Merge pull request #10 from maximilianiKIT/dev

Dev

Author: maximiliani

.github/workflows/CI.yml

@@ -7,31 +7,47 @@ name: Java CI
 
 on:
   push:
-    branches: [ main , dev]
+    branches: [main, dev]
   pull_request:
-    branches: "*"
+    branches: [main, dev]
 
 jobs:
-  build-jdk:
-    runs-on: ubuntu-latest
+  build:
+    name: Build and generate coverage report with Gradle in JDK ${{ matrix.jdk }} on ${{ matrix.os }}
     strategy:
       matrix:
-        jdk: [ 17 ]
+#        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest, macos-latest]
+        jdk: [17]
+        python-version: [3.9]
+    runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout repo
         uses: actions/checkout@v2
       - name: Set up OpenJDK
         uses: actions/setup-java@v1
         with:
           java-version: ${{ matrix.jdk }}
-      - name: Install python
-        run: sudo apt install -y python3 python3-setuptools python3-pip
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get Python location
+        run: python -c "import os, sys; print(sys.executable)"
       - name: Update pip
-        run: pip3 install --upgrade pip
+        run: python3 -m pip install --upgrade pip
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
-      - name: Build with Gradle
-        run: ./gradlew clean check jacocoTestReport
+      - name: Clean
+        run: ./gradlew clean
+#      - if: matrix.os == 'windows-latest'
+#        name: Test with Gradle on Windows
+#        run: ./gradlew build -DapplicationProperties="src\test\resources\test-config\application-test-windows.properties"
+      - if: matrix.os != 'windows-latest'
+        name: Test with Gradle on ${{ matrix.os }}
+        run: ./gradlew build -DapplicationProperties="src/test/resources/test-config/application-test.properties"
+      - name: Generate report
+        run: ./gradlew jacocoTestReport
       - name: Codecov
         uses: codecov/codecov-action@v1
         with:

.github/workflows/codeql-analysis.yml

@@ -13,7 +13,7 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ "main", "dev" ]
+    branches: [ main, dev ]
   pull_request:
     # The branches below must be a subset of the branches above
     branches: "*"
@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       actions: read
-      contents: read
+      contents: write
       security-events: write
 
     strategy:
@@ -37,20 +37,21 @@ jobs:
         # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v3
-
+    - uses: actions/checkout@v3
+    - name: Set up Python3
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
     - name: Set up OpenJDK
       uses: actions/setup-java@v1
       with:
-        java-version: ${{ matrix.jdk }}
+        java-version: 17
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v2
       with:
         languages: ${{ matrix.language }}
-        java-version: 17
         # If you wish to specify custom queries, you can do so here or in a config file.
         # By default, queries listed here will override any specified in a config file.
         # Prefix the list here with "+" to use these queries and those in the config file.
@@ -61,22 +62,57 @@ jobs:
 
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
-      with:
-        java-version: 17
+#    - name: Autobuild
+#      uses: github/codeql-action/autobuild@v2
+#      with:
+#        java-version: 17
 
       # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
 
     #   If the Autobuild fails above, remove it and uncomment the following three lines. 
     #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
 
-#   #  - run: |
-#       echo "Run, Build Application using script"
-#       ./location_of_script_within_repo/buildscript.sh
+    - run: |
+       echo "Run, Build Application using script"
+       ./gradlew build -DapplicationProperties="src/test/resources/test-config/application-test.properties"
 
     - name: Perform CodeQL Analysis
       uses: github/codeql-action/analyze@v2
       with:
-        category: "/language:${{matrix.language}}"
+        category: "/language:java
+
+  review:
+    name: Review Dependencies and create SBOM
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: write
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python3
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Set up OpenJDK
+        uses: actions/setup-java@v1
+        with:
+          java-version: 17
+
+      - name: 'Dependency Review'
+        uses: actions/dependency-review-action@v2
+
+      - name: Scan the image and upload dependency results
+        uses: anchore/sbom-action@v0
+        with:
+          artifact-name: image.spdx.json
+          dependency-snapshot: true
+

.gitignore

@@ -236,4 +236,5 @@ gradle-app.setting
 
 # End of https://www.toptal.com/developers/gitignore/api/intellij+all,java,macos,gradle,linux
 lib/gemma
-!/plugins/gemma-plugin-0.1.0.jar
+!/plugins/gemma-plugin-0.1.0-SNAPSHOT-plain.jar
+!/plugins/empty-plugin-0.0.0-SNAPSHOT-plain.jar

README.md

@@ -1,15 +1,19 @@
 # Mapping-Service
 
 [![Java CI with Gradle](https://github.com/maximilianiKIT/mapping-service/actions/workflows/CI.yml/badge.svg)](https://github.com/maximilianiKIT/mapping-service/actions/workflows/CI.yml)
-![License](https://img.shields.io/github/license/kit-data-manager/indexing-service.svg)
+[![CodeQL](https://github.com/maximilianiKIT/mapping-service/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/maximilianiKIT/mapping-service/actions/workflows/codeql-analysis.yml)
 [![codecov](https://codecov.io/gh/maximilianiKIT/mapping-service/branch/main/graph/badge.svg?token=XFhZruKFaE)](https://codecov.io/gh/maximilianiKIT/mapping-service)
+[![License](https://img.shields.io/github/license/kit-data-manager/indexing-service.svg)](https://github.com/maximilianiKIT/mapping-service/blob/c3ab1c96643b3409774eafd4c8f0843cb9ae2aa1/LICENSE)
 
 :warning:
 Not fully tested yet!
+The mapping-service provides a generic interface for mapping various documents. 
+The tools required for this, such as Gemma, JOLT, XSLT, ... can be loaded into the mapping-service as plugins, regardless of the programming language in which they were developed. 
+These tools are then made usable via the REST-API and a Web-UI. 
+The mapping schemas are stored in a database and can be managed via the REST-API and the Web-UI.
 
-The mapping service allows multiple schemas to be uploaded and managed and documents to be mapped over one of them at a time accordingly.
-Therefore, the service is extensible to other mappers, although currently only Gemma, a service that can only map JSON files, is available.
-The REST API is documented at the following link: [http://localhost:8095/swagger-ui/index.html](http://localhost:8095/swagger-ui/index.html)
+The Web-UI is accessible via the following URL: [http://\<IP or hostname>:8095](http://localhost:8095)
+The REST-API is documented at the following link: [http://\<IP or hostname>:8095/swagger-ui/index.html](http://localhost:8095/swagger-ui/index.html)
 
 ## How to build
 

build.gradle

@@ -10,6 +10,7 @@ plugins {
 
 description = 'Generic mapping service supporting different mapping implementations.'
 group = 'edu.kit.datamanager'
+version = '0.1.0-SNAPSHOT'
 
 println "Running gradle version: $gradle.gradleVersion"
 println "Building ${name} version: ${version}"
@@ -30,6 +31,7 @@ repositories {
 
 ext {
     set('snippetsDir', file('build/generated-snippets'))
+    applicationProperties = System.getProperty('applicationProperties', 'src/main/resources/application.properties')
 }
 
 dependencies {
@@ -58,7 +60,7 @@ dependencies {
     testImplementation 'org.springframework.boot:spring-boot-starter-test:2.7.3'
     testImplementation 'org.springframework.restdocs:spring-restdocs-mockmvc:2.0.6.RELEASE'
     testImplementation 'org.springframework.security:spring-security-test:5.7.3'
-    testImplementation 'org.springframework:spring-test:5.3.22'
+    testImplementation 'org.springframework:spring-test:5.3.23'
     testImplementation 'org.mockito:mockito-core:4.8.0'
     testImplementation 'org.powermock:powermock-module-junit4:2.0.9'
     testImplementation 'org.powermock:powermock-api-mockito2:2.0.9'
@@ -80,6 +82,9 @@ dependencies {
 test {
     outputs.dir snippetsDir
     finalizedBy jacocoTestReport
+    print("Running tests with configuration: ${applicationProperties}")
+    environment 'spring.config.location', applicationProperties
+//    environment 'spring.config.location', 'classpath:/test-config/'
     useJUnitPlatform()
 }
 
@@ -91,7 +96,7 @@ jacocoTestReport{
     dependsOn test
     reports {
         xml.required = true
-        html.required = false
+        html.required = true
     }
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
 

output

@@ -0,0 +1 @@
+Hello World!Input file: inputMapping schema file: schema

plugins/empty-plugin-0.0.0-SNAPSHOT-plain.jar

@@ -16,7 +16,6 @@
 @EntityScan("edu.kit.datamanager")
 @Configuration
 public class MappingServiceApplication {
-
     private static final Logger LOG = LoggerFactory.getLogger(MappingServiceApplication.class);
 
     @Bean