shiny-cromwell

Shiny app for interacting with the Fred Hutch instances of Cromwell.

The app lives at a URL only accessible to Fred Hutch folks.

This app can also be run on your local machine for any reason, e.g., if you notice memory limitations in the deployed version or you want to run it at another institution.

Running the app

Without Docker

You can run this Shiny app locally. First you'll need to install required packages:

(note: run make pkg_deps_cmd to update the below code block)

pak::pak(c("getwilds/proofr@v0.2", "getwilds/rcromwell@v3.2.1", "dplyr", "DT", "ggplot2", "glue", "httr", "jsonlite", "lubridate", "magrittr", "memoise", "purrr", "rclipboard", "RColorBrewer", "rlang", "shiny", "shinyBS", "shinydashboard", "shinydashboardPlus", "shinyFeedback", "shinyjs", "shinylogs", "shinyvalidate", "shinyWidgets", "testthat", "tibble", "uuid"))

And the above yourself in R.

Or you can run pkg_deps_install which should find and install required packages all in one step.

After installing required packages run the app. There's a few different ways to do that:

1. If you are familiar with using make commands, run make run
2. If you don't or can't use make, you can run it on the command line like Rscript -e 'shiny::runApp("app", launch.browser = TRUE)'
3. Inside of R you can run shiny::runApp("app", launch.browser = TRUE)'

All of these should open the Shiny app in your default browser. If that does not happen get in touch!

With Docker

The make command make run_docker will attempt to run the app with Docker. You'll need Docker installed and running for this to work.

Note that CTRL+C doesn't work to kill the container after running make run_docker. Yo have to use a separate terminal window or Docker Desktop to kill the container (basically the docker process doesn't receive the signal to kill its process).

Also note that docker commands can be specific to the host operating system, so if you run into errors you may need to modify the docker commands.

Debugging

• Use print statements as needed ...
• Instead of just make run, one can run the app with SHINY_LOG=true make run which activates the package shinylogs

App structure

├── app
│   ├── about.md
│   ├── buttons.R
│   ├── iputs_utils.R
│   ├── modals.R
│   ├── proof.R
│   ├── server.R
│   ├── sidebar.R
│   ├── tab-servers.R
│   ├── tab-submission.R
│   ├── tab-tracking.R
│   ├── tab-troubleshoot.R
│   ├── tab-validate.R
│   ├── tab-welcome.R
│   ├── ui.R
│   ├── ui_components.R
│   ├── utils.R
│   ├── validators.R
│   └── www
│       ├── favicon.ico
│       ├── fred-hutch.svg
│       └── js
│           └── keyup.js

Notes about the structure:

• the main app files are at app/server.R and app/ui.R
• files in www/ are automatically sourced
• code in other files in app/ - e.g., app/proof.R - are only available if pulled in with source()

We will continue to give the app more structure, possibly including Shiny modules and maybe as an R package.

License

MIT