MediaWiki

Running Jmol / JSmol

• Jmol as a standalone application.
• J(S)mol as a web applet or HTML5 object.
  • compatibility with JavaScript frameworks or libraries.
• J(S)mol embedded in wikis or blogs.
• Borrowed JSmol, or running JSmol without your own server.
• Running Jmol using Java Web Start.
• JSmol in a Jupyter notebook.
• Jmol in an Android tablet.
• Troubleshooting.

Description

MediaWiki is an open source wiki engine licensed under the GNU General Public License. It is used by many websites, including this one.

The Jmol Mediawiki Extension enables the use of the Jmol applet inside of Mediawiki pages.

Current version: 5.1, compatible with JSmol (You can check which version a Wiki is using by going to the Special:Version page in that Wiki)

Current status: (version 5, JSmol)

• The Jmol Mediawiki Extension is now using JSmol (in HTML5 modality by default, but also compatible with Java modality). Some functionality was added, apart from compatibility with MediaWiki version 1.32.

Old status: (version 4, JSmol)

• The Jmol Mediawiki Extension used JSmol (in HTML5 modality by default, but also compatible with Java modality)

Older status: (version 3, Jmol-Java)

• Security is hopefully correct now. The delay effect can be obtained by using Jmol applet in a popup window.
• The Jmol Mediawiki Extension is fully functional and stabilized. It currently needs to be modified for a few things: better security, ability to delay loading the applet.

Wikis using the Jmol Extension

If you know a Wiki using the Jmol MediaWiki Extension, please add it to the list of Wikis using Jmol.

How to use the Jmol Extension

Once the Jmol Extension is installed in the Wiki, you can start adding Jmol applets and controls.

How to know if the Extension is installed, and which version it is? Visit the Special:Version page in your wiki; the extension should be listed there.

• How to use version 5 of the Jmol Extension. Compatible with MediaWiki 1.32, PHP 7.0 and JSmol 14.29.32
• How to use version 4 of the Jmol Extension
• How to use version 3 of the Jmol Extension

Installation

(This must be done by the wiki administrator.)

The files forming the Jmol Extension are part of the Jmol source code and may hence be retrieved from the SVN system.

Installation of the Jmol extension is now described on the Jmol extension page on MediaWiki.

You can configure the Jmol extension with several settings added after the above line (default value in bold):

• $wgJmolAuthorizeChoosingSignedApplet (true, false) : Authorize users to choose between the unsigned and the signed Jmol applet.
• $wgJmolAuthorizeUploadedFile (true, false) : Authorize the use of <uploadedFileContents>.
• $wgJmolAuthorizeUrl (true, false) : Authorize the use of <urlContents>.
• $wgJmolDefaultAppletSize (400) : Size in pixels of the Jmol applet.
• $wgJmolDefaultScript : Default script.
• $wgJmolExtensionPath (extensions/Jmol) : Path to the directory where the Jmol extension is installed. This must be an absolute path, therefore if you customize it, make sure it is prepended with $wgScriptPath (see example in Jmol.php).
• $wgJmolForceNameSpace : Force the NameSpace where the applet will go looking for wiki pages containing molecular data (using <wikiPageContents>).
• $wgJmolShowWarnings (true, false) : Display warnings when users try to use disabled features.
• $wgJmolUsingSignedAppletByDefault (true, false) : Choose if the signed Jmol applet will be used by default. Note: the signed Jmol applet is signed with a default certificate. If you want to use the signed Jmol applet in your wiki, I suggest resigning the Jmol applet with your own certificate.

Note: If you want to authorize users to upload files containing molecular data (for using the <uploadedFileContents> tag), you need to do the following:

• By default, MediaWiki authorizes the uploading of files whose name ends with a limited number of extensions. For example, if you want to authorize uploading *.cml files, add $wgFileExtensions[] = 'cml'; in LocalSettings.php.
• You can add an icon in the skins/common/images/icons/ directory for each extension (for example, fileicon-cml.png). In this wiki, we are using this image, which leads to the following result.

Installation of older versions

Version 4 of the Jmol Extension is compatible with MediaWiki 1.16; installation instructions.

The Jmol Extension below v. 3.3 uses another extension, Stub Manager, so you first need to install it.

Problems yet to be solved

• Having problems with Jmol applets that are placed below the flow of a link, button, or other user interface element in markup. I get what appears to be a Java error when loading an uploaded file. --Mevans86 18:58, 13 October 2010 (UTC)

• Does not work with Media wiki 1.17 (and probably 1.15,1.16). I think there was a rewrite of mediawiki code and I get:

Warning: Parameter 1 to Jmol::tag_jmol() expected to be a reference, value given in /var/www/mediawiki/extensions/StubManager/StubManager.php on line 783

--Jacksmind 01:00, 10 October 2010 (UTC)

Hopefully this is solved with version 3.3 of the Extension, since it no longer depends on StubManager. (Still to be confirmed, but it is working fine with MW 1.16 in this site.) --AngelHerraez 12:32, 22 November 2010 (CET)

• The developers at WikiMedia / WikiMedia Commons / Wikipedia apparently advocate the use of a simpler way of inserting Jmol applets, by just linking to the (previously uploaded) model file (as it is done e.g. with images) and having the server decide upon the way to handle it, with something simpler than the current Extension (see a discussion about this).

However, in my opinion rendering of a 3D molecular model clearly calls for something more flexible than a simple, barebone viewer with default settings. Maybe we would have to resort to a simpler extension for Wikipedia and a full one for other wikis?

New tags are available since version 3.3 of the extension, which are much more simple to use (<jmolFile>, <jmolPdb>, <jmolSmiles>), but are currently not flexible. A solution to explore may be the use of HTML templates to give the opporunity to choose between differently configured viewers (with different controls and informations). --NicolasVervelle 22:44, 28 November 2010 (CET)

• An interesting feature would be the server-side automation of the snapshot ability of the Jmol application, so that images are generated into the wiki page as a thumbnail that will link to --or be replaced by-- the applet when the user clicks on the image, or on a link below it (see an example of this idea, though not server-generated).

• I have just upgraded to MediaWiki 1.18.1 and I now have:

Warning: Parameter 3 to Jmol::jmolPdbTag() expected to be a reference, value given in /var/www/SklogWiki/includesparser/Parser.php on line 3580

Any advice? --SklogWiki 19:31, 31 January 2012 (CET)

Already solved

These are left here for reference, as you may still have these problems depending on your version of MediaWiki or your version of the Jmol MediaWiki Extension.

• The installation does not work when the wiki is installed in a non-root folder of the server (e.g. http://www.myserver.com/mywiki/index.php instead of http://mywiki.myserver.com/index.php).

Fixed (2008-Nov-29) in revision 10393.

• Using <jmolAppletButton> or <jmolAppletlink> throws an error in Internet Explorer: "Invalid argument", and prevents the pop-up.

Partially fixed (2008-Dec-2) in revision 10411.

Completely fixed (2008-Dec-8) in revision 10467.

• The scripts associated to checkboxes rendered by <jmolCheckbox> have no effect on the applet.

Fixed (2008-Dec-8) in revision 10467.

This was the discussion of the problem:

(Bob) something in /skins/common/wikibits.js?97 is disabling checkboxes.
(Nico) Yes, good catch, thanks a lot. Now, I need to find a way to overcome the behaviour of setupCheckboxShiftClick(). I am going to ask on mediawiki list.
(Bugzilla) discussion

The problem was due to a conflict in the onClick event for checkboxes correctly written by the Jmol Extension and a javascript library (wikibits.js) included in MediaWiki. The offending js function is now overwritten by the extension.

• Since Jmol scripting can include a call to javascript commands, the Jmol applet inserted by the Jmol MediaWiki Extension can execute arbitrary javascript added by any user editing the page (see demo). This is an unacceptable security hole for some systems such as Wikipedia, and will prevent Jmol from being used there. There is hence a need to implement a "scripting-without-javascript" mode of the applet, i.e. a way to completely disable the javascript command in Jmol scripts run from the MediaWiki Extension.

Fixed (2008-Dec-8) in revision 10467.

No javascript will be executed by Jmol applets inserted by the Extension.

• The signed applet was not being used even when explicitly authorized in the wiki configuration ($wgJmolAuthorizeChoosingSignedApplet=true) and requested for the applet (<signed>true</signed>).

Fixed (2008-Dec-8) in revision 10467.

Now you can also have both signed and unsigned applets in the same page.

• Inserting applets with models read from php pages fails. The applet is using the <urlContents> tag and the url contains the '&' character.

Fixed (2009-Nov-13) in revision 11738, version 3.2 of the Extension.

The '&' is not tolerated by the wikicode. The solution is to use %26 (the wikicode for &) instead of the ampersand(s) in the url, content of the <urlContents> tag. The Extension will later filter those %26 codes and convert them to & so that the server correctly provides the model.

External links

• Wikipedia: Using Jmol to display molecular models
• Wikipedia: WikiProject Chemistry
• MediaWiki: Jmol Extension for MediaWiki

Contributors

AngelHerraez, NicolasVervelle, Rzepa, Mevans86, Ngreeves, Pimpim, SklogWiki, Jacksmind, EricMartz