r1995 - branches/milestone_43.x/wpi/extensions/PathwayFinder

[martijn....@bigcat.unimaas.nl]

Author: ariutta
Date: Tue Apr 11 03:54:59 2017
New Revision: 1995

Log:
Added PathwayFinder


Added:
branches/milestone_43.x/wpi/extensions/PathwayFinder/
branches/milestone_43.x/wpi/extensions/PathwayFinder/PathwayFinder.i18n.php (contents, props changed)
branches/milestone_43.x/wpi/extensions/PathwayFinder/PathwayFinder.php (contents, props changed)
branches/milestone_43.x/wpi/extensions/PathwayFinder/PathwayFinder_body.php (contents, props changed)
branches/milestone_43.x/wpi/extensions/PathwayFinder/log.txt

Added: branches/milestone_43.x/wpi/extensions/PathwayFinder/PathwayFinder.i18n.php
==============================================================================
--- (empty file)
+++ branches/milestone_43.x/wpi/extensions/PathwayFinder/PathwayFinder.i18n.php Tue Apr 11 03:54:59 2017
@@ -0,0 +1,7 @@
+<?php
+$allMessages = array(
+ 'en' => array(
+ 'pathwayfinder' => 'Pathway Finder',
+ )
+);
+?>

Added: branches/milestone_43.x/wpi/extensions/PathwayFinder/PathwayFinder.php
==============================================================================
--- (empty file)
+++ branches/milestone_43.x/wpi/extensions/PathwayFinder/PathwayFinder.php Tue Apr 11 03:54:59 2017
@@ -0,0 +1,15 @@
+<?php
+# Not a valid entry point, skip unless MEDIAWIKI is defined
+if (!defined('MEDIAWIKI')) {
+ echo <<<EOT
+To install this special page, put the following line in LocalSettings.php:
+require_once( "$IP/extensions/PathwayFinder/PathwayFinder.php" );
+EOT;
+ exit( 1 );
+}
+
+$wgAutoloadClasses['PathwayFinder'] = dirname(__FILE__) . '/PathwayFinder_body.php';
+$wgSpecialPages['PathwayFinder'] = 'PathwayFinder';
+$wgHooks['LoadAllMessages'][] = 'PathwayFinder::loadMessages';
+
+?>

Added: branches/milestone_43.x/wpi/extensions/PathwayFinder/PathwayFinder_body.php
==============================================================================
--- (empty file)
+++ branches/milestone_43.x/wpi/extensions/PathwayFinder/PathwayFinder_body.php Tue Apr 11 03:54:59 2017
@@ -0,0 +1,615 @@
+<?php
+
+class TissueAnalyzer extends SpecialPage {
+ protected $name = 'TissueAnalyzer';
+
+ function TissueAnalyzer() {
+ SpecialPage::SpecialPage ( $this->name );
+ self::loadMessages();
+ }
+
+ function execute($par) {
+ global $wgOut, $wgUser, $wgLang;
+ $this->setHeaders ();
+ $wgOut->setPagetitle ("TissueAnalyzer");
+
+ $species = (isset ( $_GET ["species"] )) ? $_GET ["species"] : "Human";
+ $cutoff = (isset ( $_GET ["cutoff"] )) ? $_GET ["cutoff"] : "5";
+ $dataset = (isset ( $_GET ["dataset"] )) ? $_GET ["dataset"] : "E-MTAB-2836";
+ $generic = (isset ( $_GET ["generic"] )) ? $_GET ["generic"] : "";
+ $select = $_GET ["select"];
+
+
+ $datasetSelect = "<SELECT name='dataset' id='dataSelect' size='1'>";
+ $path = "wpi/bin/TissueAnalyzer/datasets/datasets.config";
+ $datasetFile = fopen($path, r);
+ $hashArray = array ();
+ $speciesArray = array();
+ while ( ! feof ( $datasetFile ) ) {
+ $line = fgets ( $datasetFile );
+ $pieces = explode ( "\t", $line );
+ $id = $pieces [0];
+ if ($id === '')break;
+ $datasetSpecies = $pieces [1];
+ array_push ($speciesArray, $pieces[1]);
+ $hashArray[$id]["species"] = $datasetSpecies;
+ $hashArray[$id]["short"] = $pieces [2];
+ if (strcmp ( trim ( $species ),trim ($datasetSpecies )) == 0){
+ $datasetSelect .= (strcmp ( trim ( $dataset ), trim ( $id ) ) == 0) ? "<option selected=\"selected\">$id</option>" : "<option>$id</option>";
+ }
+ }
+ fclose ( $datasetFile );
+ $datasetSelect .="</SELECT>";
+ $speciesArray = array_unique($speciesArray);
+
+ $topTenFile = fopen("wpi/bin/TissueAnalyzer/datasets/".$dataset."_generic.txt", r);
+ $topTen = array ();
+ while (!feof($topTenFile)) {
+ array_push ( $topTen, trim (fgets($topTenFile)) );
+ }
+ fclose ( $topTenFile );
+
+ $welcomePage = false;
+ if (!isset ( $select )) {
+ $select="adipose tissue";
+ $welcomePage = true;
+ }
+
+ $this->addJs($topTen,$hashArray);
+ $this->createCriteriaDiv($select, $dataset, $cutoff, $species, $datasetSelect, $speciesArray, $generic);
+ $this->createTableResults($select, $dataset, $cutoff, $topTen);
+ $this->createViewerDivs($welcomePage, $cutoff);
+
+ return true;
+ }
+
+ function addJs($topTen,$hashArray){
+ global $wgOut;
+ $top = json_encode($topTen);
+ $hash = json_encode($hashArray);
+
+ //Add CSS
+ //Hack to add a css that's not in the skins directory
+ global $wgStylePath;
+ $oldStylePath = $wgStylePath;
+ $wgStylePath = "/wpi/lib/tissueanalyzer/";
+ $wgOut->addStyle("/fancybox/jquery.fancybox-1.3.4.css");
+ $wgStylePath = $oldStylePath;
+
+ $wgOut->addScriptFile('/wpi/lib/tissueanalyzer/fancybox/jquery.fancybox-1.3.4.js');
+ $wgOut->addScript('<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>');
+ $wgOut->addScriptFile("/wpi/lib/tissueanalyzer/ChartFancy.js");
+
+ $wgOut->addScript('
+ <script language="JavaScript">
+ function doToggleTA( elId, msg, expand, collapse ) {
+ $("#"+elId+" .toggleMe").toggle();
+ if( msg.innerHTML == expand ) {
+ msg.innerHTML = collapse;
+ $("#check").prop("checked", true);
+ checkGeneric();
+ } else {
+ msg.innerHTML = expand;
+ $("#check").prop("checked", false);check();
+ }
+ }
+ function checkGeneric() {
+ var js_array = '.$top.';
+ if ($("#check").is(":checked")){
+ $(".toggleMe").each(function() {
+ if (js_array.indexOf(this.id) != -1) {
+ $(this).show();
+ }
+ });
+ }
+ else{
+ $(".toggleMe").each(function() {
+ if (js_array.indexOf(this.id) != -1) {
+ $(this).hide();
+ }
+ });
+ }
+ }
+ </script>');
+ $wgOut->addScript('<script language="JavaScript">
+ function tissue_viewer(id,genes,pathway_name){
+ genes = genes.replace(/\./g," ");
+ $("#pwyname").attr("style","");
+ document.getElementById("pwyname").innerHTML="<b>Selected pathway:</b> " + pathway_name;
+ $("#my-legend").attr("style","");
+ $("#path_viewer").attr("src",
+ "http://www.wikipathways.org/wpi/PathwayWidget.php?id="+id+genes);
+ $("#path_viewer").attr("style","overflow:hidden;");
+ }
+ </script>');
+ $wgOut->addScript('<script type="text/javascript">
+ function updateTextInput(val) {
+ document.getElementById("cutoff_label").innerHTML=val;
+ }
+ $(function() {
+ checkGeneric();
+ $("#dataSelect").change(function() {
+ $("#tissueSelect").load("/wpi/bin/TissueAnalyzer/datasets/"+$(this).val()+"_tissues_opt.txt");
+ });
+
+ $("#speciesSelect").change(function() {
+ var speciesValue = $(this).val();
+ var hash = '.$hash.';
+ var dataSelect = document.getElementById("dataSelect");
+ dataSelect.options.length = 0;//empty the drop-down;
+ var i = 0;
+ var id = "";
+ $.each(hash,function(index, value){
+ if (value["species"]==speciesValue){
+ //console.log("index: " + index + ",value: " + value + value["species"] + speciesValue);
+ dataSelect.options[dataSelect.options.length] = new Option(index, index);
+ if (i==0){ // get the first dataset s id;
+ id = index;
+ }
+ i++;
+ }
+ });
+ $("#tissueSelect").load("/wpi/bin/TissueAnalyzer/datasets/"+id+"_tissues_opt.txt"); //update the tissue drop down with the new first id;
+ });
+ });
+ </script>');
+ }
+
+ function createCriteriaDiv($select, $dataset, $cutoff, $species, $datasetSelect, $speciesArray, $generic){
+ global $wgOut;
+
+ $speciesSelect = "<form name= action=''><SELECT name='species' id='speciesSelect' size='1'>";
+ foreach ($speciesArray as $value) {
+ $speciesSelect .= (strcmp ( trim ( $species ), $value ) == 0) ? "<option selected=\"selected\">$value</option>" : "<option>$value</option>";
+ }
+ $speciesSelect .= "</SELECT>";
+
+ $tissueSelect = "<SELECT name='select' id='tissueSelect' size='1'>";
+ $path = "wpi/bin/TissueAnalyzer/datasets/".$dataset."_tissues_opt.txt";
+ $tissuesFile = fopen ($path , r );
+ while ( ! feof ( $tissuesFile ) ) {
+ $line = fgets ( $tissuesFile );
+ $tissue = str_replace("</option>",'',$line);
+ $tissue = str_replace("<option>",'',$tissue);
+ $tissue = trim ( $tissue );
+ if ($tissue === '')
+ break;
+ $tissueSelect .= (strcmp ( trim ( $select ), trim ( $tissue ) ) == 0) ? "<option selected=\"selected\">$tissue</option>" : "<option>$tissue</option>";
+ }
+ fclose ( $tissuesFile );
+ $tissueSelect .= "</SELECT>";
+
+
+ $button = <<<HTML
+ <INPUT type="submit" name="button" value="Apply" style="cursor:pointer;font-weight:900" >
+HTML;
+
+ $slide ='
+ <input type="range" id="cutoff_id" name="cutoff" min="4" max="6" value="'.$cutoff.'" step="1" onchange="updateTextInput(this.value);">
+ <label id="cutoff_label">'.$cutoff.'</label>';
+
+ $out = <<<HTML
+ <div style="display:inline-block;width:100%;">
+ <div style="width:800px;display:inline-block;overflow:visible;border: 3px solid blue;">
+ <b>Select your criteria and then click on Apply:</b>
+ <table id='nsselect' class='allpages'>
+ <tr>
+ <td align='bottom'>Species:</td>
+ <td align='bottom'>Dataset:</td>
+
+ <td align='bottom' style='width:270px'>Tissue:</td>
+ <td align='bottom'>Active gene expression cutoff:</td>
+ </tr>
+ <tr>
+ <td align='left'>{$speciesSelect}</td>
+ <td align='left'>{$datasetSelect}</td>
+
+ <td align='left'>{$tissueSelect}</td>
+ <td align='left'>{$slide}</td>
+ <td align='right'>{$button}</td>
+ </tr>
+ </table>
+HTML;
+
+ $wgOut->addHTML($out);
+ if ($generic=="on") $checked="checked";
+ else $checked="";
+ $checkbox = '
+ <input name="generic" id="check" type="checkbox" onchange="checkGeneric(this)" '.$checked.'>
+ <label for="check">Show generic pathways</label></form></div>';
+ $wgOut->addHTML($checkbox);
+
+ $out = <<<HTML
+ <div style="display:inline-block;overflow:visible;width:100%;">
+ <label style='float:right'>
+ <a target="_blank" href="http://projects.bigcat.unimaas.nl/tissueanalyzer/quick-start/">Quick start</a>
+ </label>
+ <label style='float:right'>
+ <a target="_blank" href="http://projects.bigcat.unimaas.nl/tissueanalyzer/quick-start/">Datasets</a>
+ </label>
+ <label style='float:right'>
+ <a target="_blank" href="http://projects.bigcat.unimaas.nl/tissueanalyzer/documentation/">Documentation</a>
+ </label>
+
+ </div></div>
+HTML;
+ $out = <<<HTML
+ <style type='text/css'>
+ .navi {
+ //list-style: none;
+ margin: 0;
+ padding: 0px 0 0px 30px;
+ font-size: 135%;
+ }
+ .navi a {
+ display: block;
+ color: #000;
+ padding: 4px 0 0px 0px;
+ text-decoration: none;
+ }
+ .navi a:hover {
+ background-color: #555;
+ color: white;
+ }
+ </style>
+ <div style="display:inline-block;overflow:visible;">
+ <ul class='navi'>
+ <li><a target="_blank" href="http://projects.bigcat.unimaas.nl/tissueanalyzer/quick-start/">Quick start</a></li>
+ <li><a target="_blank" href="http://projects.bigcat.unimaas.nl/tissueanalyzer/datasets/">Datasets</a></li>
+ <li><a target="_blank" href="http://projects.bigcat.unimaas.nl/tissueanalyzer/documentation/">Documentation</a></li>
+ </ul>
+ </div>
+ </div>
+HTML;
+ $wgOut->addHTML($out);
+ }
+
+
+ function createTableResults($select, $dataset, $cutoff, $topTen){
+ global $wgOut;
+
+ $url = array ();
+ $mean = array ();
+ $perc = array ();
+ $median = array ();
+ $nami = array();
+ $path_id = array();
+ $path_rev = array();
+ $ratio = array();
+
+ $average = 0;
+ $date = '';
+ $collection = "Curated";
+ $tissue = fopen ( "wpi/data/TissueAnalyzer/$collection/$dataset/$cutoff/Tissue/$select.txt", r );
+ while ( ! feof ( $tissue ) ) {
+ $line = fgets ( $tissue );
+ if (strpos($line, '#') !== false && strpos($line, 'PDT') !== false ) {
+ $dateTmp = explode ( "\t", $line );
+ $date = $dateTmp[1]." PDT";
+ }
+ if (strpos($line, '#') !== false && strpos($line, 'PST') !== false ) {
+ $dateTmp = explode ( "\t", $line );
+ $date = $dateTmp[1]." PST";
+ }
+ $pieces = explode ( "\t", $line );
+ $name = $pieces [0];
+ $id = strstr ( $name, 'WP' );
+ $id = explode ( "_", $id );
+ $path_name = explode ( "_WP", $name );
+ $path_name = str_replace ( "Hs_", '', $path_name[0] );
+ $path_name = str_replace ( "Mm_", '', $path_name );
+ $path_name = str_replace ( "Bt_", '', $path_name );
+ $title = Title::newFromText ( ( string ) $id [0], NS_PATHWAY );
+ $pp = explode ( ".",$pieces[2]);
+ if (isset ( $title )) {
+ array_push ( $url, '<a target="_blank" href="' . $title->getFullURL () . '">' . $id[0] . '</a>' );
+ array_push ( $mean, $pieces[1] );
+ array_push ( $perc, $pp[0] );
+ array_push ( $median, $pieces[3] );
+ array_push ( $nami, $path_name);
+ array_push ( $path_id, $id[0]);
+ array_push ( $path_rev, $id[1]);
+ array_push ( $ratio,$pieces[4]);
+ }
+ }
+
+ array_multisort ($median, SORT_NUMERIC, SORT_DESC,
+ $url, SORT_STRING, SORT_DESC,
+ $mean, SORT_NUMERIC, SORT_DESC,
+ $perc, SORT_NUMERIC, SORT_DESC,
+ $ratio, SORT_NUMERIC, SORT_DESC,
+ $path_id, SORT_NUMERIC, SORT_DESC,
+ $path_rev, SORT_NUMERIC, SORT_DESC,
+ $nami, SORT_STRING, SORT_DESC );
+
+ $div = "<div style='display:inline-block;overflow:visible;width:100%'>
+ <br>
+ <label> Last build : $date</label>
+ <label id='gradient' class='scale-title' style='float:right;display: none'>Gradient color scale</label><br/>";
+ $wgOut->addHTML ( $div );
+
+ $nrShow = 20;
+ $expand = "<b>View all rows...</b>";
+ $collapse = "<b>View first ".($nrShow)." rows...</b>";
+ $button = "<table style='display:inline-block;width:300px;margin: 0.5em 0em 0em 0px'><td width='51%'><div id='viewAll' onClick='".
+ 'doToggleTA("tissueTable", this, "' . $expand . '", "' . $collapse . '")' .
+ "' style='cursor:pointer;color:#0000FF'>"."$expand<td width='45%'></table>";
+
+ $html = "<div style='display:block;overflow:visible;width:100%'>
+ <style type='text/css'>
+ .scale-title {
+ text-align: left;
+ font-weight: bold;
+ font-size: 90%;
+ }
+ .scale-labels {
+ margin: 0;
+ padding: 0;
+ float: left;
+ list-style: none;
+ }
+ .scale-labels li {
+ display: block;
+ float: left;
+ width: 50px;
+ margin-bottom: 6px;
+ text-align: center;
+ font-size: 80%;
+ list-style: none;
+ }
+ .scale-labels li span {
+ display: block;
+ float: left;
+ height: 15px;
+ width: 50px;
+ }
+ #gradient{
+ display:inline !important;
+ }
+ </style>
+ $button
+ <ul class='scale-labels' style='display:inline-block;float:right'>
+ <li><span style='background:#8c8cb9;'></span>0 - 3</li>
+ <li><span style='background:#7676c3;'></span>3 - 5 </li>
+ <li><span style='background:#5151d6;'></span>5 - 7</li>
+ <li><span style='background:#3e3edf;'></span>7 - 10 </li>
+ <li><span style='background:#0000FE;'></span> >10 </li>
+ </ul>
+ </div>";
+
+ $html .= "
+ <table id='tissueTable' class='wikitable sortable' style='display:inline-block;width:100%'>
+ <tr class='table-blue-tableheadings' id='tr_header'>
+ <td class='table-blue-headercell' style='width:44%'>Pathways</td>
+ <td class='table-blue-headercell' align='center' style='width:10%'>Linkout</td>
+ <td class='table-blue-headercell' align='center'style='width:10%'>Median</td>
+ <td class='table-blue-headercell' style='width:1%'></td>
+ <td class='table-blue-headercell' align='center' style='width:10%'>Active genes</td>
+ <td class='table-blue-headercell' align='center' style='width:10%'>Measured genes</td>
+ <td class='table-blue-headercell' align='center'style='width:10%' >Active/Measured %</td>
+ <td class='table-blue-headercell' align='center'style='width:30%' >Average expression over all tissues</td>";
+
+ for($i = 0; $i < count ( $mean ); ++ $i) {
+ $filename = "wpi/data/TissueAnalyzer/$collection/$dataset/$cutoff/Hs_$nami[$i]_$path_id[$i]_$path_rev[$i].txt";
+ $filename2 = "wpi/data/TissueAnalyzer/$collection/$dataset/$cutoff/$nami[$i]_$path_id[$i]_$path_rev[$i].txt";
+ $filename = (file_exists ( $filename )) ? $filename : $filename2;
+ $list_genes = "";
+ $active_index = 0;
+ $measure_index = 0;
+ $name = "";
+ if (file_exists ( $filename )) {
+ $file = fopen ( $filename, r );
+ while ( ! feof ( $file ) ) {
+ $line = fgets ( $file );
+ if ($line == false)
+ break;
+ if (strpos($line, '#') !== false) {
+ $averageTmp = explode ( "\t", $line );
+ $average = $averageTmp[1];
+ }
+ $pieces = explode ( "\t", $line );
+ $name = $pieces[0];
+ if ($name == $select ){
+ $genes = explode ( ",", $pieces [4] );
+ $mesure = explode ( ",", $pieces [5] );
+ $list_genes = "";
+ foreach ( $mesure as $gene ) {
+ $info = explode ( ' ', $gene );
+ if (count ( $info ) > 1) {
+ if (strpos($info[1], '&&') !== FALSE){ // Found it
+ $labels = explode ( '&&', $info[1] );
+ foreach ( $labels as $geneLabel ) {
+ $list_genes .= "&label[]=".$geneLabel;
+ $measure_index = $measure_index + 1;
+ }
+ }
+ else{
+ $list_genes .= "&label[]=".$info[1];
+ $measure_index = $measure_index + 1;
+ }
+ }
+ }
+ foreach ( $genes as $gene ) {
+ $info = explode ( ' ', $gene );
+ if (count ( $info ) > 1) {
+ if (strpos($info[1], '&&') !== FALSE){
+ $labels = explode ( '&&', $info[1] );
+ foreach ( $labels as $geneLabel ) {
+ $list_genes .= "&label[]=".$geneLabel;
+ $active_index = $active_index + 1;
+ }
+ }
+ else{
+ $list_genes .= "&label[]=".$info[1];
+ $active_index = $active_index + 1;
+ }
+ }
+ }
+ }
+ }
+ }
+ $number = explode ( "/",$ratio[$i]);
+
+ $n = intval($number[0]);
+ $m = intval($number[1]);
+
+ // Note color: %23D9A4FF => #D9A4FF
+ if (!$list_genes == ""){
+ if ($n===$m ){
+ $list_genes .= "&colors=%236A03B2";
+ for($l = 1; $l < $active_index; ++ $l){
+ $list_genes .= ",%236A03B2";
+ }
+ }
+ else{
+ $list_genes .= "&colors=%23B0B0B0";
+ for($k = 1; $k < $measure_index; ++ $k){
+ $list_genes .= ",%23B0B0B0";
+ }
+ for($l = 0; $l < $active_index; ++ $l){
+ $list_genes .= ",%236A03B2";
+ }
+ }
+ }
+ $r = 0;
+ $g = 0;
+ $b = 0;
+
+ if ( $median[$i] < 1.5 ) {
+ $r = 170;
+ $g = 170;
+ $b = 170;
+ }
+ elseif ( $median[$i] > 10) {
+ $color = 255;
+ $r = 0;
+ $g = 0;
+ $b = 255;
+ }
+ else {
+ $r = 170 - 2 *($median[$i]-1.5)/(10-1.5) * (255-170);
+ $g = 170 - 2 * ($median[$i]-1.5)/(10-1.5) * (255-170);
+ $b = 170 + ($median[$i]-1.5)/(10-1.5) * (255-170);
+ }
+ $rgb = array( $r, $g, $b );
+
+ $hex = "#";
+ $hex .= str_pad(dechex($rgb[0]), 2, "0", STR_PAD_LEFT);
+ $hex .= str_pad(dechex($rgb[1]), 2, "0", STR_PAD_LEFT);
+ $hex .= str_pad(dechex($rgb[2]), 2, "0", STR_PAD_LEFT);
+
+ if ($i < $nrShow && in_array($nami[$i], $topTen)){
+ $doShow = 'toggleMe';
+ $styleBackground = "style='background:#C7FCF9;'";
+ }
+ else if ($i < $nrShow ){
+ $doShow = '';
+ $styleBackground = '';
+ }
+ else{
+ $doShow = 'toggleMe';
+ }
+
+ $pathway_name = str_replace ( "_", " ", $nami[$i] );
+ $jsonFile = explode (".", $filename );
+ $jsonPath = "/".$jsonFile[0].".json";
+
+ $html .= <<<HTML
+ <tr class='$doShow' $styleBackground id='$nami[$i]'>
+ <td ><a href='#path_viewer' onClick='tissue_viewer("$path_id[$i]","$list_genes","$pathway_name")'> $pathway_name</a></td>
+ <td align='center' >$url[$i]</td>
+ <td align='center' >$median[$i]</td>
+ <td bgcolor='$hex' > </td>
+ <td align='center' >$number[0]</td>
+ <td align='center' >$number[1]</td>
+ <td align='center' >$perc[$i]</td>
+ <td align='center' >
+ <a id="inline" file="$jsonPath" pathway="$pathway_name" measured="$number[1]" tissue="$select" href="#data">$average</a></td>
+HTML;
+ }
+ fclose($tissue);
+ $html .= '</table>';
+ $wgOut->addHTML($html);
+ }
+
+
+
+ function createViewerDivs($welcomePage, $cutoff){
+ global $wgOut;
+ $styleViewer = '';
+ if (!$welcomePage){
+ $styleViewer = 'style="display: none;"';
+ }
+
+ $html = '<style type="text/css">
+ .my-legend .legend-title {
+ text-align: left;
+ margin-bottom: 5px;
+ font-weight: bold;
+ font-size: 90%;
+ }
+ .my-legend .legend-scale ul {
+ margin: 0;
+ margin-bottom: 5px;
+ padding: 0;
+ float: left;
+ list-style: none;
+ }
+ .my-legend .legend-scale ul li {
+ display: inline-block;
+ font-size: 80%;
+ list-style: none;
+ margin-left: 0;
+ line-height: 18px;
+ margin-bottom: 2px;
+ }
+ .my-legend ul.legend-labels li span {
+ display: block;
+ float: left;
+ height: 16px;
+ width: 30px;
+ margin-right: 5px;
+ margin-left: 0;
+ border: 1px solid #999;
+ }
+ </style>
+ </div>
+
+ <div class="my-legend" id="my-legend" '.$styleViewer.' >
+ <div class="legend-title" id="legend-title" style="display:inline-block;width:100%">Highlighting legend</div>
+ <div class="legend-scale" style="display:inline-block">
+ <ul class="legend-labels">
+ <li><span style="background:#6A03B2;"></span>Active gene (expression > '.$cutoff.')</li>
+ <li><span style="background:#B0B0B0;"></span>Not-active gene (expression < '.$cutoff.')</li>
+ </ul>
+ </div>
+ </div>
+ <div id="pwyname" '.$styleViewer.'><b>Selected pathway:</b> Fatty Acid Biosynthesis</div>
+ <div style="display:inline-block;overflow:visible;width:100%"><iframe id="path_viewer"
+ src ="http://www.wikipathways.org/wpi/PathwayWidget.php?id=WP357&label[]=ACSL4&label[]=ACSL3
+ &label[]=ACACA&label[]=ECHDC1&label[]=PECR&label[]=MECR&label[]=ACSL6&label[]=ECHDC2&label[]=ACSL5&label[]=DECR
+ 1&label[]=ACAA2&label[]=ACLY&label[]=ACSL1&label[]=ECH1&label[]=ACACB&label[]=ECHS1&label[]=PC&label[]=ACAS2&label[]=FASN
+ &label[]=ECHDC3&label[]=HADHSC&label[]=SCD&colors=%23B0B0B0,%23B0B0B0,%23B0B0B0,%23B0B0B0,%23B0B0B0,%23B0B0B0,
+ %23B0B0B0,%23B0B0B0,%23B0B0B0,%23B0B0B0,%23B0B0B0,%23B0B0B0,%236A03B2,%236A03B2,%236A03B2,%236A03B2,%236A03B2,
+ %236A03B2,%236A03B2,%236A03B2,%236A03B2,%236A03B2"
+ width="100%" height="500px" '.$styleViewer.' >
+ </iframe></div>
+ <div style="display:none"><div style="height:600px;width:1400px" id="data"></div></div>';
+
+ $wgOut->addHTML($html);
+ }
+
+ static function loadMessages() {
+ static $messagesLoaded = false;
+ global $wgMessageCache;
+ if ($messagesLoaded)
+ return true;
+ $messagesLoaded = true;
+
+ require (dirname ( __FILE__ ) . '/TissueAnalyzer.i18n.php');
+ foreach ( $allMessages as $lang => $langMessages ) {
+ $wgMessageCache->addMessages ( $langMessages, $lang );
+ }
+ return true;
+ }
+}

Added: branches/milestone_43.x/wpi/extensions/PathwayFinder/log.txt
==============================================================================