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Delete BoW/submission and change GCST #1552
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There were some complications when the author made their original submission, explained in this ticket: https://app.zenhub.com/workspaces/gwas-59df823c4a6feb3786810391/issues/gh/ebispot/goci/751 |
@eks-ebi the old GCST has been deleted from curation DB & GCST updated for the new submission, please validate |
@sajo-ebi Yes, looks great - thanks! |
I've now imported and published the new submission under PMID 39749473 |
I will check for automatic updates to the FTP folder over the following week and after next DR - will check in with developers if the old files are not being replaced |
@karatugo I have imported a new submission (with new versions of the summary statistics) for GCST90013791. There was already a file with this GCST on the FTP. Does any manual action need to be done to replace the old files? Or should it happen automatically? |
The files on ftp staging and public ftp are the same (checked md5sums). They are from Feb 2021. I can track the new files if you could show me where they are copied/moved. |
@karatugo When the new submission was created, the GCST assigned to the study was GCST90502918 (which was then manually changed back to GCST90013791 by Sajo. Could the new files still be stored under GCST90502918 in staging? |
GCST90502918 study file is from 24 Jan. |
That would be the correct one! Can you move that to replace the file for GCST90013791, and trigger new YAML creation and harmonisation? |
@karatugo As discussed in the meeting this morning, can you please do the following?
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@eks-ebi Should I delete GCST90502918 from public ftp? |
Background:
The author made a previous submission (body of work GCP000131, 1 study: GCST90013791). The submission was deleted from the deposition database, however the metadata and sumstats from the original submission still exist in the search UI: https://www.ebi.ac.uk/gwas/studies/GCST90013791.
There was also some confusion when the original submission was deleted, which means that there is another study (GCST90017149) in Mongo that is no longer needed
I have now created a new sumstats+metadata submission:
https://www.ebi.ac.uk/gwas/depo-curation/submissions/6792317da2be5f000111fd92
Thisis linked to the PMID (39749473), contains all the submitted data (sumstats and metadata) and has been fully curated. It is ready for import, but first we need to remove all traces of the old submission, and change the GCST in the new submission to match the original one (GCST90013791)
I need developer help with the following tasks:
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