Extension:Shiny

MediaWiki extensions manual

Shiny Release status: unmaintained
Implementation	Tag
Description	Allows to embed Shiny apps on pages
Author(s)	Sigbert Klinke (Sigberttalk)
Latest version	0.1 (2016-02-28)
MediaWiki	1.26+
Database changes	No
License	GNU General Public License 2.0 or later
Download	GitHub: project page git repository URL [help ] commit history Note: No localisation updates are provided by translatewiki.net .
Tags ‎<shiny>
Hooks used ParserFirstCallInit

The Shiny extension allows to embed Shiny apps in pages. The Shiny server itself uses the programming language R, which is a free software environment for statistical computing and graphics.

Warning:

This extension allows to embed and execute arbitrary R code on your web server. Currently no security measures are implemented. If you want to use the extension as a site-administrator then make sure that only trustworthy users may edit the wiki text.

Requirements

• R is a free software environment for statistical computing and graphics. It needs to be installed (probably available in your Linux distribution) and in the PATH: the command R should work on the command line.

• The Shiny server lets you put shiny web applications online. It needs to be installed separately.

Download

You can obtain the extension from GitHub.

Installation

The following subpages describe the installation process for

• Ubuntu 14.04 and
• CentOS 7

with an Apache web server. For other linux systems or web servers the description needs to be adapted.

Extension files

extension.json

stores the setup instructions.

Shiny_body.php

stores the execution code for the extension.

All other files in the <my.wiki>/extensions/Shiny could be deleted.

Configuration

The file extension.json contains three configuration variables which could be set:

 "config": {
    "ShinyR":      "/usr/bin/R",
    "ShinyAppDir": "/srv/shiny-server/mediawiki",
    "ShinyUrl":    "http://localhost/shiny/mediawiki"
 },

ShinyR

the path and command to execute R. You may query for it in your system by using the command which R

ShinyAppDir

the path where the Shiny apps are stored. Note that the actual path where app.R is stored is /srv/shiny-server/mediawiki/<my.wiki.name>/<page.title>/<shiny.app.name>

ShinyUrl

the URL which is called to access a Shiny app. Note that the actual URL for a shiny app is http://localhost/shiny/mediawiki/<my.wiki.name>/<page.title>/<shiny.app.name>

Usage

For a simple example put into a wiki page:

<shiny output="plot" name="test">
hist(rnorm(314))
</shiny>

It shows a histogram of 314 random values according to a standard normal distribution.

Some hints for development:

• For developing a Shiny app you are urged to use RStudio. If the app runs under RStudio then it will also work with MediaWiki.

shiny tag

The shiny tag can have the following attributes:

output="..."

...	corresponds to
data	dataTableOutput and renderDataTable
image	imageOutput and renderImage
plot	plotOutput and renderPlot
print	verbatimTextOutput and renderPrint
table	tableOutput and renderTable
text	textOutput and renderText
verb	print

Note if output is omitted then between the start and end tag is a fully fledged shiny app is expected.

name="..."

the name of the Shiny app. If not set then a hash value from the R program is derived.

CAUTION: Omitting the name may lead to a lot of sub-directories for the shiny server, therefore choose a name!

width="..."

the width of the windows in pixel (default: 800)

height="..."

the height of the windows in pixel (default: 600)

seamless="..."

if the Shiny app is embedded seamlessly (seamless="seamless", default) or not (any other text for seamless)

sandbox="..."

enables extra restrictions on the content that can appear in the inline frame. (default: allow-same-origin allow-scripts). The value of the attribute can either be an empty string (all the restrictions are applied), or a space-separated list of tokens that lift particular restrictions. Valid tokens are:

Token	Allows
allow-forms	the embedded browsing context to submit forms
allow-popups	to open popups (like from window.open, target="_blank", showModalDialog)
allow-same-origin	the content to be treated as being from its normal origin
allow-scripts	the embedded browsing context to run scripts (but not create pop-up windows)
allow-top-navigation	the embedded browsing context to navigate (load) content to the top-level browsing context.

Errors

In the wiki page only an <iframe ...>...</iframe> is shown instead of the Shiny app.

In case that this error occurs the extension shows the resulting HTML code instead of embedding. Check for typos/errors in the options or in your R program.

In the Shiny app only ERROR: Key / already in use is displayed

Delete from your R code the runApp(...) line.

Security

Currently no security measures are implemented.