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error updating sample set table

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6 comments

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    Samantha Velasquez

    Hi Sabrina Camp,

     

    Thank you for reporting this issue. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Add GROUP_FireCloud-Support@firecloud.org to the User email field and press enter on your keyboard.
    2. Click Save.

     

    Let us know the workspace name, as well as the relevant submission and workflow IDs. We’ll be happy to take a closer look as soon as we can.

     

    Thanks,
    Samantha

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    Sabrina Camp

    Hi! 

    The workspace name is all_germline_control_cohorts. There is no submission/ workflow ID because I am just uploading a sample set table. This is a screenshot of what it looks like. 

     

    Best,

    Sabrina

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    Samantha Velasquez

    Hi Sabrina Camp,

     

    Thanks for providing more information.

    Can you try re-uploading the tsv file? If it's still causing an error, the file may be too large and you might need to upload smaller tsv files.

     

    Best,

    Samantha

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    Samantha Velasquez

    Hi Sabrina Camp,

    After taking another look at the screenshot you provided, I think the issue here might be that you are attempting to upload what looks like a sample table as a sample set table. To understand the difference, take a look at the data tables in the following workspace as an example: https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/HCoV-19/data.

    In the sample table, each row has a unique sample_id to denote each individual sample.

    The sample_set table combines samples_ids from from the sample table as a "set."

    The screenshot below is what the tsv file for the sample_set table looks like, where the first column denotes the set, and the second column denotes the sample_id belonging to that set. Also note that the first cell contains membership:sample_set_id instead of entity:sample_set_id.

     

    If you are trying to upload a sample table, then changing the first cell to entity:sample_id instead of entity:sample_set_id should fix the upload error. However, if you are trying to upload a sample set table, make sure the tsv file is in the correct format outlined above and the first column contains membership:sample_set_id.

    I hope this helps. You can also find more information in this article: Managing data with tables.

    Please let me know if you need any further assistance.

     

    Best,

    Samantha

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    Sabrina Camp

    Hi Samantha,

    I am trying to upload columns to the sample set table. I thought that the way to do this was to have the sample_set_ids in the entity:sample_set_id column and then add other columns I would like to have in the table. 

    Thank you for the other detailed information regarding other types of tables! 

     

    Best,

    Sabrina 

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    Samantha Velasquez

    Hi Sabrina Camp,

     

    I hope the information was able to answer your question. If you are still in need of assistance, please don't hesitate to reach out!

     

    Best,

    Samantha

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