source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp @ 512

Last change on this file since 512 was 512, checked in by mbayer, 14 years ago
  • have tied the interface to the importer plugin class now -- all parameters get picked up fine by the plugin
File size: 16.8 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
11<html>
12
13<head>
14
15<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
16
17<script type="text/javascript">
18
19    //function to display or hide a given element
20    function showHideItems(myItem, myButton)
21    {
22       //this is the ID of the hidden item
23      var myItem = document.getElementById(myItem);
24
25      //this is the ID of the plus/minus button image
26      var myButton = document.getElementById(myButton);
27
28        if (myItem.style.display != "none")
29        {
30            //items are currently displayed, so hide them
31            myItem.style.display = "none";
32            swapImage(myButton,"plus");
33        }
34        else
35        {
36            //items are currently hidden, so display them
37            myItem.style.display = "block";
38            swapImage(myButton,"minus");
39        }
40    }
41
42    //function to swap an image based on its current state
43    function swapImage(myImage, state)
44    {
45        if (state == "minus")
46        {
47            myImage.src = "<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/hide.gif";
48        }
49
50        else
51        {
52            myImage.src = "<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif";
53      }
54    }
55
56</script>
57
58</head>
59
60<body>
61
62<%
63final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
64final String ID = sc.getId();
65final String requestID = request.getParameter("requestId");
66 %>
67
68<h2>Tab2MAGE Importer -- Your Experiment</h2>
69Page 1 of 3
70<p>
71
72Please configure your experiment for upload by answering the questions on this and the following two pages.
73<br>
74The answers you provide will be used to automatically create a new experiment in BASE and your raw data will be imported
75into this.
76<p>
77
78<form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
79<input type="hidden" name="ID" value="<%=ID%>"> 
80
81<table cellpadding="10">
82
83  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
84  <tr>
85    <td class="boldText">Domain:</td>
86    <td class="input"><input type="text" size="45" name="domain" value="scri.ac.uk" /></td>
87    <td >The domain tag provides information on the originator of the output MAGE-ML document. This field can contain
88    any suitable string, such as the originating internet domain name (e.g., "ebi.ac.uk").</td>
89  </tr>
90 
91  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
92  <tr>
93    <td class="boldText">Accession:</td>
94    <td class="input"><input type="text" size="45" name="accession" value="E-SCRI-001" /></td>
95    <td >The experiment accession number is a unique identifier assigned to each experiment. Accession numbers for
96    experiments submitted to ArrayExpress have the format E-XXXX-n.</td>
97  </tr>
98 
99  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
100  <tr>
101    <td class="boldText">Quality Control:</td>
102    <td class="input"><select multiple name="qualityControl">
103      <option selected="selected">biological replicate</option>
104      <option>dye swap quality control</option>
105      <option>peer review quality control</option>
106      <option>real time PCR quality control</option>
107      <option>reverse transcription PCR quality control</option>
108      <option selected="selected">spike quality control</option>
109      <option>technical replicate</option>
110    </select></td>
111    <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED
112    ontology</a>. Multiple values can be selected by holding down the Ctrl key and clicking on items.</td>
113  </tr>
114
115  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
116  <tr>
117    <td class="boldText">Experiment Design Type:</td>
118    <td class="input">
119
120    <table class="noBorder" cellpadding="3" >
121
122      <tr class="noBorder">
123        <td valign="top">Biological Property<br/>
124        </td>
125        <td colspan="2"><a onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
126          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBiologicalProperty"
127          name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
128        <div id="BiologicalProperty" style="display:none"><select multiple="multiple" name="biologicalProperty">
129          <option selected="selected">cell_component_comparison_design</option>
130          <option>cell_cycle_design</option>
131          <option>cell_type_comparison_design</option>
132          <option>cellular_process_design</option>
133          <option>development_or_differentiation_design</option>
134          <option>imprinting_design</option>
135          <option>individual_genetic_characteristics_design</option>
136          <option>innate_behavior_design</option>
137          <option>is_expressed_design</option>
138          <option>organism_part_comparison_design</option>
139          <option>organism_status_design</option>
140          <option>physiological_process_design</option>
141          <option>sex_design</option>
142          <option>species_design</option>
143          <option>strain_or_line_design</option>
144          <option>unknown_experiment_design_type</option>
145        </select></div>
146        </td>
147      </tr>
148
149      <tr class="noBorder">
150        <td>BioMolecular Annotation</td>
151        <td><a onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
152          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBioMolecularAnnotation"
153          name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
154        <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple" name="bioMolecularAnnotation">
155          <option selected="selected">RNA_stability_design</option>
156          <option>binding_site_identification_design</option>
157          <option>co-expression_design</option>
158          <option>comparative_genome_hybridization_design</option>
159          <option>genotyping_design</option>
160          <option>operon_identification_design</option>
161          <option>secreted_protein_identification_design</option>
162          <option>tiling_path_design</option>
163          <option>transcript_identification_design</option>
164          <option>translational_bias_design</option>
165          <option>unknown_experiment_design_type</option>
166        </select></div>
167        </td>
168      </tr>
169
170      <tr class="noBorder">
171        <td>Epidemiological Design</td>
172        <td><a onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" title="Show/hide items">
173        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonEpidemiologicalDesign" name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
174        <div id="EpidemiologicalDesign" style="display:none"><select multiple="multiple" name="epidemiologicalDesign">
175          <option>clinical_history_design</option>
176          <option>disease_state_design</option>
177          <option selected="selected">family_history_design</option>
178          <option>unknown_experiment_design_type</option>
179        </select></div>
180        </td>
181      </tr>
182
183      <tr class="noBorder">
184        <td>Methodological Design</td>
185        <td><a onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" title="Show/hide items">
186        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonMethodologicalDesign" name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
187        <div id="MethodologicalDesign" style="display:none"><select multiple="multiple" name="methodologicalDesign">
188          <option>all_pairs</option>
189          <option>array_platform_variation_design</option>
190          <option>dye_swap_design</option>
191          <option>ex_vivo_design</option>
192          <option>hardware_variation_design</option>
193          <option>in_vitro_design</option>
194          <option>in_vivo_design</option>
195          <option>loop_design</option>
196          <option>normalization_testing_design</option>
197          <option>operator_variation_design</option>
198          <option>optimization_design</option>
199          <option>quality_control_testing_design</option>
200          <option>reference_design</option>
201          <option>replicate_design</option>
202          <option>self_vs_self_design</option>
203          <option>software_variation_design</option>
204          <option>time_series_design</option>
205          <option>unknown_experiment_design_type</option>
206        </select></div>
207        </td>
208      </tr>
209
210      <tr class="noBorder">
211        <td>Perturbational Design</td>
212        <td><a onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" title="Show/hide items">
213        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonPerturbationalDesign" name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
214        <div id="PerturbationalDesign" style="display:none"><select multiple="multiple" name="perturbationalDesign">
215          <option>cellular_modification_design</option>
216          <option>compound_treatment_design</option>
217          <option>disease_state_design</option>
218          <option>dose_response_design</option>
219          <option>genetic_modification_design</option>
220          <option>growth_condition_design</option>
221          <option>injury_design</option>
222          <option>non-targeted_transgenic_variation_design</option>
223          <option>pathogenicity_design</option>
224          <option>stimulated_design_type</option>
225          <option>stimulus_or_stress_design</option>
226          <option>unknown_experiment_design_type</option>
227        </select></div>
228        </td>
229      </tr>
230
231      <tr class="noBorder">
232        <td>Technological Design</td>
233        <td><a onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" title="Show/hide items">
234        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonTechnologicalDesign" name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
235        <div id="TechnologicalDesign" style="display:none"><select multiple="multiple" name="technologicalDesign">
236          <option>binding_site_identification_design</option>
237          <option>cellular_modification_design</option>
238          <option>comparative_genome_hybridization_design</option>
239          <option>transcript_identification_design</option>
240        </select></div>
241        </td>
242      </tr>
243
244    </table>
245
246
247    </td>
248    <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED ontology</a>.
249    <p>Click "expand" for an item to see list boxes with specific choices.<br>
250    Multiple values can be selected by holding down the Ctrl key and clicking on items.
251    </td>
252  </tr>
253 
254  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
255  <tr>
256    <td class="boldText">Experiment Name:</td>
257    <td class="input"> 
258    <textarea rows="2" cols="30" name="experimentName">my numpty experiment</textarea>
259    </td>
260    <td>The name you have chosen for the Experiment.</td>
261  </tr>
262 
263  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
264  <tr>
265    <td class="boldText">Experiment Description:</td>
266    <td class="input">
267    <textarea rows="2" cols="30" name="description">description goes here</textarea>
268    </td>
269    <td>A short paragraph describing the purpose of the experiment.</td>
270  </tr>
271 
272  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
273  <tr>
274    <td class="boldText">Release Date:</td>
275    <td class="input"><input type="text" size="10" name="releaseDate" value="2007-12-03" /></td>
276    <td>Date for public release, in the format YYYY-MM-DD.</td>
277  </tr>
278  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
279  <tr>
280    <td class="boldText">Submission Date:</td>
281    <td class="input"><input type="text" size="10" name="submissionDate" value="2007-12-03" /></td>
282    <td>Date of submission, in the format YYYY-MM-DD.</td>
283  </tr>
284  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
285  <tr>
286    <td class="boldText">Submitter:</td>
287    <td class="input"><input type="text" size="45" name="submitter" value="Joe Bloggs" /></td>
288    <td>The name of the person responsible for submitting the experiment to the database.</td>
289  </tr>
290  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
291  <tr>
292    <td class="boldText">Organization:</td>
293    <td class="input"><input type="text" size="45" name="organization" value="SCRI" /></td>
294    <td>The organization to which the submitter is affiliated.</td>
295  </tr>
296  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
297
298  <tr class="noBorder">
299    <td class="boldText">Publication Details:</td>
300    <td  class="input"></td>
301    <td></td>
302  </tr>
303
304  <tr class="noBorder">
305    <td>Title:</td>
306    <td class="input"><textarea rows="2" cols="30" name="publicationTitle">My Ropey Paper</textarea></td>
307
308    <td rowspan="4">Publication details for any manuscript associated with the experiment. The journal field should
309    contain a standard Pubmed journal abbreviated name. The authors list is a semicolon-delimited list of names.</td>
310  </tr>
311  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
312      <tr class="noBorder">
313        <td>Authors:</td>
314        <td class="input"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
315        <td></td>
316      </tr>
317      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
318      <tr class="noBorder">
319        <td>Journal:</td>
320        <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
321        <td></td>
322      </tr>
323      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
324      <tr class="noBorder">
325        <td>Volume:</td>
326        <td class="input"><input type="text" size="10" name="volume" value="5" /></td>
327        <td></td>
328      </tr>
329      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
330      <tr class="noBorder">
331        <td>Issue:</td>
332        <td class="input"><input type="text" size="10" name="issue" value="2" /></td>
333        <td></td>
334      </tr>
335      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
336      <tr class="noBorder">
337        <td>Pages:</td>
338        <td class="input"><input type="text" size="10" name="pages" value="1234-1235" /></td>
339        <td></td>
340      </tr>
341      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
342      <tr class="noBorder">
343        <td>Year:</td>
344        <td class="input"><input type="text" size="10" name="year" value="2007" /></td>
345        <td></td>
346      </tr>
347      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
348      <tr class="noBorder">
349        <td>Pubmed ID:</td>
350        <td class="input"><input type="text" size="30" name="pubmedId" value="11009762" /></td>
351        <td></td>
352
353  </tr>
354
355  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
356</table>
357
358<p>
359
360<table class="noBorder" width="100%">
361<tr class="noBorder" ><td class="centered">
362<input type="submit"  value="Continue"/>
363</td>
364</tr>
365</table>
366
367
368
369</form>
370
371</body>
372</html>
373
374
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