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-rwxr-xr-xweb/javascript/webqtl.js184
-rw-r--r--wqflask/runserver.py6
-rw-r--r--wqflask/wqflask/search_results.py6
-rw-r--r--wqflask/wqflask/templates/search_result_page.html5
-rw-r--r--wqflask/wqflask/views.py4
5 files changed, 111 insertions, 94 deletions
diff --git a/web/javascript/webqtl.js b/web/javascript/webqtl.js
index 19ecf3b7..536e7d26 100755
--- a/web/javascript/webqtl.js
+++ b/web/javascript/webqtl.js
@@ -38,16 +38,16 @@ function makeTree(thisForm, nnn){
j += 1;
}
}
-
+
var windowName = 'formTarget' + (new Date().getTime());
var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
var html = "";
if (j > 0)
- {
+ {
var waithtml1 ="<Blockquote class='title' id='red'>Your list of "+j+" transcripts is being exported to the Gene Ontology Tree Machine for analysis. This window will soon be replaced with the main GOTM results.</Blockquote>";
}
else
- {
+ {
var waithtml1 ="<Blockquote class='title' id='red'>Your should select at least one transcript to export to the Gene Ontology Tree Machine for analysis.</Blockquote>";
}
html += waithtml1;
@@ -152,7 +152,11 @@ function showDatabase3(formName, Database,ProbeSetID,CellID){
document[formName].database.value = Database;
document[formName].ProbeSetID.value = ProbeSetID;
document[formName].CellID.value = CellID;
- document[formName].submit();
+ console.log("formName:", formName)
+ console.log("document[formName]:", document[formName])
+ console.log("submit turned off for debugging")
+ console.log("showDatabase3 is deprecated for the flask version of this site")
+ //document[formName].submit();
}
@@ -188,10 +192,10 @@ function showTrait(fmName){
var thisForm = getForm(fmName);
if (thisForm == null || showTrait.arguments.length < 2)
return;
-
+
windowName = genNewWin();
thisForm.target = windowName;
-
+
thisForm.FormID.value = "showDatabase";
thisForm.ProbeSetID.value = showTrait.arguments[1];
if (showTrait.arguments.length > 2)
@@ -205,10 +209,10 @@ function showCateGraph(fmName){
var thisForm = getForm(fmName);
if (thisForm == null || showCateGraph.arguments.length < 2)
return;
-
+
windowName = genNewWin();
thisForm.target = windowName;
-
+
thisForm.FormID.value = "showCategoryGraph";
thisForm.interval1.value = showCateGraph.arguments[1];
thisForm.interval2.value = showCateGraph.arguments[2];
@@ -219,22 +223,22 @@ function showCorrPlot(fmName){
var thisForm = getForm(fmName);
if (thisForm == null || showCorrPlot.arguments.length < 2)
return;
-
+
windowName = genNewWin();
thisForm.target = windowName;
-
+
thisForm.FormID.value = "showCorrelationPlot";
thisForm.ProbeSetID.value = showCorrPlot.arguments[1];
if (showCorrPlot.arguments.length > 2)
thisForm.CellID.value = showCorrPlot.arguments[2];
else
thisForm.CellID.value = "";
-
+
thisForm.X_geneSymbol.value = null;
thisForm.Y_geneSymbol.value = null;
thisForm.submit();
-
+
}
@@ -242,12 +246,12 @@ function showCorrPlotThird(fmName){
var thisForm = getForm(fmName);
if (thisForm == null || showCorrPlotThird.arguments.length < 3)
return;
-
+
windowName = genNewWin();
thisForm.target = windowName;
-
+
var olddb = thisForm.database.value;
-
+
thisForm.FormID.value = "showCorrelationPlot";
thisForm.database.value = showCorrPlotThird.arguments[1];
thisForm.ProbeSetID.value = showCorrPlotThird.arguments[2];
@@ -284,15 +288,15 @@ function ODE(thisForm, script){
var windowName = 'formTarget' + (new Date().getTime());
var newWindow = open("", windowName, "width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
var html = "";
- if (j == 0){
+ if (j == 0){
j = length;
trait_list2 = trait_list_all;
correlation2 = correlation_all;
llid_list2 = llid_list_all;
}
-
+
var waithtml1 ="<Blockquote class='title' id='red'>Your list of "+j+" transcripts is being exported to the ODE for analysis. This window will soon be replaced with the results.</Blockquote>";
-
+
html += waithtml1;
newWindow.document.write(html);
newWindow.document.close();
@@ -302,14 +306,14 @@ function ODE(thisForm, script){
thisForm.correlation.value = correlation2.join(',');
thisForm.id_value.value = thisForm.correlation.value;
thisForm.llid_list.value = llid_list2.join(',');
-
+
// ODE
-
+
thisForm.idtype.value = thisForm.id_type.value;
thisForm.species.value = thisForm.org.value;
thisForm.list.value = thisForm.id_list.value;
thisForm.client.value = "genenetwork";
-
+
thisForm.target = windowName;
var oldaction = thisForm.action;
thisForm.action = script;
@@ -318,13 +322,13 @@ function ODE(thisForm, script){
}
}
*/
-// 02/12/2009
+// 02/12/2009
// Lei Yan
/*scripts in the Dataediting form*/
function dataEditingFunc(thisForm,submitIdValue){
-
+
windowName = 'formTarget' + (new Date().getTime());
if (thisForm.FormID.value!='secondRegression'){
@@ -336,7 +340,7 @@ function dataEditingFunc(thisForm,submitIdValue){
}
else if (submitIdValue == "addRecord"){
- windowName = thisForm.RISet.value;
+ windowName = thisForm.RISet.value;
var name = thisForm.identification.value;
if (name != ""){
}
@@ -352,7 +356,7 @@ function dataEditingFunc(thisForm,submitIdValue){
newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
thisForm.target = windowName;
- newWindow.focus();
+ newWindow.focus();
thisForm.submitID.value = submitIdValue;
thisForm.submit();
}
@@ -394,7 +398,7 @@ function addRmvSelection(windowName, thisForm, addORrmv){
thisForm.target = windowName;
thisForm.FormID.value = addORrmv;
thisForm.submit();
- newWindow.focus();
+ newWindow.focus();
}
function batchSelection(thisForm){
@@ -424,7 +428,7 @@ function showTop10(formName, submitIdValue){
if ((submitIdValue == "markerRegression")||(submitIdValue == "compositeRegression")){
thisForm.topten.value = "topten";
}
-
+
thisForm.submitID.value = submitIdValue;
thisForm.submit();
}
@@ -441,12 +445,12 @@ function showIndividualChromosome(formName, submitIdValue, ii){
}
if (match == 0)
return;
-
+
windowName = 'formTarget' + (new Date().getTime());
newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
newWindow.focus();
thisForm.target = windowName;
-
+
if (submitIdValue == "showIntMap"){
thisForm.chromosomes.value = ii;
}
@@ -529,10 +533,10 @@ function dataWindow(form){
}
-function xchange() {
+function xchange() {
var select = document.crossChoice.RISet;
var value = select.options[select.selectedIndex].value;
-
+
if (value !="BDAI") return;
document.crossChoice.variance.checked = false;
}
@@ -580,97 +584,97 @@ function crossinfo2(){
function checkWidth(){
var width = document.getElementsByName('plotSize')[0].value
-
+
if (width < 600) {
alert("Plot size is too small - setting size to 600")
document.getElementsByName('plotSize')[0].value = 600
- }
+ }
}
function changeLineColor(){
var lineColor = document.getElementsByName('lineColorSel')[0].value
-
+
document.getElementsByName('lineColor')[0].value = lineColor
}
function changeLineSize(){
var lineSize = document.getElementsByName('lineSizeSel')[0].value
-
+
document.getElementsByName('lineSize')[0].value = lineSize
}
function changeIdColor(){
var idColor = document.getElementsByName('idColorSel')[0].value
-
+
document.getElementsByName('idColor')[0].value = idColor
}
function changeIdFont(){
var idFont = document.getElementsByName('idFontSel')[0].value
-
+
document.getElementsByName('idFont')[0].value = idFont
}
function changeIdSize(){
var idSize = document.getElementsByName('idSizeSel')[0].value
-
+
document.getElementsByName('idSize')[0].value = idSize
}
function changeSymbolColor(){
var symbolColor = document.getElementsByName('colorSel')[0].value
-
+
document.getElementsByName('symbolColor')[0].value = symbolColor
}
function changeSymbol(){
var symbol = document.getElementsByName('symbolSel')[0].value
-
+
document.getElementsByName('symbol')[0].value = symbol
}
function changeFilled(){
var filled = document.getElementsByName('fillSel')[0].value
-
+
document.getElementsByName('filled')[0].value = filled
}
function changeSize(){
var symbolSize = document.getElementsByName('sizeSel')[0].value
-
+
document.getElementsByName('symbolSize')[0].value = symbolSize
}
-function checkAll(thisForm){
+function checkAll(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
thisForm.searchResult[i].checked = true;
highlight(thisForm.searchResult[i]);
}
-}
+}
-function checkNone(thisForm){
+function checkNone(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
thisForm.searchResult[i].checked = false;
highlight(thisForm.searchResult[i]);
}
-}
+}
-function checkInvert(thisForm){
+function checkInvert(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
thisForm.searchResult[i].checked = !(thisForm.searchResult[i].checked);
highlight(thisForm.searchResult[i]);
}
-}
+}
/*Not used anymore*/
-function checkTraits2(thisForm){
+function checkTraits2(thisForm){
var length = thisForm.searchResult.length;
var category = thisForm.selectmenu.value;
for(var i = 0; i < length; i++)
@@ -720,18 +724,18 @@ function checkTraits2(thisForm){
else
{}
}
-}
+}
function checkNumeric(field,limit,resetvalue,compares,fdname)
{
- pattern = /^-?[0-9]*\.?[0-9]*$/;
+ pattern = /^-?[0-9]*\.?[0-9]*$/;
if(pattern.test(field.value)==false)
{
alert("Not numeric in " + fdname);
field.value = resetvalue;
}
- else
+ else
{
if (compares == 'gthan') {
if(field.value > limit)
@@ -748,7 +752,7 @@ function checkNumeric(field,limit,resetvalue,compares,fdname)
}
}
-function checkTraits(thisForm){
+function checkTraits(thisForm){
var length = thisForm.searchResult.length;
var andor = thisForm.selectandor.value;
var gthan = parseFloat(thisForm.selectgt.value);
@@ -780,7 +784,7 @@ function checkTraits(thisForm){
}
-function checkPM(thisForm){
+function checkPM(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
@@ -792,8 +796,8 @@ function checkPM(thisForm){
{thisForm.searchResult[i].checked = false;}
highlight(thisForm.searchResult[i]);
}
-}
-function checkMM(thisForm){
+}
+function checkMM(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
@@ -804,14 +808,14 @@ function checkMM(thisForm){
{thisForm.searchResult[i].checked = false;}
highlight(thisForm.searchResult[i]);
}
-}
+}
-function directPermuAlert(thisForm){
- if (thisForm.directPermuCheckbox.checked){
- alert("Interaction permutation will take long time to compute.\n Check this box only when necessary.");
+function directPermuAlert(thisForm){
+ if (thisForm.directPermuCheckbox.checked){
+ alert("Interaction permutation will take long time to compute.\n Check this box only when necessary.");
}
-}
+}
function cliqueDatabase(pid){
var windowName = 'clique';
@@ -869,7 +873,7 @@ function snpbrowser_function_refresh() {
for (var i=1; i<document.newSNPPadding.exonfunction.length; i++) {
document.newSNPPadding.exonfunction.options[i].selected=false;
}
- }
+ }
}
function snpbrowser_domain_refresh() {
@@ -889,7 +893,7 @@ function showHideOptions() {
var options = document.getElementById("options");
var showOptions = document.getElementsByName("showOptions")[0];
var optionsButton = document.getElementsByName("optionsButton")[0];
-
+
if (showOptions.value == '0') {
showOptions.value = '1';
optionsButton.value = "Hide Options";
@@ -898,22 +902,22 @@ function showHideOptions() {
showOptions.value = '0';
optionsButton.value = "Show Options";
}
-
- options.style.display = (options.style.display != 'none' ? 'none' : '' );
+
+ options.style.display = (options.style.display != 'none' ? 'none' : '' );
}
function editPCAName(thisForm) {
var pcaTraits = document.getElementsByName("searchResult");
-
+
var nameArray = new Array();
-
+
for (j=1; j<=pcaTraits.length; j++){
var traitName = "pcaTrait" + String(j);
var pcaTrait = document.getElementById(traitName).childNodes[0].innerHTML;
var editID = "editName" + String(j);
var editName = document.getElementsByName(editID)[0].value;
var originalName = pcaTrait.split(":")[3];
-
+
if (editName.length < 1) {
nameArray.push(originalName);
}
@@ -921,13 +925,13 @@ function editPCAName(thisForm) {
nameArray.push(editName);
}
}
-
+
var newNames = nameArray.join(",");
-
+
thisForm.newNames.value = newNames;
thisForm.searchResult = thisForm.oldSearchResult;
thisForm.FormID.value = "corMatrix";
-
+
thisForm.submit();
}
@@ -950,7 +954,7 @@ function unknownChipError(chipName){
}
/*
-Used by PartialCorrInputPage.py,
+Used by PartialCorrInputPage.py,
*/
function validateTrait(thisForm, inputRadioNames, type, method)
{
@@ -1029,7 +1033,7 @@ function validateTrait(thisForm, inputRadioNames, type, method)
}
}
-
+
}
/*
@@ -1044,7 +1048,7 @@ function changeView(i, Chr_Mb_list){
newWindow = open('',windowName,'menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900');
document.changeViewForm.target = windowName;
document.changeViewForm.chromosomes.selectedIndex = i+1;
- document.changeViewForm.startMb.value = '0.000000';
+ document.changeViewForm.startMb.value = '0.000000';
document.changeViewForm.endMb.value = Chr_Mb_list[i];
document.changeViewForm.graphWidth.value = 1280;
document.changeViewForm.submit();
@@ -1076,7 +1080,7 @@ used by networkGraphPageBody.py
function changeFormat(graphName){
var graphFormat = document.getElementById('exportFormat').value;
var traitType = document.getElementById('traitType').value;
-
+
if (graphFormat=="xgmml"){
if (traitType=="symbol"){
var graphname = graphName+ "_xgmml_symbol.txt";
@@ -1087,7 +1091,7 @@ function changeFormat(graphName){
document.getElementById('exportGraphFile').onclick = function() { window.open(graphname) };
}
}
-
+
else if (graphFormat=="plain")
{
if (traitType=="symbol")
@@ -1102,7 +1106,7 @@ function changeFormat(graphName){
}
}
-}
+}
/*
@@ -1126,13 +1130,13 @@ function set_customStrains_cookie() {
}
/*
-* moved from beta2.js
-*/
+* moved from beta2.js
+*/
function centerIntervalMapOnRange2(chr, start, stop, form) {
var oldindex = form.chromosomes.selectedIndex;
var oldstart = form.startMb.value;
var oldend = form.endMb.value;
-
+
for (var i = 1; i < form.chromosomes.length; i++){
if(form.chromosomes.options[i].text == chr){
form.chromosomes.selectedIndex = i;
@@ -1145,12 +1149,12 @@ function centerIntervalMapOnRange2(chr, start, stop, form) {
form.chromosomes.selectedIndex = oldindex;
form.startMb.value = oldstart;
form.endMb.value = oldend;
-
+
}
/*
-* moved from index3.html
-*/
+* moved from index3.html
+*/
String.prototype.trim = function(){
return this.replace(/(^\s*)|(\s*$)/g, "");
@@ -1282,13 +1286,13 @@ function showTissueCorrPlot(fmName,geneSymbol1, geneSymbol2,rank){
var thisForm = getForm(fmName);
if (thisForm == null || showTissueCorrPlot.arguments.length < 3)
return;
-
+
if (rank){
thisForm.rankOrder.value = rank;
}else{
thisForm.rankOrder.value = 0;
}
-
+
windowName = genNewWin();
thisForm.target = windowName;
@@ -1302,7 +1306,7 @@ function showTissueCorrPlot(fmName,geneSymbol1, geneSymbol2,rank){
if(typeof(thisForm.ProbeSetID2) !== 'undefined'){
thisForm.ProbeSetID2.value = 'none';
}
- thisForm.submit();
+ thisForm.submit();
}
/* Used by MarkerRegressionPage.py */
@@ -1317,7 +1321,7 @@ function validatePvalue(thisForm){
{
alert("Please enter numeric value.");
thisForm.pValue.focus();
- }
+ }
else if (pValue <0){
alert("Please enter the valid P-Value.");
thisForm.pValue.focus();
@@ -1327,7 +1331,7 @@ function validatePvalue(thisForm){
}
-
+
}
@@ -1338,9 +1342,9 @@ function showTissueAbbr(fmName,shortname, fullname){
thisForm.FormID.value = 'tissueAbbreviation';
thisForm.shortTissueName.value=shortname;
thisForm.fullTissueName.value=fullname;
-
+
thisForm.submit();
thisForm.FormID.value = 'showCorrelationPlot';
thisForm.target =''
-
+
}
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index bf73ed37..7bd82619 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -11,5 +11,11 @@ from wqflask import app
#
# For more info see: http://www.cyberciti.biz/faq/iptables-block-port/
+import logging
+logging.basicConfig(filename="/tmp/flask_gn_log", level=logging.INFO)
+
+_log = logging.getLogger("search")
+_ch = logging.StreamHandler()
+_log.addHandler(_ch)
app.run(host='0.0.0.0')
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index ee67c5de..ce7a6eef 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -5,9 +5,9 @@ from wqflask import app
from flask import render_template
###################################################
-#
+# #
# This file uses only spaces for indentation #
-#
+# #
###################################################
import string
@@ -36,7 +36,7 @@ from utility import webqtlUtil
from dbFunction import webqtlDatabaseFunction
import logging
-logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO)
+logging.basicConfig(filename="/tmp/flask_gn_log", level=logging.INFO)
_log = logging.getLogger("search")
_ch = logging.StreamHandler()
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index f79a19a7..b00355a6 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -172,7 +172,10 @@
<INPUT TYPE="checkbox" NAME="searchResult" class="checkbox" VALUE="{{ thisTrait }}" onClick="highlight(this)">
</TD>
<TD class="fs12 fwn b1 c222">
- <A HREF="javascript:showDatabase3('{{ thisFormName }}','{{thisTrait.db.name}}','{{ thisTrait.name }}','{{ thisTrait.cellid }}')" class="fs12 fwn">{{ thisTrait.name.upper() }}</A>
+ <A HREF="javascript:showDatabase3('{{ thisFormName }}','{{thisTrait.db.name}}','{{ thisTrait.name }}','{{ thisTrait.cellid }}')" class="fs12 fwn"> - </a>
+ <a href="{{ url_for('showDatabaseBXD', database=thisTrait.db.name, ProbeSetID=thisTrait.name, incparentsf1='ON', RISet='BXD')}}" class="fs12 fwn">
+ {{ thisTrait.name.upper() }}
+ </a>
</TD>
<TD class="fs12 fwn b1 c222 fsI">
<A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{thisTrait.geneid}}" TARGET="_blank" class="font_black fs12 fwn">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 88a6f6a1..b128f425 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -17,3 +17,7 @@ def index_page():
def search():
the_search = search_results.SearchResultPage(request.args)
return render_template("search_result_page.html", **the_search.__dict__)
+
+@app.route("/showDatabaseBXD")
+def showDatabaseBXD():
+ return None
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 19:15:39 +0000