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@bendichter
Last active April 6, 2021 16:43
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## set up env via bash:
conda create -n stream_nwb -c conda-forge -y python=3.7 hdf5=1.12.0 jupyter pip
conda activate stream_nwb
pip install nwbwidgets
pip install git+https://github.com/NeurodataWithoutBorders/pynwb
pip install git+https://github.com/hdmf-dev/hdmf
git clone https://github.com/satra/h5py.git
cd h5py
HDF5_DIR=~/Users/bendichter/opt/anaconda3/envs/stream_nwb/ pip install --force-reinstall --no-binary=h5py .
## test out streaming
from pynwb import NWBHDF5IO
from nwbwidgets import nwb2widget
import requests
def get_s3_url(url):
s3_url = requests.request(url=url, method='head').url
return s3_url[:s3_url.index('?')]
path = "https://dandiarchive.s3.amazonaws.com/girder-assetstore/58/07/58074d0a5a4a4086afebb4d29912c419"
io = NWBHDF5IO(get_s3_url(url), mode='r', load_namespaces=True, driver='ros3')
nwb = io.read()
nwb2widget(nwb)
@luiztauffer
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I can reproduce the problem on my windows machine, with both conda-forge installation and manual installation of hdf5.
Seems to be a problem specific to windows. I found this, it might help (search for Windows): https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0-RELEASE.txt

@luiztauffer
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we managed to make it work on a Binder deployment, if anyone is interested: https://github.com/catalystneuro/binder-nwb-stream

@satra
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satra commented Mar 21, 2021

you may want to file an issue on conda-forge for hdf5-feedstock, if it is not being compiled on windows with ROS3 VFD support.

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