source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/input.jsp @ 497

Last change on this file since 497 was 497, checked in by mbayer, 14 years ago
  • various specification related documents added (from Philippe)
  • have modified the structure of the extension -- now uses 3 separate JSP pages to collect data from user, one per tab2mage section, and data from these is stored in a data bean in the background and then retrieved in the last page
File size: 3.9 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<%@ page import="sbrn.base.*"%>
6
7<head>
8<title>Tab2MAGE Importer -- Experiment Configuration</title>
9<style type="text/css">   
10table   {border-color: #6E94B7;border-style: solid; border-width: 1px;border-collapse: collapse}
11tr {border-color: #6E94B7;border-style: solid;border-width: 1px}
12</style>
13</head>
14
15
16<body>
17
18<%
19final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
20final String ID = sc.getId();
21final String requestID = request.getParameter("requestId");
22
23 %>
24
25<h2>Tab2MAGE Importer -- Experiment Configuration</h2>
26
27<form action="index.jsp" method="get">
28<input type="hidden" name="ID" value="<%=ID%>"> 
29<input type="hidden" name="requestId" value="<%=requestID%>"> 
30<input type="hidden" name="cmd" value="SetParameters">
31<input type="hidden" name="isConfigure" value="true" />
32
33
34<table cellpadding="15">
35
36  <!-- file chooser -->
37  <tr>
38    <td>Please select the zip file on your local disk that contains the data files for import:</td>
39    <td><input type="file" name="parameter:zipFile" size="50" ></td>
40  </tr>
41
42
43  <!-- question 1 -->
44  <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
45    <td>Please select the microarray platform used in the experiment:</td>
46    <td><select name="parameter:platform">
47      <option>Affymetrix</option>
48      <option selected="selected">Genepix</option>
49    </select></td>
50  </tr>
51
52  <!-- question 2 -->
53  <tr>
54    <td>Please enter the name of the experimental organism:</td>
55    <td><input type="text" size="50" name="parameter:organism" value="barley" /></td>
56  </tr>
57
58  <!-- question 3 -->
59  <tr>
60    <td>How many different arrays designs were used ?</td>
61    <td><input type="text" size="3" name="parameter:numDesigns" / value="1"></td>
62  </tr>
63
64  <!-- question 4 -->
65  <tr>
66    <td>Was dye-swap used?</td>
67    <td>yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio"
68      name="parameter:dyeSwap" value="no" checked="checked"> <br>
69    </td>
70  </tr>
71
72  <!-- question 5 -->
73  <tr>
74    <td>Was a reference sample used?</td>
75    <td>yes <input type="radio" name="parameter:refSample" value="yes"> no <input type="radio"
76      name="parameter:refSample" value="no" checked="checked"></td>
77  </tr>
78
79  <!-- question 6 -->
80  <tr>
81    <td>How many study groups (= treatment groups) were defined in the experiment?</td>
82    <td><input type="text" size="3" name="parameter:numTreatments" value="2"/></td>
83  </tr>
84
85  <!-- question 7 -->
86  <tr>
87    <td>What were the study factors (= independent variables /experimental factors) ?
88    <p>List Study Factors and Value ranges using the following format (one per line):<br>
89    Factor 1(value1,value2,...valueN)<br>
90    Factor 2(value1,value2,...valueN)
91    <p>Example: <br>
92    Compound(aspirin,ibuprofen,acetaminophen) <br>
93    Dose(control,low,medium,high)
94    </td>
95    <td><textarea rows="8" cols="40" name="parameter:expFactors">factor1....</textarea></td>
96  </tr>
97
98  <!-- question 8 -->
99  <tr>
100    <td>How many subjects per study group (i.e. number of biological replicates)?</td>
101    <td><input type="text" size="3" name="parameter:numReplicates" value="3"/></td>
102  </tr>
103 
104  <!-- question 9 -->
105  <tr>
106    <td>List all target tissues (as a comma separated list).<br>
107    Example: liver,heart,adipose tissue</td>
108    <td><textarea rows="8" cols="40" name="parameter:tissues">tissue1,tissue2,....</textarea></td>
109  </tr>
110 
111  <!-- question 10 -->
112  <tr>
113    <td>Were samples pooled?</td>
114    <td>yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
115      name="parameter:pooling" value="no" checked="checked"></td>
116  </tr>
117 
118  <tr>
119  <td align="center" colspan="2">
120  <input type="submit" value="Continue" />
121  </td>
122  </tr>
123 
124
125
126</table>
127
128</form>
129
130</body>
131</html>
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