Removed redundant information from REST API

fixed bugs
comments
refactoring

Author: maximiliani

plugins/gemma-plugin-0.1.0.jar

@@ -31,21 +31,21 @@ public class MappingServiceApplication {
 
     private static final Logger LOG = LoggerFactory.getLogger(MappingServiceApplication.class);
 
-    @Bean
-    @Scope("prototype")
-    public Logger logger(InjectionPoint injectionPoint) {
-        Class<?> targetClass = injectionPoint.getMember().getDeclaringClass();
-        return LoggerFactory.getLogger(targetClass.getCanonicalName());
-    }
+//    @Bean
+//    @Scope("prototype")
+//    public Logger logger(InjectionPoint injectionPoint) {
+//        Class<?> targetClass = injectionPoint.getMember().getDeclaringClass();
+//        return LoggerFactory.getLogger(targetClass.getCanonicalName());
+//    }
 
-    @Bean(name = "OBJECT_MAPPER_BEAN")
-    public ObjectMapper jsonObjectMapper() {
-        return Jackson2ObjectMapperBuilder.json()
-                .serializationInclusion(JsonInclude.Include.NON_EMPTY) // Don’t include null values
-                .featuresToDisable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS) //ISODate
-                .modules(new JavaTimeModule())
-                .build();
-    }
+//    @Bean(name = "OBJECT_MAPPER_BEAN")
+//    public ObjectMapper jsonObjectMapper() {
+//        return Jackson2ObjectMapperBuilder.json()
+//                .serializationInclusion(JsonInclude.Include.NON_EMPTY) // Don’t include null values
+//                .featuresToDisable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS) //ISODate
+//                .modules(new JavaTimeModule())
+//                .build();
+//    }
 
     @Bean
     @ConfigurationProperties("repo")

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

@@ -15,8 +15,6 @@
  */
 package edu.kit.datamanager.mappingservice.configuration;
 
-import org.slf4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.web.servlet.FilterRegistrationBean;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -41,9 +39,6 @@
 @EnableGlobalMethodSecurity(prePostEnabled = true)
 public class WebSecurityConfig extends WebSecurityConfigurerAdapter {
 
-    @Autowired
-    private Logger logger;
-
     public WebSecurityConfig() {
     }
 

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

@@ -32,11 +32,16 @@
  * @author maximilianiKIT
  */
 public interface IMappingRecordDao extends JpaRepository<MappingRecord, String>, JpaSpecificationExecutor<MappingRecord> {
-    Optional<MappingRecord> findByMappingId(String mappingId);
 
-    Optional<MappingRecord> findByMappingIdAndMappingType(String mappingId, String mappingType);
+    /**
+     * Find a MappingRecords by the given ID.
+     *
+     * @param mappingId The id to search for.
+     * @return A optional of the matching MappingRecord.
+     */
+    Optional<MappingRecord> findByMappingId(String mappingId);
 
-    Iterable<MappingRecord> findByMappingIdInOrMappingTypeIn(List<String> mappingId, List<String> mappingType);
+    Iterable<MappingRecord> findByMappingIdIn(List<String> mappingId);
 
-    Page<MappingRecord> findByMappingIdInOrMappingTypeIn(List<String> mappingId, List<String> mappingType, Pageable pgbl);
+    Page<MappingRecord> findByMappingIdIn(List<String> mappingId, Pageable pgbl);
 }

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

@@ -50,9 +50,6 @@ public boolean equals(Object obj) {
         if (!Objects.equals(this.mappingId, other.mappingId)) {
             return false;
         }
-        if (!Objects.equals(this.mappingType, other.mappingType)) {
-            return false;
-        }
-        return true;
+        return Objects.equals(this.mappingType, other.mappingType);
     }
 }

src/main/java/edu/kit/datamanager/mappingservice/domain/CompositeKey.java

@@ -45,7 +45,6 @@ public class MappingRecord implements EtagSupport, Serializable {
     @NotNull(message = "The unique identify of the record.")
     private String mappingId;
 
-    @Id
     @NotNull(message = "Type of the mapping, e.g. GEMMA, XSLT, handlebars, ....")
     private String mappingType;
 

src/main/java/edu/kit/datamanager/mappingservice/domain/MappingRecord.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2018 Karlsruhe Institute of Technology.
+ * Copyright 2022 Karlsruhe Institute of Technology.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

src/main/java/edu/kit/datamanager/mappingservice/exception/MappingException.java

@@ -32,15 +32,16 @@
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;
-import java.net.URISyntaxException;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.text.SimpleDateFormat;
-import java.util.*;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Optional;
 
 /**
  * Service for managing mappings.
@@ -63,7 +64,7 @@ public class MappingService {
     private final static Logger LOGGER = LoggerFactory.getLogger(MappingService.class);
 
     @Autowired
-    public MappingService(ApplicationProperties applicationProperties) throws URISyntaxException {
+    public MappingService(ApplicationProperties applicationProperties) {
         init(applicationProperties);
     }
 
@@ -74,9 +75,7 @@ public MappingService(ApplicationProperties applicationProperties) throws URISyn
      * @param mappingRecord record of the mapping
      */
     public void createMapping(String content, MappingRecord mappingRecord) throws IOException {
-        // Right now only one mapping per mappingID is allowed. May change in future.
-        //   Optional<MappingRecord> findMapping = mappingRepo.findByMappingIdAndMappingType(mappingRecord.getMappingId(), mappingRecord.getMappingType());
-        Iterable<MappingRecord> findMapping = mappingRepo.findByMappingIdInOrMappingTypeIn(Arrays.asList(mappingRecord.getMappingId()), Arrays.asList((String) null));
+        Iterable<MappingRecord> findMapping = mappingRepo.findByMappingIdIn(Collections.singletonList(mappingRecord.getMappingId()));
         if (findMapping.iterator().hasNext()) {
             mappingRecord = findMapping.iterator().next();
             throw new MappingException("Error: Mapping '" + mappingRecord.getMappingType() + "_" + mappingRecord.getMappingId() + "' already exists!");
@@ -92,8 +91,8 @@ public void createMapping(String content, MappingRecord mappingRecord) throws IO
      * @param mappingRecord record of the mapping
      */
     public void updateMapping(String content, MappingRecord mappingRecord) throws IOException {
-        Optional<MappingRecord> findMapping = mappingRepo.findByMappingIdAndMappingType(mappingRecord.getMappingId(), mappingRecord.getMappingType());
-        if (!findMapping.isPresent()) {
+        Optional<MappingRecord> findMapping = mappingRepo.findByMappingId(mappingRecord.getMappingId());
+        if (findMapping.isEmpty()) {
             throw new MappingException("Error: Mapping '" + mappingRecord.getMappingType() + "_" + mappingRecord.getMappingId() + "' doesn't exist!");
         }
         mappingRecord.setMappingDocumentUri(findMapping.get().getMappingDocumentUri());
@@ -107,8 +106,8 @@ public void updateMapping(String content, MappingRecord mappingRecord) throws IO
      * @param mappingRecord record of the mapping
      */
     public void deleteMapping(MappingRecord mappingRecord) throws IOException {
-        Optional<MappingRecord> findMapping = mappingRepo.findByMappingIdAndMappingType(mappingRecord.getMappingId(), mappingRecord.getMappingType());
-        if (!findMapping.isPresent()) {
+        Optional<MappingRecord> findMapping = mappingRepo.findByMappingId(mappingRecord.getMappingId());
+        if (findMapping.isEmpty()) {
             throw new MappingException("Error: Mapping '" + mappingRecord.getMappingType() + "_" + mappingRecord.getMappingId() + "' doesn't exist!");
         }
         mappingRecord = findMapping.get();
@@ -120,24 +119,22 @@ public void deleteMapping(MappingRecord mappingRecord) throws IOException {
      * Execute mapping and get the location of result file. If no according
      * mapping is found the src file will be returned.
      *
-     * @param contentUrl  Content of the src file.
-     * @param mappingId   filename of the mapping
-     * @param mappingType type of the mapping.
+     * @param contentUrl Content of the src file.
+     * @param mappingId  id of the mapping
      * @return Path to result file.
      */
-    public Optional<Path> executeMapping(URI contentUrl, String mappingId, String mappingType) throws MappingPluginException {
-        Optional<Path> returnValue = Optional.empty();
+    public Optional<Path> executeMapping(URI contentUrl, String mappingId) throws MappingPluginException {
+        Optional<Path> returnValue;
         Optional<Path> download = FileUtil.downloadResource(contentUrl);
-        MappingRecord mappingRecord = null;
+        MappingRecord mappingRecord;
 
         if (download.isPresent()) {
-            LOGGER.trace("Execute Mapping for '{}', and mapping '{}/{}'.", contentUrl.toString(), mappingId, mappingType);
+            LOGGER.trace("Execute Mapping for '{}', and mapping '{}'.", contentUrl.toString(), mappingId);
             Path srcFile = download.get();
             // Get mapping file
-            Optional<MappingRecord> optionalMappingRecord = mappingRepo.findByMappingIdAndMappingType(mappingId, mappingType);
+            Optional<MappingRecord> optionalMappingRecord = mappingRepo.findByMappingId(mappingId);
             if (optionalMappingRecord.isPresent()) {
                 mappingRecord = optionalMappingRecord.get();
-                //   mappingRecord.getMappingDocumentUri();
                 Path mappingFile = Paths.get(mappingRecord.getMappingDocumentUri());
                 // execute mapping
                 Path resultFile;
@@ -150,42 +147,18 @@ public Optional<Path> executeMapping(URI contentUrl, String mappingId, String ma
                 returnValue = Optional.of(srcFile);
             }
         } else {
-            String message = contentUrl != null ? "Error: Downloading content from '" + contentUrl.toString() + "'!" : "Error: No URL provided!";
+            String message = contentUrl != null ? "Error: Downloading content from '" + contentUrl + "'!" : "Error: No URL provided!";
             throw new MappingException(message);
         }
         return returnValue;
     }
 
-    /**
-     * Execute mapping(s) and get the location of result file.
-     *
-     * @param contentUrl Content of the src file.
-     * @param mappingId  filename of the mapping
-     * @return List of paths to all result files.
-     */
-    public List<Path> executeMapping(URI contentUrl, String mappingId) throws MappingPluginException {
-        List<Path> returnValue = new ArrayList<>();
-        String noMappingType = null;
-
-        Iterator<MappingRecord> findMapping = mappingRepo.findByMappingIdInOrMappingTypeIn(Arrays.asList(mappingId), Arrays.asList(noMappingType)).iterator();
-        String mappingType = null;
-        if (findMapping.hasNext()) {
-            mappingType = findMapping.next().getMappingType();
-        }
-        Optional<Path> executeMapping = executeMapping(contentUrl, mappingId, mappingType);
-        if (executeMapping.isPresent()) {
-            returnValue.add(executeMapping.get());
-        }
-
-        return returnValue;
-    }
-
     /**
      * Initalize mappings directory and mappingUtil instance.
      *
      * @param applicationProperties Properties holding mapping directory setting.
      */
-    private void init(ApplicationProperties applicationProperties) throws URISyntaxException {
+    private void init(ApplicationProperties applicationProperties) {
         if ((applicationProperties != null) && (applicationProperties.getMappingsLocation() != null)) {
             try {
                 mappingsDirectory = Files.createDirectories(new File(applicationProperties.getMappingsLocation().getPath()).getAbsoluteFile().toPath());
@@ -205,15 +178,15 @@ private void init(ApplicationProperties applicationProperties) throws URISyntaxE
      * @throws IOException error writing file.
      */
     private void saveMappingFile(String content, MappingRecord mapping) throws IOException {
-        Path newMappingFile = null;
+        Path newMappingFile;
         if ((content != null) && (mapping != null) && (mapping.getMappingId() != null) && (mapping.getMappingType() != null)) {
             LOGGER.debug("Storing mapping file with id '{}' and type '{}'", mapping.getMappingId(), mapping.getMappingType());
             LOGGER.trace("Content of mapping: '{}'", content);
             try {
                 // 'delete' old file
                 deleteMappingFile(mapping);
                 newMappingFile = Paths.get(mappingsDirectory.toString(), mapping.getMappingId() + "_" + mapping.getMappingType() + ".mapping");
-                LOGGER.trace("Write content to '{}'", newMappingFile.toString());
+                LOGGER.trace("Write content to '{}'", newMappingFile);
                 FileUtils.writeStringToFile(newMappingFile.toFile(), content, StandardCharsets.UTF_8);
                 mapping.setMappingDocumentUri(newMappingFile.toString());
                 byte[] data = content.getBytes();
@@ -249,7 +222,7 @@ private void deleteMappingFile(MappingRecord mapping) throws IOException {
             Path deleteFile = Paths.get(mapping.getMappingDocumentUri());
             if (deleteFile.toFile().exists()) {
                 Path newFileName = Paths.get(deleteFile.getParent().toString(), deleteFile.getFileName() + date2String());
-                LOGGER.trace("Move mapping file fo '{}'", newFileName.toString());
+                LOGGER.trace("Move mapping file fo '{}'", newFileName);
                 FileUtils.moveFile(deleteFile.toFile(), newFileName.toFile());
             }
         }

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

@@ -22,49 +22,58 @@
 /**
  * Interface for mapping plugins.
  * Every plugin which implements this interface and is placed in the plugins folder will be loaded and usable via the REST-API.
+ *
+ * @author maximilianiKIT
  */
 public interface IMappingPlugin {
 
     /**
      * Name of the plugin which gets displayed in the UI and is part of the id.
+     *
      * @return The name of the plugin.
      */
     String name();
 
     /**
      * A short description of the plugin which gets displayed in the UI.
+     *
      * @return The description of the plugin.
      */
     String description();
 
     /**
      * The version of the plugin which gets displayed in the UI and is part of the id.
+     *
      * @return The version of the plugin.
      */
     String version();
 
     /**
      * A URI which refers to the plugin or the technology used by the plugin (e.g. a link to a GitHub repository).
      * This URI will be displayed in the UI.
+     *
      * @return The URI of the plugin.
      */
     String uri();
 
     /**
      * The mime type of the input data.
+     *
      * @return The mime type of the input data.
      */
     MimeType[] inputTypes();
 
     /**
      * The mime type of the output data.
+     *
      * @return The mime type of the output data.
      */
     MimeType[] outputTypes();
 
     /**
      * The id of the plugin which is used to identify the plugin.
      * By default, the id is composed of the name and the version of the plugin (e.g. testPlugin_2.1.0).
+     *
      * @return The id of the plugin.
      */
     default String id() {
@@ -79,8 +88,9 @@ default String id() {
 
     /**
      * The method which is called to execute the plugin.
-     * @param inputFile The path to the output document.
-     * @param outputFile The path to the output document.
+     *
+     * @param inputFile   The path to the output document.
+     * @param outputFile  The path to the output document.
      * @param mappingFile The path to the mapping schema.
      * @return The exit code of the plugin.
      */

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

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021 Karlsruhe Institute of Technology.
+ * Copyright 2022 Karlsruhe Institute of Technology.
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
@@ -18,6 +18,11 @@
 import java.io.File;
 import java.io.FileFilter;
 
+/**
+ * Filter for jar files.
+ *
+ * @author maximilianiKIT
+ */
 public class JARFileFilter implements FileFilter {
 
     public boolean accept(File f) {