extensions/net.sf.basedb.reggie/trunk/resources/sequencing/sequencing_ended.jsp

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2197 14 Jan 14 nicklas 1 <%@ page
2197 14 Jan 14 nicklas 2   pageEncoding="UTF-8"
2197 14 Jan 14 nicklas 3   session="false"
2197 14 Jan 14 nicklas 4   import="net.sf.basedb.core.User"
2197 14 Jan 14 nicklas 5   import="net.sf.basedb.core.DbControl"
2197 14 Jan 14 nicklas 6   import="net.sf.basedb.core.SessionControl"
2197 14 Jan 14 nicklas 7   import="net.sf.basedb.core.Application"
2197 14 Jan 14 nicklas 8   import="net.sf.basedb.clients.web.Base"  
2197 14 Jan 14 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
2197 14 Jan 14 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
2197 14 Jan 14 nicklas 11 %>
2197 14 Jan 14 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
2197 14 Jan 14 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
2197 14 Jan 14 nicklas 14 <%
3976 26 May 16 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
2197 14 Jan 14 nicklas 16 final String ID = sc.getId();
2197 14 Jan 14 nicklas 17 final float scale = Base.getScale(sc);
2197 14 Jan 14 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
5471 05 Jun 19 nicklas 19 final String pipeline = request.getParameter("pipeline");
2197 14 Jan 14 nicklas 20 DbControl dc = null;
2197 14 Jan 14 nicklas 21 try
2197 14 Jan 14 nicklas 22 {
2197 14 Jan 14 nicklas 23   dc = sc.newDbControl();
2197 14 Jan 14 nicklas 24   final User user = User.getById(dc, sc.getLoggedInUserId());
2197 14 Jan 14 nicklas 25 %>
2197 14 Jan 14 nicklas 26 <base:page type="default" >
2648 10 Sep 14 nicklas 27 <base:head 
2648 10 Sep 14 nicklas 28   scripts="~../reggie-2.js,~sequencing_ended.js" 
2648 10 Sep 14 nicklas 29   styles="path.css,~../css/reggie-2.css"
2648 10 Sep 14 nicklas 30 />
2648 10 Sep 14 nicklas 31 <base:body>
2197 14 Jan 14 nicklas 32
2197 14 Jan 14 nicklas 33   <p:path><p:pathelement 
2197 14 Jan 14 nicklas 34     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
2197 14 Jan 14 nicklas 35     /><p:pathelement title="Register sequencing ended" 
2197 14 Jan 14 nicklas 36     /></p:path>
5471 05 Jun 19 nicklas 37     
5471 05 Jun 19 nicklas 38   <div id="page-data" class="datacontainer"
5471 05 Jun 19 nicklas 39     data-pipeline="<%=HTML.encodeTags(pipeline)%>"
5471 05 Jun 19 nicklas 40   ></div>
2197 14 Jan 14 nicklas 41
2197 14 Jan 14 nicklas 42   <div class="content">
2648 10 Sep 14 nicklas 43   <form name="reggie" id="wizard" class="wizard">
2197 14 Jan 14 nicklas 44
2648 10 Sep 14 nicklas 45   <div class="step" id="step-1">
2648 10 Sep 14 nicklas 46     <div class="step-no">1</div>
2648 10 Sep 14 nicklas 47     <div class="step-title">Select sequencing run</div>
2648 10 Sep 14 nicklas 48     <div class="step-content">
2197 14 Jan 14 nicklas 49   
2648 10 Sep 14 nicklas 50       <table class="step-form">
2648 10 Sep 14 nicklas 51       <tr>
2197 14 Jan 14 nicklas 52         <td class="prompt">Sequencing run</td>
2648 10 Sep 14 nicklas 53         <td class="input">
3632 30 Nov 15 nicklas 54           <select name="seqRuns" id="seqRuns" class="required"></select>
2197 14 Jan 14 nicklas 55         </td>
2197 14 Jan 14 nicklas 56         <td class="status" id="seqRuns.status"></td>
2648 10 Sep 14 nicklas 57         <td class="help">
2648 10 Sep 14 nicklas 58           <span id="seqRuns.message" class="message"></span>
2198 15 Jan 14 nicklas 59           Select the sequencing run that has ended.
2197 14 Jan 14 nicklas 60         </td>
2197 14 Jan 14 nicklas 61       </tr>
3718 22 Jan 16 nicklas 62       <tbody class="info-section" id="autoAnalyzeSection" style="display: none;">
3718 22 Jan 16 nicklas 63       <tr>
3718 22 Jan 16 nicklas 64         <td class="prompt">Job status</td>
3718 22 Jan 16 nicklas 65         <td class="info" id="autoAnalyze">
3718 22 Jan 16 nicklas 66         </td>
3718 22 Jan 16 nicklas 67         <td class="status" id="autoAnalyze.status"></td>
3718 22 Jan 16 nicklas 68         <td class="help">
3718 22 Jan 16 nicklas 69           <span id="autoAnalyze.message" class="message"></span>
3718 22 Jan 16 nicklas 70         </td>
3718 22 Jan 16 nicklas 71       </tr>
3718 22 Jan 16 nicklas 72       </tbody>
3632 30 Nov 15 nicklas 73       <tr class="align-top">
3632 30 Nov 15 nicklas 74         <td class="prompt">RunParameters.xml</td>
3632 30 Nov 15 nicklas 75         <td class="input">
3632 30 Nov 15 nicklas 76           <table style="width: 100%;">
3632 30 Nov 15 nicklas 77           <tr>
3632 30 Nov 15 nicklas 78             <td style="width: 90%;">
3632 30 Nov 15 nicklas 79               <select name="clusters" id="clusters"></select>
3632 30 Nov 15 nicklas 80             </td>
3632 30 Nov 15 nicklas 81             <td>
3632 30 Nov 15 nicklas 82               <base:button id="searchRunArchive" title="Search..." 
3632 30 Nov 15 nicklas 83                 image="search.png" />
3632 30 Nov 15 nicklas 84             </td>
3632 30 Nov 15 nicklas 85           </tr>
3632 30 Nov 15 nicklas 86           </table>
3632 30 Nov 15 nicklas 87           - or -
3632 30 Nov 15 nicklas 88           <input type="file" name="runParametersXml" id="runParametersXml" style="width: 95%;">
3632 30 Nov 15 nicklas 89         </td>
3632 30 Nov 15 nicklas 90         <td class="status" id="runParametersXml.status"></td>
3632 30 Nov 15 nicklas 91         <td class="help">
3632 30 Nov 15 nicklas 92           <span id="runParametersXml.message" class="message"></span>
3632 30 Nov 15 nicklas 93           Search the run-archive for the <b>RunParameters.xml</b> 
3632 30 Nov 15 nicklas 94           created for the selected sequencing run or browse for
3632 30 Nov 15 nicklas 95           the file on the local file system.
3632 30 Nov 15 nicklas 96         </td>
3632 30 Nov 15 nicklas 97       </tr>
3632 30 Nov 15 nicklas 98       
2648 10 Sep 14 nicklas 99       <tbody class="info-section">
3632 30 Nov 15 nicklas 100       <tr class="section-header">
3632 30 Nov 15 nicklas 101         <td id="flowCellName" colspan="3">Flow cell information</td>
2198 15 Jan 14 nicklas 102         <td class="help"></td>
2198 15 Jan 14 nicklas 103       </tr>
2648 10 Sep 14 nicklas 104       <tr>
2648 10 Sep 14 nicklas 105         <td class="prompt">Flow cell type</td>
2648 10 Sep 14 nicklas 106         <td class="info" id="flowCellType"></td>
2412 09 May 14 nicklas 107         <td class="status"></td>
2412 09 May 14 nicklas 108         <td class="help"></td>
2412 09 May 14 nicklas 109       </tr>
2648 10 Sep 14 nicklas 110       <tr>
3632 30 Nov 15 nicklas 111         <td class="prompt">Barcode</td>
3632 30 Nov 15 nicklas 112         <td class="info" id="externalId"></td>
3632 30 Nov 15 nicklas 113         <td class="status" id="externalId.status"></td>
3632 30 Nov 15 nicklas 114         <td class="help">
3632 30 Nov 15 nicklas 115           <span id="externalId.message" class="message"></span>
3632 30 Nov 15 nicklas 116         </td>
2198 15 Jan 14 nicklas 117       </tr>
2648 10 Sep 14 nicklas 118       <tr>
2648 10 Sep 14 nicklas 119         <td class="prompt">Pools</td>
2648 10 Sep 14 nicklas 120         <td class="info" id="pools"></td>
2236 20 Feb 14 nicklas 121         <td class="status"></td>
2236 20 Feb 14 nicklas 122         <td class="help"></td>
2236 20 Feb 14 nicklas 123       </tr>
2648 10 Sep 14 nicklas 124       <tr>
5473 05 Jun 19 nicklas 125         <td class="prompt">LibPlates</td>
5473 05 Jun 19 nicklas 126         <td class="info" id="libPlates"></td>
2236 20 Feb 14 nicklas 127         <td class="status"></td>
2236 20 Feb 14 nicklas 128         <td class="help"></td>
2236 20 Feb 14 nicklas 129       </tr>
3632 30 Nov 15 nicklas 130       <tr class="section-header">
3632 30 Nov 15 nicklas 131         <td colspan="3">Sequencing information</td>
2230 17 Feb 14 nicklas 132         <td class="help"></td>
2230 17 Feb 14 nicklas 133       </tr>
2648 10 Sep 14 nicklas 134       <tr>
3632 30 Nov 15 nicklas 135         <td class="prompt">Start date</td>
3632 30 Nov 15 nicklas 136         <td class="info" id="startDate"></td>
3632 30 Nov 15 nicklas 137         <td class="status" id="startDate.status"></td>
3632 30 Nov 15 nicklas 138         <td class="help">
3632 30 Nov 15 nicklas 139           <span id="startDate.message" class="message"></span>
2225 13 Feb 14 nicklas 140         </td>
3632 30 Nov 15 nicklas 141       </tr>
3632 30 Nov 15 nicklas 142       <tr>
3632 30 Nov 15 nicklas 143         <td class="prompt">Sequencing cycles</td>
3632 30 Nov 15 nicklas 144         <td class="info" id="sequencingCycles"></td>
3632 30 Nov 15 nicklas 145         <td class="status" id="sequencingCycles.status"></td>
2648 10 Sep 14 nicklas 146         <td class="help">
3632 30 Nov 15 nicklas 147           <span id="sequencingCycles.message" class="message"></span>
2225 13 Feb 14 nicklas 148         </td>
2225 13 Feb 14 nicklas 149       </tr>
2648 10 Sep 14 nicklas 150       <tr>
3632 30 Nov 15 nicklas 151         <td class="prompt">Sequencer</td>
3632 30 Nov 15 nicklas 152         <td class="info" id="sequencer"></td>
3632 30 Nov 15 nicklas 153         <td class="status" id="sequencer.status"></td>
3632 30 Nov 15 nicklas 154         <td class="help">
3632 30 Nov 15 nicklas 155           <span id="sequencer.message" class="message"></span>
2197 14 Jan 14 nicklas 156         </td>
3632 30 Nov 15 nicklas 157       </tr>
3632 30 Nov 15 nicklas 158       <tr>
3632 30 Nov 15 nicklas 159         <td class="prompt">Position</td>
3632 30 Nov 15 nicklas 160         <td class="info" id="position"></td>
3632 30 Nov 15 nicklas 161         <td class="status" id="position.status"></td>
2648 10 Sep 14 nicklas 162         <td class="help">
3632 30 Nov 15 nicklas 163           <span id="position.message" class="message"></span>
2648 10 Sep 14 nicklas 164         </td>
2197 14 Jan 14 nicklas 165       </tr>
2648 10 Sep 14 nicklas 166       <tr>
3632 30 Nov 15 nicklas 167         <td class="prompt">Data folder</td>
3632 30 Nov 15 nicklas 168         <td class="info" id="dataFolder"></td>
3632 30 Nov 15 nicklas 169         <td class="status"></td>
3632 30 Nov 15 nicklas 170         <td class="help"></td>
3632 30 Nov 15 nicklas 171       </tr>
3632 30 Nov 15 nicklas 172       <tr>
3632 30 Nov 15 nicklas 173         <td class="prompt">Experiment</td>
3632 30 Nov 15 nicklas 174         <td class="info" id="experimentName"></td>
3632 30 Nov 15 nicklas 175         <td class="status"></td>
3632 30 Nov 15 nicklas 176         <td class="help"></td>
3632 30 Nov 15 nicklas 177       </tr>
3632 30 Nov 15 nicklas 178       <tr>
3632 30 Nov 15 nicklas 179         <td class="prompt">RunID</td>
3632 30 Nov 15 nicklas 180         <td class="info" id="runId"></td>
3632 30 Nov 15 nicklas 181         <td class="status"></td>
3632 30 Nov 15 nicklas 182         <td class="help"></td>
3632 30 Nov 15 nicklas 183       </tr>
3632 30 Nov 15 nicklas 184       <tr>
3632 30 Nov 15 nicklas 185         <td class="prompt">Run number</td>
3632 30 Nov 15 nicklas 186         <td class="info" id="runNumber"></td>
3632 30 Nov 15 nicklas 187         <td class="status"></td>
3632 30 Nov 15 nicklas 188         <td class="help"></td>
3632 30 Nov 15 nicklas 189       </tr>
3632 30 Nov 15 nicklas 190       </tbody>
3632 30 Nov 15 nicklas 191
3632 30 Nov 15 nicklas 192       <tr>
2197 14 Jan 14 nicklas 193         <td class="prompt">End date</td>
2648 10 Sep 14 nicklas 194         <td class="input">
2648 10 Sep 14 nicklas 195           <input type="text" name="endDate" id="endDate"
2648 10 Sep 14 nicklas 196             class="auto-init required" data-auto-init="focus-on-enter" data-next-focus="endTime"
2648 10 Sep 14 nicklas 197             style="width: 12em;" maxlength="10">
2648 10 Sep 14 nicklas 198           Time <input type="text" class="required" name="endTime" id="endTime"
2648 10 Sep 14 nicklas 199             class="auto-init" data-auto-init="focus-on-enter" data-next-focus="sequencingComments"
2648 10 Sep 14 nicklas 200             style="width: 6em;" maxlength="5">
2648 10 Sep 14 nicklas 201         </td>
2197 14 Jan 14 nicklas 202         <td class="status" id="endDate.status"></td>
2648 10 Sep 14 nicklas 203         <td class="help">
2648 10 Sep 14 nicklas 204           <span id="endDate.message" class="message"></span>
2648 10 Sep 14 nicklas 205           Date+time sequencing ended (YYYYMMDD, HHMM)
2648 10 Sep 14 nicklas 206         </td>
2197 14 Jan 14 nicklas 207       </tr>
2197 14 Jan 14 nicklas 208       
2648 10 Sep 14 nicklas 209       <tr class="align-top">
2197 14 Jan 14 nicklas 210         <td class="prompt">Comments</td>
2651 10 Sep 14 nicklas 211         <td class="input">
3632 30 Nov 15 nicklas 212           <textarea name="comments" id="comments" rows="6"></textarea></td>
3632 30 Nov 15 nicklas 213         <td class="status" id="comments.status"></td>
2648 10 Sep 14 nicklas 214         <td class="help">
3632 30 Nov 15 nicklas 215           <span id="comments.message" class="message"></span>
2648 10 Sep 14 nicklas 216           Comments about the sequencing.
2648 10 Sep 14 nicklas 217         </td>
2197 14 Jan 14 nicklas 218       </tr>
3632 30 Nov 15 nicklas 219       
2197 14 Jan 14 nicklas 220       </table>
2648 10 Sep 14 nicklas 221     </div>
2197 14 Jan 14 nicklas 222   </div>
2197 14 Jan 14 nicklas 223     
2648 10 Sep 14 nicklas 224   <div id="wizard-status"></div>
2197 14 Jan 14 nicklas 225   
2648 10 Sep 14 nicklas 226   <table class="navigation" id="navigation">
2648 10 Sep 14 nicklas 227   <tr>
2648 10 Sep 14 nicklas 228     <td><base:button id="gocancel" title="Cancel" /></td>
2648 10 Sep 14 nicklas 229     <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
2648 10 Sep 14 nicklas 230     <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
2648 10 Sep 14 nicklas 231     <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
2648 10 Sep 14 nicklas 232     <td id="gonext-message" class="message"></td>
2648 10 Sep 14 nicklas 233   </tr>
2197 14 Jan 14 nicklas 234   </table>
2197 14 Jan 14 nicklas 235   
2197 14 Jan 14 nicklas 236   </form>
2197 14 Jan 14 nicklas 237   </div>
2197 14 Jan 14 nicklas 238   
2197 14 Jan 14 nicklas 239 </base:body>
2197 14 Jan 14 nicklas 240 </base:page>
2197 14 Jan 14 nicklas 241 <%
2197 14 Jan 14 nicklas 242 }
2197 14 Jan 14 nicklas 243 finally
2197 14 Jan 14 nicklas 244 {
2197 14 Jan 14 nicklas 245   if (dc != null) dc.close();
2197 14 Jan 14 nicklas 246 }
2197 14 Jan 14 nicklas 247 %>

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