extensions/net.sf.basedb.reggie/trunk/resources/analysis/hisat_confirm.jsp

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4595 27 Sep 17 nicklas 1 <%@ page
4595 27 Sep 17 nicklas 2   pageEncoding="UTF-8"
4595 27 Sep 17 nicklas 3   session="false"
4595 27 Sep 17 nicklas 4   import="net.sf.basedb.core.User"
4595 27 Sep 17 nicklas 5   import="net.sf.basedb.core.DbControl"
4595 27 Sep 17 nicklas 6   import="net.sf.basedb.core.SessionControl"
4595 27 Sep 17 nicklas 7   import="net.sf.basedb.core.Application"
4595 27 Sep 17 nicklas 8   import="net.sf.basedb.clients.web.Base"  
4595 27 Sep 17 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
4595 27 Sep 17 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
4595 27 Sep 17 nicklas 11 %>
4595 27 Sep 17 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
4595 27 Sep 17 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
4595 27 Sep 17 nicklas 14 <%
4595 27 Sep 17 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
4595 27 Sep 17 nicklas 16 final String ID = sc.getId();
4595 27 Sep 17 nicklas 17 final float scale = Base.getScale(sc);
4595 27 Sep 17 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
4595 27 Sep 17 nicklas 19 DbControl dc = null;
4595 27 Sep 17 nicklas 20 try
4595 27 Sep 17 nicklas 21 {
4595 27 Sep 17 nicklas 22   dc = sc.newDbControl();
4595 27 Sep 17 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
4595 27 Sep 17 nicklas 24 %>
4595 27 Sep 17 nicklas 25 <base:page type="default" >
4595 27 Sep 17 nicklas 26 <base:head 
4595 27 Sep 17 nicklas 27   scripts="~../reggie-2.js,~hisat_confirm.js" 
4595 27 Sep 17 nicklas 28   styles="path.css,~../css/reggie-2.css"
4595 27 Sep 17 nicklas 29   >
4595 27 Sep 17 nicklas 30 <style>
4595 27 Sep 17 nicklas 31 tr.highlight
4595 27 Sep 17 nicklas 32 {
4595 27 Sep 17 nicklas 33   border-top-width: 1px;
4595 27 Sep 17 nicklas 34   border-top-style: dotted;
4595 27 Sep 17 nicklas 35 }
4595 27 Sep 17 nicklas 36
4595 27 Sep 17 nicklas 37 #alignedSequencesTable
4595 27 Sep 17 nicklas 38 {
4595 27 Sep 17 nicklas 39   width: 100%; 
4595 27 Sep 17 nicklas 40   border-collapse: collapse;
4595 27 Sep 17 nicklas 41 }
4595 27 Sep 17 nicklas 42
4595 27 Sep 17 nicklas 43 #alignedSequencesTable thead
4595 27 Sep 17 nicklas 44 {
4595 27 Sep 17 nicklas 45   border-bottom-width: 1px;
4595 27 Sep 17 nicklas 46   border-top-width: 1px;
4595 27 Sep 17 nicklas 47 }
4595 27 Sep 17 nicklas 48
4595 27 Sep 17 nicklas 49 #alignedSequencesTable td
4595 27 Sep 17 nicklas 50 {
4595 27 Sep 17 nicklas 51   text-align: center;
4595 27 Sep 17 nicklas 52   min-width: 4.5em;
4595 27 Sep 17 nicklas 53 }
4595 27 Sep 17 nicklas 54
4595 27 Sep 17 nicklas 55 #alignedSequencesTable tbody td
4595 27 Sep 17 nicklas 56 {
4595 27 Sep 17 nicklas 57   padding-top: 1px;
4595 27 Sep 17 nicklas 58   padding-bottom: 1px;
4595 27 Sep 17 nicklas 59 }
4595 27 Sep 17 nicklas 60
4595 27 Sep 17 nicklas 61 #alignedSequencesTable .italic
4595 27 Sep 17 nicklas 62 {
4595 27 Sep 17 nicklas 63   font-style: italic;
4595 27 Sep 17 nicklas 64 }
4595 27 Sep 17 nicklas 65
4620 16 Nov 17 nicklas 66 #alignedSequencesTable .icon-col
4595 27 Sep 17 nicklas 67 {
4620 16 Nov 17 nicklas 68   width: 20px;
4595 27 Sep 17 nicklas 69   max-width: 20px;
4595 27 Sep 17 nicklas 70   min-width: 0;
4595 27 Sep 17 nicklas 71 }
4595 27 Sep 17 nicklas 72
4595 27 Sep 17 nicklas 73 .file-link
4595 27 Sep 17 nicklas 74 {
4595 27 Sep 17 nicklas 75   margin-left: 0.5em;
4595 27 Sep 17 nicklas 76 }
4595 27 Sep 17 nicklas 77
4595 27 Sep 17 nicklas 78 .comment input
4595 27 Sep 17 nicklas 79 {
4595 27 Sep 17 nicklas 80   width: 95%;
4595 27 Sep 17 nicklas 81   min-width: 20em;
4595 27 Sep 17 nicklas 82 }
4595 27 Sep 17 nicklas 83
4595 27 Sep 17 nicklas 84 </style>
4595 27 Sep 17 nicklas 85 </base:head>
4595 27 Sep 17 nicklas 86 <base:body>
4595 27 Sep 17 nicklas 87
4595 27 Sep 17 nicklas 88   <p:path><p:pathelement 
4595 27 Sep 17 nicklas 89     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
4595 27 Sep 17 nicklas 90     /><p:pathelement title="Confirm Hisat alignment" 
4595 27 Sep 17 nicklas 91     /></p:path>
4595 27 Sep 17 nicklas 92
4595 27 Sep 17 nicklas 93   <div class="content">
4595 27 Sep 17 nicklas 94   <form name="reggie" id="wizard" class="wizard">
4595 27 Sep 17 nicklas 95   
4595 27 Sep 17 nicklas 96   <div class="step" id="step-1">
4595 27 Sep 17 nicklas 97     <div class="step-no">1</div>
4595 27 Sep 17 nicklas 98     <div class="step-content">
4595 27 Sep 17 nicklas 99       
4595 27 Sep 17 nicklas 100       <div id="alignedSequences"></div>
4595 27 Sep 17 nicklas 101     
4595 27 Sep 17 nicklas 102       <table class="step-form topborder" id="delete-items" style="display: none;">
4595 27 Sep 17 nicklas 103       <tr>
4595 27 Sep 17 nicklas 104         <td class="prompt"></td>
4595 27 Sep 17 nicklas 105         <td class="input" style="text-align: right; vertical-align: middle;">
4595 27 Sep 17 nicklas 106           <label>Delete items created by failed jobs
4595 27 Sep 17 nicklas 107           <input type="checkbox" name="deleteItemsCreatedByFailedJobs" id="deleteItemsCreatedByFailedJobs" checked>
4595 27 Sep 17 nicklas 108           </label>
4595 27 Sep 17 nicklas 109         </td>
4595 27 Sep 17 nicklas 110         <td class="status" id="deleteItemsCreatedByFailedJobs.status"></td>
4595 27 Sep 17 nicklas 111         <td class="help">
4595 27 Sep 17 nicklas 112           <span id="deleteItemsCreatedByFailedJobs.message" class="message"></span>
4595 27 Sep 17 nicklas 113           Recommended! <b>AlignedSequences</b> items
4595 27 Sep 17 nicklas 114           created by failed jobs are deleted to avoid cluttering in the database.
4595 27 Sep 17 nicklas 115         </td>
4595 27 Sep 17 nicklas 116       </tr>
4595 27 Sep 17 nicklas 117       </table>
4595 27 Sep 17 nicklas 118     </div>
4595 27 Sep 17 nicklas 119   </div>
4595 27 Sep 17 nicklas 120       
4595 27 Sep 17 nicklas 121   <div id="wizard-status"></div>
4595 27 Sep 17 nicklas 122
4595 27 Sep 17 nicklas 123   <table class="navigation" id="navigation">
4595 27 Sep 17 nicklas 124   <tr>
4595 27 Sep 17 nicklas 125     <td><base:button id="gocancel" title="Cancel" /></td>
4595 27 Sep 17 nicklas 126     <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
4595 27 Sep 17 nicklas 127     <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
4595 27 Sep 17 nicklas 128     <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
4595 27 Sep 17 nicklas 129     <td id="gonext-message" class="message"></td>
4595 27 Sep 17 nicklas 130   </tr>
4595 27 Sep 17 nicklas 131   </table>
4595 27 Sep 17 nicklas 132
4595 27 Sep 17 nicklas 133   </form>
4595 27 Sep 17 nicklas 134   </div>
4595 27 Sep 17 nicklas 135   
4595 27 Sep 17 nicklas 136 </base:body>
4595 27 Sep 17 nicklas 137 </base:page>
4595 27 Sep 17 nicklas 138 <%
4595 27 Sep 17 nicklas 139 }
4595 27 Sep 17 nicklas 140 finally
4595 27 Sep 17 nicklas 141 {
4595 27 Sep 17 nicklas 142   if (dc != null) dc.close();
4595 27 Sep 17 nicklas 143 }
4595 27 Sep 17 nicklas 144 %>

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