upgrade to grails 2.5

Author: mlist

application.properties

@@ -1,6 +1,6 @@
 #Grails Metadata file
-#Tue May 06 15:00:38 CEST 2014
-app.grails.version=2.2.5
+#Thu Aug 06 14:28:20 CEST 2015
+app.grails.version=2.5.0
 app.name=OpenLabFramework
-app.servlet.version=2.4
-app.version=1.3.2
+app.servlet.version=2.5
+app.version=1.4.0

grails-app/conf/BootStrap.groovy

@@ -27,7 +27,6 @@
  *
  * ############################################################################
  */
-import grails.util.GrailsUtil
 import org.openlab.barcode.BarcodeDataObject
 import org.openlab.barcode.BarcodeLabel
 import org.openlab.barcode.BarcodeSite
@@ -41,30 +40,22 @@ import org.openlab.storage.Box
 import org.openlab.storage.Compartment
 import org.openlab.storage.Freezer
 import org.openlab.storage.StorageLocation
-import org.openlab.genetracker.Recombinant
-import org.openlab.genetracker.Gene
 
 class BootStrap {
 
-    //def moduleHandlerService
-    //def applicationHandlerService
-    //def addinHandlerService
     def settingsService
-    def grailsApplication
-    def springSecurityService
     def searchableService
-    def dataSource
 
     def init = { servletContext ->
 
-        println "Database name: " + grailsApplication.config.openlab.database.name
+        println "Database name: " + grails.util.Holders.config.openlab.database.name
 
         initSettings()
         initUserbase()
         initData()
         initSecurity()
 
-        switch (GrailsUtil.environment) {
+        switch (grails.util.Environment) {
             case "development":
 
                 //initDummyData()
@@ -101,13 +92,6 @@ class BootStrap {
         if (BarcodeLabel.list().size() == 0)
             def barcodeLabel = new BarcodeLabel(name: "Label", parameters: "", barcodeType: "QR", xml: "").save()
 
-        /*
-             * Create data from original geneTracker
-             *
-            def fileName = "/home/markus/genetrackerData.xls" //"C:\\temp\\genetrackerData.xls"
-            def importer = new org.openlab.dataimport.GeneTrackerImporter(fileName)
-            importer.createAll()
-            //importer.createOnlyMasterData()*/
     }
 
     def initSearchablePlugin() {
@@ -234,6 +218,10 @@ class BootStrap {
             def requestMap = new Requestmap(url: "/appAccessToken/**", configAttribute: "ROLE_ADMIN")
             requestMap.save()
         }
+        if(!Requestmap.findByUrl("/dashboard/**")) {
+            def requestMap = new Requestmap(url: "/dashboard/**", configAttribute: "IS_AUTHENTICATED_ANONYMOUSLY")
+            requestMap.save()
+        }
     }
 
     def initDummyData() {

grails-app/conf/BuildConfig.groovy

@@ -34,84 +34,89 @@ pluginDir.eachDir {
 }
 grails.plugin.location.prototype = "prototype"
 
+grails.servlet.version = "2.5" // Change depending on target container compliance (2.5 or 3.0)
+
+forkConfig = [maxMemory: 1024, minMemory: 512, debug: false, maxPerm: 256]
+grails.project.fork = [
+        test: forkConfig, // configure settings for the test-app JVM
+        run: forkConfig, // configure settings for the run-app JVM
+        war: forkConfig, // configure settings for the run-war JVM
+        standalone: forkConfig // configure settings for the Swing console JVM
+]
+
+grails.project.target.level = 1.6
+grails.project.source.level = 1.6
 grails.project.class.dir = "target/classes"
 grails.project.test.class.dir = "target/test-classes"
 grails.project.test.reports.dir	= "target/test-reports"
 grails.project.war.file = "target/${appName}.war"
-grails.tomcat.jvmArgs= ["-Xms512m",  "-Xmx1024m", "-XX:PermSize=512m", "-XX:MaxPermSize=512m"]
+//grails.tomcat.jvmArgs= ["-Xms512m",  "-Xmx1024m", "-XX:PermSize=512m", "-XX:MaxPermSize=512m"]
+grails.project.dependency.resolver = "maven" // or ivy
+
+//grails.plugin.standalone.tomcatVersion = "7.0.52.1"
 grails.project.dependency.resolution = {
     // inherit Grails' default dependencies
     inherits( "global" ) {
         // uncomment to disable ehcache
         // excludes 'ehcache'
-        excludes "bcpg-jdk15", "bcprov-jdk15"
-
+        //excludes "bcpg-jdk15", "bcprov-jdk15"
     }
+    legacyResolve false // whether to do a secondary resolve on plugin installation, not advised and here for backwards compatibility
+
     log "warn" // log level of Ivy resolver, either 'error', 'warn', 'info', 'debug' or 'verbose'
     repositories {
-        inherits true
         grailsPlugins()
         grailsHome()
         grailsCentral()
         mavenCentral()
-        mavenRepo "http://maven.springframework.org/milestone/"
         mavenRepo "http://repo.grails.org/grails/repo/"
-
-        // uncomment the below to enable remote dependency resolution
-        // from public Maven repositories
-        //mavenLocal()
-        //mavenCentral()
-        //mavenRepo "http://snapshots.repository.codehaus.org"
-        //mavenRepo "http://repository.codehaus.org"
-        //mavenRepo "http://download.java.net/maven/2/"
-        //mavenRepo "http://repository.jboss.com/maven2/"
     }
     dependencies {
-        compile "org.grails:grails-webflow:$grailsVersion"
-        // specify dependencies here under either 'build', 'compile', 'runtime', 'test' or 'provided' scopes eg.
         runtime "hsqldb:hsqldb:1.8.0.10"
         runtime 'mysql:mysql-connector-java:5.1.16'
         runtime "net.sourceforge.jtds:jtds:1.3.1" //MS-SQL
-        compile "org.cloudfoundry:cloudfoundry-runtime:0.8.4"
         runtime 'org.bouncycastle:bcpg-jdk15on:1.50'
         runtime 'org.bouncycastle:bcprov-jdk15on:1.50'
-        runtime "org.docx4j:docx4j-ImportXHTML:3.2.2"
+        runtime ("org.docx4j:docx4j-ImportXHTML:3.2.2"){
+            excludes 'sl4j-log4j12'
+        }
         runtime "net.sf.jtidy:jtidy:r938"
-        compile "org.quartz-scheduler:quartz:1.7.3"
+        //compile "org.quartz-scheduler:quartz:1.7.3"
+        compile 'commons-beanutils:commons-beanutils:1.8.3'
     }
 
     plugins{
-        runtime ":hibernate:$grailsVersion"
-        runtime ":jquery:1.7.1"
-        runtime ":jquery-ui:1.8.24"
-        runtime ":resources:1.1.6"
-        //runtime ":database-migration:1.3.2"
-        build ":tomcat:$grailsVersion"
+        build ':tomcat:7.0.54'
+        runtime ':hibernate:3.6.10.18'
+        compile ":jquery:1.11.1"
+        compile ":jquery-ui:1.10.4"
+        runtime ":resources:1.2.14"
+        //runtime ":database-migration:1.4.0"
+        compile ':scaffolding:2.1.2'
 
-        compile ":searchable:0.6.4"
-        compile(":webflow:2.0.0") {
-            exclude 'grails-webflow'
-        }
+        compile ":searchable:0.6.9"
+        compile ":webflow:2.1.0"
 
         compile ":jquery-mobile:1.1.0.5"
-        compile ":excel-import:1.0.0"
-        compile ":spring-security-core:1.2.7.3"
+        //compile ":excel-import:1.0.0"
+        compile ":spring-security-core:1.2.7.4"
         //compile ":spring-security-acl:1.1.1"
         compile ":spring-security-cas:1.0.5"
         compile ':webxml:1.4.1'
-        compile ":spring-mobile:0.5.1"
-        compile ":standalone:1.2.3"
+        compile ":spring-mobile:1.1.3"
+        compile ":standalone:1.3"
+        compile ":quartz:1.0.2"
 
         compile ":yui:2.8.2.1"
         compile (":grails-ui:1.2.3") {
             excludes 'yui'
         }
-        compile (":richui:0.8"){
-            excludes 'yui'
-        }
+
         compile ":ajax-uploader:1.1"
         compile ":bubbling:2.1.4"
-        compile ":export:1.5"
-        compile ":joda-time:1.4"
+        compile (":export:1.6"){
+            excludes 'bcmail-jdk14', 'bcprov-jdk14', 'bctsp-jdk14'
+        }
+        compile ":joda-time:1.5"
     }
 }

grails-app/conf/Config.groovy

@@ -1,5 +1,3 @@
-import org.cloudfoundry.runtime.env.CloudEnvironment
-import org.cloudfoundry.runtime.env.RedisServiceInfo
 import org.apache.log4j.DailyRollingFileAppender
 import org.apache.log4j.Priority
 import org.apache.log4j.ConsoleAppender
@@ -44,7 +42,7 @@ import org.apache.log4j.ConsoleAppender
 //    grails.config.locations << "file:" + System.properties["${appName}.config.location"]
 // }
 
-grails.tomcat.jvmArgs= ["-Xms256m",  "-Xmx1024m", "-XX:PermSize=512m", "-XX:MaxPermSize=512m"]
+grails.tomcat.jvmArgs= ["-Xms256m",  "-Xmx1024m"]
 
 def olfLogLevel = "ERROR"
 def olfLogPattern = "%d{yyyy-MM-dd/HH:mm:ss.SSS} [%t] %x %-5p %c{2} - %m%n"
@@ -77,7 +75,7 @@ else {
 }
 
 /* */
-cgrails.mime.file.extensions = true // enables the parsing of file extensions from URLs into the request format
+grails.mime.file.extensions = true // enables the parsing of file extensions from URLs into the request format
 grails.mime.use.accept.header = false
 grails.mime.types = [html: ['text/html', 'application/xhtml+xml'],
         xml: ['text/xml', 'application/xml'],
@@ -192,6 +190,11 @@ grails.plugins.springsecurity.securityConfigType = 'Requestmap'
 
 //resource plugin
 //grails.resources.debug=true
+//grails.databinding.useSpringBinder = true
+
+// What URL patterns should be processed by the resources plugin
+grails.resources.adhoc.patterns = ['/images/*', '/css/*', '/js/*', '/plugins/*']
+grails.resources.adhoc.includes = ['/images/**', '/css/**', '/js/**', '/plugins/**']
 
 grails.resources.modules = {
     labelPrinter{
@@ -250,4 +253,7 @@ grails.views.javascript.library="prototype"
 //make sure that the restful controller is only called via secure http since the access token can easily be sniffed out otherwise
 grails.plugins.springsecurity.secureChannel.definition = [
         '/restful/**' : 'REQUIRES_SECURE_CHANNEL'
-]
+]
+
+//restore default data binding behaviour we knew from grails 2.2, i.e. empty strings are not converted to NULL anymore
+grails.databinding.convertEmptyStringsToNull = false

grails-app/conf/DataSource.groovy

@@ -1,6 +1,3 @@
-import org.cloudfoundry.runtime.env.CloudEnvironment
-import org.cloudfoundry.runtime.env.RdbmsServiceInfo
-
 /*
 * Copyright (C) 2013
 * Center for Excellence in Nanomedicine (NanoCAN)
@@ -41,7 +38,7 @@ hibernate {
 }
 
 // set per-environment serverURL stem for creating absolute links
-def cloudEnv = new CloudEnvironment()
+// def cloudEnv = new CloudEnvironment()
 
 environments {
     production {
@@ -51,7 +48,7 @@ environments {
     test {
         grails.serverURL = "http://localhost:8080/${appName}"
     }
-    cloud {
+    /*cloud {
         dataSource {
 
             dbCreate = "update"
@@ -84,18 +81,18 @@ environments {
         }
         openlab.database.name = 'cloud mySQL instance'
         grails.serverURL = "http://www.openlabframework.cfapps.io"
-    }
+    } */
     standalone {
         dataSource {
             pooled = true
-            driverClassName = "org.h2.Driver"
+            driverClassName = 'org.hsqldb.jdbcDriver'
+            url = 'jdbc:hsqldb:file:standaloneDB'
             username = "sa"
             password = ""
             dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
-            url = "jdbc:h2:file:olfDB;MVCC=TRUE"
         }
         openlab.upload.dir = "upload/"
-        openlab.database.name = 'H2 SQL instance'
+        openlab.database.name = 'HSQLDB SQL instance'
     }
 
 }

grails-app/controllers/org/openlab/content/DashboardController.groovy

@@ -44,8 +44,13 @@ class DashboardController {
             return
         }
 
-		[:]
-	}
+        if(!springSecurityService?.loggedIn){
+            redirect(action: "auth", controller: "login", params: [bodyOnly:false])
+            return
+        }
+
+        [:]
+    }
 
 	def dashboard = {
         if(!springSecurityService?.loggedIn){

grails-app/controllers/org/openlab/datasource/DataSourceController.groovy

@@ -36,23 +36,17 @@ package org.openlab.datasource
  */
 class DataSourceController {
 
-    def dataSource
+    def grailsApplication
 
     def index = {
         redirect action: show
     }
 
     def show =
         {
-            if (dataSource instanceof org.springframework.jdbc.datasource.TransactionAwareDataSourceProxy) {
-                def baseDataSource = dataSource.targetDataSource
-                [url: baseDataSource.url, driverClassName: baseDataSource.driverClassName, username: baseDataSource.username]
-            }
-
-            else {
-                [url: dataSource.jdbcUrl, driverClassName: dataSource.driverClass, username: dataSource.user]
-            }
+            def ds = grailsApplication.config.dataSource
 
+            [url: ds.url, driverClassName: ds.driverClassName, username: ds.username]
         }