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feat(deposition): Use github pages to not get rate limited, assert sequences with ena specific fields were submitted by us or the insdc_submission_group #3327

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merged 2 commits into from
Dec 4, 2024
Merged

feat(deposition): Use github pages to not get rate limited, assert sequences with ena specific fields were submitted by us or the insdc_submission_group #3327

merged 2 commits into from
Dec 4, 2024
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anna-parker
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@anna-parker anna-parker commented Dec 2, 2024 •
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resolves #3268, #3328

preview URL: http://ena-polling-fixes.loculus.org/

Summary

  1. Use github pages to reduce polling of github (we were being rate limited)
  2. Fix logger.warning syntax (error due to comma splitting strings) and use logging instance logger instead of logging base class (make ruff happy).
  3. Check if sequences with ena specific metadata fields were submitted by us or the insdc_submission_group (previously used submitter name insdc_ingest_user but this then warns us if a sequence has been curated).

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PR Checklist

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

@theosanderson
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Just to flag that because GH pages can cache stuff and because this file changes this will potentially cause a bit of confusion while the cache has yet to be updated (I recall that in the past this could be a significant length of time). But I expect this is OK for now.

@anna-parker anna-parker changed the title Use github pages to not get rate limited Use github pages to not get rate limited, assert sequences with ena specific fields were submitted by us or the insdc_submission_group Dec 2, 2024
@anna-parker anna-parker added the preview Triggers a deployment to argocd label Dec 2, 2024
@anna-parker anna-parker changed the title Use github pages to not get rate limited, assert sequences with ena specific fields were submitted by us or the insdc_submission_group feat(deposition): Use github pages to not get rate limited, assert sequences with ena specific fields were submitted by us or the insdc_submission_group Dec 2, 2024
@anna-parker anna-parker added preview Triggers a deployment to argocd and removed preview Triggers a deployment to argocd labels Dec 2, 2024
@anna-parker anna-parker marked this pull request as ready for review December 2, 2024 15:07
@anna-parker
fix logging errors and check if data was submitted by the insdc_submi…
8b01b40 
…ssion_group and not the insdc_submission_user to not warn if a sequence has been curated
@anna-parker anna-parker merged commit fdd58b6 into main Dec 4, 2024
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@anna-parker anna-parker deleted the ena-polling-fixes branch December 4, 2024 07:44
@corneliusroemer corneliusroemer mentioned this pull request Dec 4, 2024
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@theosanderson theosanderson theosanderson approved these changes

@chaoran-chen chaoran-chen chaoran-chen approved these changes

@corneliusroemer corneliusroemer Awaiting requested review from corneliusroemer

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We need to reduce the frequency at which we poll Github for curated data updates
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@anna-parker @theosanderson @chaoran-chen