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hdf5/java/test/TestH5Rref.java
Allen Byrne 3bbc4f0df4 Hdf5 1 12 merge cmake ninja and java refs (#698) 
* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* Merge CMake and java refs from dev

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-05-29 15:30:27 -05:00

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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.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.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
import hdf.hdf5lib.exceptions.HDF5FunctionArgumentException;
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 TestH5Rref {
@Rule public TestName testname = new TestName();
private static final String H5_DREG_FILE = "trefer_reg.h5";
private static final String H5_AREG_FILE = "trefer_attr.h5";
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5dsid = HDF5Constants.H5I_INVALID_HID;
long H5did = HDF5Constants.H5I_INVALID_HID;
private boolean byteArrayCheck(final byte[] array) {
for (byte b : array) {
if (b != 0) {
return false;
}
}
return true;
}
public void openH5file(String filename, String dsetname) {
try {
H5fid = H5.H5Fopen(filename,
HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5R._openH5file: " + err);
}
assertTrue("TestH5R._openH5file: H5.H5Fopen: ", H5fid >= 0);
try {
H5did = H5.H5Dopen(H5fid, dsetname, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5R._openH5file: " + err);
}
assertTrue("TestH5R._openH5file: H5.H5Dopen: ", H5did >= 0);
try {
H5dsid = H5.H5Dget_space(H5did);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5R._openH5file: " + err);
}
assertTrue("TestH5R._openH5file: H5.H5Screate_simple: ",H5dsid > 0);
}
@After
public void closeH5file() throws HDF5LibraryException {
if (H5did >= 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
if (H5dsid > 0)
try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
if (H5fid > 0)
try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
H5fid = HDF5Constants.H5I_INVALID_HID;
H5dsid = HDF5Constants.H5I_INVALID_HID;
H5did = HDF5Constants.H5I_INVALID_HID;
System.out.println();
}
@Before
public void verifyCount()
throws NullPointerException, HDF5Exception {
assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0);
System.out.print(testname.getMethodName());
}
// Test v1.12 APIs params
@Test
public void testH5Rget_object() {
int ref_type = HDF5Constants.H5R_OBJECT1;
long f_type = HDF5Constants.H5I_INVALID_HID;
int obj_type = -1;
int ndims = 1;
long ret_val = -1;
byte[][] refbuf = null;
String name = "";
String objName = "/DS_NA";
try {
openH5file(H5_DREG_FILE, objName);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: openH5file: " + err);
}
try {
f_type = H5.H5Dget_type(H5did);
int result = H5.H5Tget_class(f_type);
assertTrue("testH5Rget_object: H5Tget_class", result > 0);
String class_name = H5.H5Tget_class_name(result);
assertTrue("testH5Rget_object: H5Tget_class", class_name.compareTo("H5T_REFERENCE")==0);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: " + err);
}
finally {
try {H5.H5Tclose(f_type);} catch (Exception ex) {}
}
try {
ndims = (int)H5.H5Sget_simple_extent_npoints(H5dsid);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Sget_simple_extent_ndims: " + err);
}
refbuf = new byte[ndims][HDF5Constants.H5R_REF_BUF_SIZE];
// Read the reference from the dataset.
try {
H5.H5Dread(H5did, HDF5Constants.H5T_STD_REF,
HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, refbuf);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Rget_object: H5Dread: " + err);
}
for (int i = 0; i < ndims; i++) {
try {
ret_val = H5.H5Rget_type(refbuf[i]);
assertTrue("testH5Rget_object: H5Rget_type["+i+"]="+ret_val, ret_val == ref_type);
if (!byteArrayCheck(refbuf[i])) {
try {
obj_type = H5.H5Rget_obj_type3(refbuf[i], HDF5Constants.H5P_DEFAULT);
assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
}
catch (Throwable err2) {
err2.printStackTrace();
fail("testH5Rget_object: H5.H5Rget_obj_type3: " + err2);
}
}
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rget_type: " + err);
}
finally {
H5.H5Rdestroy(refbuf[i]);
}
}
}
@Test
public void testH5Rget_obj_type3() {
long f_type = HDF5Constants.H5I_INVALID_HID;
int ref_type = HDF5Constants.H5R_DATASET_REGION2;
int obj_type = -1;
int ndims = 1;
long ret_val = -1;
byte[][] refbuf = null;
String objName = "/Dataset1";
try {
openH5file(H5_DREG_FILE, objName);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: openH5file: " + err);
}
try {
f_type = H5.H5Dget_type(H5did);
int result = H5.H5Tget_class(f_type);
assertTrue("testH5Rget_obj_type3: H5Tget_class", result > 0);
String class_name = H5.H5Tget_class_name(result);
assertTrue("testH5Rget_obj_type3: H5Tget_class="+class_name, class_name.compareTo("H5T_REFERENCE")==0);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: " + err);
}
finally {
try {H5.H5Tclose(f_type);} catch (Exception ex) {}
}
try {
ndims = (int)H5.H5Sget_simple_extent_npoints(H5dsid);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: H5Sget_simple_extent_ndims: " + err);
}
refbuf = new byte[ndims][HDF5Constants.H5R_REF_BUF_SIZE];
// Read the reference from the dataset.
try {
H5.H5Dread(H5did, HDF5Constants.H5T_STD_REF,
HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, refbuf);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: H5Dread: " + err);
}
for (int i = 0; i < ndims; i++) {
try {
ret_val = H5.H5Rget_type(refbuf[i]);
assertTrue("testH5Rget_obj_type3: H5Rget_type["+i+"]="+ret_val, ret_val == ref_type);
if (!byteArrayCheck(refbuf[i])) {
try {
obj_type = H5.H5Rget_obj_type3(refbuf[i], HDF5Constants.H5P_DEFAULT);
assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
}
catch (Throwable err2) {
err2.printStackTrace();
fail("testH5Rget_obj_type3: H5.H5Rget_obj_type3: " + err2);
}
}
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: H5Rget_type: " + err);
}
finally {
H5.H5Rdestroy(refbuf[i]);
}
}
}
@Test
public void testH5Rget_region_dataset() {
long f_type = HDF5Constants.H5I_INVALID_HID;
long loc_id = HDF5Constants.H5I_INVALID_HID;
long loc_sid = HDF5Constants.H5I_INVALID_HID;
int ref_type = HDF5Constants.H5R_DATASET_REGION2;
int ndims = 1;
long ret_val = -1;
byte[][] refbuf = null;
String name = "";
String objName = "/Dataset1";
try {
openH5file(H5_DREG_FILE, objName);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_region_dataset: openH5file: " + err);
}
try {
f_type = H5.H5Dget_type(H5did);
int result = H5.H5Tget_class(f_type);
assertTrue("testH5Rget_region_dataset: H5Tget_class", result > 0);
String class_name = H5.H5Tget_class_name(result);
assertTrue("testH5Rget_region_dataset: H5Tget_class="+class_name, class_name.compareTo("H5T_REFERENCE")==0);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_region_dataset: " + err);
}
finally {
try {H5.H5Tclose(f_type);} catch (Exception ex) {}
}
try {
ndims = (int)H5.H5Sget_simple_extent_npoints(H5dsid);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_region_dataset: H5Sget_simple_extent_ndims: " + err);
}
refbuf = new byte[ndims][HDF5Constants.H5R_REF_BUF_SIZE];
// Read the reference from the dataset.
try {
H5.H5Dread(H5did, HDF5Constants.H5T_STD_REF,
HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, refbuf);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: H5Dread: " + err);
}
for (int i = 0; i < ndims; i++) {
try {
try {
ret_val = H5.H5Rget_type(refbuf[i]);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_region_dataset: H5Rget_type["+i+"]: " + err);
}
assertTrue("testH5Rget_region_dataset: H5Rget_type["+i+"]="+ret_val, ret_val == ref_type);
try {
loc_id = H5.H5Ropen_object(refbuf[i], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue(loc_id >= 0);
try {
loc_sid = H5.H5Ropen_region(refbuf[i], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue(loc_sid >= 0);
int region_type = -1;
try {
int reg_ndims = H5.H5Sget_simple_extent_ndims(loc_sid);
region_type = H5.H5Sget_select_type(loc_sid);
if (i == 1)
assertTrue(region_type == HDF5Constants.H5S_SEL_POINTS);
else
assertTrue(region_type == HDF5Constants.H5S_SEL_HYPERSLABS);
if (region_type == HDF5Constants.H5S_SEL_POINTS) {
long reg_npoints = H5.H5Sget_select_elem_npoints(loc_sid);
// Coordinates for get point selection
long getcoord[] = new long[reg_ndims * (int)reg_npoints];
// Known coordinates for point selection
long coord[][] = {{6,9},{2,2},{8,4},{1,6},{2,8},{3,2},
{0,4},{9,0},{7,1},{3,3}};
try {
H5.H5Sget_select_elem_pointlist(loc_sid, 0, reg_npoints, getcoord);
assertTrue("H5.H5Sget_select_elem_pointlist", coord[0][0] == getcoord[0]);
assertTrue("H5.H5Sget_select_elem_pointlist", coord[0][1] == getcoord[1]);
assertTrue("H5.H5Sget_select_elem_pointlist", coord[1][0] == getcoord[2]);
assertTrue("H5.H5Sget_select_elem_pointlist", coord[1][1] == getcoord[3]);
assertTrue("H5.H5Sget_select_elem_pointlist", coord[2][0] == getcoord[4]);
assertTrue("H5.H5Sget_select_elem_pointlist", coord[2][1] == getcoord[5]);
}
catch (Throwable err3) {
err3.printStackTrace();
fail("H5.H5Sget_select_elem_pointlist: " + err3);
}
}
else if (region_type == HDF5Constants.H5S_SEL_HYPERSLABS) {
long reg_nblocks = H5.H5Sget_select_hyper_nblocks(loc_sid);
assertTrue("H5Sget_select_hyper_nblocks", reg_nblocks == 1);
// Coordinates for get block selection
long getblocks[] = new long[reg_ndims * (int)reg_nblocks * 2];
long start[] = {2,2};
long block[] = {8,8};
try {
H5.H5Sget_select_hyper_blocklist(loc_sid, 0, reg_nblocks, getblocks);
assertTrue("H5.H5Sget_select_hyper_blocklist", start[0] == getblocks[0]);
assertTrue("H5.H5Sget_select_hyper_blocklist", start[1] == getblocks[1]);
assertTrue("H5.H5Sget_select_hyper_blocklist", (block[0]-1) == getblocks[2]);
assertTrue("H5.H5Sget_select_hyper_blocklist", (block[1]-1) == getblocks[3]);
}
catch (Throwable err3) {
err3.printStackTrace();
fail("H5.H5Sget_select_hyper_blocklist: " + err3);
}
}
}
catch (Throwable err2) {
err2.printStackTrace();
assertTrue("testH5Rget_region_dataset: H5Sget_select_type: " + err2, i > 1);
}
}
catch (Throwable err1) {
err1.printStackTrace();
fail("testH5Rget_region_dataset: " + err1);
}
finally {
try {H5.H5Sclose(loc_sid);} catch (Exception ex) {}
}
}
catch (Throwable err0) {
err0.printStackTrace();
fail("testH5Rget_region_dataset: " + err0);
}
finally {
try {H5.H5Dclose(loc_id);} catch (Exception ex) {}
}
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_region_dataset: H5Rget_type: " + err);
}
finally {
H5.H5Rdestroy(refbuf[i]);
}
} //for (int i = 0; i < ndims; i++)
}
@Test
public void testH5Rget_region_attribute() {
long f_type = HDF5Constants.H5I_INVALID_HID;
long loc_id = HDF5Constants.H5I_INVALID_HID;
long loc_sid = HDF5Constants.H5I_INVALID_HID;
int ref_type = HDF5Constants.H5R_ATTR;
int obj_type = -1;
int ndims = 1;
long ret_val = -1;
byte[][] refbuf = null;
String objName = "/Dataset3";
try {
openH5file(H5_AREG_FILE, objName);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_region_attribute: openH5file: " + err);
}
try {
f_type = H5.H5Dget_type(H5did);
int result = H5.H5Tget_class(f_type);
assertTrue("testH5Rget_region_attribute: H5Tget_class", result > 0);
String class_name = H5.H5Tget_class_name(result);
assertTrue("testH5Rget_region_attribute: H5Tget_class="+class_name, class_name.compareTo("H5T_REFERENCE")==0);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_region_attribute: " + err);
}
finally {
try {H5.H5Tclose(f_type);} catch (Exception ex) {}
}
try {
ndims = (int)H5.H5Sget_simple_extent_npoints(H5dsid);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_region_attribute: H5Sget_simple_extent_ndims: " + err);
}
refbuf = new byte[ndims][HDF5Constants.H5R_REF_BUF_SIZE];
// Read the reference from the dataset.
try {
H5.H5Dread(H5did, HDF5Constants.H5T_STD_REF,
HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, refbuf);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Rget_region_attribute: H5Dread: " + err);
}
for (int i = 0; i < ndims; i++) {
try {
ret_val = H5.H5Rget_type(refbuf[i]);
assertTrue("testH5Rget_region_attribute: H5Rget_type["+i+"]="+ret_val, ret_val == ref_type);
try {
loc_id = H5.H5Ropen_attr(refbuf[i], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue(loc_id >= 0);
if (!byteArrayCheck(refbuf[i])) {
try {
loc_sid = H5.H5Aget_space(loc_id);
assertTrue(loc_sid >= 0);
}
catch (Throwable err1) {
err1.printStackTrace();
fail("testH5Rget_region_attribute: " + err1);
}
finally {
try {H5.H5Sclose(loc_sid);} catch (Exception ex) {}
}
}
}
catch (Throwable err0) {
err0.printStackTrace();
// second attribute is null
assertTrue("testH5Rget_region_attribute: " + err0, i == 1);
}
finally {
try {H5.H5Aclose(loc_id);} catch (Exception ex) {}
}
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_region_attribute: H5Rget_type: " + err);
}
finally {
H5.H5Rdestroy(refbuf[i]);
}
}
}
// These tests need to be updated with new APIs
// @Test//
// public void testH5Rget_group() {
// long loc_id = H5fid;
// int ref_type = HDF5Constants.H5R_OBJECT2;
// long ret_val = -1;
// byte[] ref = null;
// String name = "";
// String objName = "/dset";
//
// try {
// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("testH5Rget_object: H5Rcreate_object " + err);
// }
// try {
// dataset_id= H5.H5Rdereference(H5fid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_DATASET_REGION, ref1);
//
// //Create reference on group
// ref2 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
// group_id= H5.H5Rdereference(H5gid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, ref2);
// assertNotNull(ref1);
// assertNotNull(ref2);
// assertTrue(dataset_id >= 0);
// assertTrue(group_id >= 0);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("TestH5Rdereference " + err);
// }
// finally {
// try {H5.H5Dclose(dataset_id);} catch (Exception ex) {}
// try {H5.H5Gclose(group_id);} catch (Exception ex) {}
// }
// }
// @Test//
// public void testH5Rget_attr() {
// long loc_id = H5fid;
// int ref_type = HDF5Constants.H5R_OBJECT2;
// long ret_val = -1;
// byte[] ref = null;
// String name = "";
// String objName = "/dset";
//
// try {
// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("testH5Rget_object: H5Rcreate_object " + err);
// }
// try {
// dsid = H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
// assertNotNull(ref);
// assertTrue(dsid >= 0);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("TestH5Rget_region: " + err);
// }
// finally {
// try {H5.H5Sclose(dsid);} catch (Exception ex) {}
// }
// }
}
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