mirrors/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2026-09-25 04:09:44 +03:00
Code Issues Packages Projects Releases Wiki Activity
Files
fc12e0b6c183f04add1971c796ba7d1549e6a894
hdf5/java/test/TestH5Z.java
T
Scot Breitenfeld fc12e0b6c1 Declare the H5Zf.c Fortran helpers; apply clang-format 
Two CI failures, both from the preceding commits.

Missing prototypes (hdf5 dev cmake CI). H5Pmodify_filter_by_idx_str_c
and _raw_c were defined in fortran/src/H5Zf.c but never declared in
H5f90proto.h alongside the H5Pappend_filter_*_c helpers. That broke two
different jobs for one reason:

  - "Special Workflows / gcc REL -Werror (build only)" builds with
    -Werror=missing-prototypes and rejected both definitions outright.
  - The Intel and windows-oneapi jobs failed at link with LNK2019 on
    both symbols, because H5FC_DLL on the declaration is what carries
    the dllexport attribute; with no declaration the symbols were never
    exported from hdf5_fortran.dll.

Adding the two H5FC_DLL declarations fixes both. Verified locally by
compiling H5Zf.c with -Werror=missing-prototypes, which the ordinary
build does not enable.

Formatting (clang-format Commit Changes). This job was green on the
commit before this series and has failed on every commit since; the
fault was entirely mine. Ran clang-format 17 -- the version CI pins --
over every file this series touched, C and Java alike, since the check
covers .java here too. The whole tree now passes a local run using CI's
source path and exclusion list.

Full build clean; ctest 3458/3459, the one failure being the
pre-existing ph5_f90_filtered_writes_no_sel example bug fixed upstream
in HDFGroup/hdf5#6633.
2026-08-21 09:28:51 -05:00

445 lines
18 KiB
Java
Raw Blame History

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the LICENSE file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
package test;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
import org.junit.After;
import org.junit.Before;
import org.junit.FixMethodOrder;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;
import org.junit.runners.MethodSorters;
@FixMethodOrder(MethodSorters.NAME_ASCENDING)
public class TestH5Z {
@Rule
public TestName testname = new TestName();
@Before
public void checkOpenIDs()
{
assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
System.out.print(testname.getMethodName());
}
@After
public void nextTestName()
{
System.out.println();
}
@Test
public void testH5Zfilter_avail()
{
try {
int filter_found;
filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_FLETCHER32);
assertTrue("H5.H5Zfilter_avail_FLETCHER32", filter_found > 0);
filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_NBIT);
assertTrue("H5.H5Zfilter_avail_NBIT", filter_found > 0);
filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SCALEOFFSET);
assertTrue("H5.H5Zfilter_avail_SCALEOFFSET", filter_found > 0);
filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE);
assertTrue("H5.H5Zfilter_avail_SHUFFLE", filter_found > 0);
// Just make sure H5Zfilter_avail() doesn't fail with szip/zlib
// since there is no way for us to determine if they should be present
// or not.
filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE);
filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Zfilter_avail " + err);
}
}
@Test
public void testH5Zget_filter_info()
{
try {
int filter_flag;
filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_FLETCHER32);
assertTrue("H5.H5Zget_filter_info_FLETCHER32_DECODE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
assertTrue("H5.H5Zget_filter_info_FLETCHER32_ENCODE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_NBIT);
assertTrue("H5.H5Zget_filter_info_NBIT_DECODE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
assertTrue("H5.H5Zget_filter_info_NBIT_ENCODE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SCALEOFFSET);
assertTrue("H5.H5Zget_filter_info_SCALEOFFSET_DECODE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
assertTrue("H5.H5Zget_filter_info_SCALEOFFSET_ENCODE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SHUFFLE);
assertTrue("H5.H5Zget_filter_info_DECODE_SHUFFLE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
assertTrue("H5.H5Zget_filter_info_ENCODE_SHUFFLE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE);
assertTrue("H5.H5Zget_filter_info_DEFLATE_DECODE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
assertTrue("H5.H5Zget_filter_info_DEFLATE_ENCODE_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
}
if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP)) {
filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SZIP);
// Decode should always be available, but we have no way of determining
// if encode is so don't assert on that.
assertTrue("H5.H5Zget_filter_info_DECODE_SZIP_ENABLED",
(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
}
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Zget_filter_info " + err);
}
}
@Test
public void testH5Zget_filter_class_info()
{
try {
hdf.hdf5lib.structs.H5Z_class_info_t info;
// DEFLATE (if available)
if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
info = H5.H5Zget_filter_class_info(HDF5Constants.H5Z_FILTER_DEFLATE);
assertTrue("H5Zget_filter_class_info: info must not be null", info != null);
assertTrue("H5Zget_filter_class_info: DEFLATE id",
info.id == HDF5Constants.H5Z_FILTER_DEFLATE);
assertTrue("H5Zget_filter_class_info: DEFLATE decode flag",
(info.config_flags & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) != 0);
}
// SHUFFLE
info = H5.H5Zget_filter_class_info(HDF5Constants.H5Z_FILTER_SHUFFLE);
assertTrue("H5Zget_filter_class_info: SHUFFLE info must not be null", info != null);
assertTrue("H5Zget_filter_class_info: SHUFFLE id", info.id == HDF5Constants.H5Z_FILTER_SHUFFLE);
assertTrue("H5Zget_filter_class_info: SHUFFLE decode flag",
(info.config_flags & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) != 0);
// FLETCHER32
info = H5.H5Zget_filter_class_info(HDF5Constants.H5Z_FILTER_FLETCHER32);
assertTrue("H5Zget_filter_class_info: FLETCHER32 info must not be null", info != null);
assertTrue("H5Zget_filter_class_info: FLETCHER32 id",
info.id == HDF5Constants.H5Z_FILTER_FLETCHER32);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Zget_filter_class_info " + err);
}
}
@Test(expected = HDF5LibraryException.class)
public void testH5Zget_filter_class_info_invalid() throws Throwable
{
H5.H5Zget_filter_class_info(32999);
}
@Test(expected = HDF5LibraryException.class)
public void testH5Zunregister_predefined() throws Throwable
{
int filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE);
assertTrue("H5.H5Zfilter_avail", filter_found > 0);
H5.H5Zunregister(HDF5Constants.H5Z_FILTER_SHUFFLE);
}
@Test
public void testH5Pappend_filter_string()
{
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
try {
dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
assertTrue("H5Pcreate", dcpl_id >= 0);
int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_SHUFFLE, 0, "");
assertTrue("H5Pappend_filter (string, shuffle)", ret >= 0);
int nfilters = H5.H5Pget_nfilters(dcpl_id);
assertEquals("nfilters after H5Pappend_filter", 1, nfilters);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pappend_filter_string: " + err);
}
finally {
if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
try {
H5.H5Pclose(dcpl_id);
}
catch (Exception e) { /* ignore */
}
}
}
@Test
public void testH5Pappend_filter_cdvalues()
{
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
try {
dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
assertTrue("H5Pcreate", dcpl_id >= 0);
int[] cd_values = new int[] {9};
if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_DEFLATE, 0, cd_values);
assertTrue("H5Pappend_filter (cd_values, deflate)", ret >= 0);
int nfilters = H5.H5Pget_nfilters(dcpl_id);
assertEquals("nfilters after H5Pappend_filter", 1, nfilters);
// Verify the cd_values round-trip via H5Pget_filter.
int[] cd_out = new int[1];
int[] flags_out = new int[1];
long[] cd_nelmts = new long[] {1};
String[] name_out = new String[] {""};
int filter_id =
H5.H5Pget_filter(dcpl_id, 0, flags_out, cd_nelmts, cd_out, 256, name_out, new int[1]);
assertEquals("filter id from H5Pget_filter", HDF5Constants.H5Z_FILTER_DEFLATE, filter_id);
assertEquals("cd_nelmts", 1L, cd_nelmts[0]);
assertEquals("cd_values[0] (deflate level)", 9, cd_out[0]);
}
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pappend_filter_cdvalues: " + err);
}
finally {
if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
try {
H5.H5Pclose(dcpl_id);
}
catch (Exception e) { /* ignore */
}
}
}
@Test
public void testH5Pmodify_filter_by_idx_string()
{
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
try {
dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
assertTrue("H5Pcreate", dcpl_id >= 0);
if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_DEFLATE, 0, "level=1");
assertTrue("H5Pappend_filter (string, deflate)", ret >= 0);
// Replace the configuration in place; position and ID are unchanged.
ret = H5.H5Pmodify_filter_by_idx(dcpl_id, 0, 0, "level=9");
assertTrue("H5Pmodify_filter_by_idx (string)", ret >= 0);
int nfilters = H5.H5Pget_nfilters(dcpl_id);
assertEquals("nfilters after H5Pmodify_filter_by_idx", 1, nfilters);
// The entry keeps a stored string, which reports the new value.
String[] params = new String[1];
ret = H5.H5Pget_filter_params_by_idx(dcpl_id, 0, params);
assertTrue("H5Pget_filter_params_by_idx", ret >= 0);
assertNotNull("params[0] is non-null", params[0]);
assertTrue("stored string reflects the modify: " + params[0], params[0].contains("level=9"));
}
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pmodify_filter_by_idx_string: " + err);
}
finally {
if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
try {
H5.H5Pclose(dcpl_id);
}
catch (Exception e) { /* ignore */
}
}
}
@Test
public void testH5Pmodify_filter_by_idx_cdvalues()
{
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
try {
dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
assertTrue("H5Pcreate", dcpl_id >= 0);
if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_DEFLATE, 0, "level=1");
assertTrue("H5Pappend_filter (string, deflate)", ret >= 0);
int[] cd_values = new int[] {6};
ret = H5.H5Pmodify_filter_by_idx(dcpl_id, 0, 0, cd_values);
assertTrue("H5Pmodify_filter_by_idx (cd_values)", ret >= 0);
int nfilters = H5.H5Pget_nfilters(dcpl_id);
assertEquals("nfilters after H5Pmodify_filter_by_idx", 1, nfilters);
// cd_values were replaced.
int[] cd_out = new int[1];
int[] flags_out = new int[1];
long[] cd_nelmts = new long[] {1};
String[] name_out = new String[] {""};
int filter_id =
H5.H5Pget_filter(dcpl_id, 0, flags_out, cd_nelmts, cd_out, 256, name_out, new int[1]);
assertEquals("filter id unchanged by modify", HDF5Constants.H5Z_FILTER_DEFLATE, filter_id);
assertEquals("cd_values[0] after modify", 6, cd_out[0]);
}
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pmodify_filter_by_idx_cdvalues: " + err);
}
finally {
if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
try {
H5.H5Pclose(dcpl_id);
}
catch (Exception e) { /* ignore */
}
}
}
@Test
public void testH5Pget_filter_params_by_idx()
{
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
try {
dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
assertTrue("H5Pcreate", dcpl_id >= 0);
int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_SHUFFLE, 0, "");
assertTrue("H5Pappend_filter shuffle", ret >= 0);
String[] params = new String[1];
int retval = H5.H5Pget_filter_params_by_idx(dcpl_id, 0, params);
assertTrue("H5Pget_filter_params_by_idx returned non-negative", retval >= 0);
assertNotNull("params[0] is non-null", params[0]);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pget_filter_params_by_idx: " + err);
}
finally {
if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
try {
H5.H5Pclose(dcpl_id);
}
catch (Exception e) { /* ignore */
}
}
}
@Test
public void testH5Zconfig_get_param_int()
{
try {
String cfg = "level = 6";
long[] val = new long[1];
int ret = H5.H5Zconfig_get_param(cfg, "level", val);
assertTrue("H5Zconfig_get_param (int) returned non-negative", ret >= 0);
assertEquals("H5Zconfig_get_param (int) value", 6L, val[0]);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Zconfig_get_param_int: " + err);
}
}
@Test
public void testH5Zconfig_get_param_double()
{
try {
String cfg = "scale = 1.5";
double[] val = new double[1];
int ret = H5.H5Zconfig_get_param(cfg, "scale", val);
assertTrue("H5Zconfig_get_param (double) returned non-negative", ret >= 0);
assertEquals("H5Zconfig_get_param (double) value", 1.5, val[0], 1e-10);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Zconfig_get_param_double: " + err);
}
}
@Test
public void testH5Zconfig_get_param_bool()
{
try {
String cfg = "lossless = true";
boolean[] val = new boolean[1];
int ret = H5.H5Zconfig_get_param(cfg, "lossless", val);
assertTrue("H5Zconfig_get_param (bool) returned non-negative", ret >= 0);
assertTrue("H5Zconfig_get_param (bool) value", val[0]);
String cfg2 = "lossless = false";
int ret2 = H5.H5Zconfig_get_param(cfg2, "lossless", val);
assertTrue("H5Zconfig_get_param (bool, false) returned non-negative", ret2 >= 0);
assertFalse("H5Zconfig_get_param (bool) value (false)", val[0]);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Zconfig_get_param_bool: " + err);
}
}
@Test
public void testH5Zconfig_get_param_str()
{
try {
String cfg = "mode = \"fast\"";
String[] val = new String[1];
int ret = H5.H5Zconfig_get_param(cfg, "mode", val);
assertTrue("H5Zconfig_get_param (str) returned non-negative", ret >= 0);
assertEquals("H5Zconfig_get_param (str) value", "fast", val[0]);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Zconfig_get_param_str: " + err);
}
}
@Test
public void testH5Zconfig_get_param_missing_key()
{
try {
String cfg = "level = 5";
long[] val = new long[1];
int ret = H5.H5Zconfig_get_param(cfg, "missing_key", val);
assertTrue("H5Zconfig_get_param with missing key returns 0 (not found)", ret == 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Zconfig_get_param_missing_key: " + err);
}
}
}
Reference in New Issue View Git Blame Copy Permalink