Merge pull request #34 from kit-data-manager/development

Prepare 0.1.2

Author: VolkerHartmann

.github/workflows/docker-publish.yml

@@ -0,0 +1,109 @@
+name: Docker
+
+on:
+  push:
+    # Publish `master` as Docker `latest` image.
+    branches:
+      - main
+
+    # Publish `v1.2.3` tags as releases.
+    tags:
+      - v*
+
+  # Run tests for any PRs.
+  pull_request:
+
+env:
+  # TODO: Change variable to your image's name.
+  IMAGE_NAME: indexing-service
+  # JDK version used for building jar file
+  currentBuildVersion: 17
+
+jobs:
+  # Run tests.
+  # See also https://docs.docker.com/docker-hub/builds/automated-testing/
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repo
+      uses: actions/checkout@v2
+    - name: Set up OpenJDK version ...
+      uses: actions/setup-java@v2
+      with:
+        distribution: 'zulu'
+        java-version: ${{ env.currentBuildVersion }}
+    - name: Pull elasticsearch image from docker
+      run: docker pull elasticsearch:7.9.3
+    - name: Install python
+      run: sudo apt-get install --assume-yes python3 python3-setuptools python3-pip
+    - name: Update pip
+      run: pip3 install --upgrade pip
+    - name: Install libraries via pip (xmltodict and wget)
+      run: pip3 install xmltodict wget
+    - name: Grant execute permission for gradlew
+      run: chmod +x gradlew
+    - name: Run tests
+      run:  ./gradlew jacocoTestReport
+#            docker build . --file Dockerfile
+  # Push image to GitHub Packages.
+  # See also https://docs.docker.com/docker-hub/builds/
+  push:
+    # Ensure test job passes before pushing image.
+    needs: test
+
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push'
+
+    steps:
+    - name: Checkout repo
+      uses: actions/checkout@v2
+
+    - name: Build image
+      run: |
+         docker build . --file Dockerfile --tag $IMAGE_NAME
+    - name: Log into registry
+      run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
+
+    - name: Push image
+      run: |
+        IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/$IMAGE_NAME
+        # Change all uppercase to lowercase
+        IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+        # Strip git ref prefix from version
+        VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+        # Strip "v" prefix from tag name
+        [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+        # Use Docker `latest` tag convention
+        [ "$VERSION" == "main" ] && VERSION=latest
+        echo IMAGE_ID=$IMAGE_ID
+        echo VERSION=$VERSION
+        docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+        docker push $IMAGE_ID:$VERSION
+    - name: Docker meta
+      id: docker_meta
+      uses: crazy-max/ghaction-docker-meta@v1
+      with:
+        # list of Docker images to use as base name for tags
+        images: |
+          kitdm/indexing-service
+        # add git short SHA as Docker tag
+        tag-sha: true
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v1
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v1
+    - name: Login to DockerHub
+      uses: docker/login-action@v1
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Push to Docker Hub
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        push: true
+        tags: ${{ steps.docker_meta.outputs.tags }}
+        labels: ${{ steps.docker_meta.outputs.labels }}

CHANGELOG.md

@@ -9,6 +9,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+## [0.1.2] - date 2023-02-07
+### Fixed
+- Dockerfile for dockerhub
+
+### Changed
+- Bump mockito-core from 5.0.0 to 5.1.1
+- Bump javersVersion from 6.8.2 to 6.9.1
+- Bump postgresql from 42.5.1 to 42.5.3
+- Bump tika-core from 2.6.0 to 2.7.0
+
 ## [0.1.1] - date 2023-01-30
 ### Changed
 - Bump mockito-core from 4.8.1 to 5.0.0 by @dependabot in https://github.com/kit-data-manager/indexing-service/pull/20
@@ -52,7 +62,8 @@ and mapping of metadata documents delivered by RabbitMQ
 - Mapping of metadata documents with Gemma
 - Ingest to elasticsearch
 
-[Unreleased]: https://github.com/kit-data-manager/indexing-service/compare/v0.1.1...HEAD
+[Unreleased]: https://github.com/kit-data-manager/indexing-service/compare/v0.1.2...HEAD
+[0.1.2]: https://github.com/kit-data-manager/indexing-service/compare/v0.1.1...v0.1.2
 [0.1.1]: https://github.com/kit-data-manager/indexing-service/compare/v0.1.0...v0.1.1
 [0.1.0]: https://github.com/kit-data-manager/indexing-service/compare/v0.0.4...v0.1.0
 [0.0.4]: https://github.com/kit-data-manager/indexing-service/compare/v0.0.3...v0.0.4

Dockerfile

@@ -11,19 +11,22 @@ ARG SERVICE_ROOT_DIRECTORY_DEFAULT=/spring/
 ####################################################
 # Building environment (java & git)
 ####################################################
-FROM openjdk:11-buster AS build-env-java
+FROM python:3.10 AS build-env-java
 LABEL maintainer=webmaster@datamanager.kit.edu
 LABEL stage=build-env
 
 # Install git as additional requirement
 RUN apt-get update && \
-    apt-get upgrade --assume-yes && \
-    apt-get install --assume-yes git 
+    apt-get upgrade --no-install-recommends --assume-yes && \
+    apt-get install --no-install-recommends --assume-yes git && \
+    apt-get install --no-install-recommends --assume-yes openjdk-17-jdk && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
 ####################################################
 # Building service
 ####################################################
-FROM build-env-java AS build-service-metastore2
+FROM build-env-java AS build-service-indexing
 LABEL maintainer=webmaster@datamanager.kit.edu
 LABEL stage=build-contains-sources
 
@@ -42,12 +45,12 @@ COPY . .
 RUN cp settings/application-docker.properties settings/application-default.properties
 
 # Build service in given directory
-RUN bash ./build.sh $SERVICE_DIRECTORY
+RUN bash ./build4docker.sh $SERVICE_DIRECTORY
 
 ####################################################
-# Runtime environment 4 metastore2
+# Runtime environment 4 indexing-service
 ####################################################
-FROM openjdk:11-buster AS run-service-metastore2
+FROM python:3.10 AS run-service-indexing
 LABEL maintainer=webmaster@datamanager.kit.edu
 LABEL stage=run
 
@@ -61,17 +64,20 @@ ENV REPO_NAME=${REPO_NAME_DEFAULT}
 ENV SERVICE_DIRECTORY=${SERVICE_ROOT_DIRECTORY_DEFAULT}${REPO_NAME}
 ENV REPO_PORT=${REPO_PORT_DEFAULT}
 
-# Install python3 & pip3 as additional requirement
+# Install JDK17
 RUN apt-get update && \
-    apt-get upgrade --assume-yes && \
-    apt-get install --assume-yes python3 python3-pip 
+    apt-get upgrade --no-install-recommends --assume-yes && \
+    apt-get install --no-install-recommends --assume-yes openjdk-17-jdk && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
-RUN pip3 install xmltodict wget
+# Install python3 & pip3 as additional requirement
+RUN pip3 install --no-cache-dir xmltodict==0.13.0 wget==3.2
 
 # Copy service from build container
 RUN mkdir -p ${SERVICE_DIRECTORY}
 WORKDIR ${SERVICE_DIRECTORY}
-COPY --from=build-service-metastore2 ${SERVICE_DIRECTORY} ./
+COPY --from=build-service-indexing ${SERVICE_DIRECTORY} ./
 
 ENV PYTHONIOENCODING=UTF-8
 

build.gradle

@@ -3,7 +3,7 @@ plugins {
     id "io.spring.dependency-management" version "1.1.0" 
     id "io.freefair.lombok" version "6.6.1"
     id "io.freefair.maven-publish-java" version "6.6.1"
-    id "org.owasp.dependencycheck" version "8.0.1"
+    id "org.owasp.dependencycheck" version "8.0.2"
     id 'org.asciidoctor.jvm.convert' version '3.3.2'
     id 'net.researchgate.release' version '3.0.2'
     id "com.gorylenko.gradle-git-properties" version "2.4.1"
@@ -13,7 +13,7 @@ plugins {
 
 ext {
   // versions of dependencies
-  javersVersion     = '6.8.2'
+  javersVersion     = '6.9.1'
   springDocVersion  = '1.6.14'
 }
 
@@ -71,12 +71,12 @@ dependencies {
     implementation "org.springdoc:springdoc-openapi-webmvc-core:${springDocVersion}"
 
     // driver for postgres
-    implementation "org.postgresql:postgresql:42.5.1"
+    implementation "org.postgresql:postgresql:42.5.3"
     //driver for h2
     implementation "com.h2database:h2:2.1.214"
 
     //apache
-    implementation "org.apache.tika:tika-core:2.6.0"
+    implementation "org.apache.tika:tika-core:2.7.0"
     implementation "commons-codec:commons-codec:1.15"
 
     implementation "com.github.jknack:handlebars:4.3.1"
@@ -93,7 +93,7 @@ dependencies {
     // actuator
     implementation 'de.codecentric:spring-boot-admin-starter-client:2.7.10'
 
-    runtimeOnly    'org.apache.httpcomponents:httpclient:4.5.6'
+    runtimeOnly    'org.apache.httpcomponents:httpclient:4.5.14'
 
     // Additional libraries for tests
     testImplementation "com.google.guava:guava:31.1-jre"
@@ -102,7 +102,7 @@ dependencies {
     testImplementation "org.springframework.security:spring-security-test"
 
     //Java 11 Support 
-    testImplementation "org.mockito:mockito-core:5.0.0"
+    testImplementation "org.mockito:mockito-core:5.1.1"
     testImplementation "junit:junit:4.13.2"
 
     testImplementation 'org.springframework.restdocs:spring-restdocs-mockmvc:2.0.7.RELEASE'
@@ -129,39 +129,6 @@ bootJar {
     launchScript()
 }
 
-task prepareElastic(type:Exec) {
-  println 'Start elasticsearch container'
-  if (System.getProperty('os.name').toLowerCase(Locale.ROOT).contains('windows')) {
-    println '##################################################################'
-    println 'ATTENTION: Please start elasticsearch by your own!'
-    println '##################################################################'
-  } else {
-    commandLine "bash", "./manageIndexingFramework.sh", "test"
-  }
-}
-
-task stopElastic(type:Exec) {
-  println 'Stop elasticsearch container'
-  if (System.getProperty('os.name').toLowerCase(Locale.ROOT).contains('windows')) {
-    println '##################################################################'
-    println 'ATTENTION: Please stop elasticsearch by your own!'
-    println '##################################################################'
-  } else {
-    commandLine "bash", "./manageIndexingFramework.sh", "stop_test"
-  }
-}
-
-test {
-    dependsOn prepareElastic
-    finalizedBy stopElastic, jacocoTestReport
-    environment "spring.config.location", "classpath:/test-config/"
-
-    testLogging {
-        outputs.upToDateWhen {false}
-        showStandardStreams = true
-    }
-}
-
 jacoco {
     toolVersion = "0.8.8"
 }

build.sh

@@ -50,15 +50,14 @@ function checkParameters {
   # Check if directory exists
   if [ ! -d "$INSTALLATION_DIRECTORY" ]; then
     # Create directory if it doesn't exists.
-    mkdir -p "$INSTALLATION_DIRECTORY"
-    if [ $? -ne 0 ]; then
+   if ! mkdir -p "$INSTALLATION_DIRECTORY"; then
       echo "Error creating directory '$INSTALLATION_DIRECTORY'!"
       echo "Please make sure that you have the correct access permissions for the specified directory."
       exit 1
     fi
   fi
   # Check if directory is empty
-  if [ ! -z "$(ls -A "$INSTALLATION_DIRECTORY")" ]; then
+   if [ -n "$(ls -A "$INSTALLATION_DIRECTORY")" ]; then
      echo "Directory '$INSTALLATION_DIRECTORY' is not empty!"
      echo "Please enter an empty or a new directory!"
      exit 1
@@ -74,7 +73,7 @@ it 1; }
 function printInfo {
 ################################################################################
 echo "---------------------------------------------------------------------------"
-echo $*
+echo "$*"
 echo "---------------------------------------------------------------------------"
 }
 
@@ -89,8 +88,7 @@ testForCommands="chmod cp dirname find java javac mkdir sed"
 
 for command in $testForCommands
 do 
-  type $command >> /dev/null
-  if [ $? -ne 0 ]; then
+  if ! type "$command" >> /dev/null; then
     echo "Error: command '$command' is not installed!"
     exit 1
   fi
@@ -121,11 +119,11 @@ printInfo "Build microservice of $REPO_NAME at '$INSTALLATION_DIRECTORY'"
 ################################################################################
 
 echo Build service...
-./gradlew -Prelease clean build
+./gradlew -Dprofile=release clean build
 
 
 echo "Copy configuration to '$INSTALLATION_DIRECTORY'..."
-find . -name application-default.properties -exec sed -e "s/src\/test\/resources\/python/scripts\/python/g" '{}' > "$INSTALLATION_DIRECTORY"/application.properties \;
+find ./settings -name application-default.properties -exec cp '{}' "$INSTALLATION_DIRECTORY"/application.properties \;
 
 echo "Copy jar file to '$INSTALLATION_DIRECTORY'..."
 find . -name "$REPO_NAME*.jar" -exec cp '{}' "$INSTALLATION_DIRECTORY" \;