Changeset 3 for trunk/grails-app/controllers/nl

Timestamp:

Jan 12, 2011, 9:45:08 PM (10 years ago)

Author:

robert@…

Message:

Externalized configuration; improved assay view (detail views of runs and samples); implemented uploading and parsing of FASTA and QUAL files

Location:

trunk

Files:

• . (modified) (1 prop)
• grails-app/controllers/nl/tno/metagenomics/AssayController.groovy (modified) (2 diffs)
• grails-app/controllers/nl/tno/metagenomics/FastaController.groovy (added)
• grails-app/controllers/nl/tno/metagenomics/StudyController.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/auth/LogoutController.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/integration/SynchronizeController.groovy (added)

trunk

@@ -4 +4 @@
 .classpath
 .project
+fileuploads

@@ -4 +4 @@
 .classpath
 .project
+fileuploads

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

@@ -9 +9 @@
         def fileService
         def excelService
-        def fastaService
 
         // Fields to be edited using excel file and manually
@@ -494 +493 @@
         }
 
-        /**************************************************************************
-         *
-         * Methods for handling uploaded sequence and quality files
-         *
-         *************************************************************************/
-
-        /**
-         * Processes uploaded files and tries to combine them with samples
-         */
-        def process = {
-                // load study with id specified by param.id
-                def assay = Assay.get(params.id as Long)
-
-                if (!assay) {
-                        flash.message = "No assay found with id: $params.id"
-                        redirect('action': 'errorPage')
-                        return
-                }
-
-                // Check whether files are given
-                def names = params.sequencefiles
-
-                if( !names ) {
-                        flash.message = "No files uploaded for processing"
-                        redirect('action': 'show', 'id': params.id)
-                        return
-                }
-
-                // If only 1 file is uploaded, it is given as String
-                ArrayList filenames = []
-                if( names instanceof String )
-                        filenames << names
-                else
-                        names.each { filenames << it }
-
-                /* Parses uploaded files, discards files we can not handle
-                 * 
-                 * [
-                 *              success: [
-                 *                      [filename: 'abc.fasta', type: FASTA, numSequences: 190]
-                 *                      [filename: 'cde.fasta', type: FASTA, numSequences: 140]
-                 *                      [filename: 'abc.qual', type: QUAL, numSequences: 190, avgQuality: 38]
-                 *                      [filename: 'cde.qual', type: QUAL, numSequences: 140, avgQuality: 29]
-                 *              ],
-                 *              failure: [
-                 *                      [filename: 'testing.xls', message: 'Type not recognized']
-                 *              ]
-                 * ]
-                 */
-                def parsedFiles = fastaService.parseFiles( filenames );
-
-                // Match files with samples in the database
-                def matchedFiles = fastaService.matchFiles( parsedFiles.success, assay.assaySamples );
-
-                // Sort files on filename
-                matchedFiles.sort { a,b -> a.fasta?.originalfilename <=> b.fasta?.originalfilename }
-
-                // Saved file matches in session to use them later on
-                session.processedFiles = [ parsed: parsedFiles, matched: matchedFiles ];
-
-                [assay: assay, parsedFiles: parsedFiles, matchedFiles: matchedFiles, selectedRun: params.selectedRun ]
-        }
-
-        /**
-         * Saves processed files to the database, based on the selections made by the user
-         */
-        def saveProcessedFiles = {
-                // load study with id specified by param.id
-                def assay = Assay.get(params.id as Long)
-
-                if (!assay) {
-                        flash.message = "No assay found with id: $params.id"
-                        redirect('action': 'errorPage')
-                        return
-                }
-
-                // Check whether files are given
-                def files = params.file
-
-                if( !files ) {
-                        flash.message = "No files were selected."
-                        redirect('action': 'show', 'id': params.id)
-                        return
-                }
-
-                File permanentDir = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir )
-                int numSuccesful = 0;
-                def errors = [];
-                
-                // Loop through all files Those are the numeric elements in the 'files' array
-                def digitRE = ~/^\d+$/;
-                files.findAll { it.key.matches( digitRE ) }.each { file ->
-                        def filevalue = file.value;
-                        
-                        // Check if the file is selected
-                        if( filevalue.include == "on" ) {
-                                if( fileService.fileExists( filevalue.fasta ) ) {
-                                        try {
-                                                def permanent = fastaService.savePermanent( filevalue.fasta, filevalue.qual, session.processedFiles );
-                                                
-                                                // Save the data into the database
-                                                SequenceData sd = new SequenceData();
-                                                
-                                                sd.sequenceFile = permanent.fasta
-                                                sd.qualityFile = permanent.qual
-                                                sd.numSequences = permanent.numSequences
-                                                sd.averageQuality = permanent.avgQuality
-                                                
-                                                // Couple the data to the right run and sample
-                                                def run = Run.get( filevalue.run )
-                                                if( run )
-                                                        run.addToSequenceData( sd );
-                                                        
-                                                def sample = AssaySample.get( filevalue.assaySample );
-                                                if( sample )
-                                                        sample.addToSequenceData( sd );
-                                                
-                                                if( !sd.validate() ) {
-                                                        errors << "an error occurred while saving " + filevalue.fasta + ": validation of SequenceData failed.";
-                                                } else {
-                                                        sd.save(flush:true);
-                                                }
-                                                
-                                                numSuccesful++;
-                                        } catch( Exception e ) {
-                                                errors << "an error occurred while saving " + filevalue.fasta + ": " + e.getMessage()
-                                        }
-                                }
-                        } else {
-                                // File doesn't need to be included in the system. Delete it also from disk
-                                fileService.delete( filevalue.fasta );
-                        }
-                }
-
-                // Return a message to the user
-                if( numSuccesful == 0 ) {
-                        flash.error = "None of the files were imported, because "
-                        
-                        if( errors.size() > 0 ) {
-                                errors.each {
-                                        flash.error += "<br />- " + it
-                                }
-                        } else {
-                                flash.error = "none of the files were selected for import."
-                        }
-                } else {
-                        flash.message = numSuccesful + " files have been added to the system. "
-
-                        if( errors.size() > 0 ) {
-                                flash.error += errors.size() + " errors occurred during import: "
-                                errors.each {
-                                        flash.error += "<br />- " + it
-                                }
-                        }
-                }
-                
-                redirect( action: "show", id: params.id )
-        }
-
 }

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

@@ -18 +18 @@
                 // Filter studies for the ones the user is allowed to see
                 def studies = Study.findAll();
-                [studies: studies.findAll { it.canRead( session.user ) }, gscfAddUrl: gscfService.urlAddStudy() ] 
+                [studies: studies.findAll { it.canRead( session.user ) }, gscfAddUrl: gscfService.urlAddStudy(), lastSynchronized: synchronizationService.lastFullSynchronization ] 
         }
+
 }

trunk/grails-app/controllers/nl/tno/metagenomics/auth/LogoutController.groovy

@@ -14 +14 @@
                 log.info("Session.sessionToken is now ${session.sessionToken}")
                 
-                //logout on GSCF side, and do not redirect back to metagenomics (&spring-security-redirect=${ConfigurationHolder.config.metagenomics.baseURL}/study/list)
+                //logout on GSCF side, and do not redirect back to metagenomics (&spring-security-redirect=${ConfigurationHolder.config.grails.serverURL}/study/list)
                 def redirectURL = "${ConfigurationHolder.config.gscf.baseURL}/logout/remote?consumer=${ConfigurationHolder.config.metagenomics.ConsumerID}&token=${session.sessionToken}"
                 log.info("Redirecting to: ${redirectURL}")

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

@@ -339 +339 @@
                         }
                         
-                        def url = [ 'url' : ConfigurationHolder.config.metagenomics.baseURL + '/assay/show/' + assay.id.toString() ]
+                        def url = [ 'url' : ConfigurationHolder.config.grails.serverURL + '/assay/show/' + assay.id.toString() ]
 
                         render url as JSON
                 }
-        }
+        }.metagenomics.baseURL
         
         /***************************************************/

@@ -4 +4 @@
 .classpath
 .project
+fileuploads