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hdf5/java/test/TestH5Pvirtual.java
Allen Byrne 216bff5778 #386 copyright corrections for java folder (#389) 
* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

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* Note LLVM 10 to 11 format default changes

* Update format plugin

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* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

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* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

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* HDFFV-11212 add new ref tests for JNI export dataset

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* issue with t128bit test

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* format fixes

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* Restore TRY block.

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* revert to H5_JNI_FATAL_ERROR - support functions need work

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* GH #386 java folder copyright corrections

* Whitespace
2021-02-26 09:27:15 -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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
package test;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.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 TestH5Pvirtual {
@Rule public TestName testname = new TestName();
private static final String H5_FILE = "vds.h5";
private static final String SRC_FILE[] = {
"v-0.h5",
"v-1.h5",
"v-2.h5"
};
private static final String SRC_DATASET[] = {
"A",
"B",
"C"
};
private static final int DIM_Y = 6;
private static final int VDSDIM_X = 4;
private static final int VDSDIM_Y = 6;
private static final int fill_value = -1;
long[] H5dims = { DIM_Y };
long[] VDSH5dims = { VDSDIM_X, VDSDIM_Y };
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5dsid = HDF5Constants.H5I_INVALID_HID;
long H5dssid = HDF5Constants.H5I_INVALID_HID;
long H5dvsid = HDF5Constants.H5I_INVALID_HID;
long H5did = HDF5Constants.H5I_INVALID_HID;
long H5dcplid = HDF5Constants.H5I_INVALID_HID;
long H5dapl_id = HDF5Constants.H5I_INVALID_HID;
private final void _deleteFile(String filename) {
File file = new File(filename);
if (file.exists()) {
try {file.delete();} catch (SecurityException e) {}
}
}
private final long _createDataset(long fid, long dsid, String name, long dcpl, long dapl) {
long did = HDF5Constants.H5I_INVALID_HID;
long space_id = HDF5Constants.H5I_INVALID_HID;
long[] start = {0, 0};
long[] stride = null;
long[] count = {1, 1};
long[] block = {1, VDSDIM_Y};
try {
H5dssid = H5.H5Screate_simple(1, H5dims, null);
for (int i = 0; i < 3; i++) {
start[0] = i;
/* Select i-th row in the virtual dataset; selection in the source datasets is the same. */
H5.H5Sselect_hyperslab(dsid, HDF5Constants.H5S_SELECT_SET, start, stride, count, block);
H5.H5Pset_virtual(dcpl, dsid, SRC_FILE[i], SRC_DATASET[i], H5dssid);
}
did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_NATIVE_INT, dsid,
HDF5Constants.H5P_DEFAULT, dcpl, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5Pvirtual._createDataset: ", did > 0);
return did;
}
private final void _createH5File(long fcpl, long fapl) {
int[] dset_data = new int[DIM_Y];
// Create source files and datasets
for (int i=0; i < 3; i++) {
long space_id = HDF5Constants.H5I_INVALID_HID;
long dset_id = HDF5Constants.H5I_INVALID_HID;
long file_id = HDF5Constants.H5I_INVALID_HID;
for (int j = 0; j < DIM_Y; j++) dset_data[j] = i+1;
try {
file_id = H5.H5Fcreate(SRC_FILE[i], HDF5Constants.H5F_ACC_TRUNC,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
space_id = H5.H5Screate_simple(1, H5dims, null);
dset_id = H5.H5Dcreate(file_id, SRC_DATASET[i], HDF5Constants.H5T_NATIVE_INT, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5.H5Dwrite (dset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT,
dset_data);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5Pvirtual.createH5file: " + err);
}
finally {
if (dset_id > 0)
try {H5.H5Dclose(dset_id);} catch (Exception ex) {}
if (space_id > 0)
try {H5.H5Sclose(space_id);} catch (Exception ex) {}
if (file_id > 0)
try {H5.H5Fclose(file_id);} catch (Exception ex) {}
}
}
try {
int[] fill_value = {-1};
H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5dsid = H5.H5Screate_simple(2, VDSH5dims, null);
H5dcplid = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
H5.H5Pset_fill_value(H5dcplid, HDF5Constants.H5T_NATIVE_INT, fill_value);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5Pvirtual.createH5file: " + err);
}
assertTrue("TestH5Pvirtual.createH5file: H5.H5Fcreate: ", H5fid > 0);
assertTrue("TestH5Pvirtual.createH5file: H5.H5Screate_simple: ", H5dsid > 0);
assertTrue("TestH5Pvirtual.createH5file: H5.H5Pcreate: ", H5dcplid > 0);
try {
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
}
catch (Throwable err) {
err.printStackTrace();
}
}
@Before
public void createH5file()
throws NullPointerException, HDF5Exception {
assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
System.out.print(testname.getMethodName());
_createH5File(HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
assertTrue("TestH5Pvirtual.createH5file: H5.H5Pcreate: ", H5dapl_id > 0);
}
@After
public void deleteH5file() throws HDF5LibraryException {
if (H5dapl_id > 0)
try {H5.H5Pclose(H5dapl_id);} catch (Exception ex) {}
if (H5dcplid > 0)
try {H5.H5Pclose(H5dcplid);} catch (Exception ex) {}
if (H5dsid > 0)
try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
if (H5fid > 0)
try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
for (int i = 0; i < 3; i++) {
_deleteFile(SRC_FILE[i]);
}
_deleteFile(H5_FILE);
System.out.println();
}
@Test
public void testH5Pvirtual_storage() {
int layout = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
layout = H5.H5Pget_layout (H5dcplid);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_layout: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pvirtual_storage", HDF5Constants.H5D_VIRTUAL == layout);
}
@Test
public void testH5Pget_virtual_count() {
long num_map = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
num_map = H5.H5Pget_virtual_count(H5dcplid);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_count: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pget_virtual_count: "+num_map, num_map >= 0);
assertEquals(3, num_map);
}
@Test
public void testH5Pget_source_filename() throws Throwable {
String filename = null;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
filename = (H5.H5Pget_virtual_filename (H5dcplid, 2));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_filename: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pget_source_filename: "+filename, filename.compareTo("v-2.h5") == 0);
}
@Test
public void testH5Pget_source_datasetname() throws Throwable {
String datasetname = null;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
datasetname = H5.H5Pget_virtual_dsetname (H5dcplid, 1);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_dsetname: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pget_source_datasetname: "+datasetname, datasetname.compareTo("B") == 0);
}
@Test
public void testH5Pget_selection_source_dataset() throws Throwable {
long src_space = HDF5Constants.H5I_INVALID_HID;
long src_selection = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
src_space = H5.H5Pget_virtual_srcspace (H5dcplid, 0);
src_selection = H5.H5Sget_select_type(src_space);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pget_selection_source_dataset: " + err);
}
finally {
if (src_space > 0)
try {H5.H5Sclose(src_space);} catch (Exception ex) {}
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pget_selection_source_dataset", src_selection == HDF5Constants.H5S_SEL_ALL);
}
@Test
public void testH5Pget_mapping_parameters() {
long num_map = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
try {
num_map = H5.H5Pget_virtual_count(H5dcplid);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_count: " + err);
}
for (int i = 0; i < num_map; i++) {
int vselection = -1;
long vspace = -1;
long nblocks; // Number of hyperslab blocks
long blocks[] = {-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}; // List of blocks
long[] start = {i, 0};
long[] stride = {1, 1};
long[] count = {1, 1};
long[] block = {1, VDSDIM_Y};
long q_start[] = new long[2];
long q_stride[] = new long[2];
long q_count[] = new long[2];
long q_block[] = new long[2];
boolean is_regular = false;
try {
try {
vspace = H5.H5Pget_virtual_vspace (H5dcplid, i);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_vspace: " + err);
}
try {
vselection = H5.H5Sget_select_type(vspace);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Sget_select_type: " + err);
}
assertTrue("testH5Pget_mapping_parameters["+i+"]", vselection == HDF5Constants.H5S_SEL_HYPERSLABS);
// Verify that there is only one block
nblocks = H5.H5Sget_select_hyper_nblocks(vspace);
assertTrue("H5Sget_select_hyper_nblocks", nblocks == 1);
// Retrieve the block defined
H5.H5Sget_select_hyper_blocklist(vspace, 0, nblocks, blocks);
// Verify that the correct block is defined
assertTrue("H5.H5Sget_select_hyper_blocklist["+i+"] [0]: "+blocks[0], start[0] == blocks[0]);
assertTrue("H5.H5Sget_select_hyper_blocklist["+i+"] [1]: "+blocks[1], start[1] == blocks[1]);
assertTrue("H5.H5Sget_select_hyper_blocklist["+i+"] [2]: "+blocks[2], (block[0]-1+i) == blocks[2]);
assertTrue("H5.H5Sget_select_hyper_blocklist["+i+"] [3]: "+blocks[3], (block[1]-1) == blocks[3]);
// We also can use new APIs to get start, stride, count and block
is_regular = H5.H5Sis_regular_hyperslab(vspace);
assertTrue("H5.H5Sis_regular_hyperslab", is_regular);
H5.H5Sget_regular_hyperslab (vspace, q_start, q_stride, q_count, q_block);
// Verify the hyperslab parameters
for(int u = 0; u < 2; u++) {
assertTrue("H5Sget_regular_hyperslab, start", start[u] == q_start[u]);
assertTrue("H5Sget_regular_hyperslab, stride", stride[u] == q_stride[u]);
assertTrue("H5Sget_regular_hyperslab, count", count[u] == q_count[u]);
assertTrue("H5Sget_regular_hyperslab, block", block[u] == q_block[u]);
}
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5Pget_mapping_parameters: " + err);
}
finally {
if (vspace > 0)
try {H5.H5Sclose(vspace);} catch (Exception ex) {}
}
}
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pget_mapping_parameters: " + 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_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));
}
}
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