1 | package nl.tno.metagenomics.integration |
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2 | |
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3 | import grails.test.* |
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4 | import nl.tno.metagenomics.* |
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5 | |
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6 | class TrashServiceTests extends GrailsUnitTestCase { |
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7 | def trashService |
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8 | Study trash |
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9 | |
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10 | protected void setUp() { |
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11 | super.setUp() |
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12 | mockDomain( Study ); |
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13 | mockDomain( Sample ); |
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14 | mockDomain( Assay ); |
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15 | mockDomain( AssaySample ); |
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16 | mockDomain( Run ); |
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17 | mockDomain( SequenceData ); |
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18 | |
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19 | mockLogging( TrashService.class, true ); |
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20 | |
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21 | trashService = new TrashService(); |
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22 | |
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23 | setupStudy(); |
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24 | } |
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25 | |
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26 | protected void tearDown() { |
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27 | super.tearDown() |
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28 | } |
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29 | |
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30 | protected void setupStudy() { |
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31 | // Create a study trashcan |
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32 | trash = new Study( name: "Trashcan", studyToken: "trashcan", trashcan: true ); |
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33 | trash.save(flush:true); |
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34 | |
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35 | // Setup a study with two assays, 4 samples |
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36 | Study s = new Study( name: "Study 1", studyToken: "study1" ); |
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37 | |
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38 | s.save(flush:true); |
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39 | |
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40 | // Create two assays |
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41 | Assay a1 = new Assay( id: 1, name: "Assay 1", assayToken: "assay1", study: s ); |
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42 | Assay a2 = new Assay( id: 2, name: "Assay 2", assayToken: "assay2", study: s ); |
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43 | Assay a3 = new Assay( id: 3, name: "Assay 3", assayToken: "assay3", study: s ); |
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44 | def assays = [a1, a2, a3]; |
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45 | |
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46 | assays.each { s.addToAssays( it ); it.save( flush: true ); } |
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47 | |
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48 | // Create four samples |
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49 | Sample sa1 = new Sample( id: 1, name: "Sample 1a", subject: "S1", event: "event", sampleToken: "sample1a", study: s ); |
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50 | Sample sa2 = new Sample( id: 2, name: "Sample 1b", subject: "S2", event: "event", sampleToken: "sample1b", study: s ); |
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51 | Sample sa3 = new Sample( id: 3, name: "Sample 2a", subject: "S3", event: "event", sampleToken: "sample2a", study: s ); |
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52 | Sample sa4 = new Sample( id: 4, name: "Sample 2b", subject: "S4", event: "event", sampleToken: "sample2b", study: s ); |
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53 | Sample sa5 = new Sample( id: 5, name: "Sample 3a", subject: "S5", event: "event", sampleToken: "sample3a", study: s ); |
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54 | def samples = [sa1, sa2, sa3, sa4, sa5] |
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55 | |
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56 | samples.each { s.addToSamples( it ); it.save(flush:true); } |
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57 | |
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58 | s.save(flush:true); |
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59 | |
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60 | // Create a single run |
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61 | Run run = new Run( name: "abc" ); |
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62 | run.save(flush:true); |
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63 | |
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64 | // Create desired combinations of samples and assays |
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65 | // Such that: assay1 has 2 samples with data, assay2 has 1 sample with data and assay3 has no samples with data |
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66 | AssaySample as1a = new AssaySample( oligoNumber: "123", tagSequence: "abc", tagName: "L391", sample: sa1, assay: a1 ); |
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67 | AssaySample as1b = new AssaySample( oligoNumber: "200", tagSequence: "def", tagName: "L397", sample: sa2, assay: a1 ); |
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68 | AssaySample as2a = new AssaySample( oligoNumber: "300", tagSequence: "ghi", tagName: "L421", sample: sa3, assay: a2 ); |
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69 | AssaySample as2b = new AssaySample( id: 12, sample: sa4, assay: a2); |
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70 | AssaySample as3a = new AssaySample( sample: sa5, assay: a3); |
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71 | def assaySamples= [as1a, as1b, as2a, as2b, as3a] |
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72 | |
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73 | a1.addToAssaySamples( as1a ); sa1.addToAssaySamples( as1a ); run.addToAssaySamples( as1a ); |
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74 | as1a.save(flush:true); |
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75 | |
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76 | a1.addToAssaySamples( as1b ); sa2.addToAssaySamples( as1b ); run.addToAssaySamples( as1b ); |
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77 | as1b.save(flush:true); |
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78 | |
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79 | a2.addToAssaySamples( as2a ); sa3.addToAssaySamples( as2a ); run.addToAssaySamples( as2a ); |
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80 | as2a.save(flush:true); |
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81 | |
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82 | a2.addToAssaySamples( as2b ); sa4.addToAssaySamples( as2b ); run.addToAssaySamples( as2b ); |
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83 | as2b.save(flush:true); |
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84 | |
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85 | a3.addToAssaySamples( as3a ); sa5.addToAssaySamples( as3a ); run.addToAssaySamples( as3a ); |
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86 | as3a.save(flush:true); |
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87 | |
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88 | assert as1a.sample.name == "Sample 1a" |
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89 | |
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90 | // Save samples and assays again |
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91 | assays.each { it.save(flush:true); } |
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92 | samples.each { it.save(flush:true); } |
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93 | run.save(flush:true); |
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94 | |
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95 | // Add sequencedata objects to as1a and as1b |
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96 | SequenceData sd1 = new SequenceData( assaySample: as1a, sequenceFile: "fasta1", qualityFile: "qual1", numSequences: 100, averageQuality: 10.0 ); |
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97 | SequenceData sd2 = new SequenceData( assaySample: as1a, sequenceFile: "fasta2", qualityFile: "qual2", numSequences: 30, averageQuality: 14.0 ); |
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98 | SequenceData sd3 = new SequenceData( assaySample: as1b, sequenceFile: "fasta3", qualityFile: "qual3", numSequences: 2000, averageQuality: 17.0 ); |
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99 | def sequenceData = [sd1, sd2, sd3]; |
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100 | |
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101 | as1a.addToSequenceData( sd1 ); |
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102 | as1a.addToSequenceData( sd2 ); |
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103 | as1b.addToSequenceData( sd3 ); |
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104 | |
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105 | as1a.save(flush:true); as1b.save(flush:true); |
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106 | sequenceData.each { it.save(flush:true); } |
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107 | } |
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108 | |
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109 | protected void setupTrash() { |
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110 | // Create a study trashcan |
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111 | trash = Study.findByStudyToken( "trashcan" ); |
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112 | |
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113 | // Create a trash assay |
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114 | Assay a1 = new Assay( id: 100, name: "Trash Assay 1", assayToken: "trash_assay1", study: trash ); |
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115 | def assays = [a1]; |
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116 | |
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117 | assays.each { trash.addToAssays( it ); it.save( flush: true ); } |
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118 | |
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119 | // Create three samples, two originally also present in assay 1, the other one isn't |
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120 | Sample sa1 = new Sample( id: 101, name: "Sample 1a", sampleToken: "tsample1a", subject: "fromtrash: S1", event: "fromtrash: event", study: trash ); |
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121 | Sample sa2 = new Sample( id: 102, name: "Sample 1b", sampleToken: "tsample1b", subject: "fromtrash: S2", event: "fromtrash: event", study: trash ); |
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122 | Sample sa3 = new Sample( id: 103, name: "Sample 2a", sampleToken: "tsample2a", subject: "fromtrash: S3", event: "fromtrash: event", study: trash ); |
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123 | def samples = [sa1, sa2, sa3] |
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124 | |
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125 | samples.each { trash.addToSamples( it ); it.save(flush:true); } |
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126 | |
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127 | trash.save(flush:true); |
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128 | |
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129 | // Create a single run in order to be able to save sequencedata |
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130 | Run run = new Run( name: "trashrun" ); |
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131 | run.save(flush:true); |
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132 | |
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133 | // Create desired combinations of samples and assays |
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134 | // Such that: assay1 has 2 samples with data, assay2 has 1 sample with data and assay3 has no samples with data |
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135 | AssaySample as1a = new AssaySample( id: 102, oligoNumber: "fromtrash: 1", tagSequence: "fromtrash: abc", sample: sa1, assay: a1 ); |
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136 | AssaySample as1b = new AssaySample( oligoNumber: "fromtrash: 2", tagSequence: "fromtrash: def", sample: sa2, assay: a1 ); |
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137 | AssaySample as2a = new AssaySample( oligoNumber: "fromtrash: 3", tagSequence: "fromtrash: ghi", sample: sa3, assay: a1 ); |
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138 | def assaySamples= [as1a, as1b, as2a] |
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139 | |
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140 | a1.addToAssaySamples( as1a ); sa1.addToAssaySamples( as1a ); run.addToAssaySamples( as1a ); |
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141 | as1a.save(flush:true); |
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142 | |
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143 | a1.addToAssaySamples( as1b ); sa2.addToAssaySamples( as1b ); run.addToAssaySamples( as1b ); |
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144 | as1b.save(flush:true); |
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145 | |
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146 | a1.addToAssaySamples( as2a ); sa3.addToAssaySamples( as2a ); run.addToAssaySamples( as2a ); |
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147 | as2a.save(flush:true); |
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148 | |
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149 | // Save samples and assays again |
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150 | assays.each { it.save(flush:true); } |
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151 | samples.each { it.save(flush:true); } |
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152 | run.save( flush:true ); |
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153 | |
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154 | // Add sequencedata objects to as1a and as1b |
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155 | SequenceData sd1 = new SequenceData( assaySample: as1a, sequenceFile: "fromtrash: fasta1", qualityFile: "fromtrash: qual1", numSequences: 80, averageQuality: 11.0 ); |
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156 | SequenceData sd2 = new SequenceData( assaySample: as1a, sequenceFile: "fromtrash: fasta2", qualityFile: "fromtrash: qual2", numSequences: 520, averageQuality: 14.0 ); |
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157 | SequenceData sd3 = new SequenceData( assaySample: as1b, sequenceFile: "fromtrash: fasta3", qualityFile: "fromtrash: qual3", numSequences: 2000, averageQuality: 17.0 ); |
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158 | def sequenceData = [sd1, sd2, sd3]; |
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159 | |
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160 | as1a.addToSequenceData( sd1 ); |
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161 | as1a.addToSequenceData( sd2 ); |
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162 | as1b.addToSequenceData( sd3 ); |
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163 | |
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164 | as1a.save(flush:true); as1b.save(flush:true); |
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165 | sequenceData.each { it.save(flush:true); } |
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166 | } |
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167 | |
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168 | void testStudyTrash() { |
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169 | def study = Study.findByStudyToken( "study1" ); |
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170 | |
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171 | // Check whether the starting condition is correct |
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172 | assert trash instanceof Study |
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173 | assert study instanceof Study |
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174 | assert study.assays?.size() == 3; |
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175 | assert ( !trash.assays || trash.assays.size() == 0 ); |
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176 | |
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177 | // Move data to trash and delete study |
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178 | trashService.moveToTrash( study ); |
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179 | |
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180 | // Check whether the study is really removed |
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181 | assert null == Study.findByStudyToken( "study1" ); |
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182 | |
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183 | // Check whether only the assays were kept that contain data |
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184 | assert trash.assays.size() == 2; |
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185 | |
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186 | // Check whether only the assaysamples were kept that contain data |
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187 | def assaySamples = trash.assays*.assaySamples.flatten().unique(); |
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188 | assert assaySamples.size() == 3; |
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189 | |
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190 | def assaySample = assaySamples.find { it.sample?.name == "Sample 1a"; } |
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191 | assert assaySample |
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192 | assert assaySample.oligoNumber == "123" |
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193 | assert assaySample.tagSequence == "abc" |
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194 | assert assaySample.sample.subject == "S1" |
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195 | assert assaySample.sample.event == "event" |
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196 | assert assaySample.sequenceData.size() == 2 |
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197 | |
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198 | assaySample = assaySamples.find { it.sample?.name == "Sample 1b"; } |
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199 | assert assaySample |
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200 | assert assaySample.oligoNumber == "200" |
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201 | assert assaySample.tagSequence == "def" |
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202 | assert assaySample.sample.subject == "S2" |
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203 | assert assaySample.sample.event == "event" |
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204 | assert assaySample.sequenceData.size() == 1 |
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205 | |
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206 | assaySample = assaySamples.find { it.sample?.name == "Sample 2a"; } |
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207 | assert assaySample |
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208 | assert assaySample.oligoNumber == "300" |
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209 | assert assaySample.tagSequence == "ghi" |
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210 | assert assaySample.sample.subject == "S3" |
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211 | assert assaySample.sample.event == "event" |
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212 | assert !assaySample.sequenceData || assaySample.sequenceData.size() == 0 |
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213 | |
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214 | // Check whether the assay samples contain the right sequence data |
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215 | def sequenceData = trash.assays*.assaySamples*.sequenceData.flatten().unique(); |
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216 | |
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217 | // Filter null values |
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218 | sequenceData = sequenceData.findAll { it != null }; |
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219 | assert sequenceData.size() == 3; |
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220 | |
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221 | def sd = sequenceData.find { it.sequenceFile == "fasta1"; } |
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222 | assert sd |
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223 | assert sd.qualityFile == "qual1" |
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224 | assert sd.numSequences == 100 |
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225 | assert sd.averageQuality == 10.0 |
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226 | assert sd.sample.assay.name == "Assay 1" |
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227 | assert sd.sample.sample.name == "Sample 1a" |
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228 | |
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229 | sd = sequenceData.find { it.sequenceFile == "fasta2"; } |
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230 | assert sd |
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231 | assert sd.qualityFile == "qual2" |
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232 | assert sd.numSequences == 30 |
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233 | assert sd.averageQuality == 14.0 |
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234 | assert sd.sample.assay.name == "Assay 1" |
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235 | assert sd.sample.sample.name == "Sample 1a" |
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236 | |
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237 | sd = sequenceData.find { it.sequenceFile == "fasta3"; } |
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238 | assert sd |
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239 | assert sd.qualityFile == "qual3" |
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240 | assert sd.numSequences == 2000 |
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241 | assert sd.averageQuality == 17.0 |
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242 | assert sd.sample.assay.name == "Assay 1" |
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243 | assert sd.sample.sample.name == "Sample 1b" |
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244 | } |
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245 | |
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246 | void testAssayTrash() { |
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247 | def study = Study.findByStudyToken( "study1" ); |
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248 | def assay = study.assays.find { it.assayToken == "assay1" }; |
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249 | |
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250 | // Check whether the starting condition is correct |
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251 | assert trash instanceof Study |
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252 | assert assay instanceof Assay |
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253 | assert assay.assaySamples.size() == 2; |
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254 | assert ( !trash.assays || trash.assays.size() == 0 ); |
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255 | |
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256 | // Move data to trash and delete study |
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257 | trashService.moveToTrash( assay ); |
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258 | |
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259 | // Check whether the study itself still exists |
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260 | study = Study.findByStudyToken( "study1" ) |
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261 | assert study |
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262 | assay = study.assays.find { it.assayToken == "assay1" }; |
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263 | |
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264 | study.assays.each { |
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265 | println it.name + ", " + it.assaySamples?.size() |
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266 | } |
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267 | assert !assay |
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268 | assert study.assays.size() == 2 |
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269 | |
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270 | // Check whether the assay is really removed |
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271 | assay = Assay.findByAssayToken( "assay1" ); |
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272 | assert !assay |
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273 | |
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274 | // Check whether the assay samples also have been removed |
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275 | // assert AssaySample.list().findAll { it.assay?.study?.studyToken == "study1" && it.assay?.assayToken == "assay1" }.size() == 0 |
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276 | |
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277 | // Check whether only the assays were kept that contain data |
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278 | assert trash.assays.size() == 1; |
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279 | assert trash.samples.size() == 2; |
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280 | |
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281 | // Check whether only the assaysamples were kept that contain data |
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282 | def assaySamples = trash.assays*.assaySamples.flatten().unique(); |
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283 | assert assaySamples.size() == 2; |
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284 | |
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285 | def assaySample = assaySamples.find { it.sample?.name == "Sample 1a"; } |
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286 | assert assaySample |
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287 | assert assaySample.oligoNumber == "123" |
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288 | assert assaySample.tagSequence == "abc" |
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289 | assert assaySample.sample.subject == "S1" |
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290 | assert assaySample.sample.event == "event" |
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291 | assert assaySample.sequenceData.size() == 2 |
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292 | |
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293 | assaySample = assaySamples.find { it.sample?.name == "Sample 1b"; } |
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294 | assert assaySample |
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295 | assert assaySample.oligoNumber == "200" |
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296 | assert assaySample.tagSequence == "def" |
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297 | assert assaySample.sample.subject == "S2" |
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298 | assert assaySample.sample.event == "event" |
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299 | assert assaySample.sequenceData.size() == 1 |
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300 | |
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301 | // Check whether the assay samples contain the right sequence data |
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302 | def sequenceData = trash.assays*.assaySamples*.sequenceData.flatten().unique(); |
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303 | |
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304 | // Filter null values |
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305 | sequenceData = sequenceData.findAll { it != null }; |
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306 | assert sequenceData.size() == 3; |
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307 | |
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308 | def sd = sequenceData.find { it.sequenceFile == "fasta1"; } |
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309 | assert sd |
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310 | assert sd.qualityFile == "qual1" |
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311 | assert sd.numSequences == 100 |
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312 | assert sd.averageQuality == 10.0 |
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313 | assert sd.sample.assay.name == "Assay 1" |
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314 | assert sd.sample.sample.name == "Sample 1a" |
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315 | |
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316 | sd = sequenceData.find { it.sequenceFile == "fasta2"; } |
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317 | assert sd |
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318 | assert sd.qualityFile == "qual2" |
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319 | assert sd.numSequences == 30 |
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320 | assert sd.averageQuality == 14.0 |
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321 | assert sd.sample.assay.name == "Assay 1" |
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322 | assert sd.sample.sample.name == "Sample 1a" |
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323 | |
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324 | sd = sequenceData.find { it.sequenceFile == "fasta3"; } |
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325 | assert sd |
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326 | assert sd.qualityFile == "qual3" |
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327 | assert sd.numSequences == 2000 |
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328 | assert sd.averageQuality == 17.0 |
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329 | assert sd.sample.assay.name == "Assay 1" |
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330 | assert sd.sample.sample.name == "Sample 1b" |
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331 | } |
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332 | |
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333 | void testSampleTrash() { |
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334 | def study = Study.findByStudyToken( "study1" ); |
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335 | def sample = study.samples.find { it.sampleToken == "sample1a" }; |
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336 | def assay |
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337 | |
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338 | // Check whether the starting condition is correct |
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339 | assert trash instanceof Study |
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340 | assert sample instanceof Sample |
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341 | assert sample.assaySamples.size() == 1; |
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342 | assert ( !trash.assays || trash.assays.size() == 0 ); |
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343 | |
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344 | // Move data to trash and delete study |
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345 | trashService.moveToTrash( sample ); |
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346 | |
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347 | // Check whether the study and the assay itself still exists |
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348 | study = Study.findByStudyToken( "study1" ) |
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349 | assert study |
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350 | assay = study.assays.find { it.assayToken == "assay1" }; |
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351 | assert assay |
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352 | assert study.assays.size() == 3 |
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353 | |
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354 | // Check whether the sample is really removed |
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355 | sample = Sample.findBySampleToken( "sample1a" ); |
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356 | assert !sample |
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357 | sample = study.samples.find { it.sampleToken == "sample1a" } |
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358 | assert !sample |
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359 | |
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360 | // Check whether the assay samples also have been removed |
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361 | //assert AssaySample.list().findAll { it.sample?.study?.studyToken == "study1" && it.sample?.sampleToken == "assay1" }.size() == 0 |
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362 | |
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363 | // Check whether only the assays were kept that contain data |
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364 | assert trash.assays.size() == 1; |
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365 | assert trash.samples.size() == 1; |
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366 | |
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367 | // Check whether only the assaysamples were kept that contain data and belong to sample 1 |
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368 | def assaySamples = trash.assays*.assaySamples.flatten().unique(); |
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369 | assert assaySamples.size() == 1; |
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370 | |
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371 | def assaySample = assaySamples.find { it.sample?.name == "Sample 1a"; } |
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372 | assert assaySample |
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373 | assert assaySample.assay?.name == "Assay 1" |
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374 | assert assaySample.oligoNumber == "123" |
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375 | assert assaySample.tagSequence == "abc" |
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376 | assert assaySample.sample.subject == "S1" |
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377 | assert assaySample.sample.event == "event" |
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378 | assert assaySample.sequenceData.size() == 2 |
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379 | |
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380 | // Check whether the assay samples contain the right sequence data |
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381 | def sequenceData = trash.assays*.assaySamples*.sequenceData.flatten().unique(); |
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382 | |
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383 | // Filter null values |
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384 | sequenceData = sequenceData.findAll { it != null }; |
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385 | |
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386 | assert sequenceData.size() == 2; |
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387 | |
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388 | // Filter null values |
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389 | sequenceData = sequenceData.findAll { it != null }; |
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390 | assert sequenceData.size() == 2; |
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391 | |
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392 | def sd = sequenceData.find { it.sequenceFile == "fasta1"; } |
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393 | assert sd |
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394 | assert sd.qualityFile == "qual1" |
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395 | assert sd.numSequences == 100 |
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396 | assert sd.averageQuality == 10.0 |
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397 | assert sd.sample.assay.name == "Assay 1" |
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398 | assert sd.sample.sample.name == "Sample 1a" |
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399 | |
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400 | sd = sequenceData.find { it.sequenceFile == "fasta2"; } |
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401 | assert sd |
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402 | assert sd.qualityFile == "qual2" |
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403 | assert sd.numSequences == 30 |
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404 | assert sd.averageQuality == 14.0 |
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405 | assert sd.sample.assay.name == "Assay 1" |
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406 | assert sd.sample.sample.name == "Sample 1a" |
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407 | } |
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408 | |
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409 | void testRestoreAssay() { |
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410 | setupTrash(); |
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411 | |
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412 | def study = Study.findByStudyToken( "study1" ); |
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413 | |
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414 | def trashAssay = trash.assays.find { it.assayToken == "trash_assay1" }; |
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415 | def restoreTo = study.assays.find { it.assayToken == "assay1" }; |
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416 | |
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417 | assert trashAssay |
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418 | assert restoreTo |
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419 | |
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420 | assert restoreTo.assaySamples?.size() == 2 |
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421 | |
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422 | trashService.restoreAssay( trashAssay, restoreTo ); |
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423 | |
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424 | // Check whether the sample data is moved to the other assay |
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425 | def restoredTo = study.assays.find { it.assayToken == "assay1" }; |
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426 | assert restoredTo.assaySamples?.size() == 2 |
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427 | |
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428 | // Check for the copying of oligoNumber and tagSequence |
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429 | def s = restoredTo.assaySamples.find { it.sample.sampleToken == "sample1a" } |
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430 | assert s |
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431 | assert s.oligoNumber == "fromtrash: 1"; |
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432 | assert s.tagSequence == "fromtrash: abc"; |
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433 | |
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434 | // Sample data shouldn't be copied, so remains the same |
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435 | assert s.sample.subject == "S1" |
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436 | assert s.sample.event == "event" |
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437 | |
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438 | assert s.sequenceData?.size() == 4 |
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439 | |
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440 | assert s.numSequences() == 730 |
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441 | def sequenceFiles = s.sequenceData.sequenceFile; |
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442 | assert sequenceFiles.contains( "fromtrash: fasta1" ) |
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443 | assert sequenceFiles.contains( "fromtrash: fasta2" ) |
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444 | |
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445 | // Also check the second assay sample |
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446 | s = restoredTo.assaySamples.find { it.sample.sampleToken == "sample1b" } |
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447 | assert s |
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448 | assert s.oligoNumber == "fromtrash: 2"; |
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449 | assert s.tagSequence == "fromtrash: def"; |
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450 | assert s.sequenceData?.size() == 2 |
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451 | |
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452 | assert s.numSequences() == 4000 |
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453 | sequenceFiles = s.sequenceData.sequenceFile; |
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454 | assert sequenceFiles.contains( "fromtrash: fasta3" ) |
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455 | } |
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456 | |
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457 | void testRestoreSample() { |
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458 | setupTrash(); |
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459 | |
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460 | def study = Study.findByStudyToken( "study1" ); |
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461 | |
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462 | def trashAssay = trash.assays.find { it.assayToken == "trash_assay1" }; |
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463 | def restoreToAssay = study.assays.find { it.assayToken == "assay2" }; |
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464 | |
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465 | assert trashAssay |
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466 | assert restoreToAssay |
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467 | |
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468 | def trashSample = trashAssay.assaySamples.find { it.id == 102 }; |
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469 | def restoreTo = restoreToAssay.assaySamples.find { it.id == 12 }; |
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470 | |
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471 | assert trashSample |
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472 | assert restoreTo |
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473 | |
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474 | assert restoreTo.sequenceData == null || restoreTo.sequenceData.size() == 0; |
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475 | |
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476 | trashService.restoreSample( trashSample, restoreTo ); |
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477 | |
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478 | // Check whether the sample data is moved to the other assay |
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479 | def restoredTo = restoreToAssay.assaySamples.find { it.id == 12 }; |
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480 | assert restoredTo |
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481 | |
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482 | // Check for the copying of oligoNumber and tagSequence |
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483 | assert restoredTo.oligoNumber == "fromtrash: 1"; |
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484 | assert restoredTo.tagSequence == "fromtrash: abc"; |
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485 | assert restoredTo.sequenceData?.size() == 2 |
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486 | |
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487 | // Sample data shouldn't be copied, so remains the same |
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488 | assert restoredTo.sample.subject == "S4" |
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489 | assert restoredTo.sample.event == "event" |
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490 | |
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491 | assert restoredTo.numSequences() == 600 |
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492 | def sequenceFiles = restoredTo.sequenceData.sequenceFile; |
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493 | assert sequenceFiles.contains( "fromtrash: fasta1" ) |
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494 | assert sequenceFiles.contains( "fromtrash: fasta2" ) |
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495 | |
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496 | } |
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497 | } |
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