source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp @ 513

Last change on this file since 513 was 513, checked in by mbayer, 14 years ago

have implemented a skeleton writer class which writes a dummy tab2mage file

File size: 17.4 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//we also need to figure out the name/id of the currently selected experiment that this import is getting initiated from
68ItemContext cc = sc.getCurrentContext(Item.EXPERIMENT);
69int experimentID = cc.getId();
70DbControl dc = sc.newDbControl();
71Experiment experiment = Experiment.getById(dc,experimentID);
72String expName = experiment.getName();
73dc.close();
74
75//set the experiment id in the bean so we can get at it later in the plugin
76inputDataBean.setExperimentId(new Integer(experimentID).toString());
77 %>
78 
79 experiment name = <%=expName %><br>
80 experiment ID = <%=experimentID %>
81
82<h2>Tab2MAGE Importer -- Your Experiment</h2>
83Page 1 of 3
84<p>
85
86Please configure your experiment for upload by answering the questions on this and the following two pages.
87<br>
88The answers you provide will be used to automatically create a new experiment in BASE and your raw data will be imported
89into this.
90<p>
91
92<form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
93<input type="hidden" name="ID" value="<%=ID%>"> 
94
95<table cellpadding="10">
96
97  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
98  <tr>
99    <td class="boldText">Domain:</td>
100    <td class="input"><input type="text" size="45" name="domain" value="scri.ac.uk" /></td>
101    <td >The domain tag provides information on the originator of the output MAGE-ML document. This field can contain
102    any suitable string, such as the originating internet domain name (e.g., "ebi.ac.uk").</td>
103  </tr>
104 
105  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
106  <tr>
107    <td class="boldText">Accession:</td>
108    <td class="input"><input type="text" size="45" name="accession" value="E-SCRI-001" /></td>
109    <td >The experiment accession number is a unique identifier assigned to each experiment. Accession numbers for
110    experiments submitted to ArrayExpress have the format E-XXXX-n.</td>
111  </tr>
112 
113  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
114  <tr>
115    <td class="boldText">Quality Control:</td>
116    <td class="input"><select multiple name="qualityControl">
117      <option selected="selected">biological replicate</option>
118      <option>dye swap quality control</option>
119      <option>peer review quality control</option>
120      <option>real time PCR quality control</option>
121      <option>reverse transcription PCR quality control</option>
122      <option selected="selected">spike quality control</option>
123      <option>technical replicate</option>
124    </select></td>
125    <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED
126    ontology</a>. Multiple values can be selected by holding down the Ctrl key and clicking on items.</td>
127  </tr>
128
129  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
130  <tr>
131    <td class="boldText">Experiment Design Type:</td>
132    <td class="input">
133
134    <table class="noBorder" cellpadding="3" >
135
136      <tr class="noBorder">
137        <td valign="top">Biological Property<br/>
138        </td>
139        <td colspan="2"><a onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
140          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBiologicalProperty"
141          name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
142        <div id="BiologicalProperty" style="display:none"><select multiple="multiple" name="biologicalProperty">
143          <option selected="selected">cell_component_comparison_design</option>
144          <option>cell_cycle_design</option>
145          <option>cell_type_comparison_design</option>
146          <option>cellular_process_design</option>
147          <option>development_or_differentiation_design</option>
148          <option>imprinting_design</option>
149          <option>individual_genetic_characteristics_design</option>
150          <option>innate_behavior_design</option>
151          <option>is_expressed_design</option>
152          <option>organism_part_comparison_design</option>
153          <option>organism_status_design</option>
154          <option>physiological_process_design</option>
155          <option>sex_design</option>
156          <option>species_design</option>
157          <option>strain_or_line_design</option>
158          <option>unknown_experiment_design_type</option>
159        </select></div>
160        </td>
161      </tr>
162
163      <tr class="noBorder">
164        <td>BioMolecular Annotation</td>
165        <td><a onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
166          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBioMolecularAnnotation"
167          name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
168        <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple" name="bioMolecularAnnotation">
169          <option selected="selected">RNA_stability_design</option>
170          <option>binding_site_identification_design</option>
171          <option>co-expression_design</option>
172          <option>comparative_genome_hybridization_design</option>
173          <option>genotyping_design</option>
174          <option>operon_identification_design</option>
175          <option>secreted_protein_identification_design</option>
176          <option>tiling_path_design</option>
177          <option>transcript_identification_design</option>
178          <option>translational_bias_design</option>
179          <option>unknown_experiment_design_type</option>
180        </select></div>
181        </td>
182      </tr>
183
184      <tr class="noBorder">
185        <td>Epidemiological Design</td>
186        <td><a onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" title="Show/hide items">
187        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonEpidemiologicalDesign" name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
188        <div id="EpidemiologicalDesign" style="display:none"><select multiple="multiple" name="epidemiologicalDesign">
189          <option>clinical_history_design</option>
190          <option>disease_state_design</option>
191          <option selected="selected">family_history_design</option>
192          <option>unknown_experiment_design_type</option>
193        </select></div>
194        </td>
195      </tr>
196
197      <tr class="noBorder">
198        <td>Methodological Design</td>
199        <td><a onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" title="Show/hide items">
200        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonMethodologicalDesign" name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
201        <div id="MethodologicalDesign" style="display:none"><select multiple="multiple" name="methodologicalDesign">
202          <option>all_pairs</option>
203          <option>array_platform_variation_design</option>
204          <option>dye_swap_design</option>
205          <option>ex_vivo_design</option>
206          <option>hardware_variation_design</option>
207          <option>in_vitro_design</option>
208          <option>in_vivo_design</option>
209          <option>loop_design</option>
210          <option>normalization_testing_design</option>
211          <option>operator_variation_design</option>
212          <option>optimization_design</option>
213          <option>quality_control_testing_design</option>
214          <option>reference_design</option>
215          <option>replicate_design</option>
216          <option>self_vs_self_design</option>
217          <option>software_variation_design</option>
218          <option>time_series_design</option>
219          <option>unknown_experiment_design_type</option>
220        </select></div>
221        </td>
222      </tr>
223
224      <tr class="noBorder">
225        <td>Perturbational Design</td>
226        <td><a onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" title="Show/hide items">
227        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonPerturbationalDesign" name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
228        <div id="PerturbationalDesign" style="display:none"><select multiple="multiple" name="perturbationalDesign">
229          <option>cellular_modification_design</option>
230          <option>compound_treatment_design</option>
231          <option>disease_state_design</option>
232          <option>dose_response_design</option>
233          <option>genetic_modification_design</option>
234          <option>growth_condition_design</option>
235          <option>injury_design</option>
236          <option>non-targeted_transgenic_variation_design</option>
237          <option>pathogenicity_design</option>
238          <option>stimulated_design_type</option>
239          <option>stimulus_or_stress_design</option>
240          <option>unknown_experiment_design_type</option>
241        </select></div>
242        </td>
243      </tr>
244
245      <tr class="noBorder">
246        <td>Technological Design</td>
247        <td><a onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" title="Show/hide items">
248        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonTechnologicalDesign" name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
249        <div id="TechnologicalDesign" style="display:none"><select multiple="multiple" name="technologicalDesign">
250          <option>binding_site_identification_design</option>
251          <option>cellular_modification_design</option>
252          <option>comparative_genome_hybridization_design</option>
253          <option>transcript_identification_design</option>
254        </select></div>
255        </td>
256      </tr>
257
258    </table>
259
260
261    </td>
262    <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED ontology</a>.
263    <p>Click "expand" for an item to see list boxes with specific choices.<br>
264    Multiple values can be selected by holding down the Ctrl key and clicking on items.
265    </td>
266  </tr>
267 
268  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
269  <tr>
270    <td class="boldText">Experiment Name:</td>
271    <td class="input"> 
272    <textarea rows="2" cols="30" name="experimentName"><%=expName %></textarea>
273    </td>
274    <td>The name you have chosen for the Experiment.</td>
275  </tr>
276 
277  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
278  <tr>
279    <td class="boldText">Experiment Description:</td>
280    <td class="input">
281    <textarea rows="2" cols="30" name="description">description goes here</textarea>
282    </td>
283    <td>A short paragraph describing the purpose of the experiment.</td>
284  </tr>
285 
286  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
287  <tr>
288    <td class="boldText">Release Date:</td>
289    <td class="input"><input type="text" size="10" name="releaseDate" value="2007-12-03" /></td>
290    <td>Date for public release, in the format YYYY-MM-DD.</td>
291  </tr>
292  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
293  <tr>
294    <td class="boldText">Submission Date:</td>
295    <td class="input"><input type="text" size="10" name="submissionDate" value="2007-12-03" /></td>
296    <td>Date of submission, in the format YYYY-MM-DD.</td>
297  </tr>
298  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
299  <tr>
300    <td class="boldText">Submitter:</td>
301    <td class="input"><input type="text" size="45" name="submitter" value="Joe Bloggs" /></td>
302    <td>The name of the person responsible for submitting the experiment to the database.</td>
303  </tr>
304  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
305  <tr>
306    <td class="boldText">Organization:</td>
307    <td class="input"><input type="text" size="45" name="organization" value="SCRI" /></td>
308    <td>The organization to which the submitter is affiliated.</td>
309  </tr>
310  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
311
312  <tr class="noBorder">
313    <td class="boldText">Publication Details:</td>
314    <td  class="input"></td>
315    <td></td>
316  </tr>
317
318  <tr class="noBorder">
319    <td>Title:</td>
320    <td class="input"><textarea rows="2" cols="30" name="publicationTitle">My Ropey Paper</textarea></td>
321
322    <td rowspan="4">Publication details for any manuscript associated with the experiment. The journal field should
323    contain a standard Pubmed journal abbreviated name. The authors list is a semicolon-delimited list of names.</td>
324  </tr>
325  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
326      <tr class="noBorder">
327        <td>Authors:</td>
328        <td class="input"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
329        <td></td>
330      </tr>
331      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
332      <tr class="noBorder">
333        <td>Journal:</td>
334        <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
335        <td></td>
336      </tr>
337      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
338      <tr class="noBorder">
339        <td>Volume:</td>
340        <td class="input"><input type="text" size="10" name="volume" value="5" /></td>
341        <td></td>
342      </tr>
343      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
344      <tr class="noBorder">
345        <td>Issue:</td>
346        <td class="input"><input type="text" size="10" name="issue" value="2" /></td>
347        <td></td>
348      </tr>
349      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
350      <tr class="noBorder">
351        <td>Pages:</td>
352        <td class="input"><input type="text" size="10" name="pages" value="1234-1235" /></td>
353        <td></td>
354      </tr>
355      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
356      <tr class="noBorder">
357        <td>Year:</td>
358        <td class="input"><input type="text" size="10" name="year" value="2007" /></td>
359        <td></td>
360      </tr>
361      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
362      <tr class="noBorder">
363        <td>Pubmed ID:</td>
364        <td class="input"><input type="text" size="30" name="pubmedId" value="11009762" /></td>
365        <td></td>
366
367  </tr>
368
369  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
370</table>
371
372<p>
373
374<table class="noBorder" width="100%">
375<tr class="noBorder" ><td class="centered">
376<input type="submit"  value="Continue"/>
377</td>
378</tr>
379</table>
380
381
382
383</form>
384
385</body>
386</html>
387
388
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