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scratcharchive / kachery

Content-addressable storage server with Python client
Apache License 2.0
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Issues with Kachery #5

Open MaitreyiJ opened 4 years ago

MaitreyiJ commented 4 years ago

Hi! I have been attempting to use spike forest for some spike sorting benchmarking . I was able to clone the repo and I also downloaded the dependency Kachery-but I am having the following error when I attempt to run one of the examples in this repo(running spykingCircus sorter)

with ka.config(fr='default_readonly'): (Error in this line) AttributeError: module 'kachery' has no attribute 'config'

I have tried to set the environment variable -kachery storage to some folder for temp files storage and I am not too sure how to set the password for the environment variable kachery_password.

I also attempted to run the test files in the kachery repo and I get the error-Permission denied.

I am suspecting that there is some issue with the kachery dependency. Any help/instructions will be highly helpful.

Regards Maitreyi

magland commented 4 years ago

Hi Maitreyi. Could you please confirm that you are using the right version of kachery? Did you install using pip install kachery? Try pip list to see which version is installed.

Then try a basic:

with ka.config(fr='default_readonly'):
    pass
MaitreyiJ commented 4 years ago

Yes I tried running the command, this time it doesn't fail, but gives a warning Warning: unable to load preset configurations from: https://raw.githubusercontent.com/flatironinstitute/kachery/config/config/config_2019a.json

magland commented 4 years ago

Okay, we will look into this tomorrow, thanks for the report.

MaitreyiJ commented 4 years ago

Hi ! I have been able to run the sorter now-successfully (given in the example) but there is a specific directory structure I had to follow-in terms of placing the dependencies.(kachery files)

I am currently trying to read the output files generated by the example( the Jason files) with the help of widgets/ sh links.

Thanks for the support.

magland commented 4 years ago

What do you mean by widgets/ sh links? Do you need help with this?

On Thu, May 14, 2020 at 4:12 PM MaitreyiJ notifications@github.com wrote:

Hi ! I have been able to run the sorter now-successfully (given in the example) but there is a specific directory structure I had to follow-in terms of placing the dependencies.(kachery files)

I am currently trying to read the output files generated by the example( the Jason files) with the help of widgets/ sh links.

Thanks for the support.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/flatironinstitute/kachery/issues/5#issuecomment-628862307, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA4CIQFRMMRDX7XIVEDOCTTRRRGCFANCNFSM4M657QKQ .

MaitreyiJ commented 4 years ago

Yes, I think you can help me out with this. The following screenshot was taken after running the python script example_spykingcircus.py Running the script opens the command prompt and suuccefully runs the sorter (spykingCircus) on the data-set. However the command prompt closes immediately once the spike sorting is complete and the following output is recorded in the python shell.

I am unable to understand how I should go about viewing the output files. As per the documentation , a single Jason file will contain the output . But I cant locate that file or any putput produced by the sorter.

OutputDebuggingIssues

This is what I see in the shell(in case the screenshot doesn't load properly) ===== Hither: finished [spykingcircus] with status finished after 117.37312245368958 sec Warning: problem writing .record.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\e5\7d\75\e57d75df9b97b4c275976cbdaa43f101da393c99.record.json Warning: problem writing .hints.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905.hints.json Warning: problem writing .record.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\e5\7d\75\e57d75df9b97b4c275976cbdaa43f101da393c99.record.json Warning: problem writing .hints.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905.hints.json hither.File(C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905)

magland commented 4 years ago

It appears that you are on windows. We haven't tested anything on windows. One thing you could do is to make a virtual linux machine.

On Thu, May 14, 2020 at 4:35 PM MaitreyiJ notifications@github.com wrote:

Yes, I think you can help me out with this. The following screenshot was taken after running the python script example_spykingcircus.py Running the script opens the command prompt and suuccefully runs the sorter (spykingCircus) on the data-set. However the command prompt closes immediately once the spike sorting is complete and the following output is recorded in the python shell.

I am unable to understand how I should go about viewing the output files. As per the documentation , a single Jason file will contain the output . But I cant locate that file or any putput produced by the sorter.

[image: OutputDebuggingIssues] https://user-images.githubusercontent.com/59170109/81983061-bfc8dd80-9600-11ea-947e-b88934e55e74.png

This is what I see in the shell(in case the screenshot doesn't load properly) ===== Hither: finished [spykingcircus] with status finished after 117.37312245368958 sec Warning: problem writing .record.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\e5\7d\75\e57d75df9b97b4c275976cbdaa43f101da393c99.record.json Warning: problem writing .hints.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905.hints.json Warning: problem writing .record.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\e5\7d\75\e57d75df9b97b4c275976cbdaa43f101da393c99.record.json Warning: problem writing .hints.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905.hints.json

hither.File(C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905)

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