

[4.72.3]

Fixed

• Somatic general case report small variant table can crash with unclassified variants

- HTML
Published by northwestwitch over 2 years ago

scout-browser - v4.72.2 - patch it while you can

We have patched the problems that occurred with parsing the updated OMIM files in the 4.72 release, sped up and reduced the memory footprint for the case, caseS and disease_terms.

We also introduce a few small frontend changes; increasing the download limit for STR variants to the same number as other ones, parenthood check fails are more obvious in red, and large numbers with thin spaces don't split across lines so easily.

[4.72.2]

Changed

• A gunicorn maxrequests parameter for Docker server image - default to 1200
• STR export limit increased to 500, as for other variants
• Prevent long number wrapping and use thin spaces for separation, as per standards from SI, NIST, IUPAC, BIPM.
• Speed up case retrieval and lower memory use by projecting case queries
• Make relatedness check fails stand out a little more to new users
• Speed up case retrieval and lower memory use by projecting case queries
• Speed up variant pages by projecting only the necessary keys in disease collection query ### Fixed
• Huge memory use caused by cases and variants pages pulling complete disease documents from DB
• Do not include genes fetched from HPO terms when loading diseases
• Consider the renamed fields Approved Symbol -> Approved Gene Symbol and Gene Symbols -> Gene/Locus And Other Related Symbols when parsing OMIM terms from genemap2.txt file

- HTML
Published by dnil over 2 years ago

scout-browser - Fixed high memory usage issue and jinja filter error

[4.72.1]

Fixed

• Jinja filter that renders long integers
• Case cache when looking for causatives in other cases causing the server to hang

- HTML
Published by northwestwitch over 2 years ago

scout-browser - 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 casematchingcausatives
• 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

- HTML
Published by dnil over 2 years ago

scout-browser - 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

- HTML
Published by dnil over 2 years ago

scout-browser - 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

- HTML
Published by dnil over 2 years ago

scout-browser - 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

- HTML
Published by dnil over 2 years ago

scout-browser - 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

- HTML
Published by northwestwitch almost 3 years ago

scout-browser - 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

- HTML
Published by dnil almost 3 years ago

scout-browser - 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

- HTML
Published by dnil almost 3 years ago

scout-browser - Fixed creating case reports with str variants containing comments

[4.65.2]

Fixed

• Generating general case report with str variants containing comments

- HTML
Published by northwestwitch almost 3 years ago

scout-browser - 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)

- HTML
Published by northwestwitch almost 3 years ago

scout-browser - 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 updatedat and createdat 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

- HTML
Published by dnil almost 3 years ago

scout-browser - PanelApp Green genes, ACMG modification links, research variant counting and UI fixes

[4.64]

Added

• Create/Update a gene panel containing all PanelApp green genes (scout update panelapp-green -i <cust_id>)
• Links for ACMG pathogenicity impact modification on the ACMG classification page ### Changed
• Open local observation matching cases in new windows ### Fixed
• Matching manual ranked variants are now shown also on the somatic variant page
• VarSome links to hg19/GRCh37
• Managed variants filter settings lost when navigating to additional pages
• Collect the right variant category after submitting filter form from research variantS page
• Beacon links are templated and support variants in genome build 38

- HTML
Published by dnil about 3 years ago

scout-browser - nf-core-rnafusion reports, modified ACMG, risk factors and ClinVar submission fixes

[4.63]

Added

• Display data sharing info for ClinVar, Matchmaker Exchange and Beacon in a dedicated column on Cases page
• Test for commands.download.omim.print_omim
• Display dismissed variants comments on general case report
• Modify ACMG pathogenicity impact (most commonly PVS1, PS3) based on strength of evidence with lab director's professional judgement
• REViewer button on STR variant page
• Alamut institution parameter in institute settings for Alamut Visual Plus software
• Added Manual Ranks Risk Factor, Likely Risk Factor and Uncertain Risk Factor
• Display matching manual ranks from previous cases the user has access to on VariantS and Variant pages
• Link to gnomAD gene SVs v2.1 for SV variants with gnomAD frequency
• Support for nf-core/rnafusion reports ### Changed
• Display chrY for sex unknown
• Deprecate legacy scout_load() method API call.
• Message shown when variant tag is updated for a variant
• When all ACMG classifications are deleted from a variant, the current variant classification status is also reset.
• Refactored the functions that collect causative variants
• Removed scripts/generate_test_data.py ### Fixed
• Default IGV tracks (genes, ClinVar, ClinVar CNVs) showing even if user unselects them all
• Freeze Flask-Babel below v3.0 due to issue with a locale decorator
• Thaw Flask-Babel and fix according to v3 standard. Thank you @TkTech!
• Show matching causatives on somatic structural variant page
• Visibility of gene names and functional annotations on Causatives/Verified pages
• Panel version can be manually set to floating point numbers, when modified
• Causatives page showing also non-causative variants matching causatives in other cases
• ClinVar form submission for variants with no selected transcript and HGVS
• Validating and submitting ClinVar objects not containing both Variant and Casedata info

New Contributors

• @fevac made their first contribution in https://github.com/Clinical-Genomics/scout/pull/3747

Full Changelog: https://github.com/Clinical-Genomics/scout/compare/v4.62...v4.63

- HTML
Published by dnil about 3 years ago

scout-browser - Fix bug in case group feature

[4.62.1]

Fixed

• Case page crashing when adding a case to a group without providing a valid case name

- HTML
Published by northwestwitch about 3 years ago

scout-browser - v4.62 - ClinVar API submission, Phenopackets and REViewer fallback

[4.62]

### Added - Validate ClinVar submission objects using the ClinVar API - Wrote tests for case and variant API endpoints - Create ClinVar submissions from Scout using the ClinVar API - Export Phenopacket for affected individual - Import Phenopacket from JSON file or Phenopacket API backend server - Use the new case name option for GENS requests - Pre-validate refseq:HGVS items using VariantValidator in ClinVar submission form

Fixed

• Fallback for empty alignment index for REViewer service
• Source link out for MIP 11.1 reference STR annotation
• Avoid duplicate causatives and pinned variants
• ClinVar clinical significance displays only the ACMG terms when user selects ACMG 2015 as assertion criteria
• Spacing between icon and text on Beacon and MatchMaker links on case page sidebar
• Truncate IDs and HGVS representations in ClinVar pages if longer than 25 characters
• Update ClinVar submission ID form
• Handle connection timeout when sending requests requests to external web services
• Validate any ClinVar submission regardless of its status
• Empty Phenopackets import crashes
• Stop Spinner on Phenopacket JSON download ### Changed
• Updated ClinVar submission instructions

- HTML
Published by dnil about 3 years ago

scout-browser - Patches to ClinVar submission flow

[4.61.1]

Fixed

• Added UMLS as an option of Condition ID type in ClinVar Variant downloaded files
• Missing value for Condition ID type in ClinVar Variant downloaded files
• Possibility to open, close or delete a ClinVar submission even if it doesn't have an associated name
• Save SV type, ref and alt n. copies to exported ClinVar files
• Inner and outer start and stop SV coordinates not exported in ClinVar files
• ClinVar submissions page crashing when SV files don't contain breakpoint exact coordinates
• Align OMIM diagnoses with delete diagnosis button on case page
• In ClinVar form, reset condition list and customize help when condition ID changes

- HTML
Published by dnil over 3 years ago

scout-browser - Version 4.61: ClinVar submission simplified, inheritance model colors, and more custom report types

[4.61]

Added

• Filter case list by cases with variants in ClinVar submission
• Filter case list by cases containing RNA-seq data - genefusionreports and sample-level tracks (splice junctions and RNA coverage)
• Additional case category Ignored, to be used for cases that don't fall in the existing 'inactive', 'archived', 'solved', 'prioritized' categories
• Display number of cases shown / total number of cases available for each category on Cases page
• Moved buttons to modify case status from sidebar to main case page
• Link to Mutalyzer Normalizer tool on variant's transcripts overview to retrieve official HVGS descriptions
• Option to manually load RNA MULTIQC report using the command scout load report -t multiqc_rna
• Load RNA MULTIQC automatically for a case if config file contains the multiqc_rna key/value
• Instructions in admin-guide on how to load case reports via the command line
• Possibility to filter RD variants by a specific genotype call
• Distinct colors for different inheritance models on RD Variant page
• Gene panels PDF export with case variants hits by variant type
• A couple of additional README badges for GitHub stats
• Upload and display of pipeline reference info and executable version yaml files as custom reports
• Testing CLI on hasta in PR template ### Changed
• Instructions on how to call dibs on scout-stage server in pull request template
• Deprecated CLI commands scout load <delivery_report, gene_fusion_report, coverage_qc_report, cnv_report> to replace them with command scout load report -t <report type>
• Refactored code to display and download custom case reports
• Do not export Assertion method and Assertion method citation to ClinVar submission files according to changes to ClinVar's submission spreadsheet templates.
• Simplified code to create and download ClinVar CSV files
• Colorize inheritance models badges by category on VariantS page
• Safe variants matching badge more visible on case page ### Fixed
• Non-admin users saving institute settings would clear loqusdb instance selection
• Layout of variant position, cytoband and type in SV variant summary
• Broken Build Status - GitHub badge on GitHub README page
• Visibility of text on grey badges in gene panels PDF exports
• Labels for dashboard search controls
• Dark mode visibility for ClinVar submission
• Whitespaces on outdated panel in extent report

- HTML
Published by dnil over 3 years ago

scout-browser - Mitosign, disabled rerun emails, safe variant matching and misc fixes

[4.60]

Added

• Mitochondrial deletion signatures (mitosign) can be uploaded and shown with mtDNA report
• A Type of analysis column on Causatives and Validated variants pages
• List of "safe" gene panels available for matching causatives and managed variants in institute settings, to avoid secondary findings
• svdb_origin as a synonym for FOUND_IN to complement set for variants found by all callers ### Changed
• Hide removed gene panels by default in panels page
• Removed option for filtering cancer SVs by Tumor and Normal alt AF
• Hide links to coverage report from case dynamic HPO panel if cancer analysis
• Remove rerun emails and redirect users to the analysis order portal instead
• Updated clinical SVs igv.js track (dbVar) and added example of external track from https://trackhubregistry.org/ ### Fixed
• If trying to load a badly formatted .tsv file an error message is displayed.
• Avoid showing case as rerun when first attempt at case upload failed
• Dynamic autocomplete search not working on phenomodels page
• Callers added to variant when loading case
• Now possible to update managed variant from file without deleting it first
• Missing preselected chromosome when editing a managed variant
• Preselected variant type and subtype when editing a managed variant
• Typo in dbVar ClinVar track, hg19

- HTML
Published by northwestwitch over 3 years ago

scout-browser - REViewer-Service integration and improvements

[4.59]

Added

• Button to go directly to HPO SV filter variantS page from case
• Scout-REViewer-Service integration - show REViewer picture if available
• Link to HPO panel coverage overview on Case page
• Specify a confidence threshold (green|amber|red) when loading PanelApp panels
• Functional annotations in variants lists exports (all variants)
• Cancer/Normal VAFs and COSMIC ids in in variants lists exports (cancer variants) ### Changed
• Better visualization of regional annotation for long lists of genes in large SVs in Variants tables
• Order of cells in variants tables
• More evident links to gene coverage from Variant page
• Gene panels sorted by display name in the entire Case page
• Round CADD and GnomAD values in variants export files ### Fixed
• HPO filter button on SV variantS page
• Spacing between region|function cells in SVs lists
• Labels on gene panel Chanjo report
• Fixed ambiguous duplicated response headers when requesting a BAM file from /static
• Visited color link on gene coverage button (Variant page)

- HTML
Published by northwestwitch over 3 years ago

scout-browser - Fix search on Cases and Dashboard

[4.58.1]

Fixed

• Case search with search strings that contain characters that can be escaped

- HTML
Published by northwestwitch over 3 years ago

scout-browser - New features and maintenance

[4.58]

Added

• Documentation on how to create/update PanelApp panels
• Add filter by local observations (archive) to structural variants filters
• Add more splicing consequences to SO term definitions
• Search for a specific gene in all gene panels
• Institute settings option to force show all variants on VariantS page for all cases of an institute
• Filter cases by validation pending status
• Link to The Clinical Knowledgebase (CKB) (https://ckb.jax.org/) in cancer variant's page ### Fixed
• Added a not-authorized auto-login fixture according to changes in Flask-Login 0.6.2
• Renamed cache_timeout param name of flask.sendfile function to `maxage` (Flask 2.2 compliant)
• Replaced deprecated app.config["JSON_SORT_KEYS"] with app.json.sort_keys in app settings
• Bug in gene variants page (All SNVs and INDELs) when variant gene doesn't have a hgnc id that is found in the database
• Broken export of causatives table
• Query for genes in build 38 on Search SNVs and INDELs page
• Prevent typing special characters ^<>?!=\/ in case search form
• Search matching causatives also among research variants in other cases
• Links to variants in Verified variants page
• Broken filter institute cases by pinned gene
• Better visualization of long lists of genes in large SVs on Causative and Verified Variants page
• Reintroduced missing button to export Causative variants
• Better linking and display of matching causatives and managed variants ### Changed
• State that loqusdb observation is in current case if observations count is one and no cases are shown
• Better pagination and number of variants returned by queries in Search SNVs and INDELs page
• Refactored and simplified code used for collecting gene variants for Search SNVs and INDELs page
• Fix sidebar panel icons in Case view
• Fix panel spacing in Case view
• Removed unused database sanger_ordered and case_id,category,rank_score indexes (variant collection)
• Verified variants displayed in a dedicated page reachable from institute sidebar
• Unified stats in dashboard page
• Improved gene info for large SVs and cancer SVs
• Remove the unused variant.str_variant endpoint from variant views
• Easier editing of HPO gene panel on case page
• Assign phenotype panel less cramped on Case page
• Causatives and Verified variants pages to use the same template macro
• Allow hyphens in panel names

- HTML
Published by northwestwitch over 3 years ago

scout-browser - Fixed parsing of DR key in VCF files created with Tiddit

[4.57.4]

Fixed

• Parsing of variant.FORMAT "DR" key in parse variant file

- HTML
Published by northwestwitch over 3 years ago

scout-browser - Validated variants export fixes

[4.57.3]

Fixed

• Export of STR verified variants
• Do not download as verified variants first verified and then reset to not validated
• Avoid duplicated lines in downloaded verified variants reflecting changes in variant validation status

- HTML
Published by northwestwitch over 3 years ago

scout-browser - Fixed export of verified variants and ranked cancer variants pages

[4.57.2]

Fixed

• Export of verified variants when variant gene has no transcripts
• HTTP 500 when visiting a the details page for a cancer variant that had been ranked with genmod

- HTML
Published by northwestwitch over 3 years ago

scout-browser - Fix updating/replacing a gene panel using a malformed file

[4.57.1]

Fixed

• [ ] Updating/replacing a gene panel from file with a corrupted or malformed file

- HTML
Published by northwestwitch over 3 years ago

scout-browser - Multiple loqusdb instances, dismiss counts and user events timeline

[4.57]

Added

• Display last 50 or 500 events for a user in a timeline
• Show dismiss count from other cases on matching variantS
• Save Beacon-related events in events collection
• Institute settings allow saving multiple loqusdb instances for one institute
• Display stats from multiple instances of loqusdb on variant page
• Display date and frequency of obs derived from count of local archive observations from MIP11 (requires fix in MIP) ### Changed
• Prior ACMG classifications view is no longer limited by pathogenicity ### Fixed
• Visibility of Sanger ordered badge on case page, light mode
• Some of the DataTables tables (Phenotypes and Diagnoses pages) got a bit dark in dark mode
• Remove all redundancies when displaying timeline events (some events are saved both as case-related and variant-related)
• Missing link in saved MatchMaker-related events
• Genes with mixed case gene symbols missing in PanelApp panels
• Alignment of elements on the Beacon submission modal window
• Locus info links from STR variantS page open in new browser tabs

- HTML
Published by northwestwitch over 3 years ago

scout-browser - v4.56 - CLI database update fix and a PANEL-UMI analysis category

[4.56]

Added

• Test for PanelApp panels loading
• panel-umi tag option when loading cancer analyses ### Changed
• Black text to make comments more visible in dark mode
• Loading PanelApp panels replaces pre-existing panels with same version
• Removed sidebar from Causatives page - navigation is available on the top bar for now ### Fixed
• Remove a:visited css style from all buttons
• Update of HPO terms via command line
• Background color of MIXED and PANEL-UMI sequencing types on cases page
• Fixed regex error when searching for cases with query ending with \
• Gene symbols on Causatives page lighter in dark mode
• SpliceAI tooltip of multigene variants

- HTML
Published by dnil over 3 years ago

scout-browser - v4.55 - force update and fixes

[4.55]

Changed

• Represent different tumor samples as vials in cases page
• Option to force-update the OMIM panel ### Fixed
• Low tumor purity badge alignment in cancer samples table on cancer case view
• VariantS comment popovers reactivate on hover
• Updating database genes in build 37
• ACMG classification summary hidden by sticky navbar
• Logo backgrounds fixed to white on welcome page
• Visited links turn purple again
• Style of link buttons and dropdown menus
• Update KUH and GMS logos
• Link color for Managed variants

- HTML
Published by dnil over 3 years ago

scout-browser - 4.54 - Dark Mode, Bootstrap 5

[4.54]

Added

• Dark mode, using browser/OS media preference
• Allow marking case as solved without defining causative variants
• Admin users can create missing beacon datasets from the institute's settings page
• GenCC links on gene and variant pages
• Deprecation warnings when launching the app using a .yaml config file or loading cases using .ped files ### Changed
• Improved HTML syntax in case report template
• Modified message displayed when variant rank stats could not be calculated
• Expanded instructions on how to test on CG development server (cg-vm1)
• Added more somatic variant callers (Balsamic v9 SNV, develop SV) ### Fixed
• Remove load demo case command from docker-compose.yml
• Text elements being split across pages in PDF reports
• Made login password field of type password in LDAP login form
• Gene panels HTML select in institute's settings page
• Bootstrap upgraded to version 5
• Fix some Sourcery and SonarCloud suggestions
• Escape special characters in case search on institute and dashboard pages
• Broken case PDF reports when no Madeline pedigree image can be created
• Removed text-white links style that were invisible in new pages style
• Variants pagination after pressing "Filter variants" or "Clinical filter"
• Layout of buttons Matchmaker submission panel (case page)
• Removing cases from Matchmaker (simplified code and fixed functionality)
• Reintroduce check for missing alignment files purged from server

- HTML
Published by dnil over 3 years ago

scout-browser - MIP11 compatibility adjustments and vulnerability fixes

[4.53]

Added

Changed

• Point Alamut API key docs link to new API version
• Parse dbSNP id from ID only if it says "rs", else use VEP CSQ fields
• Removed MarkupSafe from the dependencies ### Fixed
• Reintroduced loading of SVs for demo case 643595
• Successful parse of FOUND_IN should avoid GATK caller default
• All vulnerabilities flagged by SonarCloud

- HTML
Published by northwestwitch almost 4 years ago

scout-browser - Security fixes, new features and general maintenance

[4.52]

Added

• Demo cancer case gets loaded together with demo RD case in demo instance
• Parse REVELscore alongside REVELrankscore from csq field and display it on SNV variant page
• Rank score results now show the ranking range
• cDNA and protein changes displayed on institute causatives pages
• Optional SESSIONTIMEOUTMINUTES configuration in app config files
• Script to convert old OMIM case format (list of integers) to new format (list of dictionaries)
• Additional check for user logged in status before serving alignment files
• Download .cgh files from cancer samples table on cancer case page
• Number of documents and date of last update on genes page ### Changed
• Verify user before redirecting to IGV alignments and sashimi plots
• Build case IGV tracks starting from case and variant objects instead of passing all params in a form
• Unfreeze Werkzeug lib since Flask_login v.0.6 with bugfix has been released
• Sort gene panels by name (panelS and variant page)
• Removed unused server.blueprints.alignviewers.unindexed_remote_static endpoint
• User sessions to check files served by server.blueprints.alignviewers.remote_static endpoint
• Moved Beacon-related functions to a dedicated app extension
• Audit Filter now also loads filter displaying the variants for it ### Fixed
• Handle attachment_filename parameter renamed to download_name when Flask 2.2 will be released
• Removed cursor timeout param in cases find adapter function to avoid many code warnings
• Removed stream argument deprecation warning in tests
• Handle no intervals found warning in load_region test
• Beacon remove variants
• Protect remote_cors function in alignviewers view from Server-Side Request Forgery (SSRF)
• Check creation date of last document in gene collection to display when genes collection was updated last

- HTML
Published by northwestwitch almost 4 years ago

scout-browser - 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

- HTML
Published by dnil almost 4 years ago

scout-browser - Fixed missing links to matching STR causatives

[4.50.1]

Fixed

• Show matching causative STRrepid for legacy str variants (pre Stranger hgncid)

- HTML
Published by northwestwitch almost 4 years ago

scout-browser - 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 hg191kgdecoy 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

- HTML
Published by dnil almost 4 years ago

scout-browser - Report PDF export improvements and other fixes

[4.49]

Fixed

• Pydantic model types for genomebuild, madelineinfo, peddypedcheck and peddysexcheck, rankmodelversion and svrankmodel_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

- HTML
Published by northwestwitch about 4 years ago

scout-browser - Fix general report PDF export for cases with no pedigree

[4.48.1]

Fixed

• General case PDF report for recent cases with no pedigree

- HTML
Published by northwestwitch about 4 years ago

scout-browser - 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

- HTML
Published by dnil about 4 years ago

scout-browser - 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

- HTML
Published by northwestwitch about 4 years ago

scout-browser - 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, ..)

- HTML
Published by northwestwitch about 4 years ago

scout-browser - 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 flaskldap3login> 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

- HTML
Published by dnil about 4 years ago

scout-browser - 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

- HTML
Published by dnil about 4 years ago

scout-browser - Improved gene symbol alias handling in variants filtering

[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

- HTML
Published by northwestwitch about 4 years ago

scout-browser - New gene index in OMIM diagnoses and avoid dropping HPO and OMIM terms collection when updating database

[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

- HTML
Published by northwestwitch over 4 years ago

scout-browser - Fix missing indexes after genes update. Custom collections index building/updating

[4.43]

Added

• Specify which collection(s) update/build indexes for ### Changed ### Fixed
• Do not drop genes and transcripts collections when updating genes via the command line

- HTML
Published by northwestwitch over 4 years ago

scout-browser - Freeze PyMongo version, speedup creating/updating of gene panels and Phenomizer timeout problems

[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

- HTML
Published by northwestwitch over 4 years ago

scout-browser - Better cancer SV filtering, stricter config file checks on case loading and other improvements

[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 displayname 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.

- HTML
Published by northwestwitch over 4 years ago