minor changes

maximiliani · maximiliani · commit 5229d3a08dd1 · 2022-09-20T16:13:29.000+02:00
diff --git a/build.gradle b/build.gradle
@@ -52,7 +52,7 @@ dependencies {
     implementation 'javax.validation:validation-api:2.0.1.Final'
     implementation 'edu.kit.datamanager:service-base:1.0.4'
 
-    testImplementation(platform('org.junit:junit-bom:5.9.0'))
+    testImplementation platform('org.junit:junit-bom:5.9.0')
     testImplementation 'org.junit.jupiter:junit-jupiter:5.9.0'
     testImplementation 'org.junit.jupiter:junit-jupiter-migrationsupport:5.9.0'
     testImplementation 'org.springframework.boot:spring-boot-starter-test:2.7.3'
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/MappingServiceApplication.java b/src/main/java/edu/kit/datamanager/mappingservice/MappingServiceApplication.java
@@ -1,52 +1,24 @@
 package edu.kit.datamanager.mappingservice;
 
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.SerializationFeature;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 import edu.kit.datamanager.mappingservice.configuration.ApplicationProperties;
 import edu.kit.datamanager.mappingservice.plugins.PluginManager;
 import edu.kit.datamanager.mappingservice.util.PythonRunnerUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.InjectionPoint;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.domain.EntityScan;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Scope;
-import org.springframework.http.converter.json.Jackson2ObjectMapperBuilder;
-import org.springframework.scheduling.annotation.EnableScheduling;
 
 @SpringBootApplication
-@EnableScheduling
-@ComponentScan({"edu.kit.datamanager.mappingservice", "edu.kit.datamanager.configuration"})
 @EntityScan("edu.kit.datamanager")
-@ComponentScan
 @Configuration
 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(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")
     public ApplicationProperties applicationProperties() {
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/configuration/JPAPersistenceConfig.java b/src/main/java/edu/kit/datamanager/mappingservice/configuration/JPAPersistenceConfig.java
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/dao/IAclEntryDao.java b/src/main/java/edu/kit/datamanager/mappingservice/dao/IAclEntryDao.java
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/impl/MappingService.java b/src/main/java/edu/kit/datamanager/mappingservice/impl/MappingService.java
@@ -51,8 +51,7 @@ public class MappingService {
     /**
      * Repo holding all MappingRecords.
      */
-    @Autowired
-    private IMappingRecordDao mappingRepo;
+    private final IMappingRecordDao mappingRepo;
     /**
      * Path to directory holding all mapping files.
      */
@@ -64,8 +63,9 @@ public class MappingService {
     private final static Logger LOGGER = LoggerFactory.getLogger(MappingService.class);
 
     @Autowired
-    public MappingService(ApplicationProperties applicationProperties) {
+    public MappingService(ApplicationProperties applicationProperties, IMappingRecordDao mappingRepo) {
         init(applicationProperties);
+        this.mappingRepo = mappingRepo;
     }
 
     /**
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/plugins/PluginLoader.java b/src/main/java/edu/kit/datamanager/mappingservice/plugins/PluginLoader.java
@@ -64,7 +64,6 @@ public static Map<String, IMappingPlugin> loadPlugins(File plugDir) throws IOExc
         List<IMappingPlugin> IMappingPluginList = PluginLoader.createPluggableObjects(plugClasses);
         Map<String, IMappingPlugin> result = new HashMap<>();
         for (IMappingPlugin i : IMappingPluginList) {
-            System.out.println("Found Plugin: " + i.id());
             i.setup();
             result.put(i.id(), i);
         }
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/plugins/PluginManager.java b/src/main/java/edu/kit/datamanager/mappingservice/plugins/PluginManager.java
@@ -15,7 +15,6 @@
 
 package edu.kit.datamanager.mappingservice.plugins;
 
-import edu.kit.datamanager.mappingservice.util.ShellRunnerUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -119,7 +118,6 @@ public List<String> getListOfAvailableValidators() {
     public MappingPluginState mapFile(String pluginId, Path mappingFile, Path inputFile, Path outputFile) throws MappingPluginException {
         for (var entry : plugins.entrySet()) {
             if (entry.getKey().equals(pluginId)) {
-                ShellRunnerUtil.run("cat", inputFile.toString());
                 return entry.getValue().mapFile(mappingFile, inputFile, outputFile);
             }
         }
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/rest/impl/MappingAdministrationController.java b/src/main/java/edu/kit/datamanager/mappingservice/rest/impl/MappingAdministrationController.java
@@ -163,6 +163,7 @@ public ResponseEntity createMapping(@RequestPart(name = "record") final Multipar
         locationUri = WebMvcLinkBuilder.linkTo(WebMvcLinkBuilder.methodOn(this.getClass()).getMappingById(recordDocument.getMappingId())).toUri();
 
         LOG.trace("Schema record successfully persisted. Returning result.");
+        LOG.info("Successfully created mapping record with id '{}' and type '{}'.", recordDocument.getMappingId(), recordDocument.getMappingType());
         return ResponseEntity.created(locationUri).eTag("\"" + etag + "\"").body(recordDocument);
     }
 
@@ -243,6 +244,7 @@ public ResponseEntity deleteMapping(@PathVariable(value = "mappingId") String ma
             throw new MappingException("Unknown error removing map!");
         }
 
+        LOG.info("Successfully deleted mapping record with id '{}'.", mappingId);
         return new ResponseEntity<>(HttpStatus.NO_CONTENT);
     }
 
@@ -298,6 +300,7 @@ public ResponseEntity updateMapping(@PathVariable(value = "mappingId") String ma
         URI locationUri;
         locationUri = WebMvcLinkBuilder.linkTo(WebMvcLinkBuilder.methodOn(this.getClass()).getMappingById(recordDocument.getMappingId())).toUri();
 
+        LOG.info("Successfully updated mapping record with id '{}' and type '{}'.", recordDocument.getMappingId(), recordDocument.getMappingType());
         return ResponseEntity.ok().location(locationUri).eTag("\"" + etag + "\"").body(recordDocument);
     }
 
@@ -339,6 +342,13 @@ public MappingRecord getMappingById(String mappingId) throws ResourceNotFoundExc
         return record.get();
     }
 
+    /**
+     * This method merges two MappingRecords.
+     *
+     * @param managed  The existing MappingRecord.
+     * @param provided The MappingRecord to merge.
+     * @return The merged MappingRecord.
+     */
     public MappingRecord mergeRecords(MappingRecord managed, MappingRecord provided) {
         if (provided != null) {
             if (provided.getTitle() != null) {
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/rest/impl/MappingExecutionController.java b/src/main/java/edu/kit/datamanager/mappingservice/rest/impl/MappingExecutionController.java
@@ -20,7 +20,6 @@
 import edu.kit.datamanager.mappingservice.impl.MappingService;
 import edu.kit.datamanager.mappingservice.rest.IMappingExecutionController;
 import edu.kit.datamanager.mappingservice.util.FileUtil;
-import edu.kit.datamanager.mappingservice.util.ShellRunnerUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.core.io.FileSystemResource;
@@ -104,6 +103,7 @@ public ResponseEntity mapDocument(MultipartFile document, String mappingID, Http
             return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body("Internal error while accessing result");
         }
 
+        LOG.info("Successfully mapped document with mapping {}.", mappingID);
         return ResponseEntity.ok().header(HttpHeaders.CONTENT_LENGTH, String.valueOf(resultPath.toFile().length())).body(new FileSystemResource(resultPath.toFile()));
     }
 }
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/util/FileUtil.java b/src/main/java/edu/kit/datamanager/mappingservice/util/FileUtil.java
@@ -165,7 +165,7 @@ public static void removeFile(Path tempFile) {
 
     private static String guessFileExtension(byte[] schema) {
         // Cut schema to a maximum of MAX_LENGTH_OF_HEADER characters.
-        int length = schema.length > MAX_LENGTH_OF_HEADER ? MAX_LENGTH_OF_HEADER : schema.length;
+        int length = Math.min(schema.length, MAX_LENGTH_OF_HEADER);
         String schemaAsString = new String(schema, 0, length);
         LOGGER.trace("Guess type for '{}'", schemaAsString);
 
@@ -189,7 +189,7 @@ private static String guessFileExtension(byte[] schema) {
      * @return the path to the cloned repository
      */
     public static Path cloneGitRepository(String repositoryUrl, String branch) {
-        File target = new File("lib/" + repositoryUrl.trim().substring(repositoryUrl.length() - 7, repositoryUrl.length() - 1) + "_" + branch);
+        File target = new File("lib/" + repositoryUrl.trim().replace("https://", "").replace(".git", "") + "_" + branch);
         target.mkdirs();
 
         LOGGER.info("Cloning branch '{}' of repository '{}' to '{}'", branch, repositoryUrl, target.getPath());
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/util/PythonRunnerUtil.java b/src/main/java/edu/kit/datamanager/mappingservice/util/PythonRunnerUtil.java
@@ -63,7 +63,7 @@ public static void printPythonVersion() {
      * @throws MappingPluginException if an error occurs.
      */
     public static MappingPluginState runPythonScript(String arg) throws MappingPluginException {
-        return runPythonScript(arg, new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.INFO), new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.WARN));
+        return runPythonScript(arg, new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.DEBUG), new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.INFO));
     }
 
     /**
@@ -75,7 +75,7 @@ public static MappingPluginState runPythonScript(String arg) throws MappingPlugi
      * @throws MappingPluginException if an error occurs.
      */
     public static MappingPluginState runPythonScript(String script, String... args) throws MappingPluginException {
-        return runPythonScript(script, new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.INFO), new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.WARN), args);
+        return runPythonScript(script, new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.DEBUG), new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.INFO), args);
     }
 
     /**
diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
@@ -1,24 +1,17 @@
 # General Spring Boot Settings (do not change!)
 spring.main.allow-bean-definition-overriding=true
 spring.main.allow-circular-references=true
-
-# Server Settings for defining port and security
-server.port: 8095
-
-# Data transfer settings, e.g. transfer compression and multipart message size. 
+server.port=8095
+# Data transfer settings, e.g. transfer compression and multipart message size.
 # The properties max-file-size and max-request-size define the maximum size of files 
 # transferred to and from the repository. Setting them to -1 removes all limits.
-server.compression.enabled: false
-spring.servlet.multipart.max-file-size: 100MB
-spring.servlet.multipart.max-request-size: 100MB
-
-#logging settings
-logging.level.root: ERROR
-#logging.level.edu.kit: DEBUG
-logging.level.edu.kit.datamanager: INFO
-
+server.compression.enabled=false
+spring.servlet.multipart.max-file-size=100MB
+spring.servlet.multipart.max-request-size=100MB
+# Logging settings
+logging.level.root=ERROR
+logging.level.edu.kit.datamanager=INFO
 springdoc.swagger-ui.disable-swagger-default-url=true
-
 # Actuator settings
 info.app.name=Mapping-Service
 info.app.description=Generic mapping service supporting different mapping implementations.
@@ -27,31 +20,19 @@ info.app.version=1.0.0
 management.endpoint.health.probes.enabled=true
 management.endpoints.web.exposure.include=*
 
-# The jwtSecret is the mutual secret between all trusted services. This means, that if
-# authentication is enabled, the jwtSecret used by the Authentication Service to sign
-# issued JWTokens must be the same as the jwtSecret of the repository in order to 
-# be able to validate the signature. By default, the secret should be selected randomly
-# and with a sufficient length.
-repo.auth.jwtSecret:test123
-
 ###############################################################################
 # Database
 ###############################################################################
-spring.datasource.driver-class-name: org.h2.Driver
-spring.datasource.url:  jdbc:h2:file:/Users/maximilian/mps-data
-spring.datasource.username: test
-spring.datasource.password: test
-spring.jpa.hibernate.ddl-auto: update
-
+spring.datasource.driver-class-name=org.h2.Driver
+spring.datasource.url=jdbc:h2:file:///Users/maximilian/mapping-service/database
+spring.datasource.username=user
+spring.datasource.password=password
+spring.jpa.hibernate.ddl-auto=update
 
 ##################################################
-######### Mapping-Service ##########
+# Mapping-Service specific settings
 ##################################################
-
 # Absolute path to the local python interpreter
-#mapping-service.pythonLocation:file:///usr/bin/python3
 mapping-service.pythonLocation=file:///usr/local/bin/python3
-
 # Absolute path to the local gemma mappings folder
-#mapping-service.mappingsLocation:file://tmp/mappings
-mapping-service.mappingSchemasLocation:file:///Users/maximilian/mappingSchemas
+mapping-service.mappingSchemasLocation=file:///Users/maximilian/mapping-service/mappingSchemas
diff --git a/src/main/resources/mytemplate.hbs b/src/main/resources/mytemplate.hbs
diff --git a/src/main/resources/static/JS/addScheme.js b/src/main/resources/static/JS/addScheme.js
@@ -36,7 +36,7 @@ function load() {
     const http = new XMLHttpRequest();
     http.open("GET", apiUrl + "/types")
     http.send();
-    http.onload = (e) => {
+    http.onload = () => {
         const result = JSON.parse(http.responseText)
         for (let i = 0; i < result.length; i++) {
             types.push(result[i].id)
@@ -165,7 +165,7 @@ function createMapping() {
     const http = new XMLHttpRequest();
     http.open("POST", apiUrl)
     http.send(formData)
-    http.onload = (e) => {
+    http.onload = () => {
         console.log("Response: " + http.responseText)
         document.getElementById("progress").hidden = true
         document.getElementById("submit").disabled = false
@@ -237,7 +237,7 @@ function updateMapping() {
     http.open("PUT", apiUrl + "/" + id)
     http.setRequestHeader("If-Match", data.ETAG)
     http.send(formData)
-    http.onload = (e) => {
+    http.onload = () => {
         console.log("Response: " + http.responseText)
         document.getElementById("editProgress").hidden = true
         document.getElementById("update").disabled = false
@@ -314,7 +314,7 @@ function changeUIMode() {
     document.getElementById("navShow").hidden = isEdit
 }
 
-function addType(typeID, typeName, typeDescription, typeVersion, typeLink, typeMIMEOutput, typeMIMEInput) {
+function addType(typeID, typeName, typeDescription, typeVersion, typeLink, typeMIMEInput, typeMIMEOutput) {
     const element =
         `<div class="accordion-item row align-items-center clearfix">
             <div class="accordion-header" id="heading_${typeID}">
@@ -381,7 +381,7 @@ function reloadTypes() {
     const http = new XMLHttpRequest();
     http.open("GET", apiUrl + "/reloadTypes")
     http.send()
-    http.onload = (e) => {
+    http.onload = () => {
         location.reload()
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -64,7 +64,6 @@ public static Map<String, IMappingPlugin> loadPlugins(File plugDir) throws IOExc`
`64`	`64`	`List<IMappingPlugin> IMappingPluginList = PluginLoader.createPluggableObjects(plugClasses);`
`65`	`65`	`Map<String, IMappingPlugin> result = new HashMap<>();`
`66`	`66`	`for (IMappingPlugin i : IMappingPluginList) {`
`67`		`- System.out.println("Found Plugin: " + i.id());`
`68`	`67`	`i.setup();`
`69`	`68`	`result.put(i.id(), i);`
`70`	`69`	`}`
Original file line number	Diff line number	Diff line change
`@@ -15,7 +15,6 @@`
`15`	`15`
`16`	`16`	`package edu.kit.datamanager.mappingservice.plugins;`
`17`	`17`
`18`		`-import edu.kit.datamanager.mappingservice.util.ShellRunnerUtil;`
`19`	`18`	`import org.slf4j.Logger;`
`20`	`19`	`import org.slf4j.LoggerFactory;`
`21`	`20`
`@@ -119,7 +118,6 @@ public List<String> getListOfAvailableValidators() {`
`119`	`118`	`public MappingPluginState mapFile(String pluginId, Path mappingFile, Path inputFile, Path outputFile) throws MappingPluginException {`
`120`	`119`	`for (var entry : plugins.entrySet()) {`
`121`	`120`	`if (entry.getKey().equals(pluginId)) {`
`122`		`- ShellRunnerUtil.run("cat", inputFile.toString());`
`123`	`121`	`return entry.getValue().mapFile(mappingFile, inputFile, outputFile);`
`124`	`122`	`}`
`125`	`123`	`}`
Original file line number	Diff line number	Diff line change
`@@ -163,6 +163,7 @@ public ResponseEntity createMapping(@RequestPart(name = "record") final Multipar`
`163`	`163`	`locationUri = WebMvcLinkBuilder.linkTo(WebMvcLinkBuilder.methodOn(this.getClass()).getMappingById(recordDocument.getMappingId())).toUri();`
`164`	`164`
`165`	`165`	`LOG.trace("Schema record successfully persisted. Returning result.");`
	`166`	`+ LOG.info("Successfully created mapping record with id '{}' and type '{}'.", recordDocument.getMappingId(), recordDocument.getMappingType());`
`166`	`167`	`return ResponseEntity.created(locationUri).eTag("\"" + etag + "\"").body(recordDocument);`
`167`	`168`	`}`
`168`	`169`
`@@ -243,6 +244,7 @@ public ResponseEntity deleteMapping(@PathVariable(value = "mappingId") String ma`
`243`	`244`	`throw new MappingException("Unknown error removing map!");`
`244`	`245`	`}`
`245`	`246`
	`247`	`+ LOG.info("Successfully deleted mapping record with id '{}'.", mappingId);`
`246`	`248`	`return new ResponseEntity<>(HttpStatus.NO_CONTENT);`
`247`	`249`	`}`
`248`	`250`
`@@ -298,6 +300,7 @@ public ResponseEntity updateMapping(@PathVariable(value = "mappingId") String ma`
`298`	`300`	`URI locationUri;`
`299`	`301`	`locationUri = WebMvcLinkBuilder.linkTo(WebMvcLinkBuilder.methodOn(this.getClass()).getMappingById(recordDocument.getMappingId())).toUri();`
`300`	`302`
	`303`	`+ LOG.info("Successfully updated mapping record with id '{}' and type '{}'.", recordDocument.getMappingId(), recordDocument.getMappingType());`
`301`	`304`	`return ResponseEntity.ok().location(locationUri).eTag("\"" + etag + "\"").body(recordDocument);`
`302`	`305`	`}`
`303`	`306`
`@@ -339,6 +342,13 @@ public MappingRecord getMappingById(String mappingId) throws ResourceNotFoundExc`
`339`	`342`	`return record.get();`
`340`	`343`	`}`
`341`	`344`
	`345`	`+ /**`
	`346`	`+ * This method merges two MappingRecords.`
	`347`	`+ *`
	`348`	`+ * @param managed The existing MappingRecord.`
	`349`	`+ * @param provided The MappingRecord to merge.`
	`350`	`+ * @return The merged MappingRecord.`
	`351`	`+ */`
`342`	`352`	`public MappingRecord mergeRecords(MappingRecord managed, MappingRecord provided) {`
`343`	`353`	`if (provided != null) {`
`344`	`354`	`if (provided.getTitle() != null) {`
Original file line number	Diff line number	Diff line change
`@@ -20,7 +20,6 @@`
`20`	`20`	`import edu.kit.datamanager.mappingservice.impl.MappingService;`
`21`	`21`	`import edu.kit.datamanager.mappingservice.rest.IMappingExecutionController;`
`22`	`22`	`import edu.kit.datamanager.mappingservice.util.FileUtil;`
`23`		`-import edu.kit.datamanager.mappingservice.util.ShellRunnerUtil;`
`24`	`23`	`import org.slf4j.Logger;`
`25`	`24`	`import org.slf4j.LoggerFactory;`
`26`	`25`	`import org.springframework.core.io.FileSystemResource;`
`@@ -104,6 +103,7 @@ public ResponseEntity mapDocument(MultipartFile document, String mappingID, Http`
`104`	`103`	`return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body("Internal error while accessing result");`
`105`	`104`	`}`
`106`	`105`
	`106`	`+ LOG.info("Successfully mapped document with mapping {}.", mappingID);`
`107`	`107`	`return ResponseEntity.ok().header(HttpHeaders.CONTENT_LENGTH, String.valueOf(resultPath.toFile().length())).body(new FileSystemResource(resultPath.toFile()));`
`108`	`108`	`}`
`109`	`109`	`}`