extensions/net.sf.basedb.reggie/trunk/resources/sampleproc/rnaqc_bioanalyzer.jsp

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2922 12 Nov 14 nicklas 1 <%@ page
2922 12 Nov 14 nicklas 2   pageEncoding="UTF-8"
2922 12 Nov 14 nicklas 3   session="false"
2922 12 Nov 14 nicklas 4   import="net.sf.basedb.core.User"
2922 12 Nov 14 nicklas 5   import="net.sf.basedb.core.DbControl"
2922 12 Nov 14 nicklas 6   import="net.sf.basedb.core.SessionControl"
2922 12 Nov 14 nicklas 7   import="net.sf.basedb.core.Application"
2922 12 Nov 14 nicklas 8   import="net.sf.basedb.clients.web.Base"  
2922 12 Nov 14 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
2922 12 Nov 14 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
2922 12 Nov 14 nicklas 11 %>
2922 12 Nov 14 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
2922 12 Nov 14 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
2922 12 Nov 14 nicklas 14 <%
3976 26 May 16 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
2922 12 Nov 14 nicklas 16 final String ID = sc.getId();
2922 12 Nov 14 nicklas 17 final float scale = Base.getScale(sc);
2922 12 Nov 14 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
2922 12 Nov 14 nicklas 19 DbControl dc = null;
2922 12 Nov 14 nicklas 20 try
2922 12 Nov 14 nicklas 21 {
2922 12 Nov 14 nicklas 22   dc = sc.newDbControl();
2922 12 Nov 14 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
2922 12 Nov 14 nicklas 24 %>
2922 12 Nov 14 nicklas 25 <base:page type="default" >
2922 12 Nov 14 nicklas 26 <base:head 
2922 12 Nov 14 nicklas 27   scripts="~../reggie-2.js,~rnaqc_bioanalyzer.js" 
2922 12 Nov 14 nicklas 28   styles="path.css,~../css/reggie-2.css"
2922 12 Nov 14 nicklas 29 >
2922 12 Nov 14 nicklas 30 <style>
2922 12 Nov 14 nicklas 31 tr.highlight
2922 12 Nov 14 nicklas 32 {
3026 11 Dec 14 nicklas 33   border-top-width: 1px;
3026 11 Dec 14 nicklas 34   border-top-style: dotted;
2922 12 Nov 14 nicklas 35 }
2922 12 Nov 14 nicklas 36
2922 12 Nov 14 nicklas 37 #rnaQcTable
2922 12 Nov 14 nicklas 38 {
2922 12 Nov 14 nicklas 39   width: 100%; 
2922 12 Nov 14 nicklas 40   border-collapse: collapse;
2922 12 Nov 14 nicklas 41 }
2922 12 Nov 14 nicklas 42
2922 12 Nov 14 nicklas 43 #rnaQcTable th
2922 12 Nov 14 nicklas 44 {
2922 12 Nov 14 nicklas 45   padding: 4px 2px 4px 2px;
2922 12 Nov 14 nicklas 46 }
2922 12 Nov 14 nicklas 47
2922 12 Nov 14 nicklas 48 #rnaQcTable td
2922 12 Nov 14 nicklas 49 {
2922 12 Nov 14 nicklas 50   padding-top: 3px;
2922 12 Nov 14 nicklas 51   padding-bottom: 3px;
2922 12 Nov 14 nicklas 52   text-align: center;
2922 12 Nov 14 nicklas 53 }
2922 12 Nov 14 nicklas 54
2922 12 Nov 14 nicklas 55 #rnaQcTable .comments
2922 12 Nov 14 nicklas 56 {
2922 12 Nov 14 nicklas 57   text-align: left;
2922 12 Nov 14 nicklas 58   width: 50%;
2922 12 Nov 14 nicklas 59 }
2922 12 Nov 14 nicklas 60
2922 12 Nov 14 nicklas 61 #rnaQcTable .comments input
2922 12 Nov 14 nicklas 62 {
2922 12 Nov 14 nicklas 63   width: 95%;
2922 12 Nov 14 nicklas 64 }
2922 12 Nov 14 nicklas 65
2922 12 Nov 14 nicklas 66
2922 12 Nov 14 nicklas 67 </style>
2922 12 Nov 14 nicklas 68 </base:head>
2922 12 Nov 14 nicklas 69 <base:body>
2922 12 Nov 14 nicklas 70
2922 12 Nov 14 nicklas 71   <p:path><p:pathelement 
2922 12 Nov 14 nicklas 72     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
2922 12 Nov 14 nicklas 73     /><p:pathelement title="RNA quality control - Register RIN scores" 
2922 12 Nov 14 nicklas 74     /></p:path>
2922 12 Nov 14 nicklas 75
2922 12 Nov 14 nicklas 76   <div class="content">
2922 12 Nov 14 nicklas 77
2922 12 Nov 14 nicklas 78   <form name="reggie" id="wizard" class="wizard">
2922 12 Nov 14 nicklas 79   
2922 12 Nov 14 nicklas 80   <!-- 1. Select bioplate -->
2922 12 Nov 14 nicklas 81   <div class="step" id="step-1">
2922 12 Nov 14 nicklas 82     <div class="step-no">1</div>
2922 12 Nov 14 nicklas 83     <div class="step-title">Select RNA QC plate</div>
2922 12 Nov 14 nicklas 84     <div class="step-content">
2922 12 Nov 14 nicklas 85     
2922 12 Nov 14 nicklas 86       <table class="step-form">
2922 12 Nov 14 nicklas 87       <tr class="align-top">
2922 12 Nov 14 nicklas 88         <td class="prompt">Active bioplates</td>
2922 12 Nov 14 nicklas 89         <td class="input">
2922 12 Nov 14 nicklas 90           <select name="bioPlates" id="bioPlates"></select>
2922 12 Nov 14 nicklas 91         </td>
2922 12 Nov 14 nicklas 92         <td class="status" id="bioplates.status"></td>
2922 12 Nov 14 nicklas 93         <td class="help">
2922 12 Nov 14 nicklas 94           <span id="bioplates.message" class="message"></span>
2922 12 Nov 14 nicklas 95           Select the bioplate to register. The list contain RNAQC 
2922 12 Nov 14 nicklas 96           bioplates without quality score data (determined by 
2922 12 Nov 14 nicklas 97           absence of QCRunDate annotation).
2922 12 Nov 14 nicklas 98         </td>
2922 12 Nov 14 nicklas 99       </tr>
2922 12 Nov 14 nicklas 100       <tr class="align-top">
2922 12 Nov 14 nicklas 101         <td class="prompt">PDF file</td>
2922 12 Nov 14 nicklas 102         <td class="input">
2922 12 Nov 14 nicklas 103           <table style="width: 100%;">
2922 12 Nov 14 nicklas 104           <tr>
2922 12 Nov 14 nicklas 105           <td>
2922 12 Nov 14 nicklas 106             <input class="text" type="text" name="pdf" id="pdf" 
2922 12 Nov 14 nicklas 107               data-subtype="CALIPER_PDF" data-name-filter="%.pdf"
2922 12 Nov 14 nicklas 108               data-directory="/home/SCANB/RNAQC"
2922 12 Nov 14 nicklas 109             >
2922 12 Nov 14 nicklas 110           </td>
2922 12 Nov 14 nicklas 111           <td style="padding-left: 4px; width: 7em;">
2922 12 Nov 14 nicklas 112             <base:button 
2922 12 Nov 14 nicklas 113               title="Browse&hellip;"
2922 12 Nov 14 nicklas 114               id="pdf.btn"
2922 12 Nov 14 nicklas 115             />
2922 12 Nov 14 nicklas 116           </td>
2922 12 Nov 14 nicklas 117           </tr>
2922 12 Nov 14 nicklas 118           </table>    
2922 12 Nov 14 nicklas 119         </td>
2922 12 Nov 14 nicklas 120         <td class="status" id="pdf.status"></td>
2922 12 Nov 14 nicklas 121         <td class="help">
2922 12 Nov 14 nicklas 122           <span id="pdf.message" class="message"></span>
2922 12 Nov 14 nicklas 123           Select the PDF file that contains a printout with diagrams and other
2922 12 Nov 14 nicklas 124           useful documentation.
2922 12 Nov 14 nicklas 125         </td>
2922 12 Nov 14 nicklas 126       </tr>
2922 12 Nov 14 nicklas 127       <tr>
2922 12 Nov 14 nicklas 128         <td class="prompt">QC Run Date</td>
2922 12 Nov 14 nicklas 129         <td class="input">
2922 12 Nov 14 nicklas 130           <input type="text" name="qcRunDate" id="qcRunDate"
2922 12 Nov 14 nicklas 131             class="required auto-init" data-auto-init="focus-on-enter" data-next-focus="qcOperator"
2922 12 Nov 14 nicklas 132             style="width: 8em;" maxlength="10">
2922 12 Nov 14 nicklas 133             <base:icon 
2922 12 Nov 14 nicklas 134               id="qcRunDateCalendar"
2922 12 Nov 14 nicklas 135               subclass="auto-init"
2922 12 Nov 14 nicklas 136               data-auto-init="calendar"
2922 12 Nov 14 nicklas 137               data-textarea-id="qcRunDate"
2922 12 Nov 14 nicklas 138               data-date-format="yyyyMMdd"
2922 12 Nov 14 nicklas 139               data-title="QC run date"
2922 12 Nov 14 nicklas 140               image="calendar.png" 
2922 12 Nov 14 nicklas 141               tooltip="Select a date from a calendar" 
2922 12 Nov 14 nicklas 142               tabindex="-1"
2922 12 Nov 14 nicklas 143             />
2922 12 Nov 14 nicklas 144         </td>
2922 12 Nov 14 nicklas 145         <td class="status" id="qcRunDate.status"></td>
2922 12 Nov 14 nicklas 146         <td class="help">
2922 12 Nov 14 nicklas 147           <span id="qcRunDate.message" class="message"></span>
2922 12 Nov 14 nicklas 148           (YYYYMMDD or MMDD)
2922 12 Nov 14 nicklas 149         </td>
2922 12 Nov 14 nicklas 150       </tr>
2922 12 Nov 14 nicklas 151       <tr>
2922 12 Nov 14 nicklas 152         <td class="prompt">QC Operator</td>
2922 12 Nov 14 nicklas 153         <td class="input">
2922 12 Nov 14 nicklas 154           <input type="text" name="qcOperator" id="qcOperator" 
2922 12 Nov 14 nicklas 155             value="<%=HTML.encodeTags(user.getName()) %>" maxlength="255">
2922 12 Nov 14 nicklas 156         </td>
2922 12 Nov 14 nicklas 157         <td class="status" id="qcOperator.status"></td>
2922 12 Nov 14 nicklas 158         <td class="help">
2922 12 Nov 14 nicklas 159           <span id="qcOperator.message" class="message"></span>
2922 12 Nov 14 nicklas 160         </td>
2922 12 Nov 14 nicklas 161       </tr>
2922 12 Nov 14 nicklas 162       <tr class="align-top">
2922 12 Nov 14 nicklas 163         <td class="prompt">Comments</td>
2922 12 Nov 14 nicklas 164         <td class="input">
2922 12 Nov 14 nicklas 165           <textarea name="comments" id="comments" rows="4"></textarea>
2922 12 Nov 14 nicklas 166         </td>
2922 12 Nov 14 nicklas 167         <td class="status" id="comments.status"></td>
2922 12 Nov 14 nicklas 168         <td class="help">
2922 12 Nov 14 nicklas 169           <span id="comments.message" class="message"></span>
2922 12 Nov 14 nicklas 170         </td>
2922 12 Nov 14 nicklas 171       </tr>
2922 12 Nov 14 nicklas 172       </table>
2922 12 Nov 14 nicklas 173     </div>
2922 12 Nov 14 nicklas 174   </div>
2922 12 Nov 14 nicklas 175   
2922 12 Nov 14 nicklas 176   <div class="step" id="step-2">
2922 12 Nov 14 nicklas 177     <div class="step-no">2</div>
2922 12 Nov 14 nicklas 178     <div class="step-title">Register RIN values</div>
2922 12 Nov 14 nicklas 179     <div class="step-content">
2922 12 Nov 14 nicklas 180
2922 12 Nov 14 nicklas 181       <div id="rnaQc"></div>
2922 12 Nov 14 nicklas 182     </div>
2922 12 Nov 14 nicklas 183   </div>
2922 12 Nov 14 nicklas 184   
2922 12 Nov 14 nicklas 185   <div id="wizard-status"></div>
2922 12 Nov 14 nicklas 186   
2922 12 Nov 14 nicklas 187   <table class="navigation" id="navigation">
2922 12 Nov 14 nicklas 188   <tr>
2922 12 Nov 14 nicklas 189     <td><base:button id="gocancel" title="Cancel" /></td>
2922 12 Nov 14 nicklas 190     <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
2922 12 Nov 14 nicklas 191     <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
2922 12 Nov 14 nicklas 192     <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
2922 12 Nov 14 nicklas 193     <td id="gonext-message" class="message"></td>
2922 12 Nov 14 nicklas 194   </tr>
2922 12 Nov 14 nicklas 195   </table>
2922 12 Nov 14 nicklas 196
2922 12 Nov 14 nicklas 197   </form>
2922 12 Nov 14 nicklas 198   </div>
2922 12 Nov 14 nicklas 199   
2922 12 Nov 14 nicklas 200 </base:body>
2922 12 Nov 14 nicklas 201 </base:page>
2922 12 Nov 14 nicklas 202 <%
2922 12 Nov 14 nicklas 203 }
2922 12 Nov 14 nicklas 204 finally
2922 12 Nov 14 nicklas 205 {
2922 12 Nov 14 nicklas 206   if (dc != null) dc.close();
2922 12 Nov 14 nicklas 207 }
2922 12 Nov 14 nicklas 208 %>

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