Changeset 7 for trunk/grails-app/domain
- Timestamp:
- Jan 26, 2011, 5:08:25 PM (12 years ago)
- Location:
- trunk/grails-app/domain/nl/tno/metagenomics
- Files:
-
- 7 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/grails-app/domain/nl/tno/metagenomics/Assay.groovy
r2 r7 16 16 assayToken index:'assaytoken_idx' 17 17 } 18 assaySamples cascade: "all-delete-orphan" 18 19 } 19 20 -
trunk/grails-app/domain/nl/tno/metagenomics/AssaySample.groovy
r4 r7 17 17 String tagSequence // Tag originally used to identify the sample 18 18 19 static belongsTo = [ assay: Assay, sample: Sample ]19 static belongsTo = [ assay: Assay, sample: Sample, run: Run ] 20 20 static hasMany = [ sequenceData: SequenceData ] 21 21 … … 24 24 oligoNumber(nullable: true) 25 25 tagSequence(nullable: true) 26 run(nullable: true); 26 27 } 27 28 … … 30 31 numSequences index:'numsequences_idx' 31 32 } 33 sequenceData cascade: "all-delete-orphan" 32 34 } 33 35 … … 162 164 otherAssaySample.tagSequence = tagSequence; 163 165 otherAssaySample.oligoNumber = oligoNumber; 166 otherAssaySample.run = run; 164 167 165 168 // Move attached data … … 169 172 if( dataList && dataList.size() > 0 ) { 170 173 for( def j = dataList.size() - 1; j >= 0; j-- ) { 171 // Check whether the run of this sequenceData object is also connected to the assay172 def run = dataList[j].run;173 174 if( !otherAssay.runs || !otherAssay.runs.contains( run ) ) {175 otherAssay.addToRuns( run );176 }177 178 174 // Copy data 179 175 dataList[j].sample = otherAssaySample; -
trunk/grails-app/domain/nl/tno/metagenomics/Run.groovy
r3 r7 18 18 String parameterFile 19 19 20 static hasMany = [ sequenceData: SequenceData, assays: Assay]20 static hasMany = [assaySamples: AssaySample, assays: Assay] 21 21 static belongsTo = Assay // Only used to determine the owner of the many-to-many relationship assay-run 22 22 … … 71 71 */ 72 72 public int numFiles() { 73 if( ! sequenceData)73 if( !assaySamples ) 74 74 return 0 75 75 76 76 int numFiles = 0; 77 sequenceData.each { numFiles += it.numFiles() }77 assaySamples.each { numFiles += it.numFiles() } 78 78 79 79 return numFiles; … … 86 86 */ 87 87 public long numSequences() { 88 if( ! sequenceData)88 if( !assaySamples ) 89 89 return 0 90 90 91 91 long numSequences = 0; 92 sequenceData.each { numSequences += it.numSequences}92 assaySamples.each { numSequences += it.numSequences() } 93 93 94 94 return numSequences; … … 101 101 */ 102 102 public ArrayList samples( def assayId ) { 103 if( ! sequenceData)103 if( !assaySamples ) 104 104 return [] 105 105 106 106 def list = [] 107 sequenceData.each {108 if( it. sample.assay.id == assayId )109 list << it .sample107 assaySamples.each { 108 if( it.assay.id == assayId ) 109 list << it 110 110 } 111 111 -
trunk/grails-app/domain/nl/tno/metagenomics/Sample.groovy
r2 r7 16 16 assayToken index:'sampletoken_idx' 17 17 } 18 assaySamples cascade: "all-delete-orphan" 18 19 } 19 20 } -
trunk/grails-app/domain/nl/tno/metagenomics/SequenceData.groovy
r3 r7 11 11 Float averageQuality = 0.0 12 12 13 static belongsTo = [sample: AssaySample , run: Run]13 static belongsTo = [sample: AssaySample] 14 14 static constraints = { 15 15 qualityFile(nullable: true) -
trunk/grails-app/domain/nl/tno/metagenomics/Study.groovy
r4 r7 32 32 studyToken index:'studytoken_idx' 33 33 } 34 assays cascade: "all-delete-orphan" 35 samples cascade: "all-delete-orphan" 36 auth cascade: "all-delete-orphan" 34 37 } 35 38 -
trunk/grails-app/domain/nl/tno/metagenomics/auth/User.groovy
r2 r7 13 13 14 14 static hasMany = [ auth: Auth ] 15 16 static mapping = { 17 auth cascade: "all-delete-orphan" 18 } 15 19 16 20 public boolean equals( Object o ) {
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