openms / streamlit-template Goto Github PK

Update environment.yml and requirements.txt with package version numbers.

• discuss with IT how to host it (not de.NBI) and how to provide access from outside (e.g. our docker server)

Outcome: we probably can host the apps on ibmidocker. Each app gets its own docker container and port.
abiservices can act as an apache proxy (if needed)

• add dockerfile streamlit-template to install a default OpenMS environment

  • add a default installation of OpenMS (e.g., 3.0) executables to docker file (e.g., from conda)
  • add installation of OpenMS/Thirdparty tools to docker file
  • add installation of mono to enable raw file conversion
  • add cron job to docker file to automatically clean up data / delete data after a while

• think about malicious use (e.g., uploading many files) and how this could be prevented in the "online" case

• if hosted online add captcha on upload

• add download button + explanation how to run app locally to template

• document how to add a new app to the streamlit server

only if we need the streamlit_deployment repo:

• add submodule to https://github.com/OpenMS/streamlit_deployment with the streamlit-template.

Axel and me created an initial template for streamlit deployment.
I think we are at a point to test if someone can deploy it on ibmidocker

#4

Steps necessary:

• check out the repo on imbidocker
• build the image
• run docker
• check with IT how to make it accessible from outside (e.g., by adding it to our proxy ibmiservices )

User story: User wants to make his App available.

• User forks https://github.com/OpenMS/streamlit-template and adds his App code to it. Renames his repo to have a meaningful name. E.g., "Cross-Linking-App". If needed, adapts the environment.yml file for additional dependencies.
• User adds his Repo as a submodule to https://github.com/OpenMS/streamlit-deployment
• User adds his App to the local.yml docker compose script (untested), potentially ports need to be adjusted such that there is no overlap between multiple apps

This should allow to deploy multiple streamlit apps on ibmidocker. How we make it accessible through our proxy ibmiservice needs to be discussed with the IT.

e.g.

• make sure streamlit app launches without errors
• linting
• building test cases for workflow code using pytest

Would be great to add the components.

• e.g. component in submodule
• in src folder: general utility code available to everyone using the template
• e.g. one page showing the functionality

that way, the template also serves a bit like a tutorial on how web apps can be created

Switching workspaces does not work as intented in the online apps, e.g. switiching workspace and uploading files will upload them to the previous workspace.

e.g. we don't need the OpenMS source folder any more (it is currently kept because it contains the share/folder).
TODO:

• set the cmake flag -DCMAKE_INSTALL_PREFIX when generating the build system to a folder we want to install OpenMS to

call

• cmake -DCOMPONENT="library" -P build/cmake_install.cmake
• cmake -DCOMPONENT="applications" -P build/cmake_install.cmake
• cmake -DCOMPONENT="share" -P build/cmake_install.cmake

to copy files into that folder

Github action runs without errors, however opening the app will raise the following error:

The issue seems to be with streamlit version 1.30 (latest), rolling back to 1.29 resolves the issue for now.

The workflow to build should be adopted to 1.30 and perhaps include a test to check if the app launches without errors.

see e.g. https://discuss.streamlit.io/t/using-pyinstaller-or-similar-to-create-an-executable/902/86

would be interesting to check if this is possible e.g., probably similar to building a whl

I opened the existing workspace:

but I can't select the file in the workspace for raw viewing