Changeset 528
- Timestamp:
- Jan 9, 2008, 11:25:17 AM (16 years ago)
- Location:
- branches/uk_ac_ebi_Tab2MageImporter
- Files:
-
- 8 edited
Legend:
- Unmodified
- Added
- Removed
-
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp
r525 r528 120 120 121 121 <h1>Tab2MAGE Importer -- Your Experiment</h1> 122 Page 1 of 3122 Page 1 of 4 123 123 <p> 124 124 -
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp
r527 r528 88 88 <input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters"> 89 89 <input type="hidden"name="requestID" value="<%=requestID%>"> 90 <!-- these are the parameters from the input pages; need to pick them up individually from the bean here; ugly as hell but can't be done any other way -->91 <input type="hidden" name="parameter:domain" value="<%=inputDataBean.getDomain()%>">92 <input type="hidden" name="parameter:accession" value="<%=inputDataBean.getAccession()%>">93 <input type="hidden" name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>">94 <input type="hidden" name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>">95 <input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>">96 <input type="hidden" name="parameter:description" value="<%=inputDataBean.getDescription()%>">97 <input type="hidden" name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>">98 <input type="hidden" name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>">99 <input type="hidden" name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>">100 <input type="hidden" name="parameter:organization" value="<%=inputDataBean.getOrganization()%>">101 <input type="hidden" name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>">102 <input type="hidden" name="parameter:authors" value="<%=inputDataBean.getAuthors()%>">103 <input type="hidden" name="parameter:journal" value="<%=inputDataBean.getJournal()%>">104 <input type="hidden" name="parameter:volume" value="<%=inputDataBean.getVolume()%>">105 <input type="hidden" name="parameter:issue" value="<%=inputDataBean.getIssue()%>">106 <input type="hidden" name="parameter:pages" value="<%=inputDataBean.getPages()%>">107 <input type="hidden" name="parameter:year" value="<%=inputDataBean.getYear()%>">108 <input type="hidden" name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>">109 <input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>">110 <input type="hidden" name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>">111 <input type="hidden" name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>">112 <input type="hidden" name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>">113 <input type="hidden" name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>">114 <input type="hidden" name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>">115 <input type="hidden" name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>">116 <input type="hidden" name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>">117 <input type="hidden" name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>">118 <input type="hidden" name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>">119 <input type="hidden" name="parameter:experimentId" value="<%=inputDataBean.getExperimentId()%>">120 90 121 91 <input type="hidden" name="file_id" value=""> 122 <input type="hidden" name=" parameter:zipFile" value="" id="zipFile">92 <input type="hidden" name="zipFile" value="" id="zipFile"> 123 93 124 94 <h1>Tab2MAGE Importer -- Your Hybridizations</h1> 125 Page 3 of 395 Page 3 of 4 126 96 <p> 127 97 <!-- table with the input form --> … … 131 101 <tr > 132 102 <td class="boldText">Microarray platform:</td> 133 <td class="input"><select name="platform"> 103 <td class="input"> 104 <select name="platform"> 134 105 <option >Affymetrix</option> 135 106 <option >Agilent</option> -
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/mappings.jsp
r527 r528 1 <%@ page language="java" contentType="text/html; charset=ISO-8859-1" 2 pageEncoding="ISO-8859-1"%> 1 <%@ page language="java" contentType="text/html; charset=ISO-8859-1" pageEncoding="ISO-8859-1"%> 3 2 <%@ page import="java.util.*"%> 3 <%@ page import="java.util.zip.*"%> 4 4 <%@ page import="net.sf.basedb.core.*"%> 5 5 <%@ page import="net.sf.basedb.clients.web.*"%> … … 7 7 <%@ page import="uk.ac.ebi.nugo.plugins.*"%> 8 8 9 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" 10 scope="application" /> 9 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" /> 11 10 <!-- 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 --> 12 11 <jsp:setProperty name="inputDataBean" property="*" /> … … 22 21 <head> 23 22 24 <link rel="stylesheet" type="text/css" 25 href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" /> 26 <link rel="stylesheet" type="text/css" 27 href="/base/include/styles/main.css"> 28 <link rel="stylesheet" type="text/css" 29 href="/base/include/styles/size_m.css"> 30 31 <script language="JavaScript" 32 src="<%= request.getContextPath()%>/include/scripts/main.js" 33 type="text/javascript"></script> 23 <link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" /> 24 <link rel="stylesheet" type="text/css" href="/base/include/styles/main.css"> 25 <link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css"> 26 27 <script language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script> 34 28 <script language="JavaScript" type="text/javascript"> 35 29 //submits form … … 52 46 <body> 53 47 48 49 50 <form name="mappings" action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post"> 51 52 <input type="hidden" name="ID" value="<%=ID%>"> 53 <input type="hidden" name="cmd" value="SetParameters"> <input type="hidden" name="requestID" value="<%=requestID%>"> 54 55 <!-- these are the parameters from the input pages; need to pick them up individually from the bean here; ugly as hell but can't be done any other way --> 56 57 <!-- inputs from experiment.jsp page --> 58 <input type="hidden" name="parameter:domain" value="<%=inputDataBean.getDomain()%>"> 59 <input type="hidden" name="parameter:accession" value="<%=inputDataBean.getAccession()%>"> 60 <input type="hidden" name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>"> 61 <input type="hidden" name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>"> 62 <input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>"> 63 <input type="hidden" name="parameter:description" value="<%=inputDataBean.getDescription()%>"> 64 <input type="hidden" name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>"> 65 <input type="hidden" name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>"> 66 <input type="hidden" name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>"> 67 <input type="hidden" name="parameter:organization" value="<%=inputDataBean.getOrganization()%>"> 68 <input type="hidden" name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>"> 69 <input type="hidden" name="parameter:authors" value="<%=inputDataBean.getAuthors()%>"> 70 <input type="hidden" name="parameter:journal" value="<%=inputDataBean.getJournal()%>"> 71 <input type="hidden" name="parameter:volume" value="<%=inputDataBean.getVolume()%>"> 72 <input type="hidden" name="parameter:issue" value="<%=inputDataBean.getIssue()%>"> 73 <input type="hidden" name="parameter:pages" value="<%=inputDataBean.getPages()%>"> 74 <input type="hidden" name="parameter:year" value="<%=inputDataBean.getYear()%>"> 75 <input type="hidden" name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>"> 76 <input type="hidden" name="parameter:experimentId" value="<%=inputDataBean.getExperimentId()%>"> 77 <!-- inputs from protocols.jsp page --> 78 <input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>"> 79 <input type="hidden" name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>"> 80 <input type="hidden" name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>"> 81 <input type="hidden" name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>"> 82 <input type="hidden" name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>"> 83 <input type="hidden" name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>"> 84 <input type="hidden" name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>"> 85 <input type="hidden" name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>"> 86 <input type="hidden" name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>"> 87 <input type="hidden" name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>"> 88 <!-- inputs from hybridizations.jsp page --> 89 <input type="hidden" name="parameter:platform" value="<%=inputDataBean.getPlatform()%>"> 90 <input type="hidden" name="parameter:organism" value="<%=inputDataBean.getOrganism()%>"> 91 <input type="hidden" name="parameter:numDesigns" value="<%=inputDataBean.getNumDesigns()%>"> 92 <input type="hidden" name="parameter:dyeSwap" value="<%=inputDataBean.getDyeSwap()%>"> 93 <input type="hidden" name="parameter:refSample" value="<%=inputDataBean.getRefSample()%>"> 94 <input type="hidden" name="parameter:numTreatmentGroups" value="<%=inputDataBean.getNumTreatmentGroups()%>"> 95 <input type="hidden" name="parameter:expFactors" value="<%=inputDataBean.getExpFactors()%>"> 96 <input type="hidden" name="parameter:numReplicates" value="<%=inputDataBean.getNumReplicates()%>"> 97 <input type="hidden" name="parameter:tissues" value="<%=inputDataBean.getTissues()%>"> 98 <input type="hidden" name="parameter:pooling" value="<%=inputDataBean.getPooling()%>"> 99 <input type="hidden" name="file_id" value="<%=(String)request.getAttribute("file_id") %>"> 100 <input type="hidden" name="parameter:zipFile" value="<%=(String)request.getParameter("path") %>" id="zipFile"> 101 54 102 <% 103 System.out.println("all parameter values in mappings.jsp:"); 104 for (java.util.Enumeration e = request.getParameterNames(); e.hasMoreElements();) 105 { 106 String name = (String) e.nextElement(); 107 String value = request.getParameter(name); 108 System.out.println("parameter " + name + " = " + value); 109 } 110 55 111 //first extract the factor names and the possible values 56 String expFactors = inputDataBean.getExpFactors() ;112 String expFactors = inputDataBean.getExpFactors().trim(); 57 113 String[] rawFactors = expFactors.split("\n"); 58 114 … … 66 122 factorNames[i] = factorName; 67 123 //extract the possible values from between the parentheses 68 String allValues = rawFactors[i].substring(rawFactors[i].indexOf("(") + 1, rawFactors[i].indexOf(")")); 124 String allValues = rawFactors[i].substring(rawFactors[i].indexOf("(") + 1, 125 rawFactors[i].indexOf(")")); 69 126 String[] values = allValues.split(","); 70 127 factorValues[i] = values; 71 128 } 72 129 130 //here we get hold of the cartesian product of all the factor values 73 131 String[][] products = CartesianProduct.getCartesianProduct(factorValues); 132 133 //now inspect the content of the zip file and list all the individual files therein 134 135 //first parse the filepath from the input page 136 String zipFilePath = (String) request.getParameter("path"); 137 String zipFileDirStr = zipFilePath.substring(0, zipFilePath.lastIndexOf("/")); 138 String zipFileName = zipFilePath.substring(zipFilePath.lastIndexOf("/")+1); 139 140 //get hold of the appropriate BASE objects for this 141 DbControl dc = sc.newDbControl(); 142 Directory zipFileDir = Directory.getByPath(dc, new Path(zipFileDirStr, Path.Type.DIRECTORY)); 143 File zipFile = File.getFile(dc, zipFileDir, zipFileName, false); 144 145 //now inspect the file content and store the names in the List 146 Vector<String> fileNames = new Vector<String>(); 147 ZipInputStream zipStream = new ZipInputStream(zipFile.getDownloadStream(0)); 148 ZipEntry entry = zipStream.getNextEntry(); 149 while (entry != null) 150 { 151 fileNames.add(entry.getName()); 152 entry = zipStream.getNextEntry(); 153 } 154 155 String [] fileNamesArr = new String[fileNames.size()]; 156 fileNames.toArray(fileNamesArr); 157 Arrays.sort(fileNamesArr); 158 159 dc.close(); 74 160 %> 75 161 76 <form name="mappings" 77 action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/mappings.jsp" 78 method="post"><input type="hidden" name="ID" value="<%=ID%>"> 79 <input type="hidden" name="cmd" value="SetParameters"> <input 80 type="hidden" name="requestID" value="<%=requestID%>"> <!-- these are the parameters from the input pages; need to pick them up individually from the bean here; ugly as hell but can't be done any other way --> 81 82 <!-- inputs from experiment.jsp page --> <input type="hidden" 83 name="parameter:domain" value="<%=inputDataBean.getDomain()%>"> 84 <input type="hidden" name="parameter:accession" 85 value="<%=inputDataBean.getAccession()%>"> <input type="hidden" 86 name="parameter:qualityControl" 87 value="<%=inputDataBean.getQualityControl()%>"> <input 88 type="hidden" name="parameter:experimentalDesign" 89 value="<%=inputDataBean.getExperimentalDesign()%>"> <input 90 type="hidden" name="parameter:experimentName" 91 value="<%=inputDataBean.getExperimentName()%>"> <input 92 type="hidden" name="parameter:description" 93 value="<%=inputDataBean.getDescription()%>"> <input 94 type="hidden" name="parameter:releaseDate" 95 value="<%=inputDataBean.getReleaseDate()%>"> <input 96 type="hidden" name="parameter:submissionDate" 97 value="<%=inputDataBean.getSubmissionDate()%>"> <input 98 type="hidden" name="parameter:submitter" 99 value="<%=inputDataBean.getSubmitter()%>"> <input type="hidden" 100 name="parameter:organization" 101 value="<%=inputDataBean.getOrganization()%>"> <input 102 type="hidden" name="parameter:publicationTitle" 103 value="<%=inputDataBean.getPublicationTitle()%>"> <input 104 type="hidden" name="parameter:authors" 105 value="<%=inputDataBean.getAuthors()%>"> <input type="hidden" 106 name="parameter:journal" value="<%=inputDataBean.getJournal()%>"> 107 <input type="hidden" name="parameter:volume" 108 value="<%=inputDataBean.getVolume()%>"> <input type="hidden" 109 name="parameter:issue" value="<%=inputDataBean.getIssue()%>"> <input 110 type="hidden" name="parameter:pages" 111 value="<%=inputDataBean.getPages()%>"> <input type="hidden" 112 name="parameter:year" value="<%=inputDataBean.getYear()%>"> <input 113 type="hidden" name="parameter:pubmedId" 114 value="<%=inputDataBean.getPubmedId()%>"> <input type="hidden" 115 name="parameter:experimentId" 116 value="<%=inputDataBean.getExperimentId()%>"> <!-- inputs from protocols.jsp page --> 117 <input type="hidden" name="parameter:treatmentProtocol" 118 value="<%=inputDataBean.getTreatmentProtocol()%>"> <input 119 type="hidden" name="parameter:extractionProtocol" 120 value="<%=inputDataBean.getExtractionProtocol()%>"> <input 121 type="hidden" name="parameter:labelingProtocol" 122 value="<%=inputDataBean.getLabelingProtocol()%>"> <input 123 type="hidden" name="parameter:hybridizationProtocol" 124 value="<%=inputDataBean.getHybridizationProtocol()%>"> <input 125 type="hidden" name="parameter:scanningProtocol" 126 value="<%=inputDataBean.getScanningProtocol()%>"> <input 127 type="hidden" name="parameter:treatmentProtocolParams" 128 value="<%=inputDataBean.getTreatmentProtocolParams()%>"> <input 129 type="hidden" name="parameter:extractionProtocolParams" 130 value="<%=inputDataBean.getExtractionProtocolParams()%>"> <input 131 type="hidden" name="parameter:labelingProtocolParams" 132 value="<%=inputDataBean.getLabelingProtocolParams()%>"> <input 133 type="hidden" name="parameter:hybridizationProtocolParams" 134 value="<%=inputDataBean.getHybridizationProtocolParams()%>"> <input 135 type="hidden" name="parameter:scanningProtocolParams" 136 value="<%=inputDataBean.getScanningProtocolParams()%>"> <!-- inputs from hybridizations.jsp page --> 137 <input type="hidden" name="parameter:platform" 138 value="<%=inputDataBean.getPlatform()%>"> <input type="hidden" 139 name="parameter:organism" value="<%=inputDataBean.getOrganism()%>"> 140 <input type="hidden" name="parameter:numDesigns" 141 value="<%=inputDataBean.getNumDesigns()%>"> <input 142 type="hidden" name="parameter:dyeSwap" 143 value="<%=inputDataBean.getDyeSwap()%>"> <input type="hidden" 144 name="parameter:refSample" value="<%=inputDataBean.getRefSample()%>"> 145 <input type="hidden" name="parameter:numTreatmentGroups" 146 value="<%=inputDataBean.getNumTreatmentGroups()%>"> <input 147 type="hidden" name="parameter:expFactors" 148 value="<%=inputDataBean.getExpFactors()%>"> <input 149 type="hidden" name="parameter:numReplicates" 150 value="<%=inputDataBean.getNumReplicates()%>"> <input 151 type="hidden" name="parameter:tissues" 152 value="<%=inputDataBean.getTissues()%>"> <input type="hidden" 153 name="parameter:pooling" value="<%=inputDataBean.getPooling()%>"> 154 155 <input type="hidden" name="file_id" 156 value="<%=(String)request.getAttribute("file_id") %>"> <input 157 type="hidden" name="parameter:zipFile" 158 value="<%=(String)request.getAttribute("path") %>" id="zipFile"> 159 160 <table> 161 162 <h1>Tab2MAGE Importer -- File Mappings</h1> 163 Page 4 of 4 164 <p> 165 166 The table below holds a list of all possible factor value combinations used in your experiment. 167 Please select, for each combination, the appropriate file name from the drop down menu.</p><p> 168 169 <!-- this table holds the combinations of factor values --> 170 171 <table align="center" cellpadding="15"> 172 173 <!-- column header row factor names --> 174 175 <tr> 176 177 <!-- file selector header --> 178 <td class="header"><h3>File</h3></td> 179 180 <!-- factor names --> 181 <% 182 for (int i = 0; i < products[i].length; i++) 183 { 184 %> 185 <td class="header"><h3><%=factorNames[i]%></h3></td> 186 <% 187 } 188 %> 189 </tr> 190 191 <!-- now add as many rows as we have discrete combinations of factor values --> 162 192 163 193 <% … … 168 198 <tr> 169 199 200 <!-- first we need a cell with a drop down menu where we can select a filename to match the combination of factor values--> 201 202 <td class="input" name="fileinput<%=i %>"><select> 203 <% 204 for (int k = 0; k < fileNamesArr.length; k++) 205 { 206 %> 207 208 <option><%=fileNamesArr[k]%></option> 209 210 <% 211 } 212 %> 213 </select></td> 214 215 <!-- now print the values of this factor value combination, each in a separate cell --> 170 216 <% 171 217 for (int j = 0; j < products[i].length; j++) 172 218 { 173 219 %> 174 <td ><%=products[i][j]%></td>220 <td class="border"><%=products[i][j]%></td> 175 221 <% 176 222 } … … 185 231 186 232 </table> 233 234 <p> 235 236 <table align="center" class="noBorder" cellspacing="5" cellpadding="5"> 237 <tr class="noBorder"> 238 <td id="next" width="50%" style="border-style: none;"><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 style="border-style: none;"><img src="/base/images/gonext.gif" border="0"></td><td style="border-style: none;">Start Import</td></tr></table></div></div></td> 239 <td id="close" width="50%" style="border-style: none;"><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 style="border-style: none;"><img src="/base/images/cancel.gif" border="0"></td><td style="border-style: none;">Cancel</td></tr></table></div></div></td> </tr> 240 </table> 241 242 243 </form> 244 187 245 </body> 188 246 </html> -
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/protocols.jsp
r525 r528 122 122 123 123 <h1>Tab2MAGE Importer -- Your Protocols</h1> 124 Page 2 of 3124 Page 2 of 4 125 125 <p> 126 126 <table cellpadding="10"> -
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/styles.css
r524 r528 27 27 align: left; 28 28 border-top: 1px solid #6E94B7; 29 } 30 31 td.border { 32 vertical-align: middle; 33 text-align: center; 34 align: center; 35 border-color: #6E94B7; 36 border-style: solid; 37 border-width: 1px; 29 38 } 30 39 … … 70 79 vertical-align: top; 71 80 background-color: #F9F7F0; 81 text-align: center; 72 82 } 73 83 -
branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/CartesianProduct.java
r527 r528 44 44 } 45 45 } 46 47 for (int i = 0; i < products.length; i++) 48 { 49 for (int j = 0; j < products[i].length; j++) 50 { 51 System.out.print(products[i][j] + " "); 52 } 53 System.out.println(); 54 } 55 46 56 47 return products; 57 48 }
Note: See TracChangeset
for help on using the changeset viewer.