The plug-in is rather simple, but since a web search turned up nothing similar (which is kind of surprising), and someone might find it useful, I thought I’d post it here.

Here is the code for “wikindx.php”:

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<?php
/* 
Plugin Name: Wikindx
Plugin URL: http://stargrads.net/blogs/davinci/2009/09/wikindx-macro-plug-in-for-wordpress
Description: Adds a macro to WordPress to insert bibliography information from Wikindx.
Author: D. L. Yonge-Mallo
Version: 1.0
Author URI: http://stargrads.net/blogs/davinci/
*/
 
function parse_wikindx($content) {
    $WikindxPath="http://path.to/wikindx/";
 
    preg_match_all('#<wikindx( resource="([ \w]+)")?(>(.*)</wikindx>| ?/>)#Usi', $content, $wikindxs, PREG_SET_ORDER);
 
    if ( count($wikindxs) > 0 ) {
        foreach ( (array) $wikindxs as $wikindx ) {
            if( empty($wikindx[2]) ) {
                $output = "ERROR: WIKINDX MISSING RESOURCE ARGUMENT";
            } else {
                $resourceId = $wikindx[2];
                $string = file_get_contents("{$WikindxPath}cmsprint.php?action=getResource&id={$resourceId}");
                if($string) {
                    $array = unserialize(base64_decode($string));
                    $output = $array[$resourceId] . " ([{$WikindxPath}index.php?action=resourceView&id={$resourceId} details])";
 
                } else {
                    $output = "ERROR: WIKINDX RESOURCE ".$resourceId." NOT FOUND";
                }
            }
            $content = str_replace($wikindx[0], $output, $content);
        }
    }
 
    return $content;
}
add_filter('the_content', 'parse_wikindx', 2);
?>

Replace “http://path.to/wikindx/” in the above with the URL to your installation of Wikindx, obviously. For example, mine is “http://stargrads.net/bibliography/”.

Put the file into the “plugins” directory on WordPress, or if you are using WordPress^μ, then into its “mu-plugins” directory.

The plug-in creates a new macro “wikindx” with one parameter “resource”, which can be used inside WordPress posts like this:

<wikindx resource="68" />

Replace “68″ in the example with the resource ID of the bibliography entry whose information you want. (This ID can be found in the URL of the resource’s page on Wikindx.) The result is that the macro is replaced by the bibliographical information for that resource. For the above example, this would be:

R. Cleve, D. Gavinsky, and D. L. Yonge-Mallo, “Quantum Algorithms for Evaluating Min-Max Trees,” in Proc. TQC 2008, Tokyo, Japan, 2008, (details)

This plug-in can be used to good effect with Rob Miller’s Footnotes plug-in for WordPress, like this:

<ref name="CGMSY08"><wikindx resource="206" /></ref>

The result^[1] can be seen in the footnote below.

– davinci 11780

Update (Sept. 15, 2009): I’ve added the plug-in to the WordPress Plugin Directory.

Related posts:

1. Using the Ajaxified Expand Post Now plug-in with Rob Miller’s Footnotes plug-in
2. Annotate With Jarnal Plug-In Module for Wikindx
3. Using jsMath with WordPress, bbPress, and Wikindx

The AEPN plug-in truncates a post and appends an “[Expand post]” button, whenever it is displayed other than on a single page by itself. Clicking on the button fetches and displays the rest of the post. The Footnotes plug-in should be self-explanatory.

The problem with using these two plug-ins together is that if any citations are made before the fold (i.e., the <!--more--> tag), the corresponding footnotes will appear at the bottom of the (collapsed) post. When the post is subsequently expanded, those footnotes will appear again at the end of the expansion, so that they are displayed twice.

The fix for this is rather simple. In the “footnotes.php” file, surround the final if-else block with a test to see if a single post is being displayed. If so, execute the block as before. Otherwise, return the post’s content without the accompanying footer. The code should look like this:

if( is_single() ) {	
    if ( strpos($content, '<references />') === false )
        return $content . $footer;
    else
        return str_replace('<references />', $footer, $content);
} else {
    return $content;
}

When the AEPN plug-in fetches a post to expand it, it is treated as a single post, and so the footnotes will show up correctly — once, at the bottom of the expansion.

In the “ajaxified-expand-post-now.php” file, add the following lines to the top of the “getPost” function:

global $post;
$post->ID = $id;

This is needed so that the names for the footnote anchors in the expanded portion of the post are generated correctly. Citations made before the fold will link to the post’s single page, whereas citations made after it^[3] will link to the footnotes section at the bottom of the expansion, on the current page.

Finally, it may be necessary to use a so-called “kses hack” to prevent the “ref” and “references” tags needed by the Footnotes plug-in from being stripped by WordPress^μ. How to do this is beyond the scope of this post.

See also this previous post for an example of how the Footnotes plug-in can be used with the Wikindx bibliographical management system to create a bibliographical citation.

– davinci

Related posts:

1. Wikindx macro plug-in for WordPress
2. Annotate With Jarnal Plug-In Module for Wikindx

Essentially, you just need to add the following code in the header of your web site (where “path.to” should be replaced with the URL to your installation of jsMath):

<script type="text/javascript" src="http://path.to/jsMath/easy/load.js"></script>

For this web site, the above line was added to the headers of each of the template files of the component software packages.

One minor trick to getting jsMath to work with Wikindx is that all special characters have to be escaped properly\(\). For example, to get the title of Mario Szegedy’s paper^[1] on quantum walks to display correctly, as seen here, I had to enter the title as:

Spectra of Quantized Walks and a \$\sqrt{{}\delta\epsilon{}}\$-Rule

That is, where the LaTeX math syntax requires a left curly bracket, you enter “{{}”, and where it requires a right curly bracket, you enter “{}}”. The title then appears as in the footnote below.

I have created a setup help page on the wiki to record details such as these. Also, see this forum post for some macros defined for use on this site.

– davinci

Related posts:

1. Wikindx macro plug-in for WordPress
2. Using the Ajaxified Expand Post Now plug-in with Rob Miller’s Footnotes plug-in
3. Annotate With Jarnal Plug-In Module for Wikindx

To begin with, I didn’t find any ready-made projects which exactly suited my needs. The most impressive, and the one which came the closest to what I was looking for, is OpenWetWare, but its focus is on biology and biological engineering. Chemists have also gotten into the act with UsefulChem, which is hosted on wikispaces.

I did not locate any project of a similar scope or scale for physics or, perhaps ironically, computer science. The physics community is actually an early adopter of electronic scientific publishing, with its embrace of the arXiv since 1991. And the quantum community has not just one but two — count ‘em, two — whole wikis to itself: Quantiki and Qwiki. Michael Nielsen (the Mike of Mike and Ike, which is widely considered the standard text for quantum computation) has written an extensive post about the opening up of scientific culture.

Another reason for building the site myself, instead of relying on a ready-made solution, is the degree of control I would have over its customization. For a biologist or chemist, communications technologies such as blogs and wikis are only tools. But for a computer scientist, these technologies are themselves objects of study.

Following OpenWetWare’s example, I have installed MediaWiki (for wikis) and WordPress (for blogs), and I have also added bbPress (for bulletin boards) and WIKINDX (for bibliography management) into the mix.

Despite the fact that the name ★grads.net, which came to me in a fit of inspiration, suggests multiple grad(uate student)s, for now this experiment in open notebook science is mine alone.

– davinci

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