1 | package dbnp.studycapturing |
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2 | |
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3 | /** |
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4 | * Domain class describing the basic entity in the study capture part: the Study class. |
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5 | * |
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6 | * Revision information: |
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7 | * $Rev: 754 $ |
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8 | * $Author: keesvb $ |
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9 | * $Date: 2010-07-30 13:05:41 +0000 (vr, 30 jul 2010) $ |
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10 | */ |
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11 | class Study extends TemplateEntity { |
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12 | static searchable = { |
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13 | [only: ['title', 'Description']] |
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14 | } |
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15 | |
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16 | nimble.User owner // The owner of the study. A new study is automatically owned by its creator. |
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17 | String title // The title of the study |
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18 | String code // currently used as the external study ID, e.g. to reference a study in a SAM module |
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19 | Date dateCreated |
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20 | Date lastUpdated |
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21 | Date startDate |
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22 | List subjects |
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23 | List events |
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24 | List samplingEvents |
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25 | List eventGroups |
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26 | List samples |
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27 | List assays |
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28 | |
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29 | static hasMany = [ |
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30 | editors: nimble.User, // Users with read/write access to the study |
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31 | readers: nimble.User, // Users with only read access to the study |
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32 | subjects: Subject, |
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33 | samplingEvents: SamplingEvent, |
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34 | events: Event, |
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35 | eventGroups: EventGroup, |
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36 | samples: Sample, |
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37 | assays: Assay, |
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38 | persons: StudyPerson, |
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39 | publications: Publication |
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40 | ] |
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41 | |
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42 | static constraints = { |
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43 | owner(nullable: true, blank: true) |
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44 | code(nullable:false, blank:true,unique:true) |
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45 | } |
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46 | |
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47 | static mapping = { |
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48 | researchQuestion type: 'text' |
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49 | description type: 'text' |
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50 | autoTimestamp true |
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51 | } |
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52 | |
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53 | // The external study ID is currently defined as the code of the study. |
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54 | // It is used from within dbNP submodules to refer to particular study in this GSCF instance. |
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55 | def getExternalStudyId() { code } |
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56 | |
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57 | /** |
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58 | * return the domain fields for this domain class |
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59 | * @return List |
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60 | */ |
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61 | static List<TemplateField> giveDomainFields() { return Study.domainFields } |
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62 | |
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63 | static final List<TemplateField> domainFields = [ |
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64 | new TemplateField( |
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65 | name: 'title', |
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66 | type: TemplateFieldType.STRING), |
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67 | new TemplateField( |
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68 | name: 'code', |
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69 | type: TemplateFieldType.STRING, |
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70 | preferredIdentifier:true, |
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71 | comment: 'Fill out the code by which many people will recognize your study'), |
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72 | new TemplateField( |
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73 | name: 'startDate', |
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74 | type: TemplateFieldType.DATE, |
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75 | comment: 'Fill out the official start date or date of first action') |
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76 | ] |
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77 | |
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78 | /** |
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79 | * return the title of this study |
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80 | */ |
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81 | def String toString() { |
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82 | return title |
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83 | } |
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84 | |
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85 | /** |
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86 | * returns all events and sampling events that do not belong to a group |
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87 | */ |
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88 | def Set<Event> getOrphanEvents() { |
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89 | def orphans = events.findAll { event -> !event.belongsToGroup(eventGroups) } + |
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90 | samplingEvents.findAll { event -> !event.belongsToGroup(eventGroups) } |
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91 | |
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92 | return orphans |
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93 | } |
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94 | |
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95 | /** |
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96 | * Return the unique Subject templates that are used in this study |
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97 | */ |
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98 | def Set<Template> giveSubjectTemplates() { |
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99 | TemplateEntity.giveTemplates(subjects) |
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100 | } |
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101 | |
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102 | /** |
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103 | * Return the unique Event and SamplingEvent templates that are used in this study |
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104 | */ |
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105 | Set<Template> giveAllEventTemplates() { |
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106 | // For some reason, giveAllEventTemplates() + giveAllSamplingEventTemplates() |
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107 | // gives trouble when asking .size() to the result |
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108 | // So we also use giveTemplates here |
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109 | TemplateEntity.giveTemplates(events + samplingEvents) |
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110 | } |
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111 | |
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112 | /** |
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113 | * Return the unique Event templates that are used in this study |
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114 | */ |
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115 | Set<Template> giveEventTemplates() { |
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116 | TemplateEntity.giveTemplates(events) |
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117 | } |
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118 | |
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119 | /** |
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120 | * Return the unique SamplingEvent templates that are used in this study |
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121 | */ |
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122 | Set<Template> giveSamplingEventTemplates() { |
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123 | TemplateEntity.giveTemplates(samplingEvents) |
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124 | } |
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125 | |
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126 | /** |
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127 | * Returns the unique Sample templates that are used in the study |
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128 | */ |
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129 | Set<Template> giveSampleTemplates() { |
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130 | TemplateEntity.giveTemplates(samples) |
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131 | } |
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132 | /** |
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133 | * Returns the template of the study |
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134 | */ |
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135 | Template giveStudyTemplate() { |
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136 | return this.template |
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137 | } |
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138 | } |
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