Merge branch 'development' into renovate/org.apache.tika-tika-core-3.x

Author: ThomasJejkal

build.gradle

@@ -74,7 +74,7 @@ dependencies {
 
     // monitoring
     implementation 'io.micronaut.micrometer:micronaut-micrometer-registry-prometheus:5.10.2'
-    implementation 'org.springframework.boot:spring-boot-starter-actuator:3.3.4'
+    implementation 'org.springframework.boot:spring-boot-starter-actuator:3.4.5'
 
      // springdoc
     implementation "org.springdoc:springdoc-openapi-starter-webmvc-ui:${springDocVersion}"

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.3-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

src/main/java/edu/kit/datamanager/mappingservice/MappingServiceApplication.java

@@ -1,7 +1,5 @@
 package edu.kit.datamanager.mappingservice;
 
-import com.google.common.collect.ImmutableSet;
-import com.google.common.reflect.ClassPath;
 import edu.kit.datamanager.mappingservice.configuration.ApplicationProperties;
 import edu.kit.datamanager.mappingservice.plugins.PluginManager;
 import io.micrometer.core.instrument.MeterRegistry;
@@ -11,29 +9,22 @@
 import edu.kit.datamanager.security.filter.KeycloakJwtProperties;
 import edu.kit.datamanager.security.filter.KeycloakTokenFilter;
 import edu.kit.datamanager.security.filter.KeycloakTokenValidator;
-import java.io.IOException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
 import org.springframework.boot.autoconfigure.domain.EntityScan;
 import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.scheduling.annotation.EnableAsync;
 
 @SpringBootApplication
-@ComponentScan({"edu.kit.datamanager.mappingservice"})
 @EntityScan("edu.kit.datamanager")
 @Configuration
 @EnableAsync
 public class MappingServiceApplication {
 
-    private static final Logger LOG = LoggerFactory.getLogger(MappingServiceApplication.class);
-
     @Autowired
     private final MeterRegistry meterRegistry;
 
@@ -68,7 +59,7 @@ public KeycloakJwtProperties keycloakProperties() {
             value = "mapping-service.authEnabled",
             havingValue = "true",
             matchIfMissing = false)
-    public KeycloakTokenFilter keycloaktokenFilterBean() throws Exception {
+    public KeycloakTokenFilter keycloakTokenFilterBean() {
         return new KeycloakTokenFilter(KeycloakTokenValidator.builder()
                 .readTimeout(keycloakProperties().getReadTimeoutms())
                 .connectTimeout(keycloakProperties().getConnectTimeoutms())
@@ -77,17 +68,17 @@ public KeycloakTokenFilter keycloaktokenFilterBean() throws Exception {
                 .build(keycloakProperties().getJwkUrl(), keycloakProperties().getResource(), keycloakProperties().getJwtClaim()));
     }
 
-    public static void main(String[] args) throws IOException {
+    public static void main(String[] args) {
         ConfigurableApplicationContext ctx = SpringApplication.run(MappingServiceApplication.class, args);
 
         PluginManager mgr = ctx.getBean(PluginManager.class);
         System.out.println("Found plugins: ");
         mgr.getPlugins().forEach((k, v) -> {
-            System.out.println(String.format(" - %s (%s)", k, v));
+            System.out.printf(" - %s (%s)%n", k, v);
         });
         System.out.println("Using Python Version: ");
         PythonRunnerUtil.printPythonVersion();
         String port = ctx.getEnvironment().getProperty("server.port");
-        System.out.println(String.format("Mapping service is running on port %s.", port));
+        System.out.printf("Mapping service is running on port %s.%n", port);
     }
 }

src/main/java/edu/kit/datamanager/mappingservice/configuration/WebSecurityConfig.java

@@ -34,6 +34,8 @@
 import org.springframework.security.config.annotation.web.builders.HttpSecurity;
 import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
 import org.springframework.security.config.annotation.web.configuration.WebSecurityCustomizer;
+import org.springframework.security.config.annotation.web.configurers.AbstractHttpConfigurer;
+import org.springframework.security.config.annotation.web.configurers.HeadersConfigurer;
 import org.springframework.security.config.http.SessionCreationPolicy;
 import org.springframework.security.config.Customizer;
 import org.springframework.security.web.SecurityFilterChain;
@@ -50,13 +52,13 @@
  */
 @Configuration
 @EnableWebSecurity
-@EnableMethodSecurity(prePostEnabled = true)
+@EnableMethodSecurity
 public class WebSecurityConfig {
 
     private static final Logger logger = LoggerFactory.getLogger(WebSecurityConfig.class);
 
     @Autowired
-    private Optional<KeycloakTokenFilter> keycloaktokenFilterBean;
+    private Optional<KeycloakTokenFilter> keycloakTokenFilterBean;
     @Autowired
     private ApplicationProperties applicationProperties;
 
@@ -89,7 +91,7 @@ public SecurityFilterChain filterChain(HttpSecurity http) throws Exception {
             );
         } else {
             logger.trace("Authentication is DISABLED. Not securing endpoints.");
-            securedEndpointMatchers = Arrays.asList();
+            securedEndpointMatchers = List.of();
         }
 
         HttpSecurity httpSecurity = http.authorizeHttpRequests(
@@ -112,11 +114,11 @@ public SecurityFilterChain filterChain(HttpSecurity http) throws Exception {
                         session -> session.sessionCreationPolicy(SessionCreationPolicy.STATELESS));
 
         logger.info("CSRF disabled!");
-        httpSecurity = httpSecurity.csrf(csrf -> csrf.disable());
+        httpSecurity.csrf(AbstractHttpConfigurer::disable);
 
-        if (keycloaktokenFilterBean.isPresent()) {
+        if (keycloakTokenFilterBean.isPresent()) {
             logger.trace("Adding Keycloak filter to filter chain.");
-            httpSecurity.addFilterAfter(keycloaktokenFilterBean.get(), BasicAuthenticationFilter.class);
+            httpSecurity.addFilterAfter(keycloakTokenFilterBean.get(), BasicAuthenticationFilter.class);
         } else {
             logger.trace("Keycloak not configured. Skip adding keycloak filter to filter chain.");
         }
@@ -130,7 +132,7 @@ public SecurityFilterChain filterChain(HttpSecurity http) throws Exception {
         }
 
         logger.trace("Turning off cache control.");
-        httpSecurity.headers(headers -> headers.cacheControl(cache -> cache.disable()));
+        httpSecurity.headers(headers -> headers.cacheControl(HeadersConfigurer.CacheControlConfig::disable));
 
         return httpSecurity.build();
     }

src/main/java/edu/kit/datamanager/mappingservice/dao/IMappingRecordDao.java

@@ -37,7 +37,7 @@ public interface IMappingRecordDao extends JpaRepository<MappingRecord, String>,
      * Find a MappingRecords by the given ID.
      *
      * @param mappingId The id to search for.
-     * @return A optional of the matching MappingRecord.
+     * @return An optional of the matching MappingRecord.
      */
     Optional<MappingRecord> findByMappingId(String mappingId);
 

src/main/java/edu/kit/datamanager/mappingservice/impl/MappingService.java

@@ -27,6 +27,7 @@
 import edu.kit.datamanager.mappingservice.exception.MappingNotFoundException;
 import edu.kit.datamanager.mappingservice.exception.MappingServiceException;
 import edu.kit.datamanager.mappingservice.exception.MappingServiceUserException;
+import edu.kit.datamanager.mappingservice.plugins.IMappingPlugin;
 import edu.kit.datamanager.mappingservice.plugins.MappingPluginException;
 import edu.kit.datamanager.mappingservice.plugins.MappingPluginState;
 import edu.kit.datamanager.mappingservice.plugins.PluginManager;
@@ -50,9 +51,7 @@
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.text.SimpleDateFormat;
-import java.util.Collections;
-import java.util.Date;
-import java.util.Optional;
+import java.util.*;
 import java.util.concurrent.CompletableFuture;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -91,7 +90,6 @@ public class MappingService {
      */
     private Path jobsOutputDirectory;
 
-    private ApplicationProperties applicationProperties;
     private final MeterRegistry meterRegistry;
 
     /**
@@ -101,9 +99,8 @@ public class MappingService {
 
     @Autowired
     public MappingService(ApplicationProperties applicationProperties, MeterRegistry meterRegistry) {
-        this.applicationProperties = applicationProperties;
         this.meterRegistry = meterRegistry;
-        init(this.applicationProperties);
+        init(applicationProperties);
     }
 
     /**
@@ -118,32 +115,35 @@ public MappingService(ApplicationProperties applicationProperties, MeterRegistry
      */
     public MappingRecord createMapping(String content, MappingRecord mappingRecord) throws IOException {
         LOGGER.trace("Creating mapping with id {}.", mappingRecord.getMappingId());
-        // Check for valid mapping ID (should contain at least one non whitespace.
+        // Check for valid mapping ID (should contain at least one non whitespace).
         String mappingId = mappingRecord.getMappingId();
         if ((mappingId == null) || (mappingId.isBlank())) {
-            String message = String.format("MappingID shouldn't be empty or contain only whitespaces. You provide '%s'", mappingId);
+            String message = String.format("MappingID shouldn't be empty or contain only whitespaces. You provided '%s'", mappingId);
             LOGGER.error(message);
             throw new BadArgumentException(message);
         }
 
         String mappingType = mappingRecord.getMappingType();
         if ((mappingType == null) || (mappingType.isBlank() || !pluginManager.getPlugins().containsKey(mappingType))) {
-            String message = String.format("MappingType shouldn't be empty or contain only whitespaces and must be a registered plugin id. You provide '%s'", mappingType);
+            String message = String.format("MappingType shouldn't be empty or contain only whitespaces and must be a registered plugin id. You provided '%s'", mappingType);
             LOGGER.error(message);
+            Set<Map.Entry<String, IMappingPlugin>> entries = pluginManager.getPlugins().entrySet();
+            LOGGER.info("Registered plugins: ");
+            for(Map.Entry<String, IMappingPlugin> entry : entries) {
+                LOGGER.info(" * {}", entry.getKey());
+            }
+
             throw new BadArgumentException(message);
         }
 
         Iterable<MappingRecord> findMapping = mappingRepo.findByMappingIdIn(Collections.singletonList(mappingRecord.getMappingId()));
         if (findMapping.iterator().hasNext()) {
-            LOGGER.error("Unable to create mapping with id {}. Mapping id is alreadyy used.", mappingRecord.getMappingId());
+            LOGGER.error("Unable to create mapping with id {}. Mapping id is already used.", mappingRecord.getMappingId());
             mappingRecord = findMapping.iterator().next();
             throw new DuplicateMappingException("Error: Mapping '" + mappingRecord.getMappingType() + "_" + mappingRecord.getMappingId() + "' already exists!");
         }
 
-        LOGGER.trace("Saving mapping file.");
-        saveMappingFile(content, mappingRecord);
-        LOGGER.trace("Persisting mapping record.");
-        MappingRecord result = mappingRepo.save(mappingRecord);
+        MappingRecord result = persistMapping(content, mappingRecord);
         LOGGER.trace("Mapping with id {} successfully created.", result.getMappingId());
         return mappingRecord;
     }
@@ -163,10 +163,7 @@ public void updateMapping(String content, MappingRecord mappingRecord) throws Ma
 
         LOGGER.trace("Updating mapping with id {}.", mappingRecord.getMappingId());
         mappingRecord.setMappingDocumentUri(findMapping.get().getMappingDocumentUri());
-        LOGGER.trace("Saving mapping file.");
-        saveMappingFile(content, mappingRecord);
-        LOGGER.trace("Persisting mapping record.");
-        mappingRepo.save(mappingRecord);
+        persistMapping(content, mappingRecord);
         LOGGER.trace("Mapping with id {} successfully updated.", mappingRecord.getMappingId());
     }
 
@@ -189,7 +186,7 @@ public void deleteMapping(MappingRecord mappingRecord) {
         try {
             deleteMappingFile(mappingRecord);
         } catch (IOException e) {
-            LOGGER.error(String.format("Failed to delete mapping file at %s. Please remove it manually.", mappingRecord.getMappingDocumentUri()), e);
+            LOGGER.error("Failed to delete mapping file at {}. Please remove it manually.", mappingRecord.getMappingDocumentUri(), e);
         }
     }
 
@@ -432,7 +429,11 @@ public JobStatus deleteJobAndAssociatedData(String jobId) {
             //delete output file if file still exists (even after the job was removed from the queue)
             File outputFile = getOutputFile(jobId);
             if (outputFile.exists()) {
-                outputFile.delete();
+                if(outputFile.delete()){
+                    LOGGER.trace("Output file {} deleted.", outputFile);
+                }else{
+                    LOGGER.warn("Output file {} could not be deleted.", outputFile);
+                }
             } else {
                 LOGGER.debug("No output file for job {} found.", jobId);
             }
@@ -458,7 +459,11 @@ public JobStatus deleteJobAndAssociatedData(String jobId) {
 
             if (jobOutput.exists()) {
                 LOGGER.trace(" - Deleting job output");
-                jobOutput.delete();
+                if(jobOutput.delete()){
+                    LOGGER.trace(" - Output file {} deleted.", jobOutput);
+                }else{
+                    LOGGER.warn(" ! Output file {} could not be deleted.", jobOutput);
+                }
             }
             LOGGER.trace("Removing job from queue.");
             jobManager.removeJob(jobId);
@@ -488,7 +493,7 @@ private File getOutputFile(String jobId) {
     }
 
     /**
-     * Initalize mappings directory and mappingUtil instance.
+     * Initialize mappings directory and mappingUtil instance.
      *
      * @param applicationProperties Properties holding mapping directory
      * setting.
@@ -578,4 +583,11 @@ private String date2String() {
         SimpleDateFormat sdf = new SimpleDateFormat("_yyyyMMdd_HHmmss");
         return sdf.format(new Date());
     }
+
+    private MappingRecord persistMapping(String content, MappingRecord mappingRecord) throws IOException {
+        LOGGER.trace("Saving mapping file.");
+        saveMappingFile(content, mappingRecord);
+        LOGGER.trace("Persisting mapping record.");
+        return mappingRepo.save(mappingRecord);
+    }
 }

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

@@ -33,8 +33,6 @@
 import org.apache.maven.artifact.versioning.ComparableVersion;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Component;
 
 /**
  *
@@ -47,17 +45,17 @@ public abstract class AbstractPythonMappingPlugin implements IMappingPlugin {
     /**
      * The plugin name.
      */
-    private String name;
+    private final String name;
     /**
      * The URL of the Git repository where the plugin code is located.
      */
-    private String repositoryUrl;
+    private final String repositoryUrl;
 
     /**
-     * The tag which should be used to checkout a specific version from
+     * The tag which should be used to check out a specific version from
      * repositoryUrl.
      */
-    private String tag;
+    private final String tag;
 
     /**
      * The minimal python version required by the plugin
@@ -69,8 +67,8 @@ public abstract class AbstractPythonMappingPlugin implements IMappingPlugin {
      */
     private Path dir;
 
-    private String pluginVenv = "venv/PluginVenv";
-    private String venvInterpreter;
+    private final String pluginVenv = "venv/PluginVenv";
+    private final String venvInterpreter;
 
     /**
      * Default constructor for instantiating a Python-based mapping plugin. It
@@ -82,10 +80,9 @@ public abstract class AbstractPythonMappingPlugin implements IMappingPlugin {
      * the root of the Jar file. The properties file must contain one property
      * 'version' which represents an existing Git tag matching a released
      * version of the Python plugin code, e.g., version=v1.0.0
-     *
      * Furthermore, the properties file may contain a minimal Python version
      * that is required by the plugin to work. The minimal Python version is set
-     * via the 'min.python' property, e.g.., min.python=3.10.0 If the minimal
+     * via the 'min.python' property, e.g., min.python=3.10.0 If the minimal
      * Python version is not met, the plugin will be ignored.
      *
      * @param pluginName The name of the plugin.
@@ -129,20 +126,17 @@ public AbstractPythonMappingPlugin(String pluginName, String repositoryUrl) {
      * plugin to gather all information required for starting a Python process
      * executing the mapping script. The returned array must contain at least
      * the following information:
-     *
      * <ul> <li>The absolute path of the main script. It must start
      * with the working dir received as argument, where all checked-out code is
      * located.</li> <li>Script-specific parameters to provide
      * mappingFile, inputFile, and outputFile to the script execution. Depending
      * on the script implementation, the number and kind of required arguments
      * may differ.</li> </ul>
-     *
      * Example: In standalone mode, a script is called via `plugin_wrapper.py
      * sem -m mappingFile -i inputFile -o outputFile -debug`. In that case, the
      * resulting array should look as follows: [workingDir +
      * "plugin_wrapper.py", "sem", "-m", mappingFile.toString(), "-i",
      * inputFile.toString(), "-o", outputFile.toString(), "-debug"].
-     *
      * The Python call itself will be added according to the Venv used for
      * plugin execution and must not be included.
      *
@@ -244,7 +238,6 @@ public MappingPluginState mapFile(Path mappingFile, Path inputFile, Path outputF
      * This method checks if the local Python installation version is larger or
      * equal the provided version number. The version should be provided as
      * semantic version number, i.e., 3.13.2
-     *
      * The method will return TRUE if the minimal requirements are met and false
      * otherwise. False is also returned if obtaining/parsing the local python
      * version fails. for any reason.
@@ -266,7 +259,7 @@ private boolean hasMinimalPythonVersion(String versionString) {
                 LOGGER.error("Failed to obtain Python version. python --version returned with status {}.", state.getState());
             } else {
 
-                LOGGER.trace("Version command output: {}", bout.toString());
+                LOGGER.trace("Version command output: {}", bout);
 
                 String[] split = bout.toString().split(" ");