Delete project

This procedure is to delete an exported project/submission from Ingest database. If the project was submitted to DCP or EMBL-EBI archives, you should coordinate with them the deletion of that project.

Steps

1. Delete project in Terra.

   If the project has already been imported to a Terra dataset, you should coordinate the deletion with Data Import team led by jkorte@broadinstitute.org in the dcp-2 channel in HCA slack workspace

   After making sure the project is deleted in Terra, you must delete the exported files in Terra staging area. Please see the SOP on Setting up access to Terra staging area to setup your access.

   This can be done using the following command after setting up Terra access.

   gsutil -m rm -r gs://broad-dsp-monster-hca-prod-ebi-storage/prod/<project-uuid>
   

2. Delete project in the archives.

   The project data is being submitted to BioStudies, BioSamples and ENA. You should coordinate the project deletion for each archive.

   EMBL-EBI Archive	How to contact
   BioStudies	Send email to biostudies@ebi.ac.uk
   BioSamples	Send email to biosamples@ebi.ac.uk
   ENA	Complete support form https://www.ebi.ac.uk/ena/browser/support

3. Delete the spreadsheet from the broker pod.

   kubectl get pods | grep broker # get broker pod name
   kubectl exec -i -t <broker-pod-name>  -- /bin/bash
   cd /data/spreadsheets/<submission-uuid>
   rm -r /data/spreadsheets/<submission-uuid>
   

   A ticket has been filed to automate this.

4. Delete the submission via UI or API

   When a submission is deleted the upload area will be automatically deleted. This is being done by the ingest-staging-manager deployment.

   It should be possible to delete the submission via UI or the API if the submission state is Pending or Draft or Valid or Invalid.

   via UI: There should be a trash bin icon button next to the submission row in the ALL SUBMISSIONS dashboard page. Clicking the button will trigger the deletion of the submission.

   via API:

   export TOKEN='token'
   curl -X DELETE -H "Authorization: Bearer $TOKEN"  https://api.ingest.archive.data.humancellatlas.org/submissionEnvelopes/<object-id>
   

   If submission state is already submitted, the only way to delete it is via API with force flag set.

   export TOKEN='token'
   curl -X DELETE -H "Authorization: Bearer $TOKEN"  https://api.ingest.archive.data.humancellatlas.org/submissionEnvelopes/<object-id>?force=true
   

5. Delete the project in Ingest. All submissions related to the project must be deleted first.

   a. It could be deleted via delete button from the UI

   b. Or by doing the following command.

   curl -X DELETE -H "Authorization: Bearer $TOKEN"  https://api.ingest.archive.data.humancellatlas.org/projects/<object-id>