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EBISPOT
GCST changed for the submission id 632c967737db2600018dd446 GCP000432 (PMID:35870639)
The GCST was changed for the submission of 6790 studies. It is a user submission, and I added associations and uploaded it in the dep-curation app. It failed to upload as some of the variant id columns were empty. I added those missing rsids and again uploaded the file. This time it got uploaded, but the GCSTs got changed. I didn't make changes to any of the study tag.
This has to be done before the next DR.
I've attached the list of studies with original and changed GCST ids (https://app.zenhub.com/files/2995118/5cfd7cf2-7c76-4494-ba2b-d959d825b1f7/download)
@Santhi1901 this is very much complex than previously thought ,not a straight forward GCST change, the issue is the studies have been duplicated probably both unpublished studies & published studies existing in DB , I need to understand the workflow for this submission, how did we get to this scenario of studies getting duplicated in Deposition , this issue had happened once before when we had edited Depo curation without unpublishing the Pmid in Curation App, we can discuss further tomorrow
@sajo-ebi The user submitted pre-published submission (gwas-subs #613211) and later added the PMID (I am not sure when exactly the PMID was added). This submission appears in the list of pre-published submissions in the Catalog.
The sumstat validation failed multiple times due to md5sum mismatch (https://github.com/EBISPOT/goci/issues/867).
I uploaded the template with associations through depo-curation app. It failed uploading as some of the rows the variant IDs were missing. I re-uploaded again with all the errors corrected.
This time it got uploaded, but the GCSTs have changed.
This submission was never published through curation app Submission history.xlsx
The GCST has been updated for the submission & the old unused GCST have been deleted from both Mongo & Curation DB so that reuploading template doesn't retain the old GCST , need to raise a new ticket to add validation in code for submission reset to not allow reset when a submission has been edited in Depo-Curation