Hail container package issues

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Elizabeth Sheets

• March 16, 2021 17:34

The current Hail container (Python 3.7.9, hail 0.2.62) doesn't interact well with Pandas. I was able to solve the errors by installing `fsspec` and upgrading `gcsfs` (current install is 0.2.2 and the Pandas error suggested >0.3.0). I might suggest updating this container. 

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  Jason

  • March 16, 2021 20:50

  Hi Elizabeth Sheets,

  Thanks for reporting this. We'll take a closer look and get back to you as soon as we can!

  Kind regards,

  Jason

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  Jason

  • March 17, 2021 15:02

  Hi Elizabeth Sheets,

  Are there any specific Pandas functions you're having difficulty using with the Hail container? I'd love to have a reproducible issue I can show the engineers when writing up this request. Any screenshots you have would be super highly appreciated!

  Kind regards,

  Jason

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  Elizabeth Sheets

  • March 17, 2021 15:38

  I am getting the error when trying to use read_csv():

  

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  Jason

  • March 17, 2021 16:02

  Thanks for that. I did a quick test and strangely didn't have any problems using read_csv.

  

  Was anything in the environment added or changed, perhaps through a startup script? Is there any reason you can think of why we would experience different results using the command?

  Jason

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  Elizabeth Sheets

  • March 18, 2021 17:15

  Hi Jason, I don't think so, this notebook is public if you want to see if you can recreate the issue there: https://app.terra.bio/#workspaces/biodata-catalyst/BioData%20Catalyst%20GWAS%201000%20Genomes%20Tutorial/notebooks/launch/3-GWAS-genomic-data-preparation.ipynb

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  Jason

  • March 19, 2021 20:36

  Hi Elizabeth,

  Thank you for providing the notebook. I'll try to recreate the issue and get back to you as soon as I can.

  Kind regards,

  Jason

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  Elizabeth Sheets

  • March 19, 2021 21:47

  I can also invite you to my workspace (it's using open-access data) if that's easier.

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  Jason

  • March 22, 2021 21:15

  Hi Elizabeth,

  I'll let you know if we run into issues trying out the public notebook. Thank you for your patience here. we've been experiencing a higher than usual volume of support requests. We'll work to replicate this issue as soon as we're able!

  Kind regards,

  Jason

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  Jason

  • March 24, 2021 18:25

  Hi Elizabeth,

  I was able to reproduce the issue!

  We'll investigate this discrepancy and get back to you as soon as we can!

  Kind regards,

  Jason

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  Jason

  • March 25, 2021 14:23

  Hi Elizabeth,

  Just to confirm, you were able to find a workaround here and are not currently blocked due to this error, correct? I want to make sure I give our engineers the appropriate level of urgency in my filing of the issue. Let me know if you are aware of any reasons why this might need resolving sooner rather than later, and I'll be happy to communicate that to the team.

  Many thanks,

  Jason

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