Clinical-Genomics/scout issues and pull requests

#4106 - Escape protein names in case general report

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

#4105 - Hide compounds, make compound_rank_score exclusive?

Issue - State: open - Opened by dnil about 1 year ago - 4 comments
Labels: Under discussion, Easy, Frontend

#4104 - Case general report VEP http escape string consequences in transcript variant descriptions `%3D`

Issue - State: closed - Opened by dnil about 1 year ago - 1 comment
Labels: Frontend

#4103 - Revert Python to 3.8 in Dockerfiles

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

#4102 - Many slow queries..

Issue - State: closed - Opened by dnil about 1 year ago - 6 comments
Labels: enhancement, Clinical Genomics Solna instance only

#4101 - Error while opening an institute's case due to chanjo-report

Issue - State: closed - Opened by northwestwitch about 1 year ago - 8 comments
Labels: bug

#4100 - Reduce case view loading time by speeding up case retrieval in case_matching_causatives (maybe).

Pull Request - State: closed - Opened by alkc about 1 year ago - 17 comments
Labels: enhancement

#4099 - Reduce case view loading time by speeding up case retrieval in case_matching_causatives (maybe).

Pull Request - State: closed - Opened by alkc about 1 year ago - 4 comments

#4098 - Truncate long HGVS ids on case page

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

#4096 - Allow users to choose which gene to submit when a SNV variant hits multiple genes

Issue - State: closed - Opened by northwestwitch about 1 year ago
Labels: Customer Request

#4095 - Upgrade python to 3.11 in Docker images

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 10 comments

#4094 - Pretty printing looooong variant names can get a little silly esp on the case page

Issue - State: closed - Opened by dnil about 1 year ago - 1 comment
Labels: Frontend

#4093 - Fix #4092 - github actions, tests with newer python

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

#4092 - Tests with later python version?

Issue - State: closed - Opened by dnil about 1 year ago - 3 comments

#4091 - Validate internal docs links action

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

#4090 - Fix #4087, indirectly fix #2202

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

#4089 - Upgrade pydantic to version 2, validation changes and HPO term validation fix

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 23 comments

#4088 - HPO number converted to string in database documents

Issue - State: closed - Opened by northwestwitch about 1 year ago - 4 comments
Labels: bug

#4087 - Always load previous causatives

Issue - State: closed - Opened by dnil about 1 year ago - 3 comments

#4086 - Causative variants not called

Issue - State: closed - Opened by MUebe about 1 year ago - 8 comments
Labels: Clinical Genomics Solna instance only

#4085 - Where do the variants custom images appear in scout demo?

Issue - State: closed - Opened by northwestwitch about 1 year ago - 8 comments
Labels: question

#4084 - Crash on parsing hpo terms in scout setup

Issue - State: closed - Opened by Jakob37 about 1 year ago - 4 comments
Labels: duplicate

#4083 - Add some current SV calls, RD and Somatic to demo and test

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

#4082 - Minor update to bionano docs

Pull Request - State: closed - Opened by dnil about 1 year ago - 1 comment

#4081 - fix nav for newish documents - Fix #4080

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

#4080 - Docs deploy?

Issue - State: closed - Opened by dnil about 1 year ago - 2 comments
Labels: bug

#4079 - Fix loading of SVs with no INFO.END in VCF file

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 4 comments
Labels: Easy, Bugfix

#4078 - Error uploading research SV VCF

Issue - State: closed - Opened by gavinmonahan about 1 year ago - 6 comments
Labels: bug

#4077 - Missing reports

Issue - State: closed - Opened by 1ctw about 1 year ago - 2 comments
Labels: Clinical Genomics Solna instance only

#4076 - Unfreeze pymongo, test scout/pymongo with later versions of mongodb

Issue - State: closed - Opened by dnil about 1 year ago
Labels: Refactor

#4075 - Fix #3990 - RNA alignment track in RNA igv sashimi viewer

Pull Request - State: closed - Opened by dnil about 1 year ago - 5 comments
Labels: enhancement

#4074 - Filter SNVs and indels by case groups

Issue - State: open - Opened by northwestwitch about 1 year ago - 1 comment
Labels: enhancement, Customer Request

#4073 - Fix column width - fix #4071

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

#4072 - Optical mapping type and link

Issue - State: open - Opened by dnil about 1 year ago
Labels: enhancement, QualityOfLife

#4071 - The caseS page default panel still gets a little busy - rebalance

Issue - State: closed - Opened by dnil about 1 year ago
Labels: enhancement, QualityOfLife, Frontend

#4070 - Option to use different build (hg38) as basis for OMIM-AUTO

Issue - State: closed - Opened by dnil about 1 year ago - 5 comments
Labels: enhancement

#4069 - Option to export clinvar submission data as json

Issue - State: closed - Opened by northwestwitch about 1 year ago - 1 comment
Labels: enhancement

#4068 - Fix show FSHD button

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

#4067 - Freshly loaded case got FSHD activated.

Issue - State: closed - Opened by dnil about 1 year ago - 5 comments
Labels: bug

#4066 - Issues downloading the hp.obo file

Issue - State: closed - Opened by northwestwitch about 1 year ago - 4 comments

#4065 - More careful introspection on HPO updates before dropping old collection

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

#4064 - Validate new parsed HPO terms before dropping existing terms

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

#4063 - Bionano settings commented out by default in scout settings

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

#4062 - New HPO release v2023-09-01

Issue - State: closed - Opened by northwestwitch about 1 year ago - 3 comments
Labels: Clinical Genomics Solna instance only

#4061 - MEI variant link on causatives page

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

#4060 - MEI variants display on causatives view

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

#4059 - Fix #4058 - add SpliceAI link

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

#4058 - Add a linkout to SpliceAI-lookup from variant page, splice AI prediction

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

#4057 - SVType filter does not contain detailed types (DUP:INV, DUP:TANDEM, ...)

Issue - State: open - Opened by dnil about 1 year ago
Labels: enhancement

#4056 - Fix #4055 - ProteinPaint link update

Pull Request - State: closed - Opened by dnil about 1 year ago - 1 comment

#4055 - ProteinPaint gene link broken

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

#4054 - Prepare minor version 4.71

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 19 comments

#4053 - Fix visualization of cancer variants where cancer case has no affected

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

#4052 - 'dict object' has no attribute 'tumor' error in variant/variant_details.html"

Issue - State: closed - Opened by northwestwitch about 1 year ago - 7 comments
Labels: bug

#4051 - Fix #3110 - move score out of quality column somatic variantS and Fix…

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

#4050 - Fix #2786 - constrain variant_type on variantS view requests

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

#4049 - CADD scores for cancer cases

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

#4048 - Suggestion: Genespecific criteria for classification of variants with ClinGen guidelines

Issue - State: open - Opened by MariaStrandh about 1 year ago - 1 comment
Labels: enhancement, Future ideas

#4047 - Fix #3922 - display default panel on institute caseS list

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

#4046 - Fix #2294 - drop HPO term collection later into update

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

#4045 - REVEL filter variantS

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

#4044 - Fix #4043 - splice SO terms severe in clinical filter

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

#4043 - Clinical filter SNVs to include more splice variants

Issue - State: closed - Opened by dnil about 1 year ago - 2 comments
Labels: enhancement, Under discussion

#4042 - Sv observations

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

#4041 - OMIM data account expired

Issue - State: closed - Opened by northwestwitch about 1 year ago - 3 comments
Labels: Clinical Genomics Solna instance only

#4040 - Show local archive frequency/obs count on structural variantS pages

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

#4039 - Fix #4038 - remove legacy incorrectly formatted codeowners file

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

#4038 - Codeowners restored...

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

#4037 - Somatic variantS filter loqus RD archive

Pull Request - State: closed - Opened by dnil about 1 year ago - 6 comments

#4036 - Update CODEOWNERS

Pull Request - State: closed - Opened by pbiology about 1 year ago - 4 comments

#4035 - MatchMaker Exchange submission error

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

#4034 - Balsamic frequencies

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

#4033 - Move chanjo-report code to scout as an extension

Issue - State: closed - Opened by northwestwitch about 1 year ago - 1 comment
Labels: enhancement, Refactor

#4032 - Cancer germline and somatic loqusdb-observation/frequencies filter fields for cancer cases

Issue - State: closed - Opened by khurrammaqbool about 1 year ago - 2 comments
Labels: enhancement, Cancer

#4031 - Test Speedup HPO coverage

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 8 comments

#4030 - Error caused by term without description makes HPO terms update fail

Issue - State: open - Opened by northwestwitch about 1 year ago - 3 comments
Labels: bug, wontfix

#4029 - Fixed Weasyprint installation howto link

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

#4028 - Link to weasyprint installation howto no longer working on README page

Issue - State: closed - Opened by northwestwitch about 1 year ago

#4027 - Fix exploding temp vcfs folder

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 5 comments

#4026 - Fix admin docs to run docker scout on Mac - Arm processor

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

#4025 - Error while running scout demo via docker-compose

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

#4024 - Scout container tmp filling up

Issue - State: closed - Opened by Vince-janv about 1 year ago - 4 comments
Labels: bug

#4022 - Missing mtDNA coverage in Coverage report and mtDNA report in case 22157-muskel-2

Issue - State: closed - Opened by 1ctw about 1 year ago - 5 comments

#4021 - Add UMI option to cancer VCF upload

Issue - State: closed - Opened by ivadym about 1 year ago - 6 comments
Labels: Under discussion, Cancer

#4020 - Suggestion: Integrate LitVar 2.0 API call on variant pages

Issue - State: open - Opened by ehre about 1 year ago - 6 comments
Labels: enhancement, Under discussion

#4019 - Remove call to track browsers

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

#4018 - Remove method that calls netlify to track browser versions

Pull Request - State: closed - Opened by elevu over 1 year ago - 1 comment

#4017 - Swegen and loqusDB-clinical filter fields for cancer cases

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

#4016 - Remove Netlify function call to detect browser version

Issue - State: closed - Opened by elevu over 1 year ago - 1 comment
Labels: Easy

#4015 - Re-write pydantic classes in Pydantic V2 - (un)freeze dependencies

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

#4014 - Change id of reference to match IGV locus search. Fix #4013.

Pull Request - State: closed - Opened by dnil over 1 year ago - 8 comments
Labels: Easy, Bugfix

#4013 - Locus search box on RNA view IGV.js for hg38 not working

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

#4011 - Add PubMed link

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

#4010 - Make SNVs and Indels requests asynchronous to avoid page expiring

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

#4009 - Minor release v4.70

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

#4008 - Allow excluding gene panels for research

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

#4007 - Gene search PubMed

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

#4006 - Fix gunicorn workers booting by modifying Dockerfiles to use python bullseye

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 4 comments
Labels: Bugfix

#4005 - Gunicorn workers booting issue using python:3.8-slim image as Docker base image

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

#4004 - Keep RNA for DNA cases during update

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

GitHub / Clinical-Genomics/scout issues and pull requests