Cleaned up swagger documentation, made pythonLocation externally configurable, fixed some tests to also work under Windows, updated README.md

Author: ThomasJejkal

README.md

@@ -21,24 +21,45 @@ Dependencies that are needed to build and are not being downloaded via gradle:
 
 - OpenJDK 17
 - Python 3
+- pip
 
 `./gradlew -Pclean-release build`
 
-## How to start
+### Python Location
 
-`./gradlew bootRun`
+Currently, mapping-service requires Python to be installed in order to build and to run. By default, the Python location is set to `/usr/bin/python3`. In case
+your Python installation is located elsewhere or you build the mapping-service under Windows, you can provide the Python location externally, i.e.:
+
+```
+`./gradlew -Pclean-release build -DpythonLocation=file:///C:/Python310/python.EXE`
+```
 
-### Prerequisites
-Please make sure the application.properties file is configured correctly.
-Espacially the following properties (at the end of the file) are important:
-- `mapping-service.pythonLocation=file:///opt/homebrew/bin/python3` \
-Enter the loacation of your python3 installation. You can determine it by typing `which python3` in your terminal.
+## How to start
+
+Before you can start the mapping-service, you  first have to create an `application.properties` file in the source folder. As an example you may use `config/application.default.properties`
+and modify it according to your needs. Espacially the following properties (at the end of the file) are important:
+- `spring.datasource.url=jdbc:h2:file:e:/tmp/mapping-service/database`
+The path points to the location of the database in which your configured mappings are stored.
+- `mapping-service.pythonLocation=${pythonLocation:'file:///usr/bin/python3'}` \
+If no pythonLocation is provided externally (see above) the default `/usr/bin/python3` is used.
 - `mapping-service.mappingsLocation:file:///tmp/mapping-service/` \
 Enter the location where you want to store your mappings. This folder will be created if it does not exist yet.
 
 You might want to add a plugin to make the service working. Normally, there should be a gemma-plugin-x.x.x.jar in the plugins folder.
 If not, you can find its source code [here](https://github.com/maximilianiKIT/gemma-plugin).
 
+After doing this, the mapping-service is ready for the first start. This can be achieved by executing:
+
+`./gradlew bootRun`
+
+### Python Location
+
+Similar to configuring the Python location for the build process, you may also do the same for running the mapping-service via:
+
+```
+.\gradlew -DpythonLocation=file:///C:/Python310/python.EXE bootRun
+```
+
 ## License
 
 See [LICENSE file in this repository](LICENSE).

build.gradle

@@ -32,7 +32,8 @@ repositories {
 
 ext {
     set('snippetsDir', file('build/generated-snippets'))
-    applicationProperties = System.getProperty('applicationProperties', 'src/main/resources/application.properties')
+    applicationProperties = System.getProperty('applicationProperties', './src/test/resources/test-config/application-test.properties')
+    pythonLocation = System.getProperty('pythonLocation', 'file:///usr/bin/python3')
 }
 
 dependencies {
@@ -85,6 +86,7 @@ test {
     finalizedBy jacocoTestReport
     print("Running tests with configuration: ${applicationProperties}")
     environment 'spring.config.location', applicationProperties
+    environment 'pythonLocation', pythonLocation
 //    environment 'spring.config.location', 'classpath:/test-config/'
     useJUnitPlatform()
 }
@@ -117,6 +119,11 @@ springBoot {
     buildInfo()
 }
 
+bootRun {
+    systemProperty "spring.config.location", "file:$projectDir/"
+    systemProperty "pythonLocation", pythonLocation
+}
+
 bootJar {
     dependsOn asciidoctor
     from ("${asciidoctor.outputDir}/html5") {

src/main/resources/application.properties renamed to config/application.default.properties

@@ -24,7 +24,7 @@ management.endpoints.web.exposure.include=*
 # Database
 ##################################################
 spring.datasource.driver-class-name=org.h2.Driver
-spring.datasource.url=jdbc:h2:file:///tmp/mapping-service/database
+spring.datasource.url=jdbc:h2:file:e:/tmp/mapping-service/database
 spring.datasource.username=user
 spring.datasource.password=password
 spring.jpa.hibernate.ddl-auto=update
@@ -33,7 +33,7 @@ spring.jpa.hibernate.ddl-auto=update
 # Mapping-Service specific settings
 ##################################################
 # Absolute path to the local python interpreter
-mapping-service.pythonLocation=file:///usr/bin/python3
+mapping-service.pythonLocation=${pythonLocation:'file:///usr/bin/python3'}
 
 # Absolute path to the local gemma mappings folder
 mapping-service.mappingSchemasLocation=file:///tmp/mapping-service/mappingSchemas

echo.bat

@@ -0,0 +1 @@
+echo @1

output

@@ -25,6 +25,7 @@
  */
 public class JARFileFilter implements FileFilter {
 
+    @Override
     public boolean accept(File f) {
         return f.getName().toLowerCase().endsWith(".jar");
     }

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

@@ -12,7 +12,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 package edu.kit.datamanager.mappingservice.plugins;
 
 import org.slf4j.Logger;
@@ -44,21 +43,31 @@ public class PluginLoader {
      */
     static Logger LOG = LoggerFactory.getLogger(PluginLoader.class);
 
+    static ClassLoader cl = null;
+
+    public static void unload() {
+        cl = null;
+        System.gc();
+    }
+
     /**
      * Load plugins from a given directory.
      *
      * @param plugDir Directory containing plugins.
      * @return Map of plugins.
-     * @throws IOException            If there is an error with the file system.
-     * @throws MappingPluginException If there is an error with the plugin or the input.
+     * @throws IOException If there is an error with the file system.
+     * @throws MappingPluginException If there is an error with the plugin or
+     * the input.
      */
     public static Map<String, IMappingPlugin> loadPlugins(File plugDir) throws IOException, MappingPluginException {
-        if (plugDir == null || plugDir.getAbsolutePath().isBlank())
+        if (plugDir == null || plugDir.getAbsolutePath().isBlank()) {
             throw new MappingPluginException(MappingPluginState.INVALID_INPUT, "Empty input!");
+        }
         File[] plugJars = plugDir.listFiles(new JARFileFilter());
-        if (plugJars == null || plugJars.length < 1)
+        if (plugJars == null || plugJars.length < 1) {
             throw new MappingPluginException(MappingPluginState.NOT_FOUND, "No plugins found.");
-        ClassLoader cl = new URLClassLoader(PluginLoader.fileArrayToURLArray(plugJars));
+        }
+        cl = new URLClassLoader(PluginLoader.fileArrayToURLArray(plugJars));
         List<Class<IMappingPlugin>> plugClasses = PluginLoader.extractClassesFromJARs(plugJars, cl);
 
         List<IMappingPlugin> IMappingPluginList = PluginLoader.createPluggableObjects(plugClasses);
@@ -71,7 +80,6 @@ public static Map<String, IMappingPlugin> loadPlugins(File plugDir) throws IOExc
         return result;
     }
 
-
     private static URL[] fileArrayToURLArray(File[] files) throws MalformedURLException {
 
         URL[] urls = new URL[files.length];
@@ -93,22 +101,22 @@ private static List<Class<IMappingPlugin>> extractClassesFromJARs(File[] jars, C
     private static List<Class<IMappingPlugin>> extractClassesFromJAR(File jar, ClassLoader cl) throws IOException, MappingPluginException {
 
         List<Class<IMappingPlugin>> classes = new ArrayList<>();
-        JarInputStream jaris = new JarInputStream(new FileInputStream(jar));
-        JarEntry ent;
-        while ((ent = jaris.getNextJarEntry()) != null) {
-            if (ent.getName().toLowerCase().endsWith(".class")) {
-                try {
-                    Class<?> cls = cl.loadClass(ent.getName().substring(0, ent.getName().length() - 6).replace('/', '.'));
-                    if (PluginLoader.isPluggableClass(cls)) {
-                        classes.add((Class<IMappingPlugin>) cls);
+        try (JarInputStream jaris = new JarInputStream(new FileInputStream(jar))) {
+            JarEntry ent;
+            while ((ent = jaris.getNextJarEntry()) != null) {
+                if (ent.getName().toLowerCase().endsWith(".class")) {
+                    try {
+                        Class<?> cls = cl.loadClass(ent.getName().substring(0, ent.getName().length() - 6).replace('/', '.'));
+                        if (PluginLoader.isPluggableClass(cls)) {
+                            classes.add((Class<IMappingPlugin>) cls);
+                        }
+                    } catch (ClassNotFoundException e) {
+                        LOG.info("Can't load Class " + ent.getName());
+                        throw new MappingPluginException(MappingPluginState.UNKNOWN_ERROR, "Can't load Class " + ent.getName(), e);
                     }
-                } catch (ClassNotFoundException e) {
-                    LOG.info("Can't load Class " + ent.getName());
-                    throw new MappingPluginException(MappingPluginState.UNKNOWN_ERROR, "Can't load Class " + ent.getName(), e);
                 }
             }
         }
-        jaris.close();
         return classes;
     }
 

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

@@ -66,6 +66,10 @@ public static PluginManager soleInstance() {
         return soleInstance;
     }
 
+    public void unload(){
+        PluginLoader.unload();
+        plugins.clear();
+    }
     /**
      * Reloads the plugins from the 'plugins' directory.
      */