Changeset 14

Timestamp:

Feb 16, 2011, 2:24:56 PM (8 years ago)

Author:

robert@…

Message:

Implemented improved authorization (#16)
Built in select all checkboxes (#25)

Location:

trunk

Files:

• grails-app/conf/BaseFilters.groovy (modified) (1 diff)
• grails-app/conf/UrlMappings.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/AssayController.groovy (modified) (14 diffs)
• grails-app/controllers/nl/tno/metagenomics/FastaController.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/RunController.groovy (modified) (14 diffs)
• grails-app/controllers/nl/tno/metagenomics/SampleController.groovy (modified) (2 diffs)
• grails-app/controllers/nl/tno/metagenomics/StudyController.groovy (modified) (3 diffs)
• grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy (modified) (2 diffs)
• grails-app/services/nl/tno/metagenomics/SampleExcelService.groovy (modified) (5 diffs)
• grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy (modified) (11 diffs)
• grails-app/services/nl/tno/metagenomics/integration/SynchronizationService.groovy (modified) (3 diffs)
• grails-app/views/action (deleted)
• grails-app/views/assay/index.gsp (modified) (3 diffs)
• grails-app/views/common/_topnav.gsp (modified) (2 diffs)
• grails-app/views/layouts/main.gsp (modified) (1 diff)
• grails-app/views/run/index.gsp (modified) (3 diffs)
• grails-app/views/study/index.gsp (modified) (3 diffs)
• web-app/css/buttons.css (modified) (3 diffs)
• web-app/css/datatables/demo_table_jui.css (modified) (1 diff)
• web-app/js/paginate.js (modified) (1 diff)

trunk/grails-app/conf/BaseFilters.groovy

@@ -184 +184 @@
                                                 log.info "User is not authenticated during synchronizatino. Redirecting to GSCF."
                                                 redirect( url: gscfService.urlAuthRemote(params, session.sessionToken) )
+                                                return false;
                                         } catch( Exception e ) {
                                                 // Synchronization fails. Log error and continue; don't bother the user with it

trunk/grails-app/conf/UrlMappings.groovy

@@ -8 +8 @@
                 }
 
-                "/"(controller: "study")
+                "/"(controller: "run")
                 "500"(view:'/error')
         }

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

@@ -1 +1 @@
 package nl.tno.metagenomics
+
+import java.util.List;
 
 import org.codehaus.groovy.grails.commons.ConfigurationHolder
@@ -19 +21 @@
                         gscfAddUrl: gscfService.urlAddStudy() ]
         }
-        
+
         def show = {
                 def assay = getAssay( params.id );
@@ -65 +67 @@
                 }
 
+                if (!assay.study.canRead( session.user ) ) {
+                        flash.error = "You don't have the right authorizaton to access assay " + assay.name
+                        redirect(action: 'index')
+                        return null
+                }
+                
                 redirect( action: "show", id: assay.id );
         }
@@ -95 +103 @@
          */
         def parseTagExcel = {
-                def assay = getAssay( params.id );
+                def assay = getAssay( params.id, true );
                 if( !assay )
                         return
@@ -129 +137 @@
                 }
                 session.possibleFields = excelData.possibleFields
-                
+
                 [assay: assay, headers: excelData.headers, exampleData: excelData.exampleData, filename: filename, possibleFields: [ "Don't import" ] + excelData.possibleFields, bestMatches: excelData.bestMatches]
         }
@@ -137 +145 @@
          */
         def updateTagsByExcel = {
-                def assay = getAssay( params.id );
+                def assay = getAssay( params.id, true );
                 if( !assay ) {
                         // Now delete the file, since we don't need it anymore
@@ -158 +166 @@
                 // Now loop through the excel sheet and update all samples with the specified data
                 File file = new File( fileService.getUploadDir(), session.filename );
-                
+
                 if( !file.exists() || !file.canRead() ) {
                         flash.error = "Excel file has been removed since previous step. Please try again."
@@ -164 +172 @@
                         return
                 }
-                
+
                 def excelData = sampleExcelService.updateTagsByExcel( matchColumns, session.possibleFields, file, assay.assaySamples );
 
@@ -178 +186 @@
                                 flash.message += excelData.failedRows.size() + " row(s) could not be imported, because the sample names could not be found in the database."
                 }
+                
+                // Now delete the file, since we don't need it anymore
+                _deleteUploadedFileFromSession()
+
                 redirect( action: 'show', id: params.id )
         }
@@ -185 +197 @@
          */
         def updateTagsManually = {
-                def assay = getAssay( params.id );
+                def assay = getAssay( params.id, true );
                 if( !assay )
                         return
@@ -224 +236 @@
          */
         def addExistingRuns = {
-                def assay = getAssay( params.id );
+                def assay = getAssay( params.id, true );
                 if( !assay )
                         return
@@ -250 +262 @@
 
         /**
-         * Adds existing runs to this assay
+         * Removes a run from this assay
          */
         def removeRun = {
-                def assay = getAssay( params.id );
+                def assay = getAssay( params.id, true );
                 if( !assay )
                         return
@@ -300 +312 @@
                 session.filename = ''
         }
-        
-        protected Assay getAssay(def assayId) {
-                // load study with id specified by param.id
-                def assay
-                try {
-                        assay = Assay.get(assayId as Long)
-                } catch( Exception e ) {
-                        flash.error = "Incorrect id given: " + assayId
-                        redirect(controller: 'study')
-                        return null
-                }
-
-                if (!assay) {
-                        flash.error = "No assay found with id: " + assayId
-                        redirect(controller: 'study')
-                        return null
-                }
-                
-                if (!assay.study.canRead( session.user ) ) {
-                        flash.error = "You don't have the right authorizaton to access assay " + assay.name
-                        redirect(controller: 'study')
-                        return null
-                }
-                
-                return assay
-        }
-        
+
         /**
          * 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
+                def assaySamples = getAssaySamples( params );
+                def name
+
+                if( assaySamples == null ) {
+                        return
+                } else if( assaySamples*.assay.unique().size() == 1 ) {
+                        name = "Assay_" + assaySamples[0].assay?.name?.replace( ' ', '_' );
+                } else {
                         name = "assays";
-                        
+                }
+
                 // Export the sequences and quality scores
                 response.setHeader "Content-disposition", "attachment; filename=" + name.trim() + ".zip"
@@ -373 +337 @@
                 }
         }
+
+        /**
+         * Export metadata of selected samples in excel format
+         */
+        def exportMetaData = {
+                def assaySamples = getAssaySamples( params );
+                def name
+
+                if( assaySamples == null ) {
+                        return
+                } else if( assaySamples*.assay.unique().size() == 1 ) {
+                        name = "Assay_" + assaySamples[0].assay?.name?.replace( ' ', '_' );
+                } else {
+                        name = "assays";
+                }
+
+                // 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." );
+                }
+        }
+
+        
+        /**
+         * Retrieves an assay from the database, based on the assay ID given
+         * @param assayId               ID of the assay 
+         * @param writeAccess   True if you require write access to this assay. The system will check for sufficient privileges
+         * @return
+         */
+        protected Assay getAssay(def assayId, boolean writeAccess = false ) {
+                // load study with id specified by param.id
+                def assay
+                try {
+                        assay = Assay.get(assayId as Long)
+                } catch( Exception e ) {
+                        flash.error = "Incorrect id given: " + assayId
+                        redirect(action: 'index')
+                        return null
+                }
+
+                if (!assay) {
+                        flash.error = "No assay found with id: " + assayId
+                        redirect(action: 'index')
+                        return null
+                }
+
+                if ( !assay.study.canRead( session.user ) || ( writeAccess && !assay.study.canWrite( session.user ) ) ) {
+                        flash.error = "You don't have the right authorizaton to access assay " + assay.name
+                        redirect(action: 'index')
+                        return null
+                }
+                
+                return assay
+        }
+
+        
+        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 assay tokens or ids given"
+                        flash.error = message
+                        redirect( action: "index" );
+                        return;
+                }
+
+                def assaySamples = [];
+
+                // Determine which assaySamples to export
+                def assay;
+                tokens.each { token ->
+                        assay = Assay.findByAssayToken( token );
+                        if( assay && assay.study.canRead( session.user ) )
+                                assaySamples += assay.assaySamples
+                }
+                ids.each { id ->
+                        assay = Assay.get( id );
+                        if( assay && assay.study.canRead( session.user ) )
+                                assaySamples += assay.assaySamples
+                }
+
+                return assaySamples;
+        }
+
+
 }

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

@@ -69 +69 @@
                         case "run":
                                 entity = getRun( params.id );
-                                assaySamples = entity.assaySamples;
+                                assaySamples = entity.assaySamples.findAll { it.assay.study.canRead( session.user ) };
                                 break;
                         case "assay":

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

@@ -35 +35 @@
 
                 // Determine runs not used in this assay
-                def otherAssays = Assay.list( sort: "name" ).findAll { !it.runs.contains( run ) }
+                def otherAssays = Assay.list( sort: "name" ).findAll { !it.runs.contains( run ) && it.study.canRead( session.user ) }
 
                 // Send the assay information to the view
@@ -67 +67 @@
 
         def create = {
+                // Retrieve the assay from the database, but don't exit with an error if no assay is found
                 Assay a = getAssay(params.id);
                 flash.error = "";
@@ -133 +134 @@
                 }
 
+                // Check whether the user has sufficient privileges to remove the run from all assays
+                def hasPrivileges = true;
+                run.assay.each {
+                        if( !it.study.canWrite( session.user ) ) 
+                                hasPrivileges = false
+                }
+                
+                if( !hasPrivileges ) {
+                        flash.message = "Run could not be deleted because you don't have sufficient privileges to remove the run from all assays.";
+                        redirect( controller: "assay", action: "show", id: params.assayId )
+                }
+                
                 // Remove all associations
                 run.assays.each {
@@ -257 +270 @@
                 def assaySamples = run.assaySamples.findAll { it.assay.study.canWrite( session.user ) }
 
+                println "Matchcolumns: " + matchColumns
+                println "Possible fields: " + session.possibleFields
+                println "Assay samples: " + assaySamples.sample.name
+                
                 def excelData = sampleExcelService.updateTagsByExcel( matchColumns, session.possibleFields, file, assaySamples );
 
+                println excelData
+                
                 // Return a message to the user
                 if( !excelData.success ) {
@@ -270 +289 @@
                                 flash.message += excelData.failedRows.size() + " row(s) could not be imported, because the sample names could not be found in the database or you don't have the proper permissions to change them."
                 }
+
+                // Now delete the file, since we don't need it anymore
+                _deleteUploadedFileFromSession()
+
                 redirect( action: 'show', id: params.id )
         }
@@ -289 +312 @@
 
                 if( sampleParams ) {
-                        run.assaySamples.each { assaySample ->
+                        run.assaySamples.findAll { it.assay.study.canWrite( session.user ) }.each { assaySample ->
                                 def assaySampleParams = sampleParams.get( assaySample.id as String );
                                 if( assaySampleParams ) {
@@ -318 +341 @@
 
                 if( !run ) {
-                        redirect(controller: 'study')
+                        redirect(controller: 'run', action: 'index')
                         return
                 }
@@ -332 +355 @@
                         try {
                                 def assaySample = AssaySample.findById( assaySampleId as Long )
-                                if( run.assaySamples == null || !run.assaySamples.contains( assaySample ) ) {
-                                        run.addToAssaySamples( assaySample );
-                                        numAdded++;
+                                if( assaySample.assay.study.canWrite( session.user ) ) {
+                                        if( run.assaySamples == null || !run.assaySamples.contains( assaySample ) ) {
+                                                run.addToAssaySamples( assaySample );
+                                                numAdded++;
+                                        }
                                 }
                         } catch( Exception e ) {}
@@ -355 +380 @@
 
                 if( !params.assaySampleId ) {
-                        flash.message = "No sample id given"
+                        flash.error = "No sample id given"
                         redirect(action: 'show', id: params.id)
                         return
@@ -366 +391 @@
                 } catch( Exception e ) {
                         log.error e
-                        flash.message = "Incorrect assaysample id given: " + params.assaySampleId
+                        flash.error = "Incorrect assaysample id given: " + params.assaySampleId
                         redirect(action: 'show', id: params.id)
                         return
                 }
-
+                
+                if( !assaySample.assay.study.canWrite( session.user ) ) {
+                        flash.error = "You don't have sufficient privileges to remove the specified sample from this run."
+                        redirect(action: 'show', id: params.id)
+                        return
+                }
+                
                 if( run.assaySamples.contains( assaySample ) ) {
                         run.removeFromAssaySamples( assaySample );
@@ -403 +434 @@
                         try {
                                 def assay = Assay.findById( assay_id as Long )
-                                if( run.assays == null || !run.assays.contains( assay ) ) {
-                                        run.addToAssays( assay );
-                                        numAdded++;
+                                if( assay.study.canWrite( session.user ) ) {
+                                        if( run.assays == null || !run.assays.contains( assay ) ) {
+                                                run.addToAssays( assay );
+                                                numAdded++;
+                                        }
                                 }
                         } catch( Exception e ) {}
@@ -442 +475 @@
                 }
 
+                if( !assay.study.canWrite( session.user ) ) {
+                        flash.error = "You don't have sufficient privileges to remove the specified assay from this run."
+                        redirect(action: 'show', id: params.id)
+                        return
+                }
+                
                 if( run.assays.contains( assay ) ) {
                         run.removeFromAssays( assay );
@@ -456 +495 @@
          */
         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;
+                def assaySamples = getAssaySamples( params );
+
+                if( assaySamples == null )
                         return;
-                }
-
-                def assaySamples = [];
+
                 def name
 
-                if( ids.size() == 1 )
-                        name = "Run_" + Run.get( ids[ 0 ] )?.name?.replace( ' ', '_' );
+                if( assaySamples.size() == 0 ) {
+                        flash.error = "No samples found for selected runs";
+                        redirect( action: "list" );
+                        return;
+                } else if( assaySamples*.run.unique().size() == 1 )
+                        name = "Run_" + assaySamples[0].run?.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
@@ -491 +520 @@
                 }
         }
-
+        
+        /**
+         * Export metadata of selected samples in excel format
+         */
+        def exportMetaData = {
+                def assaySamples = getAssaySamples( params );
+                def name
+                
+                if( assaySamples == null )
+                        return;
+                        
+                if( assaySamples.size() == 0 ) {
+                        flash.error = "No samples found for selected runs";
+                        redirect( action: "list" );
+                        return;
+                } else if( assaySamples*.run.unique().size() == 1 ) {
+                        name = "Run_" + assaySamples[0].run?.name?.replace( ' ', '_' );
+                } else {
+                        name = "runs";
+                }
+
+                // Export the metadata
+                response.setHeader "Content-disposition", "attachment; filename=${name}.xls"
+                try {
+                        // The export functionality needs a assaysSample-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 sequences. Probably the user has cancelled the download." );
+                }
+        }
+        
+        protected List getAssaySamples( params ) {
+                def ids = params.list( 'ids' );
+                
+                ids = ids.findAll { it.isLong() }.collect { Long.parseLong( it ) }
+
+                if( !ids ) {
+                        def message = "No run ids given"
+                        flash.error = message
+                        redirect( action: "index" );
+                        return;
+                }
+
+                def assaySamples = [];
+
+                // Determine which assaySamples to export
+                ids.each { id ->
+                        def run = Run.get( id );
+                        if( run )
+                                assaySamples += run.assaySamples.findAll { it.assay.study.canRead( session.user ) }
+                }
+                
+                return assaySamples;
+        }
 
         /**

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

@@ -1 +1 @@
 package nl.tno.metagenomics
+
+import java.util.List;
 
 import org.codehaus.groovy.grails.commons.ConfigurationHolder
@@ -5 +7 @@
 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(), name );
+                   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();
+           }
+   }
+                
         
+        
+                
         /**
-         * Exports data about one or more samples in fasta format
+         * Parse the given parameters and try to extract assaysamples using ids and tokens of samples
+         * @param params
+         * @return
          */
-        def exportAsFasta = {
+        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"
-                        response.setStatus( 400, message)
-                        render message;
+                        flash.error = message
+                        redirect( action: "index" );
                         return;
                 }
-                
+
                 def assaySamples = [];
-                def name = "samples";
-                
+
                 // Determine which assaySamples to export
+                def sample;
                 tokens.each { token ->
-                        def sample = Sample.findBySampleToken( token );
-                        if( sample )
-                                assaySamples += sample.assaySamples
+                        sample = Sample.findBySampleToken( token );
+                        if( sample.study.canRead( session.user ) ) {
+                                if( sample && sample.assaySamples )
+                                        assaySamples += sample.assaySamples;
+                        }
                 }
                 ids.each { id ->
-                        def sample = Sample.get( id );
-                        if( sample )
-                                assaySamples += sample.assaySamples
+                        sample = Sample.get( id );
+                        if( sample.study.canRead( session.user ) ) {
+                                if( sample && sample.assaySamples )
+                                        assaySamples += sample.assaySamples;
+                        }
                 }
-                
-                // Export the sequences and quality scores
-                response.setHeader "Content-disposition", "attachment; filename=${name}.zip"
-                fastaService.export( assaySamples.unique(), response.getOutputStream(), name );
-                response.outputStream.flush();
+
+                return assaySamples;
         }
+
+        
 }

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

@@ -1 +1 @@
 package nl.tno.metagenomics
+
+import java.util.List;
 
 class StudyController {
@@ -6 +8 @@
         def fileService
         def trashService
+        def fastaService
+        def sampleExcelService
         
         def index = {
@@ -21 +25 @@
         }
         
-        def exportAsExcel = {
-                render "To be implemented"
+
+        /**
+         * 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*.assay*.study.unique().size() == 1 ) {
+                        name = "Study_" + assaySamples[0].assay.study.name?.replace( ' ', '_' );
+                } else {
+                        name = "studies";
+                }
+
+                // 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." );
+                }
+        }
+
+        /**
+         * 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*.assay*.study.unique().size() == 1 ) {
+                        name = "Study_" + assaySamples[0].assay.study.name?.replace( ' ', '_' );
+                } else {
+                        name = "studies";
+                }
+
+                // 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 studies using ids and tokens
+         * @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 assay tokens or ids given"
+                        flash.error = message
+                        redirect( action: "index" );
+                        return;
+                }
+
+                def assaySamples = [];
+
+                // Determine which assaySamples to export
+                def study;
+                tokens.each { token ->
+                        study = Study.findByStudyToken( token );
+                        if( study && study.canRead( session.user ) )
+                                assaySamples += study.assays*.assaySamples.flatten();
+                }
+                ids.each { id ->
+                        study = Study.get( id );
+                        if( study && study.canRead( session.user ) )
+                                assaySamples += study.assays*.assaySamples.flatten();
+                }
+
+                return assaySamples;
         }
 

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

@@ -233 +233 @@
                                         log.error "Data was requested for " + entity.toLowerCase() + " " + object.name + " but the user " + session.user.username + " doesn't have the right privileges."
                                         continue;
-                                } else {
-                                        log.error "Data was requested for " + entity.toLowerCase() + " " + object.name + ": " + session.user.username + " - " + study.canRead( session.user )
                                 }
                                 
@@ -373 +371 @@
                         switch( entity ) {
                                 case "Study":
-                                        actions[ entity ] = [ [ name: "excel", description: "Export as excel", url: createLink( controller: "study", action: "exportAsExcel", absolute: true ) ] ]
+                                        actions[ entity ] = [ 
+                                                [ name: "excel", description: "Export metadata", url: createLink( controller: "study", action: "exportMetaData", absolute: true ) ], 
+                                                [ name: "fasta", description: "Export as fasta", url: createLink( controller: "study", action: "exportAsFasta", absolute: true ) ] 
+                                        ]
                                         break;
                                 case "Assay":
-                                        actions[ entity ] = [ [ name: "fasta", description: "Export as fasta", url: createLink( controller: "assay", action: "exportAsFasta", absolute: true ) ] ]
+                                        actions[ entity ] = [ 
+                                                [ name: "fasta", description: "Export as fasta", url: createLink( controller: "assay", action: "exportAsFasta", absolute: true ) ],
+                                                [ name: "excel", description: "Export metadata", url: createLink( controller: "assay", action: "exportMetaData", absolute: true ) ]
+                                        ]
                                         break;
                                 case "Sample":
-                                        actions[ entity ] = [ [ name: "fasta", description: "Export as fasta", url: createLink( controller: "sample", action: "exportAsFasta", absolute: true ) ] ]
+                                        actions[ entity ] = [ 
+                                                [ name: "fasta", description: "Export as fasta", url: createLink( controller: "sample", action: "exportAsFasta", absolute: true ) ], 
+                                                [ name: "excel", description: "Export metadata", url: createLink( controller: "sample", action: "exportMetaData", absolute: true ) ] 
+                                        ]
                                         break;
                                 default:

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

@@ -87 +87 @@
                         
                 headers.eachWithIndex { header, idx ->
-                        // Do matching using fuzzy search. The 0.1 treshold makes sure that no match if chosen if
+                        // Do matching using fuzzy search. The 0.8 treshold makes sure that no match if chosen if
                         // there is actually no match at all.
-                        bestMatches[idx] = fuzzySearchService.mostSimilar( header, possibleFields, 0.1 );
+                        if( !header || header.toString().trim() == "" )
+                                bestMatches[idx] = null
+                        else
+                                bestMatches[idx] = fuzzySearchService.mostSimilar( header, possibleFields, 0.8 );
                 }
                 
@@ -119 +122 @@
                 def dataMatches = false;
                 possibleFields.each { columnName ->
-                        columns[ columnName ] = matchColumns.findIndexOf { it.value == columnName }
+                        def foundColumn = matchColumns.find { it.value == columnName };
+                        
+                        columns[ columnName ] = ( foundColumn && foundColumn.key.toString().isInteger() ) ? Integer.valueOf( foundColumn.key.toString() ) : -1;
 
                         if( columnName != sampleNameName && columns[ columnName ] != -1 )
@@ -125 +130 @@
                 }
 
+                println columns
+                
                 // A column to match the sample name must be present
                 if( columns[ sampleNameName ] == -1 ) {
-                        // Now delete the file, since we don't need it anymore
-                        _deleteUploadedFileFromSession()
-
                         return [ success: false, message: "There must be a column present in the excel file that matches the sample name. Please try again." ]
                 }
@@ -135 +139 @@
                 // A column with data should also be present
                 if( !dataMatches ) {
-                        // Now delete the file, since we don't need it anymore
-                        _deleteUploadedFileFromSession()
-
                         return [ success: false, message: "There are no data columns present in the excel file. No samples are updated." ]
                 }
@@ -166 +167 @@
                         String sampleName = rowData[ columns[ sampleNameName ] ] as String
 
+                        // If no sample name is found, the row is either empty or contains no sample name
+                        if( !sampleName ) { 
+                                failedRows << [ row: rowData, sampleName: "" ];
+                                continue;
+                        }
+                                
                         // Find assay by sample name. Since sample names are unique within an assay (enforced by GSCF),
                         // this will always work when only using one assay. When multiple assays are used, this might pose
                         // a problem 
+                        // TODO: Fix problem with multiple assays
                         AssaySample assaySample = assaySamples.find { it.sample.id == Sample.findByName( sampleName )?.id };
+                        println "Row: " + i + " - Sample name: " + sampleName + " - " + assaySample
 
                         // If no assaysample is found, add this row to the failed-row list

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

@@ -24 +24 @@
          */
         public String urlAuthRemote( def params, def token ) {
-                def redirectURL = "${config.gscf.baseURL}/login/auth_remote?moduleURL=${this.moduleURL()}&consumer=${this.consumerID()}&token=${token}&returnUrl=${config.grails.serverURL}"
-
+                def redirectURL = "${config.gscf.baseURL}/login/auth_remote?moduleURL=${this.moduleURL()}&consumer=${this.consumerID()}&token=${token}&"
+
+                def returnUrl = config.grails.serverURL
                 if (params.controller != null){
-                        redirectURL += "/${params.controller}"
+                        returnUrl += "/${params.controller}"
                         if (params.action != null){
-                                redirectURL += "/${params.action}"
+                                returnUrl += "/${params.action}"
                                 if (params.id != null){
-                                        redirectURL += "/${params.id}"
+                                        returnUrl += "/${params.id}"
                                 }
                         }
                 }
 
-                return redirectURL
+                // Append other parameters
+                returnUrl += "?" + params.collect {
+                        if( it.key != "controller" && it.key != "action" && it.key != "id" )
+                                return it.key.toString().encodeAsURL() + "=" + it.value.toString().encodeAsURL();
+                        else
+                                return ""
+                }.findAll { it }.join( "&" );
+                
+                return redirectURL + "returnUrl=" + returnUrl.encodeAsURL();
         }
 
@@ -65 +74 @@
          * @return Map
          */
-        public Map getUser(String sessionToken) {
+        public Map getUser(String sessionToken) throws Exception {
                 def user = [:]
-                this.callGSCF(sessionToken, "getUser").each {
-                        user[ it.key ] = it.value;
-                }
-                return user
+                try {
+                        this.callGSCF(sessionToken, "getUser").each {
+                                user[ it.key ] = it.value;
+                        }
+                        return user
+                } catch( Exception e ) {
+                        throw new Exception( "Retrieving user details from GSCF failed", e );
+                }
         }
 
@@ -80 +93 @@
          * @return ArrayList 
          */
-        public ArrayList getStudies(String sessionToken) {
+        public ArrayList getStudies(String sessionToken) throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception {
                 return this.callGSCF(sessionToken, "getStudies")
         }
@@ -92 +105 @@
          * @return ArrayList
          */
-        public ArrayList getStudies(String sessionToken, ArrayList studyTokens ) {
+        public ArrayList getStudies(String sessionToken, ArrayList studyTokens ) throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception  {
                 return this.callGSCF(sessionToken, "getStudies", [ "studyToken": studyTokens ] );
         }
@@ -104 +117 @@
          * @return ArrayList 
          */
-        public def getStudy(String sessionToken, String studyToken) throws NotAuthorizedException, ResourceNotFoundException {
+        public def getStudy(String sessionToken, String studyToken) throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception  {
                 def list
 
@@ -131 +144 @@
          * @return ArrayList 
          */
-        public ArrayList getAssays(String sessionToken, String studyToken) throws NotAuthorizedException, ResourceNotFoundException {
+        public ArrayList getAssays(String sessionToken, String studyToken) throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception  {
                 try {
                         return this.callGSCF(sessionToken, "getAssays", ["studyToken": studyToken])
@@ -150 +163 @@
          * @return ArrayList 
          */     
-        public def getAssay(String sessionToken, String studyToken, String assayToken ) throws NotAuthorizedException, ResourceNotFoundException {
+        public def getAssay(String sessionToken, String studyToken, String assayToken )throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception  {
                 def list
                 try {
@@ -178 +191 @@
          * @return ArrayList
          */
-        public def getSample(String sessionToken, String assayToken, String sampleToken) throws NotAuthorizedException, ResourceNotFoundException {
+        public def getSample(String sessionToken, String assayToken, String sampleToken) throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception  {
                 def list
 
@@ -205 +218 @@
          * @return ArrayList 
          */
-        public ArrayList getSamples(String sessionToken, String assayToken) throws NotAuthorizedException, ResourceNotFoundException {
+        public ArrayList getSamples(String sessionToken, String assayToken) throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception  {
                 // Samples of a Study limited to a single Assay
                 try {
@@ -225 +238 @@
          * @return ArrayList
          */
-        public def getSamples(String sessionToken, List sampleTokens) throws NotAuthorizedException, ResourceNotFoundException {
+        public def getSamples(String sessionToken, List sampleTokens) throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception  {
                 def list
 
@@ -249 +262 @@
          * @return ArrayList
          */
-        public HashMap getAuthorizationLevel(String sessionToken, String studyToken) throws ResourceNotFoundException {
+        public HashMap getAuthorizationLevel(String sessionToken, String studyToken) throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception  {
                 ArrayList list
 

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

@@ -67 +67 @@
                         }
                 }
+                
+                // Append other parameters
+                returnUrl += "?" + params.collect {
+                        if( it.key != "controller" && it.key != "action" && it.key != "id" )
+                                return it.key.toString().encodeAsURL() + "=" + it.value.toString().encodeAsURL(); 
+                        else
+                                return ""
+                }.findAll { it }.join( "&" );
+                
                 if( timeForFullSynchronization() ) {
                         return ConfigurationHolder.config.grails.serverURL + "/synchronize/full?redirect=" + returnUrl.encodeAsURL()
@@ -91 +100 @@
          * @return      ArrayList       List of studies or null if the synchronization has failed
          */
-        public ArrayList<Study> synchronizeStudies() throws NotAuthenticatedException, Exception {
+        public ArrayList<Study> synchronizeStudies() throws BadRequestException, NotAuthenticatedException, NotAuthorizedException, ResourceNotFoundException, Exception {
                 if( !performSynchronization() )
                         return Study.findAllWhereTrashcan(false)
@@ -140 +149 @@
                         // synchronizing and return null
                         log.error( "Exception occurred when fetching studies: " + e.getMessage() )
-                        throw new Exception( "Error while fetching studies", e)
+                        throw e
                 }
 

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

@@ -17 +17 @@
                                 <thead>
                                         <tr>
-                                                <th class="nonsortable"></th>
+                                                <th class="nonsortable"><input type="checkbox" id="checkAll" onClick="checkAllPaginated(this);" /></th>
                                                 <th>Assay</th>
                                                 <th>Study</th>
@@ -29 +29 @@
                                                         <g:each in="${study.assays}" var="assay">
                                                                 <tr>
-                                                                        <td><g:checkBox name="ids" value="${assay.id}" checked="${false}" /></td>
+                                                                        <td><g:checkBox name="ids" value="${assay.id}" checked="${false}" onClick="updateCheckAll(this);" /></td>
                                                                 
                                                                         <td><g:link controller="assay" action="show" id="${assay.id}">${assay.name}</g:link></td>
@@ -50 +50 @@
                         <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>
+                                <a class="excel" href="#" onClick="submitPaginatedForm( $( '#assayForm' ), '<g:createLink action="exportMetaData" />', '#assays', 'Please select an assay to export' ); return false;">Export metadata</a>
                         </p>
                         

trunk/grails-app/views/common/_topnav.gsp

@@ -1 +1 @@
     <!-- TOPNAV //-->
     <ul class="topnav">
-     <li><g:link controller="study">Home</g:link></li>
+     <li><g:link controller="run">Home</g:link></li>
         <li>
       <a href="#" onClick="return false;">View</a>
@@ -7 +7 @@
                 <li><g:link controller="run">Runs</g:link></li>
                 <li><g:link controller="assay">Assays</g:link></li>
+                <li><g:link controller="study">Studies</g:link></li>
       </ul>
     </li>

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

@@ -37 +37 @@
                         <div id="content">
                                 <g:if test="${lastSynchronized}">
-                                        <p>Last full synchronization: ${lastSynchronized}</p>
+                                        <!-- Last full synchronization: ${lastSynchronized} -->
                                 </g:if>
                                 <g:if test="${flash.error}">

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

@@ -30 +30 @@
                                 <thead>
                                         <tr>
-                                                <th class="nonsortable"></th>
+                                                <th class="nonsortable"><input type="checkbox" id="checkAll" onClick="checkAllPaginated(this);" /></th>
                                                 <th>Run</th>
                                                 <th># samples</th>
@@ -39 +39 @@
                                         <g:each in="${runs}" var="run">
                                                 <tr>
-                                                        <td><g:checkBox name="ids" value="${run.id}" checked="${false}" /></td>
+                                                        <td><g:checkBox name="ids" value="${run.id}" checked="${false}" onClick="updateCheckAll(this);" /></td>
                                                         <td><g:link controller="run" action="show" id="${run.id}">${run.name}</g:link></td>
                                                         <td>${run.assaySamples?.size()}</td>
@@ -50 +50 @@
                                 <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>
+                                <a class="excel" href="#" onClick="submitPaginatedForm( $( '#runForm' ), '<g:createLink action="exportMetaData" />', '#runs', 'Please select a run to export' ); return false;">Export metadata</a>
                         </p>
                 </g:else>

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

@@ -12 +12 @@
                 </g:if>
                 <g:else>
-                        <table class="paginate">
+                        <form id="assayForm">
+                        </form>
+                
+                        <table id="studies" class="paginate">
                                 <thead>
                                         <tr>
-
+                                                <th class="nonsortable"><input type="checkbox" id="checkAll" onClick="checkAllPaginated(this);" /></th>
+                                                <th>Study</th>
                                                 <th>Assay</th>
-                                                <th>Study</th>
                                                 <th># samples</th>
                                         </tr>
@@ -34 +37 @@
                                                         <g:each in="${study.assays}" var="assay">
                                                                 <tr>
+                                                                        <td><g:checkBox name="ids" value="${assay.id}" checked="${false}" onClick="updateCheckAll(this);" /></td>
+                                                                        <td><a href="${study.viewUrl()}">${study.name}</a></td>
                                                                         <td><g:link controller="assay" action="show" id="${assay.id}">${assay.name}</g:link></td>
-                                                                        <td><a href="${study.viewUrl()}">${study.name}</a></td>
                                                                         <td>${assay.assaySamples?.size()}</td>
                                                                 </tr>
@@ -43 +47 @@
                                 </tbody>
                         </table>
+                        <p class="options">
+                                <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#assayForm' ), '<g:createLink controller="assay" action="exportAsFasta" />', '#studies', 'Please select one or more studies to export' ); return false;">Export as fasta</a>
+                                <a class="excel" href="#" onClick="submitPaginatedForm( $( '#assayForm' ), '<g:createLink controller="assay" action="exportMetaData" />', '#studies', 'Please select one or more studies to export' ); return false;">Export metadata</a>
+                        </p>                    
                 </g:else>                       
         </body>

trunk/web-app/css/buttons.css

@@ -6 +6 @@
         padding-bottom: 2px;
         line-height: 20px;
-        padding-left: 28px;     
+        padding-left: 26px;     
+        
+        background-image: transparent;
+        background-repeat: no-repeat;
+        background-position: 3px 50%;
 }
 
@@ -12 +16 @@
 
 .options a.fasta {
-        background: transparent url(../plugins/famfamfam-1.0.1/images/icons/brick_go.png) 5px 50% no-repeat;
+        background-image: url(../plugins/famfamfam-1.0.1/images/icons/brick_go.png);
 }
 .options a.excel {
@@ -18 +22 @@
 }
 .options a.edit {
-        background: transparent url(../plugins/famfamfam-1.0.1/images/icons/pencil.png) 5px 50% no-repeat;
+        background-image:  url(../plugins/famfamfam-1.0.1/images/icons/pencil.png);
 }
 .options a.add {
-        background: transparent url(../plugins/famfamfam-1.0.1/images/icons/add.png) 5px 50% no-repeat;
+        background-image:  url(../plugins/famfamfam-1.0.1/images/icons/add.png);
 }
 .options a.addSequences {
-        background: transparent url(../plugins/famfamfam-1.0.1/images/icons/page_attach.png) 5px 50% no-repeat;
+        background-image:  url(../plugins/famfamfam-1.0.1/images/icons/page_attach.png);
 }
 
 .options a.addAssociation {
-        background: transparent url(../plugins/famfamfam-1.0.1/images/icons/application_add.png) 5px 50% no-repeat;
+        background-image:  url(../plugins/famfamfam-1.0.1/images/icons/application_add.png);
 }
 .options a.editAssociation {
-        background: transparent url(../plugins/famfamfam-1.0.1/images/icons/application_edit.png) 5px 50% no-repeat;
+        background-image:  url(../plugins/famfamfam-1.0.1/images/icons/application_edit.png);
 }

trunk/web-app/css/datatables/demo_table_jui.css

@@ -78 +78 @@
 .dataTables_wrapper { font-size: 10px; }
 
+/* Check all checkbox */
+input.transparent { 
+        -ms-filter: "progid:DXImageTransform.Microsoft.Alpha(Opacity=30)";
+        filter: alpha(opacity=30);
+        opacity: 0.3;
+        -moz-opacity: 0.3;
+        -khtml-opacity: 0.3;
+}
+
 /*
  * Sort arrow icon positioning

trunk/web-app/js/paginate.js

@@ -49 +49 @@
                 }
         });
+}
+
+function checkAllPaginated( input ) {
+        var paginatedTable = $(input).closest( '.paginate' );
+        var dataTable = paginatedTable.closest( '.dataTables_wrapper' );
+        var checkAll = $( '#checkAll', paginatedTable );
         
+        var oTable = paginatedTable.dataTable();
+        var inputs = $('input', oTable.fnGetNodes())
+        
+        // If any of the inputs is checked, uncheck all. Otherwise, check all
+        var check = false;
+        
+        for(var i = 0; i < inputs.length; i++ ) {
+                if( !$(inputs[i]).attr( 'checked' ) ) {
+                        check = true;
+                        break;
+                }
+        }
+        
+        inputs.each( function( idx, el ) {
+                $(el).attr( 'checked', check );
+        })
+        
+        updateCheckAll( checkAll );
+}
+
+function updateCheckAll( input ) {
+        var paginatedTable = $(input).closest( '.paginate' );
+        var dataTable = paginatedTable.closest( '.dataTables_wrapper' );
+        
+        var checkAll = $( '#checkAll', paginatedTable );
+        
+        var oTable = paginatedTable.dataTable();
+        var inputs = $('input', oTable.fnGetNodes())
+        
+        // Is none checked, are all checked or are some checked
+        var numChecked = 0
+        for(var i = 0; i < inputs.length; i++ ) {
+                if( $(inputs[i]).attr( 'checked' ) ) {
+                        numChecked++;
+                }
+        }
+        
+        checkAll.attr( 'checked', numChecked > 0 );
+        
+        if( numChecked > 0 && numChecked < inputs.length - 1 ) {
+                checkAll.addClass( 'transparent' );
+        } else {
+                checkAll.removeClass( 'transparent' );
+        }
 }