kit-data-manager · gabinoumbe · Mar 25, 2026 · Jan 26, 2026 · Jan 26, 2026 · Jan 26, 2026
diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/plugin-integration.yml b/.github/workflows/plugin-integration.yml
@@ -7,12 +7,10 @@ on:
 jobs:
   build:
     runs-on: ${{ matrix.operating-system }}
-    environment:
-      name: ${{ github.ref_name }}
     strategy:
       matrix:
         operating-system: [ubuntu-latest]
-        versions: [ { jdk: 17, mapping-service: v1.0.5 }, { jdk: 21, mapping-service: latest } ]
+        versions: [ { jdk: 17, mapping-service: v2.0.2 }, { jdk: 21, mapping-service: latest } ]
 
     steps:
     - name: Checkout repository
@@ -34,8 +32,9 @@ jobs:
         JAR_VERSION=$(./mappingservice-plugin/gradlew printVersion -q -p ./mappingservice-plugin/)
         JAR_VERSION=${JAR_VERSION##*$'\n'}
         ./mappingservice-plugin/gradlew clean jar -p ./mappingservice-plugin/
+        ls -ll ./mappingservice-plugin/build/libs/
         echo "JAR_VERSION=${JAR_VERSION}"
-        mv -v ./mappingservice-plugin/build/libs/ApeHePlugin-$JAR_VERSION-plain.jar ./mappingservice-plugin/build/libs/ApeHeplugin.jar
+        mv -v ./mappingservice-plugin/build/libs/ApeHePlugin-$JAR_VERSION.jar ./mappingservice-plugin/build/libs/ApeHeplugin.jar
       env:
         VERSION_OVERRIDE_BY_BRANCH: ${{ steps.extract_branch.outputs.branch }}
 
@@ -47,13 +46,11 @@ jobs:
 
   test:
     runs-on: ${{ matrix.operating-system }}
-    environment:
-      name: ${{ github.ref_name }}
     strategy:
       fail-fast: false
       matrix:
         operating-system: [ubuntu-latest]
-        versions: [ { jdk: 17, mapping-service: v1.0.5 }, { jdk: 21, mapping-service: latest } ]
+        versions: [ { jdk: 17, mapping-service: v2.0.2 }, { jdk: 21, mapping-service: latest } ]
     needs: build
 
     steps:
@@ -73,7 +70,7 @@ jobs:
 
     - name: Run Docker Container
       run: |
-        docker run -d -p 8095:8095 -e PIP_BREAK_SYSTEM_PACKAGES=1 -v ./plugins/ApeHeplugin.jar:/spring/mapping-service/plugins/ApeHeplugin.jar --name mapping4docker ghcr.io/kit-data-manager/mapping-service:${{ matrix.versions.mapping-service }}
+        docker run -d -p 8095:8095 -e PIP_BREAK_SYSTEM_PACKAGES=1 -e SPRING_APPLICATION_JSON='{"mapping-service.executionTimeout":300}' -v ./plugins/ApeHeplugin.jar:/spring/mapping-service/plugins/ApeHeplugin.jar --name mapping4docker ghcr.io/kit-data-manager/mapping-service:${{ matrix.versions.mapping-service }}
         echo "Waiting for mapping service to be healthy..."
         while true; do
           if ! docker ps | grep -q mapping4docker; then
@@ -84,35 +81,20 @@ jobs:
             echo "Service is running."
             break
           fi
-          echo "Waiting..."
+          echo "Waiting for the service to be ready ..."
           docker logs --tail 20 mapping4docker
           sleep 5
         done
 
-    - name: Install Hurl & Prepare JSON
-      run: |
-        curl -LO https://github.com/Orange-OpenSource/hurl/releases/download/6.0.0/hurl_6.0.0_amd64.deb
-        sudo dpkg -i hurl_6.0.0_amd64.deb
-        sudo apt install -y dos2unix
-
-        # Fetch mappingType dynamically
-        mappingType=$(curl -s http://localhost:8095/api/v1/mappingAdministration/types | jq -r '.[0].id')
-
-        echo "Using mappingType: $mappingType"
-
-        echo "{\"mappingId\":\"96\",\"mappingType\":\"$mappingType\",\"title\":\"apeHe from CI test\",\"description\":\"\",\"acl\":[]}" > record.json
-        echo '{"entry.title.value": "entry.title"}' > document.json
-
-        unix2dos -n ./mappingservice-plugin/integrationtests/basic.hurl ./mappingservice-plugin/integrationtests/basic_crlf.hurl
-
     - name: Run Tests with Hurl
       run: |
-        hurl --variable host=http://localhost:8095 --test ./mappingservice-plugin/integrationtests/basic_crlf.hurl --verbose --file-root .
+         curl --location --remote-name https://github.com/Orange-OpenSource/hurl/releases/download/6.0.0/hurl_6.0.0_amd64.deb
+         sudo dpkg -i hurl_6.0.0_amd64.deb
+         sudo apt install -y dos2unix
+         unix2dos -n ./mappingservice-plugin/integrationtests/basic.hurl ./mappingservice-plugin/integrationtests/basic_crlf.hurl
+         hurl --variable host=http://localhost:8095 --test ./mappingservice-plugin/integrationtests/basic_crlf.hurl --verbose --file-root .
       env:
         VERSION_OVERRIDE_BY_BRANCH: ${{ steps.extract_branch.outputs.branch }}
-
-    - name: Clean up temp files
-      run: rm -f record.json document.json
-
+
     - name: Stop Docker Container
-      run: docker stop mapping4docker
+      run: docker stop mapping4docker
diff --git a/CITATION.cff b/CITATION.cff
@@ -4,7 +4,7 @@ type: software
 title: APE-HE mapper
 abstract: APE-HE Mapper is a tool designed for mapping APE-HE (Advanced Photoelectric
   Effect - High Energy) metadata to a uniform, schema-compliant json format.
-version: v1.0.0
+version: v1.1.0rc
 keywords:
   - APE-HE
   - neXus

diff --git a/codemeta.json b/codemeta.json
@@ -25,7 +25,7 @@
   ],
   "name": "APE-HE mapper",
   "description": "APE-HE Mapper is a tool designed for mapping APE-HE (Advanced Photoelectric Effect - High Energy) metadata to a uniform, schema-compliant json format.",
-  "version": "v1.0.0",
+  "version": "v1.1.0rc",
   "keywords": [
     "APE-HE",
     "neXus",

diff --git a/mappingservice-plugin/build.gradle b/mappingservice-plugin/build.gradle
@@ -1,22 +1,28 @@
-import org.tomlj.Toml
+buildscript {
+    // Buildscript repositories
+    repositories {
+        mavenLocal()
+        mavenCentral()
+    }
+
+    dependencies {
+        classpath("org.tomlj:tomlj:1.1.1")
+    }
+}
 
 plugins {
-    id 'io.spring.dependency-management' version "1.1.7"
-    id 'org.springframework.boot' version "3.4.4"
     id 'java'
 }
 
-group 'edu.kit.datamanager'
+import org.tomlj.Toml
 
 repositories {
     mavenLocal()
     mavenCentral()
 }
 
 dependencies {
-    implementation 'org.springframework:spring-core:6.2.5'
-    implementation 'org.slf4j:slf4j-api:2.0.17'
-    implementation files("src/main/lib/mapping-service-plain.jar")
+    implementation 'edu.kit.datamanager:mapping-plugin-core:2.0.0'
 }
 
 if (System.getenv('VERSION_OVERRIDE_BY_BRANCH')) {
@@ -32,22 +38,24 @@ tasks.register('printVersion') {
     println project.version
 }
 
+group 'edu.kit.datamanager'
+
 //Task for creating a resource file with the version info
 tasks.register("generateVersionProps", WriteProperties) { t ->
     def generatedResourcesDir = project.layout.buildDirectory.dir(["resources", "main"].join(File.separator))
-    def outputFile = generatedResourcesDir.map { it.file("apeHepluginversion.properties") }
+    def outputFile = generatedResourcesDir.map { it.file("apehe_nxs2json.properties") }
 
     t.destinationFile = outputFile.get().asFile
     t.property("version", project.version)
 }
 
-resolveMainClassName.dependsOn("generateVersionProps")
+//resolveMainClassName.dependsOn("generateVersionProps")
 
 jar {
     dependsOn(generateVersionProps)
     archiveFileName
 }
 
-bootJar {
-    enabled = false
-}
+//bootJar {
+//    enabled = false
+//}
diff --git a/mappingservice-plugin/integrationtests/basic.hurl b/mappingservice-plugin/integrationtests/basic.hurl
@@ -8,25 +8,34 @@ HTTP 200
 # Get mapping types from the mapping service 
 # to fetch the first available id
 # ----------------------------------------------------------
-GET {{host}}/api/v1/mappingAdministration/types
+GET {{host}}/api/v1/mappingAdministration/plugins
 HTTP 200
 [Captures]
-mappingType: jsonpath "$[0].id"
+mappingType: regex "(?s)\"id\"\\s*:\\s*\"([^\"]+)\"\\s*,\\s*[^}]*?\"name\"\\s*:\\s*\"ApeHe_nxs2JSON\""
 
 # ---------------- BEGIN Test Mapping for Ape-He -----------
 
 # ----------------------------------------------------------
-# Register a dummy mapping with created files:
-# - record.json (containing the mapping scheme metadata)
-# - document.json (containing the dummy map file)
+# Register a dummy mapping with embedded JSON
 # ----------------------------------------------------------
 POST {{host}}/api/v1/mappingAdministration/
+Content-Type: multipart/form-data; boundary=boundary
 [Options]
-variable: id1=96
-[MultipartFormData]
-record: file,record.json; type=application/json
-document: file,document.json; type=application/json
-HTTP 201  # Expect plugin to be successfully created
+variable: id1=0
+```
+--boundary
+Content-Disposition: form-data; name="record"; filename="blob"
+Content-Type: application/json
+
+{"mappingId":"{{id1}}","mappingType": "{{mappingType}}","title":"APE-HE from CI test","description":"","acl":[]}
+--boundary
+Content-Disposition: form-data; name="document"; filename="blob"
+Content-Type: application/json
+
+{"entry.title.value": "entry.title"}
+--boundary--
+```
+HTTP 201
 
 # ----------------------------------------------------------
 # Execute mapping with test data

diff --git a/mappingservice-plugin/src/main/java/edu/kit/datamanager/apeHeplugin/ApeHePlugin.java b/mappingservice-plugin/src/main/java/edu/kit/datamanager/apeHeplugin/ApeHePlugin.java
@@ -1,60 +1,15 @@
 package edu.kit.datamanager.apeHeplugin;
 
-import edu.kit.datamanager.mappingservice.plugins.*;
-import edu.kit.datamanager.mappingservice.util.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.util.MimeType;
-import org.springframework.util.MimeTypeUtils;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
+import edu.kit.datamanager.mappingservice.plugins.AbstractPythonMappingPlugin;
 import java.nio.file.Path;
-import java.util.Properties;
-
-public class ApeHePlugin implements IMappingPlugin{
 
-    private static String version;
+public class ApeHePlugin extends AbstractPythonMappingPlugin{
 
-    private final Logger LOGGER = LoggerFactory.getLogger(ApeHePlugin.class);
-    private final String REPOSITORY = "https://github.com/kit-data-manager/ape_he_mapper";
-    private String TAG;
-    private Path dir;
+    private static final String REPOSITORY = "https://github.com/kit-data-manager/ape_he_mapper";
 
-    //private String pluginVenv = "venv/PluginVenv";
-    //private String venvInterpreter;
 
     public ApeHePlugin() {
-        try {
-            // Get the context class loader
-            ClassLoader classLoader = this.getClass().getClassLoader();
-            // TODO: do we need to make sure that the resource path is somehow related to the current plugin to avoid loading the wrong property file in case of identical property names?
-            URL resource = classLoader.getResource("apeHepluginversion.properties");
-            LOGGER.info("Resource file: {}", resource);
-            if (resource != null) {
-                // Load the properties file
-                try (InputStream input = resource.openStream()) {
-                    Properties properties = new Properties();
-                    properties.load(input);
-                    version = properties.getProperty("version");
-                    TAG = version;
-                }
-            } else {
-                System.err.println("Properties file not found!");
-                version = "unavailable";
-                TAG = "unavailable";
-            }
-
-            //if (System.getProperty("os.name").startsWith("Windows")) {
-            //    venvInterpreter = pluginVenv + "/Scripts/python.exe";
-            //} else {
-            //    venvInterpreter = pluginVenv + "/bin/python3";
-            //}
-
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
+        super("ApeHe_nxs2JSON", REPOSITORY);
     }
 
     @Override
@@ -68,86 +23,32 @@ public String description() {
     }
 
     @Override
-    public String version() {
-        return version;
-    }
-
-    @Override
-    public String uri() {
-        return REPOSITORY;
-    }
-
-    @Override
-    public MimeType[] inputTypes() {
-        return new MimeType[]{
-            MimeTypeUtils.parseMimeType("application/octet-stream"), 
-            MimeTypeUtils.parseMimeType("application/x-hdf5"),
-            MimeTypeUtils.parseMimeType("application/zip")
+    public String[] inputTypes() {
+        return new String[]{
+            "application/octet-stream", 
+            "application/x-hdf5",
+            "application/zip"
         };
     }
 
     @Override
-    public MimeType[] outputTypes() {
-        return new MimeType[]{
-            MimeTypeUtils.APPLICATION_JSON, 
-            MimeTypeUtils.parseMimeType("application/zip")
+    public String[] outputTypes() {
+        return new String[]{
+            "application/json", 
+            "application/zip"
         };
     }
 
     @Override
-    public void setup() {
-        LOGGER.info("Checking and installing dependencies for the tool: ");
-        //TODO: test for minimal python version?
-        try {
-            LOGGER.info("Cloning git repository {}, Tag {}", REPOSITORY, TAG);
-            dir = FileUtil.cloneGitRepository(REPOSITORY, TAG);
-            // Install Python dependencies
-
-            ProcessBuilder pb = new ProcessBuilder("python3", "-m", "pip", "install", "-r", dir + "/requirements.dist.txt");
-            pb.inheritIO();
-            Process p = pb.start();
-
-            int exitCode = p.waitFor();
-            if (exitCode != 0) {
-                LOGGER.error("Failed to install Python packages");
-            }
-
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-    }
-    /* public void setup() {
-        LOGGER.trace("Setting up mapping plugin {} {}", name(), version());
-        //TODO: test for minimal python version?
-        try {
-            LOGGER.info("Cloning git repository {}, Tag {}", REPOSITORY, TAG);
-            dir = FileUtil.cloneGitRepository(REPOSITORY, TAG);
-            // Install Python dependencies
-
-            MappingPluginState venvState = PythonRunnerUtil.runPythonScript("-m", "venv", "--system-site-packages", dir + "/" + pluginVenv);
-            if (MappingPluginState.SUCCESS().getState().equals(venvState.getState())) {
-                LOGGER.info("Venv for plugin installed successfully.");
-                LOGGER.info("Installing packages");
-                ShellRunnerUtil.run(dir + "/" + venvInterpreter, "-m", "pip", "install", "-r", dir + "/" + "requirements.dist.txt");
-            } else {
-                LOGGER.error("venv installation was not successful");
-            }
-
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-    } */
-
-    @Override
-    public MappingPluginState mapFile(Path mappingFile, Path inputFile, Path outputFile) throws MappingPluginException {
-        long startTime = System.currentTimeMillis();
-        LOGGER.trace("Run ApeHe-Mapping-Tool on '{}' with mapping '{}' -> '{}'", mappingFile, inputFile, outputFile);
-        //MappingPluginState result = ShellRunnerUtil.run(dir + "/" + venvInterpreter, dir + "/plugin_wrapper.py", "-m", mappingFile.toString(), "-i", inputFile.toString(), "-o", outputFile.toString());
-        String[] args = {"-m", mappingFile.toString(), "-i", inputFile.toString(), "-o", outputFile.toString()};
-        MappingPluginState result = PythonRunnerUtil.runPythonScript(dir + "/plugin_wrapper.py", args);
-        long endTime = System.currentTimeMillis();
-        long totalTime = endTime - startTime;
-        LOGGER.info("Execution time of mapFile: {} milliseconds", totalTime);
-        return result;
+    public String[] getCommandArray(Path workingDir, Path mappingFile, Path inputFile, Path outputFile) {
+        return new String[]{
+                workingDir + "/plugin_wrapper.py",
+                "-m",
+                mappingFile.toString(),
+                "-i",
+                inputFile.toString(),
+                "-o",
+                outputFile.toString()
+        };
     }
 }
diff --git a/mappingservice-plugin/src/main/lib/mapping-service-plain.jar b/mappingservice-plugin/src/main/lib/mapping-service-plain.jar