added Actuator

some optimization

Author: maximiliani

README.md

@@ -9,7 +9,7 @@ For mapping documents only Gemma is available currently!
 
 The mapping service allows multiple schemas to be uploaded and managed and documents to be mapped over one of them at a time accordingly.
 Therefore, the service is extensible to other mappers, although currently only Gemma, a service that can only map JSON files, is available.
-The REST API is documented at the following link: [http://localhost:8095/swagger-ui/index.html?configUrl=/v3/api-docs/swagger-config](http://localhost:8095/swagger-ui/index.html?configUrl=/v3/api-docs/swagger-config)
+The REST API is documented at the following link: [http://localhost:8095/swagger-ui/index.html](http://localhost:8095/swagger-ui/index.html)
 
 ## How to build
 

build.gradle

@@ -1,7 +1,6 @@
 plugins {
     id 'io.spring.dependency-management' version '1.0.11.RELEASE'
     id 'org.springframework.boot' version '2.6.6'
-//    id 'org.asciidoctor.convert' version '2.4.0'
     id "org.asciidoctor.jvm.convert" version "3.3.0"
     id "org.owasp.dependencycheck" version "7.0.4.1"
     id 'net.researchgate.release' version '2.8.1'
@@ -11,7 +10,7 @@ plugins {
 
 description = 'Generic mapping service supporting different mapping implementations.'
 group = 'edu.kit.datamanager'
-version = '1.0'
+version = '1.0.0'
 
 println "Building ${name} version: ${version}"
 
@@ -36,6 +35,7 @@ dependencies {
     implementation 'org.springframework.boot:spring-boot-starter-security:2.6.5'
     implementation 'org.springframework.boot:spring-boot-starter-validation:2.6.5'
     implementation 'org.springframework.boot:spring-boot-starter-web:2.6.5'
+    implementation 'org.springframework.boot:spring-boot-starter-actuator:2.6.6'
     implementation 'org.springdoc:springdoc-openapi-ui:1.6.6'
     implementation 'org.springdoc:springdoc-openapi-data-rest:1.6.6'
     implementation 'org.springdoc:springdoc-openapi-webmvc-core:1.6.6'

src/main/java/edu/kit/datamanager/mappingservice/annotations/LocalFileURL.java

@@ -37,13 +37,14 @@ public class ApplicationProperties extends GenericPluginProperties {
     /**
      * The absolute path to the python interpreter.
      */
+    @edu.kit.datamanager.annotations.ExecutableFileURL
     @Value("${mapping-service.gemma.pythonLocation}")
     private URL pythonLocation;
 
     /**
      * The path to the gemma mapping script 'mapping_single.py'
      */
-    @edu.kit.datamanager.mappingservice.annotations.LocalFileURL
+    @edu.kit.datamanager.annotations.LocalFileURL
     @Value("${mapping-service.gemma.gemmaLocation}")
     private URL gemmaLocation;
 

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

@@ -15,16 +15,12 @@
  */
 package edu.kit.datamanager.mappingservice.configuration;
 
-//import edu.kit.datamanager.security.filter.JwtAuthenticationFilter;
-//import edu.kit.datamanager.security.filter.JwtAuthenticationProvider;
-
 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;
 import org.springframework.http.HttpMethod;
-import org.springframework.security.config.annotation.authentication.builders.AuthenticationManagerBuilder;
 import org.springframework.security.config.annotation.method.configuration.EnableGlobalMethodSecurity;
 import org.springframework.security.config.annotation.web.builders.HttpSecurity;
 import org.springframework.security.config.annotation.web.builders.WebSecurity;
@@ -51,20 +47,12 @@ public class WebSecurityConfig extends WebSecurityConfigurerAdapter {
     public WebSecurityConfig() {
     }
 
-    @Override
-    public void configure(AuthenticationManagerBuilder auth) {
-//        auth.authenticationEventPublisher(new NoopAuthenticationEventPublisher()).authenticationProvider(new JwtAuthenticationProvider("test123", logger));
-    }
-
     @Override
     protected void configure(HttpSecurity http) throws Exception {
         HttpSecurity httpSecurity = http.authorizeRequests()
                 .antMatchers(HttpMethod.OPTIONS, "/**").permitAll().and().sessionManagement().sessionCreationPolicy(SessionCreationPolicy.STATELESS)
                 .and()
                 .csrf().disable();
-//                .addFilterAfter(new JwtAuthenticationFilter(authenticationManager()), BasicAuthenticationFilter.class);
-
-//        httpSecurity = httpSecurity.addFilterAfter(new NoAuthenticationFilter("test123", authenticationManager()), JwtAuthenticationFilter.class);
 
         httpSecurity.
                 authorizeRequests().

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

@@ -1,7 +1,7 @@
 # General Spring Boot Settings (do not change!)
 spring.main.allow-bean-definition-overriding=true
 spring.main.allow-circular-references=true
-spring.mvc.pathmatch.matching-strategy=ant_path_matcher
+#spring.mvc.pathmatch.matching-strategy=ant_path_matcher
 
 # Server Settings for defining port and security
 server.port: 8095
@@ -16,23 +16,18 @@ spring.servlet.multipart.max-request-size: 100MB
 #logging settings
 logging.level.root: ERROR
 #logging.level.edu.kit: DEBUG
-#logging.level.org.springframework:DEBUG
-#logging.level.org.springframework.amqp: WARN
-logging.level.edu.kit.datamanager: TRACE
+logging.level.edu.kit.datamanager: INFO
 
 springdoc.swagger-ui.disable-swagger-default-url=true
 
-###################################################################
-##################  Repository Specific Settings ##################
-###################################################################
-repo.basepath:  file:///tmp
-
-# Enable/disable (default) authentication. If authentication is enabled, a separate 
-# Authentication Service should be used in order to obtain JSON Web Tokens holding 
-# login information. The token has then to be provided within the Authentication header
-# of each HTTP request with a value of 'Bearer <TOKEN>' without quotes, replacing <TOKEN>
-# be the token obtained from the authentication service.
-repo.auth.enabled: false
+# Actuator settings
+info.app.name=Mapping-Service
+info.app.description=Generic mapping service supporting different mapping implementations.
+info.app.group=edu.kit.datamanager
+info.app.version=1.0.0
+management.endpoint.health.probes.enabled=true
+#management.endpoints.web.exposure.include=info, health, beans, configprops, loggers, prometheus, logfile, metrics, env
+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
@@ -52,5 +47,5 @@ mapping-service.gemma.pythonLocation:file:///usr/bin/python3
 mapping-service.gemma.gemmaLocation:file:src/test/resources/python/mapping_single.py
 
 # Absolute path to the local gemma mappings folder
-#metastore.indexer.mappingsLocation:file:///Users/maximilian/Documents/GitHub/mapping-service/src/test/resources/mapping/gemma
-mapping-service.mappingsLocation:file:///tmp/metastore2/mapping
+#metastore.indexer.mappingsLocation:file:src/test/resources/mapping/gemma
+mapping-service.mappingsLocation:file:///tmp/mapping-service/

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

@@ -95,8 +95,7 @@ public class MappingControllerDocumentationTest {
     private IAclEntryDao aclEntryDao;
 
     private final static String EXAMPLE_SCHEMA_ID_XML = "my_first_xsd";
-    private final static String TEMP_DIR_4_ALL = "/tmp/metastore2/";
-    private final static String TEMP_DIR_4_MAPPING = TEMP_DIR_4_ALL + "mapping/";
+    private final static String TEMP_DIR_4_MAPPING = "/tmp/mapping-service/";
     private final static String EXAMPLE_SCHEMA_ID_JSON = "my_first_json";
 
     @BeforeEach

src/main/java/edu/kit/datamanager/mappingservice/validator/LocalFileValidator.java

@@ -84,9 +84,7 @@ public class MappingServiceTest {
     @Autowired
     MappingService mappingService4Test;
 
-    private final static String TEMP_DIR_4_ALL = "/tmp/metastore2/";
-    private final static String TEMP_DIR_4_MAPPING = TEMP_DIR_4_ALL + "mapping/";
-
+    private final static String TEMP_DIR_4_MAPPING = "/tmp/mapping-service/";
 
     @BeforeEach
     public void setUp() {