Merge branch 'master' into fix-integration-tests

.travis.yml

@@ -1,31 +1,61 @@
 language: groovy
-sudo: false
 
 jdk:
-    - oraclejdk8
+  - oraclejdk8
+php:
+  - 5.6
+env:
+  - TERM=dumb; DIR=transmart-core-db-tests; PREPARE=assemble; TEST=check
+  - TERM=dumb; DIR=transmart-data; PREINSTALL="createVars setupPostgres"; INSTALL=downloadTransmartETL; TEST=dataloadingTest
+
+addons:
+  postgres: 9.4
 
 before_cache:
   - rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
+  - rm -rf $HOME/.gradle/caches/*/plugin-resolution/
 cache:
   directories:
-    - $HOME/.gradle/caches/
-    - $HOME/.gradle/wrapper/
-    - $HOME/.m2/
+    - $HOME/.gradle/caches
+    - $HOME/.gradle/wrapper
+    - $HOME/.m2
+    - $HOME/pg
+
+before_install:
+  - gradle --version
+  - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv 3375DA21
+  - echo deb http://apt.thehyve.net/internal/ trusty main | sudo tee /etc/apt/sources.list.d/hyve_internal.list
+  - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv E5267A6C
+  - echo deb http://ppa.launchpad.net/ondrej/php5/ubuntu precise main  | sudo tee /etc/apt/sources.list.d/ondrej_php5.list
+  - sudo apt-get -qq update
+  - apt-cache search php
+  - sudo apt-get install -y tk-dev php5-cli php5-json
+  - php --version
+  - echo $DIR; cd $DIR
+  - PWD=`pwd`
+  - echo $PWD
+  - ([ -z "$PREINSTALL" ] && echo "Skipping preinstall.") || (echo $PREINSTALL; sudo -i -- sh -c "cd $PWD; gradle $PREINSTALL")
+  - cd -
+
+install:
+  - echo $DIR; cd $DIR
+  - ([ -z "$INSTALL" ] && echo "Skipping install.") || (echo $INSTALL; gradle $INSTALL)
+  - cd -
 
 before_script:
-  - cd transmart-core-db-tests
-  - ./gradlew --console=plain assemble
+  - echo $DIR; cd $DIR
+  - ([ -z "$PREPARE" ] && echo "Skipping prepare.") || (echo $PREPARE; gradle $PREPARE)
   - cd -
 
 script:
-  - cd transmart-core-db-tests
-  - ./gradlew --console=plain --stacktrace check
+  - echo $DIR; cd $DIR
+  - ([ -z "$TEST" ] && echo "Skipping test.") || (echo $TEST; gradle --stacktrace $TEST)
   - cd -
 
 notifications:
   hipchat:
     rooms:
       secure: "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"
     on_success: change
-    on_failure: always
+    on_failure: change
 

Rmodules/build.gradle

@@ -75,7 +75,8 @@ dependencies {
     testCompile 'org.gmock:gmock:0.8.3'
     testCompile 'org.hamcrest:hamcrest-library:1.3'
     testCompile 'org.hamcrest:hamcrest-core:1.3'
-    compile 'quartz:quartz:1.5.1-atlassian-2'
+
+    compile 'org.grails.plugins:quartz:2.0.1'
     // https://mvnrepository.com/artifact/org.apache.commons/commons-io
     compile group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
     // https://mvnrepository.com/artifact/org.xhtmlrenderer/flying-saucer-pdf

Rmodules/grails-app/controllers/com/recomdata/transmart/data/association/DataAssociationController.groovy

@@ -40,8 +40,8 @@ class DataAssociationController {
 
         // list of required css
         def styles = [
-                servletContext.contextPath+pluginContextPath+'/css/rmodules.css',
-                servletContext.contextPath+pluginContextPath+'/css/jquery.qtip.min.css']
+                servletContext.contextPath+pluginContextPath+'/assets/rmodules.css',
+                servletContext.contextPath+pluginContextPath+'/assets/jquery.qtip.min.css']
                 //TODO: requires images: servletContext.contextPath+pluginContextPath+'/css/jquery-ui-1.10.3.custom.css']
 
         JSONObject result = new JSONObject()

Rmodules/grails-app/controllers/com/recomdata/transmart/data/association/RModulesController.groovy

@@ -19,15 +19,17 @@ package com.recomdata.transmart.data.association
 import com.google.common.collect.Maps
 import grails.converters.JSON
 import grails.core.GrailsApplication
-import grails.util.Holders
 import jobs.*
 import jobs.misc.AnalysisConstraints
 import jobs.misc.AnalysisQuartzJobAdapter
 import org.grails.web.converters.exceptions.ConverterException
 import org.grails.web.json.JSONElement
+import org.quartz.JobBuilder
 import org.quartz.JobDataMap
 import org.quartz.JobDetail
 import org.quartz.SimpleTrigger
+import org.quartz.TriggerBuilder
+import org.quartz.core.QuartzScheduler
 import org.transmartproject.core.exceptions.InvalidArgumentsException
 
 import static jobs.misc.AnalysisQuartzJobAdapter.*
@@ -55,6 +57,7 @@ class RModulesController {
     def RModulesService
     GrailsApplication grailsApplication
     def jobResultsService
+    QuartzScheduler quartzScheduler
 
     /**
      * Method called that will cancel a running job
@@ -169,9 +172,14 @@ class RModulesController {
         params.put(PARAM_USER_PARAMETERS, userParams)
         params.put(PARAM_USER_IN_CONTEXT, currentUserBean.targetSource.target)
 
-        JobDetail jobDetail   = new JobDetail(params.jobName, params.jobType, AnalysisQuartzJobAdapter)
-        jobDetail.jobDataMap  = new JobDataMap(params)
-        SimpleTrigger trigger = new SimpleTrigger("triggerNow ${Calendar.instance.time.time}", 'RModules')
+        JobDetail jobDetail   = JobBuilder.newJob(AnalysisQuartzJobAdapter)
+            .withIdentity(params.jobName, params.jobType)
+            .setJobData(params)
+            .build()
+        SimpleTrigger trigger = TriggerBuilder.newTrigger()
+            .startNow()
+            .withIdentity('RModules')
+            .build()
         quartzScheduler.scheduleJob(jobDetail, trigger)
     }
 
@@ -226,7 +234,4 @@ class RModulesController {
         constraints
     }
 
-    private static def getQuartzScheduler() {
-        Holders.grailsApplication.mainContext.quartzScheduler
-    }
 }

Rmodules/grails-app/controllers/rmodules/AnalysisFilesInterceptor.groovy

@@ -0,0 +1,29 @@
+package rmodules
+
+import org.transmartproject.core.users.User
+
+class AnalysisFilesInterceptor {
+
+    def accessLogService
+    User currentUserBean
+
+    AnalysisFilesInterceptor() {
+        match(controller: 'analysisFiles', action:'download')
+    }
+
+    boolean before() { true }
+
+    boolean after() {
+        if (params.path.toLowerCase().endsWith('.zip')) {
+            def ip = request.getHeader('X-FORWARDED-FOR') ?: request.remoteAddr
+            accessLogService.report(currentUserBean, 'Raw R Data Export',
+                    eventMessage: "User (IP: ${ip}) downloaded ${params.path} for ${params.analysisName}",
+                    requestURL: "${request.forwardURI}${request.queryString ? '?' + request.queryString : ''}")
+        }
+        true
+    }
+
+    void afterView() {
+        // no-op
+    }
+}

Rmodules/grails-app/controllers/rdc/rmodules/UrlMappings.groovy → Rmodules/grails-app/controllers/rmodules/UrlMappings.groovy

@@ -1,4 +1,4 @@
-package rdc.rmodules
+package rmodules
 
 class UrlMappings {
 

Rmodules/grails-app/services/com/recomdata/transmart/data/association/RModulesService.groovy

@@ -17,14 +17,16 @@
 package com.recomdata.transmart.data.association
 
 import com.recomdata.transmart.data.association.asynchronous.RModulesJobService
+import grails.transaction.Transactional
 import org.grails.web.json.JSONObject
+import org.quartz.JobBuilder
 import org.quartz.JobDataMap
-import org.quartz.JobDetail
-import org.quartz.SimpleTrigger
+import org.quartz.TriggerBuilder
+import org.quartz.core.QuartzScheduler
 
+@Transactional
 class RModulesService {
 
-    static transactional = true
 	static scope = 'request'
 
     static STATUS_LIST = [
@@ -39,8 +41,7 @@ class RModulesService {
 	/**
 	* quartzScheduler is available from the Quartz grails-plugin
 	*/
-    def quartzScheduler
-
+    QuartzScheduler quartzScheduler
 	def jobResultsService
 	def asyncJobService
 	def grailsApplication
@@ -211,16 +212,21 @@ class RModulesService {
 		if (jobResultsService[params.jobName]["Status"] == "Cancelled")	{return}
 
 		//com.recomdata.transmart.plugin.PluginJobExecutionService should be implemented by all Plugins
-		def jobDetail = new JobDetail(params.jobName, params.jobType, RModulesJobService.class)
+		def jobDetail = JobBuilder.newJob(RModulesJobService.class)
+			.withIdentity(params.jobName, params.jobType)
+			.build()
 		jobDetail.setJobDataMap(jobDataMap)
 
 		if (asyncJobService.updateStatus(params.jobName, jobStatusList[2]))	{
 			return
 		}
-		def trigger = new SimpleTrigger("triggerNow"+Calendar.instance.time.time, 'RModules')
+		def trigger = TriggerBuilder.newTrigger()
+			.startNow()
+			.withIdentity('RModules')
+			.build()
 		quartzScheduler.scheduleJob(jobDetail, trigger)
 	}
-	
+
 	// method for non-R jobs
 	def prepareDataForExport(userName, params) {
 		loadJobDataMap(userName, params);

Rmodules/grails-app/views/plugin/AcghFrequencyPlot.gsp

@@ -1,6 +1,6 @@
 %{--include js lib for heatmap dynamically--}%
-<r:require modules="freq_plot"/>
-<r:layoutResources disposition="defer"/>
+%{--<r:require modules="freq_plot"/>--}%
+%{--<r:layoutResources disposition="defer"/>--}%
 
 %{--Input Container--}%
 <div id="freq_plot_container" class="analysis_container"></div>

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,6 @@
+#Tue Sep 27 10:49:32 CEST 2016
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.12-bin.zip