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

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2226 13 Feb 14 nicklas 1 <%@ page
2226 13 Feb 14 nicklas 2   pageEncoding="UTF-8"
2226 13 Feb 14 nicklas 3   session="false"
2226 13 Feb 14 nicklas 4   import="net.sf.basedb.core.User"
2226 13 Feb 14 nicklas 5   import="net.sf.basedb.core.DbControl"
2226 13 Feb 14 nicklas 6   import="net.sf.basedb.core.SessionControl"
2226 13 Feb 14 nicklas 7   import="net.sf.basedb.core.Application"
2226 13 Feb 14 nicklas 8   import="net.sf.basedb.clients.web.Base"  
2226 13 Feb 14 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
2226 13 Feb 14 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
2226 13 Feb 14 nicklas 11 %>
2226 13 Feb 14 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
2226 13 Feb 14 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
2226 13 Feb 14 nicklas 14 <%
3976 26 May 16 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
2226 13 Feb 14 nicklas 16 final String ID = sc.getId();
2226 13 Feb 14 nicklas 17 final float scale = Base.getScale(sc);
2226 13 Feb 14 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
5478 10 Jun 19 nicklas 19 final String pipeline = request.getParameter("pipeline");
2226 13 Feb 14 nicklas 20 DbControl dc = null;
2226 13 Feb 14 nicklas 21 try
2226 13 Feb 14 nicklas 22 {
2226 13 Feb 14 nicklas 23   dc = sc.newDbControl();
2226 13 Feb 14 nicklas 24   final User user = User.getById(dc, sc.getLoggedInUserId());
2226 13 Feb 14 nicklas 25 %>
2226 13 Feb 14 nicklas 26 <base:page type="default" >
2639 08 Sep 14 nicklas 27 <base:head 
2639 08 Sep 14 nicklas 28   scripts="~../reggie-2.js,~sequencing_confirm.js" 
2639 08 Sep 14 nicklas 29   styles="path.css,~../css/reggie-2.css"
2639 08 Sep 14 nicklas 30 />
2639 08 Sep 14 nicklas 31 <base:body>
2226 13 Feb 14 nicklas 32
2226 13 Feb 14 nicklas 33   <p:path><p:pathelement 
2226 13 Feb 14 nicklas 34     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
2226 13 Feb 14 nicklas 35     /><p:pathelement title="Confirm sequencing completed" 
2226 13 Feb 14 nicklas 36     /></p:path>
5478 10 Jun 19 nicklas 37     
5478 10 Jun 19 nicklas 38   <div id="page-data" class="datacontainer"
5478 10 Jun 19 nicklas 39     data-pipeline="<%=HTML.encodeTags(pipeline)%>"
5478 10 Jun 19 nicklas 40   ></div>
2226 13 Feb 14 nicklas 41
2226 13 Feb 14 nicklas 42   <div class="content">
2639 08 Sep 14 nicklas 43   <form name="reggie" id="wizard" class="wizard">
2639 08 Sep 14 nicklas 44   
2639 08 Sep 14 nicklas 45   <div class="step" id="step-1">
2639 08 Sep 14 nicklas 46     <div class="step-no">1</div>
2639 08 Sep 14 nicklas 47     <div class="step-title">Select sequencing run</div>
2639 08 Sep 14 nicklas 48     <div class="step-content">
2226 13 Feb 14 nicklas 49
2639 08 Sep 14 nicklas 50       <table class="step-form">
2639 08 Sep 14 nicklas 51       <tr>
2226 13 Feb 14 nicklas 52         <td class="prompt">Sequencing run</td>
2639 08 Sep 14 nicklas 53         <td class="input">
2639 08 Sep 14 nicklas 54           <select class="required" name="seqRuns" id="seqRuns"></select>
2226 13 Feb 14 nicklas 55         </td>
2226 13 Feb 14 nicklas 56         <td class="status" id="seqRuns.status"></td>
2639 08 Sep 14 nicklas 57         <td class="help">
2639 08 Sep 14 nicklas 58           <span id="seqRuns.message" class="message"></span>
2226 13 Feb 14 nicklas 59           Select the sequencing run that has ended.
2226 13 Feb 14 nicklas 60         </td>
2226 13 Feb 14 nicklas 61       </tr>
2639 08 Sep 14 nicklas 62       <tbody class="info-section">
2639 08 Sep 14 nicklas 63       <tr>
2639 08 Sep 14 nicklas 64         <td class="prompt">Start date</td>
2639 08 Sep 14 nicklas 65         <td class="info" id="startDate" colspan="2"></td>
2226 13 Feb 14 nicklas 66         <td class="help"></td>
2226 13 Feb 14 nicklas 67       </tr>
2639 08 Sep 14 nicklas 68       <tr>
2639 08 Sep 14 nicklas 69         <td class="prompt">End date</td>
2639 08 Sep 14 nicklas 70         <td class="info" id="endDate" colspan="2"></td>
2226 13 Feb 14 nicklas 71         <td class="help"></td>
2226 13 Feb 14 nicklas 72       </tr>
2639 08 Sep 14 nicklas 73       <tr>
2639 08 Sep 14 nicklas 74         <td class="prompt">Flow cell type</td>
2639 08 Sep 14 nicklas 75         <td class="info" id="flowCellType" colspan="2"></td>
2412 09 May 14 nicklas 76         <td class="help"></td>
2412 09 May 14 nicklas 77       </tr>
2639 08 Sep 14 nicklas 78       <tr>
2639 08 Sep 14 nicklas 79         <td class="prompt">Flow cell</td>
2639 08 Sep 14 nicklas 80         <td class="info" id="flowCellInRun" colspan="2"></td>
2226 13 Feb 14 nicklas 81         <td class="help"></td>
2226 13 Feb 14 nicklas 82       </tr>
2639 08 Sep 14 nicklas 83       <tr>
2639 08 Sep 14 nicklas 84         <td class="prompt">Pools</td>
2639 08 Sep 14 nicklas 85         <td class="info" id="pools" colspan="2"></td>
2236 20 Feb 14 nicklas 86         <td class="help"></td>
2236 20 Feb 14 nicklas 87       </tr>
2639 08 Sep 14 nicklas 88       <tr>
5473 05 Jun 19 nicklas 89         <td class="prompt">LibPlates</td>
5473 05 Jun 19 nicklas 90         <td class="info" id="libPlates" colspan="2"></td>
2236 20 Feb 14 nicklas 91         <td class="help"></td>
2236 20 Feb 14 nicklas 92       </tr>
2639 08 Sep 14 nicklas 93       <tr>
2639 08 Sep 14 nicklas 94         <td class="prompt">Comments</td>
2639 08 Sep 14 nicklas 95         <td class="info" id="comments" colspan="2"></td>
2229 17 Feb 14 nicklas 96         <td class="help"></td>
2229 17 Feb 14 nicklas 97       </tr>
2641 09 Sep 14 nicklas 98       <tr>
2641 09 Sep 14 nicklas 99         <td class="prompt"></td>
2641 09 Sep 14 nicklas 100         <td class="input">
2641 09 Sep 14 nicklas 101           <base:buttongroup>
2641 09 Sep 14 nicklas 102             <base:button id="btnCheck" title="Check data files&hellip;" image="<%=home+"/images/validate.png"%>" />
2641 09 Sep 14 nicklas 103           </base:buttongroup>
2641 09 Sep 14 nicklas 104         </td>
2641 09 Sep 14 nicklas 105         <td class="status" id="check.status"></td>
2641 09 Sep 14 nicklas 106         <td class="help">
2641 09 Sep 14 nicklas 107           <span id="check.message" class="message"></span>
2641 09 Sep 14 nicklas 108           Check that data from the sequencing run exists and seems reasonable.
2641 09 Sep 14 nicklas 109         </td>
2641 09 Sep 14 nicklas 110       </tr>
2229 17 Feb 14 nicklas 111       </tbody>
2639 08 Sep 14 nicklas 112       
2639 08 Sep 14 nicklas 113       <tr>
2226 13 Feb 14 nicklas 114         <td class="prompt">Outcome</td>
2229 17 Feb 14 nicklas 115         <td class="input" colspan="2">
2639 08 Sep 14 nicklas 116           <label><input type="radio" name="outcome" id="outcomeSuccess" value="Successful"  checked
2639 08 Sep 14 nicklas 117             >Success</label> - continue with demux<br>
2228 14 Feb 14 nicklas 118           <label><input type="radio" name="outcome" id="outcomeFailed" value="Failed"
2235 19 Feb 14 nicklas 119             >Failure</label><br>
2235 19 Feb 14 nicklas 120           <img src="../images/joinbottom.gif"><label><input type="checkbox" name="flagPools" value="1" disabled checked>Flag pools for re-clustering</label>
2235 19 Feb 14 nicklas 121           
2226 13 Feb 14 nicklas 122         </td>
2226 13 Feb 14 nicklas 123         <td class="help">
2226 13 Feb 14 nicklas 124           Select the <b>Failure</b> option if further analysis of the data is not possible.
2235 19 Feb 14 nicklas 125           No child bioassay set will be created. Existing pooled libraries can optionally
2228 14 Feb 14 nicklas 126           be flagged for re-clustering on a new flow cell.
2226 13 Feb 14 nicklas 127         </td>
2226 13 Feb 14 nicklas 128       </tr>
2226 13 Feb 14 nicklas 129       </table>
2639 08 Sep 14 nicklas 130     </div>
2226 13 Feb 14 nicklas 131   </div>
2226 13 Feb 14 nicklas 132   
2639 08 Sep 14 nicklas 133   <div class="step" id="step-2">
2639 08 Sep 14 nicklas 134     <div class="step-no">2</div>
2639 08 Sep 14 nicklas 135     <div class="step-title" id="step-2-title">SequencingRun</div>
2639 08 Sep 14 nicklas 136     <div class="step-content">
2639 08 Sep 14 nicklas 137   
2639 08 Sep 14 nicklas 138       <table class="step-form">
2639 08 Sep 14 nicklas 139       <tr id="failedLanesRow">
2226 13 Feb 14 nicklas 140         <td class="prompt">Failed lanes</td>
2226 13 Feb 14 nicklas 141         <td class="input" id="failedLanes"></td>
2226 13 Feb 14 nicklas 142         <td class="status" id="failedLanes.status"></td>
2639 08 Sep 14 nicklas 143         <td class="help">
2639 08 Sep 14 nicklas 144           <span id="failedLanes.message" class="message"></span>
2226 13 Feb 14 nicklas 145           Mark the checkboxes for lanes that have failed and should not be included in the demux.
2226 13 Feb 14 nicklas 146         </td>
2226 13 Feb 14 nicklas 147       </tr>
2226 13 Feb 14 nicklas 148       
2639 08 Sep 14 nicklas 149       <tr class="align-top">
2226 13 Feb 14 nicklas 150         <td class="prompt">Comments</td>
2639 08 Sep 14 nicklas 151         <td class="input">
2651 10 Sep 14 nicklas 152           <textarea name="sequencingComments" id="sequencingComments" rows="6"></textarea>
2639 08 Sep 14 nicklas 153         </td>
2226 13 Feb 14 nicklas 154         <td class="status" id="sequencingComments.status"></td>
2639 08 Sep 14 nicklas 155         <td class="help">
2639 08 Sep 14 nicklas 156           <span id="sequencingComments.message" class="message"></span>
2639 08 Sep 14 nicklas 157           Comments about the sequencing.
2639 08 Sep 14 nicklas 158         </td>
2226 13 Feb 14 nicklas 159       </tr>
2226 13 Feb 14 nicklas 160       </table>
2639 08 Sep 14 nicklas 161     </div>
2226 13 Feb 14 nicklas 162   </div>
2226 13 Feb 14 nicklas 163     
2639 08 Sep 14 nicklas 164     <div id="wizard-status"></div>
2226 13 Feb 14 nicklas 165   
2639 08 Sep 14 nicklas 166     <table class="navigation" id="navigation">
2226 13 Feb 14 nicklas 167     <tr>
2639 08 Sep 14 nicklas 168       <td><base:button id="gocancel" title="Cancel" /></td>
2639 08 Sep 14 nicklas 169       <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
2639 08 Sep 14 nicklas 170       <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
2639 08 Sep 14 nicklas 171       <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
2639 08 Sep 14 nicklas 172       <td id="gonext-message" class="message"></td>
2226 13 Feb 14 nicklas 173     </tr>
2639 08 Sep 14 nicklas 174     </table>
2226 13 Feb 14 nicklas 175   
2226 13 Feb 14 nicklas 176   </form>
2226 13 Feb 14 nicklas 177   </div>
2226 13 Feb 14 nicklas 178   
2226 13 Feb 14 nicklas 179 </base:body>
2226 13 Feb 14 nicklas 180 </base:page>
2226 13 Feb 14 nicklas 181 <%
2226 13 Feb 14 nicklas 182 }
2226 13 Feb 14 nicklas 183 finally
2226 13 Feb 14 nicklas 184 {
2226 13 Feb 14 nicklas 185   if (dc != null) dc.close();
2226 13 Feb 14 nicklas 186 }
2226 13 Feb 14 nicklas 187 %>

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