source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp @ 511

Last change on this file since 511 was 511, checked in by mbayer, 14 years ago
  • have tidied up the interface to the point where it is usable as it is
  • have provided defaults for every field in every form for testing
File size: 17.5 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="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">
103
104    <table class="noBorder" cellpadding="1">
105
106      <tr class="noBorder">
107        <td>biological replicate</td>
108        <td><input type="checkbox" name="biological replicate" value="biological replicate" checked="checked"/></td>
109      </tr>
110
111      <tr class="noBorder">
112        <td>dye swap quality control</td>
113        <td><input type="checkbox" name="dye swap quality control" value="dye swap quality control" /></td>
114      </tr>
115
116      <tr class="noBorder">
117        <td>peer review quality control</td>
118        <td><input type="checkbox" name="peer review quality control" value="peer review quality control" /></td>
119      </tr>
120
121      <tr class="noBorder">
122        <td>real time PCR quality control</td>
123        <td><input type="checkbox" name="real time PCR quality control" value="real time PCR quality control" /></td>
124      </tr>
125
126      <tr class="noBorder">
127        <td>reverse transcription PCR quality control</td>
128        <td><input type="checkbox" name="reverse transcription PCR quality control"
129          value="reverse transcription PCR quality control" /></td>
130      </tr>
131
132      <tr class="noBorder">
133        <td>spike quality control</td>
134        <td><input type="checkbox" name="spike quality control" value="spike quality control" /></td>
135      </tr>
136
137      <tr class="noBorder">
138        <td>technical replicate</td>
139        <td><input type="checkbox" name="technical replicate" value="technical replicate" /></td>
140      </tr>
141
142    </table>
143
144  </td>
145  <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED ontology</a>. Multiple values can be selected.</td>
146  </tr>
147 
148  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
149  <tr>
150    <td class="boldText">Experiment Design Type:</td>
151    <td class="input">
152
153    <table class="noBorder" cellpadding="3" >
154
155      <tr class="noBorder">
156        <td valign="top">Biological Property<br/>
157        </td>
158        <td colspan="2"><a onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
159          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBiologicalProperty"
160          name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
161        <div id="BiologicalProperty" style="display:none"><select multiple="multiple">
162          <option selected="selected">cell_component_comparison_design</option>
163          <option>cell_cycle_design</option>
164          <option>cell_type_comparison_design</option>
165          <option>cellular_process_design</option>
166          <option>development_or_differentiation_design</option>
167          <option>imprinting_design</option>
168          <option>individual_genetic_characteristics_design</option>
169          <option>innate_behavior_design</option>
170          <option>is_expressed_design</option>
171          <option>organism_part_comparison_design</option>
172          <option>organism_status_design</option>
173          <option>physiological_process_design</option>
174          <option>sex_design</option>
175          <option>species_design</option>
176          <option>strain_or_line_design</option>
177          <option>unknown_experiment_design_type</option>
178        </select></div>
179        </td>
180      </tr>
181
182      <tr class="noBorder">
183        <td>BioMolecular Annotation</td>
184        <td><a onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
185          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBioMolecularAnnotation"
186          name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
187        <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple">
188          <option selected="selected">RNA_stability_design</option>
189          <option>binding_site_identification_design</option>
190          <option>co-expression_design</option>
191          <option>comparative_genome_hybridization_design</option>
192          <option>genotyping_design</option>
193          <option>operon_identification_design</option>
194          <option>secreted_protein_identification_design</option>
195          <option>tiling_path_design</option>
196          <option>transcript_identification_design</option>
197          <option>translational_bias_design</option>
198          <option>unknown_experiment_design_type</option>
199        </select></div>
200        </td>
201      </tr>
202
203      <tr class="noBorder">
204        <td>Epidemiological Design</td>
205        <td><a onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" title="Show/hide items">
206        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonEpidemiologicalDesign" name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
207        <div id="EpidemiologicalDesign" style="display:none"><select multiple="multiple">
208          <option>clinical_history_design</option>
209          <option>disease_state_design</option>
210          <option selected="selected">family_history_design</option>
211          <option>unknown_experiment_design_type</option>
212        </select></div>
213        </td>
214      </tr>
215
216      <tr class="noBorder">
217        <td>Methodological Design</td>
218        <td><a onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" title="Show/hide items">
219        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonMethodologicalDesign" name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
220        <div id="MethodologicalDesign" style="display:none"><select multiple="multiple">
221          <option>all_pairs</option>
222          <option>array_platform_variation_design</option>
223          <option>dye_swap_design</option>
224          <option>ex_vivo_design</option>
225          <option>hardware_variation_design</option>
226          <option>in_vitro_design</option>
227          <option>in_vivo_design</option>
228          <option>loop_design</option>
229          <option>normalization_testing_design</option>
230          <option>operator_variation_design</option>
231          <option>optimization_design</option>
232          <option>quality_control_testing_design</option>
233          <option>reference_design</option>
234          <option>replicate_design</option>
235          <option>self_vs_self_design</option>
236          <option>software_variation_design</option>
237          <option>time_series_design</option>
238          <option>unknown_experiment_design_type</option>
239        </select></div>
240        </td>
241      </tr>
242
243      <tr class="noBorder">
244        <td>Perturbational Design</td>
245        <td><a onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" title="Show/hide items">
246        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonPerturbationalDesign" name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
247        <div id="PerturbationalDesign" style="display:none"><select multiple="multiple">
248          <option>cellular_modification_design</option>
249          <option>compound_treatment_design</option>
250          <option>disease_state_design</option>
251          <option>dose_response_design</option>
252          <option>genetic_modification_design</option>
253          <option>growth_condition_design</option>
254          <option>injury_design</option>
255          <option>non-targeted_transgenic_variation_design</option>
256          <option>pathogenicity_design</option>
257          <option>stimulated_design_type</option>
258          <option>stimulus_or_stress_design</option>
259          <option>unknown_experiment_design_type</option>
260        </select></div>
261        </td>
262      </tr>
263
264      <tr class="noBorder">
265        <td>Technological Design</td>
266        <td><a onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" title="Show/hide items">
267        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonTechnologicalDesign" name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
268        <div id="TechnologicalDesign" style="display:none"><select multiple="multiple">
269          <option>binding_site_identification_design</option>
270          <option>cellular_modification_design</option>
271          <option>comparative_genome_hybridization_design</option>
272          <option>transcript_identification_design</option>
273        </select></div>
274        </td>
275      </tr>
276
277    </table>
278
279
280    </td>
281    <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED ontology</a>.
282     Multiple values can be selected.
283    <p>Click "expand" for an item to see list boxes with specific choices.<br>
284    Hold down the 'Ctrl' key and click to select multiple options.
285    </td>
286  </tr>
287 
288  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
289  <tr>
290    <td class="boldText">Experiment Name:</td>
291    <td class="input"> 
292    <textarea rows="2" cols="30" name="experimentName">my numpty experiment</textarea>
293    </td>
294    <td>The name you have chosen for the Experiment.</td>
295  </tr>
296 
297  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
298  <tr>
299    <td class="boldText">Experiment Description:</td>
300    <td class="input">
301    <textarea rows="2" cols="30" name="description">description goes here</textarea>
302    </td>
303    <td>A short paragraph describing the purpose of the experiment.</td>
304  </tr>
305 
306  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
307  <tr>
308    <td class="boldText">Release Date:</td>
309    <td class="input"><input type="text" size="10" name="" value="2007-12-03" /></td>
310    <td>Date for public release, in the format YYYY-MM-DD.</td>
311  </tr>
312  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
313  <tr>
314    <td class="boldText">Submission Date:</td>
315    <td class="input"><input type="text" size="10" name="submissionDate" value="2007-12-03" /></td>
316    <td>Date of submission, in the format YYYY-MM-DD.</td>
317  </tr>
318  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
319  <tr>
320    <td class="boldText">Submitter:</td>
321    <td class="input"><input type="text" size="45" name="submitter" value="Joe Bloggs" /></td>
322    <td>The name of the person responsible for submitting the experiment to the database.</td>
323  </tr>
324  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
325  <tr>
326    <td class="boldText">Organization:</td>
327    <td class="input"><input type="text" size="45" name="organization" value="SCRI" /></td>
328    <td>The organization to which the submitter is affiliated.</td>
329  </tr>
330  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
331
332  <tr class="noBorder">
333    <td class="boldText">Publication Details:</td>
334    <td  class="input"></td>
335    <td></td>
336  </tr>
337
338  <tr class="noBorder">
339    <td>Title:</td>
340    <td class="input"><textarea rows="2" cols="30" name="publicationTitle">My Ropey Paper</textarea></td>
341
342    <td rowspan="4">Publication details for any manuscript associated with the experiment. The journal field should
343    contain a standard Pubmed journal abbreviated name. The authors list is a semicolon-delimited list of names.</td>
344  </tr>
345  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
346      <tr class="noBorder">
347        <td>Authors:</td>
348        <td class="input"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
349        <td></td>
350      </tr>
351      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
352      <tr class="noBorder">
353        <td>Journal:</td>
354        <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Unreproducible Results</textarea></td>
355        <td></td>
356      </tr>
357      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
358      <tr class="noBorder">
359        <td>Volume:</td>
360        <td class="input"><input type="text" size="10" name="volume" value="5" /></td>
361        <td></td>
362      </tr>
363      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
364      <tr class="noBorder">
365        <td>Issue:</td>
366        <td class="input"><input type="text" size="10" name="issue" value="2" /></td>
367        <td></td>
368      </tr>
369      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
370      <tr class="noBorder">
371        <td>Pages:</td>
372        <td class="input"><input type="text" size="10" name="pages" value="1234-1235" /></td>
373        <td></td>
374      </tr>
375      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
376      <tr class="noBorder">
377        <td>Year:</td>
378        <td class="input"><input type="text" size="10" name="year" value="2007" /></td>
379        <td></td>
380      </tr>
381      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
382      <tr class="noBorder">
383        <td>Pubmed ID:</td>
384        <td class="input"><input type="text" size="30" name="pubmedId" value="11009762" /></td>
385        <td></td>
386
387  </tr>
388
389  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
390</table>
391
392<p>
393
394<table class="noBorder" width="100%">
395<tr class="noBorder" ><td class="centered">
396<input type="submit"  value="Continue"/>
397</td>
398</tr>
399</table>
400
401
402
403</form>
404
405</body>
406</html>
407
408
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