https://github.com/Sage-Bionetworks/SynapseShinyApp
Basic structure of a R Shiny application for use on Synapse
https://github.com/Sage-Bionetworks/SynapseShinyApp
Last synced: about 1 month ago
JSON representation
Basic structure of a R Shiny application for use on Synapse
- Host: GitHub
- URL: https://github.com/Sage-Bionetworks/SynapseShinyApp
- Owner: Sage-Bionetworks
- License: mit
- Created: 2015-12-04T00:09:27.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2022-04-28T21:38:04.000Z (about 3 years ago)
- Last Synced: 2024-04-11T01:26:29.276Z (about 1 year ago)
- Language: R
- Size: 145 KB
- Stars: 4
- Watchers: 9
- Forks: 8
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-synapse - SynapseShinyApp - Basic Shiny application for use on Sage Bionetwork's Synapse web portal. (R / Shiny)
README
Basic Shiny application for use on Sage Bionetworks' Synapse web portal.
## Credits
- Maintainer: [thomasyu888](https://github.com/thomasyu888)
- Contributors: [allaway](https://github.com/allaway), [duncan-palmer](https://github.com/duncan-palmer), [jkiang13](https://github.com/jkiang13), [karawoo](https://github.com/karawoo), [kdaily](https://github.com/kdaily), [vpchung](https://github.com/vpchung)
## Introduction
Shiny applications are a powerful way to develop interactive data visualization and manipulation interfaces. However, when using with Synapse, user authentication is an issue - whomever the Shiny application is running as will determine the access that users visiting the application will have.
This solution allows to determine which user is currently logged into Synapse through the web browser. These credentials are passed on to the Shiny app, and that specific user is logged in. Subsequent interactions with Synapse to pull data for the Shiny interface then happens as that user.
:warning:**HOWEVER**:warning: The Synapse R client, [synapser](https://r-docs.synapse.org/), stores authentication information in a
location that is global to the R process. This means that if one user connects
to a Shiny app, and then another user connects from another browser or computer, the second
user's authentication will supersede the first's. This can cause
hard-to-diagnose errors, and is a security issue. There are 3 ways to work
around this issue:
1. Ensure that each user gets a separate R process by customizing the
[utilization scheduler](https://support.rstudio.com/hc/en-us/articles/220546267-Scaling-and-Performance-Tuning-Applications-in-Shiny-Server-Pro)
(only available for Shiny Server Pro).
1. Write your app so that it logs in before doing any operation that interacts
with Synapse. Essentially this means writing wrappers for every synapser
function you use, e.g.:
```r
authSynGet <- function(...) {
synLogin(sessionToken = input$cookie)
synGet(...)
}
```
Placing a call to `synLogin()` before `synGet()` directly in your server
function is not necessarily sufficient, as it is still possible someone else
could log in between when your `synLogin()` and `synGet()` are executed.
1. Instead of using synapser, use the [Synapse Python client](https://python-docs.synapse.org/) + [reticulate](https://rstudio.github.io/reticulate/). The
Python client allows for creating multiple client objects, and therefore
multiple authenticated users. Please see the [reticulate branch](https://github.com/Sage-Bionetworks/SynapseShinyApp/tree/reticulate) for implementation details.
- :warning: It is important to avoid using the synapseclient.login() command without arguments, in other words, explicitly pass authToken to this function. Otherwise you will risk logging in as a user specified in .synapseConfig or .synapseSession instead of the app user.
## Usage
To create a new Shiny application based on this structure, do *not* fork this repository directly on GitHub. Instead, please use GitHub's importer following the instructions [below](#creating-a-repository).
### Creating a New Shiny App Repository
1. Go to [GitHub's importer](https://github.com/new/import?import_url=https://github.com/Sage-Bionetworks/SynapseShinyApp.git) and paste in this repository's clone URL (https://github.com/Sage-Bionetworks/SynapseShinyApp.git).
1. Choose a name for your repository.
1. Select the owner for your repository (This will probably be you, but may instead be an organization you belong to).
You can now click "Begin Import". When the process is done, you can click "Continue to repository" to visit your newly-created repository.
### Notes
If you are using a `navbarPage` instead of a `fluidPage` in your `ui.R`, use of this code:
```
tags$head(
singleton(
includeScript("www/readCookie.js")
)
),
```
will cause create a default ghost tab. Instead, you should replace the above code with this snippet:
```
header=list(tags$head(includeScript("www/readCookie.js"))),
```