Merge pull request #11 from qbicsoftware/development

Release PR

rest-api/pom.xml

@@ -54,14 +54,13 @@
       <artifactId>mysql-connector-j</artifactId>
     </dependency>
     <dependency>
-      <groupId>mysql</groupId>
-      <artifactId>mysql-connector-java</artifactId>
-      <version>8.0.33</version>
+      <groupId>org.mariadb.jdbc</groupId>
+      <artifactId>mariadb-java-client</artifactId>
     </dependency>
     <dependency>
       <groupId>org.springdoc</groupId>
       <artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
-      <version>2.3.0</version>
+      <version>2.5.0</version>
     </dependency>
     <dependency>
       <groupId>life.qbic.data-download</groupId>

rest-api/src/main/java/life/qbic/data_download/rest/config/OpenApiConfig.java

@@ -12,7 +12,7 @@
 import org.springframework.context.annotation.Configuration;
 
 @Configuration
-@OpenAPIDefinition(info = @Info(title = "My API", version = "v1"),
+@OpenAPIDefinition(info = @Info(title = "Data Download API Documentation", version = "v1"),
     security = @SecurityRequirement(name = "personal_access_token")) //globally set this
 public class OpenApiConfig {
 

rest-api/src/main/java/life/qbic/data_download/rest/config/SecurityConfig.java

@@ -18,11 +18,12 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.autoconfigure.jdbc.DataSourceProperties;
+import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.cache.CacheManager;
 import org.springframework.cache.concurrent.ConcurrentMapCacheManager;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.jdbc.datasource.DriverManagerDataSource;
 import org.springframework.security.access.PermissionEvaluator;
 import org.springframework.security.access.expression.method.DefaultMethodSecurityExpressionHandler;
 import org.springframework.security.access.expression.method.MethodSecurityExpressionHandler;
@@ -168,16 +169,17 @@ protected AclCache aclCache() {
         aclAuthorizationStrategy());
   }
 
+  @Bean(name="securityDataSourceProperties")
+  @ConfigurationProperties("qbic.access-management.datasource")
+  public DataSourceProperties dataSourceProperties() {
+    return new DataSourceProperties();
+  }
+
   @Bean("securityDataSource")
-  public DataSource dataSource(
-      @Value("${qbic.access-management.datasource.url}") String url,
-      @Value("${qbic.access-management.datasource.username}") String name,
-      @Value("${qbic.access-management.datasource.password}") String password) {
-    var ds = new DriverManagerDataSource();
-    ds.setUrl(url);
-    ds.setUsername(name);
-    ds.setPassword(password);
-    return ds;
+  public DataSource dataSource() {
+    return dataSourceProperties()
+        .initializeDataSourceBuilder()
+        .build();
   }
 
   @Bean("idSupportingLookupStrategy")

rest-api/src/main/java/life/qbic/data_download/rest/download/DownloadController.java

@@ -8,13 +8,13 @@
 import io.swagger.v3.oas.annotations.media.Schema;
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
+import io.swagger.v3.oas.annotations.tags.Tag;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.time.LocalDateTime;
 import java.time.format.DateTimeFormatter;
 import java.util.Optional;
 import java.util.UUID;
-import javax.swing.text.html.Option;
 import life.qbic.data_download.measurements.api.DataFile;
 import life.qbic.data_download.measurements.api.MeasurementData;
 import life.qbic.data_download.measurements.api.MeasurementDataProvider;
@@ -38,6 +38,7 @@
 import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
 
 @RestController
+@Tag(name = "Download Endpoints", description = "Rest endpoints related to downloading data")
 public class DownloadController {
 
   private final MeasurementDataProvider measurementDataProvider;
@@ -59,7 +60,7 @@ public DownloadController(
 
   @GetMapping(value = "/measurements/{measurementId}", produces = MediaType.APPLICATION_JSON_VALUE)
   @Operation(summary = "Download a measurement from the given measurement identifier")
-  @Parameter(name = "measurementId", required = true, description = "The identifier of the measurement to download")
+  @Parameter(name = "measurementId", required = true, description = "The identifier of the measurement to download", example = "NGSQ0001006AO-25948529211108")
   @ApiResponses(value = {
       @ApiResponse(responseCode = "200", description = "successful operation, the measurement is retrieved asynchronously", content = @Content(schema = @Schema(implementation = Void.class))),
       @ApiResponse(responseCode = "403", description = "forbidden, you do not have access to this resource", content = @Content(schema = @Schema(implementation = Void.class))),

rest-api/src/main/resources/application.properties

@@ -45,9 +45,11 @@ spring.jpa.hibernate.naming.physical-strategy=org.hibernate.boot.model.naming.Ph
 spring.jpa.open-in-view=false
 
 ### openAPI and Swagger UI endpoints
-springdoc.api-docs.enabled=true
-springdoc.swagger-ui.enabled=true
-springdoc.swagger-ui.tryItOutEnabled=false
+# https://springdoc.org/
+# https://swagger.io/docs/open-source-tools/swagger-ui/usage/configuration/ <- append to springdoc.swagger-ui.
+springdoc.swagger-ui.path=/swagger-ui.html
+# empty supported submit methods disables try it out button
+springdoc.swagger-ui.supportedSubmitMethods=[]
 
 ### Https config behind proxy
 # https://docs.spring.io/spring-boot/docs/3.2.4/reference/htmlsingle/#howto.security.enable-https