Changeset 522
- Timestamp:
- Dec 14, 2007, 6:07:34 PM (15 years ago)
- Location:
- branches/uk_ac_ebi_Tab2MageImporter
- Files:
-
- 1 deleted
- 8 edited
Legend:
- Unmodified
- Added
- Removed
-
branches/uk_ac_ebi_Tab2MageImporter/html/hybridizations.html
r521 r522 5 5 <title>Tab2MAGE Importer -- Hybridizations</title> 6 6 7 <link rel="stylesheet" type="text/css" href=" styles.css" />7 <link rel="stylesheet" type="text/css" href="../jsp/uk/ac/ebi/nugo/plugins/styles.css" /> 8 8 9 9 </head> … … 16 16 <form> 17 17 18 <!-- table with the input form --> 18 19 <table cellpadding="15"> 19 20 20 21 <!-- question 1 --> 21 22 <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px"> 22 <td class="boldText">Microarray platform used:</td> 23 <td class="input"> 24 <select name="parameter:platform"> 25 </select> 26 </td> 23 <td class="boldText">Microarray platform:</td> 24 <td class="input"><select name="parameter:platform"> 25 <option >Affymetrix</option> 26 <option >Agilent</option> 27 <option >AIDA</option> 28 <option >BZScan</option> 29 <option >ChipSkipper</option> 30 <option >GenePix</option> 31 <option >GeneTAC</option> 32 <option >Illumina</option> 33 <option >Imagene</option> 34 <option >QuantArray Biotin</option> 35 <option >QuantArray Cy</option> 36 <option >Spotfinder</option> 37 <option ><i>Custom</i></option> 38 </select></td> 39 <td>The manufacturer of the microarray chip used.</td> 27 40 </tr> 28 41 29 42 <!-- question 2 --> 30 43 <tr> 31 <td class="boldText">Name of the experimental organism:</td> 32 <td class="input"><input type="text" size="60" name="parameter:organism"/></td> 44 <td class="boldText">Experimental organism:</td> 45 <td class="input"><input type="text" size="50" name="parameter:organism" value="Solanum tuberosum"/></td> 46 <td>The full scientific name of the experimental organism used.</td> 33 47 </tr> 34 48 … … 36 50 <tr> 37 51 <td class="boldText">Number of different arrays designs used:</td> 38 <td class="input"><input type="text" size="3" name="parameter:numDesigns"/></td> 52 <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td> 53 <td>If more than one array design was used in parallel, please specify the number here.</td> 39 54 </tr> 40 55 41 56 <!-- question 4 --> 42 57 <tr> 43 <td class="boldText">Was dye-swap used?</td> 44 <td class="input">yes <input type="radio" name="parameter:dyeswap" value="yes"> no <input type="radio" name="parameter:dyeswap" value="no"> 45 <br> 58 <td class="boldText">Dye-swap</td> 59 <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio" 60 name="parameter:dyeSwap" value="no" checked="checked"> <br> 61 46 62 </td> 63 <td>If you used a dye-swap design please indicate this here.</td> 47 64 </tr> 48 65 49 66 <!-- question 5 --> 50 67 <tr> 51 <td class="boldText">Was a reference sample used?</td> 52 <td class="input">yes <input type="radio" name="parameter:refSample" value="yes"> no <input type="radio" name="parameter:refSample" 53 value="no"></td> 68 <td class="boldText">Reference sample</td> 69 <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio" 70 name="parameter:refSample" value="no" checked="checked"></td> 71 <td>If you used a reference sample please indicate this here.</td> 54 72 </tr> 55 73 56 74 <!-- question 6 --> 57 75 <tr> 58 <td class="boldText">Number of treatments used:</td> 59 <td class="input"><input type="text" size="3" name="parameter:numTreatments"/></td> 76 <td class="boldText">Number of treatment groups:</td> 77 <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="2"/></td> 78 <td>The number of permutations of factor values. <p> 79 Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3). 80 </td> 60 81 </tr> 61 82 62 83 <!-- question 7 --> 63 84 <tr> 64 <td class="boldText">Please list your experimental factors and value ranges using the following format (one per line):<br> 65 <i>Factor 1(value1,value2,...valueN)<br> 66 Factor 2(value1,value2,...valueN)</i> 67 <p>Example: <i><br>Compound(aspirin,ibuprofen,acetaminophen) 68 <br>Dose(control,low,medium,high)</i> 85 <td class="boldText">Experimental factors: 69 86 </td> 70 <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors"></textarea></td> 87 <td class="input"><textarea rows="7" cols="35" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td> 88 <td>Please list all experimental factors and value ranges using the following format (one per 89 line):<br> 90 <i>Factor 1(value1,value2,...valueN)<br></i> 91 <p>Example: <i><br> 92 Compound(aspirin,ibuprofen,acetaminophen) <br> 93 Dose(control,low,medium,high)</i></td> 71 94 </tr> 72 95 73 96 <!-- question 8 --> 74 97 <tr> 75 <td class="boldText">Number of subjects per group (i.e. number of biological replicates):</td> 76 <td class="input"><input type="text" size="3" name="parameter:numReplicates"/></td> 98 <td class="boldText">Number of subjects per group:</td> 99 <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="2"/></td> 100 <td>This is the number of biological replicates in each treatment group.</td> 77 101 </tr> 102 78 103 <!-- question 9 --> 79 104 <tr> 80 <td class="boldText"> List all target tissues (as a comma separated list).<br>81 Example: liver,heart,adipose tissue82 < /td>83 <td class="input"><textarea rows="2" cols="40" name="parameter:tissues"></textarea></td>105 <td class="boldText">Target tissues:</td> 106 <td class="input"><textarea rows="2" cols="35" name="parameter:tissues">stem</textarea></td> 107 <td>List all target tissues (as a comma separated list).<br> 108 Example: liver,heart,adipose tissue</td> 84 109 </tr> 110 85 111 <!-- question 10 --> 86 112 <tr> 87 <td class="boldText">Were samples pooled?</td> 88 <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio" name="parameter:pooling" value="no"> 89 </td> 113 <td class="boldText">Sample pooling:</td> 114 <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio" 115 name="parameter:pooling" value="no" checked="checked"></td> 116 <td>If the samples were pooled please indicate this here.</td> 90 117 </tr> 91 92 118 119 93 120 <!-- file upload --> 94 121 <tr> 95 <td class="boldText"> Please select the zip file on your local disk that contains the data files for import:</td>122 <td class="boldText">Zip file:</td> 96 123 97 <td> 98 <table border="0" cellspacing="0" cellpadding="0" class="noBorder"> 99 <tr class="noBorder"> 100 <td><input type="text" class="text required" name="path" size="50" value=""> </td> 124 <td class="input"> 125 <table class="noBorder" border="0" cellspacing="0" cellpadding="0"> 126 <tr class="noBorder" valign="middle"> 127 128 <td ><input type="text" name="path" size="40" value=""> </td> 129 101 130 <td> 102 <div class="buttonclass" onmouseover="this.className='buttonclass_hover';" 103 onmouseout="this.className='buttonclass';" onclick="browseOnClick()"> 131 <div class="buttonclass" 132 onmouseover="this.className='buttonclass_hover';" 133 onmouseout="this.className='buttonclass';" 134 onclick="browseOnClick()"> 104 135 <div class="buttonclass_inner"> 105 <table border="0" cellspacing="0" cellpadding="0"> 106 <tr> 107 <td><img src="browse.png" border="0"></td> 136 137 <table class="noBorder" cellspacing="0" cellpadding="0"> 138 <tr class="noBorder"> 139 <td> <img src="/base/images/browse.png" border="0"></td> 108 140 <td>Browse…</td> 109 141 </tr> 110 142 </table> 143 111 144 </div> 112 145 </div> 113 146 </td> 114 147 115 148 </tr> 116 149 </table> 117 150 </td> 151 152 <td>Please select the zip file on your local disk that contains the data files for import. 153 All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td> 118 154 </tr> 155 156 119 157 120 158 </table> -
branches/uk_ac_ebi_Tab2MageImporter/html/protocols.html
r511 r522 5 5 <title>Tab2MAGE Importer -- Protocols</title> 6 6 7 <link rel="stylesheet" type="text/css" href=" styles.css" />7 <link rel="stylesheet" type="text/css" href="../jsp/uk/ac/ebi/nugo/plugins/styles.css" /> 8 8 9 9 </head> -
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp
r521 r522 4 4 <%@ page import="java.util.*"%> 5 5 6 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope=" session"/>6 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application"/> 7 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 8 <jsp:setProperty name="inputDataBean" property="*"/> … … 14 14 15 15 <link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" /> 16 16 <link rel="stylesheet" type="text/css" href="/base/include/styles/main.css"> 17 <link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css"> 18 19 <script language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script> 17 20 18 21 <script type="text/javascript"> 22 function getScale() 23 { 24 return 1.0; 25 } 26 function selectArrayDesignOnClick() 27 { 28 var frm = document.forms['experimentData']; 29 var url = '<%= request.getContextPath()%>/lims/arraydesigns/index.jsp?ID=b8c5fcee801ca39c&cmd=UpdateContext&mode=selectone&callback=setArrayDesignCallback'; 30 if (frm.accession.length > 0) 31 { 32 var id = Math.abs(parseInt(frm.accession[0].value)); 33 url += '&item_id='+id; 34 } 35 Main.openPopup(url, 'SelectArrayDesign', 1000, 700); 36 } 37 function setArrayDesignCallback(id, name) 38 { 39 var frm = document.forms['experimentData']; 40 var list = frm.accession; 41 if (list.length < 1 || list[0].value == '0') // > 42 { 43 Forms.addListOption(list, 0, new Option()); 44 } 45 list[0].value = name; 46 list[0].text = name; 47 list.selectedIndex = 0; 48 parentsChanged = true; 49 } 50 //submits form 51 function submit() 52 { 53 document.experimentData.submit(); 54 } 19 55 20 56 //function to display or hide a given element … … 59 95 </head> 60 96 97 <!-- /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// --> 98 61 99 <body> 100 62 101 63 102 <% … … 84 123 85 124 Please configure your experiment for upload by answering the questions on this and the following two pages. 86 <br>87 125 The answers you provide will be used to automatically create a new experiment in BASE and your raw data will be imported 88 into this. 126 into this. All the associated objects (Hybridizations, Scans, Extracts etc.) will also be created. 89 127 <p> 90 128 91 <form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">129 <form name="experimentData" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post"> 92 130 <input type="hidden" name="ID" value="<%=ID%>"> 93 131 … … 99 137 <td class="input"><input type="text" size="45" name="domain" value="scri.ac.uk" /></td> 100 138 <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>139 any suitable string, such as the originating internet domain name (e.g. "ebi.ac.uk").</td> 102 140 </tr> 103 141 104 142 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 105 143 <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> 144 <td class="boldText">Array Acession:</td> 145 131 146 <td class="input"> 132 147 133 < table class="noBorder" cellpadding="3">134 148 <div id="accession" class="selectionlist required"> 149 <table class="noBorder" cellspacing="0" cellpadding="5"> 135 150 <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> 151 <td><select name="accession" onchange="arrayDesignOnChange()"></select></td> 152 <td> 153 <div class="buttonclass" 154 onmouseover="this.className='buttonclass_hover';" 155 onmouseout="this.className='buttonclass';" 156 onclick="selectArrayDesignOnClick()"> 157 <div class="buttonclass_inner">Select…</div> 158 </div> 159 159 </td> 160 160 </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>256 257 161 </table> 258 259 162 </div> 260 163 </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> 164 165 <td>Please select an existing array design from BASE or create a 166 new one. For ArrayExpress submissions, the array design name becomes 167 the array accession identifier. Accession numbers for experiments 168 submitted to ArrayExpress should have the format E-XXXX-n.</td> 169 265 170 </tr> 266 267 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 171 172 268 173 <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 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 310 174 175 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 176 <tr> 177 <td class="boldText">Quality Control:</td> 178 <td class="input"><select multiple name="qualityControl"> 179 <option selected="selected">biological replicate</option> 180 <option>dye swap quality control</option> 181 <option>peer review quality control</option> 182 <option>real time PCR quality control</option> 183 <option>reverse transcription PCR quality control</option> 184 <option selected="selected">spike quality control</option> 185 <option>technical replicate</option> 186 </select></td> 187 <td>A list of terms taken from the <a 188 href="http://mged.sourceforge.net/ontologies/MGEDontology.php" 189 target="_blank">MGED ontology</a>. Multiple values can be selected 190 by holding down the Ctrl key and clicking on items.</td> 191 </tr> 192 193 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 194 <tr> 195 <td class="boldText">Experiment Design Type:</td> 196 <td class="input"> 197 198 <table class="noBorder" cellpadding="3"> 199 200 <tr class="noBorder"> 201 <td valign="top">Biological Property<br /> 202 </td> 203 <td colspan="2"><a 204 onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');" 205 title="Show/hide items"> <img 206 src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" 207 border="0" id="buttonBiologicalProperty" 208 name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items --> 209 <div id="BiologicalProperty" style="display:none"><select 210 multiple="multiple" name="biologicalProperty"> 211 <option selected="selected">cell_component_comparison_design</option> 212 <option>cell_cycle_design</option> 213 <option>cell_type_comparison_design</option> 214 <option>cellular_process_design</option> 215 <option>development_or_differentiation_design</option> 216 <option>imprinting_design</option> 217 <option>individual_genetic_characteristics_design</option> 218 <option>innate_behavior_design</option> 219 <option>is_expressed_design</option> 220 <option>organism_part_comparison_design</option> 221 <option>organism_status_design</option> 222 <option>physiological_process_design</option> 223 <option>sex_design</option> 224 <option>species_design</option> 225 <option>strain_or_line_design</option> 226 <option>unknown_experiment_design_type</option> 227 </select></div> 228 </td> 229 </tr> 230 231 <tr class="noBorder"> 232 <td>BioMolecular Annotation</td> 233 <td><a 234 onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');" 235 title="Show/hide items"> <img 236 src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" 237 border="0" id="buttonBioMolecularAnnotation" 238 name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items --> 239 <div id="BioMolecularAnnotation" style="display:none"><select 240 multiple="multiple" name="bioMolecularAnnotation"> 241 <option selected="selected">RNA_stability_design</option> 242 <option>binding_site_identification_design</option> 243 <option>co-expression_design</option> 244 <option>comparative_genome_hybridization_design</option> 245 <option>genotyping_design</option> 246 <option>operon_identification_design</option> 247 <option>secreted_protein_identification_design</option> 248 <option>tiling_path_design</option> 249 <option>transcript_identification_design</option> 250 <option>translational_bias_design</option> 251 <option>unknown_experiment_design_type</option> 252 </select></div> 253 </td> 254 </tr> 255 256 <tr class="noBorder"> 257 <td>Epidemiological Design</td> 258 <td><a 259 onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" 260 title="Show/hide items"> <img 261 src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" 262 border="0" id="buttonEpidemiologicalDesign" 263 name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items --> 264 <div id="EpidemiologicalDesign" style="display:none"><select 265 multiple="multiple" name="epidemiologicalDesign"> 266 <option>clinical_history_design</option> 267 <option>disease_state_design</option> 268 <option selected="selected">family_history_design</option> 269 <option>unknown_experiment_design_type</option> 270 </select></div> 271 </td> 272 </tr> 273 274 <tr class="noBorder"> 275 <td>Methodological Design</td> 276 <td><a 277 onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" 278 title="Show/hide items"> <img 279 src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" 280 border="0" id="buttonMethodologicalDesign" 281 name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items --> 282 <div id="MethodologicalDesign" style="display:none"><select 283 multiple="multiple" name="methodologicalDesign"> 284 <option>all_pairs</option> 285 <option>array_platform_variation_design</option> 286 <option>dye_swap_design</option> 287 <option>ex_vivo_design</option> 288 <option>hardware_variation_design</option> 289 <option>in_vitro_design</option> 290 <option>in_vivo_design</option> 291 <option>loop_design</option> 292 <option>normalization_testing_design</option> 293 <option>operator_variation_design</option> 294 <option>optimization_design</option> 295 <option>quality_control_testing_design</option> 296 <option>reference_design</option> 297 <option>replicate_design</option> 298 <option>self_vs_self_design</option> 299 <option>software_variation_design</option> 300 <option>time_series_design</option> 301 <option>unknown_experiment_design_type</option> 302 </select></div> 303 </td> 304 </tr> 305 306 <tr class="noBorder"> 307 <td>Perturbational Design</td> 308 <td><a 309 onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" 310 title="Show/hide items"> <img 311 src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" 312 border="0" id="buttonPerturbationalDesign" 313 name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items --> 314 <div id="PerturbationalDesign" style="display:none"><select 315 multiple="multiple" name="perturbationalDesign"> 316 <option>cellular_modification_design</option> 317 <option>compound_treatment_design</option> 318 <option>disease_state_design</option> 319 <option>dose_response_design</option> 320 <option>genetic_modification_design</option> 321 <option>growth_condition_design</option> 322 <option>injury_design</option> 323 <option>non-targeted_transgenic_variation_design</option> 324 <option>pathogenicity_design</option> 325 <option>stimulated_design_type</option> 326 <option>stimulus_or_stress_design</option> 327 <option>unknown_experiment_design_type</option> 328 </select></div> 329 </td> 330 </tr> 331 332 <tr class="noBorder"> 333 <td>Technological Design</td> 334 <td><a 335 onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" 336 title="Show/hide items"> <img 337 src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" 338 border="0" id="buttonTechnologicalDesign" 339 name="TechnologicalDesign" /></a> <!-- begin div containing hidden items --> 340 <div id="TechnologicalDesign" style="display:none"><select 341 multiple="multiple" name="technologicalDesign"> 342 <option>binding_site_identification_design</option> 343 <option>cellular_modification_design</option> 344 <option>comparative_genome_hybridization_design</option> 345 <option>transcript_identification_design</option> 346 </select></div> 347 </td> 348 </tr> 349 350 </table> 351 352 353 </td> 354 <td>A list of terms taken from the <a 355 href="http://mged.sourceforge.net/ontologies/MGEDontology.php" 356 target="_blank">MGED ontology</a>. 357 <p>Click "expand" for an item to see list boxes with specific 358 choices.<br /> 359 <br /> 360 Multiple values can be selected by holding down the Ctrl key and 361 clicking on items. 362 </td> 363 </tr> 364 365 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 366 <tr> 367 <td class="boldText">Experiment Name:</td> 368 <td class="input"><textarea rows="2" cols="30" 369 name="experimentName"><%=expName %></textarea></td> 370 <td>The name you have chosen for the Experiment.</td> 371 </tr> 372 373 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 374 <tr> 375 <td class="boldText">Experiment Description:</td> 376 <td class="input"><textarea rows="2" cols="30" 377 name="description">description goes here</textarea></td> 378 <td>A short paragraph describing the purpose of the experiment.</td> 379 </tr> 380 381 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 382 <tr> 383 <td class="boldText">Release Date:</td> 384 <td class="input"><input type="text" size="10" 385 name="releaseDate" value="2007-12-03" /></td> 386 <td>Date for public release, in the format YYYY-MM-DD.</td> 387 </tr> 388 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 389 <tr> 390 <td class="boldText">Submission Date:</td> 391 <td class="input"><input type="text" size="10" 392 name="submissionDate" value="2007-12-03" /></td> 393 <td>Date of submission, in the format YYYY-MM-DD.</td> 394 </tr> 395 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 396 <tr> 397 <td class="boldText">Submitter:</td> 398 <td class="input"><input type="text" size="45" name="submitter" 399 value="Joe Bloggs" /></td> 400 <td>The name of the person responsible for submitting the 401 experiment to the database.</td> 402 </tr> 403 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 404 <tr> 405 <td class="boldText">Organization:</td> 406 <td class="input"><input type="text" size="45" 407 name="organization" value="SCRI" /></td> 408 <td>The organization to which the submitter is affiliated.</td> 409 </tr> 410 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 411 412 <tr class="noBorder"> 413 <td class="boldText">Publication Details:</td> 414 <td class="input"></td> 415 <td></td> 416 </tr> 417 418 <tr class="noBorder"> 419 <td>Title:</td> 420 <td class="input"><textarea rows="2" cols="30" 421 name="publicationTitle">My Ropey Paper</textarea></td> 422 423 <td rowspan="4">Publication details for any manuscript 424 associated with the experiment. <p> 425 The authors list is a semicolon-delimited list of names.<p> 426 The journal field should contain a standard Pubmed journal 427 abbreviated name. </td> 428 </tr> 429 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 430 <tr class="noBorder"> 431 <td>Authors:</td> 432 <td class="input"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td> 433 <td></td> 434 </tr> 435 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 436 <tr class="noBorder"> 437 <td>Journal:</td> 438 <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td> 439 <td></td> 440 </tr> 441 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 442 <tr class="noBorder"> 443 <td>Volume:</td> 444 <td class="input"><input type="text" size="10" name="volume" 445 value="5" /></td> 446 <td></td> 447 </tr> 448 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 449 <tr class="noBorder"> 450 <td>Issue:</td> 451 <td class="input"><input type="text" size="10" name="issue" 452 value="2" /></td> 453 <td></td> 454 </tr> 455 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 456 <tr class="noBorder"> 457 <td>Pages:</td> 458 <td class="input"><input type="text" size="10" name="pages" 459 value="1234-1235" /></td> 460 <td></td> 461 </tr> 462 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 463 <tr class="noBorder"> 464 <td>Year:</td> 465 <td class="input"><input type="text" size="10" name="year" 466 value="2007" /></td> 467 <td></td> 468 </tr> 469 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 470 <tr class="noBorder"> 471 <td>Pubmed ID:</td> 472 <td class="input"><input type="text" size="30" name="pubmedId" 473 value="11009762" /></td> 474 <td></td> 475 476 </tr> 477 478 <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ --> 479 </table> 480 481 <p> 482 483 484 <table align="center" class="noBorder" cellpadding="5"> 311 485 <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> 486 <td id="next" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="submit()"><div class="buttonclass_inner"><table class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td><img src="/base/images/gonext.gif" border="0"></td><td>Continue</td></tr></table></div></div></td> 487 <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 class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td> 384 488 </tr> 385 489 </table> -
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp
r521 r522 4 4 <%@ page import="java.util.*"%> 5 5 6 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope=" session" />6 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" /> 7 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 8 <jsp:setProperty name="inputDataBean" property="*" /> … … 20 20 21 21 <link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" /> 22 <link rel="stylesheet" type="text/css" href="/base/include/styles/main.css"> 23 <link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css"> 22 24 23 25 24 <script language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script> 26 25 27 26 <script language="JavaScript" type="text/javascript"> 27 //submits form 28 function submit() 29 { 30 document.hybridizations.submit(); 31 } 28 32 function getRoot() 29 33 { … … 125 129 <!-- question 1 --> 126 130 <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px"> 127 <td class="boldText">Microarray platform used:</td>131 <td class="boldText">Microarray platform:</td> 128 132 <td class="input"><select name="parameter:platform"> 129 133 <option >Affymetrix</option> … … 139 143 <option >QuantArray Cy</option> 140 144 <option >Spotfinder</option> 145 <option ><i>Custom</i></option> 141 146 </select></td> 147 <td>The manufacturer of the microarray chip used.</td> 142 148 </tr> 143 149 144 150 <!-- question 2 --> 145 151 <tr> 146 <td class="boldText">Name of the experimental organism:</td> 147 <td class="input"><input type="text" size="60" name="parameter:organism" value="Solanum tuberosum"/></td> 152 <td class="boldText">Experimental organism:</td> 153 <td class="input"><input type="text" size="50" name="parameter:organism" value="Solanum tuberosum"/></td> 154 <td>The full scientific name of the experimental organism used.</td> 148 155 </tr> 149 156 … … 152 159 <td class="boldText">Number of different arrays designs used:</td> 153 160 <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td> 161 <td>If more than one array design was used in parallel, please specify the number here. 162 We assume that all samples are applied once to each array design</td> 154 163 </tr> 155 164 156 165 <!-- question 4 --> 157 166 <tr> 158 <td class="boldText"> Was dye-swap used?</td>167 <td class="boldText">Dye-swap</td> 159 168 <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio" 160 169 name="parameter:dyeSwap" value="no" checked="checked"> <br> 161 </td> 170 171 </td> 172 <td>If you used a dye-swap design please indicate this here.</td> 162 173 </tr> 163 174 164 175 <!-- question 5 --> 165 176 <tr> 166 <td class="boldText"> Was a reference sample used?</td>177 <td class="boldText">Reference sample</td> 167 178 <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio" 168 179 name="parameter:refSample" value="no" checked="checked"></td> 180 <td>If you used a reference sample please indicate this here.</td> 169 181 </tr> 170 182 … … 173 185 <td class="boldText">Number of treatment groups:</td> 174 186 <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="2"/></td> 187 <td>The number of permutations of factor values. <p> 188 Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3). 189 </td> 175 190 </tr> 176 191 177 192 <!-- question 7 --> 178 193 <tr> 179 <td class="boldText">Please list your experimental factors and value ranges using the following format (one per 194 <td class="boldText">Experimental factors: 195 </td> 196 <td class="input"><textarea rows="7" cols="35" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td> 197 <td>Please list all experimental factors and value ranges using the following format (one per 180 198 line):<br> 181 199 <i>Factor 1(value1,value2,...valueN)<br></i> 182 200 <p>Example: <i><br> 183 201 Compound(aspirin,ibuprofen,acetaminophen) <br> 184 Dose(control,low,medium,high)</i> 185 </td> 186 <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td> 202 Dose(control,low,medium,high)</i></td> 187 203 </tr> 188 204 189 205 <!-- question 8 --> 190 206 <tr> 191 <td class="boldText">Number of subjects per group (i.e. number of biological replicates):</td>207 <td class="boldText">Number of subjects per group:</td> 192 208 <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="2"/></td> 209 <td>This is the number of biological replicates in each treatment group.</td> 193 210 </tr> 194 211 195 212 <!-- question 9 --> 196 213 <tr> 197 <td class="boldText">List all target tissues (as a comma separated list).<br> 214 <td class="boldText">Target tissues:</td> 215 <td class="input"><textarea rows="2" cols="35" name="parameter:tissues">stem</textarea></td> 216 <td>List all target tissues (as a comma separated list).<br> 198 217 Example: liver,heart,adipose tissue</td> 199 <td class="input"><textarea rows="2" cols="40" name="parameter:tissues">stem</textarea></td>200 218 </tr> 201 219 202 220 <!-- question 10 --> 203 221 <tr> 204 <td class="boldText"> Were samples pooled?</td>222 <td class="boldText">Sample pooling:</td> 205 223 <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio" 206 224 name="parameter:pooling" value="no" checked="checked"></td> 225 <td>If the samples were pooled please indicate this here.</td> 207 226 </tr> 208 227 209 228 210 229 <!-- file upload --> 211 <tr 212 <td class="boldText"> Please select the zip file on your local disk that contains the data files for import:</td>213 <td> 214 215 <table class="noBorder" border="0" cellspacing="0" cellpadding=" 0">216 <tr class="noBorder" >217 <td><input type="text" class="text required" name="path" size="50" value=""> </td>218 <td >230 <tr> 231 <td class="boldText">Zip file:</td> 232 233 <td class="input"> 234 <table class="noBorder" border="0" cellspacing="0" cellpadding="5"> 235 <tr class="noBorder" > 236 237 <td style="vertical-align: middle"><input type="text" name="path" size="35" value=""></td> 219 238 220 <div class="buttonclass" onmouseover="this.className='buttonclass_hover';" 221 onmouseout="this.className='buttonclass';" onclick="browseOnClick()"> 222 <div class="buttonclass_inner"> 223 224 <table border="0" cellspacing="0" cellpadding="0"> 225 <tr> 239 <td style="vertical-align: middle"> 240 <div class="buttons" 241 onmouseover="this.className='buttons_hover';" 242 onmouseout="this.className='buttons';" 243 onclick="browseOnClick()"> 244 <div class="buttons_inner"> 245 246 <table class="noBorder" cellspacing="0" cellpadding="0"> 247 <tr class="noBorder"> 226 248 <td> <img src="/base/images/browse.png" border="0"></td> 227 249 <td>Browse…</td> … … 232 254 </div> 233 255 </td> 256 234 257 </tr> 235 258 </table> 236 </td> 237 </tr> 238 239 259 </td> 260 261 <td>Please select the zip file on your local disk that contains the data files for import. 262 All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td> 263 </tr> 240 264 241 265 </table> 242 266 243 267 <p> 244 <table class="noBorder" width="100%"> 268 269 <table align="center" class="noBorder" cellpadding="5"> 245 270 <tr class="noBorder"> 246 <td class="centered"><input type="submit" value="Run Import" /></td> 247 </tr> 248 </table> 249 250 <table align="center"> 251 <tr> 252 <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>Submit</td></tr></table></div></div></td> 253 <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> 254 </tr> 271 <td id="next" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td><img src="/base/images/gonext.gif" border="0"></td><td>Run Import</td></tr></table></div></div></td> 272 <td id="close" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td> </tr> 255 273 </table> 256 274 -
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/protocols.jsp
r521 r522 5 5 <%@ page import="java.lang.*"%> 6 6 7 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope=" session" />7 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" /> 8 8 <!-- 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 --> 9 9 <jsp:setProperty name="inputDataBean" property="*" /> … … 11 11 12 12 <html> 13 13 14 <head> 15 14 16 <link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" /> 17 <link rel="stylesheet" type="text/css" href="/base/include/styles/main.css"> 18 <link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css"> 19 20 <script language="JavaScript" type="text/javascript"> 21 //submits form 22 function submit() 23 { 24 document.protocols.submit(); 25 } 26 </script> 27 15 28 </head> 29 16 30 <body> 17 31 … … 104 118 %> 105 119 106 <form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/hybridizations.jsp" method="post">120 <form name="protocols" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/hybridizations.jsp" method="post"> 107 121 <input type="hidden" name="ID" value="<%=ID%>"> 108 122 … … 122 136 <td class="header"> 123 137 <h3>Parameters</h3> 124 <p>A list of parameters for this protocol, separated by semicolons, in the format 'name(units)'. <br />125 Each parameter name should be unique within this form.<br />138 <p>A list of parameters for this protocol, separated by semicolons, in the format 'name(units)'. 139 Each parameter name must be unique within this form.<br /><br /> 126 140 Leave blank if the protocol is unparameterized.</p> 127 141 </td> … … 131 145 <td class="boldText">Treatment</td> 132 146 <td class="input"><textarea rows="8" cols="35" name="treatmentProtocol">my treatment protocol text </textarea></td> 133 <td ><textarea rows="4" cols="25" name="treatmentProtocolParams">param1</textarea></td>147 <td class="input_topaligned"><textarea rows="3" cols="35" name="treatmentProtocolParams">param1</textarea></td> 134 148 </tr> 135 149 … … 137 151 <td class="boldText">Extraction</td> 138 152 <td class="input"><textarea rows="8" cols="35" name="extractionProtocol"> my extraction protocol text </textarea></td> 139 <td ><textarea rows="4" cols="25" name="extractionProtocolParams">param2</textarea></td>153 <td class="input_topaligned"><textarea rows="3" cols="35" name="extractionProtocolParams">param2</textarea></td> 140 154 </tr> 141 155 … … 143 157 <td class="boldText">Labeling</td> 144 158 <td class="input"><textarea rows="8" cols="35" name="labelingProtocol"> my labeling protocol text </textarea></td> 145 <td ><textarea rows="4" cols="25" name="labelingProtocolParams">param3</textarea></td>159 <td class="input_topaligned"><textarea rows="3" cols="35" name="labelingProtocolParams">param3</textarea></td> 146 160 </tr> 147 161 … … 149 163 <td class="boldText">Hybridization</td> 150 164 <td class="input"><textarea rows="8" cols="35" name="hybridizationProtocol">my hybs protocol text </textarea></td> 151 <td ><textarea rows="4" cols="25" name="hybridizationProtocolParams">param4</textarea></td>165 <td class="input_topaligned"><textarea rows="3" cols="35" name="hybridizationProtocolParams">param4</textarea></td> 152 166 </tr> 153 167 … … 155 169 <td class="boldText">Scanning</td> 156 170 <td class="input"><textarea rows="8" cols="35"name="scanningProtocol"> my scanning protocol text </textarea></td> 157 <td ><textarea rows="4" cols="25" name="scanningProtocolParams"> param5</textarea></td>171 <td class="input_topaligned"><textarea rows="3" cols="35" name="scanningProtocolParams"> param5</textarea></td> 158 172 </tr> 159 173 … … 161 175 162 176 <p> 163 <table class="noBorder" width="100%">164 <tr class="noBorder">165 <td class="centered"><input type="submit" value="Continue" /></td>166 </tr>167 </table>168 177 169 <table align="center"> 170 <tr> 171 <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> 172 <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> 173 </tr> 178 <table align="center" class="noBorder" cellpadding="5"> 179 <tr class="noBorder"> 180 <td id="next" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="submit()"><div class="buttonclass_inner"><table class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td><img src="/base/images/gonext.gif" border="0"></td><td>Continue</td></tr></table></div></div></td> 181 <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 class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td> </tr> 174 182 </table> 175 183 -
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/styles.css
r521 r522 44 44 tr.noBorder { 45 45 border-style: none; 46 vertical-align: middle; 46 47 } 47 48 … … 67 68 } 68 69 70 td.input_topaligned { 71 vertical-align: top; 72 text-align: left; 73 align: left; # 74 white-space: nowrap; 75 background-color: rgb(240, 240, 240); 76 } 77 69 78 img { 70 vertical-align: bottom;79 vertical-align: middle; 71 80 } 81 82 .buttons{ 83 background: #E0E0E0; 84 border-top: 1px solid #333333; 85 border-left: 1px solid #333333; 86 border-right: 1px solid #333333; 87 border-bottom: 1px solid #333333; 88 vertical-align: middle; 89 } 90 91 92 .buttons_inner { 93 border-top: 1px solid #FFFFFF; 94 border-left: 1px solid #FFFFFF; 95 border-bottom: 1px solid #999999; 96 border-right: 1px solid #999999; 97 padding: 1px 5px 2px 5px; 98 text-align: center; 99 white-space: nowrap; 100 vertical-align: middle; 101 } 102 103 .buttons_hover { 104 background: #F0F0F0; 105 border-top: 1px solid #333333; 106 border-left: 1px solid #333333; 107 border-right: 1px solid #333333; 108 border-bottom: 1px solid #333333; 109 cursor: pointer; 110 vertical-align: middle; 111 } 112 113 .form tr { 114 vertical-align: middle; 115 }
Note: See TracChangeset
for help on using the changeset viewer.