source: trunk/grails-app/controllers/nl/tno/metagenomics/SampleController.groovy @ 24

package nl.tno.metagenomics

import java.util.List;

import org.codehaus.groovy.grails.commons.ConfigurationHolder

class SampleController {
        def fastaService
        def sampleExcelService

        def index = {
                redirect( controller: 'study' );
        }

        /**
        * Exports data about one or more studies in fasta format
        */
   def exportAsFasta = {
           def assaySamples = getAssaySamples( params );
           def name

           if( assaySamples == null ) {
                   return
           } else if( assaySamples*.sample.unique().size() == 1 ) {
                   name = "Sample_" + assaySamples[0].sample.name?.replace( ' ', '_' );
           } else {
                   name = "samples";
           }

           // Export the sequences and quality scores
           response.setHeader "Content-disposition", "attachment; filename=" + name.trim() + ".zip"
           try {
                   fastaService.export( assaySamples.unique(), response.getOutputStream() );
                   response.outputStream.flush();
           } catch( Exception e ) {
                   log.error( "Exception occurred during export of sequences. Probably the user has cancelled the download." );
           }
   }

   /**
        * Export metadata of one or more studies in excel format
        */
   def exportMetaData = {
           def assaySamples = getAssaySamples( params );
           def name

           if( assaySamples == null ) {
                   return
           } else if( assaySamples*.sample.unique().size() == 1 ) {
                   name = "Sample_" + assaySamples[0].sample.name?.replace( ' ', '_' );
           } else {
                   name = "samples";
           }

           // Export the metadata
           response.setHeader "Content-disposition", "attachment; filename=${name}.xls"
           try {
                   // The export functionality needs a assaySample-tag list, but it
                   // should be empty when only exporting metadata
                   def tags = [];
                   assaySamples.unique().each { assaySample ->
                           tags << [assaySampleId: assaySample.id, sampleName: assaySample.sample.name, assayName: assaySample.assay.name, studyName: assaySample.assay.study.name, tag: "-"]
                   }
                   sampleExcelService.exportExcelSampleData( assaySamples.unique(), tags, response.getOutputStream() );
                   response.outputStream.flush();
           } catch( Exception e ) {
                   log.error( "Exception occurred during export of metadata. Probably the user has cancelled the download." );
                   e.printStackTrace();
           }
   }
                
        
        
                
        /**
         * Parse the given parameters and try to extract assaysamples using ids and tokens of samples
         * @param params
         * @return
         */
        protected List getAssaySamples( params ) {
                def tokens = params.list( 'tokens' );
                def ids = params.list( 'ids' );
                def name;

                ids = ids.findAll { it.isLong() }.collect { Long.parseLong( it ) }

                if( !tokens && !ids ) {
                        def message = "No sample tokens or ids given"
                        flash.error = message
                        redirect( action: "index" );
                        return;
                }

                def assaySamples = [];

                // Determine which assaySamples to export
                def sample;
                tokens.each { token ->
                        sample = Sample.findBySampleToken( token );
                        if( sample.study.canRead( session.user ) ) {
                                if( sample && sample.assaySamples )
                                        assaySamples += sample.assaySamples;
                        }
                }
                ids.each { id ->
                        sample = Sample.get( id );
                        if( sample.study.canRead( session.user ) ) {
                                if( sample && sample.assaySamples )
                                        assaySamples += sample.assaySamples;
                        }
                }

                return assaySamples;
        }

        
}