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ui.py
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ui.py
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#!/usr/bin/python
#
#
# Copyright (C) 2003-2010 Institute for Systems Biology
# Seattle, Washington, USA.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
import os, glob
import cgi
import cgitb
cgitb.enable()
#from config import *
from google.appengine.ext.blobstore import BlobInfo
blobs = BlobInfo.all()
vars={'checkboxes':"",'transplantws':"/transplantdata",'survivaldatasource':"/sampledata",'genedatasource':"/genedata","jsdir":"/js","loadergif":"/images/loader.gif"}
files=[]
tr=""
lastfile = ""
namedic = {}
for blob in blobs.run():
namedic[blob.filename[:28]]=True
for basename in sorted(namedic.keys()):
#basename = blob.filename
if basename[:12] != lastfile [:12]:
vars['checkboxes'] +="<br/><br/>%s:<br/>"%basename[:12]
vars['checkboxes'] += "<input type='checkbox' id='%(file)s' name='%(file)s'/>%(file)s "%{'file':basename}
files.append(basename)
lastfile=basename
vars["files"]="['"+"','".join(files)+"']"
print "Content-type: text/html"
print
print """<?xml version="1.0" ?>
<html xmlns="http://www.w3.org/1999/xhtml"
xmlns:svg="http://www.w3.org/2000/svg"
xmlns:xlink="http://www.w3.org/1999/xlink"
lang="en-US">
<head>
<meta http-equiv='Content-Type' content='text/html; charset=utf-8' />
<title>Transplant</title>
<style>
body {
font: 8pt helvetica neue;
color: #666;
}
td {
font: 8pt helvetica neue;
color: #666;
}
input {
font: 10pt helvetica neue;
}
.outlined {
color: #666;
border-color: #F5F5F5;
border-width: 2px 2px 2px 2px;
border-style: solid;
border-spacing: 0px;
}
</style>
<script type='text/javascript' src='http://www.google.com/jsapi'></script>
<script type='text/javascript'>
google.load('visualization', '1', {packages:["table"]});
//google.load('prototype', '1.6');
</script>
<script type='text/javascript' src='%(jsdir)s/transplant.js'></script>
<script type='text/javascript' >
filenames = %(files)s;
transplantws = "%(transplantws)s";
survivaldatasource = "%(survivaldatasource)s";
genedatasource = "%(genedatasource)s";
loadingpatientinfo = true;
patients = {};
sampletypes = {};
progstyle ={"Poor":"border-color: #F5B9B9;","Good":"border-color: #B9F5B9;","Medium":"border-color: #F5F5B9;"};
samplelabels = {"10":"Blood","11":"Adjacent","01":"Tumor"};
ajloader = "%(loadergif)s";
patientrequested = {}
patientcount = 0;
patientloadedcount =0;
document.onkeypress = keyPress;
function keyPress() {
if (window.event.keyCode == 13)
{
event.returnValue=false;
event.cancel = true;
loadgeneandgrow();
}
}
function loadgeneandgrow()
{
genelocready = false;
filenamesready = false;
//Get gene location
var gene_symbol = document.getElementById('gene').value;
var querystring = "select gene_symbol, chr, start, end where gene_symbol = '"+gene_symbol+"'";
this.log("loading: " + querystring +" from " + genedatasource);
var query = new google.visualization.Query(genedatasource);
query.setQuery(querystring);
query.send(savegeneloc);
var utlpats = getQueryVariable("patients");
patientrequested = {}
for (var i in utlpats)
{
var pat = utlpats[i].split("/").pop()
log("pat " + pat + " from " + utlpats[i]);
patientrequested[pat]=true;
}
//getfilenames
/*filenames = [];
var utlpats = getQueryVariable("patients");
patientcount = utlpats.length;
patientloadedcount =0;
for (var i in utlpats)
{
var req = new XMLHttpRequest();
var patientindex = fileindex+utlpats[i]+"/Pickle";
req.open("GET", patientindex, true);
req.onreadystatechange = function (){
if (req.readyState == 4 ) {
var files = eval('(' + req.responseText + ')').references;
for (var j in files)
{
log("adding file name"+files[j].local);
filenames.push(files[j].local);
}
patientloadedcount++;
grow();
}
};
req.send(null);
}*/
}
function savegeneloc(response)
{
log("gene location data recieved");
if (response.isError()) {
log('Error in query: ' + response.getMessage() + ' ' + response.getDetailedMessage());
return;
}
var data = response.getDataTable();
var radius = parseInt(document.getElementById('radius').value);
document.getElementById('chr').value = "chr"+data.getValue(0,1);
document.getElementById('start').value = data.getValue(0,2)-radius;
document.getElementById('end').value = data.getValue(0,3)+radius;
genelocready = true;
grow();
}
function grow()
{
loadingpatientinfo = true;
document.getElementById('visdiv').innerHTML="<center><img src='"+ajloader+"'/><br/>Loading Patient Data...<\/center>";
loadthese=[];
drawthese=[];
patients = {}
sampletypes = {"10":true,"11":true,"01":true};
for (var i in filenames)
{
var filename = filenames[i];
if(document.getElementById(filename).checked)
{
loadthese.push(filename);
var patientid = filename.substring(0,12);
var sampletype = filename.substring(13,15)
log("patient '" + patientid + "' sampletype '" + sampletype + "'")
if(!patients.hasOwnProperty(patientid))
{
patients[patientid] = {samples:{}}
}
if(!patients[patientid].samples.hasOwnProperty(sampletype))
{
patients[patientid].samples[sampletype]=[];
}
patients[patientid].samples[sampletype].push(filename);
sampletypes[sampletype] = true
/*var filename = filenames[i];
loadthese.push(filename);
var patientid = filename.substring(0,12)
var sampletype = filename.substring(13,15)
log("patient '" + patientid + "' sampletype '" + sampletype + "'")
if(!patients.hasOwnProperty(patientid))
{
patients[patientid] = {samples:{}}
}
if(!patients[patientid].samples.hasOwnProperty(sampletype))
{
patients[patientid].samples[sampletype]=[];
}
patients[patientid].samples[sampletype].push(filename);
sampletypes[sampletype] = true*/
}
}
loadAll();
drawTable()
/*log("building survival query");
var orarray = []
for (var patient in patients)
{
orarray.push("(PATIENT_ID = '"+patient+"')");
}
var patientquery = "select * where " + orarray.join(" or ") + "order by `label` desc, time_years asc";
var query = new google.visualization.Query(survivaldatasource);
query.setQuery(patientquery);
log("sending query " + patientquery + " to " + survivaldatasource);
query.send(handleSurvivalResponse);*/
}
</script>
<script type='text/javascript' src='%(jsdir)s/transplantpage.js' ></script>
<style>
body { margin: 30px; text-align: left; white-space: nowrap;}
</style>
</head>
<body>
<div>
<form>
Data Files:<br/>
<input type="checkbox" id="checkallb" onchange = "script:checkallf();" /> Check All
<div style="width:95%%;height:300;overflow:auto;border:2px grey solid;">
%(checkboxes)s
</div>
<br/>
<center>
<table>
<tr>
<td>
Root Location:<br/><br/>
Gene: <input type='text' id="gene" value ="EWSR1" /><br/>
Chromosome:<input type='text' id="chr" disabled="true" /> <br/>
Start:<input type='text' id="start" disabled="true" />
End:<input type='text' id="end" disabled="true" /><br/><br/>
Break Point width:<br/>
Use Data Field:
<select id="widthfield">
<option value=5>Number of Reads</option>
<option value=8>Score</option>
<option value=false>No Decoration</option>
</select>
</td>
<td>
</td>
<td>
Tree Parameters:<br/><br/>
Maximum Branch Depth:<input type='text' id="depth" value="2"/>
Search Radius:<input type='text' id="radius" value="400000"/><br/>
<input type='checkbox' id="includesmall" checked="true"/>Include Breakpoints Found by Distance Minimum Score:<input type='text' id="minsmallscore" value="94"/><br/>
<input type='checkbox' id="includeother" checked="true"/>Include breakpoints foune by orientation or chromosome Minimum Score:<input type='text' id="minotherscore" value="94"/>
</td>
</tr>
</table>
<br/><br/>
<input type="button" value="Regrow Transplants" onclick="script:loadgeneandgrow();"/>
</center>
</form>
</div>
<div id="visdiv" style="white-space: nowrap;"></div>
</body>
</html>"""%vars