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feat(deposition): improvements and fixes #2960

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merged 14 commits into from
Oct 7, 2024
Merged

feat(deposition): improvements and fixes #2960

merged 14 commits into from
Oct 7, 2024

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anna-parker
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@anna-parker anna-parker commented Oct 7, 2024 •
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resolves #2955

preview URL: https://add-authors-to-manifest.loculus.org

Summary

  • Deposition gets its own config file so we can submit with a different taxon id than we ingest (see Improve Taxon ID Handling for Ingestion and Deposition #2955) and otherwise not use the same config as used for ingest
  • Add authors to manifest if is_broker is true
  • Update taxon_ids to be more broad in ingest and more specific in submission

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PR Checklist

  • All necessary documentation has been adapted.
  • The implemented feature is covered by an appropriate test.

@corneliusroemer corneliusroemer changed the title Add_authors_to_manifest feat: ENA deposition improvements and fixes Oct 7, 2024
@anna-parker anna-parker added the preview Triggers a deployment to argocd label Oct 7, 2024
@corneliusroemer corneliusroemer changed the title feat: ENA deposition improvements and fixes feat(deposition): improvements and fixes Oct 7, 2024
anna-parker
anna-parker commented Oct 7, 2024
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@anna-parker anna-parker marked this pull request as ready for review October 7, 2024 10:39
@corneliusroemer corneliusroemer added the needs-ppx-values-pr Requires accompanying pathoplexus/pathoplexus PR to update values.yaml label Oct 7, 2024
@anna-parker anna-parker mentioned this pull request Oct 7, 2024
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anna-parker added a commit to pathoplexus/pathoplexus that referenced this pull request Oct 7, 2024
@anna-parker
update loculus version to point to loculus-project/loculus#2960
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corneliusroemer
corneliusroemer approved these changes Oct 7, 2024
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LGTM, save 1-2 comments, have a look at them before merging

So this PR:

  • adds the is_broker variable to config
  • renames ingest to enaDeposition in some comments
  • adds the AUTHORS manifest row
  • allows setting different ingest and deposition taxon ids

@anna-parker
Ena add address (#2965)
6064eda 
* Add address

# Conflicts:
#	ena-submission/scripts/create_assembly.py

* Fix address parsing

* fix tests

* fix tests

(cherry picked from commit 673786c)

* log error
@corneliusroemer corneliusroemer merged commit 188eb04 into main Oct 7, 2024
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@corneliusroemer corneliusroemer deleted the add_authors_to_manifest branch October 7, 2024 16:05
@github-actions github-actions bot mentioned this pull request Oct 7, 2024
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@corneliusroemer corneliusroemer corneliusroemer approved these changes

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needs-ppx-values-pr Requires accompanying pathoplexus/pathoplexus PR to update values.yaml preview Triggers a deployment to argocd
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Improve Taxon ID Handling for Ingestion and Deposition
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