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index.html
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<!DOCTYPE html>
<html lang="en" xmlns:m="http://www.w3.org/1998/Math/MathML">
<head>
<!-- Meta information -->
<meta name="viewport" content="width=device-width, initial-scale=1.0"></meta>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"></meta>
<meta charset="utf-8"></meta>
<meta name="description" content=""></meta>
<meta name="author" content=""></meta>
<title>Kinomics</title>
<!-- style sheets -->
<link href="js/bootstrap/css/bootstrap.min.css" rel="stylesheet"></link>
<link href="js/qualityControl/UIsupport/nouislider.css" rel="stylesheet"></link>
<link rel="stylesheet" href="//fonts.googleapis.com/css?family=UnifrakturMaguntia"></link>
<link rel="stylesheet" href="js/qualityControl/UIsupport/jqmath-0.2.0.css"></link>
<style type="text/css">
body {
padding-top: 60px;
padding-bottom: 40px;
}
.sidebar-nav {
padding: 9px 0;
}
</style>
<!-- jQuery load this at top since everything depends on it-->
<!-- TODO: update these icons -->
<link rel="shortcut icon" href="./favicon.ico">
<link rel="apple-touch-icon-precomposed" sizes="144x144" href="http://twitter.github.com/bootstrap/assets/ico/apple-touch-icon-144-precomposed.png"></link>
<link rel="apple-touch-icon-precomposed" sizes="114x114" href="http://twitter.github.com/bootstrap/assets/ico/apple-touch-icon-114-precomposed.png"></link>
<link rel="apple-touch-icon-precomposed" sizes="72x72" href="http://twitter.github.com/bootstrap/assets/ico/apple-touch-icon-72-precomposed.png"></link>
<link rel="apple-touch-icon-precomposed" href="http://twitter.github.com/bootstrap/assets/ico/apple-touch-icon-57-precomposed.png"></link>
</head>
<body class=" hasGoogleVoiceExt">
<!-- Navigation bar at the top of the screen -->
<div class="navbar navbar-fixed-top">
<div class="navbar-inner">
<div class="container">
<button type="button" class="btn btn-navbar collapsed" data-toggle="collapse" data-target=".nav-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<!-- Branding... --> <a class="brand">Kinomics Toolbox</a>
<!-- navigate between tabs -->
<div class="nav-collapse in collapse" style="height: auto; ">
<ul class="nav">
<li class="active"><a href="#home" data-toogle="tab" id="tag1">Home</a>
</li>
<li><a href="#qualtityControl" data-toogle="tab" id="tag2">Quality Control</a>
</li>
<li><a href="#fileUpload" data-toogle="tab" id="tag3">Data</a>
</li>
<!-- TODO: change to more logical view Login tablet/phone-->
<li class="hidden-desktop">
<nav class='btn-group'>
<!-- Title -->
<a class="btn dropdown-toggle" data-toggle="dropdown" href="#">
<i class="icon-user"></i> <span class="username">Login</span>
<span class="caret"></span>
</a>
<!-- TODO: fix this stuff for the iphone login... -->
<!-- Options -->
<ul id="user-access-options" class="dropdown-menu">
<li id='auth'><a href="javascript:fuse.authenticate(function(){});">Authenticate with Google Account</a>
</li>
<li class="divider"></li>
<li><a href="javascript:s3dbfu.showmodal('loginUN');void(0);">S3DB with User Name</a>
</li>
<li><a href="javascript:s3dbfu.showmodal('loginAK');void(0);">S3DB with API Key</a>
</li>
</ul>
</nav>
</li>
<!-- TODO: change to more logical view Choose Database Phone/Tablet-->
<li class="hidden-desktop">
<nav id="tableSwitch" class="btn-group">
<!-- Title -->
<button class="btn dropdown-toggle" data-toggle="dropdown" href="#">
<span class="curData"></span>
<span class="caret"></span>
</button>
<!-- Options Phone/Tablet-->
<ul class="dropdown-menu dbSelector">
</ul>
</nav>
</li>
</ul>
<!-- Login desktop-->
<nav class='btn-group pull-right visible-desktop'>
<!-- Title -->
<a class="btn dropdown-toggle" data-toggle="dropdown" href="#">
<i class="icon-user"></i> <span class="username">Login</span>
<span class="caret"></span>
</a>
<!-- Options -->
<ul id="user-access-options" class="dropdown-menu">
<!-- TODO: fix the following line to something reasonable... -->
<li id='authFT'><a>Authenticate with Google Account</a>
</li>
<li class="divider"></li>
<li><a href="javascript:s3dbfu.showmodal('loginUN');void(0);">S3DB with User Name</a>
</li>
<li><a href="javascript:s3dbfu.showmodal('loginAK');void(0);">S3DB with API Key</a>
</li>
</ul>
</nav>
<!-- Choose Database desktop-->
<nav id="tableSwitch" class="btn-group pull-right visible-desktop">
<!-- Title -->
<button class="btn dropdown-toggle pull-right" data-toggle="dropdown" href="#">
<span class="curData"></span>
<span class="caret"></span>
</button>
<!-- Options -->
<ul class="dropdown-menu dbSelector">
</ul>
</nav>
</div>
</div>
<script id="template-upload" type="text/x-tmpl">
{ %
for (var i = 0, file; file = o.files[i]; i++) { %
} < tr class = "template-upload fade" > < td class = "preview" > < span class = "fade" > < /span></td > < td class = "name" > < span > { %= file.name %
} < /span></td > < td class = "size" > < span > { %= o.formatFileSize(file.size) %
} < /span></td > { %
if (file.error) { %
} < td class = "error"
colspan = "2" > < span class = "label label-important" > { %= locale.fileupload.error %
} < /span> {%=locale.fileupload.errors[file.error] || file.error%}</td > { %
} else if (o.files.valid && !i) { %
} < td > < div class = "progress progress-success progress-striped active"
role = "progressbar"
aria - valuemin = "0"
aria - valuemax = "100"
aria - valuenow = "0" > < div class = "bar"
style = "width:0%;" > < /div></div > < /td>
<td class="start">
{% if (!o.options.autoUpload) { %}
<button class="btn btn-primary">
<i class="icon-upload icon-white"></i > < span > { %= locale.fileupload.start %
} < /span>
</button > { %
} %
} < /td>
{% } else { %}
<td colspan="2"></td > { %
} %
} < td class = "cancel" > { %
if (!i) { %
} < button class = "btn btn-warning" > < i class = "icon-ban-circle icon-white" > < /i>
<span>{%=locale.fileupload.cancel%}</span > < /button>
{% } %}
</td > < /tr>
{% } %}
</script>
<script id="template-download" type="text/x-tmpl">
{ %
for (var i = 0, file; file = o.files[i]; i++) { %
} < tr class = "template-download fade" > { %
if (file.error) { %
} < td > < /td>
<td class="name"><span>{%=file.file_name%}</span > < /td>
<td class="size"><span>{%=o.formatFileSize(parseInt(file.file_size))%}</span > < /td>
<td class="error" colspan="2"><span class="label label-important">{%=locale.fileupload.error%}</span > { %= locale.fileupload.errors[file.error] || file.error %
} < /td>
{% } else { %}
<td class="preview"></td > < td class = "name" > { %
if (file.download_url == '#') { %
} { %= file.value %
} { %
} else { %
} < a href = "{%=file.download_url%}"
title = "{%=file.file_name%}"
download = "{%=file.file_name%}"
target = "_blank" > { %= file.file_name %
} < /a>
{% } %}
</td > < td class = "size" > < span > { %= o.formatFileSize(isNaN(parseInt(file.file_size)) ? '' : parseInt(file.file_size)) %
} < /span></td > < td colspan = "2" > < /td>
{% } %}
<td class="delete">
<button class="btn btn-danger" data-type="DELETE" data-url="{%=s3dbfu.s3dburl()%}/multiupload.php ? key = { %= file.apikey %
} & statement_id = S { %= file.statement_id %
}
">
<i class="
icon - trash icon - white "></i>
<span>{%=locale.fileupload.destroy%}</span>
</button>
</td>
</tr>
{% } %}
</script>
</div>
</div>
<!-- Location of all the tabs in the document -->
<div class="row"><div class="offset1 span10"><div id="errors"></div></div></div>
<div id="main" class="container tab-content">
<!-- Home Tab -->
<div id="home" class="tab-pane active hero-unit">
<h1>Kinomic Data Analysis and Management</h1><br />
<p>University of Alabama at Birmingham
<br>Division of Informatics
<br>Department of Radiation Oncology
<br>Department of Pathology
<br><a href="http://ibl.github.io" target="_blank">Integrative Bioinformatics Laboratory</a>
<br /><br /> Source code avaliable at: <a href="https://github.com/kinome/kinome.github.io" target="_blank">github.com</a>
</p>
</div>
<!-- Quality control tab -->
<div class="tab-pane container" id="qualtityControl">
<h1>Quality Control</h1>
<!-- TODO: dynamically generate this -->
<well class="well span11" id='tempQCMessage'>Please select at least one file to add to analysis.</well>
</div>
<!-- File manager tab -->
<div class="tab-pane" id="fileUpload">
<div id="s3dbfu-msgs"></div>
<h1>Data Manager</h1>
<div id="homediv">
<div class="container">
<!-- Default display -->
<div class="well span11" id="defaultFile">Please login to either Google or S3DB and select appropriate database to save and display files.<br /></div>
<!-- Logged in display -->
<form id="fileupload" action="" method="POST" enctype="multipart/form-data">
<div class="row">
<!-- Side Navagation bar-->
<div class="span3">
<div class="well fileOpts" id='colBrowse'>
</div>
</div>
<!-- File Upload options panel - S3DB-->
<div class="span8">
<div class="well fileOpts" id="S3DBupload">
<h4>S3DB</h4>
<div class="row fileupload-buttonbar originRow">
<div class="span">
<!-- Add files -->
<span class="btn btn-success fileinput-button inputBut">
<span><i class="icon-plus icon-white"></i> Add files...</span>
<input type="file" name="files[]" class="hiddenBut" multiple></input>
</span>
<!-- start multiple upload -->
<button type="submit" class="btn btn-primary start"><i class="icon-upload icon-white"></i><span> Start upload</span></button>
<!-- Cancel Upload -->
<button type="reset" class="btn btn-warning cancel"><i class="icon-ban-circle icon-white"></i><span> Cancel upload</span>
</button>
</div>
<!-- Progress bar for upload -->
<div class="span5 fileupload-progress fade">
<div class="progress progress-success progress-striped active" role="progressbar" aria-valuemin="0" aria-valuemax="100">
<div class="bar" style="width:0%;"></div>
</div>
<div class="progress-extended"> </div>
</div>
</div>
<div class="fileupload-loading"></div>
<br />
<div class="row">
<div class="span">
<!-- Add files -->
<p class="currentAnaDisp"></p>
</div>
</div>
</div>
</div>
<!-- File Upload options panel - Fusion Tables-->
<div class="span9">
<div class="well fileOpts" id="fusionUpload">
<h4>Fusion Tables</h4>
<div class="row fileupload-buttonbar batch">
<div class="span">
<!-- Add files -->
<span class="btn btn-success inputBut">
<span><i class="icon-plus icon-white"></i> Add files...</span>
<input type="file" name="files[]" class="hiddenBut" id= "FUSEsub" multiple></input>
</span>
<!-- start multiple upload -->
<button type="hidden" class="btn btn-primary start" id="multUp"><i class="icon-upload icon-white"></i><span> Start upload</span></button>
</div>
</div>
<div class="row fileupload-buttonbar analysis">
<div class="span">
<!-- Add files -->
<span class="btn btn-success inputBut">
<span><i class="icon-plus icon-white"></i> New Analysis...</span>
<button class="hiddenBut" id= "NEWanalysis" multiple></input>
</span>
</div>
</div>
<br />
<div class="row">
<div class="span">
<!-- Add files -->
<p class="currentAnaDisp"></p>
</div>
</div>
</div>
</div>
</div>
<!-- Table -->
<div id=tableDiv class="row">
<div class="span12">
<table role="presentation" class="table table-striped" id="fileTable">
<tbody class="files" data-toggle="modal-gallery" data-target="#modal-gallery"></tbody>
</table>
</div>
</div>
</form>
</div>
</div>
</div>
<!-- Javascript placed at the end of the document so the pages load faster
-->
<div id="javascripts">
<!-- Major Packages -->
<script src="js/general/jquery-1.7.2.min.js"></script>
<script src="js/bootstrap/js/bootstrap.min.js"></script>
<!-- Support Packages -->
<script src="js/qualityControl/UIsupport/jquery.nouislider.js"></script>
<script src="js/qualityControl/UIsupport/jqmath-etc-0.2.0.min.js"></script>
<script src="https://apis.google.com/js/client.js?onload=OnLoadCallback"></script>
<script type="text/javascript" src="js/general/jsapi.js"></script>
<!-- My Packages -->
<script src="js/general/nameSpace.js"></script>
<script src="js/general/barcodeProto.js"></script>
<script src="js/general/workersPackage.js"></script>
<script src="js/general/amdjs_1.1.0.js" type="text/javascript"></script>
<script src="js/qualityControl/qcDA.js"></script>
<script src="js/fileManagement/fmDA.js"></script>
<script src="js/fileManagement/fmDA_FT.js"></script>
<script src="js/fileManagement/fmDA_s3db.js"></script>
<script src="js/fileManagement/fusionTables.js"></script>
<!-- <script src="js/fileManagement/fileUploadManager.js"></script> -->
<!-- UI -->
<script src="js/qualityControl/qcUI.js"></script>
<script src="js/fileManagement/fmUI.js"></script>
<!-- <script src="js/general/client.js" gapi_processed="true"></script> -->
<!-- S3DB/filemanagement form -->
<!-- <script src="js/fileManagement/s3dbInferface.js"></script>
<script src="https://raw.github.com/ebadedude/S3DB-File-Upload/master/js/jquery.ui.widget.js"
type="text/javascript"></script>
<script src="https://raw.github.com/ebadedude/S3DB-File-Upload/master/js/tmpl.min.js"
type="text/javascript"></script>
<script src="https://raw.github.com/ebadedude/S3DB-File-Upload/master/js/load-image.min.js"
type="text/javascript"></script>
<script src="https://raw.github.com/ebadedude/S3DB-File-Upload/master/js/jquery.iframe-transport.js"
type="text/javascript"></script>
<script src="https://raw.github.com/ebadedude/S3DB-File-Upload/master/js/jquery.fileupload.js"
type="text/javascript"></script>
<script src="https://raw.github.com/ebadedude/S3DB-File-Upload/master/js/jquery.fileupload-fp.js"
type="text/javascript"></script>
<script src="https://raw.github.com/ebadedude/S3DB-File-Upload/master/js/jquery.fileupload-ui.js"
type="text/javascript"></script>
<script src="https://raw.github.com/ebadedude/S3DB-File-Upload/master/js/locale.js"
type="text/javascript"></script>
<script src="https://raw.github.com/ebadedude/S3DB-File-Upload/f893461cf3f9e55fa2c12a5536abc17cb7ab962b/s3dbfu.js"
type="text/javascript"></script>
-->
<!-- Makes the input botton invisible -->
<style type="text/css">
.inputBut {
overflow:hidden;
position:relative;
cursor: pointer;
_cursor: pointer;
}
.hiddenBut {
z-index: 999;
line-height: 0;
font-size: 5px;
position: absolute;
top: 0px;
left: 0px;
height:100%;
width:100%;
opacity: 0;
filter: alpha(opacity=0);
-ms-filter:"alpha(opacity=0)";
cursor: pointer;
_cursor: pointer;
margin: -200;
padding:-200;
}
</style>
<script src="js/general/wasInline.js"></script>
</div>
</body>
</html>