Fix some issues detected by sonar (#870)

* Correctly skip bytes

* Suppress warning on controlled input

* Improve exception handling

* Fix issues reported by sonar

* Format code with spotless

* Suppress some warnings

* Fix sonar issues and clean code

Author: bchapuis

baremaps-cli/src/main/java/org/apache/baremaps/cli/BaremapsException.java

@@ -0,0 +1,54 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to you under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.baremaps.cli;
+
+
+/** Signals that an exception occurred in the {@link Baremaps} CLI. */
+public class BaremapsException extends RuntimeException {
+
+  /** Constructs a {@link BaremapsException} with {@code null} as its error detail message. */
+  public BaremapsException() {}
+
+  /**
+   * Constructs an {@link BaremapsException} with the specified detail message.
+   *
+   * @param message the message
+   */
+  public BaremapsException(String message) {
+    super(message);
+  }
+
+  /**
+   * Constructs a {@link BaremapsException} with the specified cause.
+   *
+   * @param cause the cause
+   */
+  public BaremapsException(Throwable cause) {
+    super(cause);
+  }
+
+  /**
+   * Constructs a {@link BaremapsException} with the specified detail message and cause.
+   *
+   * @param message the message
+   * @param cause the cause
+   */
+  public BaremapsException(String message, Throwable cause) {
+    super(message, cause);
+  }
+}

baremaps-cli/src/main/java/org/apache/baremaps/cli/map/Dev.java

@@ -30,6 +30,7 @@
 import java.nio.file.Path;
 import java.util.concurrent.Callable;
 import java.util.function.Supplier;
+import org.apache.baremaps.cli.BaremapsException;
 import org.apache.baremaps.cli.Options;
 import org.apache.baremaps.config.ConfigReader;
 import org.apache.baremaps.maplibre.style.Style;
@@ -88,7 +89,7 @@ public Integer call() throws Exception {
         var config = configReader.read(tilesetPath);
         return objectMapper.readValue(config, Tileset.class);
       } catch (IOException e) {
-        throw new RuntimeException(e);
+        throw new BaremapsException(e);
       }
     };
 
@@ -102,7 +103,7 @@ public Integer call() throws Exception {
         var config = configReader.read(stylePath);
         return objectMapper.readValue(config, Style.class);
       } catch (IOException e) {
-        throw new RuntimeException(e);
+        throw new BaremapsException(e);
       }
     };
 

baremaps-core/src/main/java/org/apache/baremaps/database/DiffService.java

@@ -58,8 +58,11 @@ public class DiffService implements Callable<List<TileCoord>> {
   public DiffService(
       Map<Long, Coordinate> coordinateMap,
       Map<Long, List<Long>> referenceMap,
-      HeaderRepository headerRepository, Repository<Long, Node> nodeRepository,
-      Repository<Long, Way> wayRepository, Repository<Long, Relation> relationRepository, int srid,
+      HeaderRepository headerRepository,
+      Repository<Long, Node> nodeRepository,
+      Repository<Long, Way> wayRepository,
+      Repository<Long, Relation> relationRepository,
+      int srid,
       int zoom) {
     this.coordinateMap = coordinateMap;
     this.referenceMap = referenceMap;