1 | package nl.tno.metagenomics |
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2 | |
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3 | import java.util.List; |
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4 | |
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5 | import org.codehaus.groovy.grails.commons.ConfigurationHolder |
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6 | |
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7 | class SampleController { |
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8 | def fastaService |
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9 | def sampleExcelService |
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10 | |
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11 | def index = { |
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12 | redirect( controller: 'study' ); |
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13 | } |
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14 | |
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15 | /** |
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16 | * Exports data about one or more studies in fasta format |
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17 | */ |
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18 | def exportAsFasta = { |
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19 | def assaySamples = getAssaySamples( params ); |
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20 | def name |
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21 | |
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22 | if( assaySamples == null ) { |
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23 | return |
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24 | } else if( assaySamples*.sample.unique().size() == 1 ) { |
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25 | name = "Sample_" + assaySamples[0].sample.name?.replace( ' ', '_' ); |
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26 | } else { |
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27 | name = "samples"; |
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28 | } |
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29 | |
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30 | // Export the sequences and quality scores |
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31 | response.setHeader "Content-disposition", "attachment; filename=" + name.trim() + ".zip" |
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32 | try { |
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33 | fastaService.export( assaySamples.unique(), response.getOutputStream() ); |
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34 | response.outputStream.flush(); |
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35 | } catch( Exception e ) { |
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36 | log.error( "Exception occurred during export of sequences. Probably the user has cancelled the download." ); |
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37 | } |
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38 | } |
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39 | |
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40 | /** |
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41 | * Export metadata of one or more studies in excel format |
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42 | */ |
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43 | def exportMetaData = { |
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44 | def assaySamples = getAssaySamples( params ); |
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45 | def name |
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46 | |
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47 | if( assaySamples == null ) { |
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48 | return |
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49 | } else if( assaySamples*.sample.unique().size() == 1 ) { |
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50 | name = "Sample_" + assaySamples[0].sample.name?.replace( ' ', '_' ); |
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51 | } else { |
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52 | name = "samples"; |
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53 | } |
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54 | |
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55 | // Export the metadata |
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56 | response.setHeader "Content-disposition", "attachment; filename=${name}.xls" |
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57 | try { |
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58 | // The export functionality needs a assaySample-tag list, but it |
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59 | // should be empty when only exporting metadata |
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60 | def tags = []; |
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61 | assaySamples.unique().each { assaySample -> |
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62 | tags << [assaySampleId: assaySample.id, sampleName: assaySample.sample.name, assayName: assaySample.assay.name, studyName: assaySample.assay.study.name, tag: "-"] |
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63 | } |
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64 | sampleExcelService.exportExcelSampleData( assaySamples.unique(), tags, response.getOutputStream() ); |
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65 | response.outputStream.flush(); |
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66 | } catch( Exception e ) { |
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67 | log.error( "Exception occurred during export of metadata. Probably the user has cancelled the download." ); |
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68 | e.printStackTrace(); |
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69 | } |
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70 | } |
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71 | |
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72 | |
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73 | |
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74 | |
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75 | /** |
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76 | * Parse the given parameters and try to extract assaysamples using ids and tokens of samples |
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77 | * @param params |
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78 | * @return |
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79 | */ |
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80 | protected List getAssaySamples( params ) { |
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81 | def tokens = params.list( 'tokens' ); |
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82 | def ids = params.list( 'ids' ); |
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83 | def name; |
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84 | |
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85 | ids = ids.findAll { it.isLong() }.collect { Long.parseLong( it ) } |
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86 | |
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87 | if( !tokens && !ids ) { |
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88 | def message = "No sample tokens or ids given" |
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89 | flash.error = message |
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90 | redirect( action: "index" ); |
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91 | return; |
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92 | } |
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93 | |
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94 | def assaySamples = []; |
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95 | |
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96 | // Determine which assaySamples to export |
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97 | def sample; |
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98 | tokens.each { token -> |
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99 | sample = Sample.findBySampleToken( token ); |
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100 | if( sample.study.canRead( session.user ) ) { |
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101 | if( sample && sample.assaySamples ) |
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102 | assaySamples += sample.assaySamples; |
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103 | } |
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104 | } |
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105 | ids.each { id -> |
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106 | sample = Sample.get( id ); |
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107 | if( sample.study.canRead( session.user ) ) { |
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108 | if( sample && sample.assaySamples ) |
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109 | assaySamples += sample.assaySamples; |
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110 | } |
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111 | } |
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112 | |
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113 | return assaySamples; |
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114 | } |
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115 | |
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116 | |
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117 | } |
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