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hdf5/java/src-jni/test/TestH5OcopyOld.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.assertTrue;
import static org.junit.Assert.fail;
import java.io.File;
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;
public class TestH5OcopyOld {
@Rule
public TestName testname = new TestName();
private static final String FILENAME = "testRefsattributeO.h5";
private static final int DIM_X = 4;
private static final int DIM_Y = 6;
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5dsid = HDF5Constants.H5I_INVALID_HID;
long H5did1 = HDF5Constants.H5I_INVALID_HID;
long H5did2 = HDF5Constants.H5I_INVALID_HID;
long H5gcpl = HDF5Constants.H5I_INVALID_HID;
long H5gid = HDF5Constants.H5I_INVALID_HID;
long H5dsid2 = HDF5Constants.H5I_INVALID_HID;
long[] dims = {2};
private final void _deleteFile(String filename)
{
File file = new File(filename);
if (file.exists()) {
try {
file.delete();
}
catch (Exception e) {
e.printStackTrace();
}
}
}
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_I32BE, dsid, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5O._createDataset: ", did >= 0);
return did;
}
private final long _createGroup(long fid, String name)
{
long gid = HDF5Constants.H5I_INVALID_HID;
try {
H5gcpl = HDF5Constants.H5P_DEFAULT;
gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, H5gcpl, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Gcreate: " + err);
}
assertTrue("TestH5O._createGroup: ", gid >= 0);
return gid;
}
@Before
public void createH5file() throws NullPointerException, HDF5Exception
{
assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
System.out.print(testname.getMethodName());
try {
H5fid = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
H5dsid2 = H5.H5Screate(HDF5Constants.H5S_SCALAR);
H5did1 = _createDataset(H5fid, H5dsid2, "DS2", HDF5Constants.H5P_DEFAULT);
H5dsid = H5.H5Screate_simple(1, dims, null);
H5gid = _createGroup(H5fid, "/G1");
H5did2 = _createDataset(H5gid, H5dsid, "DS1", HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5O.createH5file: " + err);
}
assertTrue("TestH5O.createH5file: H5.H5Fcreate: ", H5fid >= 0);
assertTrue("TestH5O.createH5file: H5.H5Screate_simple: ", H5dsid >= 0);
assertTrue("TestH5O.createH5file: H5.H5Gcreate: ", H5gid >= 0);
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
}
@After
public void deleteH5file() throws HDF5LibraryException
{
if (H5gid > 0)
try {
H5.H5Gclose(H5gid);
}
catch (Exception ex) {
}
if (H5did2 > 0)
try {
H5.H5Dclose(H5did2);
}
catch (Exception ex) {
}
if (H5dsid > 0)
try {
H5.H5Sclose(H5dsid);
}
catch (Exception ex) {
}
if (H5dsid2 > 0)
try {
H5.H5Sclose(H5dsid2);
}
catch (Exception ex) {
}
if (H5did1 > 0)
try {
H5.H5Dclose(H5did1);
}
catch (Exception ex) {
}
if (H5fid > 0)
try {
H5.H5Fclose(H5fid);
}
catch (Exception ex) {
}
_deleteFile(FILENAME);
System.out.println();
}
@Test
public void testH5OcopyRefsAttr()
{
long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
byte rbuf0[] = null, rbuf1[] = null;
byte[] dset_data = new byte[16];
long attribute_id = HDF5Constants.H5I_INVALID_HID;
try {
rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1);
rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
// System.arraycopy(rbuf0, 0, dset_data, 0, 8);
System.arraycopy(rbuf1, 0, dset_data, 8, 8);
}
catch (Exception ex) {
fail("testH5OcopyRefsAttr: H5Rcreate failed");
}
try {
attribute_id = H5.H5Acreate(H5did2, "A1", HDF5Constants.H5T_STD_REF_OBJ, H5dsid,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5OcopyRefsAttr.H5Acreate: ", attribute_id >= 0);
H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data);
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
fail("testH5OcopyRefsAttr: H5Awrite failed");
}
finally {
try {
H5.H5Aclose(attribute_id);
}
catch (Exception exx) {
}
}
try {
ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
assertTrue("testH5OcopyRefsAttr.H5Pcreate: ", ocp_plist_id >= 0);
H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
H5.H5Ocopy(H5fid, ".", H5fid, "CPYREF", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
}
catch (Exception ex) {
fail("testH5OcopyRefsAttr: H5Ocopy failed");
}
finally {
try {
H5.H5Pclose(ocp_plist_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5OcopyRefsDatasettodiffFile()
{
byte rbuf1[] = null;
byte[] dset_data = new byte[16];
long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long H5fid2 = HDF5Constants.H5I_INVALID_HID;
try {
rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
System.arraycopy(rbuf1, 0, dset_data, 8, 8);
dataset_id =
H5.H5Dcreate(H5fid, "DSREF", HDF5Constants.H5T_STD_REF_OBJ, H5dsid, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5OcopyRefsDatasettodiffFile.H5Dcreate: ", dataset_id >= 0);
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);
H5.H5Dclose(dataset_id);
}
catch (Exception ex) {
fail("testH5OcopyRefsDatasettodiffFile: create dataset failed");
}
finally {
try {
H5.H5Dclose(dataset_id);
}
catch (Exception exx) {
}
}
try {
// create new file
H5fid2 = H5.H5Fcreate("copy_old.h5", HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
assertTrue("testH5OcopyRefsDatasettodiffFile.H5Fcreate: ", H5fid2 >= 0);
H5.H5Fflush(H5fid2, HDF5Constants.H5F_SCOPE_LOCAL);
}
catch (Exception ex) {
try {
H5.H5Fclose(H5fid2);
}
catch (Exception exx) {
}
fail("testH5OcopyRefsDatasettodiffFile: H5Fcreate failed");
}
try {
// create object copy property list id and set the flags.
ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
assertTrue("testH5OcopyRefsDatasettodiffFile.H5Pcreate: ", ocp_plist_id >= 0);
H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
// Perform copy function.
H5.H5Ocopy(H5fid, ".", H5fid2, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
}
catch (Exception ex) {
ex.printStackTrace();
fail("testH5OcopyRefsDatasettodiffFile: H5Ocopy failed");
}
finally {
try {
H5.H5Pclose(ocp_plist_id);
}
catch (Exception ex) {
}
try {
H5.H5Fclose(H5fid2);
}
catch (Exception ex) {
}
}
_deleteFile("copy_old.h5");
}
@Test
public void testH5OcopyRefsDatasettosameFile()
{
byte rbuf0[] = null, rbuf1[] = null;
byte[] dset_data = new byte[16];
long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long did = HDF5Constants.H5I_INVALID_HID;
int obj_type = -1;
byte[] read_data = new byte[16];
try {
rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1);
rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
System.arraycopy(rbuf0, 0, dset_data, 0, 8);
System.arraycopy(rbuf1, 0, dset_data, 8, 8);
// Create a dataset and write object references to it.
dataset_id =
H5.H5Dcreate(H5fid, "DSREF", HDF5Constants.H5T_STD_REF_OBJ, H5dsid, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5OcopyRefsDatasettosameFile.H5Dcreate: ", dataset_id >= 0);
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);
// Close the dataset.
H5.H5Dclose(dataset_id);
}
catch (Exception ex) {
try {
H5.H5Dclose(dataset_id);
}
catch (Exception exx) {
}
fail("testH5OcopyRefsDatasettosameFile: create dataset failed");
}
try {
ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
assertTrue("testH5OcopyRefsDatasettosameFile.H5Pcreate: ", ocp_plist_id >= 0);
H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
}
catch (Exception ex) {
try {
H5.H5Pclose(ocp_plist_id);
}
catch (Exception exx) {
}
fail("testH5OcopyRefsDatasettosameFile: H5Pset_copy_object failed");
}
// Perform copy function.
try {
H5.H5Ocopy(H5fid, "DSREF", H5fid, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
}
catch (Exception ex) {
try {
H5.H5Pclose(ocp_plist_id);
}
catch (Exception exx) {
}
fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed");
}
// Open the dataset that has been copied
try {
did = H5.H5Dopen(H5fid, "DSREF", HDF5Constants.H5P_DEFAULT);
assertTrue("testH5OcopyRefsDatasettosameFile.H5Dopen: ", did >= 0);
}
catch (Exception e) {
try {
H5.H5Dclose(did);
}
catch (Exception exx) {
}
e.printStackTrace();
fail("testH5OcopyRefsDatasettosameFile: H5Dopen failed");
}
try {
// Read the dataset object references in the read_data buffer.
H5.H5Dread(did, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, read_data);
System.arraycopy(read_data, 0, rbuf0, 0, 8);
System.arraycopy(read_data, 8, rbuf1, 0, 8);
// Get the type of object the reference points to.
obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf1);
assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf0);
assertEquals(obj_type, HDF5Constants.H5O_TYPE_GROUP);
}
catch (Exception ex) {
ex.printStackTrace();
}
finally {
try {
H5.H5Dclose(did);
}
catch (Exception ex) {
}
try {
H5.H5Pclose(ocp_plist_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5OcopyNullRef() throws Throwable
{
final long _pid_ = HDF5Constants.H5P_DEFAULT;
long sid = HDF5Constants.H5I_INVALID_HID;
long did = HDF5Constants.H5I_INVALID_HID;
long aid = HDF5Constants.H5I_INVALID_HID;
try {
sid = H5.H5Screate_simple(1, new long[] {1}, null);
assertTrue("testH5OcopyNullRef.H5Screate_simple: ", sid >= 0);
did = H5.H5Dcreate(H5fid, "Dataset_with_null_Ref", HDF5Constants.H5T_NATIVE_INT, sid, _pid_,
_pid_, _pid_);
assertTrue("testH5OcopyNullRef.H5Dcreate: ", did > 0);
aid = H5.H5Acreate(did, "Null_Ref", HDF5Constants.H5T_STD_REF_OBJ, sid, _pid_, _pid_);
assertTrue("testH5OcopyNullRef.H5Acreate: ", aid > 0);
}
catch (Exception ex) {
ex.printStackTrace();
}
finally {
try {
H5.H5Dclose(did);
}
catch (Exception exx) {
}
try {
H5.H5Aclose(aid);
}
catch (Exception exx) {
}
try {
H5.H5Sclose(sid);
}
catch (Exception exx) {
}
}
long ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
assertTrue("testH5OcopyNullRef.H5Pcreate: ", ocp_plist_id >= 0);
H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
try {
H5.H5Ocopy(H5fid, "/Dataset_with_null_Ref", H5fid, "/Dataset_with_null_Ref_cp", ocp_plist_id,
_pid_);
}
finally {
try {
H5.H5Pclose(ocp_plist_id);
}
catch (Exception exx) {
}
}
}
// @Ignore because of JIRA HDF5-9547
// @Test(expected = HDF5LibraryException.class)
// public void testH5OcopyInvalidRef() throws Throwable {
// final long _pid_ = HDF5Constants.H5P_DEFAULT;
// long sid = HDF5Constants.H5I_INVALID_HID;
// long did = HDF5Constants.H5I_INVALID_HID;
// long aid = HDF5Constants.H5I_INVALID_HID;
//
// try {
// sid = H5.H5Screate_simple(1, new long[] {1}, null);
// assertTrue("testH5OcopyInvalidRef.H5Screate_simple: ", sid >= 0);
// did = H5.H5Dcreate(H5fid, "Dataset_with_invalid_Ref", HDF5Constants.H5T_NATIVE_INT, sid,
// _pid_, _pid_, _pid_); assertTrue("testH5OcopyInvalidRef.H5Dcreate: ", did > 0); aid =
// H5.H5Acreate(did, "Invalid_Ref", HDF5Constants.H5T_STD_REF_OBJ, sid, _pid_, _pid_);
// assertTrue("testH5OcopyInvalidRef.H5Acreate: ", aid > 0);
// H5.H5Awrite(aid, HDF5Constants.H5T_STD_REF_OBJ, new long[]{-1});
// }
// catch (Exception ex) {
// ex.printStackTrace();
// }
// finally {
// try {H5.H5Dclose(did);} catch (Exception exx) {}
// try {H5.H5Aclose(aid);} catch (Exception exx) {}
// try {H5.H5Sclose(sid);} catch (Exception exx) {}
// }
//
// long ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
// assertTrue("testH5OcopyInvalidRef.H5Pcreate: ", ocp_plist_id >= 0);
// H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
// try {
// H5.H5Ocopy(H5fid, "/Dataset_with_invalid_Ref", H5fid, "/Dataset_with_invalid_Ref_cp",
// ocp_plist_id, _pid_);
// }
// finally {
// try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
// }
// }
}
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