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feat(ena-submission): Trigger ena submission #2412

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merged 3 commits into from
Aug 13, 2024
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@anna-parker anna-parker commented Aug 11, 2024

resolves #2403

preview URL: https://trigger-ena-submission.loculus.org/

Summary

  1. Get sequences that have been approved for release from https://github.com/pathoplexus/ena-submission/blob/main/approved/approved_ena_submission_list.json and add them to the submission_table (if not already there), this will trigger the ena submission process.
  2. Add a cronjob that calls get_ena_submission_list every day, sending a slack message with sequences that are ready for ena submission but need manual approval. (added in feat(ena-submission): Add ena slack notifications #2396)

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PR Checklist

image
  • Confirm cronjobs are working, changed cronjob to run every 15minutes (e.g. change from "0 0 * * *" to */15 * * * *) and then uploaded new sequences to the preview instance, slack notifications from the cron job are working as intended:
    image - additionally they are added in a loop

@anna-parker anna-parker added the preview Triggers a deployment to argocd label Aug 12, 2024
@anna-parker anna-parker added preview Triggers a deployment to argocd and removed preview Triggers a deployment to argocd labels Aug 12, 2024
@anna-parker anna-parker marked this pull request as ready for review August 12, 2024 12:18
@anna-parker anna-parker force-pushed the trigger_ena_submission branch 3 times, most recently from 27bc013 to 6cce7e5 Compare August 12, 2024 13:07
@anna-parker anna-parker added the review please PR waiting for final review label Aug 12, 2024
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@theosanderson theosanderson left a comment

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lgtm

@anna-parker anna-parker merged commit b68f2cd into main Aug 13, 2024
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@anna-parker anna-parker deleted the trigger_ena_submission branch August 13, 2024 11:37
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Configure sequence approval and test we can manually trigger submission to ENA
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