Extension:GraphViz

MediaWiki extensions manual - list

GraphViz Release status: beta
Implementation	Tag
Description	Allows to render graphs online
Author(s)	Victor Fariña, Matthew Pearson, Thomas Hummel, Gregory Szorc and others
Last version	0.9 (2011-03-14)
Database changes	no
License	FDL
Download	Download snapshot (Git master) Git [?]: repo summary tree code changes
Example	http://www.graphviz.org/Gallery.php
Parameters $wgGraphVizSettings
Hooks used ParserFirstCallInit
Check usage and version matrix

The GraphViz extension lets you create and display graphs as inline images on wiki pages, using the open-source Graphviz and Mscgen applications:

• Graphviz is a program that allows the creation of numerous types of graphs, using the DOT language.
• Mscgen is a small program that parses Message Sequence Chart descriptions. Unlike Graphviz, this program does no clever layout operations or spline routing, as this is not needed.

Automatic graph drawing has many important applications in software engineering, database and web design, networking, and in visual interfaces for many other domains.

Additionally, this extension supports multiple graphs on one page, wiki-links in graphs, and automatic pruning of old images.

Install Instructions

Graphviz

1. First, you need at least one of the external tools "Graphviz" or "MscGen" that renders your graph.
   1. Windows: Get your copy here: http://www.graphviz.org/Download.php or here http://www.mcternan.me.uk/mscgen/
   2. Unix: Same links as for windows but normally it should be preinstalled (at least graphviz - search for dot) or can be found in the package manager.
   3. Ubuntu/Debian:

sudo aptitude install graphviz graphviz-dev (test from Ubuntu 12.04 LTS)

1. Then obtain the Graphviz extension code by downloading a snapshot or getting it from SVN, or GIT

cd extensions
git clone https://gerrit.wikimedia.org/r/p/mediawiki/extensions/GraphViz.git 

1. and then put it in your MediaWiki "/extensions/GraphViz" directory.
   1. Ubuntu 10.10 comes with an earlier version of the GraphViz extension pre-installed - this is a very old version, though, so you'd be better off replacing it.
2. Add these lines to LocalSettings.php:
   

require_once("$IP/extensions/GraphViz/GraphViz.php"); //includes the extension<br />
$wgGraphVizSettings->execPath = "/path/to/graphviz/"; //Path to the Graphviz Installation

Windows Default: "C:/Program Files/Graphviz/bin/" (without dot.exe) or "C:\\Program Files\\Graphviz\\bin\\"

Other Platform : "/usr/bin/" or "/usr/local/bin/" (where the dot binary is)

• Make sure that write permissions for the "$IP/images" directory are granted.
• Make sure that internet users get read/execute access on your executables if you use server installations. (Especially under Windows.)

MscGen

The same procedure as with Graphviz - the path to MscGen has to be provided in LocalSettings.php:

$wgGraphVizSettings->mscgenPath = "/usr/bin/";

Differences from previous versions

• The variable $dotCommand that points only to the dot executable is replaced (like in Extension:GraphVizAndMSCGen) with $execPath and $mscgenPath that let you choose between several renderers.

Configuration

There are some additional configuration parameters that help you to define a basic behaviour of the extension. If you don't use these parameters they contain a default value that leads to a (hopefully) good usage of the extension. For each parameter add the line $wgGraphVizSettings->ParameterName in your LocalSettings.php after the include("extensions/Graphviz.php");-line.

Parameter	Default Value	Values	Description
execPath	"C:/Program Files/ATT/Graphviz/bin/"		(Windows) Path to the GraphViz executables with the dot.exe, circo.exe, fpdp.exe, neato.exe, twopi.exe
execPath	"/usr/bin/dot"		(Unix/linux) Path to the Graphviz executables (mainly it points to /usr/bin/ or to /usr/local/bin/) or you use $DOT_PATH
mscgenPath	-none-		Path to the MscGen-Installation
outputType	png	see #Renderer	Which image format do you want to produce?
imageFormatting	true	true, false	Do you want to define position, border or thumb for the image (not fully supported see here)
named	named	named, md5, sha1	How are the images and imagemaps named on your drive? (see #Naming of the Images)
info	false	true, false	Adds information about the parameters given, e.g. renderers used, for use on the wiki-page. Probably most useful for debugging.
install	false	true, false	Gets you an errormessage if something fails, but maybe ruins your wiki's look. This message is in English, always. (not well implemented actually)
pruneEnabled	false	true, false	Do you want an automated pruning procedure each time you render a new graph?
pruneStrategy	filenumber	filenumber, filesize	Do you want to prune if there are too many files or if they need too much disc space
pruneAmount	10000	positive number	Defines the maximum files/filesize you accept for pruneStrategy
pruneValue	0.5	0< number <=1	Defines how many files are being pruned (0.5 = 50%)

You don't need to set these values if everything works fine for you. They are used in the LocalSettings.php only for the default behaviour of all graphs in this wiki. Some parameters can be set for each individual graph (see #Renderer or #Image-Types).

Naming of the Images

There are several ways to name the graphs. Each of them has some benefits and some problems. You set the Naming-Scheme by setting $wgGraphVizSettings->named in the LocalSettings.php (See #Configuration).

Naming Type	Description	Pros/Cons	Example
named	The storagename is the name of the wikipage and the name of the graph	+ human readable + no cleanup necessary - two graphs need separate names	Graphviz_Sample---digraph+NAME.png
md5	name of your graph is based on a md5 hash of its source	+ don't worry about graphnames + pretty fast hash - permanent cleanup necesary (manually or scripted) md5 is buggy - possibility that 2 graphs have the same hash but are not the same	Graphviz_Sample---0a1e0c6bb9c6d3af6486d8f3de657f0f.png
sha1	name of your graph is based on a SHA1 hash of its source	+ don't worry about graphnames + no hash-bug as md5 - permanent cleanup necessary (manually or scripted) - not so fast as md5	Graphviz_Sample---a3862ef7e7f889778f0259657b07ba985197ef88.png

Drawing Graphs

Basically you only need to write your Graph in the dot language (or any other supported language) and put it into <graphviz>dot-commands</graphviz> or <mscgen>mscgen-commands</mscgen>.
See the #Examples for some basic graphs - you don't even need the "border" or "frame"-tags.

Mscgen

Keep in mind that mscgen uses a language _similar_ to dot but it isn't really dot. So you have to write your own code for graphviz and mscgen to display the same graph. (Furthermore the goals of graphviz and mscgen are not the same)

Another limitation when using Mscgen is that you can't use multiple graphs on one page (if you don't use hashed storage-names).

Multiple Graphs

This extension supports multiple graphs on one wiki page.

If you name the pictures by the graph names (named='named'), you just have to give the graphs different names. That means that the following two graphs can be put together on on page.

First Graph	Second Graph
<graphviz> graph NAME {... } </graphviz>	<graphviz> graph ANOTHERNAME {... } </graphviz>

This doesn't work for Mscgen graphs, because custom names aren't supported. But you can put one Mscgen graph and multiple Graphviz graphs on one page.

If your pictures are named with md5- or sha1-hashes then you can have multiple graphs of each type (Graphviz and/or Mscgen) on your page. Keep in mind that you should clean up your image-directory from time to time, because the hash changes when the code has been modified. (See #Naming of the Images)

Wiki-links

In dot you can define a URL for each node. This is normally done before defining the graph. See #Example3 for an example with Wiki-links.

In case you need an external URL, write this:

Mollusca [URL="http://www.mollusca.animal"];

And for an internal link in your wiki, write this:

Mollusca [URL="Mollusca"];

That's all.

Wiki styling

In case you want to put some kind of structure into your page you can use some image attributes as for any other image (in the style of regular MediaWiki syntax), like here: Extended image syntax).

The attributes are used like HTML attributes (e.g. <graphviz caption="Hello World">...dot...</graphviz>).

Attribute	Description	Value
caption	Adds a caption to the graph (if bordered or thumbed)	some string
alt	Alternative text for graph (if not set caption is used and at least a default string)	some string
border	Adds a border around the graph	frame, border
location	Defines the position of the graph	left, middle, center, right, none
alignment	Vertical alignment to the text	baseline, middle, sub, super, text-top, text-bottom, top, bottom
type	Several changes in design	frame, framed, thumb, thumbnail, frameless

Please bear in mind that these features are not fully identical to MediaWiki's image attributes. Differences/inconsistences are:

• In case of thumbed images the image-map isn't scaled down, so it won't fit anymore
• In case of thumbed images, they do not link to an image-page with a further description of the license and the picture in a higher resolution - we only add a (+)-sign to the caption with the direct link to the image.
• a framed and centered image will have a border with a width of 100%

Alternative: You could link to your images directly if you want to. So you could put the graph into <div style="visibility:none;"><graphviz>...</graphviz></div> and put the image of the graph anywhere into your page (or in any other page) via the "img" tag.

• If you use the named='named'-setting the graph names won't change and can be used easily.
• You have to allow linking to external images (since the images are not in the db) (and you can restrict it to your domain for security)
• you cannot use imagemaps that easily

Renderer

This extension can handle two applications for graph-drawing: Graphviz and Mscgen. Graphviz comes with several rendering engines and Mscgen has its own. For Graphviz, different renderers are ideal depending on the use case. More information on the renderers for each application can be found on their respective websites.

Renderer	Description
dot	typical hierachical layout with a "start" and an "end"
neato	"spring model" layout
fdp	like neato but better for larger graphs
sfdp	fdp multiscale version
circo	circular layout like for telecommunication networks
twopi	radial layout with "start" in the middle
mscgen	message sequence charts

You can define a renderer as the default (see #Configuration), or set it in an individual graph with an attribute (-> <graphviz renderer='neato'>...dot...</graphviz>).

Image types

Graphviz and Mscgen can produce a huge amount of different image types (see more on their websites). The GraphViz extension supports only some of them:

• Graphviz: bmp, gif, jpg, jpeg, png, svg, svgz
• Mscgen: png, svg

Note: To display vector-graphics you have to configure your wiki installation properly (-> SVG)

You can define an image type as default (-> #Configuration) or add it to the individual graph with an attribute (-> <graphviz outputType='jpg'>...dot...</graphviz>).

Examples

For a start you can try these Examples:

Example 1

"Hello World" graph for example no. 1

<graphviz border='frame' format='png'>
 digraph example1 {Hello->"World!"}
</graphviz>

Example 2

Example No. 2 rendered with neato

<graphviz renderer='neato' caption='Hello Neato'>
graph EXAMPLE2 {
   run -- intr;
   intr -- runbl;
   runbl -- run;
   run -- kernel;
   kernel -- zombie;
   kernel -- sleep;
   kernel -- runmem;
   sleep -- swap;
   swap -- runswap;
   runswap -- new;
   runswap -- runmem;
   new -- runmem;
   sleep -- runmem;
}
</graphviz>

Example 3

A more complex graph as defined by Example No. 3 (original imagemap contains (Wiki-)Links)

<graphviz caption='Hello SVG and PNG' alt='phylogenetic tree' format='png'>
digraph G {
                node [shape=plaintext];
                Mollusca [URL="Mollusca"];
                Neomeniomorpha [URL="Neomeniomorpha"];
                X1 [shape=point,label=""];
                Caudofoveata [URL="Caudofoveata"];
                Testaria [URL="Testaria"];
                Polyplacophora [URL="Polyplacophora"];
                Conchifera [URL="Conchifera"];
                Tryblidiida [URL="Tryblidiida"];
                Ganglioneura [URL="Ganglioneura"];
                Bivalvia [URL="Bivalvia"];
                X2 [shape=point,label=""];
                X3 [shape=point,label=""];
                Scaphopoda [URL="Scaphopoda"];
                Cephalopoda [URL="Cephalopoda"];
                Gastropoda [URL="Gastropoda"];
                Mollusca->X1->Testaria->Conchifera->Ganglioneura->X2->Gastropoda
                Mollusca->Neomeniomorpha
                X1->Caudofoveata
                Testaria->Polyplacophora
                Conchifera->Tryblidiida
                Ganglioneura ->Bivalvia
                X2->X3->Cephalopoda
                X3->Scaphopoda
}
</graphviz>




You can see many more examples of images created with Graphviz in this Flickr gallery.

Tutorials/online samples

See here for examples of this extension in use on other wikis:

• http://www.wikischool.de/wiki/WikiSchool:Graphviz
• http://wiki.zum.de/Hilfe:Graphviz
• http://www.wickle.com/wikis/index.php/Graphviz_extension (old)
• http://www.EcoReality.org/wiki/Test:Graphviz (comments) (maintained very well)
• http://www.nerux.org/wiki/Graphviz and http://www.nerux.org/wiki/Accueil

Pruning

Each time we create a new graph we're going to check the Image-Path for pruning. There are several options on how to prune. Configure pruning with the adequate parameters in LocalSettings.php (see #Configuration).

With the default settings you don't need any pruning, because each graph is saved accoring to its name. If you update the Graph the image-file will be replaced so there will be no unnecessary file. Reasons for pruning can be: limited storage space for images, renamed or removed graphs, graphs named with a hash.

However the best solution for pruning would be to clean up the images manually from time to time, or do it automatically with a cronjob. This saves much CPU load.

Development

Since I'm not a very experienced developer it would be nice if some "experts" could review the code or improve it on some edges.
I'm also happy if you'd notify me about bugs or problems you have (e.g. on the Discussion page).

Important points

• Check for Security Leaks
  • especially there has been mentioned: This [former] plugin does not properly sanitize user input when generating the "named" version of the files. This can lead to clobbered files and/or more serious vulnerabilities. --Andy753421 04:54, 27 July 2010 (UTC)
  • See Security for developers for specific types of vulnerabilities
• Sometimes there is an error of preg_replace: "Unknown modifier '\' on line 434" - I can't find the mistake.
  • NOTE: You need to change the string '/(\w+)\s([_:%#/\w]+)\s(\d+,\d+)\s(\d+,\d+)/' by '/(\w+)\s([_:%#\/\w]+)\s(\d+,\d+)\s(\d+,\d+)/' to correct this error

Things that should be done

• What to do with graphs that are too large? e.g. for the GET-request? Maybe some attribute in the <graphviz>-Tag that this is partial code and that it waits? Or at least shortening some commands, links, ...?
• using popen()/proc_open() instead of shell_exec() for php save-mode if possible

Nice to have features

• add uploadDir to variables
• On my local installation a graph is rerendered very often (each hour or so) even if nothing has changed on the page. (Is this only my fault?)
  • Can we reduce CPU load by preventing Graphviz from creating a new image if the page hasn't changed?
  • Can I then prune all images that are older than an hour? Or do proper installations use a cache that maybe lasts a week or so?
• Error when setting $wgGraphVizSettings->install=true on ubuntu.
• Generate Graphs without extra tools (directly in the browser): Canvas?, Base 64 Encoding see also, Extension:Graph, ...
• custom shapes for nodes in Graphviz aren't supported yet (http://www.graphviz.org/Documentation/html/shapehowto.html)
• improve pruning
  • save pruning settings (maybe settings-file in graphviz-folder or images folder, because of write access?)
    • don't prune for each graph but only check date of last pruning
  • remove files older than some date
• use the image formatting with wiki syntax with the help of MW-Renderer, so that it doesn't stay hardcoded
• put the generated graphs into the wiki-database, so that they can be handled like normal pictures

Contributions and history

• In 2004 the user Coffman created an extension to MediaWiki in response to a basic need: rendering graphs online. He found the utility Graphviz in use on another wiki application, and thought about adapting it for MediaWiki (the wiki he actually used). Exploring the Graphviz tool, he discovered an incredible tool for making graphs.
• Later on, many people improved the extension on their own or provided little bug fixes as snippets on the discussion page. This led to several functional solutions for different use cases, and to a bit of chaos.
• In 2006 Gregory Szorc independently created his own GraphViz extension, this one called "Graphviz" (small "v"), that included some helpful features like autopruning.
• Also in 2006, Ruud Schramp created the MscGen extension, adapting the code from the GraphViz extension to work with MscGen.
• In 2008 Matthew Pearson created the extension GraphVizAndMSCGen, combining the code from the GraphViz with the MscGen extension.
• In 2010 Thomas Hummel merged these and other versions, along with his own fixes, to try to create a working solution for several OSes in one file.
• In 2011 Jeroen De Dauw uploaded the resulting code onto MediaWiki SVN.

Alternatives

If you don't like this extension there are some others that I find remarkable (although I tried to put the main functionality of all of them into this extension - so thank them for their ideas also).

• The Extension by Gregory Szorc is absolutely well coded and supports auto-pruning.
• GraphViz-Version by Bytesmiths
• Extension:Graph This Extension lets you draw ASCII-Art, SVG, and Graphviz-Images without(?) the use of the Graphviz-Tool
• Extension:FreeMind uses the FreeMind-Tool to draw graphs
• Extension:Semantic_Graph also uses the FreeMind-Tool to draw (as an alternative to the #Projects based on this extension
• Extension:GraphVizAndMSCGen built upon the old graphviz-source

Projects that rely on this extension

• The "Semantic Result Formats" extension is used in conjunction with the Semantic MediaWiki extension, that bundles a number of further result formats for SMW's inline queries.
  • graph format (displays connections between pages as graphs)
  • process format (displays process graphs)
• Extension:Collaboration_Diagram (renders and visualizes a bipartite graph of any article and its editors)

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