This repo should be used for uploading sequences that have been approved for release to ENA. Once sequences are uploaded to the approved folder the ena-submission pipeline will ingest them and add them to the submission-database - triggering ENA submission. We assume only approved sequences are uploaded here and only perform minimal checks.
The loculus-get-ena-submission-list-cronjob should generate a file that is the correct format. If you are ok with the contents of this file you can rename the file as approved_ena_submission_list.json and upload it to the approved folder. (See the test folder for an example).
Note the test folder can be used to test your submissions on PPX staging. Staging reads sequences in the test folder and submits them to the ENA dev website using the ENA broker account (we do not have a separate test account the only difference is that submissions are made to the ENA dev instance but all credentials are the same as prod).
After sequences have been uploaded to the database the corresponding files can be removed, but you can also append new sequences to the approved_ena_submission_list.json.
You can use the following jq to use the submissionId as fallback for the specimenCollectorSampleId if the latter is not present:
FILE="test/approved_ena_submission_list.json"
jq '
map_values(
.metadata.specimenCollectorSampleId //= .metadata.submissionId
)
' "$FILE" | sponge "$FILE"