source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp @ 513

Last change on this file since 513 was 513, checked in by mbayer, 14 years ago

have implemented a skeleton writer class which writes a dummy tab2mage file

File size: 9.7 KB
Line 
1<%@ page import="net.sf.basedb.core.*"%>
2<%@ page import="net.sf.basedb.clients.web.*"%>
3<%@ page import="net.sf.basedb.util.*"%>
4<%@ page import="java.util.*"%>
5
6<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
7<!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name -->
8<jsp:setProperty name="inputDataBean" property="*" />
9
10<%
11final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
12final String ID = sc.getId();
13final String requestID = request.getParameter("requestId");
14 %>
15
16
17<html>
18
19<head>
20
21<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
22<link rel="stylesheet" type="text/css" href="/base/include/styles/main.css">
23<link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css">
24
25<script language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script>
26
27<script language="JavaScript" type="text/javascript">
28    function getRoot()
29    {
30      return '/base/';
31    }
32    function getScale()
33    {
34      return 1.0;
35    }
36    function doImport()
37    {
38      var frm = document.forms['hybridizations'];
39      if (Main.trimString(frm.path.value) == '')
40      {
41        alert("You must select a file to import from");
42        frm.path.focus();
43      }
44      else
45      {
46        frm.submit();
47      }
48    }
49    function browseOnClick()
50    {
51      var frm = document.forms['hybridizations'];
52      var url = '<%= request.getContextPath()%>/filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&title=Select+file+to+import&callback=setFileCallback';
53      url += '&filter:INT:location=1';
54      Main.openPopup(url, 'SelectFile', 1000, 700);
55    }
56    function setFileCallback(fileId, path)
57    {
58      var frm = document.forms['hybridizations'];
59      frm.file_id.value = fileId;
60      frm.path.value = path;
61      document.getElementById('zipFile').value = path;
62      }
63    function recentFileOnChange()
64    {
65      var frm = document.forms['hybridizations'];
66      var selected = frm.recentFile[frm.recentFile.selectedIndex];
67      setFileCallback(selected.value, selected.text);
68      frm.recentFile.selectedIndex = 0;
69    }
70
71   
72    </script>
73
74</head>
75
76<body>
77
78
79
80
81<h2>Tab2MAGE Importer -- Your Hybridizations</h2>
82Page 3 of 3
83<p>
84<form name="hybridizations"action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
85<input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters"> 
86<input type="hidden"name="requestID" value="<%=requestID%>"> 
87<!-- these are the parameters from the input pages; need to pick them up individually from the bean here; ugly as hell but can't be done any other way -->
88<input type="hidden" name="parameter:domain" value="<%=inputDataBean.getDomain()%>"> 
89<input type="hidden" name="parameter:accession" value="<%=inputDataBean.getAccession()%>"> 
90<input type="hidden" name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>"> 
91<input type="hidden" name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>"> 
92<input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>"> 
93<input type="hidden" name="parameter:description" value="<%=inputDataBean.getDescription()%>"> 
94<input type="hidden" name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>"> 
95<input type="hidden" name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>"> 
96<input type="hidden" name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>"> 
97<input type="hidden" name="parameter:organization" value="<%=inputDataBean.getOrganization()%>"> 
98<input type="hidden" name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>"> 
99<input type="hidden" name="parameter:authors" value="<%=inputDataBean.getAuthors()%>"> 
100<input type="hidden" name="parameter:journal" value="<%=inputDataBean.getJournal()%>"> 
101<input type="hidden" name="parameter:volume" value="<%=inputDataBean.getVolume()%>"> 
102<input type="hidden" name="parameter:issue" value="<%=inputDataBean.getIssue()%>"> 
103<input type="hidden" name="parameter:pages" value="<%=inputDataBean.getPages()%>"> 
104<input type="hidden" name="parameter:year" value="<%=inputDataBean.getYear()%>"> 
105<input type="hidden" name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>"> 
106<input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>"> 
107<input type="hidden" name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>"> 
108<input type="hidden" name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>"> 
109<input type="hidden" name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>"> 
110<input type="hidden" name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>"> 
111<input type="hidden" name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>"> 
112<input type="hidden" name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>"> 
113<input type="hidden" name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>"> 
114<input type="hidden" name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>"> 
115<input type="hidden" name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>"> 
116<input type="hidden" name="parameter:experimentId" value="<%=inputDataBean.getExperimentId()%>"> 
117
118<input type="hidden" name="file_id" value="">
119<input type="hidden" name="parameter:zipFile" value=""  id="zipFile">
120
121
122<!--  table with the input form -->
123<table cellpadding="15">
124
125  <!-- question 1 -->
126  <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
127    <td class="boldText">Microarray platform used:</td>
128    <td class="input"><select name="parameter:platform">
129    <option >Affymetrix</option>
130    <option >Agilent</option>
131    <option >AIDA</option>
132    <option >BZScan</option>
133    <option >ChipSkipper</option>
134    <option >GenePix</option>
135    <option >GeneTAC</option>
136    <option >Illumina</option>
137    <option >Imagene</option>
138    <option >QuantArray Biotin</option>
139    <option >QuantArray Cy</option>
140    <option >Spotfinder</option>
141    </select></td>
142  </tr>
143
144  <!-- question 2 -->
145  <tr>
146    <td class="boldText">Name of the experimental organism:</td>
147    <td class="input"><input type="text" size="60" name="parameter:organism" value="barley"/></td>
148  </tr>
149
150  <!-- question 3 -->
151  <tr>
152    <td class="boldText">Number of different arrays designs used:</td>
153    <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td>
154  </tr>
155
156  <!-- question 4 -->
157  <tr>
158    <td class="boldText">Was dye-swap used?</td>
159    <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio"
160      name="parameter:dyeSwap" value="no" checked="checked"> <br>
161    </td>
162  </tr>
163
164  <!-- question 5 -->
165  <tr>
166    <td class="boldText">Was a reference sample used?</td>
167    <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio"
168      name="parameter:refSample" value="no" checked="checked"></td>
169  </tr>
170
171  <!-- question 6 -->
172  <tr>
173    <td class="boldText">Number of treatments used:</td>
174    <td class="input"><input type="text" size="3" name="parameter:numTreatments" value="2"/></td>
175  </tr>
176
177  <!-- question 7 -->
178  <tr>
179    <td class="boldText">Please list your experimental factors and value ranges using the following format (one per
180    line):<br>
181    <i>Factor 1(value1,value2,...valueN)<br>
182    Factor 2(value1,value2,...valueN)</i>
183    <p>Example: <i><br>
184    Compound(aspirin,ibuprofen,acetaminophen) <br>
185    Dose(control,low,medium,high)</i>
186    </td>
187    <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Factor 1(value1,value2,...valueN)</textarea></td>
188  </tr>
189
190  <!-- question 8 -->
191  <tr>
192    <td class="boldText">Number of subjects per group (i.e. number of biological replicates):</td>
193    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="3"/></td>
194  </tr>
195 
196  <!-- question 9 -->
197  <tr>
198    <td class="boldText">List all target tissues (as a comma separated list).<br>
199    Example: liver,heart,adipose tissue</td>
200    <td class="input"><textarea rows="2" cols="40" name="parameter:tissues">tissues1,tissue2</textarea></td>
201  </tr>
202 
203  <!-- question 10 -->
204  <tr>
205    <td class="boldText">Were samples pooled?</td>
206    <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
207      name="parameter:pooling" value="no" checked="checked"></td>
208  </tr>
209
210
211  <!-- file upload -->
212  <tr>
213    <td class="boldText">Please select the zip file on your local disk that contains the data files for import:</td>
214
215    <td>
216    <table border="0" cellspacing="0" cellpadding="0">
217      <tr>
218        <td><input type="text" class="text required" name="path" size="50" value="">&nbsp;&nbsp;&nbsp;</td>
219        <td>
220        <div class="buttonclass" onmouseover="this.className='buttonclass_hover';"
221          onmouseout="this.className='buttonclass';" onclick="browseOnClick()">
222
223        <table border="0" cellspacing="0" cellpadding="0" class="noBorder">
224          <tr class="noBorder">
225            <td class="centered"><img src="/base/images/browse.png" border="0"></td>
226            <td>Browse&hellip;</td>
227          </tr>
228        </table>
229
230        </div>
231        </td>
232
233      </tr>
234    </table>
235    </td>
236  </tr>
237
238
239
240</table>
241
242<p>
243<table class="noBorder" width="100%">
244  <tr class="noBorder">
245    <td class="centered"><input type="submit" value="Run Import" /></td>
246  </tr>
247</table>
248
249
250</form>
251
252</body>
253</html>
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