Clinical-Genomics/scout issues and pull requests

#4208 - Add an Edit-function for authors of ACMG classifications in Scout

Issue - State: closed - Opened by TJO-Lund 11 months ago - 5 comments
Labels: enhancement, QualityOfLife

#4207 - Compacting localvariants table

Pull Request - State: closed - Opened by TereseBo 11 months ago - 6 comments

#4206 - Fix remove case from group if case has been already removed in another tab

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 5 comments

#4205 - Error in remove_case_group

Issue - State: closed - Opened by northwestwitch 11 months ago - 1 comment
Labels: bug

#4204 - Variant page loqusdbapi table could be more compact

Issue - State: closed - Opened by dnil 11 months ago
Labels: QualityOfLife, Frontend

#4203 - Minor version 4.73

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 10 comments

#4202 - Added responsiveness to ClinVar howto image

Pull Request - State: closed - Opened by TereseBo 11 months ago - 3 comments

#4201 - Add color expanded menu

Pull Request - State: closed - Opened by TereseBo 11 months ago - 6 comments

#4200 - Fix missing family name parsing

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 2 comments
Labels: Easy, Bugfix

#4199 - ClinVar submissions page has overflowing element

Issue - State: closed - Opened by TereseBo 11 months ago - 1 comment
Labels: Easy, Frontend

#4198 - Expanded menu could benefit from increased accessibility

Issue - State: closed - Opened by TereseBo 11 months ago - 1 comment
Labels: Easy, Frontend

#4197 - Case display name missing causes load to fail

Issue - State: closed - Opened by northwestwitch 11 months ago - 1 comment
Labels: bug

#4196 - Verified badge is red if false positive

Pull Request - State: closed - Opened by TereseBo 11 months ago - 2 comments

#4195 - add-scroll-to-omim-table

Pull Request - State: closed - Opened by TereseBo 11 months ago - 4 comments

#4194 - Added scrollbar to OMIM-table to prevent it from being too long.

Pull Request - State: closed - Opened by TereseBo 11 months ago - 2 comments

#4193 - Clearer STRs on case general report

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 3 comments
Labels: Easy

#4192 - 4.72.4 - GnomAD API default changed to v38

Pull Request - State: closed - Opened by dnil 11 months ago - 2 comments

#4191 - Fix #4190 - GnomAD web service defaults to hg38

Pull Request - State: closed - Opened by dnil 11 months ago - 2 comments
Labels: bug

#4190 - GnomAD link default changed to hg38 with the v4 release

Issue - State: closed - Opened by dnil 11 months ago - 3 comments
Labels: bug

#4189 - Fix #4182 - export managed variants from CLI

Pull Request - State: closed - Opened by dnil 11 months ago - 7 comments
Labels: enhancement, Customer Request

#4188 - Mei hpo button

Pull Request - State: closed - Opened by dnil 11 months ago - 2 comments
Labels: Easy, QualityOfLife

#4187 - Use HPO list button on case page for MEI

Issue - State: closed - Opened by dnil 11 months ago
Labels: enhancement, Easy, Frontend

#4186 - ClinVar pending submission format change (delayed to January)

Issue - State: closed - Opened by dnil 11 months ago - 1 comment
Labels: enhancement

#4185 - Fix #4131 again - more formatted long int and copy to clipboards

Pull Request - State: closed - Opened by dnil 11 months ago - 4 comments
Labels: Customer Request, QualityOfLife

#4184 - Update mongo test

Pull Request - State: closed - Opened by dnil 12 months ago - 3 comments

#4183 - Switch to MongoDB 7 in tests workflow

Issue - State: closed - Opened by northwestwitch 12 months ago - 1 comment

#4182 - Export managed variants from scout

Issue - State: closed - Opened by jemten 12 months ago
Labels: enhancement, Customer Request

#4181 - Patch 4.72.3

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 3 comments

#4180 - Drastic but effective fix to case report crasing for pinned somatc cancer vars

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 7 comments

#4179 - Debug case report acmg #4172

Pull Request - State: closed - Opened by dnil 12 months ago - 7 comments

#4178 - Gens cancer button

Pull Request - State: closed - Opened by dnil 12 months ago - 3 comments

#4177 - Enable GENS button for cancer view

Issue - State: closed - Opened by dnil 12 months ago
Labels: enhancement, Easy

#4176 - Clearer STRs in general case report

Issue - State: closed - Opened by dnil 12 months ago
Labels: enhancement, Customer Request

#4175 - Super long OMIM phenotypes list on case report

Issue - State: closed - Opened by northwestwitch 12 months ago - 1 comment

#4172 - missing acmg classification in report?

Issue - State: closed - Opened by dnil 12 months ago - 3 comments
Labels: bug

#4171 - Make the OMIM table scrollable on variant page

Issue - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: good first issue, Frontend

#4170 - Fix #4168 - make kinship check more obvious

Pull Request - State: closed - Opened by dnil 12 months ago - 3 comments

#4169 - Speed up variant page by projecting inheritance in disease terms query

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 2 comments

#4168 - Make kinship check more obvious

Issue - State: closed - Opened by pbiology 12 months ago - 1 comment
Labels: Easy, QualityOfLife, Frontend

#4167 - DiseaseS: handle view of susceptibility gene associations

Issue - State: open - Opened by dnil 12 months ago
Labels: enhancement

#4166 - DiseaseS: use gene symbols instead of hgnc id for Associated genes

Issue - State: closed - Opened by dnil 12 months ago - 1 comment
Labels: Easy, good first issue

#4165 - Release v4.72.2 - patch while it can be called a patch

Pull Request - State: closed - Opened by dnil 12 months ago - 9 comments

#4164 - Introduce data integrity test for OMIM downloads

Issue - State: open - Opened by dnil 12 months ago
Labels: Refactor

#4163 - Fix genemap2 parsing

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: Bugfix

#4162 - Change in header of genemap2.txt is likely having effects on the resources parsing

Issue - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: bug

#4161 - Fix #4152 - dont split large numbers, use thin space

Pull Request - State: closed - Opened by dnil 12 months ago - 2 comments

#4160 - Monitor HPO-jax-api moving to ontology.jax.org

Issue - State: closed - Opened by dnil 12 months ago - 1 comment
Labels: Task

#4159 - Fix #4139 - increase limit on STR download

Pull Request - State: closed - Opened by dnil 12 months ago - 3 comments

#4158 - Remove mim2genes-associated code in Scout

Issue - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: Refactor

#4157 - API entrypoint for pinning a variant in Scout

Issue - State: closed - Opened by mhkc 12 months ago - 5 comments
Labels: enhancement

#4156 - Do not load HPO-associated genes when loading OMIM terms

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 17 comments

#4155 - Fix #4145 - lighten by projecting case

Pull Request - State: closed - Opened by dnil 12 months ago - 4 comments

#4154 - QoL: verified badge color

Issue - State: closed - Opened by dnil 12 months ago - 6 comments
Labels: Easy, good first issue, QualityOfLife, Frontend

#4153 - Optimise memory and speed by introducing relevant variant projections

Issue - State: open - Opened by dnil 12 months ago
Labels: Refactor

#4152 - Do not split coordinates and variant lengths on 2 lines

Issue - State: closed - Opened by northwestwitch 12 months ago
Labels: enhancement, QualityOfLife

#4151 - Huge gene counts for diseases

Issue - State: closed - Opened by northwestwitch 12 months ago
Labels: bug

#4150 - Broken alamut link to mitochondrial genes on GRHc38

Issue - State: closed - Opened by mhkc 12 months ago - 1 comment
Labels: bug

#4149 - Scout gunicorn cosuming available RAM on prod server

Issue - State: closed - Opened by northwestwitch 12 months ago - 3 comments
Labels: bug

#4148 - GENS link broken

Issue - State: closed - Opened by sofievonlanthen 12 months ago - 3 comments

#4147 - Mitigate memory exhaustion by optimising disease terms queries

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 3 comments

#4146 - Max requests param for gunicorn in docker

Pull Request - State: closed - Opened by dnil 12 months ago - 9 comments

#4145 - Partially reintroduce case load speedup with projection

Issue - State: closed - Opened by dnil 12 months ago
Labels: Refactor

#4144 - Tentaive fix to server hanging

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: Bugfix

#4143 - [Solna only, possibly]: Out of memory errors on gunicorn

Issue - State: closed - Opened by dnil 12 months ago
Labels: bug

#4142 - Patch version 4.72.1

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 12 comments

#4141 - Fix jinja2 filter rendering long integers

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 3 comments

#4140 - Error in longint human friendly jinja filter

Issue - State: closed - Opened by northwestwitch 12 months ago
Labels: bug

#4139 - Filter and export page STRs limit increase

Issue - State: closed - Opened by dnil 12 months ago
Labels: enhancement, Easy, QualityOfLife

#4138 - Pydantic 2 in requirements file

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 2 comments

#4137 - Fix displaying custom case images loaded with scout version <= 4.71

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 5 comments
Labels: Easy, Bugfix

#4136 - Do not save custom images' binary data to database

Issue - State: closed - Opened by northwestwitch 12 months ago - 7 comments
Labels: enhancement

#4135 - Introduce path validation for custom images and don't crash if image is removed

Issue - State: closed - Opened by northwestwitch 12 months ago
Labels: enhancement

#4134 - Stricter genome build validation when loading case + missing tests

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 5 comments
Labels: Easy

#4133 - Improve readability of coordinates and variants size

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: enhancement, Customer Request, Easy

#4132 - Overlapping SV/SNV/MEI

Issue - State: closed - Opened by 4WGH 12 months ago - 4 comments

#4131 - nice view of size for SV

Issue - State: closed - Opened by 4WGH 12 months ago - 7 comments

#4130 - Remove warnings and unused build_phenotype module

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: Easy

#4129 - Way too many warnings when updating diseases

Issue - State: closed - Opened by northwestwitch 12 months ago

#4128 - Move load_phenotypes to setup

Issue - State: closed - Opened by dnil 12 months ago
Labels: Refactor

#4127 - Wtforms unfreeze

Pull Request - State: closed - Opened by dnil 12 months ago - 7 comments
Labels: Refactor

#4126 - unfreeze PyMongo

Pull Request - State: closed - Opened by dnil 12 months ago - 2 comments
Labels: Easy

#4125 - Version 4.72 - speedups to case, RNA alignments and Pydantic2

Pull Request - State: closed - Opened by dnil 12 months ago - 21 comments

#4124 - Disease term to gene mapping to use hg38

Issue - State: closed - Opened by dnil 12 months ago - 3 comments
Labels: enhancement

#4123 - Fix missing disease-associated HPO terms

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: Bugfix

#4122 - Remove case diagnoses even when not found in db

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: Bugfix

#4121 - Fix #4119, Fix #4120 - only re escape for re search. Fix #3571 or at …

Pull Request - State: closed - Opened by dnil 12 months ago - 4 comments

#4120 - HPO term searches order dependent

Issue - State: closed - Opened by dnil 12 months ago
Labels: bug

#4119 - Patient cohorts with spaces cannot be searched

Issue - State: closed - Opened by dnil 12 months ago
Labels: bug

#4118 - Fusion vcf view support

Pull Request - State: closed - Opened by fevac 12 months ago - 24 comments

#4117 - Diagnoses get stuck on case if the diagnosis term changes..

Issue - State: closed - Opened by dnil 12 months ago - 7 comments
Labels: bug

#4116 - Fix parsing of disease-associated HPO phenotypes

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 7 comments
Labels: Easy, Bugfix

#4115 - Diagnoses (OMIM terms) have no associated HPO phenotypes

Issue - State: closed - Opened by northwestwitch 12 months ago - 2 comments
Labels: bug

#4114 - Validate disease terms and don't drop old terms before validation ends

Pull Request - State: closed - Opened by northwestwitch 12 months ago - 6 comments

#4113 - Add diagnosis caused by mtDNA variants in Scout?

Issue - State: closed - Opened by 1ctw 12 months ago - 8 comments
Labels: enhancement, Future ideas

#4112 - New HPO release 2023-10-09

Issue - State: closed - Opened by northwestwitch 12 months ago - 15 comments
Labels: Clinical Genomics Solna instance only, Task

#4111 - RNA - aberrant expression and splicing (tomte)

Issue - State: open - Opened by dnil 12 months ago - 14 comments
Labels: enhancement

#4110 - Cancer RNA fusion view

Issue - State: closed - Opened by fevac 12 months ago
Labels: enhancement

#4109 - Simplify and possibly speed up case report

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 6 comments
Labels: Refactor

#4108 - Fix potential missing protein name bug

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

#4107 - Time case report content creation steps

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

GitHub / Clinical-Genomics/scout issues and pull requests