1 | package dbnp.studycapturing |
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2 | |
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3 | import grails.converters.* |
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4 | import grails.plugins.springsecurity.Secured |
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5 | import org.dbnp.gdt.TemplateFieldType |
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6 | import org.dbnp.gdt.RelTime |
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7 | |
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8 | |
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9 | /** |
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10 | * Controller class for studies |
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11 | */ |
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12 | class StudyController { |
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13 | def authenticationService |
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14 | |
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15 | //static allowedMethods = [save: "POST", update: "POST", delete: "POST"] |
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16 | |
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17 | def index = { |
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18 | redirect(action: "list", params: params) |
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19 | } |
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20 | |
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21 | /** |
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22 | * Shows all studies where the user has access to |
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23 | */ |
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24 | def list = { |
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25 | |
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26 | def user = authenticationService.getLoggedInUser() |
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27 | def max = Math.min(params.max ? params.int('max') : 10, 100) |
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28 | def offset = params.offset ? params.int( 'offset' ) : 0 |
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29 | def studies = Study.giveReadableStudies( user, max, offset ); |
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30 | [studyInstanceList: studies, studyInstanceTotal: Study.countReadableStudies( user ), loggedInUser: user] |
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31 | } |
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32 | |
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33 | /** |
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34 | * Shows studies for which the logged in user is the owner |
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35 | */ |
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36 | @Secured(['IS_AUTHENTICATED_REMEMBERED']) |
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37 | def myStudies = { |
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38 | def user = authenticationService.getLoggedInUser() |
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39 | def max = Math.min(params.max ? params.int('max') : 10, 100) |
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40 | def offset = params.offset ? params.int( 'offset' ) : 0 |
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41 | |
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42 | def studies = Study.findAllByOwner(user, [max:max,offset: offset]); |
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43 | render( view: "list", model: [studyInstanceList: studies, studyInstanceTotal: Study.countByOwner(user), loggedInUser: user] ) |
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44 | } |
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45 | |
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46 | /** |
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47 | * Shows a comparison of multiple studies using the show view |
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48 | * |
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49 | */ |
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50 | def list_extended = { |
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51 | // If nothing has been selected, redirect the user |
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52 | if( !params.id ) |
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53 | redirect( action: 'list' ) |
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54 | |
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55 | // Check whether one id has been selected or multiple. |
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56 | def ids = params.id |
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57 | if( ids instanceof String ) |
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58 | redirect( action: 'show', id: ids ) |
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59 | |
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60 | // Parse strings to a long |
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61 | def long_ids = [] |
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62 | ids.each { long_ids.add( Long.parseLong( it ) ) } |
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63 | |
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64 | println( long_ids ) |
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65 | |
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66 | def startTime = System.currentTimeMillis() |
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67 | def c = Study.createCriteria() |
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68 | |
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69 | def studyList = c { |
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70 | maxResults( Math.min(params.max ? params.int('max') : 10, 100) ) |
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71 | 'in'( "id", long_ids ) |
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72 | } |
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73 | render(view:'show',model:[studyList: studyList, studyInstanceTotal: Study.count(), multipleStudies: ( studyList.size() > 1 ) ] ) |
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74 | } |
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75 | |
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76 | /** |
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77 | * Shows one or more studies |
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78 | */ |
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79 | def show = { |
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80 | def startTime = System.currentTimeMillis() |
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81 | |
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82 | def studyInstance = Study.get( params.long( "id" ) ) |
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83 | if (!studyInstance) { |
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84 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), params.id])}" |
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85 | redirect(action: "list") |
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86 | } |
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87 | else { |
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88 | // Check whether the user may see this study |
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89 | def loggedInUser = authenticationService.getLoggedInUser() |
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90 | if( !studyInstance.canRead(loggedInUser) ) { |
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91 | flash.message = "You have no access to this study" |
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92 | redirect(action: "list") |
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93 | } |
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94 | |
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95 | // The study instance is packed into an array, to be able to |
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96 | // use the same view for showing the study and comparing multiple |
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97 | // studies |
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98 | [studyList: [ studyInstance ], multipleStudies: false, loggedInUser: loggedInUser, facebookLikeUrl: studyInstance.getFieldValue('published') ? "/study/show/${studyInstance?.id}" : '' ] |
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99 | } |
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100 | } |
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101 | |
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102 | /** |
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103 | * Shows the subjects tab of one or more studies. Is called when opening the subjects-tab |
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104 | * on the study overview screen. |
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105 | */ |
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106 | def show_subjects = { |
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107 | def studyList = readStudies( params.id ); |
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108 | |
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109 | if( !studyList ) |
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110 | return |
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111 | |
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112 | [studyList: studyList, studyInstanceTotal: Study.count(), multipleStudies: ( studyList.size() > 1 ), loggedInUser: authenticationService.getLoggedInUser() ] |
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113 | } |
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114 | |
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115 | /** |
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116 | * Shows the events timeline tab of one or more studies. Is called when opening the events timeline-tab |
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117 | * on the study overview screen. |
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118 | */ |
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119 | def show_events_timeline = { |
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120 | def studyList = readStudies( params.id ); |
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121 | |
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122 | if( !studyList ) |
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123 | return |
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124 | |
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125 | [studyList: studyList, studyInstanceTotal: Study.count(), multipleStudies: ( studyList.size() > 1 ), loggedInUser: authenticationService.getLoggedInUser() ] |
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126 | } |
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127 | |
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128 | /** |
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129 | * Shows the events table tab of one or more studies. Is called when opening the events table-tab |
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130 | * on the study overview screen. |
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131 | */ |
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132 | def show_events_table = { |
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133 | def studyList = readStudies( params.id ); |
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134 | |
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135 | if( !studyList ) |
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136 | return |
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137 | |
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138 | [studyList: studyList, studyInstanceTotal: Study.count(), multipleStudies: ( studyList.size() > 1 ), loggedInUser: authenticationService.getLoggedInUser() ] |
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139 | } |
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140 | |
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141 | /** |
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142 | * Shows the assays tab of one or more studies. Is called when opening the assays tab |
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143 | * on the study overview screen. |
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144 | */ |
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145 | def show_assays = { |
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146 | def studyList = readStudies( params.id ); |
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147 | |
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148 | if( !studyList ) |
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149 | return |
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150 | |
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151 | [studyList: studyList, studyInstanceTotal: Study.count(), multipleStudies: ( studyList.size() > 1 ), loggedInUser: authenticationService.getLoggedInUser() ] |
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152 | } |
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153 | |
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154 | /** |
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155 | * Shows the samples tab of one or more studies. Is called when opening the samples-tab |
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156 | * on the study overview screen. |
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157 | */ |
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158 | def show_samples = { |
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159 | def studyList = readStudies( params.id ); |
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160 | |
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161 | if( !studyList ) |
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162 | return |
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163 | |
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164 | [studyList: studyList, studyInstanceTotal: Study.count(), multipleStudies: ( studyList.size() > 1 ), loggedInUser: authenticationService.getLoggedInUser() ] |
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165 | } |
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166 | |
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167 | /** |
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168 | * Shows the persons tab of one or more studies. Is called when opening the persons tab |
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169 | * on the study overview screen. |
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170 | */ |
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171 | def show_persons = { |
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172 | def studyList = readStudies( params.id ); |
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173 | |
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174 | if( !studyList ) |
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175 | return |
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176 | |
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177 | [studyList: studyList, studyInstanceTotal: Study.count(), multipleStudies: ( studyList.size() > 1 ), loggedInUser: authenticationService.getLoggedInUser() ] |
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178 | } |
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179 | |
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180 | /** |
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181 | * Shows the publications tab of one or more studies. Is called when opening the publications tab |
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182 | * on the study overview screen. |
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183 | */ |
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184 | def show_publications = { |
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185 | def studyList = readStudies( params.id ); |
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186 | |
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187 | if( !studyList ) |
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188 | return |
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189 | |
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190 | [studyList: studyList, studyInstanceTotal: Study.count(), multipleStudies: ( studyList.size() > 1 ), loggedInUser: authenticationService.getLoggedInUser() ] |
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191 | } |
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192 | |
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193 | /** |
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194 | * Creates the javascript for showing the timeline of one or more studies |
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195 | */ |
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196 | def createTimelineBandsJs = { |
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197 | def studyList = readStudies( params.id ); |
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198 | |
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199 | if( !studyList ) |
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200 | return |
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201 | |
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202 | [studyList: studyList, studyInstanceTotal: Study.count(), multipleStudies: ( studyList.size() > 1 ) ] |
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203 | } |
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204 | |
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205 | /** |
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206 | * Reads one or more studies from the database and checks whether the logged |
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207 | * in user is allowed to access them. |
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208 | * |
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209 | * Is used by several show_-methods |
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210 | * |
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211 | * @return List with Study objects or false if an error occurred. |
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212 | */ |
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213 | private def readStudies( id ) { |
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214 | // If nothing has been selected, redirect the user |
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215 | if( !id || !( id instanceof String)) { |
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216 | response.status = 500; |
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217 | render 'No study selected'; |
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218 | return false |
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219 | } |
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220 | |
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221 | // Check whether one id has been selected or multiple. |
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222 | def ids = URLDecoder.decode( id ).split( "," ); |
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223 | |
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224 | // Parse strings to a long |
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225 | def long_ids = [] |
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226 | ids.each { long_ids.add( Long.parseLong( it ) ) } |
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227 | |
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228 | def c = Study.createCriteria() |
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229 | |
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230 | def studyList = c { |
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231 | maxResults( Math.min(params.max ? params.int('max') : 10, 100) ) |
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232 | 'in'( "id", long_ids ) |
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233 | } |
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234 | |
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235 | // Check whether the user may see these studies |
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236 | def studiesAllowed = [] |
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237 | def loggedInUser = authenticationService.getLoggedInUser() |
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238 | |
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239 | studyList.each { studyInstance -> |
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240 | if( studyInstance.canRead(loggedInUser) ) { |
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241 | studiesAllowed << studyInstance |
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242 | } |
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243 | } |
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244 | |
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245 | // If the user is not allowed to see any of the studies, return 404 |
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246 | if( studiesAllowed.size() == 0 ) { |
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247 | response.status = 404; |
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248 | render 'Selected studies not found'; |
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249 | return false |
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250 | } |
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251 | |
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252 | return studyList |
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253 | } |
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254 | |
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255 | def showByToken = { |
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256 | def studyInstance = Study.findByStudyUUID(params.id) |
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257 | if (!studyInstance) { |
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258 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), params.id])}" |
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259 | redirect(action: "list") |
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260 | } |
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261 | else { |
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262 | // Check whether the user may see this study |
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263 | def loggedInUser = authenticationService.getLoggedInUser() |
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264 | if( !studyInstance.canRead(loggedInUser) ) { |
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265 | flash.message = "You have no access to this study" |
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266 | redirect(action: "list") |
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267 | } |
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268 | |
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269 | redirect(action: "show", id: studyInstance.id) |
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270 | } |
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271 | } |
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272 | |
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273 | /** |
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274 | * Gives the events for one eventgroup in JSON format |
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275 | * |
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276 | */ |
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277 | def events = { |
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278 | def eventGroupId = Integer.parseInt( params.id ); |
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279 | def studyId = Integer.parseInt( params.study ); |
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280 | def eventGroup; |
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281 | |
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282 | // eventGroupId == -1 means that the orphaned events should be given |
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283 | if( eventGroupId == -1 ) { |
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284 | def studyInstance = Study.get( studyId ) |
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285 | |
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286 | if (studyInstance == null) { |
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287 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), studyId])}" |
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288 | redirect(action: "list"); |
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289 | return; |
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290 | } |
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291 | |
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292 | events = studyInstance.getOrphanEvents(); |
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293 | } else { |
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294 | eventGroup = EventGroup.get(params.id) |
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295 | |
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296 | if (eventGroup == null) { |
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297 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'eventgroup.label', default: 'Eventgroup'), params.id])}" |
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298 | redirect(action: "list"); |
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299 | return; |
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300 | } |
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301 | events = eventGroup?.events + eventGroup?.samplingEvents; |
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302 | } |
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303 | |
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304 | // This parameter should give the startdate of the study in milliseconds |
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305 | // since 1-1-1970 |
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306 | long startDate = Long.parseLong( params.startDate ) |
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307 | |
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308 | // Create JSON object |
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309 | def json = [ 'dateTimeFormat': 'iso8601', events: [] ]; |
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310 | |
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311 | // Add all other events |
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312 | for( event in events ) { |
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313 | def parameters = [] |
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314 | for( templateField in event.giveTemplateFields() ) { |
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315 | def value = event.getFieldValue( templateField.name ); |
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316 | if( value ) { |
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317 | if( templateField.type == TemplateFieldType.RELTIME ) |
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318 | value = new RelTime( value ).toString(); |
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319 | |
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320 | def param = templateField.name + " = " + value; |
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321 | |
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322 | if( templateField.unit ) |
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323 | param += templateField.unit; |
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324 | |
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325 | parameters << param ; |
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326 | } |
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327 | } |
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328 | |
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329 | def description = parameters.join( '<br />\n' ); |
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330 | |
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331 | if( event instanceof SamplingEvent ) { |
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332 | json.events << [ |
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333 | 'start': new Date( startDate + event.startTime * 1000 ), |
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334 | 'end': new Date( startDate + event.startTime * 1000 ), |
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335 | 'durationEvent': false, |
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336 | 'title': event.template.name, |
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337 | 'description': description |
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338 | ] |
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339 | } else { |
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340 | json.events << [ |
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341 | 'start': new Date( startDate + event.startTime * 1000 ), |
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342 | 'end': new Date( startDate + event.endTime * 1000 ), |
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343 | 'durationEvent': true, |
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344 | 'title': event.template.name, |
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345 | 'description': description |
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346 | ] |
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347 | |
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348 | } |
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349 | } |
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350 | |
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351 | // set output header to json |
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352 | response.contentType = 'application/json' |
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353 | |
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354 | render json as JSON |
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355 | } |
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356 | |
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357 | def delete = { |
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358 | def studyInstance = Study.get(params.id) |
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359 | if (studyInstance) { |
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360 | try { |
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361 | studyInstance.delete(flush: true) |
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362 | flash.message = "${message(code: 'default.deleted.message', args: [message(code: 'study.label', default: 'Study'), params.id])}" |
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363 | redirect(action: "list") |
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364 | } |
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365 | catch (org.springframework.dao.DataIntegrityViolationException e) { |
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366 | flash.message = "${message(code: 'default.not.deleted.message', args: [message(code: 'study.label', default: 'Study'), params.id])}" |
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367 | redirect(action: "show", id: params.id) |
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368 | } |
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369 | } |
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370 | else { |
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371 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), params.id])}" |
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372 | redirect(action: "list") |
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373 | } |
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374 | } |
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375 | |
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376 | /** |
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377 | * Renders assay names and id's as JSON |
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378 | */ |
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379 | def ajaxGetAssays = { |
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380 | def study = Study.read(params.id) |
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381 | |
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382 | // set output header to json |
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383 | response.contentType = 'application/json' |
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384 | |
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385 | render study?.assays?.collect{[name: it.name, id: it.id]} as JSON |
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386 | } |
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387 | |
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388 | /** |
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389 | * Exports all data from the given studies to excel. This is done using a redirect to the |
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390 | * assay controller |
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391 | * |
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392 | * @param ids ids of the studies to export |
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393 | * @param params.format "list" in order to export all assays in one big excel sheet |
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394 | * "sheets" in order to export every assay on its own sheet (default) |
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395 | * @see AssayController.exportToExcel |
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396 | */ |
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397 | def exportToExcel = { |
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398 | def ids = params.list( 'ids' ).findAll { it.isLong() }.collect { Long.valueOf( it ) }; |
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399 | |
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400 | if( !ids ) { |
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401 | flash.errorMessage = "No study ids given"; |
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402 | redirect( controller: "assay", action: "errorPage" ); |
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403 | return; |
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404 | } |
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405 | |
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406 | // Find all assay ids for these studies |
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407 | def assayIds = ids.collect { id -> |
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408 | def study = Study.get( id ); |
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409 | if( study ) { |
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410 | return study.assays.collect { assay -> assay.id } |
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411 | } else { |
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412 | return [] |
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413 | } |
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414 | }.flatten() |
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415 | |
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416 | if( !assayIds ) { |
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417 | flash.errorMessage = "No assays found for the given studies"; |
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418 | redirect( controller: "assay", action: "errorPage" ); |
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419 | return; |
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420 | } |
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421 | |
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422 | // Create url to redirect to |
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423 | def format = params.get( "format", "sheets" ) |
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424 | redirect( controller: "assay", action: "exportToExcel", params: [ "format": format, "ids": assayIds ] ); |
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425 | } |
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426 | } |
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