Extension:PagesOnDemand/PMID OnDemand

<?php
/*
 * PMID_OnDemand.php - An extension 'module' for the PagesOnDemand extension.
 * @authora Jim R. Wilson (wilson.jim.r@gmail.com) and Jim Hu (jimhu@tamu.edu)
 * @version 0.1
 * @copyright Copyright (C) 2007 Jim R. Wilson
 * @license The MIT License - http://www.opensource.org/licenses/mit-license.php 
 */
 
if ( ! defined( 'MEDIAWIKI' ) ) die();
 
# Credits
$wgExtensionCredits['other'][] = array(
    'name'=>'PMID_OnDemand',
    'author'=>'Jim Hu &lt;jimhu@tamu.edu&gt; and Jim Wilson &lt;wilson.jim.r@gmail.com&gt;',
    'description'=>'Uses PagesOnDemand to generate wiki articles about papers indexed in the National Library of Medicine PubMed database on demand.',
    'version'=>'0.1'
);
 
# Register hooks ('PagesOnDemand' hook is provided by the PagesOnDemand extension).
$wgHooks['PagesOnDemand'][] = 'wfLoadPubmedPageOnDemand';
 
/**
* Loads a demo page if the title matches a particular pattern.
* @param Title title The Title to check or create.
*/
function wfLoadPubmedPageOnDemand( $title, $article ){
 
        $myTitle = preg_replace('/^PMID:([ _]|%20)*/','PMID:', $title->getDBkey());
        $linkstring = '';
        # Short-circuit if $title isn't in the MAIN namespace or doesn't match the PMID pattern.
 if ( $title->getNamespace() != NS_MAIN || !preg_match('/^PMID:\\d+$/', $myTitle ) ) {
                return true;
        }
 
        # Create the Article's new text by getting content from PubMed EUtilities
 # Seee: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
 $ref_fields = explode(':',$myTitle);
        $data = trim(array_pop($ref_fields));
        $url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$data&retmode=xml";
        $pubmed_record = file_get_contents( $url );
 
        # exit if no pubmed id is found
 if (!$pubmed_record || strpos($pubmed_record, '<!-- Error>') > 0) return false;
 
        $xml_parser = xml_parser_create();
        xml_parse_into_struct($xml_parser, $pubmed_record, $vals, $index);
        xml_parser_free($xml_parser);
 
#     echo "<pre>";print_r($index);print_r($vals);echo "</pre>";
 #assemble author list
 $i = 0;
        foreach ($index['LASTNAME'] as $valkey){
                $author[] = $vals[$valkey]['value'].", ".$vals[$index['INITIALS'][$i]]['value'];
                $i++;
        }
 
        switch (count($author)){
                case 0:
                        $refstring = 'No author listed';
                        break;
                case 1:
                        $refstring = $author[0];
                case 2:
                        $refstring = implode (' and ',$author);
                        break;
                default:      
                        $last_auth = array_pop($author);
                        $refstring = implode(", ",$author). " and ".$last_auth;
        }
        if ($refstring != '') $refstring = "'''".$refstring."''' "; # bold author list
 #Pubdate
 $pubdate_start = array_shift($index['PUBDATE']);
        $pubdate_end = array_pop($index['PUBDATE']);
        for ($i = $pubdate_start; $i<= $pubdate_end; $i++){
                $pubdate[$vals[$i]['tag']] = @$vals[$i]['value'];
        }
 
        if (isset($pubdate['YEAR'])) $refstring .= " (".$pubdate['YEAR'].") ";       
        $refstring .= $vals[$index['ARTICLETITLE'][0]]['value'];
 
        # Journal is either in an isoabbreviation or in medlineta or in journal, title.  Use abbreviation if available.
 if (isset($index['ISOABBREVIATION'])){
                $refstring .= "''".$vals[$index['ISOABBREVIATION'][0]]['value']."'' ";
        }elseif (isset($index['MEDLINETA'])){
                        $refstring .= "''".$vals[$index['MEDLINETA'][0]]['value']."'' ";
        }elseif (isset($index['JOURNAL'])){
                foreach ($index['JOURNAL'] as $valkey){
                        if ($vals[$valkey+1]['tag'] == 'TITLE') $refstring .= "''".$vals[$valkey+1]['value']."'' ";
                }
        } 
        if (isset($index['VOLUME'])) $refstring .= "'''".$vals[$index['VOLUME'][0]]['value']."''':";
        if (isset($index['MEDLINEPGN'])) $refstring .= $vals[$index['MEDLINEPGN'][0]]['value'];
        $linkstring .= " [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=$data PubMed]";       
 
        $doistring = '';
        if(isset($index['ARTICLEID'])){
                foreach ($index['ARTICLEID'] as $key){
                        if ($vals[$key]['attributes']['IDTYPE'] == 'doi') $doistring .= "Online version:[http://dx.doi.org/".$vals[$key]['value']." ".$vals[$key]['value']."]";
                } 
        }
 
 
        if (isset($index['ABSTRACTTEXT'])){
                $abstract = $vals[$index['ABSTRACTTEXT'][0]]['value'];
        }else{
                $abstract = 'No abstract in PubMed';
        }
        # get the template
    $template = Revision::newFromTitle(Title::makeTitle(NS_TEMPLATE, 'PMID_page'));
    if (! $template){
        $text = "Template not found\n\n$refstring\n\n$abstract\n\n$linkstring";
        }else{
            $text = $template->getText();
            #strip out noinclude sections
     $text = preg_replace( '/<noinclude>.*?<\/noinclude>/s', '', $text );
                $text = str_replace('{{{REFERENCE}}}',$refstring,$text);
                $text = str_replace('{{{ABSTRACT}}}',$abstract,$text);
                $text = str_replace('{{{LINKS}}}',$linkstring,$text);
                $text = str_replace('{{{DOI}}}',$doistring,$text);
        }
        # Create the Article, supplying the new text
 # Handle case where there is an extra space after the colon
 if ($myTitle != $title->getDBkey()){
                $article = new Article($title);
                $article->doEdit( "#REDIRECT [[$myTitle]]", 'New PMID: Page!', EDIT_NEW | EDIT_FORCE_BOT );
                $title = Title::makeTitle(NS_MAIN, $myTitle);
        }
        $article = new Article($title);
        # check again that the page doesn't already exist (we previously checked the original title, not the redirected one)
 if (!$title->exists()){
                $article->doEdit( '', 'New PMID: Page!', EDIT_NEW | EDIT_FORCE_BOT );
                $article->doEdit( $text, 'Fill PMID: Page!', EDIT_UPDATE | EDIT_FORCE_BOT );
        } 
 
        # All done (returning false to kill PoD's wfRunHooks stack)
 return false;
}
?>