1 | package gscf |
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2 | |
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3 | import dbnp.studycapturing.* |
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4 | import org.dbnp.bgdt.Term |
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5 | import org.dbnp.bgdt.Ontology |
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6 | import org.dbnp.gdt.Template |
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7 | |
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8 | /** |
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9 | * SubjectTests Test |
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10 | * |
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11 | * Test the creation of a Subject and its TemplateEntity functionality on data model level |
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12 | * |
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13 | * @author keesvb |
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14 | * @since 20100510 |
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15 | * @package dbnp.studycapturing |
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16 | * |
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17 | * Revision information: |
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18 | * $Rev: 1504 $ |
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19 | * $Author: s.h.sikkema@gmail.com $ |
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20 | * $Date: 2011-02-08 09:48:41 +0000 (di, 08 feb 2011) $ |
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21 | */ |
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22 | class SubjectTests extends StudyTests { |
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23 | |
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24 | static final String testSubjectName = "Test subject" |
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25 | static final String testSubjectTemplateName = "Human" |
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26 | static final String testSubjectSpeciesTerm = "Homo sapiens" |
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27 | static final String testSubjectBMITemplateFieldName = "BMI" |
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28 | static final double testSubjectBMI = 25.32 |
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29 | static final String testSubjectGenderTemplateFieldName = "Gender" |
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30 | static final String testSubjectGender = "female" |
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31 | static final String testSubjectGenderDBName = "Female" |
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32 | |
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33 | /** |
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34 | * Set up test: create test subject to use in the tests, thereby test creation |
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35 | */ |
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36 | protected void setUp() { |
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37 | super.setUp() |
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38 | |
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39 | // Retrieve the study that should have been created in StudyTests |
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40 | def study = Study.findByTitle(testStudyName) |
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41 | assert study |
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42 | |
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43 | createSubject(study) |
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44 | } |
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45 | |
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46 | public static Subject createSubject(Study parentStudy) { |
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47 | |
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48 | // Look up human template |
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49 | def humanTemplate = Template.findByName(testSubjectTemplateName) |
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50 | assert humanTemplate |
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51 | |
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52 | def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132) |
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53 | def humanTerm = new Term( |
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54 | name: 'Homo sapiens', |
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55 | ontology: speciesOntology, |
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56 | accession: '9606') |
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57 | |
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58 | assert humanTerm.validate() |
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59 | assert humanTerm.save(flush:true) |
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60 | assert humanTerm |
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61 | |
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62 | def subject = new Subject( |
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63 | name: testSubjectName, |
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64 | template: humanTemplate, |
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65 | species: humanTerm |
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66 | ) |
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67 | |
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68 | // At this point, the sample should not validate, because it doesn't have a parent study assigned |
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69 | assert !subject.validate() |
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70 | |
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71 | // Add the subject to the retrieved parent study |
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72 | parentStudy.addToSubjects(subject) |
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73 | assert parentStudy.subjects.find { it.name == subject.name} |
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74 | |
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75 | // Now, the subject should validate |
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76 | if (!subject.validate()) { |
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77 | subject.errors.each { println it} |
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78 | } |
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79 | assert subject.validate() |
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80 | |
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81 | // Make sure the subject is saved to the database |
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82 | assert subject.save(flush: true) |
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83 | |
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84 | return subject |
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85 | |
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86 | } |
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87 | |
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88 | void testSave() { |
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89 | // Try to retrieve the subject and make sure it's the same |
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90 | def subjectDB = Subject.findByName(testSubjectName) |
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91 | assert subjectDB |
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92 | assert subjectDB.name.equals(testSubjectName) |
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93 | assert subjectDB.template.name.equals(testSubjectTemplateName) |
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94 | assert subjectDB.species.name.equals(testSubjectSpeciesTerm) |
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95 | } |
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96 | |
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97 | void testDelete() { |
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98 | def subjectDB = Subject.findByName(testSubjectName) |
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99 | subjectDB.delete() |
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100 | try { |
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101 | subjectDB.save() |
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102 | assert false // The save should not succeed since the subject is referenced by a study |
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103 | } |
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104 | catch(org.springframework.dao.InvalidDataAccessApiUsageException e) { |
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105 | subjectDB.discard() |
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106 | assert true // OK, correct exception (at least for the in-mem db, for PostgreSQL it's probably a different one...) |
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107 | } |
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108 | |
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109 | // Now, delete the subject from the study subjects collection, and then the delete action should be cascaded to the subject itself |
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110 | def study = Study.findByTitle(testStudyName) |
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111 | assert study |
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112 | study.removeFromSubjects subjectDB |
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113 | |
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114 | // Make sure the subject doesn't exist anymore at this point |
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115 | assert !Subject.findByName(testSubjectName) |
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116 | assert Subject.count() == 0 |
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117 | assert study.subjects.size() == 0 |
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118 | } |
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119 | |
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120 | |
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121 | void testValidators() { |
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122 | |
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123 | def subject = new Subject( |
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124 | name: testSubjectName + "-test" |
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125 | ); |
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126 | // Should not validate as template and species are missing |
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127 | assert !subject.validate() |
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128 | |
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129 | subject.template = Template.findByName(testSubjectTemplateName) |
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130 | // Still, species is missing |
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131 | assert !subject.validate() |
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132 | |
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133 | subject.species = Term.findByName(testSubjectSpeciesTerm) |
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134 | // Still, no parent study assigned |
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135 | assert !subject.validate() |
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136 | |
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137 | def study = Study.findByTitle(testStudyName) |
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138 | assert study |
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139 | study.addToSubjects subject |
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140 | |
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141 | // Now, the new subject should validate |
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142 | assert subject.validate() |
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143 | assert subject.save() |
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144 | |
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145 | // If the subject has the same name as another subject within the same study, it should not validate or save |
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146 | subject.name = testSubjectName |
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147 | assert !subject.validate() |
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148 | assert !subject.save() |
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149 | } |
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150 | |
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151 | /** |
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152 | * Test domain field setter of a subject, |
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153 | * by finding the appropriate species as should be defined in the Bootstrap and giveDomainFields |
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154 | * Test that species ontology is correctly defined in giveDomainFields |
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155 | * Test setFieldValue() for domain field species |
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156 | * |
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157 | */ |
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158 | void testDomainFieldSetters() { |
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159 | |
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160 | def subject = Subject.findByName(testSubjectName) |
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161 | assert subject |
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162 | |
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163 | // Remove species from subject, should not validate anymore |
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164 | subject.species = null |
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165 | assert !subject.validate() |
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166 | |
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167 | |
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168 | // Get domain fields and make sure they are name and species |
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169 | def domainFields = subject.giveDomainFields() |
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170 | assert domainFields |
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171 | assert domainFields[0].name == 'name' |
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172 | assert domainFields[1].name == 'species' |
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173 | |
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174 | // Also, make sure isDomainField() says the same |
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175 | assert subject.isDomainField(domainFields[0]) |
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176 | assert subject.isDomainField(domainFields[1]) |
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177 | assert subject.isDomainField('name') |
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178 | assert subject.isDomainField('species') |
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179 | // To be sure it just doesn't always return true :-) |
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180 | assert !subject.isDomainField('123~!name') |
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181 | assert !subject.isDomainField(testSubjectBMITemplateFieldName) |
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182 | |
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183 | // Get the ontologies from species and make sure this is 1 ontology with NCBO ID 1132 |
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184 | def speciesOntologies = domainFields[1].ontologies |
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185 | assert speciesOntologies.size() == 1 |
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186 | |
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187 | // Getting the only element in a set is hard in Grails... |
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188 | Ontology speciesOntology = speciesOntologies.asList().first() |
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189 | assert speciesOntology.ncboId == 1132 |
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190 | |
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191 | def speciesTerms = speciesOntology.giveTerms() |
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192 | def humanTerm = speciesTerms.find { it.name == testSubjectSpeciesTerm} |
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193 | assert humanTerm |
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194 | |
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195 | // Make sure giveTermByName returns the same term |
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196 | assert humanTerm == speciesOntology.giveTermByName('Homo sapiens') |
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197 | |
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198 | // Make sure the (in this test used!) Term.findByName returns the same |
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199 | // If this doesn't hold, we probably should rewrite these tests |
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200 | assert humanTerm == Term.findByName(testSubjectSpeciesTerm) |
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201 | |
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202 | // Assign species, subject should now validate and save |
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203 | subject.setFieldValue('species',humanTerm) |
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204 | if (!subject.validate()) { |
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205 | subject.errors.each { println it} |
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206 | } |
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207 | assert subject.validate() |
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208 | assert subject.save(flush:true) |
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209 | |
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210 | assert subject.getFieldValue('species') == humanTerm |
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211 | assert subject.getFieldValue('name').equals(testSubjectName) |
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212 | assert subject.getFieldValue('species') == humanTerm |
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213 | |
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214 | } |
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215 | |
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216 | /** |
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217 | * Test getFieldValue() for domain fields |
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218 | */ |
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219 | void testDomainFieldGetters() { |
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220 | |
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221 | def subjectDB = Subject.findByName(testSubjectName) |
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222 | assert subjectDB |
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223 | assert subjectDB.getFieldValue('name').equals(testSubjectName) |
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224 | assert subjectDB.getFieldValue('species') == Term.findByName(testSubjectSpeciesTerm) |
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225 | } |
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226 | |
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227 | /** |
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228 | * Test setFieldValue() and getFieldValue() for template fields |
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229 | * This cannot be done in separate tests, as the database state is reset in between |
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230 | */ |
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231 | void testTemplateFieldSetters() { |
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232 | |
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233 | def subject = Subject.findByName(testSubjectName) |
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234 | assert subject |
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235 | |
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236 | // Assign a template field using setFieldValue: BMI |
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237 | subject.setFieldValue(testSubjectBMITemplateFieldName,testSubjectBMI) |
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238 | |
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239 | // Try to retrieve it using getFieldValue |
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240 | assert subject.getFieldValue(testSubjectBMITemplateFieldName) == testSubjectBMI |
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241 | |
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242 | // Save subject |
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243 | assert subject.save(flush: true) |
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244 | |
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245 | // Try to retrieve the subject and make sure the BMI was stored |
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246 | def subjectDB = Subject.findByName(testSubjectName) |
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247 | assert subjectDB |
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248 | assert subjectDB.getFieldValue(testSubjectBMITemplateFieldName) == testSubjectBMI |
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249 | } |
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250 | |
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251 | /** |
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252 | * Test giveFields(): should return name, species and template fields |
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253 | */ |
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254 | void testGiveFields() { |
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255 | |
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256 | def subject = Subject.findByName(testSubjectName) |
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257 | assert subject |
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258 | |
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259 | // Test giveFields |
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260 | def fields = subject.giveFields() |
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261 | def i = 0 |
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262 | assert fields[i++].name == 'name' |
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263 | assert fields[i++].name == 'species' |
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264 | |
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265 | // Look up human template |
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266 | def humanTemplate = Template.findByName(testSubjectTemplateName) |
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267 | assert humanTemplate |
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268 | |
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269 | humanTemplate.fields.each { |
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270 | assert fields[i++].name.equals(it.name) |
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271 | } |
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272 | |
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273 | } |
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274 | |
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275 | void testSetGender() { |
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276 | def subject = Subject.findByName(testSubjectName) |
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277 | assert subject |
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278 | |
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279 | // Set gender |
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280 | subject.setFieldValue(testSubjectGenderTemplateFieldName,testSubjectGender) |
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281 | |
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282 | // Test if gender is set properly (to its canonical database name) via getFieldValue() |
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283 | assert subject.getFieldValue(testSubjectGenderTemplateFieldName).name == testSubjectGenderDBName |
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284 | |
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285 | // Try to save object |
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286 | assert subject.validate() |
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287 | assert subject.save(flush: true) |
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288 | |
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289 | // Try to retrieve the subject and make sure the Gender was stored properly |
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290 | def subjectDB = Subject.findByName(testSubjectName) |
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291 | assert subjectDB |
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292 | assert subjectDB.getFieldValue(testSubjectGenderTemplateFieldName).name == testSubjectGenderDBName |
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293 | } |
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294 | |
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295 | protected void tearDown() { |
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296 | super.tearDown() |
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297 | } |
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298 | |
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299 | } |
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