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karlnicholaskarlnicholas
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Generate updates for 0.1.4 version.
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‎src/test/java/org/hdf5javalib/examples/read/SeparateTypesReadTest.java‎

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package org.hdf5javalib.examples.read;
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import org.hdf5javalib.dataclass.*;
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import org.hdf5javalib.datasource.TypedDataSource;
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import org.hdf5javalib.datatype.CompoundDatatype;
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import org.hdf5javalib.examples.ResourceLoader;
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import org.hdf5javalib.hdfjava.HdfDataset;
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import org.hdf5javalib.hdfjava.HdfFileReader;
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import org.junit.jupiter.api.Test;
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import java.math.BigDecimal;
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import java.math.BigInteger;
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import java.nio.channels.SeekableByteChannel;
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import java.util.BitSet;
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import java.util.Map;
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import java.util.stream.Collectors;
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import static org.junit.jupiter.api.Assertions.*;
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public class SeparateTypesReadTest {
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public static class Compound {
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private Short a;
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private Double b;
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public Short getA() {
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return a;
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}
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public void setA(Short a) {
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this.a = a;
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}
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public Double getB() {
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return b;
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}
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public void setB(Double b) {
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this.b = b;
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}
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}
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public static class CustomCompound {
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private String name;
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private Short someShort;
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private Double someDouble;
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private CustomCompound() {
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}
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public static Builder builder() {
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return new Builder();
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}
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public String getName() {
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return name;
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}
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public void setName(String name) {
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this.name = name;
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}
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public Short getSomeShort() {
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return someShort;
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}
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public void setSomeShort(Short someShort) {
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this.someShort = someShort;
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}
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public Double getSomeDouble() {
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return someDouble;
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}
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public void setSomeDouble(Double someDouble) {
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this.someDouble = someDouble;
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}
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public static class Builder {
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private final CustomCompound instance = new CustomCompound();
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public Builder name(String name) {
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instance.setName(name);
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return this;
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}
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public Builder someShort(Short someShort) {
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instance.setSomeShort(someShort);
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return this;
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}
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public Builder someDouble(Double someDouble) {
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instance.setSomeDouble(someDouble);
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return this;
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}
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public CustomCompound build() {
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return instance;
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}
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}
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}
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@Test
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void testAllTypesSeparateH5() throws Exception {
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try (SeekableByteChannel channel = ResourceLoader.loadResourceAsChannel("all_types_separate.h5")) {
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HdfFileReader reader = new HdfFileReader(channel).readFile();
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// fixed_point
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HdfDataset fixedPointDs = reader.getDataset("/fixed_point").orElseThrow();
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TypedDataSource<HdfFixedPoint> fpSource = new TypedDataSource<>(channel, reader, fixedPointDs, HdfFixedPoint.class);
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HdfFixedPoint fp = fpSource.readScalar();
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assertEquals(42, fp.getInstance(Integer.class).intValue());
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TypedDataSource<Integer> intSource = new TypedDataSource<>(channel, reader, fixedPointDs, Integer.class);
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assertEquals(42, intSource.readScalar().intValue());
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TypedDataSource<Long> longSource = new TypedDataSource<>(channel, reader, fixedPointDs, Long.class);
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assertEquals(42L, longSource.readScalar().longValue());
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TypedDataSource<BigInteger> biSource = new TypedDataSource<>(channel, reader, fixedPointDs, BigInteger.class);
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assertEquals(BigInteger.valueOf(42), biSource.readScalar());
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TypedDataSource<BigDecimal> bdSource = new TypedDataSource<>(channel, reader, fixedPointDs, BigDecimal.class);
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assertEquals(BigDecimal.valueOf(42), bdSource.readScalar());
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TypedDataSource<String> strSource = new TypedDataSource<>(channel, reader, fixedPointDs, String.class);
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assertEquals("42", strSource.readScalar());
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// float
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HdfDataset floatDs = reader.getDataset("/float").orElseThrow();
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TypedDataSource<HdfFloatPoint> floatPointSource = new TypedDataSource<>(channel, reader, floatDs, HdfFloatPoint.class);
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HdfFloatPoint floatPoint = floatPointSource.readScalar();
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assertEquals(3.14f, floatPoint.getInstance(Float.class), 0.001f);
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TypedDataSource<Float> floatJavaSource = new TypedDataSource<>(channel, reader, floatDs, Float.class);
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assertEquals(3.14f, floatJavaSource.readScalar(), 0.001f);
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TypedDataSource<Double> doubleSource = new TypedDataSource<>(channel, reader, floatDs, Double.class);
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assertEquals(3.140000104904175, doubleSource.readScalar(), 0.000001);
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TypedDataSource<String> floatStrSource = new TypedDataSource<>(channel, reader, floatDs, String.class);
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assertEquals("3.14", floatStrSource.readScalar());
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// time
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HdfDataset timeDs = reader.getDataset("/time").orElseThrow();
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TypedDataSource<HdfTime> timeSource = new TypedDataSource<>(channel, reader, timeDs, HdfTime.class);
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HdfTime time = timeSource.readScalar();
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assertEquals(1672531200L, time.getInstance(Long.class).longValue());
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TypedDataSource<Long> timeLongSource = new TypedDataSource<>(channel, reader, timeDs, Long.class);
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assertEquals(1672531200L, timeLongSource.readScalar().longValue());
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TypedDataSource<BigInteger> timeBiSource = new TypedDataSource<>(channel, reader, timeDs, BigInteger.class);
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assertEquals(BigInteger.valueOf(1672531200L), timeBiSource.readScalar());
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TypedDataSource<String> timeStrSource = new TypedDataSource<>(channel, reader, timeDs, String.class);
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assertEquals("1672531200", timeStrSource.readScalar());
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// string
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HdfDataset stringDs = reader.getDataset("/string").orElseThrow();
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TypedDataSource<HdfString> hdfStringSource = new TypedDataSource<>(channel, reader, stringDs, HdfString.class);
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HdfString hdfString = hdfStringSource.readScalar();
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assertEquals("Hello HDF5!", hdfString.getInstance(String.class));
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TypedDataSource<String> javaStringSource = new TypedDataSource<>(channel, reader, stringDs, String.class);
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assertEquals("Hello HDF5!", javaStringSource.readScalar());
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// bitfield
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HdfDataset bitfieldDs = reader.getDataset("/bitfield").orElseThrow();
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TypedDataSource<HdfBitField> bitFieldSource = new TypedDataSource<>(channel, reader, bitfieldDs, HdfBitField.class);
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HdfBitField bitField = bitFieldSource.readScalar();
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assertEquals("10101010", bitField.getInstance(String.class));
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TypedDataSource<BitSet> bitSetSource = new TypedDataSource<>(channel, reader, bitfieldDs, BitSet.class);
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BitSet expectedBitSet = new BitSet();
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expectedBitSet.set(1);
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expectedBitSet.set(3);
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expectedBitSet.set(5);
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expectedBitSet.set(7);
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assertEquals(expectedBitSet, bitSetSource.readScalar());
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TypedDataSource<String> bitStrSource = new TypedDataSource<>(channel, reader, bitfieldDs, String.class);
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assertEquals("10101010", bitStrSource.readScalar());
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// compound
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HdfDataset compoundDs = reader.getDataset("/compound").orElseThrow();
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TypedDataSource<HdfCompound> hdfCompoundSource = new TypedDataSource<>(channel, reader, compoundDs, HdfCompound.class);
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HdfCompound hdfCompound = hdfCompoundSource.readScalar();
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assertEquals("123, 9.81", hdfCompound.getInstance(String.class));
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TypedDataSource<String> compoundStrSource = new TypedDataSource<>(channel, reader, compoundDs, String.class);
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assertEquals("123, 9.81", compoundStrSource.readScalar());
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TypedDataSource<Compound> compoundJavaSource = new TypedDataSource<>(channel, reader, compoundDs, Compound.class);
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Compound compoundJava = compoundJavaSource.readScalar();
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assertEquals(Short.valueOf((short)123), compoundJava.getA());
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assertEquals(9.81, compoundJava.getB(), 0.001);
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CompoundDatatype.addConverter(CustomCompound.class, (bytes, compoundDataType) -> {
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Map<String, HdfCompoundMember> nameToMember = compoundDataType.getInstance(HdfCompound.class, bytes)
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.getMembers()
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.stream()
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.collect(Collectors.toMap(m -> m.getDatatype().getName(), m -> m));
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return CustomCompound.builder()
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.name("Name")
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.someShort(nameToMember.get("a").getInstance(Short.class))
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.someDouble(nameToMember.get("b").getInstance(Double.class))
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.build();
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});
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TypedDataSource<CustomCompound> customCompoundSource = new TypedDataSource<>(channel, reader, compoundDs, CustomCompound.class);
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CustomCompound customCompound = customCompoundSource.readScalar();
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assertEquals("Name", customCompound.getName());
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assertEquals(Short.valueOf((short)123), customCompound.getSomeShort());
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assertEquals(9.81, customCompound.getSomeDouble(), 0.001);
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// opaque
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HdfDataset opaqueDs = reader.getDataset("/opaque").orElseThrow();
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TypedDataSource<HdfOpaque> opaqueSource = new TypedDataSource<>(channel, reader, opaqueDs, HdfOpaque.class);
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HdfOpaque opaque = opaqueSource.readScalar();
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assertEquals("DEADBEEF", opaque.getInstance(String.class));
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TypedDataSource<String> opaqueStrSource = new TypedDataSource<>(channel, reader, opaqueDs, String.class);
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assertEquals("DEADBEEF", opaqueStrSource.readScalar());
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TypedDataSource<byte[]> opaqueByteSource = new TypedDataSource<>(channel, reader, opaqueDs, byte[].class);
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byte[] expectedOpaqueBytes = {-34, -83, -66, -17};
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assertArrayEquals(expectedOpaqueBytes, opaqueByteSource.readScalar());
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// reference
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HdfDataset referenceDs = reader.getDataset("/reference").orElseThrow();
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TypedDataSource<HdfReference> referenceSource = new TypedDataSource<>(channel, reader, referenceDs, HdfReference.class);
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HdfReference reference = referenceSource.readScalar();
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assertEquals("/target", reference.getInstance(String.class));
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TypedDataSource<String> referenceStrSource = new TypedDataSource<>(channel, reader, referenceDs, String.class);
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assertEquals("/target", referenceStrSource.readScalar());
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TypedDataSource<byte[]> referenceByteSource = new TypedDataSource<>(channel, reader, referenceDs, byte[].class);
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byte[] expectedReferenceBytes = {64, 20, 0, 0, 0, 0, 0, 0};
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assertArrayEquals(expectedReferenceBytes, referenceByteSource.readScalar());
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// enum
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HdfDataset enumDs = reader.getDataset("/enum").orElseThrow();
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TypedDataSource<HdfEnum> enumSource = new TypedDataSource<>(channel, reader, enumDs, HdfEnum.class);
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HdfEnum hdfEnum = enumSource.readScalar();
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assertEquals("GREEN", hdfEnum.getInstance(String.class));
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TypedDataSource<String> enumStrSource = new TypedDataSource<>(channel, reader, enumDs, String.class);
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assertEquals("GREEN", enumStrSource.readScalar());
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// vlen
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HdfDataset vlenDs = reader.getDataset("/vlen").orElseThrow();
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TypedDataSource<HdfVariableLength> vlenSource = new TypedDataSource<>(channel, reader, vlenDs, HdfVariableLength.class);
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HdfVariableLength vlen = vlenSource.readScalar();
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assertEquals("[7, 8, 9]", vlen.getInstance(String.class));
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TypedDataSource<String> vlenStrSource = new TypedDataSource<>(channel, reader, vlenDs, String.class);
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assertEquals("[7, 8, 9]", vlenStrSource.readScalar());
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TypedDataSource<Object> vlenObjSource = new TypedDataSource<>(channel, reader, vlenDs, Object.class);
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HdfData[] vlenData = (HdfData[]) vlenObjSource.readScalar();
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assertEquals(7, vlenData[0].getInstance(Integer.class).intValue());
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assertEquals(8, vlenData[1].getInstance(Integer.class).intValue());
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assertEquals(9, vlenData[2].getInstance(Integer.class).intValue());
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// array
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HdfDataset arrayDs = reader.getDataset("/array").orElseThrow();
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TypedDataSource<HdfArray> arraySource = new TypedDataSource<>(channel, reader, arrayDs, HdfArray.class);
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HdfArray hdfArray = arraySource.readScalar();
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assertEquals("[10, 20, 30]", hdfArray.getInstance(String.class));
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TypedDataSource<String> arrayStrSource = new TypedDataSource<>(channel, reader, arrayDs, String.class);
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assertEquals("[10, 20, 30]", arrayStrSource.readScalar());
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TypedDataSource<HdfData[]> arrayDataSource = new TypedDataSource<>(channel, reader, arrayDs, HdfData[].class);
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HdfData[] arrayData = arrayDataSource.readScalar();
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assertEquals(10, arrayData[0].getInstance(Integer.class).intValue());
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assertEquals(20, arrayData[1].getInstance(Integer.class).intValue());
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assertEquals(30, arrayData[2].getInstance(Integer.class).intValue());
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assertEquals("HdfSuperblock{version=0, freeSpaceVersion=0, rootGroupVersion=0, sharedHeaderVersion=0, sizeOfOffsets=8, sizeOfLengths=8, groupLeafNodeK=4, groupInternalNodeK=16, baseAddress=0, freeSpaceAddress=<Undefined>, endOfFileAddress=11144, driverInformationAddress=<Undefined>}", reader.getSuperblock().toString());
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}
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}
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}

src/test/java/org/hdf5javalib/examples/read/HdfStringReadTest.java renamed to src/test/java/org/hdf5javalib/examples/read/StringReadTest.java

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import org.hdf5javalib.hdfjava.HdfFileReader;
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import org.junit.jupiter.api.Test;
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import java.io.IOException;
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import java.nio.channels.SeekableByteChannel;
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import java.nio.charset.StandardCharsets;
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import java.util.Arrays;
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import static org.junit.jupiter.api.Assertions.assertArrayEquals;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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public class HdfStringReadTest {
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public class StringReadTest {
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private static final String[] ASCII_EXPECTED = {"label 1 ", "label 2 ", "label 3 ", "label 4 ", "label 5 ",
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"label 6 ", "label 7 ", "label 8 ", "label 9 ", "label 10"};
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private static final String[] UTF8_EXPECTED = {"ꦠꦤ꧀ 1", "ꦠꦤ꧀ 2", "ꦠꦤ꧀ 3", "ꦠꦤ꧀ 4", "ꦠꦤ꧀ 5",

src/test/java/org/hdf5javalib/examples/read/HdfVLenTypesReadTest.java renamed to src/test/java/org/hdf5javalib/examples/read/VLenTypesReadTest.java

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import org.hdf5javalib.hdfjava.HdfFileReader;
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import org.junit.jupiter.api.Test;
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import java.io.IOException;
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import java.nio.ByteBuffer;
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import java.nio.channels.SeekableByteChannel;
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import java.nio.charset.StandardCharsets;
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import static org.junit.jupiter.api.Assertions.assertArrayEquals;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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public class HdfVLenTypesReadTest {
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public class VLenTypesReadTest {
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@Test
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public void testVlenDouble() throws Exception {

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