Ecosyste.ms: Issues

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GitHub / Clinical-Genomics/scout issues and pull requests

#4309 - Thaw cryptography

Pull Request - State: closed - Opened by dnil 10 months ago - 2 comments

#4308 - Suggested changes to indices post consult session

Pull Request - State: closed - Opened by dnil 10 months ago - 12 comments

#4307 - Switch to bootstrap icons

Issue - State: open - Opened by dnil 10 months ago
Labels: enhancement, Refactor, Frontend

#4306 - Code that needs checking before loading ORPHA terms

Issue - State: closed - Opened by northwestwitch 10 months ago - 2 comments

#4305 - Unfreeze coloredlogs

Pull Request - State: closed - Opened by dnil 10 months ago - 2 comments
Labels: Easy

#4304 - Phenomodels icons not visible

Issue - State: closed - Opened by northwestwitch 10 months ago - 2 comments
Labels: bug, Easy

#4303 - Scout view users can fail on broken entries...

Issue - State: closed - Opened by dnil 10 months ago - 1 comment

#4302 - Fix updating unexisting user crash

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 3 comments
Labels: Easy, Bugfix

#4301 - Fix #4300 - DecimalFields stepping

Pull Request - State: closed - Opened by dnil 10 months ago - 4 comments

#4300 - DecimalFields do not allow input of small numbers

Issue - State: closed - Opened by dnil 10 months ago - 1 comment
Labels: bug

#4298 - Update genes, diseases, HPO terms etc

Issue - State: closed - Opened by northwestwitch 10 months ago - 2 comments
Labels: Clinical Genomics Solna instance only

#4297 - Fusion variants's form fields are not remembered after the search

Issue - State: closed - Opened by northwestwitch 10 months ago - 1 comment

#4296 - Release version 4.75

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 6 comments

#4295 - Phenomizer connection down

Issue - State: closed - Opened by dnil 10 months ago - 10 comments
Labels: bug

#4294 - Variant page suddenly slow on main, not release branch

Issue - State: closed - Opened by dnil 10 months ago - 3 comments
Labels: Clinical Genomics Solna instance only

#4293 - Updated GnomAD gene constraints (v4) available

Issue - State: closed - Opened by dnil 10 months ago
Labels: enhancement

#4292 - Fix type of some RNA fusion variant keys

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 3 comments
Labels: Easy, Bugfix

#4291 - Remove dead functions and their tests

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 2 comments
Labels: Easy, QualityOfLife, Refactor

#4290 - Remove redundant variant index

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 2 comments

#4289 - Alamut indel links

Pull Request - State: closed - Opened by dnil 10 months ago - 12 comments
Labels: Bugfix

#4287 - Fix removing of None key/values before saving parsed variants

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 4 comments
Labels: Easy, Bugfix

#4286 - Gene filter for fusion vcf should work for fusion_gene names

Issue - State: closed - Opened by fevac 10 months ago - 9 comments
Labels: enhancement, RNA-seq

#4285 - Un-audit filter...

Issue - State: closed - Opened by dnil 10 months ago
Labels: enhancement, QualityOfLife

#4284 - Restore changelog format

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 6 comments
Labels: Easy, QualityOfLife

#4283 - Error in case GMSB-ST173MIP

Issue - State: closed - Opened by KickiLagerstedt 10 months ago - 8 comments
Labels: Clinical Genomics Solna instance only

#4282 - Fix GT ref and alt depth parsing when values are 0

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 7 comments
Labels: Easy, Bugfix

#4280 - Structural variant in genepanel?

Issue - State: closed - Opened by sofievonlanthen 10 months ago - 2 comments
Labels: enhancement, Customer Request, QualityOfLife

#4279 - Fix Alamut link for MT variants in build 38

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 4 comments
Labels: Easy, Bugfix

#4278 - Update fusion filters

Pull Request - State: closed - Opened by fevac 10 months ago - 3 comments

#4277 - Sanger email feedback

Issue - State: closed - Opened by sofievonlanthen 10 months ago - 8 comments
Labels: enhancement, Customer Request, QualityOfLife

#4276 - Display 0 instead of -1 for read junctions in fusion view

Pull Request - State: closed - Opened by fevac 10 months ago - 4 comments

#4275 - Parse and show RNA fusion found_db key/values

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 3 comments
Labels: enhancement, Easy, Bugfix

#4274 - Fix extra chars on general report

Pull Request - State: closed - Opened by dnil 10 months ago - 1 comment
Labels: Easy, QualityOfLife, Bugfix

#4273 - Left over chars on general report

Issue - State: closed - Opened by dnil 10 months ago - 1 comment
Labels: bug, QualityOfLife

#4272 - Fix Junction Reads in fusion vcf

Issue - State: closed - Opened by fevac 10 months ago
Labels: enhancement, QualityOfLife

#4271 - Add databases column fusion vcf view

Issue - State: closed - Opened by fevac 10 months ago - 2 comments
Labels: enhancement

#4270 - Add sorting in vcf columns

Issue - State: closed - Opened by fevac 10 months ago - 3 comments
Labels: wontfix

#4269 - Add additional filters for fusion vcf

Issue - State: closed - Opened by fevac 10 months ago
Labels: enhancement

#4268 - Retrieve genes transcripts and exons using the schug library

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 4 comments
Labels: Refactor

#4267 - JSONDecodeError on case MT report

Issue - State: closed - Opened by northwestwitch 10 months ago - 1 comment
Labels: bug, duplicate

#4266 - MT coverage report issue?

Issue - State: closed - Opened by dnil 10 months ago - 2 comments
Labels: bug

#4264 - Fix #4263 - activate case when visiting FSHD or SMA reports

Pull Request - State: closed - Opened by dnil 10 months ago - 3 comments

#4263 - Bionano FSHD variant view should activate case

Issue - State: closed - Opened by dnil 10 months ago
Labels: enhancement, Easy

#4262 - Add orphacodes to diseases

Pull Request - State: closed - Opened by TereseBo 10 months ago - 12 comments

#4261 - Give all load research a chance

Pull Request - State: closed - Opened by dnil 10 months ago - 3 comments

#4260 - Patch release 4.74.1

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 7 comments

#4259 - BioNanoGenomics Access 1.8 type of count fields changed?

Issue - State: closed - Opened by dnil 10 months ago - 1 comment
Labels: bug

#4258 - Deal with failed FSHD analyses..

Issue - State: closed - Opened by dnil 10 months ago - 1 comment
Labels: enhancement

#4257 - Tentatively fix #4256 - replace some now pro icons

Pull Request - State: closed - Opened by dnil 10 months ago - 3 comments
Labels: Bugfix

#4256 - Issues with viewing some icons from the hospital side...

Issue - State: closed - Opened by dnil 10 months ago - 1 comment
Labels: bug

#4254 - Improve error handling for managed variants upload

Issue - State: closed - Opened by dnil 10 months ago
Labels: enhancement

#4252 - Fix #4250 - bionano access API getFSHD changed to GET

Pull Request - State: closed - Opened by dnil 10 months ago - 3 comments
Labels: Bugfix

#4251 - Scout load research to fail late

Issue - State: closed - Opened by dnil 10 months ago - 4 comments
Labels: enhancement

#4250 - BioNano Access API update to 1.8

Issue - State: closed - Opened by dnil 10 months ago
Labels: bug

#4249 - "Haploblock" below centromeric regions in chromographs

Issue - State: open - Opened by FZ73 10 months ago - 1 comment
Labels: question, QualityOfLife

#4248 - Gens button case analysis type

Pull Request - State: closed - Opened by dnil 10 months ago - 3 comments

#4247 - A couple more fa icons fixed

Pull Request - State: closed - Opened by dnil 10 months ago - 2 comments

#4246 - Revert global styles and fix variant buttons style instead

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 3 comments
Labels: Easy

#4245 - Visited variants and cases no longer look visited

Issue - State: closed - Opened by northwestwitch 10 months ago

#4244 - Test update fontwesome

Pull Request - State: closed - Opened by dnil 10 months ago - 14 comments

#4243 - Missing icons

Issue - State: closed - Opened by northwestwitch 10 months ago - 7 comments
Labels: bug, help wanted, Easy, Frontend

#4242 - Minor release 4.74

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 6 comments

#4241 - Add commands for downloading gene-disease relation files from Orphadata

Pull Request - State: closed - Opened by TereseBo 10 months ago - 2 comments

#4240 - Compound follow multi gene

Pull Request - State: closed - Opened by dnil 10 months ago - 2 comments
Labels: Bugfix

#4239 - Do not save custom images into database documents

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 7 comments

#4238 - How to run pytest test suite locally?

Issue - State: closed - Opened by alkc 10 months ago - 2 comments
Labels: question

#4237 - Small changelog fix

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 2 comments

#4236 - Fix visited color of image links

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 2 comments
Labels: Easy, Frontend

#4235 - Audit filters specifics on case report

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 2 comments
Labels: enhancement, Easy

#4234 - Fix saving mei filters

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 2 comments
Labels: Easy, Bugfix

#4233 - Display gene panel membership in gene summary table in /variant view for variants related to multiple genes

Issue - State: closed - Opened by alkc 11 months ago - 7 comments
Labels: QualityOfLife

#4232 - Compounds follow filter hiding on variants hitting multiple genes

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

#4231 - Saving MEI research filters crash

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

#4230 - Update case document with path to mei variants

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

#4229 - Scout update case missing MEI options

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

#4228 - Re-upload misses added VCFs

Issue - State: closed - Opened by dnil 11 months ago - 9 comments
Labels: bug

#4227 - Use of clinical filter on research page unclear

Issue - State: open - Opened by dnil 11 months ago
Labels: enhancement

#4225 - Fusion variant page

Issue - State: open - Opened by dnil 11 months ago
Labels: enhancement

#4224 - Visited scout logo became pink

Issue - State: closed - Opened by northwestwitch 11 months ago
Labels: Frontend

#4223 - Convert the diagnoses page into a diagnosis search & display page

Issue - State: closed - Opened by northwestwitch 11 months ago - 1 comment
Labels: enhancement, Frontend

#4222 - Add missing OMIM terms without associated genes

Pull Request - State: closed - Opened by TereseBo 11 months ago - 8 comments

#4221 - Add test and fixtures for RNA fusion case page

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

#4220 - Add a owner + display name index to the case collection

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

#4219 - Audit clinical filter on variantS page

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

#4218 - Optionally expand comment box on variant page

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

#4217 - Visited links color

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

#4216 - Improving the indexes

Issue - State: open - Opened by northwestwitch 11 months ago - 5 comments
Labels: enhancement

#4215 - Fix MME submissions page crashing

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

#4214 - Broken Matchmaker submission page

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

#4213 - Option to submit multigene SNVs as single genes to MME

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 2 comments
Labels: Customer Request

#4212 - Added Decipher button to SNV/MEI and str variant page

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

#4211 - External links on SNV page look weird

Issue - State: closed - Opened by northwestwitch 11 months ago - 7 comments
Labels: Easy, Frontend

#4210 - Suggestion of added External Links for variants pages (Clinical SNV and INDELs).

Issue - State: open - Opened by TJO-Lund 11 months ago - 2 comments
Labels: enhancement, Easy

#4209 - Show all "Inactive cases" respectively "Active cases" on the Cases-page for each Institute in Scout

Issue - State: closed - Opened by TJO-Lund 11 months ago - 3 comments
Labels: enhancement, QualityOfLife