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datalad-nda

Playground for scripts to ease working with NDA via DataLad

scripts/datalad-nda

The main script to populate a DataLad dataset based on a downloaded NDA manifest. It has been used to produce DataLad dataset for ABCD dataset. Sample invocation:

datalad-nda/scripts/datalad-nda add2datalad \
  -i <(xzcat ~/proj/abcd/datastructure_manifest.txt.xz) \
  -d testds-content3-part10 --drop-after -J10 --develn 10 --fast

to produce a sample (super)dataset with content downloaded and indexed by git-annex, where only 10 files from a submission are downloaded.

Since GUIDs used by NDA are considered to be sensitive information, and used in the filenames of the BIDS dataset, resultant dataset is not made available publicly. Work is ongoing to establish deposition of produced datalad datasets back into NDA to provide access to researchers who have been granted access to ABCD dataset.

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datalad-nda's Issues

Trouble Adding S3 URLs from NDA manifest

Hello,

I am attempting to use the datalad-nda CLI in order to produce a datalad dataset based on the 09 2020 3165 ABCD release found on NDA. I have the manifest as an uncompressed text file, so I came up with the following command:

/home/faird/shared/code/external/utilities/datalad-nda/scripts/datalad-nda add2datalad \ -i <(cat /spaces/ngdr/workspaces/hendr522/ABCD/datalad-ABCD-BIDS/abcd316520200818/datastructure_manifest.txt) \ -d /spaces/ngdr/workspaces/hendr522/ABCD/datalad2.0-ABCD-BIDS -J 10 --fast --drop-after. I've attached the messages sent to STDOUT and STDERR in separate files
datalad2.0-nda_ABCD-BIDS_5371074_STDOUT.txt
datalad2.0-nda_ABCD-BIDS_5371074_STDERR.txt

I am using the most recent version of the datalad-nda CLI (I pulled the repo maybe a week ago) and am running datalad version 0.14.4

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