[Neuroimaging] ANN: openneuro-py, a new app for downloading OpenNeuro datasets

[Yaroslav Halchenko]

On Tue, 15 Dec 2020, Richard Höchenberger wrote:

>    Hello, just to briefly comment on this one:
>    On Tue, Dec 15, 2020 at 4:27 PM Christopher Markiewicz
>    <markiewicz at stanford.edu> wrote:

>      Hi all,

>      FWIW almost all public datasets have been pushed to GitHub and can be
>      accessed via datalad (exceptions being tracked on these issues:
>      https://github.com/OpenNeuroOrg/openneuro/issues/1741 and
>      https://github.com/OpenNeuroOrg/openneuro/issues/1743).

>          datalad install https://github.com/OpenNeuroDatasets/ds00WXYZ.git

>    I specifically wanted to avoid using datalad for several reasons:
>      * I've seen people struggle to install (esp. on macOS) and use it
>        (including myself)

please share your difficulties!  mac should be the next to the easiest
to be installed/used on.
http://handbook.datalad.org/en/latest/intro/installation.html?highlight=OSX#macos-osx

    brew install git-annex
    pip3 install datalad

should do it, but even better, instead of pip install, you do "conda install -c
conda-forge datalad" if you have conda available.  If not, soon there would be
installer (well, it is there but under active RF)
https://github.com/datalad/datalad-installer/ so you would just do smth
like

    pip install datalad_installer  # no dependencies, light and easy
    python -m datalad_installer miniconda git-annex datalad

and it should do the "right thing".   Also the effort is (very slowly)
ongoing to provide OSX build of git-annex on conda-forge.  A sloppy unfinished
approach: https://github.com/conda-forge/git-annex-feedstock/pull/107

 If not -- please file an issue so we could fix.

>      * as far as I understand, there's no way to download a specific revision
>        (version number) of a dataset using datalad 

it is just two steps procedure indeed ATM -- you would just need to
"manually" checkout corresponding version you like, e.g.

$> python3 -c 'import datalad.api as dl; ds = dl.install("https://github.com/OpenNeuroDatasets/ds000001.git"); ds.repo.checkout("1.0.0")'   

we need to make it easier, e.g. see discussion/chime-in on

	https://github.com/datalad/datalad/issues/1810#issuecomment-379365779

so we should add support for e.g.

  dl.install("https://github.com/OpenNeuroDatasets/ds000001.git@1.0.0")

or alike (already supported for RIA stores, like the one used for HCP dataset)

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW:   http://www.linkedin.com/in/yarik