GUI for Mosaic

Disclaimer: This is in active development. Please use at your own risk. This is for research purposes only.

About

This repository includes the code to an interactive app built using Streamlit. It is a user interface for Mosaic.

After installing Mosaic, install streamlit in the appropriate environment using:

pip install streamlit

the app can be launched using:

streamlit run ./app.py

For s3 access, credentials have to be added to /.aws/credentials

The downloaded h5 files must be stored under ./h5/downloads/ to be accessible throught the UI.

To Do

• The parameters render the saved values when loading an analyzed file
• Documenting the code
• Documenting the procedure to add new workflows

Architecture

Streamlit runs as script top-down and re-runs the whole thing if anything changes.

The code for loading h5 files and workflow selection is in the src/insights/tasks folder.

After H5 file is loaded the selected action in src/insights/workflows is executed. Workflows for DNA, CNV, Protein and Multi-omics have their subfolder with all the steps required to execute workflow.

Steps generally include run, compute and render with some additional steps if required by the workflow.

The mosaic-streamlit folder contains the JavaScript/Electron application with electron-forge toolchain which is used to wrap the Streamlit application and provide the desktop features.

The runner.js is used to start the Streamlit application as a child process with a few other UI elements available in main_window.js.

Build(s)

Check GitHub Actions in .github, the action workflow uses https://github.com/MissionBio/actions to automatically build Windows/macOS installers.

Sign/notarize the macOS Installer

Make sure you have Python, Node (with yarn) and XCode environments installed. To properly sign/notarize the application on macOS you need private key and certificate active in the keychain and these environment variables available:

export APPLE_DEVELOPER_ID="Developer ID Application: ..."
export APPLE_ID=...
export APPLE_PASSWORD=...

If you have Python and Node environments with all the requirements installed you can run:

$ cd build
$ ./sign-for-macos.sh

This will build the Python code with PyInstaller, copy it to the JavaScript/Electron app and build it with electron-forge toolchain. It will also codesign the application and DMG and notarize it.

Note: Make sure that you build/sign/notarize the app on the oldest macOS version you plan to support. You can use Mac/Nitro instances on AWS to sign/notarize the application.

Sign the Windows Installer

Make sure you have the SignTool installed (and check other options): https://docs.microsoft.com/en-us/dotnet/framework/tools/signtool-exe

The GitHub build generates non-admin installers so you can download a specific build and sign the installer:

$ signtool.exe sign /f F:\path\to\the\certificate.pfx /p mypassword /t http://timestamp.digicert.com .\tapestri-insights-v4-windows-v4.0.0-build-version.exe

You can verify the digital signature with:

$ signtool.exe verify .\tapestri-insights-v4-windows-v4.0.0-build-version.exe

As an alternative option you can use the electron-forge final build step to sign the application/installer. Check the documentation here: https://www.electronforge.io/config/makers/squirrel.windows#usage