Need Help?

Search our documentation and community forum

Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate.
Terra powers important scientific projects like FireCloud, AnVIL, and BioData Catalyst. Learn more.

Download sample set metadata and then cannot upload it again

Comments

9 comments

  • Avatar
    Jason Cerrato

    Hi Luda,

    Thanks for reporting this. Would you be able to share the workspace in question where you are receiving this error with GROUP_FireCloud-Support@firecloud.org? Please provide us a link of the workspace after sharing if so. 

    Kind regards,

    Jason

    0
    Comment actions Permalink
  • Avatar
    Liudmila Elagina

    Hello Jason,

     

    Unfortunately, I cannot share that particular workspace. But I shared another workspace:

    broad-firecloud-wuclonal/TCGA_GATK4_CNV_PoN

    So if you try to download sample_set metadata and then upload file sample_set_entity.tsv you will get this error:

    0
    Comment actions Permalink
  • Avatar
    Liudmila Elagina

    Hello Jason,

     

    I was wondering if you had any success replicating this error and if there is a solution for it we could use.

     

    Thank you,

    Luda

    0
    Comment actions Permalink
  • Avatar
    Jason Cerrato

    Hi Luda,

    I have not yet had a chance to take a look. Apologies for the delay here, we are experiencing a very high volume of support requests at present. I will take a look as soon as I am possibly able.

    If this is particularly urgent, please let me know and I will try to get to it sooner!

    Kind regards,

    Jason

    0
    Comment actions Permalink
  • Avatar
    Jason Cerrato

    Hi Luda,

    Just so I'm clear, do you also see this issue when you try uploading through the Terra UI? 

    Kind regards,

    Jason

    0
    Comment actions Permalink
  • Avatar
    Liudmila Elagina

    Yes, I do.

     

    0
    Comment actions Permalink
  • Avatar
    Jason Cerrato

    Hi Luda,

    Thank you for confirming. I am discussing this issue with one of our engineers now.

    Kind regards,

    Jason

    0
    Comment actions Permalink
  • Avatar
    Jason Cerrato

    Hi Luda,

    The reason why this table gets updated without issue when writing from workflows but does have issue when uploading a TSV is because updating it through workflows doesn't utilize the TSV parser, which is where the restriction is at the moment. Our engineers are currently brainstorming a solution for this restriction and I will get back to you as soon as I hear more.

    Kind regards,

    Jason

    0
    Comment actions Permalink
  • Avatar
    Jason Cerrato

    Hi Luda,

    At this time, the only way to get around the .tsv limit would be to make your changes using an API call: https://api.firecloud.org/#!/Entities/update_entity

    You mentioned you are trying to make a slight modification. What kind of change are you looking to make? We may be able to help you in figuring out how to construct the right call.

    Kind regards,

    Jason

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk