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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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243
java/test/TestH5A.java
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) {
}
}
}
}