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hdf5/java/test/TestH5G.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

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* 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

* Fix typo

* 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

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

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

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace
2021-02-26 09:27:15 -06:00

504 lines
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Java
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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.assertNotNull;
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.HDF5LibraryException;
import hdf.hdf5lib.structs.H5G_info_t;
import hdf.hdf5lib.structs.H5O_token_t;
import org.junit.After;
import org.junit.Before;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;
public class TestH5G {
@Rule public TestName testname = new TestName();
private static final String H5_FILE = "testG.h5";
private static final String H5_FILE2 = "testG2.h5";
private static final String[] GROUPS = { "/G1", "/G1/G11", "/G1/G12",
"/G1/G11/G111", "/G1/G11/G112", "/G1/G11/G113", "/G1/G11/G114" };
private static final String[] GROUPS2 = { "/G1", "/G1/G14", "/G1/G12", "/G1/G13", "/G1/G11"};
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5fid2 = HDF5Constants.H5I_INVALID_HID;
private final long _createGroup(long fid, String name) {
long gid = HDF5Constants.H5I_INVALID_HID;
try {
gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Gcreate: " + err);
}
assertTrue("TestH5G._createGroup: ", gid > 0);
return gid;
}
private final long _createGroup2(long fid, String name) {
long gid = HDF5Constants.H5I_INVALID_HID;
long gcpl = HDF5Constants.H5I_INVALID_HID;
try {
gcpl = H5.H5Pcreate(HDF5Constants.H5P_GROUP_CREATE); //create gcpl
}
catch (final Exception ex) {
fail("H5.H5Pcreate(): " + ex);
}
assertTrue("TestH5G._createGroup2: ", gcpl >= 0);
try {
H5.H5Pset_link_creation_order(gcpl, HDF5Constants.H5P_CRT_ORDER_TRACKED
+ HDF5Constants.H5P_CRT_ORDER_INDEXED); // Set link creation order
}
catch (final Exception ex) {
try {H5.H5Pclose(gcpl);} catch (final Exception exx) {}
fail("H5.H5Pset_link_creation_order: " + ex);
}
try {
gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT,
gcpl, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Gcreate: " + err);
}
finally {
try {H5.H5Pclose(gcpl);} catch (final Exception ex) {}
}
assertTrue("TestH5G._createGroup2: ", gid > 0);
return gid;
}
private final long _openGroup(long fid, String name) {
long gid = HDF5Constants.H5I_INVALID_HID;
try {
gid = H5.H5Gopen(fid, name, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
gid = HDF5Constants.H5I_INVALID_HID;
err.printStackTrace();
fail("H5.H5Gopen: " + err);
}
assertTrue("TestH5G._openGroup: ", gid > 0);
return gid;
}
private final void _deleteFile(String filename) {
File file = new File(filename);
if (file.exists()) {
try {file.delete();} catch (SecurityException e) {}
}
}
@Before
public void createH5file()
throws HDF5LibraryException, NullPointerException {
assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
System.out.print(testname.getMethodName());
try {
H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
H5fid2 = H5.H5Fcreate(H5_FILE2, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.createH5file: " + err);
}
assertTrue("TestH5G.createH5file: H5.H5Fcreate: ", H5fid > 0);
assertTrue("TestH5G.createH5file: H5.H5Fcreate: ", H5fid2 > 0);
long gid = HDF5Constants.H5I_INVALID_HID;
for (int i = 0; i < GROUPS.length; i++) {
gid = _createGroup(H5fid, GROUPS[i]);
try {H5.H5Gclose(gid);} catch (Exception ex) {}
}
for (int i = 0; i < GROUPS2.length; i++) {
gid = _createGroup2(H5fid2, GROUPS2[i]);
try {H5.H5Gclose(gid);} catch (Exception ex) {}
}
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
H5.H5Fflush(H5fid2, HDF5Constants.H5F_SCOPE_LOCAL);
}
@After
public void deleteH5file() throws HDF5LibraryException {
if (H5fid > 0) {
try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
}
if (H5fid2 > 0) {
try {H5.H5Fclose(H5fid2);} catch (Exception ex) {}
}
_deleteFile(H5_FILE);
_deleteFile(H5_FILE2);
System.out.println();
}
@Test
public void testH5Gopen() {
long gid = HDF5Constants.H5I_INVALID_HID;
for (int i = 0; i < GROUPS.length; i++) {
try {
gid = H5.H5Gopen(H5fid, GROUPS[i], HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gopen: H5.H5Gopen: " + err);
}
assertTrue("TestH5G.testH5Gopen: ", gid > 0);
try {
H5.H5Gclose(gid);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Gget_create_plist() {
long gid = HDF5Constants.H5I_INVALID_HID;
long pid = HDF5Constants.H5I_INVALID_HID;
for (int i = 0; i < GROUPS.length; i++) {
try {
gid = H5.H5Gopen(H5fid, GROUPS[i], HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_create_plist: H5.H5Gopen: " + err);
}
assertTrue("TestH5G.testH5Gget_create_plist: ", gid > 0);
try {
pid = H5.H5Gget_create_plist(gid);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_create_plist: H5.H5Gget_create_plist: " + err);
}
assertTrue("TestH5G.testH5Gget_create_plist: ", pid > 0);
try {
H5.H5Gclose(gid);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Gget_info() {
H5G_info_t info = null;
for (int i = 0; i < GROUPS.length; i++) {
try {
info = H5.H5Gget_info(H5fid);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_info: H5.H5Gget_info: " + err);
}
assertNotNull("TestH5G.testH5Gget_info: ", info);
}
}
@Test
public void testH5Gget_info_by_name() {
H5G_info_t info = null;
for (int i = 0; i < GROUPS.length; i++) {
try {
info = H5.H5Gget_info_by_name(H5fid, GROUPS[i],
HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_info_by_name: H5.H5Gget_info_by_name: " + err);
}
assertNotNull("TestH5G.testH5Gget_info_by_name: ", info);
}
}
@Test
public void testH5Gget_info_by_idx() {
H5G_info_t info = null;
for (int i = 0; i < 2; i++) {
try {
info = H5.H5Gget_info_by_idx(H5fid, "/G1",
HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC,
i, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_info_by_idx: H5.H5Gget_info_by_idx: " + err);
}
assertNotNull("TestH5G.testH5Gget_info_by_idx: ", info);
}
}
@Test
public void testH5Gget_obj_info_all() {
H5G_info_t info = null;
long gid = _openGroup(H5fid, GROUPS[0]);
try {
info = H5.H5Gget_info(gid);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_all: H5.H5Gget_info: " + err);
}
finally {
try {H5.H5Gclose(gid);} catch (Exception ex) { }
}
assertNotNull("TestH5G.testH5Gget_obj_info_all: ", info);
assertTrue("TestH5G.testH5Gget_obj_info_all: number of links is empty", info.nlinks > 0);
String objNames[] = new String[(int) info.nlinks];
int objTypes[] = new int[(int) info.nlinks];
int lnkTypes[] = new int[(int) info.nlinks];
H5O_token_t objTokens[] = new H5O_token_t[(int) info.nlinks];
int names_found = 0;
try {
names_found = H5.H5Gget_obj_info_all(H5fid, GROUPS[0], objNames,
objTypes, lnkTypes, objTokens, HDF5Constants.H5_INDEX_NAME);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_all: H5.H5Gget_obj_info_all: " + err);
}
assertTrue("number found[" + names_found + "] different than expected["
+ objNames.length + "]", names_found == objNames.length);
for (int i = 0; i < objNames.length; i++) {
assertNotNull("name #" + i + " does not exist", objNames[i]);
assertTrue("TestH5G.testH5Gget_obj_info_all: ", objNames[i].length() > 0);
}
}
@Test
public void testH5Gget_obj_info_all_gid() {
H5G_info_t info = null;
long gid = _openGroup(H5fid, GROUPS[0]);
try {
info = H5.H5Gget_info(gid);
assertNotNull("TestH5G.testH5Gget_obj_info_all_gid: ", info);
assertTrue("TestH5G.testH5Gget_obj_info_all_gid: number of links is empty", info.nlinks > 0);
String objNames[] = new String[(int) info.nlinks];
H5O_token_t objTokens[] = new H5O_token_t[(int) info.nlinks];
int lnkTypes[] = new int[(int) info.nlinks];
int objTypes[] = new int[(int) info.nlinks];
int names_found = 0;
try {
names_found = H5.H5Gget_obj_info_all(gid, null, objNames, objTypes, lnkTypes,
objTokens, HDF5Constants.H5_INDEX_NAME);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_all_gid: H5.H5Gget_obj_info_all: " + err);
}
assertTrue("TestH5G.testH5Gget_obj_info_all_gid: number found[" + names_found + "] different than expected["
+ objNames.length + "]", names_found == objNames.length);
for (int i = 0; i < objNames.length; i++) {
assertNotNull("TestH5G.testH5Gget_obj_info_all_gid: name #" + i + " does not exist", objNames[i]);
assertTrue("TestH5G.testH5Gget_obj_info_all_gid: ", objNames[i].length() > 0);
}
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_all_gid: H5.H5Gget_info: " + err);
}
finally {
try {H5.H5Gclose(gid);} catch (Exception ex) { }
}
}
@Test
public void testH5Gget_obj_info_all_gid2() {
H5G_info_t info = null;
long gid = _openGroup(H5fid, GROUPS[1]);
try {
info = H5.H5Gget_info(gid);
assertNotNull("TestH5G.testH5Gget_obj_info_all_gid2: ", info);
assertTrue("TestH5G.testH5Gget_obj_info_all_gid2: number of links is empty", info.nlinks > 0);
String objNames[] = new String[(int) info.nlinks];
H5O_token_t objTokens[] = new H5O_token_t[(int) info.nlinks];
int lnkTypes[] = new int[(int) info.nlinks];
int objTypes[] = new int[(int) info.nlinks];
int names_found = 0;
try {
names_found = H5.H5Gget_obj_info_all(gid, null, objNames, objTypes, lnkTypes,
objTokens, HDF5Constants.H5_INDEX_NAME);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_all_gid2: H5.H5Gget_obj_info_all: " + err);
}
assertTrue("TestH5G.testH5Gget_obj_info_all_gid2: number found[" + names_found + "] different than expected["
+ objNames.length + "]", names_found == objNames.length);
for (int i = 0; i < objNames.length; i++) {
assertNotNull("TestH5G.testH5Gget_obj_info_all_gid2: name #" + i + " does not exist", objNames[i]);
assertTrue("TestH5G.testH5Gget_obj_info_all_gid2: ", objNames[i].length() > 0);
}
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_all_gid2: H5.H5Gget_info: " + err);
}
finally {
try {H5.H5Gclose(gid);} catch (Exception ex) { }
}
}
@Test
public void testH5Gget_obj_info_max() {
long gid = _openGroup(H5fid, GROUPS[0]);
long groups_max_size = GROUPS.length + 1;
String objNames[] = new String[(int)groups_max_size];
int objTypes[] = new int[(int)groups_max_size];
int lnkTypes[] = new int[(int)groups_max_size];
H5O_token_t objTokens[] = new H5O_token_t[(int)groups_max_size];
int names_found = 0;
try {
names_found = H5.H5Gget_obj_info_max(gid, objNames, objTypes, lnkTypes,
objTokens, groups_max_size);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_max: H5.H5Gget_obj_info_max: " + err);
}
finally {
try {H5.H5Gclose(gid);} catch (Exception ex) { }
}
// expected number does not include root group
assertTrue("TestH5G.testH5Gget_obj_info_max: number found[" + names_found + "] different than expected["
+ (GROUPS.length - 1) + "]", names_found == (GROUPS.length - 1));
for (int i = 0; i < GROUPS.length-1; i++) {
assertNotNull("TestH5G.testH5Gget_obj_info_max: name #"+i+" does not exist",objNames[i]);
assertTrue("TestH5G.testH5Gget_obj_info_max: ", objNames[i].length()>0);
}
}
@Test
public void testH5Gget_obj_info_max_limit() {
long gid = _openGroup(H5fid, GROUPS[0]);
long groups_max_size = GROUPS.length - 3;
String objNames[] = new String[(int)groups_max_size];
int objTypes[] = new int[(int)groups_max_size];
int lnkTypes[] = new int[(int)groups_max_size];
H5O_token_t objTokens[] = new H5O_token_t[(int)groups_max_size];
int names_found = 0;
try {
names_found = H5.H5Gget_obj_info_max(gid, objNames, objTypes, lnkTypes,
objTokens, groups_max_size);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_max_limit: H5.H5Gget_obj_info_max: " + err);
}
finally {
try {H5.H5Gclose(gid);} catch (Exception ex) { }
}
assertTrue("TestH5G.testH5Gget_obj_info_max_limit: number found[" + names_found + "] different than expected["
+ groups_max_size + "]", names_found == groups_max_size);
for (int i = 0; i < objNames.length; i++) {
assertNotNull("TestH5G.testH5Gget_obj_info_max_limit: name #" + i + " does not exist", objNames[i]);
assertTrue("TestH5G.testH5Gget_obj_info_max_limit: ", objNames[i].length() > 0);
}
}
@Test
public void testH5Gget_obj_info_all_byIndexType() {
H5G_info_t info = null;
long gid = _openGroup(H5fid2, GROUPS2[0]);
try {
info = H5.H5Gget_info(gid);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_all_byIndexType: H5.H5Gget_info: " + err);
}
finally {
try {H5.H5Gclose(gid);} catch (Exception ex) { }
}
assertNotNull("TestH5G.testH5Gget_obj_info_all_byIndexType: ", info);
assertTrue("TestH5G.testH5Gget_obj_info_all_byIndexType: number of links is empty", info.nlinks > 0);
String objNames[] = new String[(int) info.nlinks];
int objTypes[] = new int[(int) info.nlinks];
int lnkTypes[] = new int[(int) info.nlinks];
H5O_token_t objTokens[] = new H5O_token_t[(int) info.nlinks];
try {
H5.H5Gget_obj_info_all(H5fid2, GROUPS2[0], objNames,
objTypes, lnkTypes, objTokens, HDF5Constants.H5_INDEX_CRT_ORDER);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_all_byIndexType: H5.H5Gget_obj_info_all: " + err);
}
assertEquals("G12",objNames[1]);
assertEquals("G13", objNames[2] );
assertEquals("G11", objNames[3] );
try {
H5.H5Gget_obj_info_all(H5fid2, GROUPS2[0], objNames,
objTypes, lnkTypes, objTokens, HDF5Constants.H5_INDEX_NAME);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5G.testH5Gget_obj_info_all_byIndexType: H5.H5Gget_obj_info_all: " + err);
}
assertEquals("G12",objNames[1]);
assertEquals("G13", objNames[2] );
assertEquals("G14", objNames[3] );
}
}
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