Clinical-Genomics/scout issues and pull requests

#3891 - Bump version to 4.66

Pull Request - State: closed - Opened by dnil over 1 year ago - 3 comments

#3890 - Gens structural variant page link individual id

Pull Request - State: closed - Opened by dnil over 1 year ago - 2 comments

#3889 - Update custom case reports load admin documentation

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 2 comments
Labels: Easy, docs

#3888 - Fix Font Awesome 6 lib integrity check

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 5 comments
Labels: Easy

#3887 - Failed integrity for Font Awesome lib

Issue - State: closed - Opened by northwestwitch over 1 year ago - 1 comment
Labels: bug, Frontend

#3886 - flag variants with polymorphism in the same codon?

Issue - State: closed - Opened by ielvers over 1 year ago - 3 comments

#3885 - Move phenomodels under a dedicated blueprint

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments
Labels: Refactor

#3884 - Filter by `SOMATICSCORE`

Issue - State: closed - Opened by khurrammaqbool over 1 year ago - 1 comment
Labels: Under discussion, Cancer

#3883 - add `SOMATICSCORE` for SVs

Issue - State: closed - Opened by khurrammaqbool over 1 year ago - 1 comment
Labels: enhancement, Cancer

#3882 - Patch release 4.65.2

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments

#3881 - Fix typo for str variants with comment in general report

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments
Labels: Bugfix

#3880 - variant_related_comments' is undefined

Issue - State: closed - Opened by northwestwitch over 1 year ago
Labels: bug

#3879 - Merge pinned and clinvar submitted vars sections on case page

Issue - State: closed - Opened by northwestwitch over 1 year ago
Labels: Easy, Frontend

#3878 - coverage report -> server error

Issue - State: closed - Opened by ielvers over 1 year ago - 4 comments
Labels: Clinical Genomics Solna instance only

#3877 - Unable to download cgh-file

Issue - State: closed - Opened by KickiLagerstedt over 1 year ago - 6 comments
Labels: Clinical Genomics Solna instance only

#3876 - Update admin docs with instructions to load the new RNA case reports

Issue - State: closed - Opened by northwestwitch over 1 year ago
Labels: Easy, docs

#3875 - Very very safe match

Pull Request - State: closed - Opened by dnil over 1 year ago - 4 comments

#3874 - No SCORE annotation on variants

Issue - State: closed - Opened by KickiLagerstedt over 1 year ago - 2 comments
Labels: question, Clinical Genomics Solna instance only

#3873 - Safe variant matching does not work as (we) intended

Issue - State: closed - Opened by ehre over 1 year ago - 8 comments
Labels: enhancement

#3872 - Cancer pin table - Fix #3866

Pull Request - State: closed - Opened by dnil over 1 year ago - 2 comments

#3871 - Fix #3870 - require importlib metadata explicitly

Pull Request - State: closed - Opened by dnil over 1 year ago - 3 comments

#3870 - Install fails missing importlib on python 3.7

Issue - State: closed - Opened by dnil over 1 year ago

#3869 - Patch release 4.65.1

Pull Request - State: closed - Opened by dnil over 1 year ago - 10 comments

#3868 - Feature request: use phenomodels to assign phenotypes on case page

Issue - State: open - Opened by northwestwitch over 1 year ago
Labels: enhancement

#3866 - Somatic pin table case report

Issue - State: closed - Opened by dnil over 1 year ago
Labels: enhancement, Cancer

#3865 - Alt fix pdf delivery

Pull Request - State: closed - Opened by dnil over 1 year ago - 5 comments

#3864 - Fix PDF delivery report

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 12 comments

#3863 - Fix svs genes visibility

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 2 comments

#3862 - Delivery report pdf conversion off?

Issue - State: closed - Opened by dnil over 1 year ago - 1 comment
Labels: bug

#3861 - Gene(s) field not so visible on SV variantS page

Issue - State: closed - Opened by northwestwitch over 1 year ago - 2 comments

#3860 - Fix SV filter form layout

Pull Request - State: closed - Opened by dnil over 1 year ago - 2 comments

#3859 - Can not dismiss structural variant on first page anymore...

Issue - State: closed - Opened by KickiLagerstedt over 1 year ago - 2 comments
Labels: bug, Frontend

#3858 - Variant disappears with clinical filter - why?

Issue - State: closed - Opened by KickiLagerstedt over 1 year ago - 11 comments
Labels: Under discussion

#3857 - Check `case_panels` stored on variant collection

Issue - State: closed - Opened by dnil over 1 year ago - 13 comments

#3856 - Replace code that downloads genes, exons and transcripts from Ensembl with schug lib

Issue - State: closed - Opened by northwestwitch over 1 year ago - 4 comments
Labels: enhancement, Refactor

#3855 - Keep variants filters section closed when navigating thru pages

Issue - State: closed - Opened by northwestwitch over 1 year ago - 1 comment
Labels: enhancement, QualityOfLife

#3854 - VariantS views duplication refactoring

Issue - State: open - Opened by dnil over 1 year ago - 1 comment
Labels: Refactor

#3853 - Retrieving stored DNA

Issue - State: closed - Opened by MUebe over 1 year ago - 1 comment

#3852 - Allow the no-keep-actions toggle to work also on what seems to be non-update loads

Issue - State: closed - Opened by dnil over 1 year ago - 3 comments
Labels: enhancement, QualityOfLife

#3851 - Option to delete events when deleting case

Issue - State: open - Opened by dnil over 1 year ago - 6 comments
Labels: enhancement, QualityOfLife

#3850 - Prepare new minor version 4.65

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 22 comments

#3849 - Fixed gene panel test pointing to the right function

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 2 comments
Labels: Easy

#3846 - Export panels in TXT format from the gene panel page

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 2 comments

#3839 - Fix #3776: show panel gene comments on variant page

Pull Request - State: closed - Opened by dnil over 1 year ago - 5 comments

#3836 - Fix #3792 - thin and allow closing dismiss bar

Pull Request - State: closed - Opened by dnil over 1 year ago - 9 comments

#3822 - Export gene panels in a scout loadable csv form from WUI

Issue - State: closed - Opened by dnil over 1 year ago
Labels: enhancement

#3819 - Fix research vars counter

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 2 comments
Labels: Bugfix

#3816 - Fix Beacon links to support variants in build 38

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 2 comments
Labels: Easy, Bugfix

#3795 - Avoid using ClinVar apitest from Scout prod - redirect data from scout-stage to apitest

Issue - State: closed - Opened by northwestwitch over 1 year ago - 6 comments
Labels: enhancement

#3792 - Enable closing of the dismiss bar (variantS page)

Issue - State: closed - Opened by ielvers over 1 year ago - 1 comment
Labels: enhancement, QualityOfLife

#3776 - Gene panel gene level comment

Issue - State: closed - Opened by dnil over 1 year ago
Labels: enhancement, Customer Request

#3762 - Simplify ClinVar form by having assertion criteria as a select or a radio button

Issue - State: closed - Opened by northwestwitch over 1 year ago - 1 comment
Labels: enhancement, Easy, QualityOfLife, Frontend

#3752 - Update SV Clinical filter

Issue - State: closed - Opened by dnil over 1 year ago - 2 comments
Labels: enhancement, Customer Request

#3749 - Convert general case report to bootstrap 5

Issue - State: closed - Opened by northwestwitch over 1 year ago - 1 comment
Labels: enhancement, Frontend

#3737 - ClinVar submission status monitor

Issue - State: closed - Opened by northwestwitch almost 2 years ago
Labels: enhancement

#3685 - Try joblib..

Pull Request - State: closed - Opened by dnil almost 2 years ago - 16 comments
Labels: Refactor

#3672 - Update most severe consequence order for SVs

Issue - State: closed - Opened by dnil almost 2 years ago - 1 comment
Labels: enhancement

#3621 - Genome_build Is Inconsistently a String or an Integer Through The System

Issue - State: closed - Opened by mikaell almost 2 years ago
Labels: Refactor

#3571 - "regular expression is invalid: \\ at end of pattern" error still not fixed.

Issue - State: closed - Opened by northwestwitch about 2 years ago - 4 comments
Labels: bug

#3523 - On diagnoses page, show number of OMIM terms available and datetime of last update

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 13 comments
Labels: enhancement

#3521 - _app_ctx_stack is deprecated and will be removed in Flask 2.3

Issue - State: closed - Opened by northwestwitch about 2 years ago - 4 comments
Labels: Refactor

#3471 - Match SVs for prior variant tag classifications etc

Issue - State: open - Opened by northwestwitch over 2 years ago - 2 comments
Labels: enhancement, Hard

#3469 - Note if individual with loqus match is in the current case

Issue - State: closed - Opened by dnil over 2 years ago - 2 comments
Labels: enhancement, QualityOfLife

#3379 - Managed variants separate for each institute?

Issue - State: closed - Opened by sofievonlanthen over 2 years ago - 3 comments
Labels: question, Under discussion

#3375 - Indels not being opened properly in Alamut Visual Plus

Issue - State: closed - Opened by mhkc over 2 years ago - 9 comments
Labels: bug

#3247 - RNA expression

Issue - State: open - Opened by 47KW over 2 years ago - 2 comments
Labels: enhancement

#3162 - cancer variantS filter load filter does not show all values with WTForms>3

Issue - State: closed - Opened by dnil over 2 years ago - 15 comments
Labels: enhancement

#3110 - Rename "Quality" column to something else in cancer variantS page or change its content?

Issue - State: closed - Opened by northwestwitch over 2 years ago

#3084 - Rename Custom Image Parameters "case" and "str"

Issue - State: closed - Opened by mikaell over 2 years ago
Labels: Easy, Refactor

#2972 - Disease transcript does not match HGVS description

Issue - State: closed - Opened by Leif-glitch almost 3 years ago - 6 comments
Labels: question

#2942 - Redundant indexes

Issue - State: open - Opened by northwestwitch almost 3 years ago - 2 comments
Labels: enhancement

#2903 - Slow mongo queries

Issue - State: open - Opened by mhkc about 3 years ago - 10 comments
Labels: bug, enhancement

#2816 - SNPedia link not loading

Issue - State: open - Opened by andreaswallberg about 3 years ago - 7 comments
Labels: enhancement, QualityOfLife

#2786 - GET parameter variant_type can be any value..

Issue - State: closed - Opened by dnil about 3 years ago
Labels: enhancement, QualityOfLife

#2759 - Automatically sending reports via email

Issue - State: closed - Opened by leahkemp about 3 years ago - 8 comments
Labels: question

#2733 - Use latest gene panel for panel overlap in variantS and variant view

Issue - State: closed - Opened by bjhall over 3 years ago - 6 comments
Labels: bug

#2693 - phenotype_groups and subject_id tags in load config

Issue - State: closed - Opened by dnil over 3 years ago - 4 comments
Labels: enhancement

#2674 - General report details for variant: ACMG criteria, GnomAD subpop info

Issue - State: open - Opened by dnil over 3 years ago - 1 comment
Labels: enhancement

#2516 - Save comments contained in an additional "comments" column when creating gene panels

Issue - State: open - Opened by northwestwitch over 3 years ago
Labels: enhancement, Customer Request

#2500 - Use Scout as JWT auth server

Issue - State: closed - Opened by mhkc over 3 years ago - 6 comments
Labels: enhancement, QualityOfLife, Task

#2357 - Create a Scout major release

Issue - State: open - Opened by northwestwitch over 3 years ago - 9 comments
Labels: enhancement, Future ideas, Under discussion, QualityOfLife, Refactor

#2339 - COSMIC annotation of germline variants in the inherited pipeline

Issue - State: open - Opened by fulyataylan over 3 years ago - 1 comment
Labels: enhancement, Easy, blocked

#2294 - Update hpo command crashes

Issue - State: closed - Opened by northwestwitch over 3 years ago
Labels: enhancement, QualityOfLife

#2286 - My Cancer genome link does not work

Issue - State: closed - Opened by heronikdin over 3 years ago - 10 comments
Labels: Under discussion, Cancer

#2222 - HGNC lsdb linkout

Issue - State: closed - Opened by dnil almost 4 years ago - 1 comment
Labels: enhancement, Under discussion

#2202 - Create a collection containing all causative variants

Issue - State: closed - Opened by northwestwitch almost 4 years ago - 2 comments
Labels: enhancement, Clinical Genomics Solna instance only

#2188 - Simplifying how config files or variables are passed?

Issue - State: closed - Opened by northwestwitch almost 4 years ago - 2 comments
Labels: enhancement, Refactor

#2159 - Use Orphanet to describe diseases, together with OMIM

Issue - State: closed - Opened by northwestwitch almost 4 years ago - 11 comments
Labels: enhancement, Intermediate

#2068 - Highlight panel matching genes in variants gene column

Issue - State: closed - Opened by dnil about 4 years ago - 1 comment
Labels: enhancement, Customer Request, Easy

#2027 - Update (SV) frequency filter to best available, and show freq on variants table

Issue - State: closed - Opened by dnil about 4 years ago - 2 comments
Labels: enhancement

#2002 - Change pdf export library js solution #1997

Pull Request - State: closed - Opened by elevu about 4 years ago - 7 comments

#1932 - Events to event log for upload, re-uploads etc

Issue - State: closed - Opened by dnil over 4 years ago - 3 comments
Labels: enhancement

#1907 - Integration of chromosomal segments lists for annotation and filtering

Issue - State: open - Opened by TJO-Lund over 4 years ago - 10 comments
Labels: enhancement, Hard

#1827 - Hotspots of mutation in IGV

Issue - State: closed - Opened by northwestwitch over 4 years ago - 1 comment
Labels: enhancement, Customer Request, Cancer, QualityOfLife

#1825 - Cosmic track in IGV

Issue - State: closed - Opened by northwestwitch over 4 years ago - 5 comments
Labels: enhancement, Customer Request, Cancer, QualityOfLife, Clinical Genomics Solna instance only

#1783 - Opening IGV on a repeat region sometimes causes the view to crash or stall

Issue - State: closed - Opened by northwestwitch over 4 years ago - 9 comments
Labels: enhancement

#1682 - Display exon number and VAF % on the variant page

Issue - State: closed - Opened by christacosta over 4 years ago - 14 comments
Labels: enhancement, Customer Request, Cancer, QualityOfLife

#1621 - alamut to show bam file

Issue - State: open - Opened by patrikgrenfeldt over 4 years ago - 9 comments
Labels: enhancement, Cancer, blocked

#1584 - Custom annotation

Pull Request - State: closed - Opened by bjhall almost 5 years ago - 11 comments

#1571 - Show GnomAD ratio to expected and Z-score for missense variation

Issue - State: closed - Opened by dnil almost 5 years ago - 1 comment
Labels: enhancement, Intermediate

GitHub / Clinical-Genomics/scout issues and pull requests