Introduce retry to connect to db server after time-out (#113)

* Introduce retry count

* Hide data source details

* Add javadocs

* Bump mariadb-java-client 2.7.3 => 3.0.6

pom.xml

@@ -217,7 +217,7 @@
 		<dependency>
 			<groupId>org.mariadb.jdbc</groupId>
 			<artifactId>mariadb-java-client</artifactId>
-			<version>2.7.3</version>
+			<version>3.0.6</version>
 		</dependency>
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>

src/main/groovy/life/qbic/DataSource.groovy

@@ -20,6 +20,7 @@ interface DataSource {
      * execution of the connection object with a try-with-resource statement or call the
      * {@link AutoCloseable#close()} method explicitly.</p>
      * @return a connection to the datasource
+     * @throws {@link TimeOutException} when a connection cannot be acquired from the data source
      */
-    Connection getConnection()
+    Connection getConnection() throws TimeOutException
 }

src/main/groovy/life/qbic/QBiCDataSource.groovy

@@ -1,8 +1,11 @@
 package life.qbic
 
+import groovy.util.logging.Log4j2
+
 import javax.inject.Inject
 import javax.inject.Singleton
 import java.sql.Connection
+import java.sql.SQLTimeoutException
 
 /**
  * <b>QBiCDataSource Class</b>
@@ -12,19 +15,37 @@ import java.sql.Connection
  * @since 1.2.1
  */
 @Singleton
+@Log4j2
 class QBiCDataSource implements DataSource {
 
-    javax.sql.DataSource source
+    private final static int MAX_RETRY_COUNT = 3
+
+    private final javax.sql.DataSource source
 
-    @Inject QBiCDataSource (javax.sql.DataSource source) {
+    @Inject
+    QBiCDataSource(javax.sql.DataSource source) {
         this.source = source
     }
 
     /**
      * {@InheritDocs}
      */
     @Override
-    Connection getConnection() {
+    Connection getConnection() throws TimeOutException {
+        Connection connection = null
+        int turn = 1
+        while (!connection) {
+            if (turn == MAX_RETRY_COUNT) {
+                throw new TimeOutException("Maximum number of tries reached ($MAX_RETRY_COUNT), connection to database server timed out repeatedly.")
+            }
+            try {
+                connection = this.source.getConnection()
+            } catch (SQLTimeoutException e) {
+                log.error("Turn $turn to get connection failed.")
+                log.error("Connection to database server timed out.", e)
+            }
+            turn++;
+        }
         return this.source.connection
     }
 }

src/main/groovy/life/qbic/TimeOutException.java

@@ -0,0 +1,23 @@
+package life.qbic;
+
+/**
+ * Timeout Exception
+ * <p>
+ * Is thrown when connections to a data source cannot be established.
+ *
+ * @since 2.2.3
+ */
+public class TimeOutException extends RuntimeException {
+
+  public TimeOutException() {
+  }
+
+  public TimeOutException(String message) {
+    super(message);
+  }
+
+  public TimeOutException(String message, Throwable cause) {
+    super(message, cause);
+  }
+
+}

src/main/groovy/life/qbic/db/MariaDBManager.groovy

@@ -3,7 +3,9 @@ package life.qbic.db
 import groovy.sql.GroovyRowResult
 import groovy.sql.Sql
 import groovy.util.logging.Log4j2
+import life.qbic.DataSource
 import life.qbic.QBiCDataSource
+import life.qbic.TimeOutException
 import life.qbic.api.rest.v2.samples.SampleStatusDto
 import life.qbic.datamodel.identifiers.SampleCodeFunctions
 import life.qbic.datamodel.people.Address
@@ -27,7 +29,6 @@ import org.codehaus.groovy.runtime.DefaultGroovyMethods
 
 import javax.inject.Inject
 import javax.inject.Singleton
-import javax.sql.DataSource
 import java.sql.Connection
 import java.sql.SQLException
 import java.sql.Timestamp
@@ -49,7 +50,15 @@ class MariaDBManager implements IQueryService, INotificationService, SampleEvent
 
   @Inject
   MariaDBManager(QBiCDataSource dataSource) {
-    this.dataSource = dataSource.getSource()
+    this.dataSource = dataSource
+  }
+
+  private Connection getConnection() throws UnrecoverableException {
+    try {
+      return dataSource.getConnection()
+    } catch (TimeOutException exception) {
+      throw new UnrecoverableException("Connection to data source timed out", exception)
+    }
   }
 
   void addNewLocation(String sampleId, Location location) throws IllegalArgumentException {