Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
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
#4681 - Stylistic updates to the "calculate matching causatives" toggle
Issue -
State: closed - Opened by Jakob37 19 days ago
#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
#4668 - Extremely slow loading of variant pages when loqusdb instance can't be reached
Issue -
State: closed - Opened by northwestwitch 28 days ago
- 3 comments
#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
#4661 - "scout setup demo" is loading also research variants, but they are not shown as a category of available vars on case page
Issue -
State: closed - Opened by northwestwitch about 1 month ago
- 2 comments
Labels: bug
#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
#4637 - MT report crashes for cases where one or more samples are not in chanjo database
Issue -
State: closed - Opened by northwestwitch about 2 months ago
Labels: bug
#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