source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp @ 528

Last change on this file since 528 was 528, checked in by mbayer, 14 years ago

file mappings now fully implemented on UI side -- still need to pick up mappings in the actual plugin though
File size: 8.5 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="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()%>/plugins/uk/ac/ebi/nugo/plugins/mappings.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
91<input type="hidden" name="file_id" value="">
92<input type="hidden" name="zipFile" value=""  id="zipFile">
93
94<h1>Tab2MAGE Importer -- Your Hybridizations</h1>
95Page 3 of 4
96<p>
97<!--  table with the input form -->
98<table cellpadding="15">
99
100  <!-- question 1 -->
101  <tr >
102    <td class="boldText">Microarray platform:</td>
103    <td class="input">
104    <select name="platform">
105    <option >Affymetrix</option>
106    <option >Agilent</option>
107    <option >AIDA</option>
108    <option >BZScan</option>
109    <option >ChipSkipper</option>
110    <option >GenePix</option>
111    <option >GeneTAC</option>
112    <option >Illumina</option>
113    <option >Imagene</option>
114    <option >QuantArray Biotin</option>
115    <option >QuantArray Cy</option>
116    <option >Spotfinder</option>
117    <option ><i>Custom</i></option>
118    </select></td>
119    <td>The manufacturer of the microarray chip used.</td>
120  </tr>
121
122  <!-- question 2 -->
123  <tr>
124    <td class="boldText">Experimental organism:</td>
125    <td class="input"><input type="text" size="50" name="organism" value="Solanum tuberosum"/></td>
126    <td>The full scientific name of the experimental organism used.</td>
127  </tr>
128
129  <!-- question 3 -->
130  <tr>
131    <td class="boldText">Number of different arrays designs used:</td>
132    <td class="input"><input type="text" size="3" name="numDesigns" value="1"/></td>
133    <td>If more than one array design was used in parallel, please specify the number here.
134    We assume that all samples are applied once to each array design</td>
135  </tr>
136
137  <!-- question 4 -->
138  <tr>
139    <td class="boldText">Dye-swap</td>
140    <td class="input">yes <input type="radio" name="dyeSwap" value="yes"> no <input type="radio"
141      name="parameter:dyeSwap" value="no" checked="checked"> <br>
142     
143    </td>
144    <td>If you used a dye-swap design please indicate this here.</td>
145  </tr>
146
147  <!-- question 5 -->
148  <tr>
149    <td class="boldText">Reference sample</td>
150    <td class="input">yes <input type="radio" name="refSample" value="yes" > no <input type="radio"
151      name="parameter:refSample" value="no" checked="checked"></td>
152    <td>If you used a reference sample please indicate this here.</td>
153  </tr>
154
155  <!-- question 6 -->
156  <tr>
157    <td class="boldText">Number of treatment groups:</td>
158    <td class="input"><input type="text" size="3" name="numTreatmentGroups" value="2"/></td>
159    <td>The number of permutations of factor values. <p>
160    Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
161    </td>
162  </tr>
163
164  <!-- question 7 -->
165  <tr>
166    <td class="boldText">Experimental factors:
167    </td>
168    <td class="input"><textarea rows="7" cols="32" name="expFactors">Strain(mutant,wildtype)</textarea></td>
169    <td>Please list all experimental factors and value ranges using the following format (one per
170    line):<br>
171    <i>Factor 1(value1,value2,...valueN)<br></i>
172    <p>Example: <i><br>
173    Compound(aspirin,ibuprofen) <br>
174    Dose(control,low,medium,high)</i></td>
175  </tr>
176
177  <!-- question 8 -->
178  <tr>
179    <td class="boldText">Number of subjects per group:</td>
180    <td class="input"><input type="text" size="3" name="numReplicates" value="2"/></td>
181    <td>This is the number of biological replicates in each treatment group.</td>
182  </tr>
183 
184  <!-- question 9 -->
185  <tr>
186    <td class="boldText">Target tissues:</td>
187    <td class="input"><textarea rows="2" cols="32" name="tissues">stem</textarea></td>
188    <td>List all target tissues (as a comma separated list).<br>
189    Example: liver,heart</td>
190  </tr>
191 
192  <!-- question 10 -->
193  <tr>
194    <td class="boldText">Sample pooling:</td>
195    <td class="input">yes <input type="radio" name="pooling" value="yes"> no <input type="radio"
196      name="parameter:pooling" value="no" checked="checked"></td>
197    <td>If the samples were pooled please indicate this here.</td>
198  </tr>
199
200
201  <!-- file upload -->
202  <tr>
203    <td class="boldText">Zip file:</td>
204
205    <td class="input">
206    <table class="noBorder" border="0" cellspacing="0" cellpadding="5">
207      <tr class="noBorder" >
208     
209        <td style="vertical-align: middle;border-style: none;"><input type="text" name="path" size="35" value=""></td>
210       
211        <td  style="vertical-align: middle;border-style: none;">
212        <div class="buttons"
213          onmouseover="this.className='buttons_hover';"
214          onmouseout="this.className='buttons';"
215          onclick="browseOnClick()">
216        <div class="buttons_inner">
217
218        <table class="noBorder" cellspacing="0" cellpadding="0">
219          <tr class="noBorder">
220            <td style="border-style: none;">&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
221            <td style="border-style: none;">Browse&hellip;</td>
222          </tr>
223        </table>
224
225        </div>
226        </div>
227        </td>
228       
229      </tr>
230    </table>
231    </td>
232
233    <td>Please select the zip file on your local disk that contains the data files for import.
234   All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td>
235  </tr>
236
237</table>
238
239<p>
240
241  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
242  <tr class="noBorder">
243    <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>
244    <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>
245  </table>
246
247
248</form>
249
250</body>
251</html>
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