URL: http://metabolomics.jp/
*/
if ( !defined( 'MEDIAWIKI' ) ) {
die( 'This file is a MediaWiki extension, see ExMolFunctions.php.' );
}
$wgExtensionCredits['parserhook'][] = array(
'name' => 'ExMolFunctions',
'version' => '0.1',
'author' => 'K, Suwa',
'description' => 'Link and page which receive template and arguments',
'url' => 'http://metabolomics.jp/wiki/Help:Extension/ExMolFunctions',
);
$wgHooks['ParserBeforeStrip'][] = 'efExMolFunctionsView';
$wgHooks['ArticleSave'][] = 'efExMolFunctionsDataInsert';
global $egMolNamespace;
$egMolNamespace = "Mol";
function efExMolFunctionsView( &$parser, &$text, &$strip_state ) {
global $wgTitle, $egMolNamespace;
if( ereg( "^$egMolNamespace:.*$", $wgTitle ) && ereg( "\nM END *(\n|$)", $text ) !== FALSE ) {
$text = "[[Image:{{PAGENAME}}.png]]\n" . $text . "\n
";
}
return true;
}
function efExMolFunctionsDataInsert( &$parser, &$user, &$text, &$summary, $minor, $watch, $sectionanchor, &$flags ) {
global $wgExtraNamespaces, $egMolNamespace, $egJavaBin, $egMolCalculatorJar, $egMolImageJar, $egTmpPath, $wgTitle, $egMolPath;
# check namespace
$targetNamespace = $parser->getTitle()->getNamespace();
$molNamespace = array_search( $egMolNamespace, $wgExtraNamespaces );
if( $molNamespace === FALSE || $targetNamespace != $molNamespace )
return true;
# process
$procText = $text;
$lines = split( "\n", $procText );
$wikitext = '';
# calculate
$mol = "";
for( $i = 0; $i < count( $lines ); $i ++ ){
if( stripos( $lines[$i], 'S SKP' ) === 0 ){
$count = trim( substr( $lines[$i], 6 ) );
$i += $count;
} else
$mol .= $lines[$i] . "\n";
}
$mol = escapeshellcmd( escapeshellarg( $mol ) );
$res = `$egJavaBin -jar $egMolCalculatorJar $mol`;
$data = split( "\n", $res );
$datas = array();
$datas['formula'] = trim( substr( $data[0], 8 ) );
$datas['extmass'] = trim( substr( $data[1], 10 ) );
$datas['avemass'] = trim( substr( $data[2], 12 ) );
$datas['smiles'] = trim( substr( $data[3], 7 ) );
$page_title = $wgTitle->getText();
# parameter
$width = 100;
$height = 100;
$autodraw = '';
$option = '';
# insert
if( stripos( $procText, 'S SKP' ) === FALSE ) {
# insert
for( $i = 0; $i < count( $lines ); $i ++ ) {
$pos = stripos( $lines[$i], 'M END' );
if( $pos !== FALSE && $pos == 0 ) {
$wikitext .= "S SKP 5\n";
$wikitext .= 'ID ' . $page_title. "\n";
$wikitext .= 'FORMULA ' . $datas['formula']. "\n";
$wikitext .= 'EXACTMASS ' . $datas['extmass']. "\n";
$wikitext .= 'AVERAGEMASS ' . $datas['avemass']. "\n";
$wikitext .= 'SMILES ' . $datas['smiles']. "\n";
$wikitext .= $lines[$i]. "\n";
} else {
$wikitext .= $lines[$i]. "\n";
}
}
} else {
# fix
$molflags = array();
$idflag = false;
$molflags['formula'] = false;
$molflags['extmass'] = false;
$molflags['avemass'] = false;
$molflags['smiles'] = false;
for( $i = 0; $i < count( $lines ); $i ++ ) {
if( stripos( $lines[$i], 'S SKP' ) === 0 ) {
$count = trim( substr( $lines[$i], 6 ) );
$tmptext = '';
for( $j = 1; $j <= $count; $j ++ ) {
$pos = stripos( $lines[$i+$j], 'ID ' );
if( $pos !== FALSE && $pos == 0 ) {
$idflag = true;
}
$pos = stripos( $lines[$i+$j], 'FORMULA ' );
if( $pos !== FALSE && $pos == 0 ) {
$molflags['formula'] = true;
}
$pos = stripos( $lines[$i+$j], 'EXACTMASS ' );
if( $pos !== FALSE && $pos == 0 ) {
$molflags['extmass'] = true;
}
$pos = stripos( $lines[$i+$j], 'AVERAGEMASS ' );
if( $pos !== FALSE && $pos == 0 ) {
$molflags['avemass'] = true;
}
$pos = stripos( $lines[$i+$j], 'SMILES ' );
if( $pos !== FALSE && $pos == 0 ) {
$molflags['smiles'] = true;
}
$pos = stripos( $lines[$i+$j], 'X ' );
if( $pos !== FALSE && $pos == 0 && strlen( $lines[$i+$j] ) > 3 ) {
$width = trim( substr( $lines[$i+$j], 2 ) );
if( !ereg( '^[0-9]+$', $width ) )
$width = 100;
if( $width > 1000 )
$width = 1000;
}
$pos = stripos( $lines[$i+$j], 'Y ' );
if( $pos !== FALSE && $pos == 0 && strlen( $lines[$i+$j] ) > 3 ) {
$height = trim( substr( $lines[$i+$j], 2 ) );
if( !ereg( '^[0-9]+$', $height ) )
$height = 100;
if( $height > 1000 )
$height = 1000;
}
$pos = stripos( $lines[$i+$j], 'AUTODRAW ' );
if( $pos !== FALSE && $pos == 0 && strlen( $lines[$i+$j] ) > 10 ) {
$autodraw = trim( substr( $lines[$i+$j], 9 ) );
if( strcasecmp( $autodraw, 'true' ) != 0 )
$autodraw = '-a';
else
$autodraw = '';
}
$pos = stripos( $lines[$i+$j], 'OPTION ' );
if( $pos !== FALSE && $pos == 0 && strlen( $lines[$i+$j] ) > 8 ) {
$option = escapeshellarg( escapeshellcmd( trim( substr( $lines[$i+$j], 7 ) ) ) );
}
$tmptext .= $lines[$i+$j] . "\n";
}
if( !$idflag ) {
$tmptext .= 'ID ' . $page_title . "\n";
$count ++;
}
if( !$molflags['formula'] ) {
$tmptext .= 'FORMULA ' . $datas['formula'] . "\n";
$count ++;
}
if( !$molflags['extmass'] ) {
$tmptext .= 'EXACTMASS ' . $datas['extmass'] . "\n";
$count ++;
}
if( !$molflags['avemass'] ) {
$tmptext .= 'AVERAGEMASS ' . $datas['avemass'] . "\n";
$count ++;
}
if( !$molflags['smiles'] ) {
$tmptext .= 'SMILES ' . $datas['smiles'] . "\n";
$count ++;
}
while( strlen( $count ) < 3 )
$count = ' ' . $count;
$wikitext .= "S SKP" . $count . "\n" . $tmptext;
$i += $j - 1;
} else {
$wikitext .= $lines[$i] . "\n";
}
}
}
# if( stripos( $wikitext, '' ) !== 0 )
# $wikitext = '' . $wikitext;
# $wikitext = trim( $wikitext );
# if( strripos( $wikitext, '
' ) != strlen( $wikitext ) - 6 )
# $wikitext .= "\n
";
$text = ereg_replace( " *\n", " \n", $wikitext );
# create and add/update image
$id = $parser->getTitle()->getText();
# create image and save to egTmpPath
$file = "$egTmpPath/$id.png";
$nfile = "$egTmpPath/" . $id . "n.png";
$delete_flag = false;
if( !isset( $_SERVER["DOCUMENT_ROOT"] ) || strlen( $_SERVER["DOCUMENT_ROOT"] ) == 0 ) {
$path = "/tmp";
$delete_flag = true;
} else {
$path = $_SERVER["DOCUMENT_ROOT"] . $egMolPath . "/" . substr( $id, 0, 4 );
if( !file_exists( $path ) ){
mkdir( $path );
} else if( !is_dir( $path ) ){
$path = "/tmp";
$delete_flag = true;
}
}
# `$egJavaBin -jar $egMolImageJar $file '$wikitext' $width $height $autodraw $option`;
# temporary change. ###
/* $molfile = "$path/$id.mol";
$mfh = fopen( "$molfile", "w" );
fwrite( $mfh, "$wikitext" );
fclose( $mfh );
`DISPLAY=localhost:1.0 $egJavaBin -jar $egMolImageJar $autodraw -p -s 15 -l 2 -o "$egTmpPath" "$molfile"`;
# over ################
$base = wfBaseName( $file );
$title = Title::makeTitleSafe( NS_IMAGE, $base );
if( !is_object( $title ) ){
# error
return true;
}
$image = wfLocalFile( $title );
$archive = $image->publish( $file );
if( WikiError::isError( $archive ) || !$archive->isGood() ) {
# error
return true;
}
if( !$image->recordUpload( $archive->value, "", "" ) ) {
return true;
# error
}
unlink( $file );
if( $delete_flag )
unlink( $molfile );
*/
efExMolFunctionsCreateImage( $path, $id, $file, $wikitext, $autodraw, $delete_flag, "" );
efExMolFunctionsCreateImage( $path, $id . "n", $nfile, $wikitext, $autodraw, $delete_flag, "-n" );
return true;
}
function efExMolFunctionsCreateImage( $path, $id, $file, $wikitext, $autodraw, $delete_flag, $number_flag )
{
global $egJavaBin, $egMolImageJar, $egTmpPath;
$molfile = "$path/$id.mol";
$mfh = fopen( "$molfile", "w" );
fwrite( $mfh, "$wikitext" );
fclose( $mfh );
`DISPLAY=localhost:1.0 $egJavaBin -jar $egMolImageJar $autodraw $number_flag -p -s 15 -l 2 -o "$egTmpPath" "$molfile"`;
$base = wfBaseName( $file );
$title = Title::makeTitleSafe( NS_IMAGE, $base );
if( !is_object( $title ) ){
# error
return true;
}
$image = wfLocalFile( $title );
$archive = $image->publish( $file );
if( WikiError::isError( $archive ) || !$archive->isGood() ) {
# error
return true;
}
if( !$image->recordUpload( $archive->value, "", "" ) ) {
return true;
# error
}
unlink( $file );
if( $delete_flag )
unlink( $molfile );
}