Merge branch 'dev' into release

.gitignore

@@ -6,6 +6,7 @@ Thumbs.db
 .gradle
 build/
 gradlew*
+gradle/wrapper
 
 # IDEs
 # - IntelliJ IDEA

.travis.yml

@@ -21,9 +21,10 @@ cache:
     - $HOME/pg
 
 before_install:
-  - curl -f -L https://services.gradle.org/distributions/gradle-3.5.1-bin.zip -o gradle-3.5.1-bin.zip
-  - unzip gradle-3.5.1-bin.zip
-  - GRADLE_HOME="$(pwd)/gradle-3.5.1"
+  - GRADLE_VERSION=4.10.3
+  - curl -f -L "https://services.gradle.org/distributions/gradle-${GRADLE_VERSION}-bin.zip" -o "gradle-${GRADLE_VERSION}-bin.zip"
+  - unzip "gradle-${GRADLE_VERSION}-bin.zip"
+  - GRADLE_HOME="$(pwd)/gradle-${GRADLE_VERSION}"
   - GRADLE_SCRIPT="${GRADLE_HOME}/bin/gradle"
   - $GRADLE_SCRIPT --version
   - groovy --version

build.gradle

@@ -1,90 +1,68 @@
 buildscript {
     ext {
-        assetPipelineVersion = '2.11.6'
-        grailsVersion = '3.2.13'
-        guavaVersion = '19.0'
+        assetPipelineVersion = '2.15.1'
+        grailsVersion = '3.3.11'
+        guavaVersion = '29.0-jre'
         jansiVersion = '1.14'
-        protobufVersion = '3.1.0'
+        protobufVersion = '3.12.2'
     }
     repositories {
         mavenLocal()
         mavenCentral()
         maven { url 'https://plugins.gradle.org/m2/' }
         maven { url 'https://repo.grails.org/grails/core' }
         maven { url 'https://dl.bintray.com/grails/plugins' }
-        // maven { url 'https://repo.transmartfoundation.org/content/repositories/public' }
         maven { url 'https://repo.thehyve.nl/content/repositories/public' }
     }
     dependencies {
         classpath "org.grails:grails-gradle-plugin:$grailsVersion"
         classpath "com.google.guava:guava:$guavaVersion"
         classpath "com.bertramlabs.plugins:asset-pipeline-gradle:$assetPipelineVersion"
-        classpath 'org.grails.plugins:hibernate5:6.0.4'
+        classpath 'org.grails.plugins:hibernate5:6.1.12'
         classpath "com.google.protobuf:protobuf-java:${protobufVersion}"
         classpath "com.google.protobuf:protobuf-java-util:${protobufVersion}"
-        classpath 'org.grails.plugins:views-gradle:1.0.12'
+        classpath 'org.grails.plugins:views-gradle:1.2.10'
         classpath 'net.linguica.gradle:maven-settings-plugin:0.5'
         classpath "org.fusesource.jansi:jansi:${jansiVersion}"
-        classpath 'org.owasp:dependency-check-gradle:3.2.1'
+        classpath 'org.owasp:dependency-check-gradle:5.3.2.1'
     }
 }
 
-// Workaround suggested in https://github.com/gradle/gradle/issues/778
-org.fusesource.jansi.AnsiConsole.out.println('[init jansi library conflict workaround]')
-
 apply plugin: 'idea'
 apply plugin: 'maven-publish'
 apply plugin: 'org.owasp.dependencycheck'
 
 ext {
     transmartVersion = '17.2.7'
 
-    assetPipelineVersion = '2.11.6'
-    gradleWrapperVersion = '3.5.1'
-    grailsVersion = '3.2.13'
-    guavaVersion = '19.0'
-    jacksonVersion = '2.10.1'
-    liquibaseVersion = '3.7.0'
-    ojdb7Version = '12.1.0.1'
-    openCsvVersion = '5.0'
-    postgresqlVersion = '42.2.5.jre7'
-    protobufVersion = '3.1.0'
-    quartzVersion = '2.0.13'
-    springSecurityPluginVersion = '3.2.3'
-    springSecurityVersion = '4.1.4.RELEASE'
-    keycloakVersion = '6.0.1'
-}
-
-task wrapper(type: Wrapper) {
-    gradleVersion = gradleWrapperVersion
+    assetPipelineVersion = '2.15.1'
+    grailsVersion = '3.3.11'
+    guavaVersion = '29.0-jre'
+    hibernateVersion = '5.1.17.Final'
+    jacksonVersion = '2.11.0'
+    keycloakVersion = '10.0.2'
+    liquibaseVersion = '3.10.0'
+    ojdb8Version = '12.2.0.1'
+    openCsvVersion = '5.2'
+    postgresqlVersion = '42.2.14.jre7'
+    protobufVersion = '3.12.2'
+    quartzPluginVersion = '2.0.13'
+    quartzVersion = '2.3.2'
+    springSecurityVersion = '4.2.17.RELEASE'
+    tomcatVersion = '8.5.56'
 }
 
 version = transmartVersion
 group = 'org.transmartproject'
 
 allprojects {
-    ext {
-        assetPipelineVersion = assetPipelineVersion
-        guavaVersion = guavaVersion
-        jacksonVersion = jacksonVersion
-        liquibaseVersion = liquibaseVersion
-        ojdb7Version = ojdb7Version
-        openCsvVersion = openCsvVersion
-        postgresqlVersion = postgresqlVersion
-        protobufVersion = protobufVersion
-        quartzVersion = quartzVersion
-        springSecurityPluginVersion = springSecurityPluginVersion
-        springSecurityVersion = springSecurityVersion
-    }
     repositories {
         repositories {
             mavenLocal()
             mavenCentral()
             maven { url 'https://repo.grails.org/grails/core' }
-            // maven { url 'https://repo.transmartfoundation.org/content/repositories/public/' }
             maven { url 'https://repo.thehyve.nl/content/groups/public/' }
             maven { url 'https://dl.bintray.com/bluesliverx/grails-plugins' }
-            // maven { url 'https://jcenter.bintray.com' }
         }
     }
 }
@@ -95,6 +73,7 @@ subprojects { project ->
 
     apply plugin: 'eclipse'
     apply plugin: 'idea'
+    apply plugin: 'org.owasp.dependencycheck'
 
     if (project.name =~ /^(transmart-core-db-tests|transmart-core-db|transmart-rest-api|transmart-api-server)$/) {
         if (project.name =~ /^(transmart-api-server)$/) {

docker/README.md

@@ -52,7 +52,7 @@ Publish the image to [Docker Hub](https://hub.docker.com/r/thehyve/transmart-api
 
 ```bash
 docker login
-TRANSMART_VERSION="17.2.7"
+TRANSMART_VERSION="17.2.8"
 docker tag transmart-api-server "thehyve/transmart-api-server:${TRANSMART_VERSION}"
 docker push "thehyve/transmart-api-server:${TRANSMART_VERSION}"
 ```

docker/docker-compose.yml

@@ -16,7 +16,7 @@ services:
 
   transmart-api-server:
     container_name: transmart-api-server
-    image: thehyve/transmart-api-server:17.2.7
+    image: thehyve/transmart-api-server:17.2.8
     ports:
       - 9081:8081
     environment:

docker/transmart-api-server/Dockerfile

@@ -3,7 +3,7 @@ LABEL maintainer="[email protected]" \
       service="transmart-api-server" \
       description="This is the Docker image of the tranSMART API server"
 
-ARG TRANSMART_VERSION="17.2.7"
+ARG TRANSMART_VERSION="17.2.8"
 
 ENV TRANSMART_USER_NAME transmart
 ENV TRANSMART_GROUP_NAME "${TRANSMART_USER_NAME}"

docs/README.md

@@ -1,6 +1,6 @@
-# tranSMART 17.2.7 Installation
+# tranSMART 17.2.8 Installation
 
-Below are the installation instructions for tranSMART version 17.2.7. If you already have an older version of tranSMART, follow the [upgrade guide](upgrade.md) instead.
+Below are the installation instructions for tranSMART version 17.2.8. If you already have an older version of tranSMART, follow the [upgrade guide](upgrade.md) instead.
 
   1. [Prerequisites](#1-prerequisites)
   2. [Setup database](#2-setup-database)
@@ -22,7 +22,7 @@ as well.
 * For all components:
     * JDK 8
 * For building tranSMART from sources:
-    * [gradle](https://gradle.org). Any version `> 2.12` and `<= 3.5.1` should suffice (version `3.5.1` is recommended). Other versions may cause some build issues.
+    * [gradle](https://gradle.org). Any version `> 2.12` and `<= 4.10.3` should suffice (version `4.10.3` is recommended). Other versions may cause some build issues.
 
 
 ## 2. Setup database
@@ -102,7 +102,7 @@ Deployment artefacts are published to [the Nexus repository of The Hyve](https:/
 To fetch and run `transmart-api-server`:
 ```bash
 # Fetch artefacts from Maven
-TRANSMART_VERSION=17.2.7
+TRANSMART_VERSION=17.2.8
 curl -f -L https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-api-server/${TRANSMART_VERSION}/transmart-api-server-${TRANSMART_VERSION}.war -o transmart-api-server-${TRANSMART_VERSION}.war && \
 # Run it with:
 java -jar -Dspring.config.location=/path/to/config.yaml transmart-api-server-${TRANSMART_VERSION}.war

gradle.properties

@@ -1,2 +1 @@
-grailsVersion=3.2.13
-gradleWrapperVersion=3.5.1
+gradleWrapperVersion=4.10.3

gradle/codenarc/ruleset.groovy

@@ -272,7 +272,7 @@ ruleset {
 	SerializableClassMustDefineSerialVersionUID
 
 	// rulesets/size.xml
-	AbcComplexity
+//	AbcComplexity
 	ClassSize
 //	CrapMetric
 	CyclomaticComplexity

open-api/swagger.yaml

@@ -13,12 +13,11 @@ info:
 
     # OAuth2
 
-    All tranSMART REST API calls need an [Authorization header](https://wiki.transmartfoundation.org/display/transmartwiki/tranSMART+REST+API).
+    All tranSMART REST API calls need an Authorization header with a valid authentication token:
 
-    ```
-
-    Authorization:Bearer {token}
 
+    ```
+    Authorization: Bearer {token}
     ```
 
 
@@ -531,6 +530,7 @@ info:
     [observations.proto](../transmart-rest-api/src/protobuf/v2/observations.proto).
     Information on [google
     protobuf](https://developers.google.com/protocol-buffers/).
+
 paths:
   /versions:
     get:
@@ -3063,9 +3063,18 @@ paths:
         '200':
           description: Successfull response
 
+security:
+  - OpenID:
+      - openid
 
 components:
 
+  securitySchemes:
+    OpenID:
+      type: http
+      scheme: bearer
+      bearerFormat: JWT
+
   schemas:
 
     Version:
@@ -3724,7 +3733,7 @@ components:
         name:
           type: string
         modifierCode:
-          type: string  
+          type: string
         dimensionType:
           type: string
           enum: [subject, attribute]

transmart-api-server/build.gradle

@@ -6,47 +6,62 @@ dependencyManagement {
 }
 
 dependencies {
-    //Grails 3 dependencies
-    compile "org.springframework.boot:spring-boot-starter-logging"
-    compile "org.springframework.boot:spring-boot-autoconfigure"
+    profile "org.grails.profiles:rest-api"
+
+    console("org.grails:grails-console") {
+        exclude group: 'org.fusesource.jansi', module: 'jansi'
+    }
+
+    compile "com.fasterxml.jackson.core:jackson-core:${jacksonVersion}"
+    compile "com.fasterxml.jackson.core:jackson-annotations:${jacksonVersion}"
+    compile "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}"
     compile "org.grails:grails-core"
-    compile "org.springframework.boot:spring-boot-starter-actuator"
-    compile "org.springframework.boot:spring-boot-starter-tomcat"
+    compile "org.grails:grails-logging"
     compile "org.grails:grails-plugin-url-mappings"
     compile "org.grails:grails-plugin-rest"
     compile "org.grails:grails-plugin-codecs"
     compile "org.grails:grails-plugin-interceptors"
     compile "org.grails:grails-plugin-services"
     compile "org.grails:grails-plugin-datasource"
     compile "org.grails:grails-plugin-databinding"
-    compile "org.grails:grails-plugin-async"
     compile "org.grails:grails-web-boot"
-    compile "org.grails:grails-logging"
+    compile "org.grails.plugins:async"
     compile "org.grails.plugins:cache"
+    compile "org.grails.plugins:database-migration:3.0.4"
     compile "org.grails.plugins:hibernate5"
-    compile "org.hibernate:hibernate-core:5.1.2.Final"
-    compile "org.hibernate:hibernate-ehcache:5.1.2.Final"
     compile "org.grails.plugins:views-json"
     compile "org.grails.plugins:views-json-templates"
-    compile "org.grails.plugins:database-migration:3.0.4"
+    compile "org.hibernate:hibernate-core:${hibernateVersion}"
+    compile "org.hibernate:hibernate-ehcache:${hibernateVersion}"
+    compile("org.keycloak:keycloak-legacy-spring-boot-starter") {
+        exclude group: 'com.fasterxml.jackson.core', module: 'jackson-core'
+        exclude group: 'com.fasterxml.jackson.core', module: 'jackson-databind'
+    }
     compile "org.liquibase:liquibase-core:${liquibaseVersion}"
-    console("org.grails:grails-console") {
-        exclude group: 'org.fusesource.jansi', module: 'jansi'
+    compile "org.postgresql:postgresql:${postgresqlVersion}"
+    compile "org.springframework.boot:spring-boot-autoconfigure"
+    compile("org.springframework.boot:spring-boot-starter-actuator") {
+        exclude group: 'com.fasterxml.jackson.core', module: 'jackson-databind'
     }
-    profile "org.grails.profiles:rest-api"
+    compile "org.springframework.boot:spring-boot-starter-logging"
+    compile "org.springframework.boot:spring-boot-starter-security"
+    compile "org.springframework.boot:spring-boot-starter-tomcat"
+    compile "org.springframework.security:spring-security-config:${springSecurityVersion}"
+    compile "org.springframework.security:spring-security-core:${springSecurityVersion}"
+    compile "org.springframework.security:spring-security-web:${springSecurityVersion}"
+    compile "org.apache.tomcat:tomcat-annotations-api:${tomcatVersion}"
+    compile "org.apache.tomcat.embed:tomcat-embed-core:${tomcatVersion}"
+    compile "org.apache.tomcat.embed:tomcat-embed-el:${tomcatVersion}"
+    compile "org.apache.tomcat.embed:tomcat-embed-websocket:${tomcatVersion}"
 
-    //Custom dependencies
     compile project(':transmart-rest-api')
     compile project(':transmart-schemas')
 
-    compile "org.keycloak:keycloak-legacy-spring-boot-starter"
-    compile "org.springframework.boot:spring-boot-starter-security"
-
-    testCompile 'org.spockframework:spock-core:1.1-groovy-2.4'
-
     runtime('ch.qos.logback.contrib:logback-jackson:0.1.5') {
         exclude group: 'com.fasterxml.jackson.core', module: 'jackson-databind'
     }
+
+    testCompile 'org.spockframework:spock-core:1.1-groovy-2.4'
 }
 
 bootRun {

transmart-api-server/grails-app/conf/application.yml

@@ -42,7 +42,7 @@ hibernate:
         region.factory_class: org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory
 
 dataSource:
-    url: jdbc:postgresql://localhost:5432/transmart?currentSchema=public
+    url: jdbc:postgresql://localhost:${PGPORT:5432}/transmart?currentSchema=public
     driverClassName: org.postgresql.Driver
     username: biomart_user
     password: biomart_user
@@ -95,10 +95,10 @@ environments:
             verify-token-audience: true
     development:
         keycloak:
-            realm: dev
+            realm: ${KEYCLOAK_REALM:dev}
             bearer-only: true
-            auth-server-url: http://localhost:8080/auth
-            resource: transmart
+            auth-server-url: ${KEYCLOAK_SERVER_URL:http://localhost:8080}/auth
+            resource: ${KEYCLOAK_CLIENT_ID:transmart}
             use-resource-role-mappings: true
             verify-token-audience: true
 #            disable-trust-manager: false  # when true, SSL certificate checking is disabled. Do not use that in production!
@@ -109,4 +109,9 @@ environments:
 # org.transmartproject.security.denyAccessToUsersWithoutRole: false  # when true, users without any role are denied access.
 # If true, the ROLE_PUBLIC role can be used to grant access to users
 
+---
 # org.transmartproject.system.writeLogToDatabase: true  # write log messages to the searchapp.search_app_access_log table
+
+environments:
+    development:
+        org.transmartproject.system.writeLogToDatabase: false

transmart-api-server/grails-app/init/org/transmartproject/api/server/Application.groovy

@@ -16,7 +16,7 @@ class Application extends GrailsAutoConfiguration {
         { ->
             // Configure data source health indicator based
             // on the dataSource in the application context.
-            databaseHealthCheck(DataSourceHealthIndicator, dataSource)
+            databaseHealthCheck(DataSourceHealthIndicator, ref('dataSource'))
         }
     }
 }

transmart-copy/README.md

@@ -6,11 +6,11 @@ only substituting indexes for database identifiers for subjects, trial visits an
 
 ### Download
 The latest version can be downloaded here:
-[transmart-copy-17.2.7.jar](https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-copy/17.2.7/transmart-copy-17.2.7.jar).
+[transmart-copy-17.2.8.jar](https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-copy/17.2.8/transmart-copy-17.2.8.jar).
 
 ```bash
 # Download transmart-copy
-curl -f -L https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-copy/17.2.7/transmart-copy-17.2.7.jar -o transmart-copy.jar
+curl -f -L https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-copy/17.2.8/transmart-copy-17.2.8.jar -o transmart-copy.jar
 ```
 
 ### Usage