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Add INSDC accession to results of ena submission and upload to backend. #2845

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merged 8 commits into from
Sep 24, 2024

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anna-parker
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@anna-parker anna-parker commented Sep 19, 2024

resolves #

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Summary

  1. Maps results of successful ENA assembly submission to insdc_accession_base and insdc_accession_full and uploads these results to Loculus - handles the case with a single and also a multi-segment organism:
image
  1. Tested locally and updated README with exact commands for local testing and additional warnings.
  2. Refactored code to have --test flag (determines if ENA dev or prod is used) that is set at config level to make code clearer.

Screenshot

PR Checklist

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

@anna-parker anna-parker marked this pull request as ready for review September 22, 2024 14:25
@anna-parker anna-parker added the preview Triggers a deployment to argocd label Sep 22, 2024
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@corneliusroemer corneliusroemer left a comment

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Looks great - haven't tested or reviewed closely, will familiarize myself with the code once we've got the submission running.

@anna-parker anna-parker merged commit b264449 into main Sep 24, 2024
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@anna-parker anna-parker deleted the add_insdcAccession branch September 24, 2024 13:06
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2 participants