1 | package dbnp.studycapturing |
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2 | |
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3 | import dbnp.data.* |
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4 | import grails.converters.* |
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5 | import grails.plugins.springsecurity.Secured |
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6 | import dbnp.authentication.AuthenticationService |
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7 | import dbnp.authentication.SecUser |
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8 | import org.codehaus.groovy.grails.plugins.web.taglib.ValidationTagLib |
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9 | |
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10 | /** |
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11 | * ajaxflow Controller |
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12 | * |
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13 | * @author Jeroen Wesbeek |
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14 | * @since 20101220 |
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15 | * |
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16 | * Revision information: |
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17 | * $Rev: 66849 $ |
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18 | * $Author: duh $ |
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19 | * $Date: 2010-12-08 15:12:54 +0100 (Wed, 08 Dec 2010) $ |
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20 | */ |
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21 | @Secured(['IS_AUTHENTICATED_REMEMBERED']) |
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22 | class StudyWizardController { |
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23 | def pluginManager |
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24 | def authenticationService |
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25 | def validationTagLib = new ValidationTagLib() |
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26 | |
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27 | /** |
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28 | * index method, redirect to the webflow |
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29 | * @void |
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30 | */ |
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31 | def index = { |
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32 | // Grom a development message |
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33 | if (pluginManager.getGrailsPlugin('grom')) "redirecting into the webflow".grom() |
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34 | |
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35 | def jump = [:] |
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36 | |
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37 | // allow quickjumps to: |
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38 | // edit a study : /wizard?jump=edit&id=1 |
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39 | // create a study : /wizard?jump=create |
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40 | if (params.get('jump')) { |
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41 | switch (params.get('jump')) { |
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42 | case 'create': |
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43 | jump = [ |
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44 | action: 'create' |
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45 | ] |
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46 | break |
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47 | case 'edit': |
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48 | jump = [ |
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49 | action : 'edit', |
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50 | id : params.get('id') |
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51 | ] |
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52 | break |
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53 | default: |
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54 | break |
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55 | } |
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56 | } |
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57 | |
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58 | // store in session |
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59 | session.jump = jump |
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60 | |
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61 | /** |
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62 | * Do you believe it in your head? |
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63 | * I can go with the flow |
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64 | * Don't say it doesn't matter (with the flow) matter anymore |
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65 | * I can go with the flow (I can go) |
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66 | * Do you believe it in your head? |
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67 | */ |
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68 | redirect(action: 'pages') |
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69 | } |
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70 | |
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71 | /** |
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72 | * WebFlow definition |
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73 | * @void |
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74 | */ |
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75 | def pagesFlow = { |
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76 | // start the flow |
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77 | onStart { |
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78 | // Grom a development message |
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79 | if (pluginManager.getGrailsPlugin('grom')) "entering the WebFlow".grom() |
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80 | |
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81 | // define variables in the flow scope which is availabe |
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82 | // throughout the complete webflow also have a look at |
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83 | // the Flow Scopes section on http://www.grails.org/WebFlow |
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84 | // |
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85 | // The following flow scope variables are used to generate |
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86 | // wizard tabs. Also see common/_tabs.gsp for more information |
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87 | // define flow variables |
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88 | flow.page = 0 |
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89 | flow.pages = [ |
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90 | //[title: 'Templates'], // templates |
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91 | [title: 'Start'], // load or create a study |
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92 | [title: 'Subjects'], // subjects |
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93 | [title: 'Events'], // events and event grouping |
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94 | //[title: 'Event Groups'], // groups |
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95 | [title: 'Samples'], // samples |
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96 | [title: 'Assays'], // assays |
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97 | //[title: 'Assay Groups'], // assays |
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98 | [title: 'Confirmation'], // confirmation page |
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99 | [title: 'Done'] // finish page |
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100 | ] |
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101 | flow.jump = session.jump |
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102 | |
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103 | success() |
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104 | } |
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105 | |
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106 | // render the main wizard page which immediately |
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107 | // triggers the 'next' action (hence, the main |
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108 | // page dynamically renders the study template |
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109 | // and makes the flow jump to the study logic) |
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110 | mainPage { |
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111 | render(view: "/studyWizard/index") |
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112 | onRender { |
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113 | // Grom a development message |
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114 | if (pluginManager.getGrailsPlugin('grom')) "rendering the main Ajaxflow page (index.gsp)".grom() |
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115 | |
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116 | // let the view know we're in page 1 |
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117 | flow.page = 1 |
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118 | success() |
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119 | } |
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120 | on("next").to "handleJump" |
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121 | } |
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122 | |
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123 | // handle the jump parameter |
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124 | // |
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125 | // I came to get down [2x] |
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126 | // So get out your seats and jump around |
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127 | // Jump around [3x] |
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128 | // Jump up Jump up and get down |
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129 | // Jump [18x] |
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130 | handleJump { |
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131 | action { |
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132 | // Grom a development message |
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133 | if (pluginManager.getGrailsPlugin('grom')) "entering handleJump".grom() |
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134 | |
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135 | if (flow.jump && flow.jump.action == 'edit') { |
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136 | if (flow.jump.id) { |
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137 | // load study |
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138 | if (this.loadStudy(flow, flash, [studyid:flow.jump.id],authenticationService.getLoggedInUser())) { |
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139 | toStudyPage() |
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140 | } else { |
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141 | toStartPage() |
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142 | } |
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143 | } else { |
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144 | toModifyPage() |
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145 | } |
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146 | } else if (flow.jump && flow.jump.action == 'create') { |
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147 | if (!flow.study) flow.study = new Study() |
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148 | toStudyPage() |
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149 | } else { |
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150 | toStartPage() |
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151 | } |
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152 | } |
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153 | on("toStartPage").to "start" |
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154 | on("toStudyPage").to "study" |
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155 | on("toModifyPage").to "modify" |
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156 | } |
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157 | |
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158 | // create or modify a study |
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159 | start { |
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160 | render(view: "_start") |
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161 | onRender { |
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162 | // Grom a development message |
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163 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_start.gsp".grom() |
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164 | |
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165 | flow.page = 1 |
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166 | success() |
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167 | } |
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168 | on("next") { |
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169 | // clean the flow scope |
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170 | flow.remove('study') |
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171 | |
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172 | // create a new study instance |
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173 | if (!flow.study) flow.study = new Study() |
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174 | |
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175 | // set 'quicksave' variable to false |
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176 | flow.quickSave = false |
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177 | }.to "study" |
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178 | on("modify").to "modify" |
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179 | on("import").to "redirectToImport" |
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180 | } |
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181 | |
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182 | // redirect to the import wizard |
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183 | redirectToImport { |
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184 | render(view: "_redirect") |
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185 | onRender { |
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186 | // Grom a development message |
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187 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_redirect.gsp".grom() |
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188 | |
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189 | flash.uri = "/importer/index" |
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190 | } |
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191 | on("next").to "start" |
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192 | } |
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193 | |
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194 | // load a study to modify |
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195 | modify { |
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196 | render(view: "_modify") |
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197 | onRender { |
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198 | // Grom a development message |
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199 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_modify.gsp".grom() |
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200 | |
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201 | flow.page = 1 |
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202 | flash.showCancel = true |
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203 | success() |
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204 | } |
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205 | on("cancel") { |
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206 | flow.remove('study') |
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207 | |
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208 | success() |
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209 | }.to "start" |
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210 | on("next") { |
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211 | // load study |
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212 | if (this.loadStudy(flow, flash, params, authenticationService.getLoggedInUser())) { |
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213 | success() |
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214 | } else { |
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215 | error() |
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216 | } |
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217 | }.to "study" |
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218 | } |
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219 | |
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220 | // render and handle the study page |
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221 | study { |
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222 | render(view: "_study") |
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223 | onRender { |
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224 | // Grom a development message |
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225 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_study.gsp".grom() |
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226 | |
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227 | flow.page = 1 |
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228 | |
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229 | // since this controller was refactored it's technically |
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230 | // safe to enable quicksave throughout the application. |
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231 | // However, we must keep an eye on the quality of the |
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232 | // studies as this change makes it easier to create dummy |
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233 | // studies which will create garbage in out database. |
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234 | flow.quickSave = true |
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235 | |
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236 | success() |
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237 | } |
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238 | on("refresh") { |
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239 | // handle form data |
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240 | studyPage(flow, flash, params) |
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241 | |
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242 | // force refresh of the template |
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243 | if (flow.study.template && flow.study.template instanceof Template) { |
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244 | flow.study.template.refresh() |
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245 | } |
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246 | |
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247 | // reset errors |
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248 | flash.wizardErrors = [:] |
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249 | success() |
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250 | }.to "study" |
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251 | on("switchTemplate") { |
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252 | // handle form data |
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253 | studyPage(flow, flash, params) |
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254 | |
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255 | // reset errors |
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256 | flash.wizardErrors = [:] |
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257 | success() |
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258 | }.to "study" |
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259 | on("previous") { |
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260 | // handle form data |
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261 | studyPage(flow, flash, params) |
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262 | |
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263 | // reset errors |
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264 | flash.wizardErrors = [:] |
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265 | success() |
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266 | }.to "start" |
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267 | on("next") { |
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268 | studyPage(flow, flash, params) ? success() : error() |
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269 | }.to "subjects" |
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270 | on("quickSave") { |
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271 | studyPage(flow, flash, params) ? success() : error() |
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272 | }.to "waitForSave" |
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273 | } |
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274 | |
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275 | // render and handle subjects page |
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276 | subjects { |
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277 | render(view: "_subjects") |
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278 | onRender { |
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279 | // Grom a development message |
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280 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_subjects.gsp".grom() |
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281 | |
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282 | flow.page = 2 |
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283 | |
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284 | if (!flash.values || !flash.values.addNumber) flash.values = [addNumber:1] |
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285 | |
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286 | success() |
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287 | } |
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288 | on("refresh") { |
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289 | // remember the params in the flash scope |
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290 | flash.values = params |
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291 | |
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292 | // refresh templates |
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293 | if (flow.study.subjects) { |
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294 | flow.study.giveSubjectTemplates().each() { |
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295 | it.refresh() |
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296 | } |
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297 | } |
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298 | |
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299 | success() |
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300 | }.to "subjects" |
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301 | on("add") { |
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302 | // handle form data |
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303 | addSubjects(flow, flash, params) ? success() : error() |
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304 | }.to "subjects" |
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305 | on("delete") { |
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306 | // handle form data |
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307 | subjectPage(flow, flash, params) |
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308 | |
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309 | // reset errors |
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310 | flash.wizardErrors = [:] |
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311 | |
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312 | // remove subject |
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313 | def subjectToRemove = flow.study.subjects.find { it.identifier == (params.get('do') as int) } |
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314 | if (subjectToRemove) { |
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315 | flow.study.deleteSubject( subjectToRemove ) |
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316 | } |
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317 | }.to "subjects" |
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318 | on("previous") { |
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319 | // handle form data |
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320 | subjectPage(flow, flash, params) |
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321 | |
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322 | // reset errors |
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323 | flash.wizardErrors = [:] |
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324 | success() |
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325 | }.to "study" |
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326 | on("next") { |
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327 | // handle form data |
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328 | subjectPage(flow, flash, params) ? success() : error() |
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329 | }.to "events" |
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330 | on("quickSave") { |
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331 | // handle form data |
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332 | subjectPage(flow, flash, params) ? success() : error() |
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333 | }.to "waitForSave" |
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334 | } |
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335 | |
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336 | // render events page |
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337 | events { |
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338 | render(view: "_events") |
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339 | onRender { |
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340 | // Grom a development message |
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341 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_events.gsp".grom() |
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342 | |
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343 | flow.page = 3 |
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344 | |
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345 | // add initial eventGroup to study |
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346 | if (!flow.study.eventGroups?.size()) { |
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347 | flow.study.addToEventGroups( |
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348 | new EventGroup(name: 'Group 1') |
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349 | ) |
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350 | } |
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351 | |
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352 | success() |
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353 | } |
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354 | on("clear") { |
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355 | // remove all events |
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356 | (flow.study.events + flow.study.samplingEvents).each() { event -> |
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357 | if (event instanceof SamplingEvent) { |
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358 | flow.study.deleteSamplingEvent( event ) |
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359 | } else { |
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360 | flow.study.deleteEvent( event ) |
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361 | } |
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362 | } |
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363 | |
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364 | success() |
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365 | }.to "events" |
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366 | on("switchTemplate") { |
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367 | // handle form data |
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368 | eventPage(flow, flash, params) |
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369 | |
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370 | // get template |
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371 | def type = params.get('eventType') |
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372 | def template= Template.findByName( params.get( type + 'Template' ) ) |
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373 | |
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374 | // change template and/or instance? |
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375 | if (!flow.event || (flow.event instanceof Event && type == "sample") || (flow.event instanceof SamplingEvent && type == "event")) { |
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376 | // create new instance |
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377 | flow.event = (type == "event") ? new Event(template: template) : new SamplingEvent(template: template) |
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378 | } else { |
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379 | flow.event.template = template |
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380 | } |
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381 | |
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382 | // reset errors |
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383 | flash.wizardErrors = [:] |
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384 | success() |
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385 | |
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386 | }.to "events" |
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387 | on("refresh") { |
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388 | // handle form data |
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389 | eventPage(flow, flash, params) |
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390 | |
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391 | // refresh templates |
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392 | flow.study.giveEventTemplates().each() { |
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393 | it.refresh() |
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394 | } |
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395 | |
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396 | // refresh event template |
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397 | if (flow.event?.template) flow.event.template.refresh() |
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398 | |
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399 | // reset errors |
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400 | flash.wizardErrors = [:] |
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401 | success() |
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402 | }.to "events" |
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403 | on("add") { |
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404 | // handle form data |
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405 | eventPage(flow, flash, params) |
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406 | |
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407 | // reset errors |
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408 | flash.wizardErrors = [:] |
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409 | |
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410 | // add event to study |
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411 | if (flow.event instanceof SamplingEvent) { |
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412 | flow.study.addToSamplingEvents( flow.event ) |
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413 | } else { |
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414 | flow.study.addToEvents( flow.event ) |
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415 | } |
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416 | |
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417 | // validate event |
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418 | if (flow.event.validate()) { |
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419 | // remove event from the flowscope |
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420 | flow.remove('event') |
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421 | |
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422 | success() |
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423 | } else { |
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424 | // event does not validate |
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425 | // remove from study |
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426 | if (flow.event instanceof SamplingEvent) { |
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427 | flow.study.removeFromSamplingEvents( flow.event ) |
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428 | } else { |
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429 | flow.study.removeFromEvents( flow.event ) |
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430 | } |
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431 | |
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432 | // append errors |
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433 | this.appendErrors(flow.event, flash.wizardErrors) |
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434 | error() |
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435 | } |
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436 | }.to "events" |
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437 | on("deleteEvent") { |
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438 | // handle form data |
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439 | eventPage(flow, flash, params) |
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440 | |
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441 | // reset errors |
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442 | flash.wizardErrors = [:] |
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443 | |
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444 | // find matching (sampling) event |
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445 | def event = flow.study.events.find { it.getIdentifier() == (params.get('do') as int) } |
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446 | def samplingEvent = flow.study.samplingEvents.find { it.getIdentifier() == (params.get('do') as int) } |
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447 | |
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448 | // perform delete |
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449 | if (event) flow.study.deleteEvent( event ) |
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450 | if (samplingEvent) flow.study.deleteSamplingEvent( samplingEvent ) |
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451 | }.to "events" |
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452 | on("addEventGroup") { |
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453 | // handle form data |
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454 | eventPage(flow, flash, params) |
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455 | |
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456 | // set work variables |
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457 | def groupName = 'Group ' |
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458 | def tempGroupIterator = 1 |
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459 | def tempGroupName = groupName + tempGroupIterator |
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460 | |
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461 | // make sure group name is unique |
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462 | if (flow.study.eventGroups) { |
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463 | while (flow.study.eventGroups.find { it.name == tempGroupName }) { |
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464 | tempGroupIterator++ |
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465 | tempGroupName = groupName + tempGroupIterator |
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466 | } |
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467 | } |
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468 | groupName = tempGroupName |
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469 | |
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470 | // add a new eventGroup |
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471 | flow.study.addToEventGroups( |
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472 | new EventGroup( |
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473 | name : groupName |
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474 | ) |
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475 | ) |
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476 | |
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477 | // reset errors |
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478 | flash.wizardErrors = [:] |
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479 | success() |
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480 | }.to "events" |
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481 | on("deleteEventGroup") { |
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482 | // handle form data |
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483 | eventPage(flow, flash, params) |
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484 | |
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485 | // reset errors |
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486 | flash.wizardErrors = [:] |
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487 | |
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488 | // remove eventGroup |
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489 | def eventGroupToRemove = flow.study.eventGroups.find { it.getIdentifier() == (params.get('do') as int) } |
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490 | }.to "events" |
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491 | on("duplicate") { |
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492 | // handle form data |
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493 | eventPage(flow, flash, params) |
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494 | |
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495 | // reset errors |
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496 | flash.wizardErrors = [:] |
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497 | |
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498 | // clone event |
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499 | def event = null |
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500 | (((flow.study.events) ? flow.study.events : []) + ((flow.study.samplingEvents) ? flow.study.samplingEvents : [])).find { it.getIdentifier() == (params.get('do') as int) }.each { |
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501 | event = (it instanceof SamplingEvent) ? new SamplingEvent() : new Event() |
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502 | |
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503 | // set template |
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504 | event.template = it.template |
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505 | |
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506 | // copy data |
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507 | it.giveFields().each() { field -> |
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508 | event.setFieldValue( |
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509 | field.name, |
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510 | it.getFieldValue(field.name) |
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511 | ) |
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512 | } |
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513 | |
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514 | // assign duplicate event to study |
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515 | if (event instanceof SamplingEvent) { |
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516 | flow.study.addToSamplingEvents(event) |
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517 | } else { |
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518 | flow.study.addToEvents(event) |
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519 | } |
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520 | } |
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521 | |
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522 | success() |
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523 | }.to "events" |
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524 | on("previous") { |
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525 | // handle form data |
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526 | eventPage(flow, flash, params) |
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527 | |
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528 | // reset errors |
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529 | flash.wizardErrors = [:] |
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530 | success() |
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531 | }.to "subjects" |
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532 | on("next") { |
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533 | // handle form data |
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534 | eventPage(flow, flash, params) ? success() : error() |
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535 | }.to "eventsNext" |
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536 | on("quickSave") { |
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537 | // handle form data |
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538 | eventPage(flow, flash, params) ? success() : error() |
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539 | }.to "waitForSave" |
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540 | } |
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541 | |
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542 | // decide to show a warning page or not |
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543 | eventsNext { |
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544 | action { |
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545 | // Grom a development message |
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546 | if (pluginManager.getGrailsPlugin('grom')) ".entering eventsNext".grom() |
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547 | |
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548 | def assigned = false |
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549 | |
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550 | // check if all sampling events are in an eventGroup |
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551 | flow.study.samplingEvents.each() { samplingEvent -> |
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552 | // iterate through eventGroups |
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553 | flow.study.eventGroups.each() { eventGroup -> |
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554 | if ( eventGroup.samplingEvents.find { it.equals(samplingEvent) } ) { |
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555 | assigned = true |
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556 | } |
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557 | } |
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558 | } |
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559 | |
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560 | if (assigned) { |
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561 | toGroupsPage() |
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562 | } else { |
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563 | toWarningPage() |
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564 | } |
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565 | } |
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566 | on("toWarningPage").to "unassignedSamplingEventWarning" |
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567 | on("toGroupsPage").to "groups" |
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568 | } |
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569 | |
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570 | // warning page for unassigned samplingEvent |
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571 | unassignedSamplingEventWarning { |
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572 | render(view: "_unassigned_samplingEvent_warning") |
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573 | onRender { |
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574 | // Grom a development message |
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575 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_unnassigned_samplingEvent_warning.gsp".grom() |
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576 | |
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577 | flow.page = 3 |
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578 | success() |
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579 | } |
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580 | on("next").to "groups" |
---|
581 | on("previous").to "events" |
---|
582 | } |
---|
583 | |
---|
584 | // groups page |
---|
585 | groups { |
---|
586 | render(view: "_groups") |
---|
587 | onRender { |
---|
588 | // Grom a development message |
---|
589 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_groups.gsp".grom() |
---|
590 | |
---|
591 | flow.page = 3 |
---|
592 | success() |
---|
593 | } |
---|
594 | on("previous") { |
---|
595 | // handle form data |
---|
596 | groupPage(flow, flash, params) ? success() : error() |
---|
597 | }.to "events" |
---|
598 | on("next") { |
---|
599 | // handle form data |
---|
600 | groupPage(flow, flash, params) ? success() : error() |
---|
601 | }.to "samples" |
---|
602 | on("quickSave") { |
---|
603 | // handle form data |
---|
604 | groupPage(flow, flash, params) ? success() : error() |
---|
605 | }.to "waitForSave" |
---|
606 | } |
---|
607 | |
---|
608 | // sample 'previous' page with warning |
---|
609 | samplePrevious { |
---|
610 | render(view: "_samples_previous_warning") |
---|
611 | onRender { |
---|
612 | // Grom a development message |
---|
613 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_samples_previous_warning.gsp".grom() |
---|
614 | |
---|
615 | flow.page = 4 |
---|
616 | } |
---|
617 | on("next").to "samples" |
---|
618 | on("previous").to "groups" |
---|
619 | } |
---|
620 | |
---|
621 | // samples page |
---|
622 | samples { |
---|
623 | render(view: "_samples") |
---|
624 | onRender { |
---|
625 | // Grom a development message |
---|
626 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_samples.gsp".grom() |
---|
627 | |
---|
628 | flow.page = 4 |
---|
629 | success() |
---|
630 | } |
---|
631 | on("switchTemplate") { |
---|
632 | // handle form data |
---|
633 | samplePage(flow, flash, params) |
---|
634 | |
---|
635 | // ignore errors |
---|
636 | flash.wizardErrors = [:] |
---|
637 | |
---|
638 | succes() |
---|
639 | }.to "samples" |
---|
640 | on("refresh") { |
---|
641 | // handle samples |
---|
642 | samplePage(flow, flash, params) |
---|
643 | |
---|
644 | // refresh all sample templates |
---|
645 | flow.study.giveSampleTemplates().each() { |
---|
646 | it.refresh() |
---|
647 | } |
---|
648 | |
---|
649 | // ignore errors |
---|
650 | flash.wizardErrors = [:] |
---|
651 | |
---|
652 | success() |
---|
653 | }.to "samples" |
---|
654 | on("regenerate") { |
---|
655 | // handle samples |
---|
656 | samplePage(flow, flash, params) |
---|
657 | |
---|
658 | // remove all samples from the study |
---|
659 | flow.study.samples.findAll{true}.each() { sample -> |
---|
660 | flow.study.removeFromSamples(sample) |
---|
661 | } |
---|
662 | |
---|
663 | // ignore errors |
---|
664 | flash.wizardErrors = [:] |
---|
665 | |
---|
666 | success() |
---|
667 | }.to "samples" |
---|
668 | on("previous") { |
---|
669 | // handle samples |
---|
670 | samplePage(flow, flash, params) |
---|
671 | |
---|
672 | // ignore errors |
---|
673 | flash.wizardErrors = [:] |
---|
674 | |
---|
675 | success() |
---|
676 | }.to "samplePrevious" |
---|
677 | on("next") { |
---|
678 | // handle form data |
---|
679 | samplePage(flow, flash, params) ? success() : error() |
---|
680 | }.to "assays" |
---|
681 | on("quickSave") { |
---|
682 | // handle form data |
---|
683 | samplePage(flow, flash, params) ? success() : error() |
---|
684 | }.to "waitForSave" |
---|
685 | } |
---|
686 | |
---|
687 | // assays page |
---|
688 | assays { |
---|
689 | render(view: "_assays") |
---|
690 | onRender { |
---|
691 | // Grom a development message |
---|
692 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_assays.gsp".grom() |
---|
693 | |
---|
694 | flow.page = 5 |
---|
695 | } |
---|
696 | on("refresh") { |
---|
697 | // handle form data |
---|
698 | assayPage(flow, flash, params) |
---|
699 | |
---|
700 | // force refresh of the template |
---|
701 | if (flow.assay && flow.assay.template && flow.assay.template instanceof Template) { |
---|
702 | flow.assay.template.refresh() |
---|
703 | } |
---|
704 | |
---|
705 | // reset errors |
---|
706 | flash.wizardErrors = [:] |
---|
707 | success() |
---|
708 | }.to "assays" |
---|
709 | on("switchTemplate") { |
---|
710 | // handle form data |
---|
711 | assayPage(flow, flash, params) |
---|
712 | |
---|
713 | // find assay template |
---|
714 | def template = Template.findByName(params.get('template')) |
---|
715 | if (flow.assay) { |
---|
716 | // set template |
---|
717 | flow.assay.template = template |
---|
718 | if (template) { |
---|
719 | flow.assay.setFieldValue( |
---|
720 | 'externalAssayID', |
---|
721 | ucwords(flow.study.code).replaceAll("([ ]{1,})", "") + '_' + ucwords(template.name).replaceAll("([ ]{1,})", "") |
---|
722 | ) |
---|
723 | } |
---|
724 | } else { |
---|
725 | // create a new assay instance |
---|
726 | flow.assay = new Assay(template: template) |
---|
727 | if (template) { |
---|
728 | flow.assay.setFieldValue( |
---|
729 | 'externalAssayID', |
---|
730 | ucwords(flow.study.code).replaceAll("([ ]{1,})", "") + '_' + ucwords(template.name).replaceAll("([ ]{1,})", "") |
---|
731 | ) |
---|
732 | } |
---|
733 | } |
---|
734 | |
---|
735 | // reset errors |
---|
736 | flash.wizardErrors = [:] |
---|
737 | success() |
---|
738 | }.to "assays" |
---|
739 | on("add") { |
---|
740 | // handle form data |
---|
741 | assayPage(flow, flash, params) |
---|
742 | |
---|
743 | // reset errors |
---|
744 | flash.wizardErrors = [:] |
---|
745 | |
---|
746 | // add assay to study |
---|
747 | flow.study.addToAssays( flow.assay ) |
---|
748 | |
---|
749 | // validate assay |
---|
750 | if (flow.assay.validate()) { |
---|
751 | // remove assay from the flowscope |
---|
752 | flow.remove('assay') |
---|
753 | success() |
---|
754 | } else { |
---|
755 | // assay does not validate |
---|
756 | // remove from study |
---|
757 | flow.study.removeFromAssays( flow.assay ) |
---|
758 | |
---|
759 | // append errors |
---|
760 | this.appendErrors(flow.assay, flash.wizardErrors) |
---|
761 | error() |
---|
762 | } |
---|
763 | }.to "assays" |
---|
764 | on("deleteAssay") { |
---|
765 | // handle form data |
---|
766 | assayPage(flow, flash, params) |
---|
767 | |
---|
768 | // reset errors |
---|
769 | flash.wizardErrors = [:] |
---|
770 | |
---|
771 | // find this assay |
---|
772 | def assay = flow.study.assays.find { it.getIdentifier() == (params.get('do') as int) } |
---|
773 | |
---|
774 | // perform delete |
---|
775 | if (assay) flow.study.deleteAssay( assay ) |
---|
776 | }.to "assays" |
---|
777 | on("previous") { |
---|
778 | // handle form data |
---|
779 | assayPage(flow, flash, params) |
---|
780 | |
---|
781 | // ignore errors |
---|
782 | flash.wizardErrors = [:] |
---|
783 | |
---|
784 | success() |
---|
785 | }.to "samples" |
---|
786 | on("next") { |
---|
787 | // handle form data |
---|
788 | assayPage(flow, flash, params) ? success() : error() |
---|
789 | }.to "assayNext" |
---|
790 | on("quickSave") { |
---|
791 | // handle form data |
---|
792 | assayPage(flow, flash, params) ? success() : error() |
---|
793 | }.to "waitForSave" |
---|
794 | } |
---|
795 | |
---|
796 | // assayNext |
---|
797 | assayNext { |
---|
798 | action { |
---|
799 | // Grom a development message |
---|
800 | if (pluginManager.getGrailsPlugin('grom')) "entering assayNext".grom() |
---|
801 | |
---|
802 | // have we got samples and assays? |
---|
803 | if (flow.study.assays && flow.study.samples) { |
---|
804 | // yes, go to the group page |
---|
805 | toAssayGroups() |
---|
806 | } else { |
---|
807 | // no need to show the group page as |
---|
808 | // there's nothing to group |
---|
809 | toConfirm() |
---|
810 | } |
---|
811 | } |
---|
812 | on("toAssayGroups").to "assayGroups" |
---|
813 | on("toConfirm").to "confirm" |
---|
814 | } |
---|
815 | |
---|
816 | // assay grouping page |
---|
817 | assayGroups { |
---|
818 | render(view: "_assay_groups") |
---|
819 | onRender { |
---|
820 | // Grom a development message |
---|
821 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_assay_groups.gsp".grom() |
---|
822 | |
---|
823 | flow.page = 5 |
---|
824 | } |
---|
825 | on("previous") { |
---|
826 | // handle form data |
---|
827 | assayGroupPage(flow, flash, params) |
---|
828 | |
---|
829 | // ignore errors |
---|
830 | flash.wizardErrors = [:] |
---|
831 | |
---|
832 | success() |
---|
833 | }.to "assays" |
---|
834 | on("next") { |
---|
835 | // handle form data |
---|
836 | assayGroupPage(flow, flash, params) ? success() : error() |
---|
837 | }.to "confirm" |
---|
838 | on("quickSave") { |
---|
839 | // handle form data |
---|
840 | assayGroupPage(flow, flash, params) ? success() : error() |
---|
841 | }.to "waitForSave" |
---|
842 | } |
---|
843 | |
---|
844 | // confirm Previous |
---|
845 | confirmPrevious { |
---|
846 | action { |
---|
847 | // Grom a development message |
---|
848 | if (pluginManager.getGrailsPlugin('grom')) "entering confirmPrevious".grom() |
---|
849 | |
---|
850 | // have we got samples and assays? |
---|
851 | if (flow.study.assays && flow.study.samples) { |
---|
852 | // yes, go to the group page |
---|
853 | toAssayGroups() |
---|
854 | } else { |
---|
855 | // no need to show the group page as |
---|
856 | // there's nothing to group |
---|
857 | toAssays() |
---|
858 | } |
---|
859 | } |
---|
860 | on("toAssayGroups").to "assayGroups" |
---|
861 | on("toAssays").to "assays" |
---|
862 | } |
---|
863 | |
---|
864 | // confirmation |
---|
865 | confirm { |
---|
866 | render(view: "_confirmation") |
---|
867 | onRender { |
---|
868 | // Grom a development message |
---|
869 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_confirmation.gsp".grom() |
---|
870 | |
---|
871 | flow.page = 6 |
---|
872 | } |
---|
873 | on("toStudy").to "study" |
---|
874 | on("toSubjects").to "subjects" |
---|
875 | on("toEvents").to "events" |
---|
876 | on("toGroups").to "groups" |
---|
877 | on("toSamples").to "samples" |
---|
878 | on("toAssays").to "assays" |
---|
879 | on("toAssayGroups").to "assayGroups" |
---|
880 | on("previous").to "confirmPrevious" |
---|
881 | on("next").to "waitForSave" |
---|
882 | on("quickSave").to "waitForSave" |
---|
883 | } |
---|
884 | |
---|
885 | waitForSave { |
---|
886 | render(view: "_wait") |
---|
887 | onRender { |
---|
888 | // Grom a development message |
---|
889 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_wait.gsp".grom() |
---|
890 | |
---|
891 | flow.page = 7 |
---|
892 | } |
---|
893 | on("next").to "save" |
---|
894 | } |
---|
895 | |
---|
896 | // store all study data |
---|
897 | save { |
---|
898 | action { |
---|
899 | // Grom a development message |
---|
900 | if (pluginManager.getGrailsPlugin('grom')) "entering save".grom() |
---|
901 | |
---|
902 | flash.wizardErrors = [:] |
---|
903 | |
---|
904 | // persist data to the database |
---|
905 | try { |
---|
906 | // save study |
---|
907 | // Grom a development message |
---|
908 | if (pluginManager.getGrailsPlugin('grom')) "saving study".grom() |
---|
909 | |
---|
910 | // Make sure the owner of the study is set right |
---|
911 | flow.study.owner = authenticationService.getLoggedInUser() |
---|
912 | |
---|
913 | if (!flow.study.save(flush:true)) { |
---|
914 | this.appendErrors(flow.study, flash.wizardErrors) |
---|
915 | throw new Exception('error saving study') |
---|
916 | } |
---|
917 | log.info ".saved study "+flow.study+" (id: "+flow.study.id+")" |
---|
918 | |
---|
919 | success() |
---|
920 | } catch (Exception e) { |
---|
921 | // rollback |
---|
922 | this.appendErrorMap(['exception': e.toString() + ', see log for stacktrace' ], flash.wizardErrors) |
---|
923 | |
---|
924 | // stacktrace in flash scope |
---|
925 | flash.debug = e.getStackTrace() |
---|
926 | |
---|
927 | error() |
---|
928 | } |
---|
929 | } |
---|
930 | on("error").to "error" |
---|
931 | on(Exception).to "error" |
---|
932 | on("success").to "done" |
---|
933 | } |
---|
934 | |
---|
935 | // error storing data |
---|
936 | error { |
---|
937 | render(view: "_error") |
---|
938 | onRender { |
---|
939 | // Grom a development message |
---|
940 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_error.gsp".grom() |
---|
941 | |
---|
942 | flow.page = 6 |
---|
943 | } |
---|
944 | on("next").to "waitForSave" |
---|
945 | on("previous").to "samples" |
---|
946 | } |
---|
947 | |
---|
948 | // render finish page |
---|
949 | done { |
---|
950 | render(view: "_done") |
---|
951 | onRender { |
---|
952 | // Grom a development message |
---|
953 | if (pluginManager.getGrailsPlugin('grom')) "rendering the partial: pages/_done.gsp".grom() |
---|
954 | |
---|
955 | flow.page = 7 |
---|
956 | } |
---|
957 | onEnd { |
---|
958 | // clean flow scope |
---|
959 | flow.clear() |
---|
960 | } |
---|
961 | } |
---|
962 | } |
---|
963 | |
---|
964 | /** |
---|
965 | * load a study |
---|
966 | * @param Map LocalAttributeMap (the flow scope) |
---|
967 | * @param Map localAttributeMap (the flash scope) |
---|
968 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
969 | * @returns boolean |
---|
970 | */ |
---|
971 | def loadStudy(flow, flash, params, user) { |
---|
972 | flash.wizardErrors = [:] |
---|
973 | |
---|
974 | // load study |
---|
975 | try { |
---|
976 | // load study |
---|
977 | def study = (params.studyid) ? Study.findById( params.studyid ) : Study.findByTitle( params.study ) |
---|
978 | |
---|
979 | // Check whether the user is allowed to edit this study. If it is not allowed |
---|
980 | // the used should had never seen a link to this page, so he should never get |
---|
981 | // here. That's why we just return false |
---|
982 | if (!study.canWrite(user)){ |
---|
983 | return false |
---|
984 | } |
---|
985 | |
---|
986 | // Grails tends to lazily initialize objects. While in theory this |
---|
987 | // is a nice feature, it does not work well with our complex setup |
---|
988 | // using the Identity class to match POST variables with object |
---|
989 | // instances. This lazy initialization caused two issues: |
---|
990 | // #147 and #223, and both are now resolved by forcing objects to |
---|
991 | // be instantiated / initialized when a study is loaded from the |
---|
992 | // database |
---|
993 | study.template |
---|
994 | study.hasMany.each { name, type -> |
---|
995 | // dynamically instantiate all identity classes |
---|
996 | if (type.toString() =~ "dbnp.studycapturing") { |
---|
997 | study.getProperty( name ).each { } |
---|
998 | } |
---|
999 | } |
---|
1000 | |
---|
1001 | // store study in the flowscope |
---|
1002 | flow.study = study |
---|
1003 | |
---|
1004 | // set 'quicksave' variable |
---|
1005 | flow.quickSave = true |
---|
1006 | |
---|
1007 | return true |
---|
1008 | } catch (Exception e) { |
---|
1009 | // rollback |
---|
1010 | this.appendErrorMap(['exception': e.getMessage() + ', see log for stacktrace'], flash.wizardErrors) |
---|
1011 | |
---|
1012 | return false |
---|
1013 | } |
---|
1014 | } |
---|
1015 | |
---|
1016 | /** |
---|
1017 | * Handle the wizard study page |
---|
1018 | * |
---|
1019 | * @param Map LocalAttributeMap (the flow scope) |
---|
1020 | * @param Map localAttributeMap (the flash scope) |
---|
1021 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1022 | * @returns boolean |
---|
1023 | */ |
---|
1024 | def studyPage(flow, flash, params) { |
---|
1025 | flash.values = params |
---|
1026 | flash.wizardErrors = [:] |
---|
1027 | |
---|
1028 | // instantiate study of it is not yet present |
---|
1029 | if (!flow.study) flow.study = new Study() |
---|
1030 | |
---|
1031 | // did the study template change? |
---|
1032 | if (params.get('template').size() && flow.study.template?.name != params.get('template')) { |
---|
1033 | // set the template |
---|
1034 | flow.study.template = Template.findByName(params.remove('template')) |
---|
1035 | } |
---|
1036 | |
---|
1037 | // does the study have a template set? |
---|
1038 | if (flow.study.template && flow.study.template instanceof Template) { |
---|
1039 | // yes, iterate through template fields |
---|
1040 | flow.study.giveFields().each() { |
---|
1041 | // and set their values |
---|
1042 | flow.study.setFieldValue(it.name, params.get(it.escapedName())) |
---|
1043 | } |
---|
1044 | } |
---|
1045 | |
---|
1046 | // handle publications |
---|
1047 | handlePublications(flow, flash, params) |
---|
1048 | |
---|
1049 | // handle contacts |
---|
1050 | handleContacts(flow, flash, params) |
---|
1051 | |
---|
1052 | // handle users (readers, writers) |
---|
1053 | handleUsers(flow, flash, params, 'readers') |
---|
1054 | handleUsers(flow, flash, params, 'writers') |
---|
1055 | |
---|
1056 | // handle public checkbox |
---|
1057 | if (params.get("publicstudy")) { |
---|
1058 | flow.study.publicstudy = params.get("publicstudy") |
---|
1059 | } |
---|
1060 | |
---|
1061 | // have we got a template? |
---|
1062 | if (flow.study.template && flow.study.template instanceof Template) { |
---|
1063 | // validate the study |
---|
1064 | if (flow.study.validate()) { |
---|
1065 | // instance is okay |
---|
1066 | return true |
---|
1067 | } else { |
---|
1068 | // validation failed |
---|
1069 | this.appendErrors(flow.study, flash.wizardErrors) |
---|
1070 | return false |
---|
1071 | } |
---|
1072 | } else { |
---|
1073 | // no, return an error that the template is not set |
---|
1074 | this.appendErrorMap(['template': g.message(code: 'select.not.selected.or.add', args: ['template'])], flash.wizardErrors) |
---|
1075 | return false |
---|
1076 | } |
---|
1077 | } |
---|
1078 | |
---|
1079 | /** |
---|
1080 | * re-usable code for handling publications form data in a web flow |
---|
1081 | * @param Map LocalAttributeMap (the flow scope) |
---|
1082 | * @param Map localAttributeMap (the flash scope) |
---|
1083 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1084 | * @returns boolean |
---|
1085 | */ |
---|
1086 | def handlePublications(flow, flash, params) { |
---|
1087 | flash.wizardErrors = [:] |
---|
1088 | |
---|
1089 | if (!flow.study.publications) flow.study.publications = [] |
---|
1090 | |
---|
1091 | // Check the ids of the pubblications that should be attached |
---|
1092 | // to this study. If they are already attached, keep 'm. If |
---|
1093 | // studies are attached that are not in the selected (i.e. the |
---|
1094 | // user deleted them), remove them |
---|
1095 | def publicationIDs = params.get('publication_ids') |
---|
1096 | if (publicationIDs) { |
---|
1097 | // Find the individual IDs and make integers |
---|
1098 | publicationIDs = publicationIDs.split(',').collect { Integer.parseInt(it, 10) } |
---|
1099 | |
---|
1100 | // First remove the publication that are not present in the array |
---|
1101 | flow.study.publications.removeAll { publication -> !publicationIDs.find { id -> id == publication.id } } |
---|
1102 | |
---|
1103 | // Add those publications not yet present in the database |
---|
1104 | publicationIDs.each { id -> |
---|
1105 | if (!flow.study.publications.find { publication -> id == publication.id }) { |
---|
1106 | def publication = Publication.get(id) |
---|
1107 | if (publication) { |
---|
1108 | flow.study.addToPublications(publication) |
---|
1109 | } else { |
---|
1110 | log.info('.publication with ID ' + id + ' not found in database.') |
---|
1111 | } |
---|
1112 | } |
---|
1113 | } |
---|
1114 | |
---|
1115 | } else { |
---|
1116 | log.info('.no publications selected.') |
---|
1117 | flow.study.publications.clear() |
---|
1118 | } |
---|
1119 | |
---|
1120 | } |
---|
1121 | |
---|
1122 | /** |
---|
1123 | * re-usable code for handling contacts form data in a web flow |
---|
1124 | * @param Map LocalAttributeMap (the flow scope) |
---|
1125 | * @param Map localAttributeMap (the flash scope) |
---|
1126 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1127 | * @return boolean |
---|
1128 | */ |
---|
1129 | def handleContacts(flow, flash, params) { |
---|
1130 | flash.wizardErrors = [:] |
---|
1131 | |
---|
1132 | if (!flow.study.persons) flow.study.persons = [] |
---|
1133 | |
---|
1134 | // Check the ids of the contacts that should be attached |
---|
1135 | // to this study. If they are already attached, keep 'm. If |
---|
1136 | // studies are attached that are not in the selected (i.e. the |
---|
1137 | // user deleted them), remove them |
---|
1138 | |
---|
1139 | // Contacts are saved as [person_id]-[role_id] |
---|
1140 | def contactIDs = params.get('contacts_ids') |
---|
1141 | if (contactIDs) { |
---|
1142 | // Find the individual IDs and make integers |
---|
1143 | contactIDs = contactIDs.split(',').collect { |
---|
1144 | def parts = it.split('-') |
---|
1145 | return [person: Integer.parseInt(parts[0]), role: Integer.parseInt(parts[1])] |
---|
1146 | } |
---|
1147 | |
---|
1148 | // First remove the contacts that are not present in the array |
---|
1149 | flow.study.persons.removeAll { |
---|
1150 | studyperson -> !contactIDs.find { ids -> (ids.person == studyperson.person.id) && (ids.role == studyperson.role.id) } |
---|
1151 | } |
---|
1152 | |
---|
1153 | // Add those contacts not yet present in the database |
---|
1154 | contactIDs.each { ids -> |
---|
1155 | if (!flow.study.persons.find { studyperson -> (ids.person == studyperson.person.id) && (ids.role == studyperson.role.id) }) { |
---|
1156 | def person = Person.get(ids.person) |
---|
1157 | def role = PersonRole.get(ids.role) |
---|
1158 | if (person && role) { |
---|
1159 | // Find a studyperson object with these parameters |
---|
1160 | def studyPerson = StudyPerson.findAll().find { studyperson -> studyperson.person.id == person.id && studyperson.role.id == role.id } |
---|
1161 | |
---|
1162 | // If if does not yet exist, save the example |
---|
1163 | if (!studyPerson) { |
---|
1164 | studyPerson = new StudyPerson( |
---|
1165 | person: person, |
---|
1166 | role: role |
---|
1167 | ) |
---|
1168 | studyPerson.save(flush: true) |
---|
1169 | } |
---|
1170 | |
---|
1171 | flow.study.addToPersons(studyPerson) |
---|
1172 | } else { |
---|
1173 | log.info('.person ' + ids.person + ' or Role ' + ids.role + ' not found in database.') |
---|
1174 | } |
---|
1175 | } |
---|
1176 | } |
---|
1177 | } else { |
---|
1178 | log.info('.no persons selected.') |
---|
1179 | flow.study.persons.clear() |
---|
1180 | } |
---|
1181 | |
---|
1182 | } |
---|
1183 | |
---|
1184 | /** |
---|
1185 | * re-usable code for handling contacts form data in a web flow |
---|
1186 | * @param Map LocalAttributeMap (the flow scope) |
---|
1187 | * @param Map localAttributeMap (the flash scope) |
---|
1188 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1189 | * @param String 'readers' or 'writers' |
---|
1190 | * @return boolean |
---|
1191 | */ |
---|
1192 | def handleUsers(flow, flash, params, type) { |
---|
1193 | flash.wizardErrors = [:] |
---|
1194 | |
---|
1195 | def users = [] |
---|
1196 | |
---|
1197 | if (type == "readers") { |
---|
1198 | users = flow.study.readers ?: [] |
---|
1199 | } else if (type == "writers") { |
---|
1200 | users = flow.study.writers ?: [] |
---|
1201 | } |
---|
1202 | |
---|
1203 | // Check the ids of the contacts that should be attached |
---|
1204 | // to this study. If they are already attached, keep 'm. If |
---|
1205 | // studies are attached that are not in the selected (i.e. the |
---|
1206 | // user deleted them), remove them |
---|
1207 | |
---|
1208 | // Users are saved as user_id |
---|
1209 | def userIDs = params.get(type + '_ids') |
---|
1210 | if (userIDs) { |
---|
1211 | // Find the individual IDs and make integers |
---|
1212 | userIDs = userIDs.split(',').collect { Integer.parseInt(it, 10) } |
---|
1213 | |
---|
1214 | // First remove the publication that are not present in the array |
---|
1215 | users.removeAll { user -> !userIDs.find { id -> id == user.id } } |
---|
1216 | |
---|
1217 | // Add those publications not yet present in the database |
---|
1218 | userIDs.each { id -> |
---|
1219 | if (!users.find { user -> id == user.id }) { |
---|
1220 | def user = SecUser.get(id) |
---|
1221 | if (user) { |
---|
1222 | users.add(user) |
---|
1223 | } else { |
---|
1224 | log.info('.user with ID ' + id + ' not found in database.') |
---|
1225 | } |
---|
1226 | } |
---|
1227 | } |
---|
1228 | |
---|
1229 | } else { |
---|
1230 | log.info('.no users selected.') |
---|
1231 | users.clear() |
---|
1232 | } |
---|
1233 | |
---|
1234 | if (type == "readers") { |
---|
1235 | if (flow.study.readers) |
---|
1236 | flow.study.readers.clear() |
---|
1237 | users.each { flow.study.addToReaders(it) } |
---|
1238 | } else if (type == "writers") { |
---|
1239 | if (flow.study.writers) |
---|
1240 | flow.study.writers.clear() |
---|
1241 | |
---|
1242 | users.each { flow.study.addToWriters(it) } |
---|
1243 | } |
---|
1244 | } |
---|
1245 | |
---|
1246 | /** |
---|
1247 | * Handle the wizard subject page |
---|
1248 | * |
---|
1249 | * @param Map LocalAttributeMap (the flow scope) |
---|
1250 | * @param Map localAttributeMap (the flash scope) |
---|
1251 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1252 | * @returns boolean |
---|
1253 | */ |
---|
1254 | def subjectPage(flow, flash, params) { |
---|
1255 | def errors = false |
---|
1256 | flash.wizardErrors = [:] |
---|
1257 | |
---|
1258 | // remember the params in the flash scope |
---|
1259 | flash.values = params |
---|
1260 | |
---|
1261 | // iterate through subjects |
---|
1262 | flow.study.subjects.each() { subject -> |
---|
1263 | // iterate through (template and domain) fields |
---|
1264 | subject.giveFields().each() { field -> |
---|
1265 | // set field |
---|
1266 | subject.setFieldValue( |
---|
1267 | field.name, |
---|
1268 | params.get('subject_' + subject.getIdentifier() + '_' + field.escapedName()) |
---|
1269 | ) |
---|
1270 | } |
---|
1271 | |
---|
1272 | // validate subject |
---|
1273 | if (!subject.validate()) { |
---|
1274 | errors = true |
---|
1275 | this.appendErrors(subject, flash.wizardErrors, 'subject_' + subject.getIdentifier() + '_') |
---|
1276 | } |
---|
1277 | } |
---|
1278 | |
---|
1279 | return !errors |
---|
1280 | } |
---|
1281 | |
---|
1282 | /** |
---|
1283 | * Add a number of subjects to a study |
---|
1284 | * |
---|
1285 | * required params entities: |
---|
1286 | * -addNumber (int) |
---|
1287 | * -species (string) |
---|
1288 | * -template (string) |
---|
1289 | * |
---|
1290 | * @param Map LocalAttributeMap (the flow scope) |
---|
1291 | * @param Map localAttributeMap (the flash scope) |
---|
1292 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1293 | * @returns boolean |
---|
1294 | */ |
---|
1295 | def addSubjects(flow, flash, params) { |
---|
1296 | // remember the params in the flash scope |
---|
1297 | flash.values = params |
---|
1298 | |
---|
1299 | // handle the subject page |
---|
1300 | subjectPage(flow, flash, params) |
---|
1301 | |
---|
1302 | // (re)set error message |
---|
1303 | flash.wizardErrors = [:] |
---|
1304 | |
---|
1305 | // set work variables |
---|
1306 | def errors = false |
---|
1307 | def number = params.get('addNumber') as int |
---|
1308 | def species = Term.findByName(params.get('species')) |
---|
1309 | def template = Template.findByName(params.get('template')) |
---|
1310 | |
---|
1311 | // can we add subjects? |
---|
1312 | if (number > 0 && species && template) { |
---|
1313 | // add subjects to study |
---|
1314 | number.times { |
---|
1315 | // work variables |
---|
1316 | def subjectName = 'Subject ' |
---|
1317 | def subjectIterator = 1 |
---|
1318 | def tempSubjectName = subjectName + subjectIterator |
---|
1319 | |
---|
1320 | // make sure subject name is unique |
---|
1321 | if (flow.study.subjects) { |
---|
1322 | while (flow.study.subjects.find { it.name == tempSubjectName }) { |
---|
1323 | subjectIterator++ |
---|
1324 | tempSubjectName = subjectName + subjectIterator |
---|
1325 | } |
---|
1326 | } |
---|
1327 | subjectName = tempSubjectName |
---|
1328 | |
---|
1329 | // create a subject instance |
---|
1330 | def subject = new Subject( |
---|
1331 | name : subjectName, |
---|
1332 | species : species, |
---|
1333 | template : template |
---|
1334 | ) |
---|
1335 | |
---|
1336 | // add it to the study |
---|
1337 | flow.study.addToSubjects( subject ) |
---|
1338 | |
---|
1339 | // validate subject |
---|
1340 | if (subject.validate()) { |
---|
1341 | log.info ".added subject "+subject |
---|
1342 | } else { |
---|
1343 | // whoops? |
---|
1344 | flow.study.removeFromSubjects( subject ) |
---|
1345 | |
---|
1346 | // append errors |
---|
1347 | this.appendErrors(subject, flash.wizardErrors) |
---|
1348 | errors = true |
---|
1349 | } |
---|
1350 | } |
---|
1351 | } else { |
---|
1352 | // add feedback |
---|
1353 | errors = true |
---|
1354 | if (number < 1) this.appendErrorMap(['addNumber': 'Enter a positive number of subjects to add'], flash.wizardErrors) |
---|
1355 | if (!species) this.appendErrorMap(['species': g.message(code: 'select.not.selected.or.add', args: ['species'])], flash.wizardErrors) |
---|
1356 | if (!template) this.appendErrorMap(['template': g.message(code: 'select.not.selected.or.add', args: ['template'])], flash.wizardErrors) |
---|
1357 | } |
---|
1358 | |
---|
1359 | return !errors |
---|
1360 | } |
---|
1361 | |
---|
1362 | /** |
---|
1363 | * Handle the wizard event page |
---|
1364 | * |
---|
1365 | * @param Map LocalAttributeMap (the flow scope) |
---|
1366 | * @param Map localAttributeMap (the flash scope) |
---|
1367 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1368 | * @returns boolean |
---|
1369 | */ |
---|
1370 | def eventPage(flow, flash, params) { |
---|
1371 | def errors = false |
---|
1372 | flash.wizardErrors = [:] |
---|
1373 | |
---|
1374 | // remember the params in the flash scope |
---|
1375 | flash.values = params |
---|
1376 | |
---|
1377 | // handle the 'add event' form |
---|
1378 | if (flow.event) { |
---|
1379 | flow.event.giveFields().each() { field -> |
---|
1380 | // set field |
---|
1381 | flow.event.setFieldValue( |
---|
1382 | field.name, |
---|
1383 | params.get(field.escapedName()) |
---|
1384 | ) |
---|
1385 | } |
---|
1386 | } |
---|
1387 | |
---|
1388 | // handle the eventGroup names and grouping |
---|
1389 | def name = "" |
---|
1390 | def tempName= "" |
---|
1391 | flow.study.eventGroups.each() { eventGroup -> |
---|
1392 | // iterate through templates |
---|
1393 | flow.study.giveAllEventTemplates().each() { template -> |
---|
1394 | tempName = params.get( 'eventGroup_' + eventGroup.getIdentifier() + '_' + template.getIdentifier() ) |
---|
1395 | |
---|
1396 | // is the name different? |
---|
1397 | if (tempName != eventGroup.name) { |
---|
1398 | name = tempName |
---|
1399 | } |
---|
1400 | } |
---|
1401 | |
---|
1402 | // should the name change? |
---|
1403 | if (name) { |
---|
1404 | // yes, change it |
---|
1405 | eventGroup.name = name |
---|
1406 | name = "" |
---|
1407 | } |
---|
1408 | |
---|
1409 | // handle eventGrouping |
---|
1410 | ( ((flow.study.events) ? flow.study.events : []) + ((flow.study.samplingEvents) ? flow.study.samplingEvents : []) ) .each() { event -> |
---|
1411 | if (params.get( 'event_' + event.getIdentifier() + '_group_' + eventGroup.getIdentifier() )) { |
---|
1412 | // add to eventGroup |
---|
1413 | if (event instanceof SamplingEvent) { |
---|
1414 | // check if we are already in this eventGroup |
---|
1415 | if (!eventGroup.samplingEvents.find { it.equals(event) }) { |
---|
1416 | // no, add it |
---|
1417 | eventGroup.addToSamplingEvents(event) |
---|
1418 | |
---|
1419 | // iterate through subjects for this eventGroup |
---|
1420 | eventGroup.subjects.each() { subject -> |
---|
1421 | // instantiate a sample for this subject / event |
---|
1422 | def samplingEventName = ucwords(event.template.name) |
---|
1423 | def eventGroupName = ucwords(eventGroup.name).replaceAll("([ ]{1,})", "") |
---|
1424 | def sampleName = (ucwords(subject.name) + '_' + samplingEventName + '_' + eventGroupName + '_' + new RelTime(event.startTime).toString()).replaceAll("([ ]{1,})", "") |
---|
1425 | def tempSampleIterator = 0 |
---|
1426 | def tempSampleName = sampleName |
---|
1427 | |
---|
1428 | // make sure sampleName is unique |
---|
1429 | if (flow.study.samples) { |
---|
1430 | while (flow.study.samples.find { it.name == tempSampleName }) { |
---|
1431 | tempSampleIterator++ |
---|
1432 | tempSampleName = sampleName + "_" + tempSampleIterator |
---|
1433 | } |
---|
1434 | sampleName = tempSampleName |
---|
1435 | } |
---|
1436 | |
---|
1437 | // instantiate a sample |
---|
1438 | flow.study.addToSamples( |
---|
1439 | new Sample( |
---|
1440 | parentSubject : subject, |
---|
1441 | parentEvent : event, |
---|
1442 | parentEventGroup: eventGroup, |
---|
1443 | name : sampleName, |
---|
1444 | template : (event.sampleTemplate) ? event.sampleTemplate : '' |
---|
1445 | ) |
---|
1446 | ) |
---|
1447 | } |
---|
1448 | } |
---|
1449 | } else { |
---|
1450 | eventGroup.addToEvents(event) |
---|
1451 | } |
---|
1452 | } else { |
---|
1453 | // remove from eventGroup |
---|
1454 | if (event instanceof SamplingEvent) { |
---|
1455 | // iterate through subjects (if we have them) |
---|
1456 | eventGroup.subjects.each() { subject -> |
---|
1457 | // find all samples for this subject / event |
---|
1458 | flow.study.samples.findAll { (it.parentEvent.equals(event) && it.parentSubject.equals(subject) ) }.each() { |
---|
1459 | // delete this sample |
---|
1460 | flow.study.removeFromSamples( it ) |
---|
1461 | it.delete() |
---|
1462 | } |
---|
1463 | } |
---|
1464 | |
---|
1465 | eventGroup.removeFromSamplingEvents(event) |
---|
1466 | } else { |
---|
1467 | eventGroup.removeFromEvents(event) |
---|
1468 | } |
---|
1469 | } |
---|
1470 | } |
---|
1471 | } |
---|
1472 | |
---|
1473 | // handle the (sampling) events |
---|
1474 | ( ((flow.study.events) ? flow.study.events : []) + ((flow.study.samplingEvents) ? flow.study.samplingEvents : []) ) .each() { event -> |
---|
1475 | event.giveFields().each() { field -> |
---|
1476 | event.setFieldValue( |
---|
1477 | field.name, |
---|
1478 | params.get( 'event_' + event.getIdentifier() + '_' + field.escapedName() ) |
---|
1479 | ) |
---|
1480 | } |
---|
1481 | |
---|
1482 | // validate event |
---|
1483 | if (!event.validate()) { |
---|
1484 | errors = true |
---|
1485 | this.appendErrors(event, flash.wizardErrors) |
---|
1486 | } |
---|
1487 | } |
---|
1488 | |
---|
1489 | return !errors |
---|
1490 | } |
---|
1491 | |
---|
1492 | /** |
---|
1493 | * Handle the wizard group page |
---|
1494 | * |
---|
1495 | * @param Map LocalAttributeMap (the flow scope) |
---|
1496 | * @param Map localAttributeMap (the flash scope) |
---|
1497 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1498 | * @returns boolean |
---|
1499 | */ |
---|
1500 | def groupPage(flow, flash, params) { |
---|
1501 | def errors = false |
---|
1502 | flash.wizardErrors = [:] |
---|
1503 | |
---|
1504 | // remember the params in the flash scope |
---|
1505 | flash.values = params |
---|
1506 | |
---|
1507 | // iterate through groups |
---|
1508 | flow.study.eventGroups.each() { eventGroup -> |
---|
1509 | // iterate through subjects |
---|
1510 | flow.study.subjects.each() { subject -> |
---|
1511 | if (params.get('subject_' + subject.getIdentifier() + '_group_' + eventGroup.getIdentifier() )) { |
---|
1512 | // check if this subject is already part of this eventGroup |
---|
1513 | if ( !eventGroup.subjects.find { it.equals(subject) } ) { |
---|
1514 | // add to eventGroup |
---|
1515 | eventGroup.addToSubjects(subject) |
---|
1516 | |
---|
1517 | // iterate through samplingEvents |
---|
1518 | eventGroup.samplingEvents.each() { samplingEvent -> |
---|
1519 | def samplingEventName = ucwords(samplingEvent.template.name) |
---|
1520 | def eventGroupName = ucwords(eventGroup.name) |
---|
1521 | def sampleName = (ucwords(subject.name) + '_' + samplingEventName + '_' + eventGroupName + '_' + new RelTime(samplingEvent.startTime).toString()).replaceAll("([ ]{1,})", "") |
---|
1522 | def tempSampleIterator = 0 |
---|
1523 | def tempSampleName = sampleName |
---|
1524 | |
---|
1525 | // make sure sampleName is unique |
---|
1526 | if (flow.study.samples) { |
---|
1527 | while (flow.study.samples.find { it.name == tempSampleName }) { |
---|
1528 | tempSampleIterator++ |
---|
1529 | tempSampleName = sampleName + "_" + tempSampleIterator |
---|
1530 | } |
---|
1531 | sampleName = tempSampleName |
---|
1532 | } |
---|
1533 | |
---|
1534 | // instantiate a sample |
---|
1535 | flow.study.addToSamples( |
---|
1536 | new Sample( |
---|
1537 | parentSubject : subject, |
---|
1538 | parentEvent : samplingEvent, |
---|
1539 | parentEventGroup: eventGroup, |
---|
1540 | name : sampleName, |
---|
1541 | template : (samplingEvent.sampleTemplate) ? samplingEvent.sampleTemplate : '' |
---|
1542 | ) |
---|
1543 | ) |
---|
1544 | } |
---|
1545 | } else { |
---|
1546 | } |
---|
1547 | } else { |
---|
1548 | // check if this subject is a member of this eventGroup |
---|
1549 | if (eventGroup.subjects.find { it.equals(subject) }) { |
---|
1550 | // remove from eventGroup |
---|
1551 | eventGroup.removeFromSubjects(subject) |
---|
1552 | |
---|
1553 | // iterate through samplingEvents |
---|
1554 | eventGroup.samplingEvents.each() { samplingEvent -> |
---|
1555 | flow.study.samples.findAll { (it.parentEvent.equals(samplingEvent) && it.parentSubject.equals(subject) && it.parentEventGroup.equals(eventGroup)) }.each() { |
---|
1556 | // delete this sample |
---|
1557 | flow.study.removeFromSamples(it) |
---|
1558 | it.delete() |
---|
1559 | } |
---|
1560 | } |
---|
1561 | } |
---|
1562 | } |
---|
1563 | } |
---|
1564 | } |
---|
1565 | } |
---|
1566 | |
---|
1567 | /** |
---|
1568 | * Handle the wizard samples page |
---|
1569 | * |
---|
1570 | * @param Map LocalAttributeMap (the flow scope) |
---|
1571 | * @param Map localAttributeMap (the flash scope) |
---|
1572 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1573 | * @returns boolean |
---|
1574 | */ |
---|
1575 | def samplePage(flow, flash, params) { |
---|
1576 | def errors = false |
---|
1577 | flash.wizardErrors = [:] |
---|
1578 | |
---|
1579 | // remember the params in the flash scope |
---|
1580 | flash.values = params |
---|
1581 | |
---|
1582 | // iterate through samples |
---|
1583 | flow.study.samples.each() { sample -> |
---|
1584 | // iterate through sample fields |
---|
1585 | sample.giveFields().each() { field -> |
---|
1586 | def value = params.get('sample_'+sample.getIdentifier()+'_'+field.escapedName()) |
---|
1587 | |
---|
1588 | // set field value |
---|
1589 | if (!(field.name == 'name' && !value)) { |
---|
1590 | log.info "setting "+field.name+" to "+value |
---|
1591 | sample.setFieldValue(field.name, value) |
---|
1592 | } |
---|
1593 | } |
---|
1594 | |
---|
1595 | // has the template changed? |
---|
1596 | def templateName = params.get('template_' + sample.getIdentifier()) |
---|
1597 | if (templateName && sample.template?.name != templateName) { |
---|
1598 | sample.template = Template.findByName(templateName) |
---|
1599 | } |
---|
1600 | |
---|
1601 | // validate sample |
---|
1602 | if (!sample.validate()) { |
---|
1603 | errors = true |
---|
1604 | this.appendErrors(sample, flash.wizardErrors, 'sample_' + sample.getIdentifier() + '_' ) |
---|
1605 | log.info 'error-> sample_'+sample.getIdentifier() |
---|
1606 | } |
---|
1607 | } |
---|
1608 | |
---|
1609 | return !errors |
---|
1610 | } |
---|
1611 | |
---|
1612 | /** |
---|
1613 | * Handle the wizard assays page |
---|
1614 | * |
---|
1615 | * @param Map LocalAttributeMap (the flow scope) |
---|
1616 | * @param Map localAttributeMap (the flash scope) |
---|
1617 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1618 | * @returns boolean |
---|
1619 | */ |
---|
1620 | def assayPage(flow, flash, params) { |
---|
1621 | def errors = false |
---|
1622 | flash.wizardErrors = [:] |
---|
1623 | |
---|
1624 | // remember the params in the flash scope |
---|
1625 | flash.values = params |
---|
1626 | |
---|
1627 | // handle the 'add assay' form |
---|
1628 | if (flow.assay) { |
---|
1629 | flow.assay.giveFields().each() { field -> |
---|
1630 | // set field |
---|
1631 | flow.assay.setFieldValue( |
---|
1632 | field.name, |
---|
1633 | params.get(field.escapedName()) |
---|
1634 | ) |
---|
1635 | } |
---|
1636 | } |
---|
1637 | |
---|
1638 | // handle the assay data |
---|
1639 | flow.study.assays.each() { assay -> |
---|
1640 | // set data |
---|
1641 | assay.giveFields().each() { field -> |
---|
1642 | assay.setFieldValue( |
---|
1643 | field.name, |
---|
1644 | params.get( 'assay_' + assay.getIdentifier() + '_' + field.escapedName() ) |
---|
1645 | ) |
---|
1646 | } |
---|
1647 | |
---|
1648 | // validate assay |
---|
1649 | if (!assay.validate()) { |
---|
1650 | errors = true |
---|
1651 | this.appendErrors(assay, flash.wizardErrors, 'assay_' + assay.getIdentifier() + '_') |
---|
1652 | } |
---|
1653 | } |
---|
1654 | |
---|
1655 | return !errors |
---|
1656 | } |
---|
1657 | |
---|
1658 | /** |
---|
1659 | * Handle the wizard assayGroups page |
---|
1660 | * |
---|
1661 | * @param Map LocalAttributeMap (the flow scope) |
---|
1662 | * @param Map localAttributeMap (the flash scope) |
---|
1663 | * @param Map GrailsParameterMap (the flow parameters = form data) |
---|
1664 | * @returns boolean |
---|
1665 | */ |
---|
1666 | def assayGroupPage(flow, flash, params) { |
---|
1667 | def errors = false |
---|
1668 | flash.wizardErrors = [:] |
---|
1669 | |
---|
1670 | // remember the params in the flash scope |
---|
1671 | flash.values = params |
---|
1672 | |
---|
1673 | // iterate through samples |
---|
1674 | flow.study.samples.each() { sample -> |
---|
1675 | // iterate through assays |
---|
1676 | flow.study.assays.each() { assay -> |
---|
1677 | if (params.get( 'sample_' + sample.getIdentifier() + '_assay_' + assay.getIdentifier() )) { |
---|
1678 | // add sample to assay |
---|
1679 | assay.addToSamples( sample ) |
---|
1680 | } else { |
---|
1681 | // remove sample from assay |
---|
1682 | assay.removeFromSamples( sample ) |
---|
1683 | } |
---|
1684 | } |
---|
1685 | } |
---|
1686 | |
---|
1687 | return !errors |
---|
1688 | } |
---|
1689 | |
---|
1690 | /** |
---|
1691 | * groovy / java equivalent of php's ucwords function |
---|
1692 | * |
---|
1693 | * Capitalize all first letters of separate words |
---|
1694 | * |
---|
1695 | * @param String |
---|
1696 | * @return String |
---|
1697 | */ |
---|
1698 | public static ucwords(String text) { |
---|
1699 | def newText = '' |
---|
1700 | |
---|
1701 | // change case to lowercase |
---|
1702 | text = text.toLowerCase() |
---|
1703 | |
---|
1704 | // iterate through words |
---|
1705 | text.split(" ").each() { |
---|
1706 | newText += it[0].toUpperCase() + it.substring(1) + " " |
---|
1707 | } |
---|
1708 | |
---|
1709 | return newText.substring(0, newText.size()-1) |
---|
1710 | } |
---|
1711 | |
---|
1712 | /** |
---|
1713 | * return the object from a map of objects by searching for a name |
---|
1714 | * @param String name |
---|
1715 | * @param Map map of objects |
---|
1716 | * @return Object |
---|
1717 | */ |
---|
1718 | def getObjectByName(name, map) { |
---|
1719 | def result = null |
---|
1720 | map.each() { |
---|
1721 | if (it.name == name) { |
---|
1722 | result = it |
---|
1723 | } |
---|
1724 | } |
---|
1725 | |
---|
1726 | return result |
---|
1727 | } |
---|
1728 | |
---|
1729 | /** |
---|
1730 | * transform domain class validation errors into a human readable |
---|
1731 | * linked hash map |
---|
1732 | * @param object validated domain class |
---|
1733 | * @return object linkedHashMap |
---|
1734 | */ |
---|
1735 | def getHumanReadableErrors(object) { |
---|
1736 | def errors = [:] |
---|
1737 | object.errors.getAllErrors().each() { error -> |
---|
1738 | // error.codes.each() { code -> println code } |
---|
1739 | |
---|
1740 | // generally speaking g.message(...) should work, |
---|
1741 | // however it fails in some steps of the wizard |
---|
1742 | // (add event, add assay, etc) so g is not always |
---|
1743 | // availably. Using our own instance of the |
---|
1744 | // validationTagLib instead so it is always |
---|
1745 | // available to us |
---|
1746 | errors[ error.getArguments()[0] ] = validationTagLib.message(error: error) |
---|
1747 | } |
---|
1748 | |
---|
1749 | return errors |
---|
1750 | } |
---|
1751 | |
---|
1752 | /** |
---|
1753 | * append errors of a particular object to a map |
---|
1754 | * @param object |
---|
1755 | * @param map linkedHashMap |
---|
1756 | * @void |
---|
1757 | */ |
---|
1758 | def appendErrors(object, map) { |
---|
1759 | this.appendErrorMap(getHumanReadableErrors(object), map) |
---|
1760 | } |
---|
1761 | |
---|
1762 | def appendErrors(object, map, prepend) { |
---|
1763 | this.appendErrorMap(getHumanReadableErrors(object), map, prepend) |
---|
1764 | } |
---|
1765 | |
---|
1766 | /** |
---|
1767 | * append errors of one map to another map |
---|
1768 | * @param map linkedHashMap |
---|
1769 | * @param map linkedHashMap |
---|
1770 | * @void |
---|
1771 | */ |
---|
1772 | def appendErrorMap(map, mapToExtend) { |
---|
1773 | map.each() {key, value -> |
---|
1774 | mapToExtend[key] = ['key': key, 'value': value, 'dynamic': false] |
---|
1775 | } |
---|
1776 | } |
---|
1777 | |
---|
1778 | def appendErrorMap(map, mapToExtend, prepend) { |
---|
1779 | map.each() {key, value -> |
---|
1780 | mapToExtend[prepend + key] = ['key': key, 'value': value, 'dynamic': true] |
---|
1781 | } |
---|
1782 | } |
---|
1783 | |
---|
1784 | /** |
---|
1785 | * Parses a RelTime string and returns a nice human readable string |
---|
1786 | * |
---|
1787 | * @return Human Readable string or a HTTP response code 400 on error |
---|
1788 | */ |
---|
1789 | def ajaxParseRelTime = { |
---|
1790 | if (params.reltime == null) { |
---|
1791 | response.status = 400 |
---|
1792 | render('reltime parameter is expected') |
---|
1793 | } |
---|
1794 | |
---|
1795 | try { |
---|
1796 | def reltime = RelTime.parseRelTime(params.reltime) |
---|
1797 | render reltime.toPrettyString() |
---|
1798 | } catch (IllegalArgumentException e) { |
---|
1799 | response.status = 400 |
---|
1800 | render(e.getMessage()) |
---|
1801 | } |
---|
1802 | } |
---|
1803 | |
---|
1804 | /** |
---|
1805 | * Proxy for searching PubMed articles (or other articles from the Entrez DB). |
---|
1806 | * |
---|
1807 | * This proxy is needed because it is not allowed to fetch XML directly from a different |
---|
1808 | * domain using javascript. So we have the javascript call a function on our own domain |
---|
1809 | * and the proxy will fetch the data from Entrez |
---|
1810 | * |
---|
1811 | * @since 20100609 |
---|
1812 | * @param _utility The name of the utility, without the complete path. Example: 'esearch.fcgi' |
---|
1813 | * @return XML |
---|
1814 | */ |
---|
1815 | def entrezProxy = { |
---|
1816 | // Remove unnecessary parameters |
---|
1817 | params.remove( "action" ) |
---|
1818 | params.remove( "controller" ) |
---|
1819 | |
---|
1820 | def url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils"; |
---|
1821 | def util = params.remove( "_utility" ) |
---|
1822 | def paramString = params.collect { k, v -> k + '=' + v.encodeAsURL() }.join( '&' ); |
---|
1823 | |
---|
1824 | def fullUrl = url + '/' + util + '?' + paramString; |
---|
1825 | |
---|
1826 | // Return the output of the request |
---|
1827 | // render fullUrl; |
---|
1828 | render( |
---|
1829 | text: new URL( fullUrl ).getText(), |
---|
1830 | contentType: "text/xml", |
---|
1831 | encoding: "UTF-8" |
---|
1832 | ); |
---|
1833 | } |
---|
1834 | } |
---|