source: extensions/net.sf.basedb.reggie/trunk/resources/batch/import-external-specimen.jsp @ 6212

Last change on this file since 6212 was 6212, checked in by Nicklas Nordborg, 15 months ago

References #1295: Registration of specimen handled by external lab

Added possibility to select an "Operator" when importing that override values from the JSON files.

File size: 6.7 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 th
52{
53  padding: 4px;
54}
55
56#importItemsTable td
57{
58  text-align: center;
59  min-width: 4.5em;
60}
61
62#importItemsTable tbody td
63{
64  padding: 1px 2px;
65}
66
67#importItemsTable td.icon, #importItemsTable td.import
68{
69  width: 20px;
70  min-width: 20px;
71}
72
73#importItemsTable td.valid
74{
75  text-align: left;
76}
77
78.file-data
79{
80  font-style: italic;
81  opacity: 0.5;
82}
83
84</style>
85</base:head>
86<base:body>
87
88  <p:path><p:pathelement 
89    title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
90    /><p:pathelement title="Import externally processed samples" 
91    /></p:path>
92
93  <div class="content">
94  <form name="reggie" id="wizard" class="wizard">
95 
96    <div class="step" id="step-1">
97      <div class="step-no">1</div>
98      <div class="step-content">
99 
100        <div id="itemTable"></div>
101       
102      </div>
103    </div>
104 
105    <div class="step" id="step-2">
106      <div class="step-no">2</div>
107      <div class="step-title">Import options</div>
108      <div class="step-content">
109 
110        <table class="step-form">
111        <tbody>
112          <tr>
113            <td class="prompt">Operator</td>
114            <td class="input">
115              <select name="operator" id="operator">
116                <option value="CMD">CMD
117                <option value="">- Use JSON -
118              </option>
119            </td>
120            <td class="status" id="operator.status"></td>
121            <td class="help">
122              <span id="operator.message" class="message"></span>
123              The external operator. If the <i>Use JSON</i> option is selected
124              the operator information is taken from the JSON file.
125            </td>
126          </tr>
127        </tbody>
128        <tbody>
129          <tr class="section-header">
130            <td colspan="4">FASTQ Import</td>
131          </tr>
132          <tr>
133            <td class="subprompt">Auto-analyze</td>
134            <td class="input">
135              <label><input type="radio" name="autoAnalyze" id="autoAnalyzeYes" disabled>Yes</label>
136              <label><input type="radio" name="autoAnalyze" id="autoAnalyzeNo" disabled>No</label>
137            </td>
138            <td class="status" id="autoAnalyze.status"></td>
139            <td class="help">
140              <span id="autoAnalyze.message" class="message"></span>
141              If the auto-analyze option is enabled, Reggie will automatically start
142              importing the FASTQ files after a successful JSON import.
143            </td>
144          </tr>
145          <tr>
146            <td class="subprompt">Protocol</td>
147            <td class="input">
148              <select name="mergeProtocol" id="mergeProtocol" disabled></select>
149            </td>
150            <td class="status" id="mergeProtocol.status"></td>
151            <td class="help">
152              <span id="mergeProtocol.message" class="message"></span>
153              Select the protocol used for merging.
154            </td>
155          </tr>
156          <tr>
157            <td class="subprompt">Software</td>
158            <td class="input">
159              <select name="mergeSoftware" id="mergeSoftware" disabled></select>
160            </td>
161            <td class="status" id="mergeSoftware.status"></td>
162            <td class="help">
163              <span id="mergeSoftware.message" class="message"></span>
164              Select the software to use for merging the FASTQ files.
165            </td>
166          </tr>
167        </tbody>
168        <tbody>
169          <tr class="section-header">
170            <td colspan="4">Open Grid Scheduler</td>
171          </tr>
172          <tr>
173            <td class="subprompt">Open Grid Cluster</td>
174            <td class="input">
175              <select name="clusters" id="clusters" class="required" disabled></select>
176            </td>
177            <td class="status" id="clusters.status"></td>
178            <td class="help">
179              <span id="clusters.message" class="message"></span>
180              Select the cluster to use for running the analysis.
181            </td>
182          </tr>
183          <tr>
184            <td class="subprompt">Job priority</td>
185            <td class="input">
186              <select name="priority" id="priority" disabled></select>
187            </td>
188            <td class="status" id="priority.status"></td>
189            <td class="help">
190              <span id="priority.message" class="message"></span>
191              Select the priority of the analysis jobs.
192            </td>
193          </tr>
194          <tr>
195            <td class="subprompt">Auto-confirm</td>
196            <td class="input"><input type="checkbox" name="autoConfirm" checked disabled></td>
197            <td class="status" id="autoConfirm.status"></td>
198            <td class="help">
199              <span id="autoConfirm.message" class="message"></span>
200              If the FASTQ analysis is successful, with at least 10M reads
201              after trimmomatic and valid fragment size values, it is
202              automatically confirmed and alignment is started.
203            </td>
204          </tr>
205          <tr>
206            <td class="subprompt">Debug</td>
207            <td class="input"><input type="checkbox" name="debug" disabled></td>
208            <td class="status" id="debug.status"></td>
209            <td class="help">
210              <span id="debug.message" class="message"></span>
211              When running in debug mode only part of the sequenced data is used and
212              temporary files are not removed from the cluster nodes.
213            </td>
214          </tr>
215        </tbody>
216        </table>
217      </div>
218    </div>
219 
220    <div id="wizard-status"></div>
221    <div id="wizard-progress"></div>
222
223    <table class="navigation" id="navigation">
224    <tr>
225      <td><base:button id="gocancel" title="Cancel" /></td>
226      <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
227      <td><base:button id="goregister" title="Register" image="<%=home+"/images/gonext.png"%>" /></td>
228      <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
229      <td id="gonext-message" class="message"></td>
230    </tr>
231    </table>
232  </form>
233  </div>
234 
235</base:body>
236</base:page>
237<%
238}
239finally
240{
241  if (dc != null) dc.close();
242}
243%>
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