Changeset 29 for trunk/grails-app
- Timestamp:
- Apr 5, 2011, 3:59:22 PM (11 years ago)
- Location:
- trunk/grails-app/services/nl/tno/metagenomics
- Files:
-
- 8 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/grails-app/services/nl/tno/metagenomics/FastaService.groovy
r24 r29 1 package nl.tno.m etagenomics1 package nl.tno.massSequencing 2 2 3 3 import java.io.BufferedWriter; … … 46 46 47 47 if( !directory ) { 48 directory = fileService.absolutePath( ConfigurationHolder.config.m etagenomics.fileDir )48 directory = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir ) 49 49 } 50 50 … … 361 361 */ 362 362 public def savePermanent( String fastaFile, String qualFile, def processedFiles ) { 363 File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.m etagenomics.fileDir );363 File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir ); 364 364 def returnStructure = [:]; 365 365 … … 411 411 // Retrieve the filename from configuration, if none is given 412 412 if( !name ) 413 name = ConfigurationHolder.config.m etagenomics.exportFilename413 name = ConfigurationHolder.config.massSequencing.exportFilename 414 414 415 415 // Determine the directory the uploaded files are stored in 416 File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.m etagenomics.fileDir );416 File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir ); 417 417 418 418 // First check whether qual files should be exported or not -
trunk/grails-app/services/nl/tno/metagenomics/SampleExcelService.groovy
r24 r29 1 package nl.tno.m etagenomics1 package nl.tno.massSequencing 2 2 3 3 import org.springframework.web.context.request.RequestContextHolder; -
trunk/grails-app/services/nl/tno/metagenomics/files/ExcelService.groovy
r24 r29 1 package nl.tno.m etagenomics.files1 package nl.tno.massSequencing.files 2 2 3 3 import java.text.DecimalFormat -
trunk/grails-app/services/nl/tno/metagenomics/files/FileService.groovy
r20 r29 13 13 * $Date$ 14 14 */ 15 package nl.tno.m etagenomics.files15 package nl.tno.massSequencing.files 16 16 17 17 import org.codehaus.groovy.grails.commons.ApplicationHolder … … 97 97 def File getUploadDir() { 98 98 // Find the file upload directory name from the configuration 99 String uploadDir = ConfigurationHolder.config.m etagenomics.fileUploadDir99 String uploadDir = ConfigurationHolder.config.massSequencing.fileUploadDir 100 100 101 101 if( !uploadDir ) … … 322 322 323 323 if( !age ) { 324 age = ConfigurationHolder.config.m etagenomics.fileUploadMaxAge324 age = ConfigurationHolder.config.massSequencing.fileUploadMaxAge 325 325 } 326 326 -
trunk/grails-app/services/nl/tno/metagenomics/imports/FuzzySearchService.groovy
r21 r29 1 package nl.tno.m etagenomics.imports1 package nl.tno.massSequencing.imports 2 2 3 3 class FuzzySearchService { -
trunk/grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy
r19 r29 1 package nl.tno.m etagenomics.integration1 package nl.tno.massSequencing.integration 2 2 3 3 import grails.converters.JSON … … 378 378 */ 379 379 private String consumerID() { 380 return config.m etagenomics.consumerID380 return config.massSequencing.consumerID 381 381 } 382 382 -
trunk/grails-app/services/nl/tno/metagenomics/integration/SynchronizationService.groovy
r24 r29 1 package nl.tno.m etagenomics.integration2 3 import nl.tno.m etagenomics.*4 import nl.tno.m etagenomics.auth.*1 package nl.tno.massSequencing.integration 2 3 import nl.tno.massSequencing.* 4 import nl.tno.massSequencing.auth.* 5 5 import org.codehaus.groovy.grails.commons.ConfigurationHolder 6 6 … … 25 25 */ 26 26 protected performSynchronization() { 27 def conf = ConfigurationHolder.config.m etagenomics.synchronization;27 def conf = ConfigurationHolder.config.massSequencing.synchronization; 28 28 29 29 // If nothing is entered in configuration, return true (default value) … … 46 46 long difference = SynchronizationService.lastFullSynchronization.getTime() - today.getTime() 47 47 48 if( difference / 1000 > ConfigurationHolder.config.m etagenomics.fullSynchronization )48 if( difference / 1000 > ConfigurationHolder.config.massSequencing.fullSynchronization ) 49 49 return true 50 50 else -
trunk/grails-app/services/nl/tno/metagenomics/integration/TrashService.groovy
r22 r29 1 package nl.tno.m etagenomics.integration2 3 import nl.tno.m etagenomics.*4 import nl.tno.m etagenomics.auth.Auth;1 package nl.tno.massSequencing.integration 2 3 import nl.tno.massSequencing.* 4 import nl.tno.massSequencing.auth.Auth; 5 5 6 6 … … 29 29 } 30 30 } 31 31 32 // Remove sequence data first, since it gives problems when keeping it 33 if( study.assays ) { 34 l = [] + study.assays*.assaySamples*.sequenceData?.flatten() 35 36 l.each { 37 if( it ) 38 it.sample.removeFromSequenceData( it ); 39 } 40 } 32 41 study.delete(flush:true); 33 42 } … … 53 62 } 54 63 55 l = []56 64 if( assay.assaySamples ) { 57 l += assay.assaySamples 65 // Remove sequence data first, since it gives problems when keeping it 66 l = [] + assay.assaySamples*.sequenceData?.flatten() 67 68 l.each { 69 if( it ) { 70 it.sample.removeFromSequenceData( it ); 71 } 72 } 73 74 l = [] + assay.assaySamples 58 75 59 76 l.each { … … 63 80 } 64 81 82 83 65 84 def study = assay.study 66 85 if( study ) { … … 79 98 def l = [] 80 99 if( sample.assaySamples ) { 81 l += sample.assaySamples 100 // Remove sequence data first, since it gives problems when keeping it 101 l = [] + sample.assaySamples*.sequenceData?.flatten() 102 103 l.each { 104 if( it ) { 105 it.sample.removeFromSequenceData( it ); 106 } 107 } 108 109 l =[] + sample.assaySamples 82 110 83 111 l.each {
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