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Delete BoW/submission and change GCST #1552

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4 of 6 tasks
eks-ebi opened this issue Jan 24, 2025 · 13 comments
Open
4 of 6 tasks

Delete BoW/submission and change GCST #1552

eks-ebi opened this issue Jan 24, 2025 · 13 comments
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@eks-ebi
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eks-ebi commented Jan 24, 2025

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:

  • Make sure we have deleted everything linked to the original body of work (GCP000131) and the existing study (GCST90013791) - I think it is already deleted from deposition db, but it would be worth double checking. I think the existing data for this GCST also needs to be removed from Oracle so it does not appear in the search UI, downloads etc.
  • Delete GCST90017149 from deposition db (this is not needed, and does not need to be replaced by anything)
  • Change the GCST for the new submission (6792317da2be5f000111fd92) from GCST90502918 > GCST90013791 to match what the author has cited in their paper
  • Once the GCST is updated, I will import the new submission and publish to Catalog
  • Make sure the old summary statistics have been removed from the FTP: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90013001-GCST90014000/GCST90013791/
  • Make sure the summary statistics from the new submission have been copied to the correct GCST folder in the FTP: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90013001-GCST90014000/GCST90013791/
@eks-ebi eks-ebi changed the title Delete BoW and submission and change GCST Delete BoW/submission and change GCST Jan 24, 2025
@eks-ebi
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eks-ebi commented Jan 27, 2025

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
This might help to explain what happened back then.

@sajo-ebi
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sajo-ebi commented Feb 4, 2025

@eks-ebi the old GCST has been deleted from curation DB & GCST updated for the new submission, please validate

@eks-ebi
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eks-ebi commented Feb 4, 2025

@sajo-ebi Yes, looks great - thanks!

@eks-ebi
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eks-ebi commented Feb 4, 2025

I've now imported and published the new submission under PMID 39749473

@eks-ebi
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eks-ebi commented Feb 4, 2025

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

@eks-ebi
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eks-ebi commented Feb 5, 2025

@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?
It looks like the old files are still there for the time being: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90013001-GCST90014000/GCST90013791/ (time stamps from January 2025, whereas the new files should be from February 2025)

@karatugo
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karatugo commented Feb 5, 2025

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.

@eks-ebi
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eks-ebi commented Feb 5, 2025

@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?

@karatugo
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karatugo commented Feb 5, 2025

GCST90502918 study file is from 24 Jan.

@eks-ebi
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eks-ebi commented Feb 5, 2025

That would be the correct one! Can you move that to replace the file for GCST90013791, and trigger new YAML creation and harmonisation?

@eks-ebi
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eks-ebi commented Feb 6, 2025

@karatugo As discussed in the meeting this morning, can you please do the following?

  1. delete all of the files that are currently under GCST90013791
  2. move the new file which is currently under GCST90502918 into the folder for GCST90013791, and rename them as GCST90013791
  3. do anything else that needs to be done to generate new YAMLs/harmonised files for the new file

@eks-ebi eks-ebi assigned karatugo and unassigned ljwh2 and sajo-ebi Feb 12, 2025
@karatugo
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  • Deleted all of the files that are currently under GCST90013791 both on ftp staging and public ftp
  • Moved all files which is currently under GCST90502918 into the folder for GCST90013791, and renamed them as GCST90013791
  • yaml will be generated in 2 days
  • harmonised folder also deleted, should generated harmonised files automatically after ftp sync is done in 2 days

@karatugo
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@eks-ebi Should I delete GCST90502918 from public ftp?

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