Creating and Deploying EDP R/Shiny Applications¶

Shiny is an R package that makes it easy to build interactive web apps straight from R. Developers can use it to build standalone web apps and dashboards. Shiny can also be extended with custom CSS and JavaScript. The best way to get started with Shiny is to follow the Shiny Tutorial.

EDP users can create new Shiny apps through the R API client by creating EDP applications. EDP applications represent unique OAuth2 credentials that enable a third-party system to obtain EDP access tokens on behalf of EDP users. By default, applications created on the EDP are accessible only to users in the same organization.

Note: the EDP R package is currently published under the name ``solvebio``, so the R examples below use ``library(solvebio)``.

Getting Started¶

To get started, developers should ensure they have the latest EDP R package and install the shiny R package, and can also opt to install the shinyjs R package.

# Install the EDP R package
install.packages("solvebio")

# Install Shiny
install.packages("shiny")

# Install ShinyJS (optional, for token cookie storage)
install.packages("shinyjs")

The user should authenticate their R session using their QuartzBio credentials, and can then start using the EDP R package to create apps. Each time a user creates a new app, a unique client ID is generated. Users should make sure to save their client IDs to a safe place after creation. Users can always contact EDP Support to retrieve a list of their apps (with their client IDs) in the future.

To create an app, users can enter the following R commands. Doing so will create the app and allow the user to view its client ID:

library(solvebio)

# The redirect URL (protocol, host, and port) must exactly match
# the local development URL.
redirect_uris <- "http://127.0.0.1:3838/"

#EDP supports wildcard URIs. If a hosted app has a dynamic value in the URL, such as:
"https://my-app.my-dash-apps.net/notebookSession/123456/_oauth-redirect"
#here `123456` is a session ID that changes for each session, then the redirect URI can be provided as:
"https://my-app.my-dash-apps.net/notebookSession/*/_oauth-redirect"

# Creates the app (only once per application)
# using the standard Shiny OAuth2 redirect URL:
my_app <- Application.create(name = "My Shiny App", redirect_uris = redirect_uris)

# Prints the app's client ID:
cat(my_app$client_id)

Users can contact EDP Support to retrieve the relevant client ID if lost.

Authenticating Users¶

The primary advantage of using the R Shiny integration with EDP is the ability to authenticate users. This enables developers to create applications that dynamically understand the access permissions of a user in the EDP. For example, a developer can create an application allowing access to other users’ vaults without actually having access themselves.

To authenticate with the EDP, developers can use the client ID in the Protected Server R function (solvebio::protectedServer) in their app.R file:

library(shiny)
library(shinyjs)
library(solvebio)

# Set Shiny to use port 3838 (for development only)
options(shiny.port = 3838)

server <- function(input, output, session) {
    output$current_user <- renderText({
        # To use the current user's EDP credentials,
        # retrieve the `env` from the session:
        env <- session$userData$solvebio_env

        # Pass the env to any EDP R function:
        user <- User.retrieve(env=env)
        paste("Logged-in as: ", user$full_name)
    })
}

ui <- fluidPage(
        # Optional code for token cookie support
        shiny::tags$head(
            shiny::tags$script(src = "https://cdnjs.cloudflare.com/ajax/libs/js-cookie/2.2.0/js.cookie.js")
        ),
        useShinyjs(),
        extendShinyjs(text = solvebio::protectedServerJS(),
            functions = c("enableCookieAuth", "getCookie", "setCookie", "rmCookie")),

        # UI code:
        titlePanel("Welcome to your EDP Shiny app!"),
        mainPanel(textOutput("current_user"))
)

# Wraps the base server and returns a new protected server function
# Setting client_secret is optional but will encrypt OAuth2 tokens in browser cookies
protected_server <- solvebio::protectedServer(server, client_id="YOUR CLIENT ID", client_secret=NULL)

# On the last line of the file, declares the Shiny app with the protected_server
shinyApp(ui = ui, server = protected_server)

Updating Applications¶

Users can update the redirect URIs of their EDP R applications as needed, such as when moving from a local development environment to a production environment:

library(solvebio)

# Retrieves app (the first that matches the name, owned by the current user)
my_app <- Application.all(name='My Shiny App', user=User.retrieve()$id)$data

# Adds the 'write' scope and set the production redirect URI.
Application.update(my_app$client_id, scopes = "read write", redirect_uris = "https://my-app.my-dash-apps.net/_oauth-redirect")

Deleting Applications¶

Users can delete EDP R applications by issuing the following commands. Deleting the application in this way will revoke the relevant authentication credentials and client ID.

library(solvebio)

# Retrieves app (the first that matches the name, owned by the current user)
my_app <- Application.all(name='My Shiny App', user=User.retrieve()$id)$data

# Deletes the app
Application.delete(my_app$client_id)

Note: this is irreversible. A new client ID will need to be created and populated in the app if the app needs to be deployed in the future.

Deploying Shiny Apps¶

The recommended way to deploy Shiny apps is to use Shiny Server Pro (which may require a separate license). Users with an on-premises Shiny Server can contact their local sysadmin for help deploying the app.

Users who want to test their Shiny apps using a public server can use Shinyapps.io or Heroku. Users should keep in mind that their data may be accessible by a third-party system if they choose one of these options.

Example Shiny App¶

The Example R/EDP Shiny App is a simple Shiny app wrapped by EDP’s “protected server”, requiring users to authorize the app with their QuartzBio account via OAuth2. The app presents the user with a list of datasets in their personal vault.

In order to run the app, two environment variables are required:

CLIENT_ID: The client ID of the user’s EDP application.
APP_URL: The full URL (host, port, and path if necessary) of the user’s app once it is deployed (defaults to http://127.0.0.1:3838).

Running Locally¶

After creating a client ID, the user should write it to a .Renviron file in the app’s directory as shown above (see Updating Applications):

CLIENT_ID=your-client-id

The user can then install the dependencies for the app by running init.R:

Rscript init.R

To run the app locally, the user can run the code through RStudio or run the following command in their shell:

R -e "shiny::runApp(port=3838)"

After running the command, the user can open http://127.0.0.1:3838 in their web browser to open the app.

Deploying to ShinyApps.io¶

First, the user should create a ShinyApps account. The user can follow the instructions to install rsconnect and log in with their credentials.

Users should make sure to create their EDP app and set up their .Renviron file (as shown in the section above) before deploying.

To deploy, the user can open R in the app’s directory and run:

library(rsconnect)
deployApp()

This may take a few minutes, and should automatically open up the user’s browser to the app URL.

Deploying to Heroku¶

First, the user should create a Heroku account. Deploying to Heroku requires a special buildpack that supports R and Shiny, so the user will need to create the app using the Heroku command line tools.

The custom buildpack needs the following files:

Aptfile: contains additional system dependencies.
run.R: signals to Heroku that this is an R Shiny app.
init.R: install additional R dependencies.

First, the user should create their app on Heroku:

heroku create --buildpack http://github.com/virtualstaticvoid/heroku-buildpack-r.git#heroku-16

Once their app is created, the user should set up the following environment variables:

# Sets EDP app's client ID
heroku config:set CLIENT_ID=<your client id>

# Sets app's public URL (e.g. `https://<APP NAME>.herokuapp.com`)
heroku config:set APP_URL=https://<your app>.herokuapp.com

Finally, the user can deploy the app:

git push heroku master

Note: the first deploy can take upwards of 20 minutes to complete.

Applications Endpoints¶

This API reference is organized by resource type and endpoint. Each resource type has one or more data representations and one or more methods. Methods do not accept URL parameters or request bodies unless specified.

Note: if your EDP endpoint is ``sponsor.edp.aws.quartz.bio``, you would use ``sponsor.api.edp.aws.quartz.bio``.

All the endpoints below share the same base URL:

BASE = https://<EDP_API_HOST>/v2

Method	HTTP Request	Description	Authorization	Response
create	`POST {BASE}/applications`	Create an application.	This request requires an authorized user with permission to create new applications.	The response contains a single Application resource.
delete	`DELETE {BASE}/applications/{CLIENT_ID}`	Delete an application.	This request requires an authorized user with permission to modify the target application.	The response returns “HTTP 200 OK” when successful.
get	`GET {BASE}/applications/{CLIENT_ID}`	Retrieve metadata about an application.	This request requires an authorized user with permission to view the target application.	The response contains an Application resource.
secret	`GET {BASE}/applications/{CLIENT_ID}/secret`	Retrieve an application’s secret key.	This request requires an authorized user with permission to view the target application’s secret key.	The response contains an Application resource with an additional `client_secret` attribute.

The create request accepts the following properties:

Property	Value	Description
name	string	(required) A user-visible name for the app.
redirect_uris	string	(required) A list of space-separated valid redirection endpoint URIs. Endpoints can use regex format, like `https://my-app.my-dash-apps.net/notebookSession/*/_oauth-redirect`
description	string	A user-friendly description of the app.
help_url	string	The URL where documentation about the app can be found.
scopes	string	OAuth2 scopes required to use the app (`read` or `read write`).
source_url	string	The URL where the app’s source code can be found.
tags	string (list)	A list of arbitrary tags to categorize the app.
web_url	string	The URL where the app can be accessed by users.