URL: http://metabolomics.jp/
*/
if ( !defined( 'MEDIAWIKI' ) ) {
die( 'This file is a MediaWiki extension, see MassFunctions.php.' );
}
$wgExtensionFunctions[] = 'efSetupMassFunctions';
$wgExtensionCredits['parserhook'][] = array(
'name' => 'MassFunctions',
'version' => '0.2',
'author' => 'K, Suwa',
'description' => 'Mass functions',
'url' => 'http://metabolomics.jp/wiki/Help:Extension/MassFunctions',
);
$wgHooks['LanguageGetMagic'][] = 'efMassFunctionsLanguageGetMagic';
class MassFunctions {
var $url = 'http://www.massbank.jp/api/services/MassBankAPI?wsdl';
/**
* Output Mass viewer applet
* e.g. {{#masstemplate:KO00001}} => ""
*
* @param $parser Parser Parent parser
* @param $keioid target id
* @return string Parts string
*/
function spectraApplet( ) {
global $egMassJarPath;
$argv = func_get_args();
$num = count( $argv );
if( $num <= 1 || $num % 2 == 0 )
return $num;
$count = ( $num - 1 ) / 2;
$html = "{{#javawithparam:DisplayAll.class\n|DisplayAll3.jar\n|$egMassJarPath\n|100%\n|" . (200*$count) . "\n|num=" . $count . ";";
$exFunctions = new ExFunctions();
for( $i = 1; $i <= $count; $i ++ ){
$peak = substr( trim( $exFunctions->searchLine( $argv[0], "^peak1=", "Persist", $argv[$i*2-1] ) ), 16 );
$prec = trim( $exFunctions->searchLine( $argv[0], " PRECURSOR_M/Z ", "Persist", $argv[$i*2-1] ) );
if( strlen( $prec ) > 0 )
$prec = substr( $prec, 40 );
$html .= "id" . $i . "=" . $argv[$i*2-1] . ";name" . $i . "=" . $argv[$i*2] . ";precursor" . $i . "=$prec;peak" . $i . "=$peak;";
}
$html = substr( $html, 0, strlen( $html ) - 1 ) . "}}\n\n";
return array( $html, 'noparse' => false );
}
/**
* Output Mass record
* e.g. {{#masstemplate:KO00001}} => "...
"
*
* @param $parser Parser Parent parser
* @param $keioid target id
* @return string Parts string
*/
function massRecordInfoWithApp( &$parser, $keioid ) {
global $egMassJarPath;
$ids = array( $keioid );
$params = array("ids" => $ids );
$soap = new SoapClient( $this->url );
try {
$res = $soap->getRecordInfo( $params );
} catch (SoapFault $e) {
return "";
}
$ret = $res->return;
$info = $ret->info;
$lines = split( "\n", $info );
$precursor = "";
$peak = "";
$title = "";
for( $i = 0; $i < count( $lines ); $i ++ ){
if( preg_match( '/^MS\$FOCUSED_ION: PRECURSOR_M\/Z .*$/', $lines[$i] ) ){
$precursor = trim( substr( $lines[$i], 30 ) );
} else if( preg_match( '/^PK\$PEAK: m\/z int. rel.int.$/', $lines[$i] ) ){
$i ++;
for( ; $i < count( $lines ); $i ++ ){
if( preg_match( '/^ .*$/', $lines[$i] ) ){
$mz = split( ' ', trim( $lines[$i] ) );
$peak .= $mz[0] . "," . $mz[2] . ":";
} else
break;
}
} else if( preg_match( '/^RECORD_TITLE:.*$/', $lines[$i] ) ){
$title = preg_replace( '/;/', ':', trim( substr( $lines[$i], 13 ) ) );
}
}
return array( "Applet
\n\n{{#javawithparam:DisplayAll.class\n|DisplayAll3.jar\n|$egMassJarPath\n|100%\n|200\n|num=1;\nid1=$keioid;\nname1=$title;\nprecursor1=$precursor;\npeak1=$peak\n}}\n\nImage
\n\n[[Image:Mass:$keioid.png]]\n\n\n" . $info . "\n
\n", 'noparse' => false );
}
}
function efSetupMassFunctions() {
global $wgParser;
$massFunctions = new MassFunctions;
$wgParser->setFunctionHook( 'spectraapplet', array( &$massFunctions, 'spectraApplet' ) );
$wgParser->setFunctionHook( 'massrecordinfowithapp', array( &$massFunctions, 'massRecordInfoWithApp' ) );
}
function efMassFunctionsLanguageGetMagic( &$magicWords, $langCode ) {
$magicWords['spectraapplet'] = array( 0, 'spectraapplet' );
$magicWords['massrecordinfowithapp'] = array( 0, 'massrecordinfowithapp' );
return true;
}