extensions/net.sf.basedb.reggie/trunk/resources/dnaseq-analysis/pon_build.jsp

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7395 06 Nov 23 nicklas 1 <%@ page
7395 06 Nov 23 nicklas 2   pageEncoding="UTF-8"
7395 06 Nov 23 nicklas 3   session="false"
7395 06 Nov 23 nicklas 4   import="net.sf.basedb.core.User"
7395 06 Nov 23 nicklas 5   import="net.sf.basedb.core.DbControl"
7395 06 Nov 23 nicklas 6   import="net.sf.basedb.core.SessionControl"
7395 06 Nov 23 nicklas 7   import="net.sf.basedb.core.Application"
7395 06 Nov 23 nicklas 8   import="net.sf.basedb.clients.web.Base"  
7395 06 Nov 23 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
7395 06 Nov 23 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
7395 06 Nov 23 nicklas 11 %>
7395 06 Nov 23 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
7395 06 Nov 23 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
7395 06 Nov 23 nicklas 14 <%
7395 06 Nov 23 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
7395 06 Nov 23 nicklas 16 final String ID = sc.getId();
7395 06 Nov 23 nicklas 17 final float scale = Base.getScale(sc);
7395 06 Nov 23 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
7395 06 Nov 23 nicklas 19 DbControl dc = null;
7395 06 Nov 23 nicklas 20 try
7395 06 Nov 23 nicklas 21 {
7395 06 Nov 23 nicklas 22   dc = sc.newDbControl();
7395 06 Nov 23 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
7395 06 Nov 23 nicklas 24 %>
7395 06 Nov 23 nicklas 25 <base:page type="default" >
7395 06 Nov 23 nicklas 26 <base:head 
7395 06 Nov 23 nicklas 27   scripts="~../reggie-2.js,~pon_build.js" 
7395 06 Nov 23 nicklas 28   styles="path.css,~../css/reggie-2.css"
7395 06 Nov 23 nicklas 29 />
7395 06 Nov 23 nicklas 30 <base:body>
7395 06 Nov 23 nicklas 31
7395 06 Nov 23 nicklas 32   <p:path><p:pathelement 
7395 06 Nov 23 nicklas 33     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
7395 06 Nov 23 nicklas 34     /><p:pathelement title="Panel-of-normals: Build panel" 
7395 06 Nov 23 nicklas 35     /></p:path>
7395 06 Nov 23 nicklas 36
7395 06 Nov 23 nicklas 37   <div class="content">
7395 06 Nov 23 nicklas 38   <form name="reggie" id="wizard" class="wizard">
7395 06 Nov 23 nicklas 39
7395 06 Nov 23 nicklas 40   <div class="step" id="step-1">
7395 06 Nov 23 nicklas 41     <div class="step-no">1</div>
7395 06 Nov 23 nicklas 42     <div class="step-title">Select list with panel-of-normals</div>
7395 06 Nov 23 nicklas 43     <div class="step-content">
7395 06 Nov 23 nicklas 44     
7395 06 Nov 23 nicklas 45       <table class="step-form">
7395 06 Nov 23 nicklas 46       <tr class="align-top">
7395 06 Nov 23 nicklas 47         <td class="prompt">Item list</td>
7395 06 Nov 23 nicklas 48         <td class="input">
7395 06 Nov 23 nicklas 49         
7395 06 Nov 23 nicklas 50           <table style="width: 100%;">
7395 06 Nov 23 nicklas 51           <tr>
7395 06 Nov 23 nicklas 52           <td>
7395 06 Nov 23 nicklas 53             <select class="required" name="itemList" id="itemList"></select>
7395 06 Nov 23 nicklas 54           </td>
7395 06 Nov 23 nicklas 55           <td style="padding-left: 4px; width: 7em;">
7395 06 Nov 23 nicklas 56             <base:button title="Select&hellip;" id="btnSelectList" />
7395 06 Nov 23 nicklas 57           </td>
7395 06 Nov 23 nicklas 58           </tr>
7395 06 Nov 23 nicklas 59           </table>
7395 06 Nov 23 nicklas 60
7395 06 Nov 23 nicklas 61         </td>
7395 06 Nov 23 nicklas 62         <td class="status" id="itemList.status"></td>
7395 06 Nov 23 nicklas 63         <td class="help"><span id="itemList.message" class="message"></span>
7395 06 Nov 23 nicklas 64           Select a list containing the panel-of-normals that should be used to
7395 06 Nov 23 nicklas 65           build the database. All results must be confirmed before they can be used.
7395 06 Nov 23 nicklas 66         </td>
7395 06 Nov 23 nicklas 67       </tr>
7442 17 Nov 23 nicklas 68       <tr>
7442 17 Nov 23 nicklas 69         <td class="prompt">External operator</td>
7442 17 Nov 23 nicklas 70         <td class="input"><span id="externalOperator"></span></td>
7442 17 Nov 23 nicklas 71         <td class="status"></td>
7442 17 Nov 23 nicklas 72         <td class="help">
7442 17 Nov 23 nicklas 73           All items in the panel-of-normals should be from the same operator.
7442 17 Nov 23 nicklas 74         </td>
7442 17 Nov 23 nicklas 75       </tr>
7395 06 Nov 23 nicklas 76       </table>
7395 06 Nov 23 nicklas 77     </div>
7395 06 Nov 23 nicklas 78   </div>
7395 06 Nov 23 nicklas 79   
7395 06 Nov 23 nicklas 80   
7395 06 Nov 23 nicklas 81   <div class="step" id="step-2">
7395 06 Nov 23 nicklas 82     <div class="step-no">2</div>
7395 06 Nov 23 nicklas 83     <div class="step-title">Parameters</div>
7395 06 Nov 23 nicklas 84     <div class="step-content">
7395 06 Nov 23 nicklas 85
7395 06 Nov 23 nicklas 86       <table class="step-form">
7395 06 Nov 23 nicklas 87       <tbody>
7395 06 Nov 23 nicklas 88         <tr class="section-header">
7395 06 Nov 23 nicklas 89           <td colspan="4">Job scheduler</td>
7395 06 Nov 23 nicklas 90         </tr>
7395 06 Nov 23 nicklas 91         <tr>
7395 06 Nov 23 nicklas 92           <td class="subprompt">Cluster</td>
7395 06 Nov 23 nicklas 93           <td class="input">
7395 06 Nov 23 nicklas 94             <select name="clusters" id="clusters" class="required"></select></td>
7395 06 Nov 23 nicklas 95           <td class="status" id="clusters.status"></td>
7395 06 Nov 23 nicklas 96           <td class="help">
7395 06 Nov 23 nicklas 97             <span id="clusters.message" class="message"></span>
7395 06 Nov 23 nicklas 98             Select the cluster to use for running the software.
7395 06 Nov 23 nicklas 99           </td>
7395 06 Nov 23 nicklas 100         </tr>
7395 06 Nov 23 nicklas 101         <tr id="job-priority" style="display: none;">
7395 06 Nov 23 nicklas 102           <td class="subprompt">Job priority</td>
7395 06 Nov 23 nicklas 103           <td class="input">
7395 06 Nov 23 nicklas 104             <select name="priority" id="priority"></select>
7395 06 Nov 23 nicklas 105           </td>
7395 06 Nov 23 nicklas 106           <td class="status" id="priority.status"></td>
7395 06 Nov 23 nicklas 107           <td class="help">
7395 06 Nov 23 nicklas 108             <span id="priority.message" class="message"></span>
7395 06 Nov 23 nicklas 109             Select the priority of the job.
7395 06 Nov 23 nicklas 110           </td>
7395 06 Nov 23 nicklas 111         </tr>
7395 06 Nov 23 nicklas 112         <tr id="job-partition" style="display: none;">
7395 06 Nov 23 nicklas 113           <td class="subprompt">Job partition</td>
7395 06 Nov 23 nicklas 114           <td class="input">
7395 06 Nov 23 nicklas 115             <select name="partition" id="partition"></select>
7395 06 Nov 23 nicklas 116           </td>
7395 06 Nov 23 nicklas 117           <td class="status" id="partition.status"></td>
7395 06 Nov 23 nicklas 118           <td class="help">
7395 06 Nov 23 nicklas 119             <span id="partition.message" class="message"></span>
7395 06 Nov 23 nicklas 120             Select the partition/queue that the job should be submitted to.
7395 06 Nov 23 nicklas 121           </td>
7395 06 Nov 23 nicklas 122         </tr>
7395 06 Nov 23 nicklas 123         </tbody>
7395 06 Nov 23 nicklas 124         <tbody class="info-section">
7395 06 Nov 23 nicklas 125           <tr class="align-top">
7395 06 Nov 23 nicklas 126             <td class="subprompt">Job options</td>
7395 06 Nov 23 nicklas 127             <td class="info input">
7395 06 Nov 23 nicklas 128               <div id="submitOptions" class="item-description code"></div>
7395 06 Nov 23 nicklas 129               <textarea id="submitOptionsOverride" name="submitOptionsOverride" rows="4" style="display: none;"></textarea>
7395 06 Nov 23 nicklas 130             </td>
7395 06 Nov 23 nicklas 131             <td class="status" id="submitOptions.status">
7395 06 Nov 23 nicklas 132               <input type="checkbox" id="override" name="override" title="Override the default options" disabled>
7395 06 Nov 23 nicklas 133             </td>
7395 06 Nov 23 nicklas 134             <td class="help">
7395 06 Nov 23 nicklas 135               Parameters are configured in the &lt;wgs-variant-call&gt;/&lt;submit&gt; 
7395 06 Nov 23 nicklas 136               section in reggie-config.xml. Select the checkbox to manually 
7395 06 Nov 23 nicklas 137               override the default options.
7395 06 Nov 23 nicklas 138             </td>
7395 06 Nov 23 nicklas 139           </tr>
7395 06 Nov 23 nicklas 140         </tbody>
7395 06 Nov 23 nicklas 141         <tbody>
7395 06 Nov 23 nicklas 142         <tr>
7395 06 Nov 23 nicklas 143           <td class="subprompt">Debug</td>
7395 06 Nov 23 nicklas 144           <td class="input"><input type="checkbox" name="debug"></td>
7395 06 Nov 23 nicklas 145           <td class="status" id="debug.status"></td>
7395 06 Nov 23 nicklas 146           <td class="help">
7395 06 Nov 23 nicklas 147             <span id="debug.message" class="message"></span>
7395 06 Nov 23 nicklas 148             When running in debug mode temporary files are not removed from the
7395 06 Nov 23 nicklas 149             cluster node.
7395 06 Nov 23 nicklas 150           </td>
7395 06 Nov 23 nicklas 151         </tr>
7395 06 Nov 23 nicklas 152       </tbody>
7395 06 Nov 23 nicklas 153       </table>
7395 06 Nov 23 nicklas 154     </div>
7395 06 Nov 23 nicklas 155   </div>
7395 06 Nov 23 nicklas 156     
7395 06 Nov 23 nicklas 157     <div id="wizard-status"></div>
7395 06 Nov 23 nicklas 158     <div id="wizard-progress"></div>
7395 06 Nov 23 nicklas 159   
7395 06 Nov 23 nicklas 160     <table class="navigation" id="navigation">
7395 06 Nov 23 nicklas 161     <tr>
7395 06 Nov 23 nicklas 162       <td><base:button id="gocancel" title="Cancel" /></td>
7395 06 Nov 23 nicklas 163       <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
7395 06 Nov 23 nicklas 164       <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
7395 06 Nov 23 nicklas 165       <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
7395 06 Nov 23 nicklas 166       <td id="gonext-message" class="message"></td>
7395 06 Nov 23 nicklas 167     </tr>
7395 06 Nov 23 nicklas 168     </table>
7395 06 Nov 23 nicklas 169   
7395 06 Nov 23 nicklas 170   </form>
7395 06 Nov 23 nicklas 171   </div>
7395 06 Nov 23 nicklas 172   
7395 06 Nov 23 nicklas 173 </base:body>
7395 06 Nov 23 nicklas 174 </base:page>
7395 06 Nov 23 nicklas 175 <%
7395 06 Nov 23 nicklas 176 }
7395 06 Nov 23 nicklas 177 finally
7395 06 Nov 23 nicklas 178 {
7395 06 Nov 23 nicklas 179   if (dc != null) dc.close();
7395 06 Nov 23 nicklas 180 }
7395 06 Nov 23 nicklas 181 %>

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