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Develop HDFFV-11310 (#1811)

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* Rework java vl check in read/write. Handle old refs in h5dump

* Committing clang-format changes

* Java changes allow default VL reads

* Fix JNI utility for old refs

* HDFFV-11310 - implement vlen read/write for atomic types.

* format check fix

* Mostly format fixes

* More format issues

* Two format changes

* Use JNI names for sizeof

* format change

* fix size typo

* Change to older method to initialize list

* remove unused var

* format fix

* switch writeVL functions to use datatype instead of java type

* Add VL option to generic read/write check

* Correct function name typo

* Add JIRA issue

* Correct note to match change in code.

* HDFFV-11318 add VL references as byte arrays

* Add release note and format changes

* Another format update

* Fix unreleased allocations

* Fix format

* format correction

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
This commit is contained in:
Allen Byrne
2022-07-11 15:59:52 -05:00
committed by GitHub
parent 663321087a
commit b9d1d66ab8
20 changed files with 2711 additions and 573 deletions
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469
java/test/TestH5R.java
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@@ -19,6 +19,9 @@ import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
@@ -528,4 +531,470 @@ public class TestH5R {
byte[] ref = null;
H5.H5Rget_attr_name(ref);
}
@Test
public void testH5RVLattr_ref()
{
String attr_obj_name = "VLObjRefdata";
String attr_reg_name = "VLRegRefdata";
long attr_obj_id = HDF5Constants.H5I_INVALID_HID;
long attr_reg_id = HDF5Constants.H5I_INVALID_HID;
long atype_obj_id = HDF5Constants.H5I_INVALID_HID;
long atype_reg_id = HDF5Constants.H5I_INVALID_HID;
long aspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
byte[] ref1 = null;
byte[] ref2 = null;
byte[] ref3 = null;
byte[] ref4 = null;
try {
// Create reference on dataset
ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid);
assertNotNull(ref1);
ref2 = H5.H5Rcreate(H5gid, "dset2", HDF5Constants.H5R_DATASET_REGION, H5dsid);
assertNotNull(ref2);
ref3 = H5.H5Rcreate(H5gid, "/dset", HDF5Constants.H5R_OBJECT, -1);
assertNotNull(ref3);
// Create reference on group
ref4 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
assertNotNull(ref3);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5RVLattr_ref: " + err);
}
ArrayList[] vl_obj_data = new ArrayList[4];
ArrayList[] vl_reg_data = new ArrayList[4];
try {
// Write Object Reference data
vl_obj_data[0] = new ArrayList<byte[]>(Arrays.asList(ref3));
vl_obj_data[1] = new ArrayList<byte[]>(Arrays.asList(ref3, ref4));
vl_obj_data[2] = new ArrayList<byte[]>(Arrays.asList(ref3, ref3, ref3));
vl_obj_data[3] = new ArrayList<byte[]>(Arrays.asList(ref4, ref4, ref4, ref4));
Class dataClass = vl_obj_data.getClass();
assertTrue("testH5RVLattr_ref.getClass: " + dataClass, dataClass.isArray());
try {
atype_obj_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_OBJ);
assertTrue("testH5RVLattr_ref.H5Tvlen_create: ", atype_obj_id >= 0);
}
catch (Exception err) {
if (atype_obj_id > 0)
try {
H5.H5Tclose(atype_obj_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_obj_id = H5.H5Acreate(H5did, attr_obj_name, atype_obj_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLattr_ref: ", attr_obj_id >= 0);
H5.H5AwriteVL(attr_obj_id, atype_obj_id, vl_obj_data);
}
catch (Exception err) {
if (attr_obj_id > 0)
try {
H5.H5Aclose(attr_obj_id);
}
catch (Exception ex) {
}
if (atype_obj_id > 0)
try {
H5.H5Tclose(atype_obj_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
// Write Region Reference data
vl_reg_data[0] = new ArrayList<byte[]>(Arrays.asList(ref1));
vl_reg_data[1] = new ArrayList<byte[]>(Arrays.asList(ref1, ref2));
vl_reg_data[2] = new ArrayList<byte[]>(Arrays.asList(ref1, ref1, ref1));
vl_reg_data[3] = new ArrayList<byte[]>(Arrays.asList(ref2, ref2, ref2, ref2));
dataClass = vl_reg_data.getClass();
assertTrue("testH5RVLattr_ref.getClass: " + dataClass, dataClass.isArray());
try {
atype_reg_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_DSETREG);
assertTrue("testH5RVLattr_ref.H5Tvlen_create: ", atype_reg_id >= 0);
}
catch (Exception err) {
if (atype_reg_id > 0)
try {
H5.H5Tclose(atype_reg_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_reg_id = H5.H5Acreate(H5did, attr_reg_name, atype_reg_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLattr_ref: ", attr_reg_id >= 0);
H5.H5AwriteVL(attr_reg_id, atype_reg_id, vl_reg_data);
}
catch (Exception err) {
if (attr_reg_id > 0)
try {
H5.H5Aclose(attr_reg_id);
}
catch (Exception ex) {
}
if (atype_reg_id > 0)
try {
H5.H5Tclose(atype_reg_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
for (int j = 0; j < dims.length; j++) {
lsize *= dims[j];
}
// Read Object Reference data
ArrayList[] vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5AreadVL(attr_obj_id, atype_obj_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
((byte[])vl_obj_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
((byte[])vl_obj_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
((byte[])vl_obj_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
((byte[])vl_obj_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
// Read Region Reference data
vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5AreadVL(attr_reg_id, atype_reg_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
((byte[])vl_reg_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
((byte[])vl_reg_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
((byte[])vl_reg_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
((byte[])vl_reg_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
finally {
if (attr_reg_id > 0)
try {
H5.H5Aclose(attr_reg_id);
}
catch (Exception ex) {
}
if (attr_obj_id > 0)
try {
H5.H5Aclose(attr_obj_id);
}
catch (Exception ex) {
}
if (atype_reg_id > 0)
try {
H5.H5Tclose(atype_reg_id);
}
catch (Exception ex) {
}
if (atype_obj_id > 0)
try {
H5.H5Tclose(atype_obj_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5RVLdset_ref()
{
String dset_obj_name = "VLObjRefdata";
String dset_reg_name = "VLRegRefdata";
long dset_obj_id = HDF5Constants.H5I_INVALID_HID;
long dset_reg_id = HDF5Constants.H5I_INVALID_HID;
long dtype_obj_id = HDF5Constants.H5I_INVALID_HID;
long dtype_reg_id = HDF5Constants.H5I_INVALID_HID;
long dspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
byte[] ref1 = null;
byte[] ref2 = null;
byte[] ref3 = null;
byte[] ref4 = null;
try {
// Create reference on dataset
ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid);
assertNotNull(ref1);
ref2 = H5.H5Rcreate(H5gid, "dset2", HDF5Constants.H5R_DATASET_REGION, H5dsid);
assertNotNull(ref2);
ref3 = H5.H5Rcreate(H5gid, "/dset", HDF5Constants.H5R_OBJECT, -1);
assertNotNull(ref3);
// Create reference on group
ref4 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
assertNotNull(ref3);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5RVLattr_ref: " + err);
}
ArrayList[] vl_obj_data = new ArrayList[4];
ArrayList[] vl_reg_data = new ArrayList[4];
try {
// Write Object Reference data
vl_obj_data[0] = new ArrayList<byte[]>(Arrays.asList(ref3));
vl_obj_data[1] = new ArrayList<byte[]>(Arrays.asList(ref3, ref4));
vl_obj_data[2] = new ArrayList<byte[]>(Arrays.asList(ref3, ref3, ref3));
vl_obj_data[3] = new ArrayList<byte[]>(Arrays.asList(ref4, ref4, ref4, ref4));
Class dataClass = vl_obj_data.getClass();
assertTrue("testH5RVLdset_ref.getClass: " + dataClass, dataClass.isArray());
try {
dtype_obj_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_OBJ);
assertTrue("testH5RVLdset_ref.H5Tvlen_create: ", dtype_obj_id >= 0);
}
catch (Exception err) {
if (dtype_obj_id > 0)
try {
H5.H5Tclose(dtype_obj_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + err);
}
try {
dspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(dspace_id > 0);
dset_obj_id =
H5.H5Dcreate(H5fid, dset_obj_name, dtype_obj_id, dspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLdset_ref: ", dset_obj_id >= 0);
H5.H5DwriteVL(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_obj_data);
}
catch (Exception err) {
if (dset_obj_id > 0)
try {
H5.H5Dclose(dset_obj_id);
}
catch (Exception ex) {
}
if (dtype_obj_id > 0)
try {
H5.H5Tclose(dtype_obj_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + err);
}
finally {
if (dspace_id > 0)
try {
H5.H5Sclose(dspace_id);
}
catch (Exception ex) {
}
}
// Write Region Reference data
vl_reg_data[0] = new ArrayList<byte[]>(Arrays.asList(ref1));
vl_reg_data[1] = new ArrayList<byte[]>(Arrays.asList(ref1, ref2));
vl_reg_data[2] = new ArrayList<byte[]>(Arrays.asList(ref1, ref1, ref1));
vl_reg_data[3] = new ArrayList<byte[]>(Arrays.asList(ref2, ref2, ref2, ref2));
dataClass = vl_reg_data.getClass();
assertTrue("testH5RVLdset_ref.getClass: " + dataClass, dataClass.isArray());
try {
dtype_reg_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_DSETREG);
assertTrue("testH5RVLdset_ref.H5Tvlen_create: ", dtype_reg_id >= 0);
}
catch (Exception err) {
if (dtype_reg_id > 0)
try {
H5.H5Tclose(dtype_reg_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + err);
}
try {
dspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(dspace_id > 0);
dset_reg_id =
H5.H5Dcreate(H5fid, dset_reg_name, dtype_reg_id, dspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLdset_ref: ", dset_reg_id >= 0);
H5.H5DwriteVL(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_reg_data);
}
catch (Exception err) {
if (dset_reg_id > 0)
try {
H5.H5Dclose(dset_reg_id);
}
catch (Exception ex) {
}
if (dtype_reg_id > 0)
try {
H5.H5Tclose(dtype_reg_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + err);
}
finally {
if (dspace_id > 0)
try {
H5.H5Sclose(dspace_id);
}
catch (Exception ex) {
}
}
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
for (int j = 0; j < dims.length; j++) {
lsize *= dims[j];
}
// Read Object Reference data
ArrayList[] vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5DreadVL(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
((byte[])vl_obj_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
((byte[])vl_obj_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
((byte[])vl_obj_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
((byte[])vl_obj_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
// Read Region Reference data
vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5DreadVL(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
((byte[])vl_reg_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
((byte[])vl_reg_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
((byte[])vl_reg_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
((byte[])vl_reg_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + err);
}
finally {
if (dset_reg_id > 0)
try {
H5.H5Dclose(dset_reg_id);
}
catch (Exception ex) {
}
if (dset_obj_id > 0)
try {
H5.H5Dclose(dset_obj_id);
}
catch (Exception ex) {
}
if (dtype_reg_id > 0)
try {
H5.H5Tclose(dtype_reg_id);
}
catch (Exception ex) {
}
if (dtype_obj_id > 0)
try {
H5.H5Tclose(dtype_obj_id);
}
catch (Exception ex) {
}
}
}
}