Deleting entire data tables

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tmajarian

• July 21, 2021 14:53

Hi-

I have multiple workspaces with 5+ data tables in each. I would like to delete each table in its entirety in each workspace -- to remove all data tables but keep the workspaces themselves. I am aware of how to do this through the GUI & API (although I am having issues with each) on an entity-by-entity basis. Is there a quicker/better way to bulk delete entire data tables?

 

Thanks!

-Tim

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  Samantha (she/her)

  • July 21, 2021 16:36

  Hi tmajarian,

   

  Thanks for reaching out. If you want to delete the entire data table at once, you can select all rows in the table to delete, which will effectively delete the table itself. Unfortunately, there's no way to delete multiple tables at once.

  

  Can you elaborate on the issues you are having using the API?

   

  Best,

  Samantha

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  tmajarian

  • July 21, 2021 17:42

  Hi Samantha-

  Sure. I'm actually having what seems to be the same issue with both the GUI and API. Using the method you described, I am getting a "failed to fetch" error:

  

  Using the API to delete the same entities gives me a time out error: ReadTimeout: HTTPSConnectionPool(host='api.firecloud.org', port=443): Read timed out. (read timeout=120).

   

  These tables were imported using Biodata Catalyst Gen3. 

   

  Thanks for looking into this for me.

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  Samantha (she/her)

  • July 21, 2021 18:31

  Hi tmajarian,

   

  How many rows are in the table you are trying to delete? If possible, can you please share your workspace with GROUP_FireCloud-Support@firecloud.org and let us know the name of your workspace so we can take a closer look?

   

  Best,

  Samantha

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  tmajarian

  • July 21, 2021 18:33

  There are only 9 rows in the table. The workspace is named "NIH_interop_BDCatalyst". I will share the workspace.

   

  Thanks!

   

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  Samantha (she/her)

  • July 21, 2021 19:19

  Hi tmajarian,

  I cloned the workspace and was able to reproduce the error when attempting to delete the "study" table. I'll bring this to our engineers to look into and let you know what they say.

  Best,

  Samantha

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  Samantha (she/her)

  • July 22, 2021 14:10

  Hi tmajarian,

  I brought this to our engineers and they think the deletion is timing out because Terra needs to make sure that there are no other entities in the workspace that contain references to any of the 9 entities, but there are a lot of references here so it's a bit slow. Deletion would probably still fail even if it didn't time out because you can't delete any entity that has references to it. If you try to just delete one of those rows instead of all 9, you should be able to get a more helpful error message.

  When I tried to delete one of the rows in the study table in the clone I created, the error message indicates that there are 21008 entities that reference it.

  

  

   

  Best,

  Samantha

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  tmajarian

  • July 22, 2021 15:01

  Thanks! I am using the API to delete entities in batches which is working for me.

  -Tim

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