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.
585 lines
20 KiB
Java
585 lines
20 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.assertTrue;
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import static org.junit.Assert.fail;
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import java.io.File;
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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.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 TestH5Pvirtual {
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@Rule
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public TestName testname = new TestName();
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private static final String H5_FILE = "vds.h5";
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private static final String SRC_FILE[] = {"v-0.h5", "v-1.h5", "v-2.h5"};
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private static final String SRC_DATASET[] = {"A", "B", "C"};
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private static final int DIM_Y = 6;
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private static final int VDSDIM_X = 4;
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private static final int VDSDIM_Y = 6;
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private static final int fill_value = -1;
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long[] H5dims = {DIM_Y};
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long[] VDSH5dims = {VDSDIM_X, VDSDIM_Y};
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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 H5dssid = HDF5Constants.H5I_INVALID_HID;
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long H5dvsid = HDF5Constants.H5I_INVALID_HID;
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long H5did = HDF5Constants.H5I_INVALID_HID;
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long H5dcplid = HDF5Constants.H5I_INVALID_HID;
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long H5dapl_id = HDF5Constants.H5I_INVALID_HID;
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private final void _deleteFile(String filename)
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{
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File file = new File(filename);
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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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}
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}
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}
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private final long _createDataset(long fid, long dsid, String name, long dcpl, long dapl)
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{
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long did = HDF5Constants.H5I_INVALID_HID;
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long space_id = HDF5Constants.H5I_INVALID_HID;
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long[] start = {0, 0};
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long[] stride = null;
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long[] count = {1, 1};
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long[] block = {1, VDSDIM_Y};
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try {
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H5dssid = H5.H5Screate_simple(1, H5dims, null);
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for (int i = 0; i < 3; i++) {
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start[0] = i;
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/* Select i-th row in the virtual dataset; selection in the source datasets is the same. */
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H5.H5Sselect_hyperslab(dsid, HDF5Constants.H5S_SELECT_SET, start, stride, count, block);
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H5.H5Pset_virtual(dcpl, dsid, SRC_FILE[i], SRC_DATASET[i], H5dssid);
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}
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did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_NATIVE_INT, dsid, HDF5Constants.H5P_DEFAULT, dcpl,
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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("TestH5Pvirtual._createDataset: ", did > 0);
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return did;
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}
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private final void _createH5File(long fcpl, long fapl)
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{
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int[] dset_data = new int[DIM_Y];
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// Create source files and datasets
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for (int i = 0; i < 3; i++) {
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long space_id = HDF5Constants.H5I_INVALID_HID;
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long dset_id = HDF5Constants.H5I_INVALID_HID;
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long file_id = HDF5Constants.H5I_INVALID_HID;
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for (int j = 0; j < DIM_Y; j++)
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dset_data[j] = i + 1;
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try {
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file_id = H5.H5Fcreate(SRC_FILE[i], HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.H5P_DEFAULT);
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space_id = H5.H5Screate_simple(1, H5dims, null);
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dset_id = H5.H5Dcreate(file_id, SRC_DATASET[i], HDF5Constants.H5T_NATIVE_INT, space_id,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.H5P_DEFAULT);
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H5.H5Dwrite(dset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
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HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("TestH5Pvirtual.createH5file: " + err);
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}
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finally {
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if (dset_id > 0)
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try {
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H5.H5Dclose(dset_id);
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}
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catch (Exception ex) {
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}
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if (space_id > 0)
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try {
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H5.H5Sclose(space_id);
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}
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catch (Exception ex) {
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}
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if (file_id > 0)
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try {
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H5.H5Fclose(file_id);
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}
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catch (Exception ex) {
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}
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}
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}
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try {
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int[] fill_value = {-1};
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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, VDSH5dims, null);
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H5dcplid = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
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H5.H5Pset_fill_value(H5dcplid, HDF5Constants.H5T_NATIVE_INT, fill_value);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("TestH5Pvirtual.createH5file: " + err);
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}
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assertTrue("TestH5Pvirtual.createH5file: H5.H5Fcreate: ", H5fid > 0);
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assertTrue("TestH5Pvirtual.createH5file: H5.H5Screate_simple: ", H5dsid > 0);
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assertTrue("TestH5Pvirtual.createH5file: H5.H5Pcreate: ", H5dcplid > 0);
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try {
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H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
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}
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catch (Throwable err) {
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err.printStackTrace();
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}
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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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_createH5File(HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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H5dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
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assertTrue("TestH5Pvirtual.createH5file: H5.H5Pcreate: ", H5dapl_id > 0);
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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 (H5dapl_id > 0)
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try {
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H5.H5Pclose(H5dapl_id);
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}
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catch (Exception ex) {
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}
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if (H5dcplid > 0)
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try {
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H5.H5Pclose(H5dcplid);
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}
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catch (Exception ex) {
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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 (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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for (int i = 0; i < 3; i++) {
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_deleteFile(SRC_FILE[i]);
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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
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public void testH5Pvirtual_storage()
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{
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int layout = -1;
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H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
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try {
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layout = H5.H5Pget_layout(H5dcplid);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Pget_layout: " + err);
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}
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finally {
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if (H5dssid > 0)
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try {
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H5.H5Sclose(H5dssid);
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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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}
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assertTrue("testH5Pvirtual_storage", HDF5Constants.H5D_VIRTUAL == layout);
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}
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@Test
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public void testH5Pget_virtual_count()
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{
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long num_map = -1;
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H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
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try {
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num_map = H5.H5Pget_virtual_count(H5dcplid);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Pget_virtual_count: " + err);
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}
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finally {
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if (H5dssid > 0)
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try {
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H5.H5Sclose(H5dssid);
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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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}
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assertTrue("testH5Pget_virtual_count: " + num_map, num_map >= 0);
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assertEquals(3, num_map);
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}
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@Test
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public void testH5Pget_source_filename() throws Throwable
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{
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String filename = null;
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H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
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try {
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filename = (H5.H5Pget_virtual_filename(H5dcplid, 2));
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Pget_virtual_filename: " + err);
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}
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finally {
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if (H5dssid > 0)
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try {
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H5.H5Sclose(H5dssid);
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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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}
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assertTrue("testH5Pget_source_filename: " + filename, filename.compareTo("v-2.h5") == 0);
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}
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@Test
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public void testH5Pget_source_datasetname() throws Throwable
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{
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String datasetname = null;
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H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
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try {
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datasetname = H5.H5Pget_virtual_dsetname(H5dcplid, 1);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Pget_virtual_dsetname: " + err);
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}
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finally {
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if (H5dssid > 0)
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try {
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H5.H5Sclose(H5dssid);
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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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}
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assertTrue("testH5Pget_source_datasetname: " + datasetname, datasetname.compareTo("B") == 0);
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}
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@Test
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public void testH5Pget_selection_source_dataset() throws Throwable
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{
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long src_space = HDF5Constants.H5I_INVALID_HID;
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long src_selection = -1;
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H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
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try {
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src_space = H5.H5Pget_virtual_srcspace(H5dcplid, 0);
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src_selection = H5.H5Sget_select_type(src_space);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Pget_selection_source_dataset: " + err);
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}
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finally {
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if (src_space > 0)
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try {
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H5.H5Sclose(src_space);
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}
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catch (Exception ex) {
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}
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if (H5dssid > 0)
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try {
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H5.H5Sclose(H5dssid);
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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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}
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assertTrue("testH5Pget_selection_source_dataset", src_selection == HDF5Constants.H5S_SEL_ALL);
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}
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@Test
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public void testH5Pget_mapping_parameters()
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{
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long num_map = -1;
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H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
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try {
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try {
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num_map = H5.H5Pget_virtual_count(H5dcplid);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Pget_virtual_count: " + err);
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}
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for (int i = 0; i < num_map; i++) {
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int vselection = -1;
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long vspace = -1;
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long nblocks; // Number of hyperslab blocks
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long blocks[] = {-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}; // List of blocks
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long[] start = {i, 0};
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long[] stride = {1, 1};
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long[] count = {1, 1};
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long[] block = {1, VDSDIM_Y};
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long q_start[] = new long[2];
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long q_stride[] = new long[2];
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long q_count[] = new long[2];
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long q_block[] = new long[2];
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boolean is_regular = false;
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try {
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try {
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vspace = H5.H5Pget_virtual_vspace(H5dcplid, i);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Pget_virtual_vspace: " + err);
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}
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try {
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vselection = H5.H5Sget_select_type(vspace);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sget_select_type: " + err);
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}
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assertTrue("testH5Pget_mapping_parameters[" + i + "]",
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vselection == HDF5Constants.H5S_SEL_HYPERSLABS);
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// Verify that there is only one block
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nblocks = H5.H5Sget_select_hyper_nblocks(vspace);
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assertTrue("H5Sget_select_hyper_nblocks", nblocks == 1);
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// Retrieve the block defined
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H5.H5Sget_select_hyper_blocklist(vspace, 0, nblocks, blocks);
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// Verify that the correct block is defined
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assertTrue("H5.H5Sget_select_hyper_blocklist[" + i + "] [0]: " + blocks[0],
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start[0] == blocks[0]);
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assertTrue("H5.H5Sget_select_hyper_blocklist[" + i + "] [1]: " + blocks[1],
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start[1] == blocks[1]);
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assertTrue("H5.H5Sget_select_hyper_blocklist[" + i + "] [2]: " + blocks[2],
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(block[0] - 1 + i) == blocks[2]);
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assertTrue("H5.H5Sget_select_hyper_blocklist[" + i + "] [3]: " + blocks[3],
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(block[1] - 1) == blocks[3]);
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// We also can use new APIs to get start, stride, count and block
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is_regular = H5.H5Sis_regular_hyperslab(vspace);
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assertTrue("H5.H5Sis_regular_hyperslab", is_regular);
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H5.H5Sget_regular_hyperslab(vspace, q_start, q_stride, q_count, q_block);
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// Verify the hyperslab parameters
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for (int u = 0; u < 2; u++) {
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assertTrue("H5Sget_regular_hyperslab, start", start[u] == q_start[u]);
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assertTrue("H5Sget_regular_hyperslab, stride", stride[u] == q_stride[u]);
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assertTrue("H5Sget_regular_hyperslab, count", count[u] == q_count[u]);
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assertTrue("H5Sget_regular_hyperslab, block", block[u] == q_block[u]);
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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("H5.testH5Pget_mapping_parameters: " + err);
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}
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finally {
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if (vspace > 0)
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try {
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H5.H5Sclose(vspace);
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}
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catch (Exception ex) {
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}
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}
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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("testH5Pget_mapping_parameters: " + err);
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}
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finally {
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if (H5dssid > 0)
|
|
try {
|
|
H5.H5Sclose(H5dssid);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (H5did > 0)
|
|
try {
|
|
H5.H5Dclose(H5did);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Pset_get_virtual_view()
|
|
{
|
|
int ret_val = -1;
|
|
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
|
|
try {
|
|
ret_val = H5.H5Pget_virtual_view(H5dapl_id);
|
|
assertTrue("H5Pget_virtual_view", ret_val >= 0);
|
|
assertEquals(HDF5Constants.H5D_VDS_LAST_AVAILABLE, ret_val);
|
|
H5.H5Pset_virtual_view(H5dapl_id, HDF5Constants.H5D_VDS_FIRST_MISSING);
|
|
ret_val = H5.H5Pget_virtual_view(H5dapl_id);
|
|
assertTrue("H5Pget_virtual_view", ret_val >= 0);
|
|
assertEquals(HDF5Constants.H5D_VDS_FIRST_MISSING, ret_val);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5Pset_get_virtual_view: " + err);
|
|
}
|
|
finally {
|
|
if (H5dssid > 0)
|
|
try {
|
|
H5.H5Sclose(H5dssid);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (H5did > 0)
|
|
try {
|
|
H5.H5Dclose(H5did);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Pset_get_virtual_printf_gap()
|
|
{
|
|
long ret_val = -1;
|
|
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
|
|
try {
|
|
ret_val = H5.H5Pget_virtual_printf_gap(H5dapl_id);
|
|
assertTrue("H5Pget_virtual_printf_gap", ret_val >= 0);
|
|
assertEquals(0, ret_val);
|
|
H5.H5Pset_virtual_printf_gap(H5dapl_id, 2);
|
|
ret_val = H5.H5Pget_virtual_printf_gap(H5dapl_id);
|
|
assertTrue("H5Pget_virtual_printf_gap", ret_val >= 0);
|
|
assertEquals(2, ret_val);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5Pset_get_virtual_printf_gap: " + err);
|
|
}
|
|
finally {
|
|
if (H5dssid > 0)
|
|
try {
|
|
H5.H5Sclose(H5dssid);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (H5did > 0)
|
|
try {
|
|
H5.H5Dclose(H5did);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Pset_virtual_prefix()
|
|
{
|
|
String prefix = "tmp";
|
|
try {
|
|
H5.H5Pset_virtual_prefix(H5dapl_id, prefix);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5Pset_virtual_prefix: " + err);
|
|
}
|
|
}
|
|
|
|
@Test(expected = NullPointerException.class)
|
|
public void testH5Pset_virtual_prefix_null() throws Throwable
|
|
{
|
|
H5.H5Pset_virtual_prefix(H5dapl_id, null);
|
|
}
|
|
|
|
@Test
|
|
public void testH5Pget_virtual_prefix()
|
|
{
|
|
String prefix = "tmp";
|
|
String pre = "";
|
|
|
|
try {
|
|
H5.H5Pset_virtual_prefix(H5dapl_id, prefix);
|
|
pre = H5.H5Pget_virtual_prefix(H5dapl_id);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5Pget_virtual_prefix: " + err);
|
|
}
|
|
assertTrue("The prefix: ", prefix.equals(pre));
|
|
}
|
|
}
|