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Issues list

Add x-record-total to get-original-metadata backend related to the loculus backend component feature Feature proposal ingest Ingest pipeline
#2847 opened Sep 19, 2024 by corneliusroemer
1
Investigate adding a distributed lock for ingest backend related to the loculus backend component deployment Code changes targetting the deployment infrastructure ingest Ingest pipeline
#2843 opened Sep 19, 2024 by anna-parker
2
We currently include stop codons in protein sequences discussion Open questions preprocessing Issues related to the preprocessing component
#2841 opened Sep 18, 2024 by theosanderson
8
ena-submission: Better logging of webin-cli errors insdc tasks related to ENA/INSDC submission
#2840 opened Sep 18, 2024 by anna-parker
Renaming file is not enough to change the docker image cache hash in our CI bug Something isn't working github_actions Pull requests that update GitHub Actions code
#2838 opened Sep 18, 2024 by corneliusroemer
1
1
Only allow historical countries before a country-specific cutoff, something submitted in 2010 shouldn't say "USSR" feature Feature proposal ingest Ingest pipeline
#2836 opened Sep 18, 2024 by corneliusroemer
5
Create "region/continent" field derived from country in preprocessing feature Feature proposal ingest Ingest pipeline
#2835 opened Sep 18, 2024 by corneliusroemer
Include extra metadata from Genbank that is in the full Genbank files but not (yet) parsed and emitted by NCBI virus feature Feature proposal ingest Ingest pipeline
#2834 opened Sep 18, 2024 by corneliusroemer
1
Ingest: get nucleotide accessions to ignore from extended metadata table high_priority Work on this as soon as possible (potentially post-MVP) ingest Ingest pipeline insdc tasks related to ENA/INSDC submission
#2832 opened Sep 18, 2024 by corneliusroemer
@anna-parker
5
ena-submission: refactoring comments insdc tasks related to ENA/INSDC submission
#2831 opened Sep 18, 2024 by anna-parker
4 tasks
@anna-parker
Fix ingest in one go ingest Ingest pipeline
#2830 opened Sep 18, 2024 by corneliusroemer
2 tasks
@corneliusroemer @anna-parker
The ingest logs contain the ingest user's password codesmell For warnings/lints without immediate harm but to be fixed eventually ingest Ingest pipeline
#2827 opened Sep 18, 2024 by fengelniederhammer
1
Add groups table to tables whose updates invalidate eleased data cache backend related to the loculus backend component bug Something isn't working
#2824 opened Sep 17, 2024 by corneliusroemer
Revoked and non-latest sequences are entirely inaccessible through the Search UI
#2816 opened Sep 17, 2024 by theosanderson
Rename "ENA submission" to "ENA Deposition" insdc tasks related to ENA/INSDC submission
#2811 opened Sep 16, 2024 by theosanderson
Test ENA submission updates insdc tasks related to ENA/INSDC submission tests Test related issues
#2809 opened Sep 16, 2024 by corneliusroemer
Make swagger UI sections more logical for API consumers: regroup and separate public/private endpoints backend related to the loculus backend component codesmell For warnings/lints without immediate harm but to be fixed eventually documentation Improvements or additions to documentation refactoring Code requires refactoring
#2805 opened Sep 16, 2024 by corneliusroemer
4 tasks
In ingest, populate the version comment field with a diff versus the previous version feature Feature proposal ingest Ingest pipeline
#2804 opened Sep 16, 2024 by corneliusroemer
5
Diff view of Loculus versions feature Feature proposal website Tasks related to the web application
#2803 opened Sep 16, 2024 by corneliusroemer
2
Command line interface (CLI) cli related to the command line interface component epic A major task that should be broken down into smaller tasks feature Feature proposal
#2801 opened Sep 15, 2024 by chaoran-chen Priority 1 (highest)
1
Review and potentially restructure configuration config Configuration related issues, i.e. helm processing discussion Open questions refactoring Code requires refactoring
#2800 opened Sep 15, 2024 by chaoran-chen Release v1.0
Config file validation config Configuration related issues, i.e. helm processing feature Feature proposal
#2798 opened Sep 15, 2024 by chaoran-chen Release v1.0
Config file schema config Configuration related issues, i.e. helm processing feature Feature proposal
#2796 opened Sep 15, 2024 by chaoran-chen Release v1.0
Review code and identify things to refactor and missing tests backend related to the loculus backend component ingest Ingest pipeline insdc tasks related to ENA/INSDC submission preprocessing Issues related to the preprocessing component website Tasks related to the web application
#2795 opened Sep 15, 2024 by chaoran-chen Priority 1 (highest)
How to handle seqs that INSDC doesn't accept (gappy)? discussion Open questions insdc tasks related to ENA/INSDC submission
#2794 opened Sep 15, 2024 by chaoran-chen Priority 1 (highest)
ProTip! Exclude everything labeled bug with -label:bug.