Ecosyste.ms: Issues

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GitHub / Clinical-Genomics/scout issues and pull requests

#4688 - Unfreeze Werkzeug again

Issue - State: open - Opened by dnil 13 days ago
Labels: enhancement

#4687 - Version 4.84 - fix load order, chanjo-report extension load warning, …

Pull Request - State: closed - Opened by dnil 14 days ago - 4 comments

#4686 - How we calculate VAF in scout

Issue - State: open - Opened by northwestwitch 17 days ago - 1 comment
Labels: question, Customer Request

#4685 - Linter python versions

Pull Request - State: closed - Opened by dnil 18 days ago - 3 comments

#4684 - Workaround fix #4682 - sort case file load order alphabetically

Pull Request - State: closed - Opened by dnil 18 days ago - 3 comments

#4683 - Swap menu chevrons

Pull Request - State: closed - Opened by dnil 19 days ago - 2 comments

#4682 - SV variants and large SNVs collide in variant_id

Issue - State: closed - Opened by dnil 19 days ago
Labels: bug

#4680 - Fix gene links

Pull Request - State: closed - Opened by northwestwitch 19 days ago - 2 comments
Labels: Easy, Bugfix

#4679 - Link to HGNC portal broken on gene page

Issue - State: closed - Opened by northwestwitch 19 days ago
Labels: bug

#4678 - Pydantic gene

Pull Request - State: closed - Opened by northwestwitch 20 days ago - 6 comments
Labels: Easy, Refactor

#4677 - Load genes missing Ensembl ID using cytoband coordinates

Pull Request - State: open - Opened by northwestwitch 23 days ago - 3 comments

#4676 - Clearer chanjo-report error message only when needed

Pull Request - State: closed - Opened by northwestwitch 24 days ago - 3 comments
Labels: Easy

#4675 - Import chanjo-report warning emitted before log level set

Issue - State: closed - Opened by dnil 24 days ago
Labels: QualityOfLife, Refactor

#4674 - Safer variant updates in variantS controllers

Pull Request - State: closed - Opened by northwestwitch 24 days ago - 2 comments
Labels: Easy, Refactor, Bugfix

#4673 - Flash an alert when loqus instance is not reachable

Pull Request - State: closed - Opened by northwestwitch 26 days ago - 4 comments

#4672 - nf-core/raredisease MT variants loading

Issue - State: closed - Opened by dnil 27 days ago - 4 comments

#4671 - Upgrade python to 3.11 in the Dockerfiles

Pull Request - State: closed - Opened by northwestwitch 27 days ago - 3 comments

#4670 - When updating the OMIM panel with --force, update also the date

Issue - State: open - Opened by northwestwitch 27 days ago - 1 comment
Labels: QualityOfLife

#4669 - Warnings when loqusdb-api is not reachable

Issue - State: closed - Opened by dnil 28 days ago
Labels: enhancement

#4667 - Minor release 4.83

Pull Request - State: closed - Opened by northwestwitch 28 days ago - 17 comments

#4666 - CLI option to link a panel to multiple institutes

Issue - State: closed - Opened by Jakob37 28 days ago - 6 comments

#4665 - CLI option to remove an institute

Issue - State: open - Opened by Jakob37 28 days ago - 4 comments
Labels: enhancement, Intermediate

#4664 - Changelog reminder version

Pull Request - State: closed - Opened by dnil about 1 month ago - 7 comments

#4663 - Automation: check CHANGELOG changes for latest version/unreleased

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

#4662 - Fix automatically loading research variants when loading a case

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

#4660 - Optimise safe genes by avoiding duplicates when collecting genes from many panels

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

#4659 - Small event projection

Pull Request - State: closed - Opened by dnil about 1 month ago - 7 comments

#4658 - Speedup case page by saving in database (institute document) the list of safe genes for the institute

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

#4657 - A small projection on panels, and use sets instead of explicit loops

Pull Request - State: closed - Opened by dnil about 1 month ago - 5 comments

#4656 - time case controller

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

#4655 - Speeding up case page interactions

Issue - State: open - Opened by Jakob37 about 1 month ago - 5 comments
Labels: enhancement

#4654 - Parse drop

Pull Request - State: open - Opened by dnil about 1 month ago - 3 comments

#4652 - Update issue templates

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

#4651 - Chanjo as extension

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

#4650 - Attempt at speeding up tests

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 6 comments

#4649 - Lost access to Scout

Issue - State: closed - Opened by Lucpen about 1 month ago - 2 comments

#4648 - Can't connect to chanjo database

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

#4647 - Fix PanelApp panel not saving genes with empty `EnsembleGeneIds` list

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

#4646 - Fix #4645 - benign modifiers

Pull Request - State: closed - Opened by dnil about 1 month ago - 3 comments
Labels: Bugfix

#4645 - ACMG benign modifiers apply to is_likely_pathogenic and is_pathogenic

Issue - State: closed - Opened by ViktorHy about 1 month ago
Labels: bug

#4644 - Modify OMIM-AUTO panel to include genes in both builds

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

#4643 - Fix #4642 - dont crash on missing phenotype terms

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

#4642 - Empty phenotype_terms - after editing genes perhaps?

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

#4641 - Deployments on cg-vm1 fail

Issue - State: closed - Opened by northwestwitch about 2 months ago - 2 comments
Labels: wontfix, blocked

#4640 - Hide mtDNA and coverage reports for WTS cases

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 4 comments
Labels: Easy

#4639 - Hide not-applicable reports for e.g. tomte cases

Issue - State: closed - Opened by dnil about 2 months ago
Labels: enhancement, RNA-seq

#4638 - Fix MT-report crash when one of the samples is not in chanjo db

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 3 comments
Labels: Easy, Bugfix

#4636 - Add better error handling for chanjo report fails.

Pull Request - State: closed - Opened by dnil about 2 months ago - 3 comments

#4635 - Test any chanjo-report branch

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 6 comments

#4634 - Provide SVG logo

Pull Request - State: closed - Opened by dnil about 2 months ago - 9 comments

#4633 - Add SVG logos

Issue - State: closed - Opened by dnil about 2 months ago
Labels: enhancement, Easy, Task

#4632 - Case reupload event

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

#4631 - Edit ACMG classifications

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

#4629 - CLI events

Pull Request - State: closed - Opened by dnil about 2 months ago - 6 comments

#4628 - chromograph view

Issue - State: closed - Opened by 4WGH about 2 months ago - 3 comments

#4627 - Hardcoded secret key

Issue - State: closed - Opened by Asterius27 about 2 months ago - 2 comments
Labels: Under discussion

#4626 - Version 4.82.2 - a patch release

Pull Request - State: closed - Opened by dnil about 2 months ago - 3 comments

#4625 - Fix #4624 - show ExHu STR sizes again

Pull Request - State: closed - Opened by dnil about 2 months ago - 4 comments

#4624 - STR estimated size from old cases...

Issue - State: closed - Opened by dnil about 2 months ago - 1 comment
Labels: bug

#4623 - Non confirmed sex warning

Pull Request - State: closed - Opened by Jakob37 about 2 months ago - 7 comments

#4622 - Add non confirmed sex warning to tables

Pull Request - State: closed - Opened by Jakob37 about 2 months ago - 4 comments

#4621 - Clearer warning for sample sex mismatch

Issue - State: closed - Opened by Jakob37 about 2 months ago - 1 comment
Labels: Customer Request, QualityOfLife

#4620 - Revert installation of flask-ldapconn

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 6 comments
Labels: Bugfix

#4619 - Change LDAP library?

Issue - State: closed - Opened by northwestwitch about 2 months ago - 1 comment
Labels: Under discussion

#4618 - Freeze werkzeug again

Pull Request - State: closed - Opened by dnil about 2 months ago - 3 comments

#4617 - debug Alchy load and route...

Pull Request - State: closed - Opened by dnil 2 months ago - 3 comments

#4616 - '_bcf_float_missing' error executing scout from local installation

Issue - State: closed - Opened by northwestwitch 2 months ago - 5 comments
Labels: duplicate

#4615 - Fix installation of libraries in second build stage of Dockerfile

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

#4614 - No chanjo-report endpoint found

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

#4613 - Revert to primary flask-ldapconn once its PyPi is up to date

Issue - State: closed - Opened by dnil 2 months ago - 2 comments
Labels: Easy, Refactor, blocked

#4612 - Unfreeze werkzeug

Pull Request - State: closed - Opened by dnil 2 months ago - 4 comments

#4611 - Prod/stage divide for CLINVAR settings

Issue - State: open - Opened by dnil 2 months ago
Labels: enhancement

#4610 - Werkzeug vuln <3.0.3

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

#4609 - ncRNA genes and the clinical filter

Issue - State: open - Opened by ielvers 2 months ago - 9 comments
Labels: enhancement, Under discussion

#4608 - Fix case crashing when evaluating ClinVar vars among pinned not loaded variants

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

#4607 - Error adding variant to ClinVar

Issue - State: closed - Opened by northwestwitch 2 months ago - 1 comment
Labels: bug

#4606 - Avoid chanjo2 queries when there are no genes available for stats

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 7 comments
Labels: Easy, QualityOfLife

#4605 - User friendly error message for no default panel

Issue - State: closed - Opened by Jakob37 2 months ago - 2 comments
Labels: enhancement, Easy

#4604 - Shall we parse and add to DB obsolete HPO terms?

Issue - State: closed - Opened by northwestwitch 2 months ago - 4 comments
Labels: Under discussion

#4603 - Prepare minor version 4.82

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 14 comments

#4602 - Fix diagnoses API search crashing with empty search string

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 6 comments
Labels: Easy, Bugfix

#4601 - Empty API diagnoses query crashes

Issue - State: closed - Opened by dnil 2 months ago - 1 comment
Labels: bug

#4600 - Use latest gene panel for panel overlap in variantS, variant view and case report

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 4 comments
Labels: Bugfix

#4599 - Use latest gene panel for panel overlap in variantS, variant view and case report

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

#4598 - Display errors loading managed variants from file on relative web page

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 6 comments
Labels: enhancement, Easy

#4597 - Flag coverage dropouts induced by repeat expansions in long-read data

Issue - State: open - Opened by fellen31 2 months ago - 1 comment
Labels: enhancement, LRS

#4596 - "Classify-link" on the Clinical Structural variants-variant page

Issue - State: open - Opened by SofieCMD 2 months ago - 2 comments
Labels: enhancement, Customer Request, Intermediate

#4595 - ClinVar submission status button

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

#4594 - Stricter control over ClinVar condition IDs provided in ClinVar form

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

#4593 - Fix end coordinates in ClinVar for indels

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 3 comments
Labels: Easy, Bugfix

#4592 - Typehead diseases when query contains source substring

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

#4591 - Fix ORPHA dropdown and preselected diagnoses on ClinVar form

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

#4590 - ClinVar submission error - variant location for indel

Issue - State: closed - Opened by dnil 2 months ago - 1 comment
Labels: bug

#4589 - Fix ClinVar form parsing to not include : in conditionType.id when condition is Orphanet

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

#4588 - Autocompletion on case page diagnosis field to include entry number

Issue - State: closed - Opened by dnil 2 months ago
Labels: QualityOfLife

#4587 - Fix installation of wkhtmltopdf in GitHub action

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