source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp @ 548

Last change on this file since 548 was 548, checked in by mbayer, 13 years ago

new page added to gather additional info needed for autogeneration of t2m file

File size: 9.5 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/potato_small.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 selected="selected">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="Hordeum vulgare"/></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">
142    <table class="noBorder" cellpadding="4">
143      <tr>
144        <td class="noBorder"><input type="radio" name="dyeSwap" value="yes"></td>
145        <td class="noBorder">yes</td>
146      </tr>
147
148      <tr>
149        <td class="noBorder"><input type="radio" name="dyeSwap" value="no" checked="checked"></td>
150        <td class="noBorder">no</td>
151      </tr>
152    </table>     
153    </td>
154    <td>If you used a dye-swap design please indicate this here.</td>
155  </tr>
156
157  <!-- question 5 -->
158  <tr>
159    <td class="boldText">Reference sample</td>
160    <td class="input"> 
161    <table class="noBorder" cellpadding="4">
162      <tr>
163        <td class="noBorder"><input type="radio" name="refSample" value="yes"></td>
164        <td class="noBorder">yes</td>
165      </tr>
166
167      <tr>
168        <td class="noBorder"><input type="radio"name="refSample" value="no"  checked="checked"></td>
169        <td class="noBorder">no</td>
170      </tr>
171    </table>       
172    </td>
173    <td>If you used a reference sample please indicate this here.</td>
174  </tr>
175
176  <!-- question 6 -->
177  <tr>
178    <td class="boldText">Number of treatment groups:</td>
179    <td class="input"><input type="text" size="3" name="numTreatmentGroups" value="2"/></td>
180    <td>The number of discrete combinations of factor values, i.e. the product of the number of factor levels(values) from all factors. <p>
181    Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
182    </td>
183  </tr>
184
185  <!-- question 7 -->
186  <tr>
187    <td class="boldText">Experimental factors:
188    </td>
189    <td class="input"><textarea rows="7" cols="32" name="expFactors">Strain(mutant,wildtype)</textarea></td>
190    <td>Please list all experimental factors and value ranges using the following format (one per
191    line):<br>
192    <i>Factor 1(value1,value2,...valueN)<br></i>
193    <p>Example: <i><br>
194    Compound(aspirin,ibuprofen) <br>
195    Dose(control,low,medium,high)</i></td>
196  </tr>
197
198  <!-- question 8 -->
199  <tr>
200    <td class="boldText">Number of subjects per group:</td>
201    <td class="input"><input type="text" size="3" name="numReplicates" value="2"/></td>
202    <td>This is the number of biological replicates in each treatment group.</td>
203  </tr>
204 
205  <!-- question 8a -->
206  <tr>
207    <td class="boldText">Subject (replicate) labels:</td>
208    <td class="input"><textarea rows="8" cols="32" name="subjectNames"></textarea></td>
209    <td>Please provide a list of labels(names) for the experimental subjects, one per line,
210     in no particular order (copy and paste from Excel works).</td>
211  </tr> 
212 
213  <!-- question 9 -->
214  <tr>
215    <td class="boldText">Target tissues:</td>
216    <td class="input"><textarea rows="4" cols="32" name="tissues">stem</textarea></td>
217    <td>List all target tissues one per line, in no particular order (copy and paste from Excel works).</td>
218  </tr>
219 
220  <!-- question 10 -->
221  <tr>
222    <td class="boldText">Sample pooling:</td>
223    <td class="input">
224    <table class="noBorder" cellpadding="4">
225      <tr>
226        <td class="noBorder"><input type="radio" name="pooling" value="yes"></td>
227        <td class="noBorder">yes</td>
228      </tr>
229      <tr>
230        <td class="noBorder"><input type="radio" name="pooling" value="no" checked="checked"></td>
231        <td class="noBorder">no</td>
232      </tr>
233    </table>   
234    </td>
235    <td>If the samples were pooled please indicate this here.</td>
236  </tr>
237
238
239  <!-- file upload -->
240  <tr>
241    <td class="boldText">Zip file:</td>
242
243    <td class="input">
244    <table class="noBorder" border="0" cellspacing="0" cellpadding="5">
245      <tr class="noBorder" >
246     
247        <td style="vertical-align: middle;border-style: none;"><input type="text" name="path" size="35" value=""></td>
248       
249        <td  style="vertical-align: middle;border-style: none;">
250        <div class="buttons"
251          onmouseover="this.className='buttons_hover';"
252          onmouseout="this.className='buttons';"
253          onclick="browseOnClick()">
254        <div class="buttons_inner">
255
256        <table class="noBorder" cellspacing="0" cellpadding="0">
257          <tr class="noBorder">
258            <td style="border-style: none;">&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
259            <td style="border-style: none;">Browse&hellip;</td>
260          </tr>
261        </table>
262
263        </div>
264        </div>
265        </td>
266       
267      </tr>
268    </table>
269    </td>
270
271    <td>Please select the zip file on your local disk that contains the data files for import.
272   All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td>
273  </tr>
274
275</table>
276
277<p>
278
279  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
280  <tr class="noBorder">
281    <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>
282    <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>
283  </table>
284
285
286</form>
287
288</body>
289</html>
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