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neurodata / ndstore

code for storing neurodata images and image annotations
http://neurodata.io
Apache License 2.0
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Unable to ingest nifti #374

Open vikramc1 opened 8 years ago

vikramc1 commented 8 years ago

After copying & pasting the "putnifti.py" file to my working directory, I ran:

python putnifti.py '52.91.173.4/nd' 'FA_Maps' 'dti' 'KKI2009_113_1_DTI_aligned.nii'

The resulting url was printed as: http://52.91.173.4/nd/ca/FA_Maps/dti/nii/

The resulting error was: Failed http://52.91.173.4/nd/ocp/ca/FA_Maps/dti/nii/. Exception HTTP Error 502: Bad Gateway.

@jovo @randalburns @kunallillaney @gkiar

kunallillaney commented 8 years ago

@vikramc1 @gkiar Use mri.neurodata.io. Let me know if there is an issue.

jovo commented 8 years ago

:couple_holding_hands:!!!

On Mon, Oct 31, 2016 at 6:40 PM, Kunal Lillaney notifications@github.com wrote:

@vikramc1 https://github.com/vikramc1 @gkiar https://github.com/gkiar Use mri.neurodata.io. Let me know if there is an issue.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/neurodata/ndstore/issues/374#issuecomment-257441589, or mute the thread https://github.com/notifications/unsubscribe-auth/AACjcnF3BctbiGHHZruOJbt13lX51Uyhks5q5m5BgaJpZM4KlS8z .

the glass is all full: half water, half air. neurodata.io, jovo calendar https://calendar.google.com/calendar/embed?src=joshuav%40gmail.com&ctz=America/New_York

vikramc1 commented 8 years ago

attempted to create a channel for my project on mri.neurodata.io and got the following error:

Failed to create channel. (1049, "Unknown database 'kki2009'")

EDIT:

I accidentally chose the 'Link to existing database' option when creating the project. Problem fixed.

vikramc1 commented 8 years ago

Still having some issues ingesting.

Command I typed: python putnifti.py 'mri.neurodata.io/nd' 'kki2009' 'dti' 'dti/KKI2009_113_1_DTI_aligned.nii.gz'

First argument: baseurl Second argument: token Third argument: channel Fourth argument: filename

(putnifti.py taken from here)

URL generated: http://mri.neurodata.io/nd/ca/kki2009/dti/nii/ Error encountered: Failed http://mri.neurodata.io/nd/ca/kki2009/dti/nii/. Exception HTTP Error 502: Bad Gateway.

Additional Information:

@kunallillaney

kunallillaney commented 8 years ago

@vikramc1 Email me the file you are trying to post.

vikramc1 commented 8 years ago

sent to you on slack

On Nov 3, 2016, at 11:40 AM, Kunal Lillaney notifications@github.com<mailto:notifications@github.com> wrote:

@vikramc1https://github.com/vikramc1 Email me the file you are trying to post.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/neurodata/ndstore/issues/374#issuecomment-258180432, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGwm1of03RA5ngVAOdkJ6eDZGD8Nudzxks5q6gCHgaJpZM4KlS8z.

kunallillaney commented 8 years ago

@vikramc1 Should be resolved now. Try again. It will take some time for it to finish. I would run it in a screen/tmux.

jovo commented 8 years ago

thanks @kunallillaney

vikramc1 commented 8 years ago

Still not working but with a different error.

Tried: python putnifti.py 'mri.neurodata.io/nd' 'kki2009' 'dti' 'dti/KKI2009_113_1_DTI_aligned.nii.gz' Web url generated: http://mri.neurodata.io/nd/ca/kki2009/dti/nii/ Error received: Failed http://mri.neurodata.io/nd/ca/kki2009/dti/nii/. Exception HTTP Error 504: Gateway Timeout.

jovo commented 8 years ago

@kunallillaney perhaps you can provide an example of this working? @perlman @randburns

On Mon, Nov 7, 2016 at 10:37 AM, vikramc1 notifications@github.com wrote:

Tried: python putnifti.py 'mri.neurodata.io/nd' 'kki2009' 'dti' 'dti/KKI2009_113_1_DTI_aligned.nii.gz' Web url generated: http://mri.neurodata.io/nd/ca/kki2009/dti/nii/ Error received: Failed http://mri.neurodata.io/nd/ca/kki2009/dti/nii/. Exception HTTP Error 504: Gateway Timeout.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/neurodata/ndstore/issues/374#issuecomment-258868855, or mute the thread https://github.com/notifications/unsubscribe-auth/AACjckBSTU9uaaliRIEFRf-HhR937FR0ks5q70WcgaJpZM4KlS8z .

the glass is all full: half water, half air. neurodata.io, jovo calendar https://calendar.google.com/calendar/embed?src=joshuav%40gmail.com&ctz=America/New_York

kunallillaney commented 8 years ago

@vikramc1 Just a sanity check. Are you actually typing single quotation marks in your command line arguments?

vikramc1 commented 8 years ago

Yes I am

kunallillaney commented 8 years ago

@vikramc1 Why are you doing that, because they are strings? When you pass command-line arguments to a python script you do not do that.

Here is the command to run. python putnifti.py mri.neurodata.io/nd kki2009 dti dti/KKI2009_113_1_DTI_aligned.nii.gz

Do ensure here that the path to the file is correct from the point where you run your script.

vikramc1 commented 8 years ago

@kunallillaney I tried that and got the same error: Failed http://mri.neurodata.io/nd/ca/kki2009/dti/nii/. Exception HTTP Error 504: Gateway Timeout.

kunallillaney commented 8 years ago

@vikramc1 I messaged you on slack. Also, I posted the same file via my computer and it worked. So I am not sure what you are doing wrong(Maybe the file path is wrong). This can be easily verified in person. :)

kunallillaney commented 8 years ago

@vikramc1 I have identified the issue but there is no easy fix for it as of now. @randalburns @perlman The NGINX web-server is timing out after 10mins(we have set the UWSGI read timeout to 600secs) because the job takes longer then that. I can increase this number arbitrarily but that will lead to security issues.

kunallillaney commented 8 years ago

@vikramc1 Were you able to get all the data in? The timeout fix can hopefully work in the short-term. Also let me know if you can view the data . I sent you a sample URL and XY doc link over slack.