source: extensions/net.sf.basedb.reggie/trunk/resources/analysis/check_data_files.jsp @ 5531

Last change on this file since 5531 was 5531, checked in by Nicklas Nordborg, 3 years ago

References #1161: Update picard to 2.20

Implemented a method for parsing output from picard and extracting lines that could be related to an error (non-zero exit code). hopefully it will be able to present the actual error message to user near the top of the output while skippen other unrelated informational messages.

File size: 4.0 KB
Line 
1<%@ page
2  pageEncoding="UTF-8"
3  session="false"
4  import="net.sf.basedb.core.User"
5  import="net.sf.basedb.core.DbControl"
6  import="net.sf.basedb.core.SessionControl"
7  import="net.sf.basedb.core.Application"
8  import="net.sf.basedb.util.Values"
9  import="net.sf.basedb.clients.web.Base" 
10  import="net.sf.basedb.clients.web.util.HTML"
11  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
12%>
13<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
14<%
15final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
16final String ID = sc.getId();
17final float scale = Base.getScale(sc);
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  int seqRunId = Values.getInt(request.getParameter("seqrun"));
26  String readString = Values.getStringOrNull(request.getParameter("readString"));
27  String omitLanes = Values.getStringOrNull(request.getParameter("omitLanes"));
28%>
29<base:page type="popup" title="Check data files">
30<base:head 
31  scripts="~check_data_files.js,~../reggie-2.js" 
32  styles="path.css,~../css/reggie-2.css"
33>
34<style>
35
36#lanes-section tr
37{
38  vertical-align: baseline;
39}
40
41#lanes-section .status
42{
43  width: 20px;
44  max-width: 20px;
45  min-width: 20px;
46  background-repeat: no-repeat;
47  background-position: 50% 2px;
48}
49
50#lanes-section .status.checking
51{
52  background-image: url('../images/loading-small.gif');
53}
54
55#lanes-section .checking .message
56{
57  font-weight: bold;
58  font-style: italic;
59  color: #999999;
60}
61
62#lanes-section .status.valid
63{
64  background-image: url('../images/ok.png');
65}
66
67#lanes-section .status.warning
68{
69  background-image: url('../images/warning.png');
70}
71
72#lanes-section .status.invalid
73{
74  background-image: url('../images/error.png');
75  color: #CC0000;
76}
77
78#lanes-section .invalid .message
79{
80  color: #CC0000;
81  max-height: 5em;
82  overflow: auto;
83  white-space: pre-wrap;
84  border-bottom: 1px solid #A0A0A0;
85}
86
87
88</style>
89</base:head>
90<base:body>
91  <h1>Check data files</h1>
92
93  <div id="page-data" class="datacontainer"
94    data-seqrun-id="<%=seqRunId%>"
95    data-omit-lanes="[<%=omitLanes == null ? "" : omitLanes%>]"
96  ></div>
97 
98  <form name="reggie" id="wizard" class="wizard">
99  <div class="content bottomborder">
100    <table class="fullform input100">
101    <tr>
102      <th>Sequencing run</th>
103      <td colspan="2">
104        <span id="sequencingrun"></span>, <b>Flow cell:</b> <span id="flowCellId"></span> (<span id="flowCellType"></span>)
105      </td>
106    </tr>
107    <tr>
108      <th>Data files folder</th>
109      <td id="dataFilesFolder" colspan="2"></td>
110    </tr>
111    <tr>
112      <th>Program</th>
113      <td colspan="2">
114        <label><input type="radio" name="program" value="genseq" checked>genseq_check_illumina_dir.pl</label><br>
115        <label><input type="radio" name="program" value="picard">Picard CheckIlluminaDirectory</label><br>
116      </td>
117    </tr>
118    <tr>
119      <th>ReadString</th>
120      <td colspan="2">
121        <input type="text" name="readString" id="readString" class="text required" 
122          value="<%=HTML.encodeTags(readString) %>"
123          style="width: 15em;">
124        (<span id="sequencingCycles"></span>)
125      </td>
126    </tr>
127    <tr>
128      <th>Cluster node</th>
129      <td colspan="2">
130        <table>
131        <tr>
132          <td><select name="clusters" id="clusters" class="required" style="min-width: 15em; margin-right: 1em;"></select></td>
133          <td>
134            <base:button id="check" title="Check selected lanes" style="display: none;" image="<%=home+"/images/validate.png"%>" />
135          </td>
136        </table>
137      </td>
138    </tr>
139   
140    <tbody id="lanes-section"></tbody>
141   
142    <tr class="dynamic">
143      <th></th>
144      <td colspan="2">
145        <div id="wizard-status"></div>
146      </td>
147    </tr>
148    </table>
149  </div>
150  </form>
151 
152  <base:buttongroup subclass="dialogbuttons" id="dialogbuttons">
153    <base:button id="close" title="Close" />
154  </base:buttongroup>
155 
156</base:body>
157</base:page>
158<%
159}
160finally
161{
162  if (dc != null) dc.close();
163}
164%>
Note: See TracBrowser for help on using the repository browser.