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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 13:59:52 -07:00
committed by GitHub
co-authored by github-actions
parent 663321087a
commit b9d1d66ab8
20 changed files with 2711 additions and 573 deletions
Download Patch File Download Diff File Expand all files Collapse all files
java/test/TestH5A.java
+224 -19
View File
@@ -20,6 +20,8 @@ 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;
@@ -637,9 +639,8 @@ public class TestH5A {
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_INC, 0, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder ",
attr_info.corder ==
0); // should equal 0 as this is the order of 1st attribute created.
assertTrue("Corder ", attr_info.corder ==
0); // should equal 0 as this is the order of 1st attribute created.
assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr_id));
// Verify info for 2nd attribute, in increasing creation order
@@ -653,33 +654,29 @@ public class TestH5A {
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_DEC, 0, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder",
attr_info.corder ==
1); // should equal 1 as this is the order of 2nd attribute created.
assertTrue("Corder", attr_info.corder ==
1); // should equal 1 as this is the order of 2nd attribute created.
// verify info for 1st attribute, in decreasing creation order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_DEC, 1, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder",
attr_info.corder ==
0); // should equal 0 as this is the order of 1st attribute created.
assertTrue("Corder", attr_info.corder ==
0); // should equal 0 as this is the order of 1st attribute created.
// verify info for 1st attribute, in increasing name order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_NAME,
HDF5Constants.H5_ITER_INC, 1, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder",
attr_info.corder ==
0); // should equal 0 as this is the order of 1st attribute created.
assertTrue("Corder", attr_info.corder ==
0); // should equal 0 as this is the order of 1st attribute created.
// verify info for 2nd attribute, in decreasing name order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_NAME,
HDF5Constants.H5_ITER_DEC, 1, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder",
attr_info.corder ==
1); // should equal 1 as this is the order of 2nd attribute created.
assertTrue("Corder", attr_info.corder ==
1); // should equal 1 as this is the order of 2nd attribute created.
}
catch (Throwable err) {
err.printStackTrace();
@@ -1075,7 +1072,7 @@ public class TestH5A {
HDF5Constants.H5P_DEFAULT);
assertTrue("testH5Awrite_readVL: ", attr_id >= 0);
H5.H5AwriteVL(attr_id, atype_id, str_data);
H5.H5Awrite_VLStrings(attr_id, atype_id, str_data);
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
@@ -1087,7 +1084,7 @@ public class TestH5A {
strs[j] = "";
}
try {
H5.H5AreadVL(attr_id, atype_id, strs);
H5.H5Aread_VLStrings(attr_id, atype_id, strs);
}
catch (Exception ex) {
ex.printStackTrace();
@@ -1162,12 +1159,12 @@ public class TestH5A {
fail("H5.H5Acreate: " + err);
}
/* Close the property list, and get the attribute's property list */
// Close the property list, and get the attribute's property list
H5.H5Pclose(plist_id);
plist_id = H5.H5Aget_create_plist(attribute_id);
assertTrue(plist_id > 0);
/* Get the character encoding and ensure that it is the default (ASCII) */
// Get the character encoding and ensure that it is the default (ASCII)
try {
char_encoding = H5.H5Pget_char_encoding(plist_id);
}
@@ -1371,4 +1368,212 @@ public class TestH5A {
}
}
}
@Test
public void testH5AVLwr()
{
String attr_int_name = "VLIntdata";
String attr_dbl_name = "VLDbldata";
long attr_int_id = HDF5Constants.H5I_INVALID_HID;
long attr_dbl_id = HDF5Constants.H5I_INVALID_HID;
long atype_int_id = HDF5Constants.H5I_INVALID_HID;
long atype_dbl_id = HDF5Constants.H5I_INVALID_HID;
long aspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
ArrayList[] vl_int_data = new ArrayList[4];
ArrayList[] vl_dbl_data = new ArrayList[4];
try {
// Write Integer data
vl_int_data[0] = new ArrayList<Integer>(Arrays.asList(1));
vl_int_data[1] = new ArrayList<Integer>(Arrays.asList(2, 3));
vl_int_data[2] = new ArrayList<Integer>(Arrays.asList(4, 5, 6));
vl_int_data[3] = new ArrayList<Integer>(Arrays.asList(7, 8, 9, 10));
Class dataClass = vl_int_data.getClass();
assertTrue("testH5AVLwr.getClass: " + dataClass, dataClass.isArray());
try {
atype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
assertTrue("testH5AVLwr.H5Tvlen_create: ", atype_int_id >= 0);
}
catch (Exception err) {
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_int_id = H5.H5Acreate(H5did, attr_int_name, atype_int_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AVLwr: ", attr_int_id >= 0);
H5.H5AwriteVL(attr_int_id, atype_int_id, vl_int_data);
}
catch (Exception err) {
if (attr_int_id > 0)
try {
H5.H5Aclose(attr_int_id);
}
catch (Exception ex) {
}
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
// Write Double data
vl_dbl_data[0] = new ArrayList<Double>(Arrays.asList(1.1));
vl_dbl_data[1] = new ArrayList<Double>(Arrays.asList(2.2, 3.3));
vl_dbl_data[2] = new ArrayList<Double>(Arrays.asList(4.4, 5.5, 6.6));
vl_dbl_data[3] = new ArrayList<Double>(Arrays.asList(7.7, 8.8, 9.9, 10.0));
dataClass = vl_dbl_data.getClass();
assertTrue("testH5AVLwr.getClass: " + dataClass, dataClass.isArray());
try {
atype_dbl_id = H5.H5Tvlen_create(HDF5Constants.H5T_NATIVE_DOUBLE);
assertTrue("testH5AVLwr.H5Tvlen_create: ", atype_dbl_id >= 0);
}
catch (Exception err) {
if (atype_dbl_id > 0)
try {
H5.H5Tclose(atype_dbl_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_dbl_id = H5.H5Acreate(H5did, attr_dbl_name, atype_dbl_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AVLwr: ", attr_dbl_id >= 0);
H5.H5AwriteVL(attr_dbl_id, atype_dbl_id, vl_dbl_data);
}
catch (Exception err) {
if (attr_dbl_id > 0)
try {
H5.H5Aclose(attr_dbl_id);
}
catch (Exception ex) {
}
if (atype_dbl_id > 0)
try {
H5.H5Tclose(atype_dbl_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwr: " + 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 Integer data
ArrayList[] vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<Integer>();
try {
H5.H5AreadVL(attr_int_id, atype_int_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5AVLwr:" + vl_readbuf[0].get(0),
vl_int_data[0].get(0).equals(vl_readbuf[0].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[1].get(0),
vl_int_data[1].get(0).equals(vl_readbuf[1].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[2].get(0),
vl_int_data[2].get(0).equals(vl_readbuf[2].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[3].get(0),
vl_int_data[3].get(0).equals(vl_readbuf[3].get(0)));
// Read Double data
vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<Double>();
try {
H5.H5AreadVL(attr_dbl_id, atype_dbl_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5AVLwr:" + vl_readbuf[0].get(0),
vl_dbl_data[0].get(0).equals(vl_readbuf[0].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[1].get(0),
vl_dbl_data[1].get(0).equals(vl_readbuf[1].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[2].get(0),
vl_dbl_data[2].get(0).equals(vl_readbuf[2].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[3].get(0),
vl_dbl_data[3].get(0).equals(vl_readbuf[3].get(0)));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
finally {
if (attr_dbl_id > 0)
try {
H5.H5Aclose(attr_dbl_id);
}
catch (Exception ex) {
}
if (attr_int_id > 0)
try {
H5.H5Aclose(attr_int_id);
}
catch (Exception ex) {
}
if (atype_dbl_id > 0)
try {
H5.H5Tclose(atype_dbl_id);
}
catch (Exception ex) {
}
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
}
}
}
java/test/TestH5D.java
+219 -2
View File
@@ -17,6 +17,9 @@ 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;
@@ -961,8 +964,8 @@ public class TestH5D {
assertTrue("H5Dvlen_get_buf_size " + vl_size + " == " + str_data_bytes, vl_size == str_data_bytes);
}
@Test(expected = IllegalArgumentException.class)
public void testH5Dvlen_read_invalid_buffer() throws Throwable
@Test
public void testH5Dvlen_read_default_buffer() throws Throwable
{
String[] str_data = {"Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.",
"Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!",
@@ -1013,4 +1016,218 @@ public class TestH5D {
assertTrue("testH5Dvlen_write_read " + str_wdata[v] + " == " + str_rdata[v],
str_wdata[v] == str_wdata[v]);
}
@Test
public void testH5DVLwr()
{
String dset_int_name = "VLIntdata";
String dset_dbl_name = "VLDbldata";
long dset_int_id = HDF5Constants.H5I_INVALID_HID;
long dset_dbl_id = HDF5Constants.H5I_INVALID_HID;
long dtype_int_id = HDF5Constants.H5I_INVALID_HID;
long dtype_dbl_id = HDF5Constants.H5I_INVALID_HID;
long dspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
ArrayList[] vl_int_data = new ArrayList[4];
ArrayList[] vl_dbl_data = new ArrayList[4];
try {
// Write Integer data
vl_int_data[0] = new ArrayList<Integer>(Arrays.asList(1));
vl_int_data[1] = new ArrayList<Integer>(Arrays.asList(2, 3));
vl_int_data[2] = new ArrayList<Integer>(Arrays.asList(4, 5, 6));
vl_int_data[3] = new ArrayList<Integer>(Arrays.asList(7, 8, 9, 10));
Class dataClass = vl_int_data.getClass();
assertTrue("testH5DVLwr.getClass: " + dataClass, dataClass.isArray());
try {
dtype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
assertTrue("testH5DVLwr.H5Tvlen_create: ", dtype_int_id >= 0);
}
catch (Exception err) {
if (dtype_int_id > 0)
try {
H5.H5Tclose(dtype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5DVLwr: " + err);
}
try {
dspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(dspace_id > 0);
dset_int_id =
H5.H5Dcreate(H5fid, dset_int_name, dtype_int_id, dspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5DVLwr: ", dset_int_id >= 0);
H5.H5DwriteVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_int_data);
}
catch (Exception err) {
if (dset_int_id > 0)
try {
H5.H5Dclose(dset_int_id);
}
catch (Exception ex) {
}
if (dtype_int_id > 0)
try {
H5.H5Tclose(dtype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5DVLwr: " + err);
}
finally {
if (dspace_id > 0)
try {
H5.H5Sclose(dspace_id);
}
catch (Exception ex) {
}
}
// Write Double data
vl_dbl_data[0] = new ArrayList<Double>(Arrays.asList(1.1));
vl_dbl_data[1] = new ArrayList<Double>(Arrays.asList(2.2, 3.3));
vl_dbl_data[2] = new ArrayList<Double>(Arrays.asList(4.4, 5.5, 6.6));
vl_dbl_data[3] = new ArrayList<Double>(Arrays.asList(7.7, 8.8, 9.9, 10.0));
dataClass = vl_dbl_data.getClass();
assertTrue("testH5DVLwr.getClass: " + dataClass, dataClass.isArray());
try {
dtype_dbl_id = H5.H5Tvlen_create(HDF5Constants.H5T_NATIVE_DOUBLE);
assertTrue("testH5DVLwr.H5Tvlen_create: ", dtype_dbl_id >= 0);
}
catch (Exception err) {
if (dtype_dbl_id > 0)
try {
H5.H5Tclose(dtype_dbl_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5DVLwr: " + err);
}
try {
dspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(dspace_id > 0);
dset_dbl_id =
H5.H5Dcreate(H5fid, dset_dbl_name, dtype_dbl_id, dspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5DVLwr: ", dset_dbl_id >= 0);
H5.H5DwriteVL(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_dbl_data);
}
catch (Exception err) {
if (dset_dbl_id > 0)
try {
H5.H5Dclose(dset_dbl_id);
}
catch (Exception ex) {
}
if (dtype_dbl_id > 0)
try {
H5.H5Tclose(dtype_dbl_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5DVLwr: " + 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 Integer data
ArrayList[] vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<Integer>();
try {
H5.H5DreadVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5DVLwr:" + vl_readbuf[0].get(0),
vl_int_data[0].get(0).equals(vl_readbuf[0].get(0)));
assertTrue("testH5DVLwr:" + vl_readbuf[1].get(0),
vl_int_data[1].get(0).equals(vl_readbuf[1].get(0)));
assertTrue("testH5DVLwr:" + vl_readbuf[2].get(0),
vl_int_data[2].get(0).equals(vl_readbuf[2].get(0)));
assertTrue("testH5DVLwr:" + vl_readbuf[3].get(0),
vl_int_data[3].get(0).equals(vl_readbuf[3].get(0)));
// Read Double data
vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<Double>();
try {
H5.H5DreadVL(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5DVLwr:" + vl_readbuf[0].get(0),
vl_dbl_data[0].get(0).equals(vl_readbuf[0].get(0)));
assertTrue("testH5DVLwr:" + vl_readbuf[1].get(0),
vl_dbl_data[1].get(0).equals(vl_readbuf[1].get(0)));
assertTrue("testH5DVLwr:" + vl_readbuf[2].get(0),
vl_dbl_data[2].get(0).equals(vl_readbuf[2].get(0)));
assertTrue("testH5DVLwr:" + vl_readbuf[3].get(0),
vl_dbl_data[3].get(0).equals(vl_readbuf[3].get(0)));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5DVLwr: " + err);
}
finally {
if (dset_dbl_id > 0)
try {
H5.H5Dclose(dset_dbl_id);
}
catch (Exception ex) {
}
if (dset_int_id > 0)
try {
H5.H5Dclose(dset_int_id);
}
catch (Exception ex) {
}
if (dtype_dbl_id > 0)
try {
H5.H5Tclose(dtype_dbl_id);
}
catch (Exception ex) {
}
if (dtype_int_id > 0)
try {
H5.H5Tclose(dtype_int_id);
}
catch (Exception ex) {
}
}
}
}
java/test/TestH5R.java
+469
View File
@@ -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) {
}
}
}
}
java/test/testfiles/JUnit-TestH5A.txt
+2 -1
View File
@@ -6,6 +6,7 @@ JUnit version 4.11
.testH5Aiterate
.testH5Aopen_by_idx
.testH5Aopen_invalidname
.testH5AVLwr
.testH5Aopen
.testH5Aget_info_by_name
.testH5Aget_create_plist
@@ -30,5 +31,5 @@ JUnit version 4.11
Time: XXXX
OK (28 tests)
OK (29 tests)
java/test/testfiles/JUnit-TestH5D.txt
+3 -2
View File
@@ -4,6 +4,7 @@ JUnit version 4.11
.testH5Dcreate
.testH5Dget_offset
.testH5Dget_type
.testH5DVLwr
.testH5Dfill
.testH5Dopen
.testH5Dcreate_anon
@@ -11,15 +12,15 @@ JUnit version 4.11
.testH5Dget_storage_size_empty
.testH5Diterate
.testH5Dget_access_plist
.testH5Dvlen_read_invalid_buffer
.testH5Dvlen_get_buf_size
.testH5Dget_space_closed
.testH5Dget_space_status
.testH5Dvlen_write_read
.testH5Dget_space
.testH5Dget_type_closed
.testH5Dvlen_read_default_buffer
Time: XXXX
OK (19 tests)
OK (20 tests)
java/test/testfiles/JUnit-TestH5R.txt
+3 -1
View File
@@ -4,6 +4,8 @@ JUnit version 4.11
.testH5Ropen_region_Nullref
.testH5Requal_Nullref1
.testH5Requal_Nullref2
.testH5RVLdset_ref
.testH5RVLattr_ref
.testH5Rget_object
.testH5Rget_obj_type3_Nullref
.testH5Ropen_object_Nullref
@@ -24,5 +26,5 @@ JUnit version 4.11
Time: XXXX
OK (22 tests)
OK (24 tests)