From ffb19cd33761f429de58e9c3df8b3116fbe70a1d Mon Sep 17 00:00:00 2001
From: Tim <tim@raro.dev>
Date: Mon, 31 Jul 2023 13:48:02 +0200
Subject: [PATCH] [Fix] Fix the reflexion warning on ontology generation in
 s-pipes-modules

---
 .../main/java/RdfAnnotationProcessorMojo.java | 41 +++++++++++++------
 s-pipes-modules/pom.xml                       | 37 ++++++++---------
 2 files changed, 46 insertions(+), 32 deletions(-)

diff --git a/s-pipes-modules-utils/s-pipes-module-creator-maven-plugin/src/main/java/RdfAnnotationProcessorMojo.java b/s-pipes-modules-utils/s-pipes-module-creator-maven-plugin/src/main/java/RdfAnnotationProcessorMojo.java
index 4de3cc2d..621c5775 100644
--- a/s-pipes-modules-utils/s-pipes-module-creator-maven-plugin/src/main/java/RdfAnnotationProcessorMojo.java
+++ b/s-pipes-modules-utils/s-pipes-module-creator-maven-plugin/src/main/java/RdfAnnotationProcessorMojo.java
@@ -52,21 +52,32 @@ public class RdfAnnotationProcessorMojo extends AbstractMojo {
     @Parameter(defaultValue = "${project}", readonly = true, required = true)
     MavenProject project;
 
-    @Parameter(defaultValue = "${project.groupId}", readonly = true, required = true)
-    String javaModuleName;
-
-    @Parameter(required = false, readonly = true)
-    String moduleClassName;
+    /**
+     * The mode in which the plugin is running. 2 values are supported:
+     * <ul>
+     *  <li><b>RDF_FOR_MODULE</b> - Generate an RDF ontology for a single module.
+     *  Presumes that the pom.xml belongs to the module itself.</li>
+     *  <li><b>RDF_FOR_ALL_CHILDREN</b> - Generate an RDF ontology that contains
+     *  all modules from this Maven project's submodules. In this mode, the plugin will try to
+     *  look through all available classes and find those annotated as SPipes Modules.</li>
+     * </ul>
+     * Defaults to <b>RDF_FOR_ALL_CHILDREN</b> if no mode is explicitly specified.
+     */
+    @Parameter(readonly = true)
+    GenerationMode mode;
 
-    @Parameter(required = false, readonly = true)
+    /**
+     * The Java module which should be scanned for the SPipes Module classes.
+     */
+    @Parameter(required = true, readonly = true)
     String modulePackageName;
 
-    @Parameter(required = false, readonly = true)
+    /**
+     * Filename of the ontology file generated by the plugin.
+     */
+    @Parameter(required = true, readonly = true)
     String ontologyFilename;
 
-    @Parameter(required = false, readonly = true)
-    GenerationMode mode;
-
     enum GenerationMode {
         RDF_FOR_MODULE,
         RDF_FOR_ALL_CHILDREN
@@ -105,6 +116,7 @@ public void execute() throws MojoExecutionException {
 
     }
 
+    @SuppressWarnings("unchecked") // Maven returns untyped list which must be manually retyped
     private void generateRdfForAllModules() throws MalformedURLException, ClassNotFoundException, FileNotFoundException {
         //read all submodules
         getLog().info("Generating an RDF for all sub-modules");
@@ -113,7 +125,8 @@ private void generateRdfForAllModules() throws MalformedURLException, ClassNotFo
 
             //find module's main class
             var moduleClasses = readAllModuleClasses(submodule);
-            getLog().info("Module: " + submodule.getName() + " | Classes: [" + moduleClasses.stream()
+            getLog().info("Scanned maven module '" + submodule.getName() + "' and found " + moduleClasses.size()
+                    + " SPipes Module(s): [" + moduleClasses.stream()
                     .map(Class::getSimpleName)
                     .collect(Collectors.joining(", ")) + "]");
 
@@ -129,7 +142,7 @@ private void generateRdfForAllModules() throws MalformedURLException, ClassNotFo
         }
         writeModelToStdout(model);
         try {
-            writeToTargetFolderFile(model, "all-modules.ttl");
+            writeToTargetFolderFile(model, ontologyFilename);
         } catch (IOException e) {
             getLog().error("Failed to write model to the output file", e);
         }
@@ -164,7 +177,9 @@ private Set<Class<?>> readAllModuleClasses(MavenProject project) throws Malforme
         var reflectionConfig = new ConfigurationBuilder()
                 .setUrls(ClasspathHelper.forClassLoader(classLoader))
                 .setScanners(new SubTypesScanner(false), new TypeAnnotationsScanner())
-                .filterInputsBy(new FilterBuilder().includePackage(modulePackageName));
+                .filterInputsBy(new FilterBuilder().includePackage(modulePackageName))
+                .setExpandSuperTypes(false);
+
         var classSearcher = new Reflections(reflectionConfig);
 
         //Find classes with the module annotation
diff --git a/s-pipes-modules/pom.xml b/s-pipes-modules/pom.xml
index b566649f..a6f7f996 100644
--- a/s-pipes-modules/pom.xml
+++ b/s-pipes-modules/pom.xml
@@ -51,25 +51,24 @@
                 </configuration>
             </plugin>
 
-<!--            <plugin>-->
-<!--                <groupId>cz.cvut.kbss</groupId>-->
-<!--                <artifactId>s-pipes-module-creator-maven-plugin</artifactId>-->
-<!--                <version>${project.parent.version}</version>-->
-<!--                <inherited>false</inherited>-->
-<!--                <executions>-->
-<!--                    <execution>-->
-<!--                        <goals>-->
-<!--                            <goal>process-annotations</goal>-->
-<!--                        </goals>-->
-<!--                        <configuration>-->
-<!--                            <mode>RDF_FOR_ALL_CHILDREN</mode>-->
-<!--                            <moduleClassName>FoobarModule</moduleClassName>-->
-<!--                            <modulePackageName>cz.cvut.spipes.modules</modulePackageName>-->
-<!--                            <ontologyFilename>test-own-artifact-generated.ttl</ontologyFilename>-->
-<!--                        </configuration>-->
-<!--                    </execution>-->
-<!--                </executions>-->
-<!--            </plugin>-->
+            <plugin>
+                <groupId>cz.cvut.kbss</groupId>
+                <artifactId>s-pipes-module-creator-maven-plugin</artifactId>
+                <version>${project.parent.version}</version>
+                <inherited>false</inherited>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>process-annotations</goal>
+                        </goals>
+                        <configuration>
+                            <mode>RDF_FOR_ALL_CHILDREN</mode>
+                            <modulePackageName>cz.cvut.spipes</modulePackageName>
+                            <ontologyFilename>all-modules.ttl</ontologyFilename>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
 
         </plugins>
     </build>