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Merge pull request #285 from AjitPS/master
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@AjitPS
AjitPS authored Jul 23, 2018
2 parents 4e5d632 + 88dd033 commit c62aef9
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Showing 8 changed files with 281 additions and 175 deletions.
2 changes: 2 additions & 0 deletions common/client-base/src/main/webapp/html/css/style.css
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Expand Up @@ -684,6 +684,8 @@ a.contact-button :hover {
/* Gene View: interactive evidence summary filter */
#evidenceSummary2 {cursor:pointer; padding-top:5px; padding-bottom:5px;}
#loadingDiv_GeneView {float:right; color:darkOrange; font-size:15px; font-weight:bold; width:120px; height:25px; display:none;}
#revertGeneView.unhover { cursor:pointer; border: none; width:30px; height:30px; background:url("../image/reset_filter.png") no-repeat; }
#revertGeneView.hover { cursor:pointer; border: none; width:30px; height:30px; background:url("../image/reset_filter_hover.png") no-repeat; }

/* Suggestor box */
/* #suggestor_search_area {} */
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116 changes: 87 additions & 29 deletions common/client-base/src/main/webapp/html/javascript/utils.js
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Expand Up @@ -817,15 +817,15 @@ function searchKeyword(){

activateButton('resultsTable');
createGenesTable(data.geneTable, keyword, candidateGenes);
createEvidenceTable(data.evidenceTable);
createEvidenceTable(data.evidenceTable, keyword);
}
});
}
}

/*
* Function
* Generates the new lightweight Network graph, using cytoscapeJS.
* Generates the network using KnetMaps
* @author: Ajit Singh.
*/
function generateCyJSNetwork(url,requestParams){
Expand Down Expand Up @@ -938,7 +938,7 @@ var table = "";
table = table + '<p class="margin_left"><a download="genes.tsv" href="data:application/octet-stream;base64,'+btoa(text)+'" target="_blank">Download as TAB delimited file</a><br />';
table = table + 'Select gene(s) and click "View Network" button to see the network.<span id="hintSortableTable" class="hint hint-small" ></span></p>';
table = table + '<form name="checkbox_form">';
table = table + 'Max number of genes to show: ';
table = table + '<u>Max</u> number of genes to show: ';
table = table + '<select value="'+rows+'" id="numGenes">';
//table = table + '<select value="'+results+'" id="numGenes">';
table = table + '<option value="1000"'+(rows==1000?'selected':'')+'>1000</option>';
Expand All @@ -955,7 +955,8 @@ var table = "";
// dynamic Evidence Summary to be displayed above Gene View table
// table = table + interactive_summary_Legend;
table = table + '<div id="evidence_Summary_Legend" class="evidenceSummary">'+ interactive_summary_Legend +
'<input id="revertGeneView" type="button" value="Undo All" title= "Revert all filtering changes">'+'</div>';
'<input id="revertGeneView" type="button" value="" class="unhover" title= "Revert all filtering/sorting changes">'+'</div>';

table = table + '<div id= "geneViewTable" class = "scrollTable">';
table = table + '<table id = "tablesorter" class="tablesorter">';
table = table + '<thead>';
Expand All @@ -970,11 +971,11 @@ var table = "";
table = table + '<th width="60">'+values[3]+'</th>';
table = table + '<th width="70">'+values[4]+'</th>';
}
//table = table + '<th width="70">'+values[5]+'</th>';
table = table + '<th width="70">'+values[6]+'</th>';
//table = table + '<th width="70">'+values[5]+'</th>'; // hide TAXID (if single organism)
// table = table + '<th width="70">'+values[6]+'</th>'; // hide score for now (18/07/18)
// table = table + '<th width="85">'+values[7]+'</th>'; // user yes/no; DISABLED (13/09/17)
if(reference_genome == true){ //QTL
table = table + '<th width="70">'+values[8]+'</th>';
//table = table + '<th width="70">'+values[8]+'</th>'; // hide QTL for now (18/07/18)
}
table = table + '<th width="220">'+values[9]+'</th>';
table = table + '<th width="70">Select</th>';
Expand Down Expand Up @@ -1134,7 +1135,7 @@ var table = "";

var select = '<td><input id="checkboxGene_'+i+'" type="checkbox" name= "candidates" value="'+values[1]+'"></td>';
//table = table + gene + chr + start + end + score + withinQTL + usersList + evidence + select;
table = table + gene + geneName + taxid + chr + start + score + /*usersList +*/ withinQTL + evidence + select;
table = table + gene + geneName + taxid + chr + start + /*score + /*usersList +*/ /*withinQTL +*/ evidence + select; // hide score & QTL for now (18/07/18)
table = table + '</tr>';
}
table = table+'</tbody>';
Expand Down Expand Up @@ -1213,6 +1214,14 @@ var table = "";
// $("#loadingDiv_GeneView").css("display","none"); // clear
});

$("#revertGeneView").mouseenter(function(e) {
$("#revertGeneView").removeClass('unhover').addClass('hover');
});

$("#revertGeneView").mouseout(function(e) {
$("#revertGeneView").removeClass('hover').addClass('unhover');
});

/*
* if select all targets is checked find all targets and check them.
*/
Expand Down Expand Up @@ -1285,7 +1294,7 @@ function containsKey(keyToTest, array){
* Function
*
*/
function createEvidenceTable(text){
function createEvidenceTable(text, keyword){
var table = "";
var summaryArr = new Array();
var summaryText = '';
Expand All @@ -1307,7 +1316,7 @@ function createEvidenceTable(text){
table = table + '<th width="78">'+header[2]+'</th>';
table = table + '<th width="60">'+header[3]+'</th>';
table = table + '<th width="103">'+header[4]+'</th>';
table = table + '<th width="50">'+header[5]+'</th>';
// table = table + '<th width="50">'+header[5]+'</th>'; // hide QTL for now (18/07/18)
table = table + '</tr>';
table = table + '</thead>';
table = table + '<tbody class="scrollTable">';
Expand All @@ -1332,10 +1341,28 @@ function createEvidenceTable(text){
} */
table = table + '<td>'+evidenceValue+'</td>';
table = table + '<td>'+values[2]+'</td>';

//table = table + '<td><a href="javascript:;" onclick="evidencePath('+values[6]+');">'+values[3]+'</a></td>';
table = table + '<td><a href="javascript:;" class="generateEvidencePath" title="Display in the new KnetMaps" id="generateEvidencePath_'+ev_i+'">'+values[3]+'</a></td>';
table = table + '<td>'+values[4]+'</td>'; // user genes
table = table + '<td>'+values[5]+'</td>';
table = table + '<td><a href="javascript:;" class="generateEvidencePath" title="Display in KnetMaps" id="generateEvidencePath_'+ev_i+'">'+values[3]+'</a></td>'; // all genes

// table = table + '<td>'+values[4]+'</td>'; // user genes
// For user genes, add option to visualize their Networks in KnetMaps via web services (api_url)
var userGenes= 0;
if(values[4].length > 0) {
userGenes= 1; // i.e., min. 1 user gene found
values[4]= values[4].trim();
if(values[4].includes(",")) { // for multiple user genes
userGenes= values[4].split(",").length; // total user genes found
}
// launch evidence network using 'userGenes'.
table = table + '<td><a href="javascript:;" class="userGenes_evidenceNetwork" title="Display in KnetMaps" id="userGenes_evidenceNetwork_'+ev_i+'">'+userGenes+'</a></td>';
}
else {
userGenes= 0;
table = table + '<td>'+userGenes+'</td>'; // zero user genes
}

// table = table + '<td>'+values[5]+'</td>'; // hide QTL for now (18/07/18)
table = table + '</tr>';
//Calculates the summary box
if (containsKey(values[0],summaryArr)){
Expand Down Expand Up @@ -1377,25 +1404,56 @@ function createEvidenceTable(text){
evidencePath(values[6]);
});

/*
* click handler for generating the evidence path network for user genes (using user_genes and search keywords, passed to api_url
* @author: Ajit Singh (19/07/2018)
*/
$(".userGenes_evidenceNetwork").bind("click", {x: evidenceTable}, function(e) {
e.preventDefault();
var evidenceNum = $(e.target).attr("id").replace("userGenes_evidenceNetwork_","");
var values = e.data.x[evidenceNum].split("\t");

var evi_userGenes= values[4].trim(); // user gene(s) provided
// Add comma-separated user genes to a new (candidates) list
var ug_list= [];
if(evi_userGenes.includes(",")) {
var vals= evi_userGenes.split(",");
for(var i=0; i < vals.length; i++) {
ug_list.push(vals[i]);
}
}
else {
ug_list.push(evi_userGenes);
}

var search_keywords= keyword.trim(); // user search keyword(s) used
// search_keywords= search_keywords.replace(/"/g, '\"').trim(); // replace all keyword double quotes with separator/quote

// console.log("generate userGenes_evidenceNetwork: keywords: "+ search_keywords +", userGenes_list: "+ ug_list);
// Generate Network
generateCyJSNetwork(api_url+'/network', {keyword:search_keywords, list:ug_list});
});

$("#tablesorterEvidence").tablesorter({
sortList: [[3,1]], //sort by score in decending order
textExtraction: function(node) { // Sort TYPE column
var attr = $(node).attr('type-sort-value');
if (typeof attr !== 'undefined' && attr !== false) {
return attr;
}
return $(node).text();
}
});
sortList: [[3,1]], //sort by score in decending order
textExtraction: function(node) { // Sort TYPE column
var attr = $(node).attr('type-sort-value');
if (typeof attr !== 'undefined' && attr !== false) {
return attr;
}
return $(node).text();
}
});

//Shows the evidence summary box
for(key in summaryArr){
var contype= key.trim();
//if (key !== "Trait") {
summaryText = summaryText+'<div class="evidenceSummaryItem"><div class="evidence_item evidence_item_'+key+' title="'+key+'"></div>'+summaryArr[key]+'</div>';
/* }
else { // For Trait, display tooltip text as GWAS instead.
summaryText = summaryText+'<div class="evidenceSummaryItem"><div class="evidence_item evidence_item_'+key+'" title="GWAS"></div>'+summaryArr[key]+'</div>';
} */
var contype= key.trim();
// if (key !== "Trait") {
summaryText= summaryText+'<div class="evidenceSummaryItem"><div class="evidence_item evidence_item_'+key+' title="'+key+'"></div>'+summaryArr[key]+'</div>';
/* }
else { // For Trait, display tooltip text as GWAS instead.
summaryText= summaryText+'<div class="evidenceSummaryItem"><div class="evidence_item evidence_item_'+key+'" title="GWAS"></div>'+summaryArr[key]+'</div>';
}*/

}

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1 change: 1 addition & 0 deletions common/server-datasource-ondexlocal/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@
<dependency>
<groupId>net.sourceforge.ondex.modules</groupId>
<artifactId>cyjs_json</artifactId>
<version>2.1.1-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
10 changes: 9 additions & 1 deletion ...e-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexLocalDataSource.java
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Expand Up @@ -212,7 +212,7 @@ from user gene list (Set<ONDEXConcept> userGenes) */

// temporary...
/* String genomaps_filename= Paths.get(this.getProperty("DataPath"), System.currentTimeMillis()+"_genomaps.xml").toString();
this.ondexServiceProvider.writeGenomapsFile(genomaps_filename, xmlGViewer);
this.ondexServiceProvider.writeResultsFile(genomaps_filename, xmlGViewer);
*/

log.debug("1.) Genomaps annotation ");
Expand All @@ -223,11 +223,19 @@ from user gene list (Set<ONDEXConcept> userGenes) */
// Gene table file
String geneTable = this.ondexServiceProvider.writeGeneTable(genes, userGenes, request.getQtl(),
request.getListMode());
// temporary...
/* String gv_filename= Paths.get(this.getProperty("DataPath"), System.currentTimeMillis()+"_GeneTable.tab").toString();
this.ondexServiceProvider.writeResultsFile(gv_filename, geneTable); */

log.debug("2.) Gene table ");

// Evidence table file
String evidenceTable = this.ondexServiceProvider.writeEvidenceTable(qtlnetminerResults.getLuceneConcepts(),
userGenes, request.getQtl());
// temporary...
/* String ev_filename= Paths.get(this.getProperty("DataPath"), System.currentTimeMillis()+"_EvidenceTable.tab").toString();
this.ondexServiceProvider.writeResultsFile(ev_filename, evidenceTable); */

log.debug("3.) Evidence table ");

// Document count (only related with genes)
Expand Down
35 changes: 30 additions & 5 deletions ...e-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java
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Expand Up @@ -1840,7 +1840,7 @@ public String writeAnnotationXML(String api_url, ArrayList<ONDEXConcept> genes,
}

// temporary...
public void writeGenomapsFile(String filename, String sb_string) {
public void writeResultsFile(String filename, String sb_string) {
try {
BufferedWriter out = new BufferedWriter(new FileWriter(filename));
out.write(sb_string);
Expand Down Expand Up @@ -2174,15 +2174,35 @@ public String writeEvidenceTable(HashMap<ONDEXConcept, Float> luceneConcepts, Se
Set<Integer> listOfGenes = mapConcept2Genes.get(lc.getId());
Integer numberOfGenes = listOfGenes.size();
// Creates numberOfUserGenes and numberOfQTL
Integer numberOfUserGenes = 0;
//Integer numberOfUserGenes = 0;
String user_genes="";
Integer numberOfQTL = 0;

for (int log : listOfGenes) {

ONDEXConcept gene = graph.getConcept(log);
if ((userGenes != null) && (gene != null) && (userGenes.contains(gene))) {
numberOfUserGenes++;
}
// numberOfUserGenes++;
// retain gene Accession/Name (18/07/18)
String geneAcc="";
for(ConceptAccession acc : gene.getConceptAccessions()) {
String accValue= acc.getAccession();
geneAcc = accValue;
if(acc.getElementOf().getId().equalsIgnoreCase("TAIR") && accValue.startsWith("AT")
&& (accValue.indexOf(".") == -1)) {
geneAcc = accValue;
break;
}
else if(acc.getElementOf().getId().equalsIgnoreCase("PHYTOZOME")) {
geneAcc = accValue;
break;
}
}
// use shortest preferred concept name
/* String geneName = getShortestPreferedName(gene.getConceptNames());
geneAcc= geneName; */
user_genes= user_genes + geneAcc +",";
}

if (mapGene2QTL.containsKey(log)) {
numberOfQTL++;
Expand Down Expand Up @@ -2307,8 +2327,13 @@ public String writeEvidenceTable(HashMap<ONDEXConcept, Float> luceneConcepts, Se
// }
// }
}

// omit last comma from user_genes String
if(user_genes.contains(",")) {
user_genes= user_genes.substring(0, user_genes.length()-1);
}
// writes the row
out.append(type + "\t" + name + "\t" + fmt.format(score) + "\t" + numberOfGenes + "\t" + numberOfUserGenes
out.append(type + "\t" + name + "\t" + fmt.format(score) + "\t" + numberOfGenes + "\t" + /*numberOfUserGenes*/ user_genes
+ "\t" + numberOfQTL + "\t" + ondexId + "\n");
}
//log.info("Evidence table generated...");
Expand Down
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