Cannot access jupyter notebook

[SimonZamora]

Hi there,

Firstly, I want to express my appreciation for making Deepvats open source. It's a fantastic tool that I believe will benefit countless individuals!

I'm currently in the process of setting up Deepvats to analyze some time-series data related to movement kinematics. However, I've encountered an issue with the Jupyter notebooks setup that's preventing me from diving into my analysis.

When I run docker-compose up -d, it seems unable to access a file named delete_entity_project.sh. While this file was present in older versions, it appears to be missing in the current setup.

Here's a snippet of the output I'm seeing from Docker Compose and the error I've found in the logs:

simonz@DESKTOP-TDPKSLO:~/deepvats-master/docker$ docker compose ps -a
NAME IMAGE COMMAND SERVICE CREATED STATUS PORTS
deppvats_test_jupyter_1 dvats-jupyter:simonz "/usr/local/bin/entr…" jupyter 18 minutes ago Exited (127) 7 seconds ago
deppvats_test_rstudio-server_1 dvats-rstudio:simonz "/usr/local/bin/entr…" rstudio-server 18 minutes ago Up About a minute 0.0.0.0:8787->8787/tcp, :::8787->8787/tcp

simonz@DESKTOP-TDPKSLO:~/deepvats-master/docker$ docker compose logs
deppvats_test_jupyter_1 | drwxrwxrwx 13 1000 1000 4096 Apr 30 09:56 .
deppvats_test_jupyter_1 | drwxr-xr-x 1 simonz simonz 4096 Apr 30 10:14 ..
deppvats_test_jupyter_1 | drwxrwxrwx 2 1000 1000 4096 Apr 30 09:55 .devcontainer
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 26 Mar 14 11:57 .gitattributes
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 1927 Mar 14 11:57 .gitignore
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 416 Mar 14 11:57 .pre-commit-config.yaml
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 2348 Mar 14 11:57 CONTRIBUTING.md
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 11357 Mar 14 11:57 LICENSE
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 111 Mar 14 11:57 MANIFEST.in
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 417 Mar 14 11:57 Makefile
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 8279 Mar 14 11:57 README.md
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 1176 Mar 14 11:57 build_base_image.sh
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 446 Mar 14 11:57 clean-jupyter-files.sh
deppvats_test_jupyter_1 | drwxrwxrwx 2 simonz 1000 4096 Apr 30 09:56 data
deppvats_test_jupyter_1 | drwxrwxrwx 4 1000 1000 4096 Apr 30 09:56 docker
deppvats_test_jupyter_1 | drwxrwxrwx 4 1000 1000 4096 Apr 30 09:55 docs
deppvats_test_jupyter_1 | drwxrwxrwx 2 simonz 1000 4096 Apr 30 09:55 dvats
deppvats_test_jupyter_1 | drwxrwxrwx 2 1000 1000 4096 Apr 30 09:55 imgs
deppvats_test_jupyter_1 | drwxrwxrwx 4 1000 1000 4096 Apr 30 09:55 nbs
deppvats_test_jupyter_1 | drwxrwxrwx 3 1000 1000 4096 Apr 30 09:55 nbs_pipeline
deppvats_test_jupyter_1 | drwxrwxrwx 2 1000 1000 4096 Apr 30 09:55 paper
deppvats_test_jupyter_1 | drwxrwxrwx 2 simonz 1000 4096 Apr 30 09:55 r_shiny_app
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 606 Mar 14 11:57 settings.ini
deppvats_test_jupyter_1 | -rwxrwxrwx 1 1000 1000 1913 Mar 14 11:57 setup.py
deppvats_test_jupyter_1 | drwxrwxrwx 2 1000 1000 4096 Apr 30 09:55 tchub
deppvats_test_jupyter_1 | Defaulting to user installation because normal site-packages is not writeable
deppvats_test_jupyter_1 | Obtaining file:///home/simonz/work
deppvats_test_jupyter_1 | Preparing metadata (setup.py) ... done
deppvats_test_jupyter_1 | Installing collected packages: dvats
deppvats_test_jupyter_1 | Running setup.py develop for dvats
deppvats_test_jupyter_1 | Successfully installed dvats-0.0.1
deppvats_test_jupyter_1 | patonlab simonz Deepvats
deppvats_test_jupyter_1 | /usr/local/bin/entrypoint.sh: line 15: /usr/local/bin/delete_entity_project.sh: No such file or directory

This issue is hindering my ability to utilize the Jupyter notebooks, although I can still use the RStudio app without any problems. I'm eager to explore the capabilities of the Jupyter environment for my analysis.

Do you have any suggestions on how I might address this issue? Any guidance or assistance you can provide would be greatly appreciated.

Thanks again for your invaluable support!

Cheers!

Simon Z

[Inmaculada Santamaria-Valenzuela]

Thank you very much for your issue and for using our application. The solution will soon be in the master branch. In the meantime, you can delete line 15 from docker\entrypoint.sh to make it work correctly.

Apologies for the delay. If you need anything else, feel free to contact us again.

Best regards,
Inmaculada

[SimonZamora]

Hi!

Thanks for your response! I managed to resolve the issue. However, I did notice some problems in the code: the TSNE and PCA projections are broken, and the indexing of the start and end positions of the windows doesn't work depending on the date format.

I'd be happy to share some of the fixes I implemented :)

Thanks for the great work! I really like the app and find it very useful.

Cheers,

Simon

[Inmaculada Santamaria-Valenzuela]

Hi, Simon!
Thanks a lot for using the app and for your usefull messages. I will take a look to those issues.
If you want to share those fixes (and doesn't fit here), you can contact us via e-mail: [e-mail].
Also, I would be glad if you could tell the test-case that you are using for testing the indexes.

Thanks,
Inmaculada

[Inmaculada Santamaria-Valenzuela]

Hi, Simon.
Could you make Pull Requests with your proporsals?
Thanks a lot,
Inmaculada