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b754dcb8f2727f38b9f2ca1b99562fddfd9de158
hdf5/java/src-jni/test/TestH5.java
T
Allen Byrne b754dcb8f2 Move Java wrappers to FFM using jextract and java 25 (#5957) 
FFM build requires Java 25, Jextract 25.
Generates FFM bindings during configure.
JNI is default when the requirements are not met or can be forced.
Presets added for maven and FFM - JNI is default selection.
Enhanced Maven options will work with either JNI or FFM
New Workflows for testing and maven uploads.
Extensive documentation changes for java.
2025-11-04 14:03:06 -06:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the LICENSE file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
package test;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Reader;
import java.io.StreamTokenizer;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
import org.junit.After;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;
/**
* @author xcao
*
*/
public class TestH5 {
@Rule
public TestName testname = new TestName();
private static final String H5_FILE = "testData.h5";
private static final String EXPORT_FILE = "testExport.txt";
private static final String H5_REGION_FILE = "trefer_reg.h5";
private static final String EXPORT_REGION_FILE = "testExportReg.txt";
private static final String H5_ATTR_FILE = "trefer_attr.h5";
private static final String EXPORT_ATTR_FILE = "testExportAttr.txt";
private static final String H5_DREG_FILE = "tdatareg.h5";
private static final String EXPORT_DREG_FILE = "testExportDReg.txt";
private static final String H5_AREG_FILE = "tattrreg.h5";
private static final String EXPORT_AREG_FILE = "testExportAReg.txt";
private static final int DIM_X = 4;
private static final int DIM_Y = 6;
private static final int DIM_BLKS = 36;
private static final int DIM_PNTS = 10;
private static final int DIM_ATTR = 12;
private static final int RANK = 2;
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5dsid = HDF5Constants.H5I_INVALID_HID;
long H5did = HDF5Constants.H5I_INVALID_HID;
long[] H5dims = {DIM_X, DIM_Y};
private final void _deleteFile(String filename)
{
File file = null;
try {
file = new File(filename);
}
catch (Throwable err) {
}
if (file.exists()) {
try {
file.delete();
}
catch (SecurityException e) {
}
}
}
private final long _createDataset(long fid, long dsid, String name, long dapl)
{
long did = HDF5Constants.H5I_INVALID_HID;
try {
did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32LE, dsid, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5._createDataset: ", did > 0);
return did;
}
private final void _createH5File()
{
try {
H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
H5dsid = H5.H5Screate_simple(2, H5dims, null);
H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5Pfapl.createH5file: " + err);
}
assertTrue("TestH5.createH5file: H5.H5Fcreate: ", H5fid > 0);
assertTrue("TestH5.createH5file: H5.H5Screate_simple: ", H5dsid > 0);
assertTrue("TestH5.createH5file: _createDataset: ", H5did > 0);
try {
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
}
catch (Throwable err) {
err.printStackTrace();
}
}
private final void _closeH5File()
{
if (H5did >= 0)
try {
H5.H5Dclose(H5did);
}
catch (Exception ex) {
}
if (H5dsid > 0)
try {
H5.H5Sclose(H5dsid);
}
catch (Exception ex) {
}
if (H5fid > 0)
try {
H5.H5Fclose(H5fid);
}
catch (Exception ex) {
}
H5fid = HDF5Constants.H5I_INVALID_HID;
H5dsid = HDF5Constants.H5I_INVALID_HID;
H5did = HDF5Constants.H5I_INVALID_HID;
}
public void _openH5File(String filename, String dsetname)
{
try {
H5fid = H5.H5Fopen(filename, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5._openH5file: " + err);
}
assertTrue("TestH5._openH5file: H5.H5Fopen: ", H5fid >= 0);
try {
H5did = H5.H5Dopen(H5fid, dsetname, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5._openH5file: " + err);
}
assertTrue("TestH5._openH5file: H5.H5Dopen: ", H5did >= 0);
try {
H5dsid = H5.H5Dget_space(H5did);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5._openH5file: " + err);
}
assertTrue("TestH5._openH5file: H5.H5Screate_simple: ", H5dsid > 0);
}
public final void _deleteH5file()
{
_closeH5File();
_deleteFile(H5_FILE);
}
@After
public void closeH5File() throws HDF5LibraryException
{
_closeH5File();
assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
System.out.println();
}
@Before
public void verifyCount() throws NullPointerException, HDF5Exception
{
assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
System.out.print(testname.getMethodName());
}
/**
* Test method for {@link hdf.hdf5lib.H5#J2C(int)}.
* NOTE:
* H5F_ACC_DEBUG no longer prints any special debug info. Even though the symbol is
* being retained hdf java does not access the symbol.
*/
@Test
public void testJ2C()
{
int H5F_ACC_RDONLY = 0x0000;
int H5F_ACC_RDWR = 0x0001;
int H5F_ACC_TRUNC = 0x0002;
int H5F_ACC_EXCL = 0x0004;
int H5F_ACC_CREAT = 0x0010;
int H5F_OBJ_FILE = 0x0001;
int H5F_OBJ_DATASET = 0x0002;
int H5F_OBJ_GROUP = 0x0004;
int H5F_OBJ_DATATYPE = 0x0008;
int H5F_OBJ_ATTR = 0x0010;
int H5F_OBJ_ALL = H5F_OBJ_FILE | H5F_OBJ_DATASET | H5F_OBJ_GROUP | H5F_OBJ_DATATYPE | H5F_OBJ_ATTR;
int H5F_OBJ_LOCAL = 0x0020;
int definedValues[] = {H5F_ACC_RDONLY, H5F_ACC_RDWR, H5F_ACC_TRUNC, H5F_ACC_EXCL,
H5F_ACC_CREAT, H5F_OBJ_FILE, H5F_OBJ_DATASET, H5F_OBJ_GROUP,
H5F_OBJ_DATATYPE, H5F_OBJ_ATTR, H5F_OBJ_ALL, H5F_OBJ_LOCAL};
int j2cValues[] = {
HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5F_ACC_TRUNC,
HDF5Constants.H5F_ACC_EXCL, HDF5Constants.H5F_ACC_CREAT, HDF5Constants.H5F_OBJ_FILE,
HDF5Constants.H5F_OBJ_DATASET, HDF5Constants.H5F_OBJ_GROUP, HDF5Constants.H5F_OBJ_DATATYPE,
HDF5Constants.H5F_OBJ_ATTR, HDF5Constants.H5F_OBJ_ALL, HDF5Constants.H5F_OBJ_LOCAL};
for (int i = 0; i < definedValues.length; i++) {
assertEquals(definedValues[i], j2cValues[i]);
}
assertFalse(H5F_ACC_RDONLY == HDF5Constants.H5F_ACC_RDWR);
assertFalse(H5F_OBJ_FILE == HDF5Constants.H5F_OBJ_GROUP);
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5error_off()}.
*/
@Test
public void testH5error_off()
{
try {
H5.H5error_off();
}
catch (Throwable err) {
fail("H5.H5error_off failed: " + err);
}
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5open()}.
*/
@Test
public void testH5open()
{
try {
H5.H5open();
}
catch (Throwable err) {
fail("H5.H5open failed: " + err);
}
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5garbage_collect()}.
*/
@Test
public void testH5garbage_collect()
{
try {
H5.H5garbage_collect();
}
catch (Throwable err) {
fail("H5.H5garbage_collect failed: " + err);
}
}
/**
* Test method for
* {@link hdf.hdf5lib.H5#H5set_free_list_limits(int, int, int, int, int, int)}
* .
*/
@Test
public void testH5set_free_list_limits()
{
int reg_global_lim = 1;
int reg_list_lim = 1;
int arr_global_lim = 1;
int arr_list_lim = 1;
int blk_global_lim = 1;
int blk_list_lim = 1;
try {
H5.H5set_free_list_limits(reg_global_lim, reg_list_lim, arr_global_lim, arr_list_lim,
blk_global_lim, blk_list_lim);
}
catch (Throwable err) {
fail("H5.H5set_free_list_limits failed: " + err);
}
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5get_libversion(int[])}.
*/
@Test
public void testH5get_libversion()
{
int libversion[] = {2, 0, 0};
try {
H5.H5get_libversion(libversion);
}
catch (Throwable err) {
fail("H5.H5get_libversion: " + err);
}
for (int i = 0; i < 3; i++)
assertEquals(H5.LIB_VERSION[i], libversion[i]);
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5get_libversion(int[])}
* to ensure a null libversion parameter causes the function to
* fail.
*/
@Test
public void testH5get_libversion_null_param()
{
try {
H5.H5get_libversion(null);
}
catch (Throwable err) {
return;
}
fail("H5.H5get_libversion: succeeded with a null libversion parameter!");
}
/**
* Test method for
* {@link hdf.hdf5lib.H5#H5check_version(int, int, int)}.
*/
@Test
public void testH5check_version()
{
int majnum = 2, minnum = 0, relnum = 0;
try {
H5.H5check_version(majnum, minnum, relnum);
}
catch (Throwable err) {
fail("H5.H5check_version failed: " + err);
}
try {
H5.H5check_version(-1, 0, 0);
}
catch (Throwable err) {
fail("H5.H5check_version failed: " + err);
}
}
@Test
public void testIsSerializable()
{
H5 test = new H5();
ByteArrayOutputStream out = new ByteArrayOutputStream();
ObjectOutputStream oos;
try {
oos = new ObjectOutputStream(out);
oos.writeObject(test);
oos.close();
}
catch (IOException err) {
err.printStackTrace();
fail("ObjectOutputStream failed: " + err);
}
assertTrue(out.toByteArray().length > 0);
}
@SuppressWarnings("static-access")
@Test
public void serializeToDisk()
{
try {
H5 test = new H5();
FileOutputStream fos = new FileOutputStream("temph5.ser");
ObjectOutputStream oos = new ObjectOutputStream(fos);
oos.writeObject(test);
oos.close();
}
catch (Exception ex) {
fail("Exception thrown during test: " + ex.toString());
}
try {
FileInputStream fis = new FileInputStream("temph5.ser");
ObjectInputStream ois = new ObjectInputStream(fis);
H5 test = (hdf.hdf5lib.H5)ois.readObject();
ois.close();
assertTrue("H5.LIB_VERSION[0]", test.LIB_VERSION[0] == H5.LIB_VERSION[0]);
assertTrue("H5.LIB_VERSION[1]", test.LIB_VERSION[1] == H5.LIB_VERSION[1]);
// assertTrue("H5.LIB_VERSION[2]", test.LIB_VERSION[2]==H5.LIB_VERSION[2]);
// Clean up the file
new File("temph5.ser").delete();
}
catch (Exception ex) {
fail("Exception thrown during test: " + ex.toString());
}
}
@Ignore
public void testH5export_dataset()
{
int[][] dset_data = new int[DIM_X][DIM_Y];
int[][] dset_indata = new int[DIM_X][DIM_Y];
int FILLVAL = 99;
_createH5File();
// Initialize the dataset.
for (int indx = 0; indx < DIM_X; indx++)
for (int jndx = 0; jndx < DIM_Y; jndx++)
dset_data[indx][jndx] = FILLVAL;
try {
if (H5did >= 0)
H5.H5Dwrite(H5did, HDF5Constants.H5T_STD_I32LE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
_closeH5File();
_openH5File(H5_FILE, "/dset");
try {
H5.H5export_dataset(EXPORT_FILE, H5fid, "/dset", 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_FILE);
try {
Reader reader = new FileReader(EXPORT_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
int jndx = 0;
while (streamTokenizer.nextToken() != StreamTokenizer.TT_EOF) {
if (streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx][jndx] = (int)streamTokenizer.nval;
jndx++;
if (jndx >= DIM_Y) {
jndx = 0;
indx++;
}
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for (int row = 0; row < DIM_X; row++)
for (int col = 0; col < DIM_Y; col++) {
assertTrue("H5export_dataset: <" + row + "," + col + ">" + dset_indata[row][col] + "=99",
dset_indata[row][col] == 99);
}
_deleteH5file();
}
@Ignore
public void testH5export_region()
{
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108, 111,
126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
int[] dset_indata = new int[DIM_BLKS + DIM_PNTS];
String objName = "/Dataset1";
_openH5File(H5_REGION_FILE, objName);
try {
H5.H5export_dataset(EXPORT_REGION_FILE, H5fid, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_REGION_FILE);
try {
Reader reader = new FileReader(EXPORT_REGION_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
while (streamTokenizer.nextToken() != StreamTokenizer.TT_EOF) {
if (streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for (int row = 0; row < DIM_X; row++)
assertTrue("testH5export_region: <" + row + ">" + dset_indata[row],
dset_indata[row] == dset_data_expect[row]);
}
@Ignore
public void testH5export_attribute()
{
int[] dset_data_expect = {0, 3, 6, 9, 1, 4, 7, 10, 2, 5, 8, 11};
int[] dset_indata = new int[DIM_ATTR];
String objName = "/Dataset3";
_openH5File(H5_ATTR_FILE, objName);
try {
H5.H5export_dataset(EXPORT_ATTR_FILE, H5did, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_ATTR_FILE);
try {
Reader reader = new FileReader(EXPORT_ATTR_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
int jndx = 0;
while (streamTokenizer.nextToken() != StreamTokenizer.TT_EOF) {
if (streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for (int row = 0; row < DIM_X; row++)
assertTrue("testH5export_attribute: <" + row + ">" + dset_indata[row],
dset_indata[row] == dset_data_expect[row]);
}
@Ignore
public void testH5export_regdataset()
{
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108, 111,
126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
int[] dset_indata = new int[DIM_BLKS + DIM_PNTS];
String objName = "/Dataset1";
_openH5File(H5_DREG_FILE, objName);
try {
H5.H5export_dataset(EXPORT_DREG_FILE, H5fid, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_DREG_FILE);
try {
Reader reader = new FileReader(EXPORT_DREG_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
while (streamTokenizer.nextToken() != StreamTokenizer.TT_EOF) {
if (streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for (int row = 0; row < DIM_X; row++)
assertTrue("testH5export_regdataset: <" + row + ">" + dset_indata[row],
dset_indata[row] == dset_data_expect[row]);
}
@Ignore
public void testH5export_attrdataset()
{
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108, 111,
126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
int[] dset_indata = new int[DIM_BLKS + DIM_PNTS];
String dsetName = "/Dataset1";
String objName = "Attribute1";
_openH5File(H5_AREG_FILE, dsetName);
try {
H5.H5export_attribute(EXPORT_AREG_FILE, H5did, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_attribute failed: " + err);
}
File file = new File(EXPORT_AREG_FILE);
try {
Reader reader = new FileReader(EXPORT_AREG_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
int jndx = 0;
while (streamTokenizer.nextToken() != StreamTokenizer.TT_EOF) {
if (streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for (int row = 0; row < DIM_X; row++)
assertTrue("testH5export_attrdataset: <" + row + ">" + dset_indata[row],
dset_indata[row] == dset_data_expect[row]);
}
}
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