Minor improvements

Author: maximiliani

.github/workflows/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

build.gradle

@@ -33,15 +33,15 @@ ext {
 }
 
 dependencies {
-    implementation 'org.eclipse.jgit:org.eclipse.jgit:6.2.0.202206071550-r'
-    implementation 'org.springframework.boot:spring-boot-starter-data-jpa:2.6.7'
-    implementation 'org.springframework.boot:spring-boot-starter-security:2.6.7'
-    implementation 'org.springframework.boot:spring-boot-starter-validation:2.6.7'
-    implementation 'org.springframework.boot:spring-boot-starter-web:2.6.7'
-    implementation 'org.springframework.boot:spring-boot-starter-actuator:2.6.7'
-    implementation 'org.springdoc:springdoc-openapi-ui:1.6.7'
-    implementation 'org.springdoc:springdoc-openapi-data-rest:1.6.7'
-    implementation 'org.springdoc:springdoc-openapi-webmvc-core:1.6.7'
+    implementation 'org.eclipse.jgit:org.eclipse.jgit:6.3.0.202209071007-r'
+    implementation 'org.springframework.boot:spring-boot-starter-data-jpa:2.7.3'
+    implementation 'org.springframework.boot:spring-boot-starter-security:2.7.3'
+    implementation 'org.springframework.boot:spring-boot-starter-validation:2.7.3'
+    implementation 'org.springframework.boot:spring-boot-starter-web:2.7.3'
+    implementation 'org.springframework.boot:spring-boot-starter-actuator:2.7.3'
+    implementation 'org.springdoc:springdoc-openapi-ui:1.6.11'
+    implementation 'org.springdoc:springdoc-openapi-data-rest:1.6.11'
+    implementation 'org.springdoc:springdoc-openapi-webmvc-core:1.6.11'
     implementation 'org.javers:javers-spring-boot-starter-sql:6.6.5'
     implementation 'org.apache.httpcomponents:httpclient:4.5.13'
     implementation 'org.apache.commons:commons-collections4:4.4'
@@ -50,28 +50,28 @@ dependencies {
     implementation 'com.google.guava:guava:31.1-jre'
     implementation 'commons-io:commons-io:2.11.0'
     implementation 'javax.validation:validation-api:2.0.1.Final'
-    implementation 'edu.kit.datamanager:service-base:1.0.1'
+    implementation 'edu.kit.datamanager:service-base:1.0.4'
 
-    testImplementation(platform('org.junit:junit-bom:5.8.2'))
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
-    testImplementation 'org.junit.jupiter:junit-jupiter-migrationsupport:5.8.2'
-    testImplementation 'org.springframework.boot:spring-boot-starter-test:2.6.7'
+    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'
     testImplementation 'org.springframework.restdocs:spring-restdocs-mockmvc:2.0.6.RELEASE'
-    testImplementation 'org.springframework.security:spring-security-test:5.6.3'
-    testImplementation 'org.springframework:spring-test:5.3.19'
-    testImplementation 'org.mockito:mockito-core:4.5.1'
+    testImplementation 'org.springframework.security:spring-security-test:5.7.3'
+    testImplementation 'org.springframework:spring-test:5.3.22'
+    testImplementation 'org.mockito:mockito-core:4.8.0'
     testImplementation 'org.powermock:powermock-module-junit4:2.0.9'
     testImplementation 'org.powermock:powermock-api-mockito2:2.0.9'
-    testImplementation 'net.bytebuddy:byte-buddy:1.12.9'
-    testImplementation 'org.junit.vintage:junit-vintage-engine:5.8.2'
+    testImplementation 'net.bytebuddy:byte-buddy:1.12.16'
+    testImplementation 'org.junit.vintage:junit-vintage-engine:5.9.0'
 
-    annotationProcessor 'org.springframework.boot:spring-boot-configuration-processor:2.6.7'
+    annotationProcessor 'org.springframework.boot:spring-boot-configuration-processor:2.7.3'
     annotationProcessor 'org.projectlombok:lombok:1.18.24'
 
     compileOnly 'org.projectlombok:lombok:1.18.24'
 
-    runtimeOnly 'com.h2database:h2:2.1.212'
-    runtimeOnly 'org.postgresql:postgresql:42.3.4'
+    runtimeOnly 'com.h2database:h2:2.1.214'
+    runtimeOnly 'org.postgresql:postgresql:42.5.0'
     runtimeOnly 'org.apache.httpcomponents:httpclient:4.5.13'
 
     asciidoctorExt 'org.springframework.restdocs:spring-restdocs-asciidoctor:2.0.6.RELEASE'

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

@@ -29,6 +29,8 @@
 @Configuration
 public class MappingServiceApplication {
 
+    private static final Logger LOG = LoggerFactory.getLogger(MappingServiceApplication.class);
+
     @Bean
     @Scope("prototype")
     public Logger logger(InjectionPoint injectionPoint) {
@@ -53,9 +55,10 @@ public ApplicationProperties applicationProperties() {
 
     public static void main(String[] args) {
         SpringApplication.run(MappingServiceApplication.class, args);
-        System.out.println("Mapping service is running! Access it at http://localhost:8095");
 
-        PluginManager.soleInstance().getListOfAvailableValidators().forEach(System.out::println);
+        PluginManager.soleInstance().getListOfAvailableValidators().forEach((value) -> LOG.info("Found validator: " + value));
         PythonRunnerUtil.printPythonVersion();
+
+        System.out.println("Mapping service is running! Access it at http://localhost:8095");
     }
 }

src/main/resources/application.properties

@@ -40,7 +40,7 @@ repo.auth.jwtSecret:test123
 
 # Absolute path to the local python interpreter
 #mapping-service.pythonLocation:file:///usr/bin/python3
-mapping-service.pythonLocation=file:///opt/homebrew/bin/python3
+mapping-service.pythonLocation=file:///usr/local/bin/python3
 
 # Absolute path to the local gemma mappings folder
 #mapping-service.mappingsLocation:file://tmp/mappings

src/test/resources/exampleUserInput/simple.mapping

@@ -1,17 +1,17 @@
 {
-  "$schema": "http://json-schema.org/draft-07/schema#",
-  "$id": "http://example.com/product.schema.json",
-  "title": "Simple Mapping",
-  "description": "Data resource mapping from json",
-  "type": "object",
-  "properties":{
-  "Publisher":{
-   "path": "publisher",
-   "type": "string"
-   },
-   "Publication Date":{
-   "path": "publicationDate",
-   "type": "string"
-   }
-  }
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "http://example.com/product.schema.json",
+    "title": "Simple Mapping",
+    "description": "Data resource mapping from json",
+    "type": "object",
+    "properties":{
+        "Author":{
+            "path": "publisher",
+            "type": "string"
+        },
+        "Release Date":{
+            "path": "publicationDate",
+            "type": "string"
+        }
+    }
 }