Changeset 2030

Timestamp:

Sep 22, 2011, 5:10:17 PM (11 years ago)

Author:

robert@…

Message:

Added galaxy export functionality in assayController

Location:

trunk/grails-app

Files:

• controllers/dbnp/studycapturing/AssayController.groovy (modified) (1 diff)
• views/assay/galaxyExport.gsp (added)

trunk/grails-app/controllers/dbnp/studycapturing/AssayController.groovy

@@ -211 +211 @@
                 handleError() {
                         render(view: 'errorPage')
+                }
+        }
+        
+        /**
+         * This method is called when a user wants to fetch data from GSCF
+         */
+        def galaxyExport = {
+                def galaxy_url = params.get( "GALAXY_URL" );
+                def tool_id = params.get( "tool_id" );
+                
+                // Without galaxy url, we can't do anything
+                if( !galaxy_url || !tool_id ) {
+                        redirect( action: "assayExport" );
+                }
+                
+                def user            = authenticationService.getLoggedInUser()
+                def userStudies    = Study.giveReadableStudies(user)
+                
+                [ galaxy_url: galaxy_url, tool_id: tool_id, userStudies: userStudies ]
+        }
+        
+        def sendToGalaxy = {
+                // Generate the url to redirect the user to
+                def galaxy_url = params.get( "GALAXY_URL" );
+                def tool_id = params.get( "tool_id" );
+                
+                // Without galaxy url, we can't do anything
+                if( !galaxy_url || !tool_id  ) {
+                        redirect( action: "assayExport" );
+                }
+                
+                def assayId = params.long( "assayId" );
+                def assay = assayId ? Assay.get( assayId ) : null;
+                
+                // If no assay is given, return to galaxyExport screen
+                if( !assay ) {
+                        redirect( action: "galaxyExport", params: [ "GALAXY_URL": galaxy_url ] );
+                }
+                
+                // create a random session token that will be used to allow to module to
+                // sync with gscf prior to presenting the measurement data
+                def sessionToken = UUID.randomUUID().toString()
+                def consumer = "galaxy";
+
+                // put the session token to work
+                authenticationService.logInRemotely( consumer, sessionToken, authenticationService.getLoggedInUser() )
+                
+                // Create a url where the data can be fetched
+                def fetchUrl = g.createLink( absolute: true, controller: "assay", action: "fetchGalaxyData", params: [ assayToken: assay.assayUUID, sessionToken: sessionToken ] );
+                
+                // Generate url to redirect the user to
+                def url = galaxy_url + "?tool_id=" + URLEncoder.encode( tool_id.toString(), "UTF-8" ) + "&URL=" + URLEncoder.encode( fetchUrl.toString(), "UTF-8" ) 
+                
+                log.trace "Redirecting galaxy user back to " + url;
+                
+                redirect( url: url );
+        }
+        
+        // This method is accessible for each user. However, he should return with a valid
+        // session token
+        @Secured(['true'])
+        def fetchGalaxyData = {
+                // Check accessibility
+                def consumer = "galaxy";
+                def user = authenticationService.getRemotelyLoggedInUser( consumer, params.sessionToken );
+                if( !user ) {
+                        response.status = 401;
+                        render "You must be logged in";
+                        return
+                }
+                
+                // Invalidate session token
+                authenticationService.logOffRemotely( consumer, params.sessionToken );
+                
+                // retrieve assay
+                def assay = Assay.findByAssayUUID( params.assayToken );
+                
+                if( !assay ) {
+                        response.status = 404;
+                        render "No assay found";
+                        return
+                }
+                
+                // Return assay data
+                def fieldMap = assayService.collectAssayTemplateFields( assay )
+                def measurementTokens = fieldMap.remove('Module Measurement Data');
+                def assayData = assayService.collectAssayData(assay, fieldMap, measurementTokens)
+                def rowData            = assayService.convertColumnToRowStructure(assayData)
+                                
+                def outputDelimiter = '\t'
+                def outputFileExtension = 'txt'
+
+                def filename = "export.$outputFileExtension"
+                response.setHeader("Content-disposition", "attachment;filename=\"${filename}\"")
+                response.setContentType("application/octet-stream")
+                try {
+                        assayService.exportRowWiseDataToCSVFile(rowData, response.outputStream, outputDelimiter, java.util.Locale.US)
+                } catch (Exception e) {
+                        flash.errorMessage = e.message
+                        redirect action: 'errorPage'
                 }
         }