1 | /** |
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2 | * ExporterController Controler |
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3 | * |
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4 | * Description of my controller |
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5 | * |
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6 | * @author your email (+name?) |
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7 | * @since 2010mmdd |
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8 | * @package ??? |
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9 | * |
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10 | * Revision information: |
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11 | * $Rev$ |
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12 | * $Author$ |
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13 | * $Date$ |
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14 | */ |
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15 | package dbnp.exporter |
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16 | |
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17 | import dbnp.studycapturing.* |
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18 | |
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19 | import org.apache.poi.hssf.util.HSSFColor |
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20 | import org.apache.poi.* |
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21 | import org.apache.poi.hssf.usermodel.* |
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22 | import org.apache.poi.poifs.filesystem.POIFSFileSystem |
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23 | import org.apache.poi.ss.usermodel.DataFormatter |
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24 | import java.util.zip.ZipEntry |
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25 | import java.util.zip.ZipOutputStream |
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26 | import java.util.zip.ZipInputStream |
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27 | import javax.servlet.ServletOutputStream |
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28 | |
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29 | import grails.plugins.springsecurity.Secured |
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30 | |
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31 | class ExporterController { |
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32 | |
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33 | def AuthenticationService |
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34 | def ImporterService |
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35 | |
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36 | /* |
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37 | * List of all studies for selection the study to export |
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38 | * Using the same code as 'list' into StudyController |
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39 | */ |
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40 | def index = { |
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41 | |
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42 | def user = AuthenticationService.getLoggedInUser() |
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43 | def max = Math.min(params.max ? params.int('max') : 10, 100) |
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44 | |
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45 | def c = dbnp.studycapturing.Study.createCriteria() |
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46 | |
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47 | def studies = Study.giveReadableStudies(user, max); |
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48 | [studyInstanceList: studies, studyInstanceTotal: studies.count()] |
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49 | } |
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50 | |
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51 | def export = { |
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52 | |
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53 | def studies = [] |
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54 | for ( j in dbnp.studycapturing.Study.list() ){ |
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55 | if (params.containsKey(j.code)){ |
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56 | studies.add(j) |
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57 | } |
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58 | } |
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59 | |
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60 | if(studies.size()>1){ |
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61 | // Create a ZIP file containing all the SimpleTox files |
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62 | def files = [] |
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63 | for (studyInstance in studies){ |
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64 | downloadFile(studyInstance,false) |
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65 | files.add(new File("web-app/fileuploads/"+studyInstance.code+"_SimpleTox.xls")) |
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66 | } |
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67 | |
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68 | response.setContentType( "application/zip" ) ; |
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69 | response.addHeader( "Content-Disposition", "attachment; filename=\"GSCF_SimpleToxStudies.zip\"" ) ; |
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70 | |
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71 | // get a ZipOutputStream, so we can zip our files together |
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72 | ZipOutputStream outZip = new ZipOutputStream( response.getOutputStream() ); |
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73 | |
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74 | // add SimpleTox files to the zip |
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75 | for (outFiles in files){ |
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76 | |
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77 | FileInputStream inStream = null |
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78 | try |
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79 | { |
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80 | // Add ZIP entry to output stream. |
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81 | outZip.putNextEntry( new ZipEntry( outFiles.getName() ) ) ; |
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82 | |
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83 | inStream = new FileInputStream( outFiles ) |
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84 | |
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85 | // Transfer bytes from the file to the ZIP file |
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86 | byte[] buf = new byte[ 4096 ] ; |
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87 | int len |
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88 | while( ( len = inStream.read( buf ) ) > 0 ) |
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89 | { |
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90 | outZip.write( buf, 0, len ) |
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91 | } |
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92 | } |
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93 | catch( Exception ex ) { } |
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94 | finally |
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95 | { |
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96 | // Complete the entry |
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97 | try{ outZip.closeEntry() } catch( Exception ex ) { } |
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98 | try{ inStream.close() } catch( Exception ex ) { } |
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99 | } |
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100 | outFiles.delete() |
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101 | } |
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102 | outZip.flush() |
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103 | outZip.close() |
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104 | } |
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105 | |
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106 | |
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107 | else { |
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108 | def studyInstance = studies.getAt(0) |
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109 | // make the file downloadable |
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110 | if ((studyInstance!=null) && (studyInstance.samples.size()>0)){ |
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111 | downloadFile(studyInstance,true) |
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112 | } |
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113 | else { |
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114 | flash.message= "Error while exporting the file, please try again or choose another file" |
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115 | redirect(action:index) |
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116 | } |
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117 | |
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118 | } |
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119 | |
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120 | } |
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121 | /* |
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122 | * the export method will create a SimpleTox format for the selected study |
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123 | */ |
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124 | def downloadFile(studyInstance, boolean dl) { |
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125 | // the attributes list for the SimpleTox format |
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126 | def attributes_list = ["SubjectID","DataFile","HybName","SampleName","ArrayType","Label","StudyTitle","Array_ID", |
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127 | "Species"] |
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128 | println studyInstance.samples.size() |
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129 | println "StudyInstance :" + studyInstance |
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130 | |
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131 | // The first row contains the attributes names |
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132 | HSSFWorkbook wb = new HSSFWorkbook() |
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133 | HSSFSheet sheet = wb.createSheet() |
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134 | HSSFRow row = sheet.createRow((short)0) |
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135 | for (i in 0..attributes_list.size()){ |
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136 | row.createCell((short)i).setCellValue(attributes_list[i]) |
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137 | } |
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138 | |
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139 | // Adding the next lines |
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140 | for (s in 1..studyInstance.samples.size()){ |
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141 | // creating new line for every sample |
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142 | HSSFRow sub = sheet.createRow((short)s) |
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143 | def sample = studyInstance.samples.getAt(s-1) |
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144 | |
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145 | writeMandatoryFields(sub,sample,studyInstance) |
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146 | |
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147 | try { |
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148 | // adding the subject domain + template properties |
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149 | writeSubjectProperties(sub,sample,row) |
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150 | |
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151 | // adding the samplingEvent domain + template properties |
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152 | writeSamplingEventProperties(sub,sample,row) |
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153 | |
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154 | // adding EventGroup domain + template properties |
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155 | // writeEventGroupProperties(sub,sample,rows) |
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156 | |
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157 | // adding Sample domain + template properties |
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158 | writeSampleProperties(sub,sample,row) |
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159 | } |
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160 | catch (Exception e){ |
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161 | println "Error adding properties" |
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162 | } |
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163 | } |
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164 | |
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165 | // Make the file downlodable |
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166 | if(dl) { |
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167 | println "Creation for downloading the file "+studyInstance.title+"_SimpleTox.xls" |
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168 | response.setHeader("Content-disposition", "attachment;filename=\"${studyInstance.code}_SimpleTox.xls\"") |
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169 | response.setContentType("application/octet-stream") |
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170 | wb.write(response.outputStream) |
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171 | response.outputStream.close() |
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172 | } |
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173 | |
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174 | // Create the file and save into ZIP |
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175 | if(!dl){ |
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176 | FileOutputStream fileOut = new FileOutputStream("web-app/fileuploads/"+studyInstance.code+"_SimpleTox.xls", true) |
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177 | wb.write(fileOut) |
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178 | fileOut.close() |
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179 | } |
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180 | } |
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181 | |
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182 | def writeMandatoryFields(sub,sample,study) { |
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183 | // adding subject name in row 1 |
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184 | sample.parentSubject ? sub.createCell((short)0).setCellValue(sample.parentSubject.name) : "not defined" |
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185 | // adding sample in row 4 |
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186 | sample.name!=null ? sub.createCell((short)3).setCellValue(sample.name) : "not defined" |
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187 | // adding label (EventGroup) in row 6 |
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188 | for (ev in EventGroup.list()){ |
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189 | if(sample.parentSubject){ |
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190 | if ( (sample.parentSubject.name) && (ev.subjects.name.contains(sample.parentSubject.name))) { |
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191 | sub.createCell((short)5).setCellValue(ev.name) |
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192 | break |
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193 | } |
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194 | else { |
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195 | sub.createCell((short)5).setCellValue(" ") |
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196 | }} |
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197 | else { |
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198 | sub.createCell((short)5).setCellValue(" ") |
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199 | } |
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200 | } |
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201 | // adding study title in row 7 |
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202 | sub.createCell((short)6).setCellValue(study.title) |
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203 | // Species row 9 |
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204 | // sample.parentSubject.species.name!=null ? sub.createCell((short)8).setCellValue(sample.parentSubject.species.name) : "not defined" |
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205 | sample.parentSubject ? sub.createCell((short)8).setCellValue(sample.parentSubject.species.name) : "not defined" |
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206 | } |
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207 | |
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208 | // writing subject properties |
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209 | def writeSubjectProperties(sub,sample,row) { |
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210 | println "----- SUBJECT -----" |
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211 | for (u in 0..sample.parentSubject.giveFields().unique().size()-1){ |
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212 | TemplateField tf = sample.parentSubject.giveFields().getAt(u) |
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213 | println tf.name |
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214 | row.createCell((short)9+u).setCellValue(tf.name) |
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215 | sample.parentSubject.getFieldValue(tf.name) ? sub.createCell((short)9+u).setCellValue(sample.parentSubject.getFieldValue(tf.name).toString()) : "not define" |
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216 | } |
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217 | } |
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218 | |
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219 | // writing samplingEvent properties |
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220 | def writeSamplingEventProperties(sub,sample,row){ |
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221 | println "----- SAMPLING EVENT -----" |
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222 | for (t in 0..sample.parentEvent.giveFields().unique().size()-1){ |
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223 | TemplateField tf =sample.parentEvent.giveFields().getAt(t) |
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224 | println tf.name |
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225 | row.createCell((short)9+sample.parentSubject.giveFields().unique().size()+t).setCellValue("samplingEvent-"+tf.name) |
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226 | sample.parentEvent.getFieldValue(tf.name) ? sub.createCell((short)9+sample.parentSubject.giveFields().unique().size()+t).setCellValue(sample.parentEvent.getFieldValue(tf.name).toString()) : "not define" |
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227 | } |
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228 | } |
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229 | |
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230 | // writing EventGroup properties |
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231 | def writeEventGroupProperties(sub,sample,row){ |
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232 | |
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233 | } |
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234 | |
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235 | // writing sample properties |
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236 | def writeSampleProperties(sub,sample,row){ |
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237 | println "----- SAMPLE -----" |
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238 | for (v in 0..sample.giveFields().unique().size()-1){ |
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239 | TemplateField tf =sample.giveFields().getAt(v) |
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240 | println tf.name |
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241 | row.createCell((short)9+sample.parentSubject.giveFields().unique().size()+v+sample.parentEvent.giveFields().unique().size()).setCellValue("sample-"+tf.name) |
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242 | sample.getFieldValue(tf.name) ? sub.createCell((short)9+sample.parentSubject.giveFields().unique().size()+v+sample.parentEvent.giveFields().unique().size()).setCellValue(sample.getFieldValue(tf.name).toString()) : "not define" |
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243 | } |
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244 | } |
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245 | } |
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