Fixed autowire of applicationProperties in AbstractPythongMappingPlugin, fixed dependency duplication issue, tests may still fail

Author: ThomasJejkal

build.gradle

@@ -82,7 +82,11 @@ dependencies {
     implementation 'com.google.guava:guava:33.4.8-jre'
     implementation 'commons-io:commons-io:2.19.0'
     implementation 'javax.validation:validation-api:2.0.1.Final'
-    implementation 'edu.kit.datamanager:service-base:1.3.3'
+    implementation ('edu.kit.datamanager:service-base:1.3.3'){
+        //exclude dependency as spring boot includes 
+        //org.glassfish.jaxb:jaxb-core:4.0.5 which leads to a duplication conflict
+       	exclude group: "com.sun.xml.bind"
+    }
     // apache
     implementation "org.apache.tika:tika-core:2.9.3"
 

src/main/java/edu/kit/datamanager/mappingservice/plugins/AbstractPythonMappingPlugin.java

@@ -40,16 +40,15 @@
  *
  * @author jejkal
  */
-@Component
 public abstract class AbstractPythonMappingPlugin implements IMappingPlugin {
 
     private final Logger LOGGER = LoggerFactory.getLogger(AbstractPythonMappingPlugin.class);
 
     /**
-     * Application properties autowired at instantiation time.
+     * Application properties autowired at instantiation time via
+     * setApplicationProperties.
      */
-    @Autowired
-    private final ApplicationProperties applicationProperties;
+    private ApplicationProperties applicationProperties;
     /**
      * The plugin name.
      */
@@ -130,6 +129,17 @@ public AbstractPythonMappingPlugin(String pluginName, String repositoryUrl) {
         }
     }
 
+    /**
+     * Setter to autowire ApplicationProperties into all implementations of this
+     * abstract class.
+     *
+     * @param applicationProperties The applicationProperties bean.
+     */
+    @Autowired
+    public final void setApplicationProperties(ApplicationProperties applicationProperties) {
+        this.applicationProperties = applicationProperties;
+    }
+
     /**
      * Abstract method that is supposed to be implemented by each Python mapping
      * plugin to gather all information required for starting a Python process

src/main/java/edu/kit/datamanager/mappingservice/plugins/impl/GemmaPlugin.java

@@ -16,19 +16,13 @@
 package edu.kit.datamanager.mappingservice.plugins.impl;
 
 import edu.kit.datamanager.mappingservice.plugins.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.util.MimeType;
 import org.springframework.util.MimeTypeUtils;
 import java.nio.file.Path;
 
 public class GemmaPlugin extends AbstractPythonMappingPlugin {
 
-    private final Logger LOGGER = LoggerFactory.getLogger(GemmaPlugin.class);
     private static final String GEMMA_REPOSITORY = "https://github.com/kit-data-manager/gemma.git";
-    private static final String GEMMA_BRANCH = "master";
-    private static Path gemmaDir;
-    private boolean initialized = false;
 
     public GemmaPlugin() {
         super("GEMMA", GEMMA_REPOSITORY);
@@ -58,17 +52,4 @@ public String[] getCommandArray(Path workingDir, Path mappingFile, Path inputFil
             outputFile.toString()
         };
     }
-
-  /*  @Override
-    public MappingPluginState mapFile(Path mappingFile, Path inputFile, Path outputFile) throws MappingPluginException {
-        if (initialized) {
-            LOGGER.trace("Running plugin '{}' v{} on '{}' with mapping '{}' -> '{}'", name(), version(), inputFile, mappingFile, outputFile);
-            return PythonRunnerUtil.runPythonScript(gemmaDir + "/mapping_single.py", mappingFile.toString(), inputFile.toString(), outputFile.toString());
-        } else {
-            LOGGER.error("Plugin '" + name() + "' " + version() + " not initialized. Returning EXECUTION_ERROR.");
-            MappingPluginState result = MappingPluginState.EXECUTION_ERROR();
-            result.setDetails("Plugin not initialized, probably due to missing dependencies or external plugin repository.");
-            return result;
-        }
-    }*/
 }

src/main/resources/gemma.properties

@@ -0,0 +1,2 @@
+version=master
+min.python=3.0.0

src/test/java/edu/kit/datamanager/mappingservice/util/FileUtilTest.java

@@ -322,7 +322,7 @@ public void testFixFileExtensionWrongFile() {
     @Test
     void cloneValidGitRepository() {
         Path util = null;
-        
+
         try {
             util = FileUtil.cloneGitRepository("https://github.com/kit-data-manager/mapping-service.git", "main", "/tmp/test");
         } catch (Exception e) {
@@ -340,7 +340,6 @@ void cloneValidGitRepository() {
     @Test
     void cloneInvalidGitRepository() {
         assertThrows(MappingServiceException.class, () -> FileUtil.cloneGitRepository("test", "test", "test"));
-        assertThrows(MappingServiceException.class, () -> FileUtil.cloneGitRepository("test", "test"));
     }
 
     @AfterEach

src/test/resources/test-config/application-test.properties

@@ -67,6 +67,7 @@ eureka.client.enabled: false
 mapping-service.pythonExecutable=${pythonExecutable:file:///usr/bin/python}
 # Absolute path to the folder where all plugins are located
 mapping-service.pluginLocation=file:///tmp/mapping-service/plugins
+mapping-service.codeLocation=file:///tmp/mapping-service/code
 # Absolute path to the local gemma mappings folder
 mapping-service.mappingSchemasLocation=file:///tmp/mapping-service/schemas
 # Folder where job output files for async mapping executions are stored