Add a command line tool for linting ACLs

.gitattributes

@@ -0,0 +1,2 @@
+/gemma-cli/src/main/config/bash_completion.d/* linguist-generated=true
+/gemma-cli/src/main/config/fish/completions/* linguist-generated=true

.jenkins/Jenkinsfile

@@ -44,7 +44,6 @@ pipeline {
             steps {
                 checkout scm
                 script {
-                    testdbUrl = sh script: 'mvn help:evaluate -Dexpression=gemma.testdb.build.url -q -DforceStdout', returnStdout: true
                     gemmaVersion = sh script: 'mvn help:evaluate -Dexpression=project.version -q -DforceStdout', returnStdout: true
                     baseCodeVersion = sh script: 'mvn help:evaluate -Dartifact=baseCode:baseCode -Dexpression=project.version -q -DforceStdout', returnStdout: true
                     buildHash = env.GIT_COMMIT
@@ -101,7 +100,7 @@ pipeline {
         stage('Run quick unit tests') {
             steps {
                 setBuildStatus "Tests", "Tests for build #${env.BUILD_NUMBER} have started...", 'PENDING'
-                sh 'mvn -B test --fail-at-end -DexcludedGroups=SlowTest -DskipVersionFile'
+                sh 'mvn -B test --fail-at-end -DexcludedGroups=SlowTest'
             }
             post {
                 always {
@@ -118,7 +117,7 @@ pipeline {
         stage('Package') {
             steps {
                 setBuildStatus "Package", "Package for build #${env.BUILD_NUMBER} have started...", 'PENDING'
-                sh 'mvn -B package -DskipTests -DskipVersionFile'
+                sh 'mvn -B package -DskipTests'
             }
             post {
                 success {
@@ -157,8 +156,10 @@ pipeline {
                         }
                     }
                     steps {
-                        setBuildStatus "Slow tests", "Slow tests #${env.BUILD_NUMBER} have started...", 'PENDING'
-                        sh 'mvn -B test --fail-at-end -Dgroups=SlowTest -DskipWebpack -DskipVersionFile'
+                        lock('gemma-slow-tests') {
+                            setBuildStatus "Slow tests", "Slow tests #${env.BUILD_NUMBER} have started...", 'PENDING'
+                            sh 'mvn -B test --fail-at-end -Dgroups=SlowTest -DskipWebpack'
+                        }
                     }
                     post {
                         always {
@@ -185,8 +186,8 @@ pipeline {
                     }
                     steps {
                         setBuildStatus "Integration tests", "Integration tests #${env.BUILD_NUMBER} have started...", 'PENDING'
-                        lock('database/' + testdbUrl) {
-                            sh 'mvn -B verify --fail-at-end -DskipUnitTests -Dmaven.javadoc.skip=true -DskipWebpack -DskipVersionFile'
+                        lock('database/gemdtest') {
+                            sh 'mvn -B verify --fail-at-end -DskipUnitTests -DskipJavadoc -DskipWebpack'
                         }
                     }
                     post {
@@ -202,6 +203,9 @@ pipeline {
                     }
                 }
                 stage('SonarQube Analysis') {
+                    tools {
+                        jdk 'Java 17'
+                    }
                     when {
                         anyOf {
                             branch 'master'
@@ -213,9 +217,11 @@ pipeline {
                         }
                     }
                     steps {
-                        setBuildStatus "SonarQube Analysis", "SonarQube analysis for build #${env.BUILD_NUMBER} has started...", 'PENDING'
-                        withSonarQubeEnv('UBC SonarQube') {
-                            sh "mvn dependency-check:check sonar:sonar -Dsonar.projectKey=mslg -Dsonar.projectName='MSL - Gemma'"
+                        lock('gemma-sonarqube-analysis') {
+                            setBuildStatus "SonarQube Analysis", "SonarQube analysis for build #${env.BUILD_NUMBER} has started...", 'PENDING'
+                            withSonarQubeEnv('UBC SonarQube') {
+                                sh "mvn package -DskipTests -DskipJavadoc -DskipWebpack dependency-check:check org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=mslg -Dsonar.projectName='MSL - Gemma'"
+                            }
                         }
                     }
                     post {
@@ -241,7 +247,7 @@ pipeline {
                         }
                     }
                     steps {
-                        sh 'mvn -B deploy -DskipTests -DskipWebpack -DskipVersionFile'
+                        sh 'mvn -B deploy -DskipTests -DskipJavadoc -DskipWebpack'
                     }
                 }
                 stage('Deploy Maven website') {
@@ -255,7 +261,7 @@ pipeline {
                         }
                     }
                     steps {
-                        sh 'mvn -B site-deploy -DskipWebpack -DskipVersionFile'
+                        sh 'mvn -B site-deploy -DskipWebpack'
                         script {
                             if (dataDir != null) {
                                 sh "ln -Tsf ${params.MAVEN_SITES_DIR}/gemma/gemma-${gemmaVersion} ${dataDir}/gemma-devsite"

gemma-cli/deploy.sh

@@ -3,6 +3,12 @@
 #
 # Deploy the Gemma CLI
 #
+# Usage: ./deploy <ref>
+#
+# The <ref> argument is a name under which the CLI is deployed. Note that this
+# script is designed to re-use an existing deployment under that name to
+# minimize the amount of data transferred with rsync.
+#
 # Environment variables:
 # GEMMA_CLI_DEPLOY_SERVER: The server to deploy the Gemma CLI to.
 # GEMMA_CLI_PREFIX:        The prefix for the Gemma CLI deployment directory (defaults to /space/opt/gemma-cli).

gemma-cli/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>gemma</artifactId>
         <groupId>gemma</groupId>
-        <version>1.32.2</version>
+        <version>1.32.6-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>gemma-cli</artifactId>
@@ -61,7 +61,7 @@
         <dependency>
             <groupId>commons-cli</groupId>
             <artifactId>commons-cli</artifactId>
-            <version>1.9.0</version>
+            <version>1.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>