- A lot of plugin related improvments

- Fixed a bug in study data tables

grails-app/conf/BuildConfig.groovy

@@ -30,22 +30,11 @@ grails.project.dependency.resolution = {
     log "warn" // log level of Ivy resolver, either 'error', 'warn', 'info', 'debug' or 'verbose'
     legacyResolve true
     repositories {
-
-        grailsPlugins()
         grailsHome()
-        mavenLocal()
+        grailsPlugins()
         grailsCentral()
         mavenCentral()
-
-        // grails 1.3.9 does not seem to properly inherit maven repo's from plugins
-        // so explicitely put mavenrepos in here. When upgraded to Grails 2.x this can
-        // probably be removed
-        mavenRepo "http://repo.grails.org/grails/plugins/"
-        mavenRepo "http://nexus.dbnp.org/content/repositories/releases"
-        //mavenRepo "http://repository.springsource.com/maven/bundles/release"
-        //mavenRepo "http://repository.springsource.com/maven/bundles/external"
-        //mavenRepo "http://repository.springsource.com/maven/libraries/release"
-        //mavenRepo "http://repository.springsource.com/maven/libraries/external"
+        mavenLocal()
 
         // Repository for ISATAB tools
         //mavenRepo "http://frog.oerc.ox.ac.uk:8080/nexus-2.1.2/content/repositories/releases"
@@ -80,36 +69,34 @@ grails.project.dependency.resolution = {
         compile('org.codehaus.groovy.modules.http-builder:http-builder:0.5.0') { excludes "commons-logging", "xml-apis", "groovy" }
     }
     plugins {
-        // plugins for the build system only
-        build ":tomcat:7.0.55.3"
-
-        compile(
-                ":hibernate4:4.3.10",
+        // Plugins for the build system only
+        build ":tomcat:7.0.70"
 
-                ":jquery:1.11.1",
-                ':jquery-ui:1.10.4',
-
-                ":resources:1.2.14",
-                ":spring-security-core:2.0.0",
-
-                ':matrix-importer:0.2.5.0',
-                ':dbxp-module-base:0.6.2.0',
-
-                ":famfamfam:1.0.1",
-                ":mail:1.0.7",
-                ":quartz:1.0.2",
-                ":ajaxflow:0.2.4",
-                ":webflow:2.1.0",
-                ":scaffolding:2.1.2"
-        )
+        // Plugins needed at runtime but not for compilation
+        runtime ":hibernate4:4.3.10"
+        runtime ":jquery:1.11.1"
+        runtime ":resources:1.2.14"
 
+        // Plugins needed for compilation
+        compile ":spring-security-core:2.0.0"
+        compile ':jquery-ui:1.10.4'
+        compile ":mail:1.0.7"
+        compile ":famfamfam:1.0.1"
+        compile ":quartz:1.0.2"
+        compile ":ajaxflow:0.2.4"
+        compile ":webflow:2.1.0"
+        compile ":scaffolding:2.1.2"
         compile ":yui-war-minify:1.5"
 
         if (System.getProperty("grails.env") == "development") {
             // development mode only Plugins
             compile(":console:1.5.4")
         }
 
+        // Now included as local plugins
+//        compile ":matrix-importer:0.2.5.0"
+//        compile ":dbxp-module-base:0.6.2.0"
+
         // add { transative = false } to ignore dependency transition
     }
 }
@@ -118,5 +105,5 @@ grails.plugin.location.'gdt' = './local-plugins/GDT'
 grails.plugin.location.'dbxpSam' = './local-plugins/SAM'
 grails.plugin.location.'dbxp-base' = './local-plugins/dbxpBase'
 
-//grails.plugin.location.'dbxpModuleBase' = '../dbxpModuleBase'
-//grails.plugin.location.'matrix-importer' = '../matrixImporter'
+grails.plugin.location.'dbxpModuleBase' = './local-plugins/dbxpModuleBase'
+grails.plugin.location.'matrix-importer' = './local-plugins/matrixImporter'

grails-app/conf/DataSource.groovy

@@ -7,7 +7,8 @@ dataSource {
 hibernate {
     cache.use_second_level_cache = true
     cache.use_query_cache = false
-    cache.region.factory_class = 'net.sf.ehcache.hibernate.EhCacheRegionFactory'
+//    cache.region.factory_class = 'net.sf.ehcache.hibernate.SingletonEhCacheRegionFactory' // Hibernate 3
+    cache.region.factory_class = 'org.hibernate.cache.ehcache.EhCacheRegionFactory' // Hibernate 4
 }
 // environment specific settings
 environments {

grails-app/services/dbnp/studycapturing/StudyEditService.groovy

@@ -26,6 +26,7 @@ class StudyEditService {
 	 		int			ids				Total list of filtered ids
 	 */
     def getEntitiesForTemplate( searchParams, study, template ) {
+
 		def query = generateHQL( searchParams, study, template )
 
 		// Also count the total number of results in the dataset
@@ -103,22 +104,26 @@ class StudyEditService {
 	 */
 	def generateOutput( query, searchParams, entity ) {
 		def output = [:]
-		
+
 		// First select the number of results
-		def filteredIds = entity.executeQuery( "SELECT DISTINCT s.id FROM " + query.from + " WHERE " + query.where, query.params );
+		def filteredIds = entity.executeQuery( "SELECT DISTINCT s.id FROM " + query.from + " WHERE " + query.where, query.params )
 		output.totalFiltered = filteredIds.size()
 		output.ids = filteredIds
-
-		// Now find the results themselves
-		def hql = "SELECT " + query.select + " FROM " + query.from + " WHERE " + query.where + " " + ( query.order ? " ORDER BY " + query.order : "" )
-		output.entities = entity.executeQuery( hql, query.params, [ max: searchParams.max, offset: searchParams.offset ] )
 
-                if( query.chooseFirst ) {
-                    output.entities = output.entities.collect { it[0] }
-                }
+		// Now if filteredIds is not empty find the results themselves by that list
+		if ( filteredIds.size() != 0 ) {
+			def hql = "SELECT " + query.select + " FROM " + entity.simpleName + " " + query.select + " WHERE id IN :ids" + ( query.order ? " ORDER BY " + query.order : "" )
+			output.entities = entity.executeQuery( hql, [ ids: filteredIds ], [ max: searchParams.max, offset: searchParams.offset ] )
+		}
+		else {
+			output.entities = []
+		}
+
+		if( query.chooseFirst ) {
+			output.entities = output.entities.collect { it[0] }
+		}
 
 		output
-
 	}
 
 	/**
@@ -290,7 +295,7 @@ class StudyEditService {
 
 
 		// Create an HQL query as it gives us the most flexibility in searching and ordering
-		def from = " Sample s "
+		def from = " Sample s"
 		def joins = []
 		def whereClause = []
 		def hqlParams = [ study: study ]

local-plugins/GDT/grails-app/conf/BuildConfig.groovy

@@ -27,22 +27,17 @@ grails.project.dependency.resolution = {
     }
 
     plugins {
-        build(  ":tomcat:7.0.55",
-                //Temporary static version of Rest Client Builder due to compile error
-                ":rest-client-builder:1.0.3"
-        ) {
-            // plugin only plugin, should not be transitive to the application
-            export = false
-        }
+        // Plugins for the build system only
+        build ":tomcat:7.0.70"
+        build ":rest-client-builder:1.0.3"
 
-        compile(":hibernate4:4.3.6.1",
-		":jquery:1.8.3",
-		":webflow:2.0.8.1",
-        ":ajaxflow:0.2.4",
-                ":rest:0.8",
-                ":webflow:2.1.0"
-        ) {
-            export = false
-        }
+        // Plugins needed at runtime but not for compilation
+        runtime ":hibernate4:4.3.10"
+        runtime ":jquery:1.11.1"
+
+        // Plugins needed for compilation
+        compile ":ajaxflow:0.2.4"
+        compile ":webflow:2.1.0"
+        compile ":rest:0.8"
     }
 }

local-plugins/SAM/grails-app/conf/BuildConfig.groovy

@@ -30,32 +30,38 @@ grails.project.dependency.resolution = {
     }
     plugins {
 
-        build(  ":tomcat:7.0.55",
-                ":release:2.2.1",
-                //Temporary static version of Rest Client Builder due to compile error
-                ":rest-client-builder:1.0.3"
-        ) {
-            // plugin only plugin, should not be transitive to the application
-            export = false
-        }
+        // Plugins for the build system only
+        build ":tomcat:7.0.70"
+        build ":release:2.2.1"
+        //Temporary static version of Rest Client Builder due to compile error
+        build ":rest-client-builder:1.0.3"
+
+        // Plugins needed at runtime but not for compilation
+        runtime ":hibernate4:4.3.10"
+        runtime ":jquery:1.11.1"
+        runtime ":resources:1.2.14"
 
-        compile(
-            ":hibernate4:4.3.6.1",
-            ':famfamfam:1.0.1',
-            ':matrix-importer:0.2.5.0',
-            ':ajaxflow:latest.integration',
-            ':resources:latest.integration',
-            ':jquery:latest.integration',
-            ':jquery-datatables:1.7.5',
-            ':jquery-ui:1.8.15') {
-            export = false
+        // Plugins needed for compilation
+        compile ':jquery-ui:1.10.4'
+        compile ":famfamfam:1.0.1"
+        compile ":ajaxflow:0.2.4"
+        compile ":jquery-datatables:1.7.5"
+
+        if (System.getProperty("grails.env") == "development") {
+            // development mode only Plugins
+            compile(":console:1.5.4")
         }
+
+        // Now included as local plugins
+//        compile ":matrix-importer:0.2.5.0"
+//        compile ":dbxp-module-base:0.6.2.0"
     }
 }
 
-//grails.plugin.location.'dbxpModuleBase' = '../dbxpModuleBase'
-//grails.plugin.location.'matrixImporter' = '../../../matrixImporter'
 grails.plugin.location.'gdt' = '../GDT'
 grails.plugin.location.'dbxpBase' = '../dbxpBase'
 
+//grails.plugin.location.'dbxpModuleBase' = '../dbxpModuleBase'
+grails.plugin.location.'matrixImporter' = '../matrixImporter'
+
 //grails.server.port.http = "8182"  // The modern way of setting the server port

local-plugins/dbxpModuleBase/.gitignore

@@ -0,0 +1,19 @@
+.project
+.classpath
+*.iws
+ws
+*Db.properties
+*Db.script
+.settings
+eclipse
+stacktrace.log
+target
+/plugins
+/web-app/plugins
+/web-app/WEB-INF/classes
+.idea
+*.iml
+/target-eclipse/*
+grails-dbxp-module-base-*.zip
+grails-dbxp-module-base-*.zip.sha1
+plugin.xml

local-plugins/dbxpModuleBase/DbxpModuleBaseGrailsPlugin.groovy

@@ -0,0 +1,39 @@
+class DbxpModuleBaseGrailsPlugin {
+    // the plugin version
+    def version = "0.6.2.0"
+    // the version or versions of Grails the plugin is designed for
+    def grailsVersion = "1.3.7 > *"
+
+    // the other plugins this plugin depends on are declared in BuildConfig.groovy
+	def dependsOn		= [jquery: "1.7.1 > *", jqueryDatatables: "1.7.5 > *", jqueryUi: "1.7.1 > *" ]
+	// resources that are excluded from plugin packaging
+    def pluginExcludes = [
+            "grails-app/views/error.gsp",
+            "grails-app/views/index.gsp",
+            "grails-app/controllers/test"
+    ]
+
+	def author			= "Robert Horlings"
+	def authorEmail 	= "robert@isdat.nl"
+	def title			= "Base for Phenotype Database modules that communicate with GSCF"
+	def description 	= '''\\
+dbxpModuleBase is a Grails plugin that provides basic functionality to create a dbXP module that contains molecular
+data for studies defined in GSCF, the Generic Study Capture Framework.
+dbxpModuleBase is part of the Phenotype Database software ecosystem.
+
+As of version 0.6.2.0 this module is ready for grails 2.4.0 and higher
+'''
+	def documentation   = "https://github.com/thehyve/dbxpModuleBase/blob/master/README.md"
+	def license         = "APACHE"
+	def issueManagement = [system: "github", url: "https://github.com/thehyve/dbxpModuleBase/issues"]
+	def scm             = [url: "https://github.com/thehyve/dbxpModuleBase"]
+	def organization    = [name: "Phenotype Foundatiom", url: "http://phenotypefoundation.org/" ]
+	def developers      = [
+			[ name: "Kees van Bochove", email: "kees@thehyve.nl" ],
+			[ name: "Robert Horlings", email: "robert@isdat.nl" ],
+			[ name: "Siemen Sikkema", email: "s.h.sikkema@gmail.com" ],
+			[ name: "Jeroen Wesbeek", email: "work@osx.eu" ],
+			[ name: "Taco Steemers", email: "taco@thehyve.nl" ],
+			[ name: "Tjeerd van Dijk", email: "tjeerd@thehyve.nl" ]
+	]
+}

local-plugins/dbxpModuleBase/README.md

@@ -0,0 +1,28 @@
+dbxpModuleBase
+====
+
+A Grails plugin that can serve as the basis for a dbXP module.
+dbxpModuleBase provides basic module services such as synchronisation of a proxy Study-Sample-Assay cache with GSCF.
+
+## How to publish changes
+To create a new version of dbxpModuleBase and publish it on nexus.nmcdsp.org:
+
+### Make sure that ~/.grails/settings.groovy contains username and password for Nexus:
+```
+~/.grails $ cat settings.groovy
+grails.project.dependency.distribution = {
+ remoteRepository(id:"pluginReleases", url:"http://nexus.nmcdsp.org/content/repositories/releases/") {
+     authentication username: "admin", password: "** ask Jeroen or Kees **"
+ }
+}
+```
+
+### Make sure maven-publisher plugin is installed
+```
+grails install-plugin maven-publisher
+```
+
+### Deploy the upgrade
+```
+grails maven-deploy --repository=pluginReleases
+```

local-plugins/dbxpModuleBase/application.properties

@@ -0,0 +1,4 @@
+#Grails Metadata file
+#Thu Jul 19 13:22:53 CEST 2012
+app.grails.version=2.3.9
+app.name=dbxpModuleBase

local-plugins/dbxpModuleBase/grails-app/conf/BuildConfig.groovy

@@ -0,0 +1,57 @@
+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/${appName}-${appVersion}.war"
+grails.project.dependency.resolution = {
+    // inherit Grails' default dependencies
+    inherits("global") {
+        // uncomment to disable ehcache
+        // excludes 'ehcache'
+    }
+    log "warn" // log level of Ivy resolver, either 'error', 'warn', 'info', 'debug' or 'verbose'
+    repositories {
+        grailsPlugins()
+        grailsHome()
+        grailsCentral()
+
+        mavenRepo "http://nexus.nmcdsp.org/content/repositories/releases"
+//		mavenRepo "http://nexus.nmcdsp.org/content/repositories/snapshots"
+
+        // 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/"
+    }
+	plugins {
+		build(		":release:latest.integration",
+				":rest-client-builder:latest.integration"
+		) {
+			// plugin only plugin, should not be transitive to the application
+			export = false
+		}
+
+		compile(
+			':resources:latest.integration'
+		) {
+			// no need to export the plugins to application (dependencies are declared in plugin descriptor file)
+			export = false
+		}
+        compile(
+                ':jquery:latest.integration',
+                ':jquery-datatables:1.7.5',
+                ':jquery-ui:latest.integration',
+                ':famfamfam:1.0.1',
+       ) {
+            export = true
+        }
+	}
+    dependencies {
+        // specify dependencies here under either 'build', 'compile', 'runtime', 'test' or 'provided' scopes eg.
+
+        // runtime 'mysql:mysql-connector-java:5.1.13'
+    }
+}