mirror of
https://github.com/HDFGroup/hdf5.git
synced 2026-09-25 04:09:44 +03:00
Allen Byrne
b754dcb8f2
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.
1001 lines
36 KiB
Java
1001 lines
36 KiB
Java
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the LICENSE file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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package test;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertTrue;
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import static org.junit.Assert.fail;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import hdf.hdf5lib.H5;
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import hdf.hdf5lib.HDF5Constants;
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import hdf.hdf5lib.exceptions.HDF5Exception;
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import hdf.hdf5lib.exceptions.HDF5FunctionArgumentException;
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import hdf.hdf5lib.exceptions.HDF5LibraryException;
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import org.junit.After;
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import org.junit.Before;
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import org.junit.Ignore;
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import org.junit.Rule;
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import org.junit.Test;
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import org.junit.rules.TestName;
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public class TestH5R {
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@Rule
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public TestName testname = new TestName();
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private static final String H5_FILE = "testH5R.h5";
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private static final int DIM_X = 4;
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private static final int DIM_Y = 6;
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long H5fid = HDF5Constants.H5I_INVALID_HID;
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long H5dsid = HDF5Constants.H5I_INVALID_HID;
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long H5did = HDF5Constants.H5I_INVALID_HID;
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long H5gid = HDF5Constants.H5I_INVALID_HID;
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long H5did2 = HDF5Constants.H5I_INVALID_HID;
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long[] H5dims = {DIM_X, DIM_Y};
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int[][] dset_data = new int[DIM_X][DIM_Y];
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int FILLVAL = 99;
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private final void _deleteFile(String filename)
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{
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File file = null;
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try {
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file = new File(filename);
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}
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catch (Throwable err) {
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}
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if (file.exists()) {
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try {
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file.delete();
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}
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catch (SecurityException e) {
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e.printStackTrace();
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}
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}
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assertFalse("TestH5R._deleteFile file still exists ", file.exists());
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}
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private final long _createDataset(long fid, long dsid, String name, long dapl)
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{
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long did = HDF5Constants.H5I_INVALID_HID;
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try {
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did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.H5P_DEFAULT, dapl);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Dcreate: " + err);
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}
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assertTrue("TestH5R._createDataset: ", did > 0);
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return did;
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}
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private final long _createGroup(long fid, String name)
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{
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long gid = HDF5Constants.H5I_INVALID_HID;
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try {
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gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Gcreate: " + err);
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}
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assertTrue("TestH5R._createGroup: ", gid > 0);
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return gid;
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}
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@Before
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public void createH5file() throws NullPointerException, HDF5Exception
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{
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assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
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System.out.print(testname.getMethodName());
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try {
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H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.H5P_DEFAULT);
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H5dsid = H5.H5Screate_simple(2, H5dims, null);
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H5gid = _createGroup(H5fid, "Group1");
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H5did2 = _createDataset(H5gid, H5dsid, "dset2", HDF5Constants.H5P_DEFAULT);
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H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
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// Initialize the dataset.
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for (int indx = 0; indx < DIM_X; indx++)
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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dset_data[indx][jndx] = FILLVAL;
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try {
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if (H5did >= 0)
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H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
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HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data[0]);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("TestH5R.createH5file: " + err);
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}
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assertTrue("TestH5R.createH5file: H5.H5Fcreate: ", H5fid > 0);
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assertTrue("TestH5R.createH5file: H5.H5Screate_simple: ", H5dsid > 0);
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assertTrue("TestH5R.createH5file: _createDataset: ", H5did > 0);
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H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
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}
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@After
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public void deleteH5file() throws HDF5LibraryException
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{
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if (H5dsid > 0)
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try {
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H5.H5Sclose(H5dsid);
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}
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catch (Exception ex) {
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}
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if (H5did > 0)
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try {
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H5.H5Dclose(H5did);
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}
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catch (Exception ex) {
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}
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if (H5fid > 0)
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try {
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H5.H5Fclose(H5fid);
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}
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catch (Exception ex) {
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}
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if (H5gid > 0)
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try {
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H5.H5Gclose(H5gid);
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}
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catch (Exception ex) {
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}
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if (H5did2 > 0)
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try {
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H5.H5Dclose(H5did2);
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}
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catch (Exception ex) {
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}
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_deleteFile(H5_FILE);
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System.out.println();
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}
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// Test v1.12 APIs params
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@Test
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public void testH5Rget_object()
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{
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int ref_type = HDF5Constants.H5R_OBJECT2;
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long ret_val = -1;
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byte[] ref = null;
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String name = "";
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String objName = "/dset";
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try {
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ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Rget_object: H5Rcreate_object " + err);
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}
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try {
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ret_val = H5.H5Rget_type(ref);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Rget_object: H5Rget_type: " + err);
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}
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assertTrue("testH5Rget_object: H5Rget_type", ret_val == ref_type);
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try {
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name = H5.H5Rget_file_name(ref);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Rget_object: H5Rget_file_name: " + err);
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}
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assertTrue("testH5Rget_object: H5Rget_file_name", H5_FILE.equals(name));
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try {
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name = H5.H5Rget_obj_name(ref, HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Rget_object: H5Rget_obj_name: " + err);
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}
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assertTrue("The name of the object: ", objName.equals(name));
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H5.H5Rdestroy(ref);
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}
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@Test
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public void testH5Rget_obj_type3()
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{
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int obj_type = -1;
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byte[] ref = null;
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String objName = "/dset";
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try {
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ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Rget_obj_type3: H5Rcreate_object " + err);
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}
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try {
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obj_type = H5.H5Rget_obj_type3(ref, HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Rget_obj_type3: H5.H5Rget_obj_type3: " + err);
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}
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assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
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H5.H5Rdestroy(ref);
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}
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@Test
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public void testH5Rcreate_regionref_object()
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{
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byte[] ref = null;
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String objName = "/dset";
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long start[] = {2, 2}; // Starting location of hyperslab
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long stride[] = {1, 1}; // Stride of hyperslab
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long count[] = {1, 1}; // Element count of hyperslab
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long block[] = {3, 3}; // Block size of hyperslab
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// Select 3x3 hyperslab for reference
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try {
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H5.H5Sselect_hyperslab(H5dsid, HDF5Constants.H5S_SELECT_SET, start, stride, count, block);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Rget_object: H5Sselect_hyperslab " + err);
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}
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try {
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ref = H5.H5Rcreate_region(H5fid, objName, H5dsid, HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Rget_object: H5Rcreate_region " + err);
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}
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assertNotNull(ref);
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H5.H5Rdestroy(ref);
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}
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// These tests need to be updated with new APIs
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// @Test//
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// public void testH5Rget_group() {
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// long loc_id = H5fid;
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// int ref_type = HDF5Constants.H5R_OBJECT2;
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// long ret_val = -1;
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// byte[] ref = null;
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// String name = "";
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// String objName = "/dset";
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//
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// try {
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// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
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// }
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// catch (Throwable err) {
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// err.printStackTrace();
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// fail("testH5Rget_object: H5Rcreate_object " + err);
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// }
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// try {
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// dataset_id= H5.H5Rdereference(H5fid, HDF5Constants.H5P_DEFAULT,
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// HDF5Constants.H5R_DATASET_REGION, ref1);
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//
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// //Create reference on group
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// ref2 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
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// group_id= H5.H5Rdereference(H5gid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT,
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// ref2); assertNotNull(ref1); assertNotNull(ref2); assertTrue(dataset_id >= 0);
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// assertTrue(group_id >= 0);
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// }
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// catch (Throwable err) {
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// err.printStackTrace();
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// fail("TestH5Rdereference " + err);
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// }
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// finally {
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// try {H5.H5Dclose(dataset_id);} catch (Exception ex) {}
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// try {H5.H5Gclose(group_id);} catch (Exception ex) {}
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// }
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// }
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// @Test//
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// public void testH5Rget_region_dataset() {
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// long loc_id = H5fid;
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// int ref_type = HDF5Constants.H5R_OBJECT2;
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// long ret_val = -1;
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// byte[] ref = null;
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// String name = "";
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// String objName = "/dset";
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//
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// try {
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// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
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// }
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// catch (Throwable err) {
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// err.printStackTrace();
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// fail("testH5Rget_object: H5Rcreate_object " + err);
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// }
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// try {
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// dsid = H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
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// assertNotNull(ref);
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// assertTrue(dsid >= 0);
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// }
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// catch (Throwable err) {
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// err.printStackTrace();
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// fail("TestH5Rget_region: " + err);
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// }
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// finally {
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// try {H5.H5Sclose(dsid);} catch (Exception ex) {}
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// }
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// }
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// @Test//
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// public void testH5Rget_attr() {
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// long loc_id = H5fid;
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// int ref_type = HDF5Constants.H5R_OBJECT2;
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// long ret_val = -1;
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// byte[] ref = null;
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// String name = "";
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// String objName = "/dset";
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//
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// try {
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// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
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// }
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// catch (Throwable err) {
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// err.printStackTrace();
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// fail("testH5Rget_object: H5Rcreate_object " + err);
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// }
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// try {
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// dsid = H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
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// assertNotNull(ref);
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// assertTrue(dsid >= 0);
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// }
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// catch (Throwable err) {
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// err.printStackTrace();
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// fail("TestH5Rget_region: " + err);
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// }
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// finally {
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// try {H5.H5Sclose(dsid);} catch (Exception ex) {}
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// }
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// }
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// Test parameters to H5Rcreate_object
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@Test(expected = NullPointerException.class)
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public void testH5Rcreate_object_Nullname() throws Throwable
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{
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String name = null;
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H5.H5Rcreate_object(H5fid, name, HDF5Constants.H5P_DEFAULT);
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}
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@Test(expected = HDF5FunctionArgumentException.class)
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public void testH5Rcreate_object_Invalidloc() throws Throwable
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{
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String name = "";
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H5.H5Rcreate_object(-1, name, HDF5Constants.H5P_DEFAULT);
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}
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// Test parameters to H5Rcreate_region
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@Test(expected = NullPointerException.class)
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public void testH5Rcreate_region_Nullname() throws Throwable
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{
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String name = null;
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H5.H5Rcreate_region(H5fid, name, -1, HDF5Constants.H5P_DEFAULT);
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}
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@Test(expected = HDF5FunctionArgumentException.class)
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public void testH5Rcreate_region_Invalidloc() throws Throwable
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{
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String name = "";
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H5.H5Rcreate_region(-1, name, -1, HDF5Constants.H5P_DEFAULT);
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}
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// Test parameters to H5Rcreate_attr
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@Test(expected = NullPointerException.class)
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public void testH5Rcreate_attr_Nullname() throws Throwable
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{
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String name = null;
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String attrname = "";
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H5.H5Rcreate_attr(H5fid, name, attrname, HDF5Constants.H5P_DEFAULT);
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}
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@Test(expected = NullPointerException.class)
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public void testH5Rcreate_attr_Nullattrname() throws Throwable
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{
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String name = "";
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String attrname = null;
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H5.H5Rcreate_attr(H5fid, name, attrname, HDF5Constants.H5P_DEFAULT);
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}
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@Test(expected = HDF5FunctionArgumentException.class)
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public void testH5Rcreate_attr_Invalidloc() throws Throwable
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{
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String name = "";
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String attrname = "";
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H5.H5Rcreate_attr(-1, name, attrname, HDF5Constants.H5P_DEFAULT);
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}
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// Test parameters to H5Rdestroy
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@Test(expected = NullPointerException.class)
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public void testH5Rdestroy_Nullref() throws Throwable
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{
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byte[] ref = null;
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H5.H5Rdestroy(ref);
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}
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// Test parameters to H5Rget_type
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@Test(expected = NullPointerException.class)
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public void testH5Rget_type_Nullref() throws Throwable
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{
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byte[] ref = null;
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H5.H5Rget_type(ref);
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}
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// Test parameters to H5Requal
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@Test(expected = NullPointerException.class)
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public void testH5Requal_Nullref1() throws Throwable
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{
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byte[] ref1 = null;
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byte[] ref2 = {0, 0, 0, 0};
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H5.H5Requal(ref1, ref2);
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}
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@Test(expected = NullPointerException.class)
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public void testH5Requal_Nullref2() throws Throwable
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{
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byte[] ref1 = {0, 0, 0, 0};
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byte[] ref2 = null;
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H5.H5Requal(ref1, ref2);
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}
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// Test parameters to H5Rcopy
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@Test(expected = NullPointerException.class)
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public void testH5Rcopy_Nullref1() throws Throwable
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{
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byte[] ref1 = null;
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byte[] ref2 = H5.H5Rcopy(ref1);
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}
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// Test parameters to H5Ropen_object
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@Test(expected = NullPointerException.class)
|
|
public void testH5Ropen_object_Nullref() throws Throwable
|
|
{
|
|
byte[] ref = null;
|
|
H5.H5Ropen_object(ref, -1, -1);
|
|
}
|
|
|
|
// Test parameters to H5Ropen_region
|
|
@Test(expected = NullPointerException.class)
|
|
public void testH5Ropen_region_Nullref() throws Throwable
|
|
{
|
|
byte[] ref = null;
|
|
H5.H5Ropen_region(ref, -1, -1);
|
|
}
|
|
|
|
// Test parameters to H5Ropen_attr
|
|
@Test(expected = NullPointerException.class)
|
|
public void testH5Ropen_attr_Nullref() throws Throwable
|
|
{
|
|
byte[] ref = null;
|
|
H5.H5Ropen_attr(ref, -1, -1);
|
|
}
|
|
|
|
// Test parameters to H5Rget_obj_type3
|
|
@Test(expected = NullPointerException.class)
|
|
public void testH5Rget_obj_type3_Nullref() throws Throwable
|
|
{
|
|
byte[] ref = null;
|
|
H5.H5Rget_obj_type3(ref, -1);
|
|
}
|
|
|
|
// Test parameters to H5Rget_file_name
|
|
@Test(expected = NullPointerException.class)
|
|
public void testH5Rget_file_name_Nullref() throws Throwable
|
|
{
|
|
byte[] ref = null;
|
|
H5.H5Rget_file_name(ref);
|
|
}
|
|
|
|
// Test parameters to H5Rget_obj_name
|
|
@Test(expected = NullPointerException.class)
|
|
public void testH5Rget_obj_name_Nullref() throws Throwable
|
|
{
|
|
byte[] ref = null;
|
|
H5.H5Rget_obj_name(ref, -1);
|
|
}
|
|
|
|
// Test parameters to H5Rget_attr_name
|
|
@Test(expected = NullPointerException.class)
|
|
public void testH5Rget_attr_name_Nullref() throws Throwable
|
|
{
|
|
byte[] ref = null;
|
|
H5.H5Rget_attr_name(ref);
|
|
}
|
|
|
|
@Test
|
|
public void testH5RVLattr_ref()
|
|
{
|
|
String attr_obj_name = "VLObjRefdata";
|
|
String attr_reg_name = "VLRegRefdata";
|
|
long attr_obj_id = HDF5Constants.H5I_INVALID_HID;
|
|
long attr_reg_id = HDF5Constants.H5I_INVALID_HID;
|
|
long atype_obj_id = HDF5Constants.H5I_INVALID_HID;
|
|
long atype_reg_id = HDF5Constants.H5I_INVALID_HID;
|
|
long aspace_id = HDF5Constants.H5I_INVALID_HID;
|
|
long[] dims = {4};
|
|
long lsize = 1;
|
|
byte[] ref1 = null;
|
|
byte[] ref2 = null;
|
|
byte[] ref3 = null;
|
|
byte[] ref4 = null;
|
|
|
|
try {
|
|
// Create reference on dataset
|
|
ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid);
|
|
assertNotNull(ref1);
|
|
ref2 = H5.H5Rcreate(H5gid, "dset2", HDF5Constants.H5R_DATASET_REGION, H5dsid);
|
|
assertNotNull(ref2);
|
|
ref3 = H5.H5Rcreate(H5gid, "/dset", HDF5Constants.H5R_OBJECT, -1);
|
|
assertNotNull(ref3);
|
|
|
|
// Create reference on group
|
|
ref4 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
|
|
assertNotNull(ref3);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5RVLattr_ref: " + err);
|
|
}
|
|
|
|
ArrayList[] vl_obj_data = new ArrayList[4];
|
|
ArrayList[] vl_reg_data = new ArrayList[4];
|
|
try {
|
|
// Write Object Reference data
|
|
vl_obj_data[0] = new ArrayList<byte[]>(Arrays.asList(ref3));
|
|
vl_obj_data[1] = new ArrayList<byte[]>(Arrays.asList(ref3, ref4));
|
|
vl_obj_data[2] = new ArrayList<byte[]>(Arrays.asList(ref3, ref3, ref3));
|
|
vl_obj_data[3] = new ArrayList<byte[]>(Arrays.asList(ref4, ref4, ref4, ref4));
|
|
Class dataClass = vl_obj_data.getClass();
|
|
assertTrue("testH5RVLattr_ref.getClass: " + dataClass, dataClass.isArray());
|
|
|
|
try {
|
|
atype_obj_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_OBJ);
|
|
assertTrue("testH5RVLattr_ref.H5Tvlen_create: ", atype_obj_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (atype_obj_id > 0)
|
|
try {
|
|
H5.H5Tclose(atype_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLattr_ref: " + err);
|
|
}
|
|
|
|
try {
|
|
aspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(aspace_id > 0);
|
|
attr_obj_id = H5.H5Acreate(H5did, attr_obj_name, atype_obj_id, aspace_id,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5RVLattr_ref: ", attr_obj_id >= 0);
|
|
|
|
H5.H5Awrite(attr_obj_id, atype_obj_id, vl_obj_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (attr_obj_id > 0)
|
|
try {
|
|
H5.H5Aclose(attr_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (atype_obj_id > 0)
|
|
try {
|
|
H5.H5Tclose(atype_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLattr_ref: " + err);
|
|
}
|
|
finally {
|
|
if (aspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(aspace_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
|
|
// Write Region Reference data
|
|
vl_reg_data[0] = new ArrayList<byte[]>(Arrays.asList(ref1));
|
|
vl_reg_data[1] = new ArrayList<byte[]>(Arrays.asList(ref1, ref2));
|
|
vl_reg_data[2] = new ArrayList<byte[]>(Arrays.asList(ref1, ref1, ref1));
|
|
vl_reg_data[3] = new ArrayList<byte[]>(Arrays.asList(ref2, ref2, ref2, ref2));
|
|
dataClass = vl_reg_data.getClass();
|
|
assertTrue("testH5RVLattr_ref.getClass: " + dataClass, dataClass.isArray());
|
|
|
|
try {
|
|
atype_reg_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_DSETREG);
|
|
assertTrue("testH5RVLattr_ref.H5Tvlen_create: ", atype_reg_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (atype_reg_id > 0)
|
|
try {
|
|
H5.H5Tclose(atype_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLattr_ref: " + err);
|
|
}
|
|
|
|
try {
|
|
aspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(aspace_id > 0);
|
|
attr_reg_id = H5.H5Acreate(H5did, attr_reg_name, atype_reg_id, aspace_id,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5RVLattr_ref: ", attr_reg_id >= 0);
|
|
|
|
H5.H5Awrite(attr_reg_id, atype_reg_id, vl_reg_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (attr_reg_id > 0)
|
|
try {
|
|
H5.H5Aclose(attr_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (atype_reg_id > 0)
|
|
try {
|
|
H5.H5Tclose(atype_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLattr_ref: " + err);
|
|
}
|
|
finally {
|
|
if (aspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(aspace_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
|
|
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
|
|
|
|
for (int j = 0; j < dims.length; j++) {
|
|
lsize *= dims[j];
|
|
}
|
|
|
|
// Read Object Reference data
|
|
ArrayList[] vl_readbuf = new ArrayList[4];
|
|
for (int j = 0; j < lsize; j++)
|
|
vl_readbuf[j] = new ArrayList<byte[]>();
|
|
|
|
try {
|
|
H5.H5Aread(attr_obj_id, atype_obj_id, vl_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
|
|
((byte[])vl_obj_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
|
|
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
|
|
((byte[])vl_obj_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
|
|
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
|
|
((byte[])vl_obj_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
|
|
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
|
|
((byte[])vl_obj_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
|
|
|
|
// Read Region Reference data
|
|
vl_readbuf = new ArrayList[4];
|
|
for (int j = 0; j < lsize; j++)
|
|
vl_readbuf[j] = new ArrayList<byte[]>();
|
|
|
|
try {
|
|
H5.H5Aread(attr_reg_id, atype_reg_id, vl_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
|
|
((byte[])vl_reg_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
|
|
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
|
|
((byte[])vl_reg_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
|
|
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
|
|
((byte[])vl_reg_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
|
|
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
|
|
((byte[])vl_reg_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLattr_ref: " + err);
|
|
}
|
|
finally {
|
|
if (attr_reg_id > 0)
|
|
try {
|
|
H5.H5Aclose(attr_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (attr_obj_id > 0)
|
|
try {
|
|
H5.H5Aclose(attr_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (atype_reg_id > 0)
|
|
try {
|
|
H5.H5Tclose(atype_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (atype_obj_id > 0)
|
|
try {
|
|
H5.H5Tclose(atype_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5RVLdset_ref()
|
|
{
|
|
String dset_obj_name = "VLObjRefdata";
|
|
String dset_reg_name = "VLRegRefdata";
|
|
long dset_obj_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dset_reg_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_obj_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_reg_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dspace_id = HDF5Constants.H5I_INVALID_HID;
|
|
long[] dims = {4};
|
|
long lsize = 1;
|
|
byte[] ref1 = null;
|
|
byte[] ref2 = null;
|
|
byte[] ref3 = null;
|
|
byte[] ref4 = null;
|
|
|
|
try {
|
|
// Create reference on dataset
|
|
ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid);
|
|
assertNotNull(ref1);
|
|
ref2 = H5.H5Rcreate(H5gid, "dset2", HDF5Constants.H5R_DATASET_REGION, H5dsid);
|
|
assertNotNull(ref2);
|
|
ref3 = H5.H5Rcreate(H5gid, "/dset", HDF5Constants.H5R_OBJECT, -1);
|
|
assertNotNull(ref3);
|
|
|
|
// Create reference on group
|
|
ref4 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
|
|
assertNotNull(ref3);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5RVLattr_ref: " + err);
|
|
}
|
|
|
|
ArrayList[] vl_obj_data = new ArrayList[4];
|
|
ArrayList[] vl_reg_data = new ArrayList[4];
|
|
try {
|
|
// Write Object Reference data
|
|
vl_obj_data[0] = new ArrayList<byte[]>(Arrays.asList(ref3));
|
|
vl_obj_data[1] = new ArrayList<byte[]>(Arrays.asList(ref3, ref4));
|
|
vl_obj_data[2] = new ArrayList<byte[]>(Arrays.asList(ref3, ref3, ref3));
|
|
vl_obj_data[3] = new ArrayList<byte[]>(Arrays.asList(ref4, ref4, ref4, ref4));
|
|
Class dataClass = vl_obj_data.getClass();
|
|
assertTrue("testH5RVLdset_ref.getClass: " + dataClass, dataClass.isArray());
|
|
|
|
try {
|
|
dtype_obj_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_OBJ);
|
|
assertTrue("testH5RVLdset_ref.H5Tvlen_create: ", dtype_obj_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (dtype_obj_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLdset_ref: " + err);
|
|
}
|
|
|
|
try {
|
|
dspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(dspace_id > 0);
|
|
dset_obj_id =
|
|
H5.H5Dcreate(H5fid, dset_obj_name, dtype_obj_id, dspace_id, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5RVLdset_ref: ", dset_obj_id >= 0);
|
|
|
|
H5.H5Dwrite(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_obj_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (dset_obj_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_obj_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLdset_ref: " + err);
|
|
}
|
|
finally {
|
|
if (dspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(dspace_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
|
|
// Write Region Reference data
|
|
vl_reg_data[0] = new ArrayList<byte[]>(Arrays.asList(ref1));
|
|
vl_reg_data[1] = new ArrayList<byte[]>(Arrays.asList(ref1, ref2));
|
|
vl_reg_data[2] = new ArrayList<byte[]>(Arrays.asList(ref1, ref1, ref1));
|
|
vl_reg_data[3] = new ArrayList<byte[]>(Arrays.asList(ref2, ref2, ref2, ref2));
|
|
dataClass = vl_reg_data.getClass();
|
|
assertTrue("testH5RVLdset_ref.getClass: " + dataClass, dataClass.isArray());
|
|
|
|
try {
|
|
dtype_reg_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_DSETREG);
|
|
assertTrue("testH5RVLdset_ref.H5Tvlen_create: ", dtype_reg_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (dtype_reg_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLdset_ref: " + err);
|
|
}
|
|
|
|
try {
|
|
dspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(dspace_id > 0);
|
|
dset_reg_id =
|
|
H5.H5Dcreate(H5fid, dset_reg_name, dtype_reg_id, dspace_id, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5RVLdset_ref: ", dset_reg_id >= 0);
|
|
|
|
H5.H5Dwrite(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_reg_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (dset_reg_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_reg_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLdset_ref: " + err);
|
|
}
|
|
finally {
|
|
if (dspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(dspace_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
|
|
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
|
|
|
|
for (int j = 0; j < dims.length; j++) {
|
|
lsize *= dims[j];
|
|
}
|
|
|
|
// Read Object Reference data
|
|
ArrayList[] vl_readbuf = new ArrayList[4];
|
|
for (int j = 0; j < lsize; j++)
|
|
vl_readbuf[j] = new ArrayList<byte[]>();
|
|
|
|
try {
|
|
H5.H5Dread(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
|
|
((byte[])vl_obj_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
|
|
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
|
|
((byte[])vl_obj_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
|
|
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
|
|
((byte[])vl_obj_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
|
|
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
|
|
((byte[])vl_obj_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
|
|
|
|
// Read Region Reference data
|
|
vl_readbuf = new ArrayList[4];
|
|
for (int j = 0; j < lsize; j++)
|
|
vl_readbuf[j] = new ArrayList<byte[]>();
|
|
|
|
try {
|
|
H5.H5Dread(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
|
|
((byte[])vl_reg_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
|
|
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
|
|
((byte[])vl_reg_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
|
|
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
|
|
((byte[])vl_reg_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
|
|
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
|
|
((byte[])vl_reg_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.testH5RVLdset_ref: " + err);
|
|
}
|
|
finally {
|
|
if (dset_reg_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dset_obj_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_reg_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_reg_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_obj_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_obj_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
}
|