source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp @ 521

Last change on this file since 521 was 521, checked in by mbayer, 14 years ago

some minor bug fixes

File size: 18.0 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
18<script type="text/javascript">
19
20    //function to display or hide a given element
21    function showHideItems(myItem, myButton)
22    {
23       //this is the ID of the hidden item
24      var myItem = document.getElementById(myItem);
25
26      //this is the ID of the plus/minus button image
27      var myButton = document.getElementById(myButton);
28
29        if (myItem.style.display != "none")
30        {
31            //items are currently displayed, so hide them
32            myItem.style.display = "none";
33            swapImage(myButton,"plus");
34        }
35        else
36        {
37            //items are currently hidden, so display them
38            myItem.style.display = "block";
39            swapImage(myButton,"minus");
40        }
41    }
42
43    //function to swap an image based on its current state
44    function swapImage(myImage, state)
45    {
46        if (state == "minus")
47        {
48            myImage.src = "<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/hide.gif";
49        }
50
51        else
52        {
53            myImage.src = "<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif";
54      }
55    }
56
57</script>
58
59</head>
60
61<body>
62
63<%
64final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
65final String ID = sc.getId();
66final String requestID = request.getParameter("requestId");
67
68//we also need to figure out the name/id of the currently selected experiment that this import is getting initiated from
69ItemContext cc = sc.getCurrentContext(Item.EXPERIMENT);
70int experimentID = cc.getId();
71DbControl dc = sc.newDbControl();
72Experiment experiment = Experiment.getById(dc,experimentID);
73String expName = experiment.getName();
74dc.close();
75
76//set the experiment id in the bean so we can get at it later in the plugin
77inputDataBean.setExperimentId(new Integer(experimentID).toString());
78 %>
79 
80
81<h2>Tab2MAGE Importer -- Your Experiment</h2>
82Page 1 of 3
83<p>
84
85Please configure your experiment for upload by answering the questions on this and the following two pages.
86<br>
87The answers you provide will be used to automatically create a new experiment in BASE and your raw data will be imported
88into this.
89<p>
90
91<form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
92<input type="hidden" name="ID" value="<%=ID%>"> 
93
94<table cellpadding="10">
95
96  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
97  <tr>
98    <td class="boldText">Domain:</td>
99    <td class="input"><input type="text" size="45" name="domain" value="scri.ac.uk" /></td>
100    <td >The domain tag provides information on the originator of the output MAGE-ML document. This field can contain
101    any suitable string, such as the originating internet domain name (e.g., "ebi.ac.uk").</td>
102  </tr>
103 
104  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
105  <tr>
106    <td class="boldText">Accession:</td>
107    <td class="input"><input type="text" size="45" name="accession" value="E-SCRI-001" /></td>
108    <td >The experiment accession number is a unique identifier assigned to each experiment. Accession numbers for
109    experiments submitted to ArrayExpress have the format E-XXXX-n.</td>
110  </tr>
111 
112  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
113  <tr>
114    <td class="boldText">Quality Control:</td>
115    <td class="input"><select multiple name="qualityControl">
116      <option selected="selected">biological replicate</option>
117      <option>dye swap quality control</option>
118      <option>peer review quality control</option>
119      <option>real time PCR quality control</option>
120      <option>reverse transcription PCR quality control</option>
121      <option selected="selected">spike quality control</option>
122      <option>technical replicate</option>
123    </select></td>
124    <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED
125    ontology</a>. Multiple values can be selected by holding down the Ctrl key and clicking on items.</td>
126  </tr>
127
128  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
129  <tr>
130    <td class="boldText">Experiment Design Type:</td>
131    <td class="input">
132
133    <table class="noBorder" cellpadding="3" >
134
135      <tr class="noBorder">
136        <td valign="top">Biological Property<br/>
137        </td>
138        <td colspan="2"><a onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
139          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBiologicalProperty"
140          name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
141        <div id="BiologicalProperty" style="display:none"><select multiple="multiple" name="biologicalProperty">
142          <option selected="selected">cell_component_comparison_design</option>
143          <option>cell_cycle_design</option>
144          <option>cell_type_comparison_design</option>
145          <option>cellular_process_design</option>
146          <option>development_or_differentiation_design</option>
147          <option>imprinting_design</option>
148          <option>individual_genetic_characteristics_design</option>
149          <option>innate_behavior_design</option>
150          <option>is_expressed_design</option>
151          <option>organism_part_comparison_design</option>
152          <option>organism_status_design</option>
153          <option>physiological_process_design</option>
154          <option>sex_design</option>
155          <option>species_design</option>
156          <option>strain_or_line_design</option>
157          <option>unknown_experiment_design_type</option>
158        </select></div>
159        </td>
160      </tr>
161
162      <tr class="noBorder">
163        <td>BioMolecular Annotation</td>
164        <td><a onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
165          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBioMolecularAnnotation"
166          name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
167        <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple" name="bioMolecularAnnotation">
168          <option selected="selected">RNA_stability_design</option>
169          <option>binding_site_identification_design</option>
170          <option>co-expression_design</option>
171          <option>comparative_genome_hybridization_design</option>
172          <option>genotyping_design</option>
173          <option>operon_identification_design</option>
174          <option>secreted_protein_identification_design</option>
175          <option>tiling_path_design</option>
176          <option>transcript_identification_design</option>
177          <option>translational_bias_design</option>
178          <option>unknown_experiment_design_type</option>
179        </select></div>
180        </td>
181      </tr>
182
183      <tr class="noBorder">
184        <td>Epidemiological Design</td>
185        <td><a onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" title="Show/hide items">
186        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonEpidemiologicalDesign" name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
187        <div id="EpidemiologicalDesign" style="display:none"><select multiple="multiple" name="epidemiologicalDesign">
188          <option>clinical_history_design</option>
189          <option>disease_state_design</option>
190          <option selected="selected">family_history_design</option>
191          <option>unknown_experiment_design_type</option>
192        </select></div>
193        </td>
194      </tr>
195
196      <tr class="noBorder">
197        <td>Methodological Design</td>
198        <td><a onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" title="Show/hide items">
199        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonMethodologicalDesign" name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
200        <div id="MethodologicalDesign" style="display:none"><select multiple="multiple" name="methodologicalDesign">
201          <option>all_pairs</option>
202          <option>array_platform_variation_design</option>
203          <option>dye_swap_design</option>
204          <option>ex_vivo_design</option>
205          <option>hardware_variation_design</option>
206          <option>in_vitro_design</option>
207          <option>in_vivo_design</option>
208          <option>loop_design</option>
209          <option>normalization_testing_design</option>
210          <option>operator_variation_design</option>
211          <option>optimization_design</option>
212          <option>quality_control_testing_design</option>
213          <option>reference_design</option>
214          <option>replicate_design</option>
215          <option>self_vs_self_design</option>
216          <option>software_variation_design</option>
217          <option>time_series_design</option>
218          <option>unknown_experiment_design_type</option>
219        </select></div>
220        </td>
221      </tr>
222
223      <tr class="noBorder">
224        <td>Perturbational Design</td>
225        <td><a onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" title="Show/hide items">
226        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonPerturbationalDesign" name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
227        <div id="PerturbationalDesign" style="display:none"><select multiple="multiple" name="perturbationalDesign">
228          <option>cellular_modification_design</option>
229          <option>compound_treatment_design</option>
230          <option>disease_state_design</option>
231          <option>dose_response_design</option>
232          <option>genetic_modification_design</option>
233          <option>growth_condition_design</option>
234          <option>injury_design</option>
235          <option>non-targeted_transgenic_variation_design</option>
236          <option>pathogenicity_design</option>
237          <option>stimulated_design_type</option>
238          <option>stimulus_or_stress_design</option>
239          <option>unknown_experiment_design_type</option>
240        </select></div>
241        </td>
242      </tr>
243
244      <tr class="noBorder">
245        <td>Technological Design</td>
246        <td><a onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" title="Show/hide items">
247        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonTechnologicalDesign" name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
248        <div id="TechnologicalDesign" style="display:none"><select multiple="multiple" name="technologicalDesign">
249          <option>binding_site_identification_design</option>
250          <option>cellular_modification_design</option>
251          <option>comparative_genome_hybridization_design</option>
252          <option>transcript_identification_design</option>
253        </select></div>
254        </td>
255      </tr>
256
257    </table>
258
259
260    </td>
261    <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED ontology</a>.
262    <p>Click "expand" for an item to see list boxes with specific choices.<br>
263    Multiple values can be selected by holding down the Ctrl key and clicking on items.
264    </td>
265  </tr>
266 
267  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
268  <tr>
269    <td class="boldText">Experiment Name:</td>
270    <td class="input"> 
271    <textarea rows="2" cols="30" name="experimentName"><%=expName %></textarea>
272    </td>
273    <td>The name you have chosen for the Experiment.</td>
274  </tr>
275 
276  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
277  <tr>
278    <td class="boldText">Experiment Description:</td>
279    <td class="input">
280    <textarea rows="2" cols="30" name="description">description goes here</textarea>
281    </td>
282    <td>A short paragraph describing the purpose of the experiment.</td>
283  </tr>
284 
285  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
286  <tr>
287    <td class="boldText">Release Date:</td>
288    <td class="input"><input type="text" size="10" name="releaseDate" value="2007-12-03" /></td>
289    <td>Date for public release, in the format YYYY-MM-DD.</td>
290  </tr>
291  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
292  <tr>
293    <td class="boldText">Submission Date:</td>
294    <td class="input"><input type="text" size="10" name="submissionDate" value="2007-12-03" /></td>
295    <td>Date of submission, in the format YYYY-MM-DD.</td>
296  </tr>
297  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
298  <tr>
299    <td class="boldText">Submitter:</td>
300    <td class="input"><input type="text" size="45" name="submitter" value="Joe Bloggs" /></td>
301    <td>The name of the person responsible for submitting the experiment to the database.</td>
302  </tr>
303  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
304  <tr>
305    <td class="boldText">Organization:</td>
306    <td class="input"><input type="text" size="45" name="organization" value="SCRI" /></td>
307    <td>The organization to which the submitter is affiliated.</td>
308  </tr>
309  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
310
311  <tr class="noBorder">
312    <td class="boldText">Publication Details:</td>
313    <td  class="input"></td>
314    <td></td>
315  </tr>
316
317  <tr class="noBorder">
318    <td>Title:</td>
319    <td class="input"><textarea rows="2" cols="30" name="publicationTitle">My Ropey Paper</textarea></td>
320
321    <td rowspan="4">Publication details for any manuscript associated with the experiment. The journal field should
322    contain a standard Pubmed journal abbreviated name. The authors list is a semicolon-delimited list of names.</td>
323  </tr>
324  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
325      <tr class="noBorder">
326        <td>Authors:</td>
327        <td class="input"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
328        <td></td>
329      </tr>
330      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
331      <tr class="noBorder">
332        <td>Journal:</td>
333        <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
334        <td></td>
335      </tr>
336      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
337      <tr class="noBorder">
338        <td>Volume:</td>
339        <td class="input"><input type="text" size="10" name="volume" value="5" /></td>
340        <td></td>
341      </tr>
342      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
343      <tr class="noBorder">
344        <td>Issue:</td>
345        <td class="input"><input type="text" size="10" name="issue" value="2" /></td>
346        <td></td>
347      </tr>
348      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
349      <tr class="noBorder">
350        <td>Pages:</td>
351        <td class="input"><input type="text" size="10" name="pages" value="1234-1235" /></td>
352        <td></td>
353      </tr>
354      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
355      <tr class="noBorder">
356        <td>Year:</td>
357        <td class="input"><input type="text" size="10" name="year" value="2007" /></td>
358        <td></td>
359      </tr>
360      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
361      <tr class="noBorder">
362        <td>Pubmed ID:</td>
363        <td class="input"><input type="text" size="30" name="pubmedId" value="11009762" /></td>
364        <td></td>
365
366  </tr>
367
368  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
369</table>
370
371<p>
372
373<table class="noBorder" width="100%">
374<tr class="noBorder" ><td class="centered">
375<input type="submit"  value="Continue"/>
376</td>
377</tr>
378</table>
379
380  <table align="center">
381  <tr>
382    <td id="next" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="submit();"><div class="buttonclass_inner"><table border="0" cellspacing="0" cellpadding="0"><tr><td><img src="/base/images/gonext.gif" border="0"></td><td>Continue</td></tr></table></div></div></td>
383    <td id="close" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="window.close();"><div class="buttonclass_inner"><table border="0" cellspacing="0" cellpadding="0"><tr><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>
384  </tr>
385  </table>
386
387</form>
388
389</body>
390</html>
391
392
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