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pypi NSRR outside AWS

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robkon +0 points · almost 2 years ago

Hi All

I have nsrr pypi package installed on top of python 3.8.9 running on Mac OS 12. I am trying to build out a script to download files from the Mesa dataset that I have been granted access to. I would like to download one edf file at a time, conduct a spectral analysis, save the output then remove the local file. This method saves a lot of local disk space.

When I run the nsrr package and check user access the response object returns "'Error: service is available only from AWS cloud'. I assume that AWS cloud has some properties which allow access that the NSRR API_SERVER checks for.

With this in mind how should python developers access a permissioned dataset from their development environment on a laptop?

regards and thank you


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Shyamal +0 points · almost 2 years ago

Hi Robert,

Python package 'nsrr' (NSRR Cloud - https://github.com/nsrr/nsrr-cloud ) is built to support sleep researchers who are AWS cloud users only. For now, we have only this supported capability for python developers. To get started with NSRR Cloud, please refer to https://nsrr.github.io/nsrr-cloud/. Currently only CFS dataset is hosted in NSRR Cloud. And, we are actively working to add support for additional datasets in NSRR Cloud.

For any development environment other than AWS, we recommend users to utilize original Ruby gem (https://github.com/nsrr/nsrr-gem). First, you would have to go to https://sleepdata.org to identify MESA study folder strcuture and file naming for EDF's . Now use the following options in ruby command:

  1. Dataset name in the format of "dataset/folder1/folder2/" (ex: mesa/files/polysomnography/edfs) and,
  2. File name in the format of '--file="file_name_regex.ext"' (ex: mesa-sleep-0001.edf).

Let us know if you need any other help.