Changeset 13

Timestamp:

Feb 10, 2011, 5:03:02 PM (12 years ago)

Author:

robert@…

Message:

Improved user interface and implemented basic export functionality

Location:

trunk

Files:

• grails-app/conf/Config.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/AssayController.groovy (modified) (2 diffs)
• grails-app/controllers/nl/tno/metagenomics/RunController.groovy (modified) (3 diffs)
• grails-app/controllers/nl/tno/metagenomics/SampleController.groovy (added)
• grails-app/controllers/nl/tno/metagenomics/StudyController.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/integration/ActionController.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy (modified) (1 diff)
• grails-app/services/nl/tno/metagenomics/FastaService.groovy (modified) (4 diffs)
• grails-app/services/nl/tno/metagenomics/SampleExcelService.groovy (modified) (5 diffs)
• grails-app/services/nl/tno/metagenomics/files/FileService.groovy (modified) (1 diff)
• grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy (modified) (8 diffs)
• grails-app/services/nl/tno/metagenomics/integration/SynchronizationService.groovy (modified) (1 diff)
• grails-app/views/assay/index.gsp (modified) (3 diffs)
• grails-app/views/assay/show.gsp (modified) (2 diffs)
• grails-app/views/layouts/main.gsp (modified) (2 diffs)
• grails-app/views/run/index.gsp (modified) (3 diffs)
• grails-app/views/run/show.gsp (modified) (4 diffs)
• web-app/css/buttons.css (added)
• web-app/js/forms.js (added)

trunk/grails-app/conf/Config.groovy

@@ -41 +41 @@
 // Otherwise, it should be given as an absolute path (e.g. '/home/user/sequences')
 // The directory should be writable by the webserver user
-metagenomics.fileUploadDir = "filuploads/temp"
+metagenomics.fileUploadDir = "fileuploads/temp"
 
 // Maximum age that uploaded files should be kept on the server before deleting them. When a user uploads a file,

trunk/grails-app/controllers/nl/tno/metagenomics/AssayController.groovy

@@ -11 +11 @@
         def excelService
         def sampleExcelService
+        def fastaService
 
         def index = {
@@ -326 +327 @@
         }
         
-
+        /**
+         * Exports data about one or more assays in fasta format
+         */
+        def exportAsFasta = {
+                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 assay tokens or ids given"
+                        response.setStatus( 400, message)
+                        render message;
+                        return;
+                }
+                                
+                def assaySamples = [];
+                
+                // Determine which assaySamples to export
+                def assay;
+                tokens.each { token ->
+                        assay = Assay.findByAssayToken( token );
+                        if( assay )
+                                assaySamples += assay.assaySamples
+                }
+                ids.each { id ->
+                        assay = Assay.get( id );
+                        if( assay )
+                                assaySamples += assay.assaySamples
+                }
+
+                if( ( ids.size() + tokens.size() ) == 1 && assay )
+                        name = "Assay_" + assay?.name?.replace( ' ', '_' );
+                else
+                        name = "assays";
+                        
+                // Export the sequences and quality scores
+                response.setHeader "Content-disposition", "attachment; filename=" + name.trim() + ".zip"
+                try {
+                        fastaService.export( assaySamples.unique(), response.getOutputStream(), name );
+                        response.outputStream.flush();
+                } catch( Exception e ) {
+                        log.error( "Exception occurred during export of sequences. Probably the user has cancelled the download." );
+                }
+        }
 }

trunk/grails-app/controllers/nl/tno/metagenomics/RunController.groovy

@@ -9 +9 @@
         def synchronizationService
         def sampleExcelService
+        def fastaService
 
         def index = {
@@ -25 +26 @@
                 // Make sure the newest data is available
                 synchronizationService.sessionToken = session.sessionToken
-                synchronizationService.synchronizeStudies();
+                synchronizationService.user = session.user
+                try { 
+                        synchronizationService.synchronizeStudies();
+                } catch( Exception e ) {
+                        log.error "Exception occurred during synchronization in " + params.controller + ": " + e.getMessage()
+                        redirect( url: synchronizationService.gscfService.urlAuthRemote(params, session.sessionToken) )
+                }
 
                 // Determine runs not used in this assay
@@ -445 +452 @@
         }
 
+        /**
+         * Exports data about one or more runs in fasta format
+         */
+        def exportAsFasta = {
+                def ids = params.list( 'ids' );
+
+                ids = ids.findAll { it.isLong() }.collect { Long.parseLong( it ) }
+
+                if( !ids ) {
+                        def message = "No run ids given"
+                        response.setStatus( 400, message)
+                        render message;
+                        return;
+                }
+
+                def assaySamples = [];
+                def name
+
+                if( ids.size() == 1 )
+                        name = "Run_" + Run.get( ids[ 0 ] )?.name?.replace( ' ', '_' );
+                else
+                        name = "runs";
+
+                // Determine which assaySamples to export
+                ids.each { id ->
+                        def run = Run.get( id );
+                        if( run )
+                                assaySamples += run.assaySamples
+                }
+
+                // Export the sequences and quality scores
+                response.setHeader "Content-disposition", "attachment; filename=${name}.zip"
+                try {
+                        fastaService.export( assaySamples.unique(), response.getOutputStream(), name );
+                        response.outputStream.flush();
+                } catch( Exception e ) {
+                        log.error( "Exception occurred during export of sequences. Probably the user has cancelled the download." );
+                }
+        }
+
 
         /**

trunk/grails-app/controllers/nl/tno/metagenomics/StudyController.groovy

@@ -20 +20 @@
                         lastSynchronized: synchronizationService.lastFullSynchronization ] 
         }
+        
+        def exportAsExcel = {
+                render "To be implemented"
+        }
 
 }

trunk/grails-app/controllers/nl/tno/metagenomics/integration/ActionController.groovy

@@ -3 +3 @@
 
 class ActionController {
-        def fastaService
-        
-        /**
-         * Exports data in fasta format
-         */
-        def fasta = {
-                def entity = params.entity;
-                def tokens = params.tokens;
-                
-                if( !tokens ) {
-                        def message = "No entity tokens given"
-                        response.setStatus( 400, message)
-                        render message;
-                        return;
-                }
-                
-                if( tokens instanceof String )
-                        tokens = [tokens]
-                
-                def assaySamples = [];
-                def name = "testfile";
-                
-                switch( params.entity ) {
-                        case "Study":
-                                // Determine which assaySamples to export
-                                tokens.each { token ->
-                                        def study = Study.findByStudyToken( token );
-                                        if( study )
-                                                assaySamples += study.assay*.assaySamples.flatten()
-                                }
-                                break;
-                        case "Assay":
-                                // Determine which assaySamples to export
-                                tokens.each { token ->
-                                        def assay = Assay.findByAssayToken( token );
-                                        if( assay )
-                                                assaySamples += assay.assaySamples
-                                }
-                                break;
-                        case "Sample":
-                                // Determine which assaySamples to export
-                                tokens.each { token ->
-                                        def sample = Sample.findBySampleToken( token );
-                                        if( sample )
-                                                assaySamples += sample.assaySamples
-                                }
-                                break;
-                        default:
-                                def message = "Specified entity can't be handled by this module."
-                                response.setStatus( 400, message)
-                                render message;
-                                return;
-                }
-                
-                // Export the sequences and quality scores
-                response.setHeader "Content-disposition", "attachment; filename=${name}.zip"
-                fastaService.export( assaySamples.unique(), response.getOutputStream(), name );
-                response.outputStream.flush();
-        }
+
 }

trunk/grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy

@@ -373 +373 @@
                         switch( entity ) {
                                 case "Study":
-                                        actions[ entity ] = [ [ name: "excel", description: "Export as excel" ] ]
+                                        actions[ entity ] = [ [ name: "excel", description: "Export as excel", url: createLink( controller: "study", action: "exportAsExcel", absolute: true ) ] ]
                                         break;
                                 case "Assay":
-                                        actions[ entity ] = [ [ name: "fasta", description: "Export as fasta" ] ]
+                                        actions[ entity ] = [ [ name: "fasta", description: "Export as fasta", url: createLink( controller: "assay", action: "exportAsFasta", absolute: true ) ] ]
                                         break;
                                 case "Sample":
-                                        actions[ entity ] = [ [ name: "fasta", description: "Export as fasta" ] ]
+                                        actions[ entity ] = [ [ name: "fasta", description: "Export as fasta", url: createLink( controller: "sample", action: "exportAsFasta", absolute: true ) ] ]
                                         break;
                                 default:

trunk/grails-app/services/nl/tno/metagenomics/FastaService.groovy

@@ -3 +3 @@
 import java.io.BufferedWriter;
 import java.io.File;
+import java.io.Writer;
 import java.util.ArrayList;
 import java.util.zip.ZipEntry
@@ -11 +12 @@
         def fileService
         def fuzzySearchService
+        def sampleExcelService
 
         static transactional = true
@@ -428 +430 @@
 
                                 // Save the tag for exporting
-                                tags << [assaySampleId: assaySample.id, sampleName: assaySample.sample.name, assayName: assaySample.assay.name, tag: tag]
+                                tags << [assaySampleId: assaySample.id, sampleName: assaySample.sample.name, assayName: assaySample.assay.name, studyName: assaySample.assay.study.name, tag: tag]
                         }
                 }
@@ -481 +483 @@
                 }
                 
+                // Export a tab delimited file with tags
+                zipFile.putNextEntry( new ZipEntry( name + "_sample-tag.tab" ) );
+                exportSampleTagFile( tags, zipWriter );
+                zipWriter.flush();
+                zipFile.closeEntry();
+
+                // Export an excel file with information about the samples
+                zipFile.putNextEntry( new ZipEntry( name + ".xls" ) );
+                sampleExcelService.exportExcelSampleData( assaySamples, tags, zipFile );
+                zipFile.closeEntry();
+                
                 zipFile.close();
-
-                // Export a tab delimited file with tags
-                //exportSampleTagFile( tags );
+        }
+        
+        /**
+         * Creates a tab delimited file with two columns and column headers "Sequence" and "Samplename"
+         * @param tags          Map with newly created tags
+         * @param zipWriter     Writer to write the data to
+         */
+        protected void exportSampleTagFile( List tags, Writer zipWriter ) {
+                zipWriter.write( "Sequence" + "\t" + "Samplename" + "\n" );
+                
+                // Check whether the sample names are unique. If they aren't, the assay and study names
+                // are appended to the sample name
+                def sampleNames = tags*.sampleNames;
+                if( sampleNames.unique().size() < sampleNames.size() ) {
+                        tags.each {
+                                it.uniqueName = it.sampleName + " (" + it.assayName + " / " + it.studyName + ")";
+                        }
+                } else {
+                        tags.each {
+                                it.uniqueName = it.sampleName;
+                        }
+                }
+                
+                tags.each {
+                        zipWriter.write( it.tag + "\t" + it.uniqueName + "\n" );
+                }
         }
 

trunk/grails-app/services/nl/tno/metagenomics/SampleExcelService.groovy

@@ -1 +1 @@
 package nl.tno.metagenomics
+
+import org.springframework.web.context.request.RequestContextHolder;
 
 class SampleExcelService {
         def excelService
         def fuzzySearchService
+        def gscfService
         
     static transactional = true
@@ -15 +18 @@
         def possibleFields = [sampleNameName, runName, tagNameName, tagSequenceName, oligoNumberName]
         
-    def downloadSampleExcel( def assaySamples, boolean includeRun = true ) {
+    /**
+     * Download a sample excel file with information about the metagenomics data of the assaySamples (i.e. all assaySample properties)
+     * @param assaySamples      AssaySamples for which the information should be exported
+     * @param includeRun        Whether to include a column with run name or not
+     * @return
+     */
+        def downloadSampleExcel( def assaySamples, boolean includeRun = true ) {
                 def sheetIndex = 0;
                 
@@ -50 +59 @@
                 excelService.autoSizeColumns( wb, sheetIndex, 0..2)
 
-                return wb;              
+                return wb;
     }
         
+        /**
+         * Parses a given excel file and tries to match the column names with assaySample properties
+         * @param file  
+         * @return
+         */
         def parseTagsExcel( File file, boolean includeRun = true ) {
                 def sheetIndex = 0
@@ -81 +95 @@
         }
         
+        /**
+         * Updates given assay samples with data from the excel file
+         * @param matchColumns          Indicated which columns from the excel file should go into which field of the assaySample
+         * @param possibleFields        List with possible fields to enter
+         * @param file                          Excel file with the data
+         * @param assaySamples          Assay Samples to be updated
+         * @return
+         */
         def updateTagsByExcel( def matchColumns, def possibleFields, File file, def assaySamples ) {
                 def sheetIndex = 0
@@ -187 +209 @@
                 }
         }
+        
+        /**
+         * Exports all known data about the samples to an excel file
+         * @param assaySamples  Assaysamples to export information about
+         * @param tags                  Tags associated with the assay samples
+         * @param stream                Outputstream to write the data to       
+         * @return
+         */
+        def exportExcelSampleData( List<AssaySample> assaySamples, def tags, OutputStream stream ) {
+                if( assaySamples == null )
+                        assaySamples = []
+
+                // Gather data from GSCF.
+                def sampleTokens = assaySamples*.sample.unique()*.sampleToken;
+                def sessionToken = RequestContextHolder.currentRequestAttributes().getSession().sessionToken
+                def gscfData
+                try {
+                        gscfData = gscfService.getSamples( sessionToken, sampleTokens );
+                } catch( Exception e ) {
+                        log.error "Exception occurred while fetching sample data from gscf: " + e.getMessage();
+                        return;
+                }
+                
+                // Determine which fields to show from the GSCF data
+                def gscfFields = []
+                def subjectFields = []
+                def eventFields = []
+                def moduleFields = [ "Sample name", "Assay name", "Study name", "Run name", "# sequences", "Artificial tag sequence", "Original tag sequence", "Tag name", "Oligo number" ]
+                gscfData.each { sample ->
+                        sample.each { key, value ->
+                                if( key == "subjectObject" ) {
+                                        value.each { subjectKey, subjectValue -> 
+                                                if( subjectValue && !value.isNull( subjectKey ) && !subjectFields.contains( subjectKey ) )
+                                                        subjectFields << subjectKey
+                                        }
+                                } else if( key == "eventObject" ) {
+                                        value.each { eventKey, eventValue -> 
+                                                if( eventValue && !value.isNull( eventKey ) && !eventFields.contains( eventKey ) )
+                                                        eventFields << eventKey
+                                        }
+                                } else if( value && !sample.isNull( key ) && !gscfFields.contains( key ) ) {
+                                        gscfFields << key
+                                }
+                        }
+                }
+                
+                // Handle specific fields and names in GSCF
+                def fields = handleSpecificFields( [ "module": moduleFields, "gscf": gscfFields, "subject": subjectFields, "event": eventFields ] );
+
+                // Put the module data in the right format (and sorting the samples by name)
+                def data = []
+                assaySamples.toList().sort { it.sample.name }.each { assaySample ->
+                        // Lookup the tag for this assaySample
+                        def currentTag = tags.find { it.assaySampleId == assaySample.id };
+                        
+                        // First add the module data
+                        def row = [
+                                assaySample.sample.name,
+                                assaySample.assay.name,
+                                assaySample.assay.study.name,
+                                assaySample.run?.name,
+                                assaySample.numSequences(),
+                                currentTag?.tag,
+                                assaySample.tagName,
+                                assaySample.tagSequence,
+                                assaySample.oligoNumber
+                        ]
+                        
+                        // Afterwards add the gscfData including subject and event data
+                        def gscfRow = gscfData.find { it.sampleToken == assaySample.sample.sampleToken };
+                        if( gscfRow ) {
+                                fields[ "names" ][ "gscf" ].each { field ->
+                                        row << prepare( gscfRow, field );
+                                }
+                                fields[ "names" ][ "subject" ].each { field ->
+                                        row << prepare( gscfRow.optJSONObject( "subjectObject" ), field );
+                                }
+                                fields[ "names" ][ "event" ].each { field ->
+                                        row << prepare( gscfRow.optJSONObject( "eventObject" ), field );
+                                }
+                        }
+                        
+                        data << row;
+                        
+                }
+                
+                // Create excel file
+                def sheetIndex = 0;
+                        
+                // Create an excel sheet
+                def wb = excelService.create();
+
+                // Put the headers on the first row
+                excelService.writeHeader( wb, fields[ "descriptions" ][ "all" ], sheetIndex );
+                excelService.writeData( wb, data, sheetIndex, 1 );
+
+                // Auto resize columns
+                excelService.autoSizeColumns( wb, sheetIndex, 0..fields[ "names" ][ "all" ].size()-1)
+
+                // Write the data to the output stream
+                wb.write( stream );
+        }
+        
+        protected String prepare( def object, def fieldName ) {
+                if( object.isNull( fieldName ) )
+                        return "";
+                
+                // If the field is a object, return the 'name' property
+                def obj = object.optJSONObject( fieldName ) 
+                if( obj )
+                        return obj.optString( "name" )
+                else
+                        return object.optString( fieldName );
+        }
+        
+        protected handleSpecificFields( def inputFields ) {
+                def fields = [
+                        "names": [ 
+                                "all": [] 
+                        ],
+                        "descriptions": [
+                                "all": []
+                        ]
+                ]
+                
+                inputFields.each { key, value ->
+                        def names = [];
+                        def descriptions = []
+                        switch( key ) { 
+                                case "gscf":
+                                        value.each {
+                                                if( it != "sampleToken" && it != "name" ) {
+                                                        names << it;
+                                                        if( it == "startTime" )
+                                                                descriptions << "Event start time";
+                                                        else
+                                                                descriptions << it
+                                                }
+                                        }
+                                        break;
+                                case "subject":
+                                        value.each {
+                                                if( it != "name" ) {
+                                                        names << it;
+                                                        descriptions << it
+                                                }
+                                        }
+                                        break;
+                                case "event":
+                                        value.each {
+                                                if( it != "startTime" ) {
+                                                        names << it;
+                                                        descriptions << it
+                                                }
+                                        }
+                                        break;
+                                default:
+                                        names = value; descriptions = value;
+                                        break;
+                        }
+                        
+                        fields[ "names" ][ key ] = names;
+                        fields[ "names" ][ "all" ] += names;
+                        fields[ "descriptions" ][ key ] = descriptions;
+                        fields[ "descriptions" ][ "all" ] += descriptions;
+                }       
+                
+                return fields;
+
+        }
+        
 }

trunk/grails-app/services/nl/tno/metagenomics/files/FileService.groovy

@@ -100 +100 @@
 
                 if( !uploadDir )
-                uploadDir = "fileuploads"
+                        uploadDir = "fileuploads"
 
                 return absolutePath( uploadDir );

trunk/grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy

@@ -12 +12 @@
  */
 class GscfService {
-
         def config = ConfigurationHolder.config
 
         static transactional = true
-
-
 
         /**
@@ -51 +48 @@
                 return "${config.gscf.baseURL}/study/showByToken/" + studyToken
         }
-        
-        /**
-        * Returns the url to add a new study in GSCF
-        *
-        * @return                       URL to redirect the user to
-        */
-   public String urlAddStudy( String studyToken ) {
-           return config.gscf.baseURL + config.gscf.addStudyPath
-   }
-
-   /**
-   * Retrieves the currently logged in user from GSCF
-   *
-   * @param sessionToken String
-   *
-   * @return Map
-   */
-  public Map getUser(String sessionToken) {
-          def user = [:]
-          this.callGSCF(sessionToken, "getUser").each {
-                  user[ it.key ] = it.value;
-          }
-          return user
-  }
-   
+
+        /**
+         * Returns the url to add a new study in GSCF
+         *
+         * @return                      URL to redirect the user to
+         */
+        public String urlAddStudy( String studyToken ) {
+                return config.gscf.baseURL + config.gscf.addStudyPath
+        }
+
+        /**
+         * Retrieves the currently logged in user from GSCF
+         *
+         * @param sessionToken String
+         *
+         * @return Map
+         */
+        public Map getUser(String sessionToken) {
+                def user = [:]
+                this.callGSCF(sessionToken, "getUser").each {
+                        user[ it.key ] = it.value;
+                }
+                return user
+        }
+
         /**
          * Retrieve a list of Studies from the GSCF
@@ -87 +84 @@
         }
 
-        
+
         /**
          * Retrieve a list of Studies from the GSCF
@@ -116 +113 @@
                 } catch( ResourceNotFoundException e ) {
                         throw new ResourceNotFoundException( "Study with token " + studyToken + " not found in GSCF" )
-                        throw e // Other exceptions are thrown as they appear
-                }
+                } // Other exceptions are thrown as they appear
 
                 // Return only the first element of the list, since we are only interested in one study
-                if( list.size() == 0 ) {
+                if( list?.size() ) {
+                        return list[0];
+                } else {
                         return []
-                } else {
-                        return list[0];
                 }
         }
@@ -172 +168 @@
         }
 
-        /** 
-         * Retrieve a list of Samples from the GSCF
-         * 
-         * @param sessionToken String
-         * @param assay Assay (parameter assay is optional, only used when you want to limit the list of samples of an Assay within a Study)
-         * 
-         * @return ArrayList 
-         */
-        public ArrayList getSamples(String sessionToken, String assayToken) throws NotAuthorizedException, ResourceNotFoundException {
-                // Samples of a Study limited to a single Assay
-                try {
-                        return this.callGSCF(sessionToken, "getSamples", ["assayToken":assayToken])
-                } catch( NotAuthorizedException e ) {
-                        throw new NotAuthorizedException( "User is not authorized to access study for assay with token " + assayToken )
-                } catch( ResourceNotFoundException e ) {1
-                        throw new ResourceNotFoundException( "Assay with token " + assayToken + " not found in GSCF" )
-                } // Other exceptions are thrown as they appear
-
-        }
-
+        
         /**
          * Retrieve a single Sample from the GSCF
-         * 
+         *
          * @param sessionToken String
          * @param assay Assay
-         * @param sample Sample  
-         * 
-         * @return ArrayList 
+         * @param sample Sample
+         *
+         * @return ArrayList
          */
         public def getSample(String sessionToken, String assayToken, String sampleToken) throws NotAuthorizedException, ResourceNotFoundException {
@@ -219 +196 @@
 
         }
+        
+        /** 
+         * Retrieve a list of Samples from the GSCF
+         * 
+         * @param sessionToken String
+         * @param assay Assay (parameter assay is optional, only used when you want to limit the list of samples of an Assay within a Study)
+         * 
+         * @return ArrayList 
+         */
+        public ArrayList getSamples(String sessionToken, String assayToken) throws NotAuthorizedException, ResourceNotFoundException {
+                // Samples of a Study limited to a single Assay
+                try {
+                        return this.callGSCF(sessionToken, "getSamples", ["assayToken":assayToken])
+                } catch( NotAuthorizedException e ) {
+                        throw new NotAuthorizedException( "User is not authorized to access study for assay with token " + assayToken )
+                } catch( ResourceNotFoundException e ) {1
+                        throw new ResourceNotFoundException( "Assay with token " + assayToken + " not found in GSCF" )
+                } // Other exceptions are thrown as they appear
+
+        }
+
+        /**
+         * Retrieve a list of samples from the GSCF
+         *
+         * @param sessionToken String
+         * @param sampleTokens List of sampleTokens
+         *
+         * @return ArrayList
+         */
+        public def getSamples(String sessionToken, List sampleTokens) throws NotAuthorizedException, ResourceNotFoundException {
+                def list
+
+                try {
+                        list = this.callGSCF(sessionToken, "getSamples", ["sampleToken": sampleTokens])
+                } catch( NotAuthorizedException e ) {
+                        throw new NotAuthorizedException( "User is not authorized to access samples" )
+                } catch( ResourceNotFoundException e ) {
+                        throw new ResourceNotFoundException( "Samples with token " + sampleTokens + " not found in GSCF" )
+                } // Other exceptions are thrown as they appear
+
+                // Return only the first element of the list, since we are only interested in one sample
+                return list
+        }
+
 
         /**
@@ -273 +294 @@
 
                 // concat all Rest Call specific arguments behind addr
-                restParams.each {parameter -> 
+                restParams.each {parameter ->
                         // If a list is given as value, the parameter should show up multiple times
                         if( parameter.value instanceof Collection ) {
@@ -281 +302 @@
                         } else {
                                 addr += "&${parameter.key}=" + parameter.value.toString().encodeAsURL()
-                        } 
+                        }
                 }
 

trunk/grails-app/services/nl/tno/metagenomics/integration/SynchronizationService.groovy

@@ -261 +261 @@
                         // Can't retrieve data. Maybe sessionToken has expired or invalid. Anyway, stop
                         // synchronizing and return null
+                        e.printStackTrace()
                         log.error( "Exception occurred when fetching study " + study.studyToken + ": " + e.getMessage() )
                         throw new Exception( "Error while fetching study " + study.studyToken, e)

trunk/grails-app/views/assay/index.gsp

@@ -12 +12 @@
                 </g:if>
                 <g:else>
-                        <table class="paginate">
+                        <form id="assayForm">
+                        </form>
+                        <table id="assays" class="paginate">
                                 <thead>
                                         <tr>
+                                                <th class="nonsortable"></th>
                                                 <th>Assay</th>
                                                 <th>Study</th>
@@ -26 +29 @@
                                                         <g:each in="${study.assays}" var="assay">
                                                                 <tr>
+                                                                        <td><g:checkBox name="ids" value="${assay.id}" checked="${false}" /></td>
+                                                                
                                                                         <td><g:link controller="assay" action="show" id="${assay.id}">${assay.name}</g:link></td>
                                                                         <td><a href="${study.viewUrl()}">${study.name}</a></td>
@@ -43 +48 @@
                                 </tbody>
                         </table>
+                        <p class="options">
+                                <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#assayForm' ), '<g:createLink action="exportAsFasta" />', '#assays', 'Please select an assay to export' ); return false;">Export as fasta</a>
+                        </p>
+                        
                 </g:else>                       
         </body>

trunk/grails-app/views/assay/show.gsp

@@ -100 +100 @@
                         </tbody>
                 </table>
+                <p class="options">
+                        <g:if test="${editable}">
+                                <a class="editAssociation" onClick="showEnterTagsDialog();" href="#">Edit sample data</a>
+                        </g:if>
+                        <g:else>
+                                <a class="editAssociation disabled" onClick="return false;" href="#">Edit sample data</a>
+                        </g:else>
+                        <g:if test="${!editable || assay.runs == null || assay.runs.size() == 0}">
+                                <a class="addSequences disabled" onClick="return false;" href="#">Add sequence files</a>
+                        </g:if>
+                        <g:else>
+                                <a class="addSequences" onClick="showAddFilesDialog();" href="#">Add sequence files</a>
+                        </g:else>
+                </p>
+
                 <g:if test="${editable}">
-                        <input type="button" value="Edit sample data" onClick="showEnterTagsDialog();">
-                        <input type="button" value="Add sequence files" onClick="showAddFilesDialog();" <g:if test="${assay.runs == null || assay.runs.size() == 0}">disabled="disabled"</g:if>>
                         <g:render template="enterTagsDialog" model="[assay: assay, sortedAssaySamples: assaySamples]" />
                         <g:render template="addFilesDialog" model="[assay: assay]" />
@@ -162 +175 @@
                 </table>
         </g:else>
+        <p class="options">
+                <g:if test="${editable}">
+                        <a class="addAssociation" onClick="showAddRunDialog();" href="#">Add run</a>
+                </g:if>
+                <g:else>
+                        <a class="addAssociation disabled" onClick="return false;" href="#">Add run</a>
+                </g:else>
+        </p>
+
         <g:if test="${editable}">
-                <input type="button" value="Add run" onClick="showAddRunDialog();">
                 <g:render template="addRunDialog" model="[assay: assay]" />
                 <div id="editRunDialog" class="dialog"></div>

trunk/grails-app/views/layouts/main.gsp

@@ -8 +8 @@
                 <link rel="stylesheet" href="${resource(dir: 'css', file: session.style + '.css')}"/>
                 <link rel="stylesheet" href="${resource(dir: 'css', file: 'login_panel.css')}"/>
+                <link rel="stylesheet" href="${resource(dir: 'css', file: 'buttons.css')}"/>
                 <link rel="shortcut icon" href="${resource(dir: 'images', file: 'favicon.ico')}" type="image/x-icon"/>
                 
@@ -21 +22 @@
                 </script>
                 <script type="text/javascript" src="${resource(dir: 'js', file: 'paginate.js')}"></script>
+                <script type="text/javascript" src="${resource(dir: 'js', file: 'forms.js')}"></script>
                 
                 <g:layoutHead/>

trunk/grails-app/views/run/index.gsp

@@ -25 +25 @@
                 </g:if>
                 <g:else>
-                        <table class="paginate">
+                        <form id="runForm">
+                        </form>
+                        <table id="runs" class="paginate">
                                 <thead>
                                         <tr>
+                                                <th class="nonsortable"></th>
                                                 <th>Run</th>
                                                 <th># samples</th>
@@ -36 +39 @@
                                         <g:each in="${runs}" var="run">
                                                 <tr>
+                                                        <td><g:checkBox name="ids" value="${run.id}" checked="${false}" /></td>
                                                         <td><g:link controller="run" action="show" id="${run.id}">${run.name}</g:link></td>
                                                         <td>${run.assaySamples?.size()}</td>
@@ -43 +47 @@
                                 </tbody>
                         </table>
+                        <p class="options">
+                                <a class="add" href="#" onClick="showAddRunDialog(); return false;">Add run</a>
+                                <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#runForm' ), '<g:createLink action="exportAsFasta" />', '#runs', 'Please select a run to export' ); return false;">Export as fasta</a>
+                        </p>
                 </g:else>
                 <g:render template="addRunDialog" />

trunk/grails-app/views/run/show.gsp

@@ -56 +56 @@
                 <label>Machine</label>: ${run.machine}<br />
                 <label>Parameters</label>: <g:uploadedFile value="${run.parameterFile}" /><br />
-                <a href="#" onClick="showEditRunDialog( ${run.id} ); return false;">Edit run</a>
         </div>
         <div class="blok_data">
@@ -79 +78 @@
                 <label># files</label>: ${run.numFiles()}<br />
         </div>
+        <p class="options">
+                <a class="edit" href="#" onClick="showEditRunDialog( ${run.id} ); return false;">Edit run</a>
+        </p>
         
         <!-- Samples -->
@@ -137 +139 @@
                 </table>
                 <g:if test="${editable}">
-                        <% def writableAssaySamples = assaySamples.findAll { it.assay.study.canWrite( session.user ) } %>
+                        <p class="options">
+                                <% def writableAssaySamples = assaySamples.findAll { it.assay.study.canWrite( session.user ) } %>
+                                <a class="addAssociation" onClick="showAddSamplesDialog();" href="#">Add samples</a>
+
+                                <g:if test="${writableAssaySamples.size() > 0}">
+                                        <a class="editAssociation" onClick="showEnterTagsDialog();" href="#">Edit sample data</a>
+                                </g:if>
+                                <g:else>
+                                        <a class="editAssociation disabled" onClick="return false;" href="#">Edit sample data</a>
+                                </g:else>
+
+                                <g:if test="${writableAssaySamples.size() == 0 || !run.assays?.size()}">
+                                        <a class="addSequences disabled" onClick="return false;" href="#">Add sequence files</a>
+                                </g:if>
+                                <g:else>
+                                        <a class="addSequences" onClick="showAddFilesDialog();" href="#">Add sequence files</a>
+                                </g:else>
+
+                        </p>
                         <g:if test="${writableAssaySamples.size() > 0}">
-                                <input type="button" value="Edit sample data" onClick="showEnterTagsDialog();">
-                                <input type="button" value="Add sequence files" onClick="showAddFilesDialog();" <g:if test="${run.assays == null || run.assays.size() == 0}">disabled="disabled"</g:if>>
                                 <g:render template="enterTagsDialog" model="[run: run, writableAssaySamples: writableAssaySamples]" />
                                 <g:render template="addFilesDialog" model="[run: run]" />
                         </g:if>
-                        <g:else>
-                                <input type="button" value="Edit sample data" disabled="disabled">
-                                <input type="button" value="Add sequence files" disabled="disabled">
-                        </g:else>
-                        <input type="button" value="Add sample" onClick="showAddSamplesDialog();">
+                        
                         <g:render template="addSamplesDialog" model="[run: run]" />
+                        
                 </g:if>
                 <div id="showSampleDialog" class="dialog"></div>
@@ -208 +223 @@
         <% def writableAssays = otherAssays.findAll { it.study.canWrite( session.user ) } %>
         <g:if test="${editable}">
+                <p class="options">
+                        <g:if test="${writableAssays.size() > 0}">
+                                <a class="addAssociation" href="#" onClick="showAddAssayDialog();">Add assay</a>
+                        </g:if>
+                        <g:else>
+                                <a class="addAssociation disabled" href="#" onClick="return false;">Add assay</a>
+                        </g:else>
+                </p>
                 <g:if test="${writableAssays.size() > 0}">
-                        <input type="button" value="Add assay" onClick="showAddAssayDialog();" />
                         <g:render template="addAssayDialog" model="[run: run, writableAssays: writableAssays]" />
                 </g:if>
-                <g:else>
-                        <input type="button" value="Add assay" disabled="disabled" />
-                </g:else>
         </g:if> 
         <div id="showRunDialog" class="dialog"></div>