source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp @ 517

Last change on this file since 517 was 517, checked in by mbayer, 14 years ago

writer now also writes hybs section out but still needs to be integrated with the rest of the code

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 treatment groups:</td>
174    <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="12"/></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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