source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp @ 523

Last change on this file since 523 was 523, checked in by mbayer, 14 years ago

some more tweaks to the interface, mostly for making it work with IE

File size: 11.2 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="application" />
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
23
24<script language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script>
25
26<script language="JavaScript" type="text/javascript">
27  //submits form
28  function submit()
29  {
30    document.hybridizations.submit();
31  }
32    function getRoot()
33    {
34      return '/base/';
35    }
36    function getScale()
37    {
38      return 1.0;
39    }
40    function doImport()
41    {
42      var frm = document.forms['hybridizations'];
43      if (Main.trimString(frm.path.value) == '')
44      {
45        alert("You must select a file to import from");
46        frm.path.focus();
47      }
48      else
49      {
50        frm.submit();
51      }
52    }
53    function browseOnClick()
54    {
55      var frm = document.forms['hybridizations'];
56      var url = '<%= request.getContextPath()%>/filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&title=Select+file+to+import&callback=setFileCallback';
57      url += '&filter:INT:location=1';
58      Main.openPopup(url, 'SelectFile', 1000, 700);
59    }
60    function setFileCallback(fileId, path)
61    {
62      var frm = document.forms['hybridizations'];
63      frm.file_id.value = fileId;
64      frm.path.value = path;
65      document.getElementById('zipFile').value = path;
66      }
67    function recentFileOnChange()
68    {
69      var frm = document.forms['hybridizations'];
70      var selected = frm.recentFile[frm.recentFile.selectedIndex];
71      setFileCallback(selected.value, selected.text);
72      frm.recentFile.selectedIndex = 0;
73    }
74
75   
76    </script>
77
78</head>
79
80<body>
81
82
83
84
85<h2>Tab2MAGE Importer -- Your Hybridizations</h2>
86Page 3 of 3
87<p>
88<form name="hybridizations"action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
89<input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters"> 
90<input type="hidden"name="requestID" value="<%=requestID%>"> 
91<!-- 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 -->
92<input type="hidden" name="parameter:domain" value="<%=inputDataBean.getDomain()%>"> 
93<input type="hidden" name="parameter:accession" value="<%=inputDataBean.getAccession()%>"> 
94<input type="hidden" name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>"> 
95<input type="hidden" name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>"> 
96<input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>"> 
97<input type="hidden" name="parameter:description" value="<%=inputDataBean.getDescription()%>"> 
98<input type="hidden" name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>"> 
99<input type="hidden" name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>"> 
100<input type="hidden" name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>"> 
101<input type="hidden" name="parameter:organization" value="<%=inputDataBean.getOrganization()%>"> 
102<input type="hidden" name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>"> 
103<input type="hidden" name="parameter:authors" value="<%=inputDataBean.getAuthors()%>"> 
104<input type="hidden" name="parameter:journal" value="<%=inputDataBean.getJournal()%>"> 
105<input type="hidden" name="parameter:volume" value="<%=inputDataBean.getVolume()%>"> 
106<input type="hidden" name="parameter:issue" value="<%=inputDataBean.getIssue()%>"> 
107<input type="hidden" name="parameter:pages" value="<%=inputDataBean.getPages()%>"> 
108<input type="hidden" name="parameter:year" value="<%=inputDataBean.getYear()%>"> 
109<input type="hidden" name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>"> 
110<input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>"> 
111<input type="hidden" name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>"> 
112<input type="hidden" name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>"> 
113<input type="hidden" name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>"> 
114<input type="hidden" name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>"> 
115<input type="hidden" name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>"> 
116<input type="hidden" name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>"> 
117<input type="hidden" name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>"> 
118<input type="hidden" name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>"> 
119<input type="hidden" name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>"> 
120<input type="hidden" name="parameter:experimentId" value="<%=inputDataBean.getExperimentId()%>"> 
121
122<input type="hidden" name="file_id" value="">
123<input type="hidden" name="parameter:zipFile" value=""  id="zipFile">
124
125
126<!--  table with the input form -->
127<table cellpadding="15">
128
129  <!-- question 1 -->
130  <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
131    <td class="boldText">Microarray platform:</td>
132    <td class="input"><select name="parameter:platform">
133    <option >Affymetrix</option>
134    <option >Agilent</option>
135    <option >AIDA</option>
136    <option >BZScan</option>
137    <option >ChipSkipper</option>
138    <option >GenePix</option>
139    <option >GeneTAC</option>
140    <option >Illumina</option>
141    <option >Imagene</option>
142    <option >QuantArray Biotin</option>
143    <option >QuantArray Cy</option>
144    <option >Spotfinder</option>
145    <option ><i>Custom</i></option>
146    </select></td>
147    <td>The manufacturer of the microarray chip used.</td>
148  </tr>
149
150  <!-- question 2 -->
151  <tr>
152    <td class="boldText">Experimental organism:</td>
153    <td class="input"><input type="text" size="50" name="parameter:organism" value="Solanum tuberosum"/></td>
154    <td>The full scientific name of the experimental organism used.</td>
155  </tr>
156
157  <!-- question 3 -->
158  <tr>
159    <td class="boldText">Number of different arrays designs used:</td>
160    <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td>
161    <td>If more than one array design was used in parallel, please specify the number here.
162    We assume that all samples are applied once to each array design</td>
163  </tr>
164
165  <!-- question 4 -->
166  <tr>
167    <td class="boldText">Dye-swap</td>
168    <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio"
169      name="parameter:dyeSwap" value="no" checked="checked"> <br>
170     
171    </td>
172    <td>If you used a dye-swap design please indicate this here.</td>
173  </tr>
174
175  <!-- question 5 -->
176  <tr>
177    <td class="boldText">Reference sample</td>
178    <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio"
179      name="parameter:refSample" value="no" checked="checked"></td>
180    <td>If you used a reference sample please indicate this here.</td>
181  </tr>
182
183  <!-- question 6 -->
184  <tr>
185    <td class="boldText">Number of treatment groups:</td>
186    <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="2"/></td>
187    <td>The number of permutations of factor values. <p>
188    Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
189    </td>
190  </tr>
191
192  <!-- question 7 -->
193  <tr>
194    <td class="boldText">Experimental factors:
195    </td>
196    <td class="input"><textarea rows="7" cols="32" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td>
197    <td>Please list all experimental factors and value ranges using the following format (one per
198    line):<br>
199    <i>Factor 1(value1,value2,...valueN)<br></i>
200    <p>Example: <i><br>
201    Compound(aspirin,ibuprofen) <br>
202    Dose(control,low,medium,high)</i></td>
203  </tr>
204
205  <!-- question 8 -->
206  <tr>
207    <td class="boldText">Number of subjects per group:</td>
208    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="2"/></td>
209    <td>This is the number of biological replicates in each treatment group.</td>
210  </tr>
211 
212  <!-- question 9 -->
213  <tr>
214    <td class="boldText">Target tissues:</td>
215    <td class="input"><textarea rows="2" cols="32" name="parameter:tissues">stem</textarea></td>
216    <td>List all target tissues (as a comma separated list).<br>
217    Example: liver,heart</td>
218  </tr>
219 
220  <!-- question 10 -->
221  <tr>
222    <td class="boldText">Sample pooling:</td>
223    <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
224      name="parameter:pooling" value="no" checked="checked"></td>
225    <td>If the samples were pooled please indicate this here.</td>
226  </tr>
227
228
229  <!-- file upload -->
230  <tr>
231    <td class="boldText">Zip file:</td>
232
233    <td class="input">
234    <table class="noBorder" border="0" cellspacing="0" cellpadding="5">
235      <tr class="noBorder" >
236     
237        <td style="vertical-align: middle"><input type="text" name="path" size="35" value=""></td>
238       
239        <td  style="vertical-align: middle">
240        <div class="buttons"
241          onmouseover="this.className='buttons_hover';"
242          onmouseout="this.className='buttons';"
243          onclick="browseOnClick()">
244        <div class="buttons_inner">
245
246        <table class="noBorder" cellspacing="0" cellpadding="0">
247          <tr class="noBorder">
248            <td>&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
249            <td>Browse&hellip;</td>
250          </tr>
251        </table>
252
253        </div>
254        </div>
255        </td>
256       
257      </tr>
258    </table>
259    </td>
260
261    <td>Please select the zip file on your local disk that contains the data files for import.
262   All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td>
263  </tr>
264
265</table>
266
267<p>
268
269  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
270  <tr class="noBorder">
271    <td id="next" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/gonext.gif" border="0"></td><td>Run Import</td></tr></table></div></div></td>
272    <td id="close" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>  </tr>
273  </table>
274
275
276</form>
277
278</body>
279</html>
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