source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp @ 525

Last change on this file since 525 was 525, checked in by mbayer, 13 years ago
  • basic Affy support implemented
  • next steps required now: mappings filenames to factor values, annotation handling, more complex two channel experiments (dye swaps, no ref sample)
File size: 11.6 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<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  //submits form
29  function submit()
30  {
31    document.hybridizations.submit();
32  }
33    function getRoot()
34    {
35      return '/base/';
36    }
37    function getScale()
38    {
39      return 1.0;
40    }
41    function doImport()
42    {
43      var frm = document.forms['hybridizations'];
44      if (Main.trimString(frm.path.value) == '')
45      {
46        alert("You must select a file to import from");
47        frm.path.focus();
48      }
49      else
50      {
51        frm.submit();
52      }
53    }
54    function browseOnClick()
55    {
56      var frm = document.forms['hybridizations'];
57      var url = '<%= request.getContextPath()%>/filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&title=Select+file+to+import&callback=setFileCallback';
58      url += '&filter:INT:location=1';
59      Main.openPopup(url, 'SelectFile', 1000, 700);
60    }
61    function setFileCallback(fileId, path)
62    {
63      var frm = document.forms['hybridizations'];
64      frm.file_id.value = fileId;
65      frm.path.value = path;
66      document.getElementById('zipFile').value = path;
67      }
68    function recentFileOnChange()
69    {
70      var frm = document.forms['hybridizations'];
71      var selected = frm.recentFile[frm.recentFile.selectedIndex];
72      setFileCallback(selected.value, selected.text);
73      frm.recentFile.selectedIndex = 0;
74    }
75
76   
77    </script>
78
79</head>
80
81<body>
82
83
84
85
86
87<form name="hybridizations"action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
88<input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters"> 
89<input type="hidden"name="requestID" value="<%=requestID%>"> 
90<!-- 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 -->
91<input type="hidden" name="parameter:domain" value="<%=inputDataBean.getDomain()%>"> 
92<input type="hidden" name="parameter:accession" value="<%=inputDataBean.getAccession()%>"> 
93<input type="hidden" name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>"> 
94<input type="hidden" name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>"> 
95<input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>"> 
96<input type="hidden" name="parameter:description" value="<%=inputDataBean.getDescription()%>"> 
97<input type="hidden" name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>"> 
98<input type="hidden" name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>"> 
99<input type="hidden" name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>"> 
100<input type="hidden" name="parameter:organization" value="<%=inputDataBean.getOrganization()%>"> 
101<input type="hidden" name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>"> 
102<input type="hidden" name="parameter:authors" value="<%=inputDataBean.getAuthors()%>"> 
103<input type="hidden" name="parameter:journal" value="<%=inputDataBean.getJournal()%>"> 
104<input type="hidden" name="parameter:volume" value="<%=inputDataBean.getVolume()%>"> 
105<input type="hidden" name="parameter:issue" value="<%=inputDataBean.getIssue()%>"> 
106<input type="hidden" name="parameter:pages" value="<%=inputDataBean.getPages()%>"> 
107<input type="hidden" name="parameter:year" value="<%=inputDataBean.getYear()%>"> 
108<input type="hidden" name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>"> 
109<input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>"> 
110<input type="hidden" name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>"> 
111<input type="hidden" name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>"> 
112<input type="hidden" name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>"> 
113<input type="hidden" name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>"> 
114<input type="hidden" name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>"> 
115<input type="hidden" name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>"> 
116<input type="hidden" name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>"> 
117<input type="hidden" name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>"> 
118<input type="hidden" name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>"> 
119<input type="hidden" name="parameter:experimentId" value="<%=inputDataBean.getExperimentId()%>"> 
120
121<input type="hidden" name="file_id" value="">
122<input type="hidden" name="parameter:zipFile" value=""  id="zipFile">
123
124<h1>Tab2MAGE Importer -- Your Hybridizations</h1>
125Page 3 of 3
126<p>
127<!--  table with the input form -->
128<table cellpadding="15">
129
130  <!-- question 1 -->
131  <tr >
132    <td class="boldText">Microarray platform:</td>
133    <td class="input"><select name="parameter:platform">
134    <option >Affymetrix</option>
135    <option >Agilent</option>
136    <option >AIDA</option>
137    <option >BZScan</option>
138    <option >ChipSkipper</option>
139    <option >GenePix</option>
140    <option >GeneTAC</option>
141    <option >Illumina</option>
142    <option >Imagene</option>
143    <option >QuantArray Biotin</option>
144    <option >QuantArray Cy</option>
145    <option >Spotfinder</option>
146    <option ><i>Custom</i></option>
147    </select></td>
148    <td>The manufacturer of the microarray chip used.</td>
149  </tr>
150
151  <!-- question 2 -->
152  <tr>
153    <td class="boldText">Experimental organism:</td>
154    <td class="input"><input type="text" size="50" name="parameter:organism" value="Solanum tuberosum"/></td>
155    <td>The full scientific name of the experimental organism used.</td>
156  </tr>
157
158  <!-- question 3 -->
159  <tr>
160    <td class="boldText">Number of different arrays designs used:</td>
161    <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td>
162    <td>If more than one array design was used in parallel, please specify the number here.
163    We assume that all samples are applied once to each array design</td>
164  </tr>
165
166  <!-- question 4 -->
167  <tr>
168    <td class="boldText">Dye-swap</td>
169    <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio"
170      name="parameter:dyeSwap" value="no" checked="checked"> <br>
171     
172    </td>
173    <td>If you used a dye-swap design please indicate this here.</td>
174  </tr>
175
176  <!-- question 5 -->
177  <tr>
178    <td class="boldText">Reference sample</td>
179    <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio"
180      name="parameter:refSample" value="no" checked="checked"></td>
181    <td>If you used a reference sample please indicate this here.</td>
182  </tr>
183
184  <!-- question 6 -->
185  <tr>
186    <td class="boldText">Number of treatment groups:</td>
187    <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="2"/></td>
188    <td>The number of permutations of factor values. <p>
189    Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
190    </td>
191  </tr>
192
193  <!-- question 7 -->
194  <tr>
195    <td class="boldText">Experimental factors:
196    </td>
197    <td class="input"><textarea rows="7" cols="32" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td>
198    <td>Please list all experimental factors and value ranges using the following format (one per
199    line):<br>
200    <i>Factor 1(value1,value2,...valueN)<br></i>
201    <p>Example: <i><br>
202    Compound(aspirin,ibuprofen) <br>
203    Dose(control,low,medium,high)</i></td>
204  </tr>
205
206  <!-- question 8 -->
207  <tr>
208    <td class="boldText">Number of subjects per group:</td>
209    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="2"/></td>
210    <td>This is the number of biological replicates in each treatment group.</td>
211  </tr>
212 
213  <!-- question 9 -->
214  <tr>
215    <td class="boldText">Target tissues:</td>
216    <td class="input"><textarea rows="2" cols="32" name="parameter:tissues">stem</textarea></td>
217    <td>List all target tissues (as a comma separated list).<br>
218    Example: liver,heart</td>
219  </tr>
220 
221  <!-- question 10 -->
222  <tr>
223    <td class="boldText">Sample pooling:</td>
224    <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
225      name="parameter:pooling" value="no" checked="checked"></td>
226    <td>If the samples were pooled please indicate this here.</td>
227  </tr>
228
229
230  <!-- file upload -->
231  <tr>
232    <td class="boldText">Zip file:</td>
233
234    <td class="input">
235    <table class="noBorder" border="0" cellspacing="0" cellpadding="5">
236      <tr class="noBorder" >
237     
238        <td style="vertical-align: middle;border-style: none;"><input type="text" name="path" size="35" value=""></td>
239       
240        <td  style="vertical-align: middle;border-style: none;">
241        <div class="buttons"
242          onmouseover="this.className='buttons_hover';"
243          onmouseout="this.className='buttons';"
244          onclick="browseOnClick()">
245        <div class="buttons_inner">
246
247        <table class="noBorder" cellspacing="0" cellpadding="0">
248          <tr class="noBorder">
249            <td style="border-style: none;">&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
250            <td style="border-style: none;">Browse&hellip;</td>
251          </tr>
252        </table>
253
254        </div>
255        </div>
256        </td>
257       
258      </tr>
259    </table>
260    </td>
261
262    <td>Please select the zip file on your local disk that contains the data files for import.
263   All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td>
264  </tr>
265
266</table>
267
268<p>
269
270  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
271  <tr class="noBorder">
272    <td id="next" width="50%" style="border-style: none;"><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 style="border-style: none;"><img src="/base/images/gonext.gif" border="0"></td><td style="border-style: none;">Run Import</td></tr></table></div></div></td>
273    <td id="close" width="50%" style="border-style: none;"><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 style="border-style: none;"><img src="/base/images/cancel.gif" border="0"></td><td style="border-style: none;">Cancel</td></tr></table></div></div></td>  </tr>
274  </table>
275
276
277</form>
278
279</body>
280</html>
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