source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp @ 543

Last change on this file since 543 was 543, checked in by mbayer, 13 years ago

submit mechanism has been changed to interactive -- submit.jsp now requires user to review and accept the current set of parameter values; this is because jsp forwarding was causing endless problems

File size: 8.8 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  //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()%>/plugins/uk/ac/ebi/nugo/plugins/userchoice2.jsp?ID=<%=ID%>" method="post">
88<input type="hidden" name="ID" value="<%=ID%>"> 
89<input type="hidden" name="cmd" value="SetParameters"> 
90<input type="hidden"name="requestId" value="<%=requestId%>"> 
91
92<input type="hidden" name="file_id" value="">
93<input type="hidden" name="zipFile" value="/home/michab/affyTestFiles.zip"  id="zipFile">
94
95<h1>Tab2MAGE Import Wizard -- Your Hybridizations</h1>
96
97<p>
98<!--  table with the input form -->
99<table cellpadding="15">
100
101  <!-- question 1 -->
102  <tr >
103    <td class="boldText">Microarray platform:</td>
104    <td class="input">
105    <select name="platform">
106    <option >Affymetrix</option>
107    <option >Agilent</option>
108    <option >AIDA</option>
109    <option >BZScan</option>
110    <option >ChipSkipper</option>
111    <option >GenePix</option>
112    <option >GeneTAC</option>
113    <option >Illumina</option>
114    <option >Imagene</option>
115    <option >QuantArray Biotin</option>
116    <option >QuantArray Cy</option>
117    <option >Spotfinder</option>
118    <option ><i>Custom</i></option>
119    </select></td>
120    <td>The manufacturer of the microarray chip used.</td>
121  </tr>
122
123  <!-- question 2 -->
124  <tr>
125    <td class="boldText">Experimental organism:</td>
126    <td class="input"><input type="text" size="50" name="organism" value="Solanum tuberosum"/></td>
127    <td>The full scientific name of the experimental organism used.</td>
128  </tr>
129
130  <!-- question 3 -->
131  <tr>
132    <td class="boldText">Number of different arrays designs used:</td>
133    <td class="input"><input type="text" size="3" name="numDesigns" value="1"/></td>
134    <td>If more than one array design was used in parallel, please specify the number here.
135    We assume that all samples are applied once to each array design</td>
136  </tr>
137
138  <!-- question 4 -->
139  <tr>
140    <td class="boldText">Dye-swap</td>
141    <td class="input">yes <input type="radio" name="dyeSwap" value="yes"> no <input type="radio"
142      name="dyeSwap" value="no" checked="checked"> <br>
143     
144    </td>
145    <td>If you used a dye-swap design please indicate this here.</td>
146  </tr>
147
148  <!-- question 5 -->
149  <tr>
150    <td class="boldText">Reference sample</td>
151    <td class="input">yes <input type="radio" name="refSample" value="yes" > no <input type="radio"
152      name="refSample" value="no" checked="checked"></td>
153    <td>If you used a reference sample please indicate this here.</td>
154  </tr>
155
156  <!-- question 6 -->
157  <tr>
158    <td class="boldText">Number of treatment groups:</td>
159    <td class="input"><input type="text" size="3" name="numTreatmentGroups" value="2"/></td>
160    <td>The number of permutations of factor values. <p>
161    Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
162    </td>
163  </tr>
164
165  <!-- question 7 -->
166  <tr>
167    <td class="boldText">Experimental factors:
168    </td>
169    <td class="input"><textarea rows="7" cols="32" name="expFactors">Strain(mutant,wildtype)</textarea></td>
170    <td>Please list all experimental factors and value ranges using the following format (one per
171    line):<br>
172    <i>Factor 1(value1,value2,...valueN)<br></i>
173    <p>Example: <i><br>
174    Compound(aspirin,ibuprofen) <br>
175    Dose(control,low,medium,high)</i></td>
176  </tr>
177
178  <!-- question 8 -->
179  <tr>
180    <td class="boldText">Number of subjects per group:</td>
181    <td class="input"><input type="text" size="3" name="numReplicates" value="2"/></td>
182    <td>This is the number of biological replicates in each treatment group.</td>
183  </tr>
184 
185  <!-- question 8a -->
186  <tr>
187    <td class="boldText">Subject (replicate) labels:</td>
188    <td class="input"><textarea rows="8" cols="32" name="subjectNames">plant1</textarea></td>
189    <td>Please provide a list of labels(names) for the experimental subjects, one per line,
190     in no particular order (copy and paste from Excel works).</td>
191  </tr> 
192 
193  <!-- question 9 -->
194  <tr>
195    <td class="boldText">Target tissues:</td>
196    <td class="input"><textarea rows="4" cols="32" name="tissues">stem</textarea></td>
197    <td>List all target tissues one per line, in no particular order (copy and paste from Excel works).</td>
198  </tr>
199 
200  <!-- question 10 -->
201  <tr>
202    <td class="boldText">Sample pooling:</td>
203    <td class="input">yes <input type="radio" name="pooling" value="yes"> no <input type="radio"
204      name="pooling" value="no" checked="checked"></td>
205    <td>If the samples were pooled please indicate this here.</td>
206  </tr>
207
208
209  <!-- file upload -->
210  <tr>
211    <td class="boldText">Zip file:</td>
212
213    <td class="input">
214    <table class="noBorder" border="0" cellspacing="0" cellpadding="5">
215      <tr class="noBorder" >
216     
217        <td style="vertical-align: middle;border-style: none;"><input type="text" name="path" size="35" value=""></td>
218       
219        <td  style="vertical-align: middle;border-style: none;">
220        <div class="buttons"
221          onmouseover="this.className='buttons_hover';"
222          onmouseout="this.className='buttons';"
223          onclick="browseOnClick()">
224        <div class="buttons_inner">
225
226        <table class="noBorder" cellspacing="0" cellpadding="0">
227          <tr class="noBorder">
228            <td style="border-style: none;">&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
229            <td style="border-style: none;">Browse&hellip;</td>
230          </tr>
231        </table>
232
233        </div>
234        </div>
235        </td>
236       
237      </tr>
238    </table>
239    </td>
240
241    <td>Please select the zip file on your local disk that contains the data files for import.
242   All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td>
243  </tr>
244
245</table>
246
247<p>
248
249  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
250  <tr class="noBorder">
251    <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;">Next</td></tr></table></div></div></td>
252    <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>
253  </table>
254
255
256</form>
257
258</body>
259</html>
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