source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp @ 518

Last change on this file since 518 was 518, checked in by mbayer, 14 years ago

integration of generated tab2mage file with the rest of the code is now partially implemented but not complete (routine check-in for rollback)

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="Solanum tuberosum"/></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="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></i>
182    <p>Example: <i><br>
183    Compound(aspirin,ibuprofen,acetaminophen) <br>
184    Dose(control,low,medium,high)</i>
185    </td>
186    <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td>
187  </tr>
188
189  <!-- question 8 -->
190  <tr>
191    <td class="boldText">Number of subjects per group (i.e. number of biological replicates):</td>
192    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="2"/></td>
193  </tr>
194 
195  <!-- question 9 -->
196  <tr>
197    <td class="boldText">List all target tissues (as a comma separated list).<br>
198    Example: liver,heart,adipose tissue</td>
199    <td class="input"><textarea rows="2" cols="40" name="parameter:tissues">stem</textarea></td>
200  </tr>
201 
202  <!-- question 10 -->
203  <tr>
204    <td class="boldText">Were samples pooled?</td>
205    <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
206      name="parameter:pooling" value="no" checked="checked"></td>
207  </tr>
208
209
210  <!-- file upload -->
211  <tr>
212    <td class="boldText">Please select the zip file on your local disk that contains the data files for import:</td>
213
214    <td>
215    <table border="0" cellspacing="0" cellpadding="0">
216      <tr>
217        <td><input type="text" class="text required" name="path" size="50" value="">&nbsp;&nbsp;&nbsp;</td>
218        <td>
219        <div class="buttonclass" onmouseover="this.className='buttonclass_hover';"
220          onmouseout="this.className='buttonclass';" onclick="browseOnClick()">
221        <div class="buttonclass_inner">
222        <table border="0" cellspacing="0" cellpadding="0">
223          <tr>
224            <td><img src="/base/images/browse.png" border="0"></td>
225            <td>Browse&hellip;</td>
226          </tr>
227        </table>
228        </div>
229        </div>
230        </td>
231
232      </tr>
233    </table>
234    </td>
235  </tr>
236
237
238
239</table>
240
241<p>
242<table class="noBorder" width="100%">
243  <tr class="noBorder">
244    <td class="centered"><input type="submit" value="Run Import" /></td>
245  </tr>
246</table>
247
248
249</form>
250
251</body>
252</html>
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