SonarQube cleanup

Author: karlnicholas

.gitignore

@@ -44,3 +44,4 @@ hdf5/*/*.h5
 /src/main/resources/h5ex_tutr/att/*.h5
 /src/main/resources/h5ex_d/*.h5
 /src/main/resources/h5ex_d/*.data
+/src/main/resources/h5ex_g/

src/main/java/org/hdf5javalib/examples/h5ex_g/h5ex_g_read.java

@@ -0,0 +1,56 @@
+package org.hdf5javalib.examples.h5ex_g;
+
+import org.hdf5javalib.datasource.TypedDataSource;
+import org.hdf5javalib.utils.HdfDisplayUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Objects;
+import java.util.stream.Stream;
+
+/**
+ * Demonstrates reading and processing compound data from an HDF5 file.
+ * <p>
+ * The {@code CompoundRead} class serves as an example application that reads
+ * a compound dataset from an HDF5 file, processes it using a {@link TypedDataSource},
+ * and displays the results. It showcases filtering and mapping operations on the
+ * dataset, as well as conversion to a custom Java class.
+ * </p>
+ */
+public class h5ex_g_read {
+    private static final Logger log = LoggerFactory.getLogger(h5ex_g_read.class);
+    /**
+     * Entry point for the application.
+     *
+     * @param args command-line arguments (not used)
+     */
+    public static void main(String[] args) {
+        new h5ex_g_read().run();
+    }
+
+    /**
+     * Executes the main logic of reading and displaying compound data from an HDF5 file.
+     */
+    private void run() {
+        try {
+            // List all .h5 files in HDF5Examples resources directory
+            Path dirPath = Paths.get(Objects.requireNonNull(h5ex_g_read.class.getClassLoader().getResource("h5ex_g")).toURI());
+            try ( Stream<Path> streamList = Files.list(dirPath) ) {
+                streamList.filter(p -> p.toString().endsWith(".h5"))
+                        .forEach(p -> {
+                            log.info("Running {}", p.getFileName());
+                            HdfDisplayUtils.displayFileContent(p);
+                        });
+
+            }
+        } catch (URISyntaxException | IOException e) {
+            throw new IllegalStateException(e);
+        }
+    }
+
+}

src/test/java/org/hdf5javalib/examples/h5ex_g/H5exGReadTest.java

@@ -0,0 +1,92 @@
+package org.hdf5javalib.examples.h5ex_g;
+
+import org.hdf5javalib.examples.ResourceLoader;
+import org.hdf5javalib.hdfjava.HdfDataset;
+import org.hdf5javalib.hdfjava.HdfFileReader;
+import org.junit.jupiter.api.Test;
+
+import java.nio.channels.SeekableByteChannel;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+public class H5exGReadTest {
+
+    @Test
+    void testCompact1() throws Exception {
+        try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("h5ex_g/h5ex_g_compact1.h5")) {
+            new HdfFileReader(channel).readFile();
+        }
+    }
+
+    @Test
+    void testCompact2() throws Exception {
+        try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("h5ex_g/h5ex_g_compact2.h5")) {
+            HdfFileReader reader = new HdfFileReader(channel).readFile();
+            reader.getGroup("/G1").orElseThrow();
+        }
+    }
+
+    @Test
+    void testCOrder() throws Exception {
+        try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("h5ex_g/h5ex_g_corder.h5")) {
+            HdfFileReader reader = new HdfFileReader(channel).readFile();
+            reader.getDataset("/index_group").orElseThrow().close();
+        }
+    }
+
+    @Test
+    void testCreate() throws Exception {
+        try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("h5ex_g/h5ex_g_create.h5")) {
+            new HdfFileReader(channel).readFile();
+        }
+    }
+
+    @Test
+    void testIntermediate() throws Exception {
+        try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("h5ex_g/h5ex_g_intermediate.h5")) {
+            new HdfFileReader(channel).readFile();
+        }
+    }
+
+    @Test
+    void testIterate() throws Exception {
+        try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("h5ex_g/h5ex_g_iterate.h5")) {
+            HdfFileReader reader = new HdfFileReader(channel).readFile();
+            reader.getDataset("/DS1").orElseThrow().close();
+            reader.getDataset("/DT1").orElseThrow().close();
+            reader.getDataset("/G1/DS2").orElseThrow().close();
+            HdfDataset dataset = reader.getDataset("/L1").orElseThrow();
+            assertEquals("/G1/DS2", dataset.getHardLink());
+            dataset.close();
+        }
+    }
+
+    @Test
+    void testPhase() throws Exception {
+        try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("h5ex_g/h5ex_g_phase.h5")) {
+            HdfFileReader reader = new HdfFileReader(channel).readFile();
+            reader.getGroup("/G0").orElseThrow();
+        }
+    }
+
+    @Test
+    void testTraverse() throws Exception {
+        try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("h5ex_g/h5ex_g_traverse.h5")) {
+            HdfFileReader reader = new HdfFileReader(channel).readFile();
+            reader.getDataset("/group1/dset1").orElseThrow().close();
+            HdfDataset dataSet = reader.getDataset("/group1/group3/dset2").orElseThrow();
+            assertEquals("/group1/dset1", dataSet.getHardLink());
+        }
+    }
+
+    @Test
+    void testVisit() throws Exception {
+        try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("h5ex_g/h5ex_g_visit.h5")) {
+            HdfFileReader reader = new HdfFileReader(channel).readFile();
+            reader.getDataset("/group1/dset1").orElseThrow().close();
+            HdfDataset dataSet = reader.getDataset("/group1/group3/dset2").orElseThrow();
+            assertEquals("/group1/dset1", dataSet.getHardLink());
+            dataSet.close();
+        }
+    }
+}