source: extensions/net.sf.basedb.reggie/trunk/resources/batch/import-external-specimen.jsp @ 6211

Last change on this file since 6211 was 6211, checked in by Nicklas Nordborg, 15 months ago

References #1295: Registration of specimen handled by external lab

Implemented support for auto-starting FASTQ import after a successful JSON import.

File size: 5.9 KB
Line 
1<%@ page
2  pageEncoding="UTF-8"
3  session="false"
4  import="net.sf.basedb.core.Application"
5  import="net.sf.basedb.core.User"
6  import="net.sf.basedb.core.DbControl"
7  import="net.sf.basedb.core.SessionControl"
8  import="net.sf.basedb.clients.web.Base"
9  import="net.sf.basedb.clients.web.util.HTML"
10  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
11  import="net.sf.basedb.util.Values"
12%>
13<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
14<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
15<%
16final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
17final String ID = sc.getId();
18final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
19DbControl dc = null;
20try
21{
22  dc = sc.newDbControl();
23  final User user = User.getById(dc, sc.getLoggedInUserId());
24%>
25<base:page type="default" >
26<base:head 
27  scripts="~../reggie-2.js,~import-external-specimen.js" 
28  styles="path.css,~../css/reggie-2.css"
29>
30<style>
31
32
33#importItemsTable
34{
35  width: 100%;
36  border-collapse: collapse;
37}
38
39#importItemsTable tr.highlight
40{
41  border-top-width: 1px;
42  border-top-style: dotted;
43}
44
45#importItemsTable thead
46{
47  border-bottom-width: 1px;
48  border-top-width: 1px;
49}
50
51#importItemsTable td
52{
53  text-align: center;
54  min-width: 4.5em;
55}
56
57#importItemsTable tbody td
58{
59  padding: 1px 2px;
60}
61
62#importItemsTable td.icon
63{
64  width: 20px;
65  min-width: 20px;
66}
67
68#importItemsTable td.valid
69{
70  text-align: left;
71}
72
73</style>
74</base:head>
75<base:body>
76
77  <p:path><p:pathelement 
78    title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
79    /><p:pathelement title="Import externally processed samples" 
80    /></p:path>
81
82  <div class="content">
83  <form name="reggie" id="wizard" class="wizard">
84 
85    <div class="step" id="step-1">
86      <div class="step-no">1</div>
87      <div class="step-content">
88 
89        <div id="itemTable"></div>
90       
91      </div>
92    </div>
93 
94    <div class="step" id="step-2">
95      <div class="step-no">2</div>
96      <div class="step-title">FASTQ import options</div>
97      <div class="step-content">
98 
99        <table class="step-form">
100        <tbody>
101          <tr>
102            <td class="subprompt">Auto-analyze</td>
103            <td class="input">
104              <label><input type="radio" name="autoAnalyze" id="autoAnalyzeYes" disabled>Yes</label>
105              <label><input type="radio" name="autoAnalyze" id="autoAnalyzeNo" disabled>No</label>
106            </td>
107            <td class="status" id="autoAnalyze.status"></td>
108            <td class="help">
109              <span id="autoAnalyze.message" class="message"></span>
110              If the auto-analyze option is enabled, Reggie will automatically start
111              importing the FASTQ files after a successful JSON import.
112            </td>
113          </tr>
114          <tr>
115            <td class="subprompt">Protocol</td>
116            <td class="input">
117              <select name="mergeProtocol" id="mergeProtocol" disabled></select>
118            </td>
119            <td class="status" id="mergeProtocol.status"></td>
120            <td class="help">
121              <span id="mergeProtocol.message" class="message"></span>
122              Select the protocol used for merging.
123            </td>
124          </tr>
125          <tr>
126            <td class="subprompt">Software</td>
127            <td class="input">
128              <select name="mergeSoftware" id="mergeSoftware" disabled></select>
129            </td>
130            <td class="status" id="mergeSoftware.status"></td>
131            <td class="help">
132              <span id="mergeSoftware.message" class="message"></span>
133              Select the software to use for merging the FASTQ files.
134            </td>
135          </tr>
136        </tbody>
137        <tbody>
138          <tr class="section-header">
139            <td colspan="4">Open Grid Scheduler</td>
140          </tr>
141          <tr>
142            <td class="subprompt">Open Grid Cluster</td>
143            <td class="input">
144              <select name="clusters" id="clusters" class="required" disabled></select>
145            </td>
146            <td class="status" id="clusters.status"></td>
147            <td class="help">
148              <span id="clusters.message" class="message"></span>
149              Select the cluster to use for running the analysis.
150            </td>
151          </tr>
152          <tr>
153            <td class="subprompt">Job priority</td>
154            <td class="input">
155              <select name="priority" id="priority" disabled></select>
156            </td>
157            <td class="status" id="priority.status"></td>
158            <td class="help">
159              <span id="priority.message" class="message"></span>
160              Select the priority of the analysis jobs.
161            </td>
162          </tr>
163          <tr>
164            <td class="subprompt">Auto-confirm</td>
165            <td class="input"><input type="checkbox" name="autoConfirm" checked disabled></td>
166            <td class="status" id="autoConfirm.status"></td>
167            <td class="help">
168              <span id="autoConfirm.message" class="message"></span>
169              If the FASTQ analysis is successful, with at least 10M reads
170              after trimmomatic and valid fragment size values, it is
171              automatically confirmed and alignment is started.
172            </td>
173          </tr>
174          <tr>
175            <td class="subprompt">Debug</td>
176            <td class="input"><input type="checkbox" name="debug" disabled></td>
177            <td class="status" id="debug.status"></td>
178            <td class="help">
179              <span id="debug.message" class="message"></span>
180              When running in debug mode only part of the sequenced data is used and
181              temporary files are not removed from the cluster nodes.
182            </td>
183          </tr>
184        </tbody>
185        </table>
186      </div>
187    </div>
188 
189    <div id="wizard-status"></div>
190    <div id="wizard-progress"></div>
191
192    <table class="navigation" id="navigation">
193    <tr>
194      <td><base:button id="gocancel" title="Cancel" /></td>
195      <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
196      <td><base:button id="goregister" title="Register" image="<%=home+"/images/gonext.png"%>" /></td>
197      <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
198      <td id="gonext-message" class="message"></td>
199    </tr>
200    </table>
201  </form>
202  </div>
203 
204</base:body>
205</base:page>
206<%
207}
208finally
209{
210  if (dc != null) dc.close();
211}
212%>
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