Merge pull request #167 from AtlasOfLivingAustralia/develop

Merge develop to master

Author: sughics

.travis.yml

@@ -1,11 +1,12 @@
 language: groovy
 jdk:
-- openjdk8
+- openjdk11
 sudo: false
 branches:
   only:
     - master
     - develop
+    - feature_oidcIntegration
 before_cache:
   - rm -f  $HOME/.gradle/caches/modules-2/modules-2.lock
   - rm -fr $HOME/.gradle/caches/*/plugin-resolution/
@@ -21,5 +22,6 @@ after_success:
   - '[ "${TRAVIS_PULL_REQUEST}" = "false" ] && travis_retry ./gradlew publish'
 env:
   global:
+    - JAVA_TOOL_OPTIONS=-Dhttps.protocols=TLSv1.2
     - secure: OqyYLYoeTw2ifeopsXEQnLDF8DA5j12iSH9mKGXjE6abkrhXCghWOtb+jGstRvJr/ZrpJfFK3VOkistgkf6y8/RYxB7a0MJsr+1GUXtdHhtPbUcShJDybj6AlbgPCI2J4VdIQSB+ey2XZKOMOO3+XwbsczrTHBh5KpBHdI7Tw8I=
     - secure: XvAZn/Iv/HVBcR3DiDrNhOvMy4LVvrH0eM7jims9Kyhwb6YvZc8aD2MpgfR9pEcKpyy5zSx/EKYKbB6rf5tzjjEOSgCCrYfoqNB2e1/pqNnzMsblEpRC3IsHOYs7bQwckKOclQ1pP/6BzjxSKzZNQG+dQT+KhfPPmWj4Ky+hmN0=

build.gradle

@@ -19,26 +19,29 @@ buildscript {
     }
     dependencies {
         classpath "org.grails:grails-gradle-plugin:$grailsVersion"
-        classpath "com.bertramlabs.plugins:asset-pipeline-gradle:2.14.1"
-        classpath "org.grails.plugins:hibernate5:${gormVersion-".RELEASE"}"
+        classpath "com.bertramlabs.plugins:asset-pipeline-gradle:3.3.2"
+        classpath "org.grails.plugins:hibernate5:7.0.2"
+        classpath 'org.grails.plugins:quartz:2.0.13'
     }
 }
 
 plugins {
     id "com.gorylenko.gradle-git-properties" version "1.4.17"
 }
 
-version "1.6"
+
+version "2.0.0-SNAPSHOT"
 group "au.org.ala"
 
 apply plugin:"eclipse"
 apply plugin:"idea"
 apply plugin:"war"
 apply plugin:"org.grails.grails-web"
 apply plugin:"org.grails.grails-gsp"
-apply plugin:"asset-pipeline"
+apply plugin:"com.bertramlabs.asset-pipeline"
 
-apply from: 'https://raw.githubusercontent.com/AtlasOfLivingAustralia/travis-build-configuration/master/travis_grails_publish.gradle'
+//apply from: 'https://raw.githubusercontent.com/AtlasOfLivingAustralia/travis-build-configuration/master/travis_grails_publish.gradle'
+apply from: "${project.projectDir}/gradle/publish.gradle"
 
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
@@ -75,20 +78,21 @@ dependencies {
     compile "org.grails:grails-plugin-services"
     compile "org.grails:grails-plugin-url-mappings"
     compile "org.grails:grails-plugin-interceptors"
-    compile "org.grails.plugins:cache"
     compile "org.grails.plugins:async"
     compile "org.grails.plugins:scaffolding"
     compile "org.grails.plugins:events"
     compile "org.grails.plugins:hibernate5"
-    compile "org.hibernate:hibernate-core:5.1.16.Final"
-    compile "org.hibernate:hibernate-ehcache:5.1.16.Final"
+//    compile "org.hibernate:hibernate-core:5.4.0.Final"
+//    compile "org.hibernate:hibernate-ehcache:5.4.0.Final"
+    compile "org.hibernate:hibernate-jcache"
+
     compile "org.grails.plugins:gsp"
     console "org.grails:grails-console"
     profile "org.grails.profiles:web"
     runtime "org.glassfish.web:el-impl:2.1.2-b03"
     runtime "com.h2database:h2"
     runtime "org.apache.tomcat:tomcat-jdbc"
-    runtime "com.bertramlabs.plugins:asset-pipeline-grails:2.15.1"
+    runtime "com.bertramlabs.plugins:asset-pipeline-grails:3.3.2"
 
     //compile "org.grails.plugins:grails-plugin-converters" // only needed for grails 3.3
     //testCompile "org.grails:grails-plugin-testing"
@@ -98,20 +102,20 @@ dependencies {
     testCompile "org.grails:grails-test-mixins:3.3.0"
 
     // Grails plugin dependencies
-    runtime "org.grails.plugins:ala-bootstrap3:3.2.3", noCache
-    compile "org.grails.plugins:ala-ws-security-plugin:2.0", noCache
-    compile "org.grails.plugins:ala-ws-plugin:2.0", noCache
-    compile "org.grails.plugins:ala-auth:3.1.3", noCache
-    compile "org.grails.plugins:ala-admin-plugin:2.1"
+    runtime "org.grails.plugins:ala-bootstrap3:4.1.0", noCache
+    compile "org.grails.plugins:ala-ws-security-plugin:4.1.1", noCache
+    compile "org.grails.plugins:ala-ws-plugin:3.1.0", noCache
+    compile "org.grails.plugins:ala-auth:5.1.0", noCache
+    compile "org.grails.plugins:ala-admin-plugin:2.3.0"
     //compile 'au.org.ala:userdetails-service-client:1.4.0' // TODO remove this line once updated version is included in ala-auth
 
-    compile 'org.grails.plugins:external-config:1.1.1'
-    compile 'org.grails.plugins:mail:2.0.0.RC6'
+    compile 'org.grails.plugins:external-config:2.0.0'
+    compile 'org.grails.plugins:mail:3.0.0'
     compile 'org.grails.plugins:http-builder-helper:1.0.2.ALA'
     compile 'org.grails.plugins:schwartz-monitor:2.0.1.ALA-SNAPSHOT'
-    compile 'org.grails.plugins:quartz:2.0.12'
-    compile 'org.grails.plugins:cache:4.0.1'
-    compile 'org.grails.plugins:cache-ehcache:3.0.0.M1'
+    compile 'org.grails.plugins:quartz:2.0.13'
+    compile 'org.grails.plugins:cache:4.0.2'
+    compile 'org.grails.plugins:cache-ehcache:3.0.0'
 
     // regular JAR dependencies
     runtime 'mysql:mysql-connector-java:8.0.25'
@@ -127,11 +131,12 @@ dependencies {
     //runtime 'org.apache.httpcomponents:httpclient:4.2.2'
     compile 'com.jayway.jsonpath:json-path:0.5.6'
     compile 'com.jayway.jsonpath:json-path-assert:0.5.6'
+    compile 'au.org.ala.plugins:openapi:1.1.0'
 }
 
 bootRun {
     jvmArgs('-Dspring.output.ansi.enabled=always')
-    addResources = true
+    sourceResources sourceSets.main
     String springProfilesActive = 'spring.profiles.active'
     systemProperty springProfilesActive, System.getProperty(springProfilesActive)
 }

gradle.properties

@@ -1,3 +1,3 @@
-grailsVersion=3.3.9
-gormVersion=6.1.11.RELEASE
-gradleWrapperVersion=3.5
+grailsVersion=4.1.1
+gormVersion=7.0.8.RELEASE
+gradleWrapperVersion=5.0

gradle/publish.gradle

@@ -0,0 +1,32 @@
+apply plugin:"maven-publish"
+
+publishing {
+    repositories {
+        maven {
+            name 'Nexus'
+            url "https://nexus.ala.org.au/content/repositories/${project.version.endsWith('-SNAPSHOT') ? 'snapshots' : 'releases' }"
+            credentials {
+                username = System.getenv('TRAVIS_DEPLOY_USERNAME')
+                password = System.getenv('TRAVIS_DEPLOY_PASSWORD')
+            }
+        }
+    }
+    publications {
+        mavenJar(MavenPublication) {
+            pom.withXml {
+                def pomNode = asNode()
+                pomNode.dependencyManagement.replaceNode {}
+
+                // simply remove dependencies without a version
+                // version-less dependencies are handled with dependencyManagement
+                // see https://github.com/spring-gradle-plugins/dependency-management-plugin/issues/8 for more complete solutions
+                pomNode.dependencies.dependency.findAll {
+                    it.version.text().isEmpty()
+                }.each {
+                    it.replaceNode {}
+                }
+            }
+            from components.web
+        }
+    }
+}

gradle/wrapper/gradle-wrapper.jar

@@ -1,6 +1,5 @@
-#Tue Aug 08 11:44:31 AEST 2017
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-5.1.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-3.4.1-all.zip

gradle/wrapper/gradle-wrapper.properties

@@ -28,16 +28,16 @@ APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+DEFAULT_JVM_OPTS='"-Xmx64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
 
-warn ( ) {
+warn () {
     echo "$*"
 }
 
-die ( ) {
+die () {
     echo
     echo "$*"
     echo
@@ -155,7 +155,7 @@ if $cygwin ; then
 fi
 
 # Escape application args
-save ( ) {
+save () {
     for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
     echo " "
 }
@@ -169,4 +169,4 @@ if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
   cd "$(dirname "$0")"
 fi
 
-exec "$JAVACMD" "$@"
+exec "$JAVACMD" "$@"

gradlew

@@ -8,14 +8,14 @@
 @rem Set local scope for the variables with windows NT shell
 if "%OS%"=="Windows_NT" setlocal
 
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
-
 set DIRNAME=%~dp0
 if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m"
+
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome
 
@@ -46,10 +46,9 @@ echo location of your Java installation.
 goto fail
 
 :init
-@rem Get command-line arguments, handling Windowz variants
+@rem Get command-line arguments, handling Windows variants
 
 if not "%OS%" == "Windows_NT" goto win9xME_args
-if "%@eval[2+2]" == "4" goto 4NT_args
 
 :win9xME_args
 @rem Slurp the command line arguments.
@@ -60,11 +59,6 @@ set _SKIP=2
 if "x%~1" == "x" goto execute
 
 set CMD_LINE_ARGS=%*
-goto execute
-
-:4NT_args
-@rem Get arguments from the 4NT Shell from JP Software
-set CMD_LINE_ARGS=%$
 
 :execute
 @rem Setup the command line

gradlew.bat

@@ -38,12 +38,12 @@ spring:
     groovy:
         template:
             check-template-location: false
-
 # Spring Actuator Endpoints are Disabled by Default
-endpoints:
-    enabled: true
     jmx:
-        enabled: true
+        unique-names: true
+management:
+    endpoints:
+        enabled-by-default: true
 
 ---
 grails:
@@ -97,10 +97,6 @@ grails:
                 scriptlets: html
                 taglib: none
                 staticparts: none
-endpoints:
-    jmx:
-        unique-names: true
-    enabled: true
 ---
 headerAndFooter:
     baseURL: "https://www.ala.org.au/commonui-bs3-2019"
@@ -117,7 +113,7 @@ siteDefaultLanguage: "en"
 security:
     cas:
         adminRole: ROLE_ADMIN
-        uriFilterPattern: "/,/alaAdmin.*,/testAuth.*,/query/.*,/admin/?.*,/admin/user/.*,/admin/user/debug/.*,/admin/debug/all,/notification/myAlerts,/notification/changeFrequency,/notification/addMyAlert,/notification/addMyAlert/.*,/notification/deleteMyAlert/.*,/notification/deleteMyAlert/.*,/notification/deleteMyAlertWR/.*,/webservice/.*,/webservice/createTaxonAlert,/webservice/taxonAlerts,/webservice/createRegionAlert,/webservice/regionAlerts,/webservice/deleteTaxonAlert/.*,/webservice/create*,/webservice/createSpeciesGroupRegionAlert,/ws/.*,/ws/createTaxonAlert,/ws/taxonAlerts,/ws/createRegionAlert,/ws/regionAlerts,/ws/deleteTaxonAlert/.*,/ws/createTaxonRegionAlert,/ws/createSpeciesGroupRegionAlert,/admin/runChecksNow"
+        uriFilterPattern: ["/","/alaAdmin/*","/testAuth/*","/query/*","/admin/*","/admin/user/*","/admin/user/debug/*","/admin/debug/all","/notification/myAlerts","/notification/changeFrequency","/notification/addMyAlert","/notification/addMyAlert/*","/notification/deleteMyAlert/*","/notification/deleteMyAlert/*","/notification/deleteMyAlertWR/*","/webservice/*","/webservice/createTaxonAlert","/webservice/taxonAlerts","/webservice/createRegionAlert","/webservice/regionAlerts","/webservice/deleteTaxonAlert/*","/webservice/create*","/webservice/createSpeciesGroupRegionAlert","/ws/*","/ws/createTaxonAlert","/ws/taxonAlerts","/ws/createRegionAlert","/ws/regionAlerts","/ws/deleteTaxonAlert/*","/ws/createTaxonRegionAlert","/ws/createSpeciesGroupRegionAlert","/admin/runChecksNow"]
 
 postie:
     emailSender: "atlas-alerts@ala.org.au"
@@ -195,7 +191,7 @@ hibernate:
         use_second_level_cache: true
         use_query_cache: true
         region:
-            factory_class: org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory
+            factory_class: org.hibernate.cache.jcache.internal.JCacheRegionFactory
 
 dataSource:
     pooled: true
@@ -249,4 +245,33 @@ environments:
             dbCreate: none
 
 myannotation:
-    enabled: false
+    enabled: false
+
+security:
+    cas:
+        enabled: false
+    oidc:
+        enabled: true
+        discoveryUri: https://auth-dev.ala.org.au/cas/oidc/.well-known
+        scope: openid,profile,email,ala,roles,user_defined
+#        allowUnsignedIdTokens: true
+    jwt:
+        enabled: true
+        discoveryUri: https://auth-dev.ala.org.au/cas/oidc/.well-known
+        fallbackToLegacyBehaviour: true
+
+openapi:
+    title: Alerts REST services
+    description: REST services for interacting with the alerts webapp
+    terms: https://www.ala.org.au/terms
+    contact:
+        name: Support
+        email: support@ala.org.au
+    license:
+        name: Mozilla Public License 1.1
+        url: https://www.mozilla.org/en-US/MPL/1.1/
+    version: '@info.app.version@'
+    cachetimeoutms: 0
+
+webservice:
+    jwt: true

grails-app/conf/application.yml

@@ -118,6 +118,7 @@ root(WARN, [APPENDER])
 //                'au.org.ala'
         ],
         (DEBUG): [ // DEBUG and TRACE should only be enabled for non-production environments
+                   'au.org.ala.alerts'
         ],
         (TRACE): [
         ]

grails-app/conf/logback.groovy

@@ -14,11 +14,13 @@
 package au.org.ala.alerts
 
 import au.org.ala.web.AlaSecured
+import grails.gorm.transactions.Transactional
 import grails.util.Holders
 import groovy.json.JsonSlurper
 import org.apache.http.client.methods.HttpPost
 import org.apache.http.impl.client.DefaultHttpClient
 
+@Transactional
 @AlaSecured(value = 'ROLE_ADMIN', redirectController = 'notification', redirectAction = 'myAlerts', message = "You don't have permission to view that page.")
 class AdminController {
 
@@ -253,7 +255,7 @@ class AdminController {
             def query = Query.get(1)
             def frequency = Frequency.get(1)
             def queryResult = QueryResult.findByQuery(query) ?: new QueryResult(query: query, frequency: frequency)
-            emailService.sendGroupEmail(query, [user.email], queryResult, [], frequency, 0, "", "")
+            emailService.sendGroupEmail(query, [user.email], queryResult, [], frequency, 0, "", "", [:], [:])
             msg = "Email was sent to ${user.email} - check tomcat logs for ERROR message with value \"Error sending email to addresses:\""
         } else {
             msg = "User was not found or not logged in"

grails-app/controllers/au/org/ala/alerts/AdminController.groovy

@@ -2,7 +2,9 @@ package au.org.ala.alerts
 
 import grails.converters.JSON
 import org.apache.http.HttpStatus
+import grails.gorm.transactions.Transactional
 
+@Transactional
 class NotificationController {
 
     def notificationService
@@ -94,7 +96,7 @@ class NotificationController {
     }
 
     def changeFrequency = {
-        def user = userService.getUser()
+        def user = getUser()
         log.debug("Changing frequency to: " + params.frequency + " for user ${user}")
         notificationService.updateFrequency(user, params.frequency)
         return null

grails-app/controllers/au/org/ala/alerts/NotificationController.groovy

@@ -1,9 +1,11 @@
 package au.org.ala.alerts
 
 import au.org.ala.web.AlaSecured
+import grails.gorm.transactions.Transactional
 import grails.util.Holders
 import org.springframework.dao.DataIntegrityViolationException
 
+@Transactional
 class QueryController {
 
     static allowedMethods = [save: "POST", update: "POST", update: "PUT", delete: "POST"]