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JNI: Improve varlen datatype handling in H5A/H5D read/write functions (#2156)

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* Improve JNI VL datatype read/write to handle complex combinations

* Implement VL of VL JNI writes and reads

* Add Java VLofVL test for attributtes

* Changes to address review issues

* Fix H5Aread vl blocks
This commit is contained in:
Allen Byrne 2022-10-25 23:33:30 -05:00 committed by GitHub
parent ad2d77397a
commit 9c61f7b1e1
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GPG Key ID: 4AEE18F83AFDEB23
12 changed files with 1089 additions and 971 deletions
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574
java/src/jni/h5aImp.c
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@ -156,13 +156,15 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf,
jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
jbyte *readBuf = NULL;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean readBufIsCopy;
jbyte *readBuf = NULL;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
size_t typeSize;
H5T_class_t type_class;
jsize vl_array_len; // Only used by vl_data_class types
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@ -174,40 +176,60 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t
if (vl_data_class) {
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
}
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
}
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Aread: read buffer not critically pinned");
if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Aread: failed to allocate raw VL read buffer");
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Aread: read buffer not pinned");
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Aread: read buffer not critically pinned");
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Aread: read buffer not pinned");
}
}
if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (vl_data_class) {
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf);
}
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
dims[0] = (hsize_t)vl_array_len;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
if (sid >= 0)
H5Sclose(sid);
}
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
if (vl_data_class) {
HDfree(readBuf);
}
else {
UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
else {
UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
}
}
@ -223,38 +245,52 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf,
jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
jbyte *writeBuf = NULL;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean writeBufIsCopy;
jbyte *writeBuf = NULL;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
size_t typeSize;
H5T_class_t type_class;
jsize vl_array_len; // Only used by vl_data_class types
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer is NULL");
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
}
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite: write buffer not critically pinned");
if (vl_data_class) {
/* Get size of data array */
if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer length < 0");
}
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Awrite: failed to allocate raw VL write buffer");
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Awrite: write buffer not pinned");
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite: write buffer not critically pinned");
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Awrite: write buffer not pinned");
}
}
if (vl_data_class) {
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
}
if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0)
@ -262,14 +298,24 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
if ((status >= 0) && vl_data_class) {
dims[0] = (hsize_t)vl_array_len;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
}
if (vl_data_class) {
HDfree(writeBuf);
}
else {
UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
else {
UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
}
}
@ -1064,244 +1110,9 @@ done:
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
H5T_class_t type_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n = 0;
htri_t vl_data_class;
herr_t status = FAIL;
jbyteArray *readBuf = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: read buffer is NULL");
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (vl_data_class) {
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: readBuf length < 0");
}
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_VLEN) {
size_t typeSize;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
void *rawBuf = NULL;
jobjectArray jList = NULL;
size_t i, j, x;
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (!(memb = H5Tget_super(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AreadVL: failed to allocate raw VL read buffer");
if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)rawBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Cache class types */
/* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
/*
jmethodID boolValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
*/
jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
jmethodID shortValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
jmethodID floatValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
jmethodID doubleValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
// retrieve the java.util.List interface class
jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z");
/* Convert each element to a list */
for (i = 0; i < (size_t)n; i++) {
hvl_t vl_elem;
// The list we're going to return:
if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
/* Get the number of sequence elements */
HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
jsize nelmts = (jsize)vl_elem.len;
if (vl_elem.len != (size_t)nelmts)
H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadVL: overflow of number of VL elements");
if (nelmts < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: number of VL elements < 0");
jobject jobj = NULL;
for (j = 0; j < (size_t)nelmts; j++) {
switch (vlClass) {
/* case H5T_BOOL: {
jboolean boolValue;
for (x = 0; x < vlSize; x++) {
((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
} */
case H5T_INTEGER: {
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue;
for (x = 0; x < vlSize; x++) {
((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj =
ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jshort): {
jshort shortValue;
for (x = 0; x < vlSize; x++) {
((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
shortValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jint): {
jint intValue;
for (x = 0; x < vlSize; x++) {
((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jlong): {
jlong longValue;
for (x = 0; x < vlSize; x++) {
((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj =
ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
}
break;
}
case H5T_FLOAT: {
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue;
for (x = 0; x < vlSize; x++) {
((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
(double)floatValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jdouble): {
jdouble doubleValue;
for (x = 0; x < vlSize; x++) {
((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
doubleValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
}
break;
}
case H5T_REFERENCE: {
jboolean bb;
jbyte *barray = NULL;
jsize byteArraySize = (jsize)vlSize;
if (vlSize != (size_t)byteArraySize)
H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadVL: overflow of byteArraySize");
if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
"readVL reference: byte array not pinned");
for (x = 0; x < vlSize; x++) {
barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x];
}
if (barray)
UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "H5AreadVL: invalid class type");
break;
}
// Add it to the list
ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
} /* end for */
if (rawBuf)
HDfree(rawBuf);
}
else {
if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
if (sid >= 0)
H5Sclose(sid);
}
UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
status = Java_hdf_hdf5lib_H5_H5Aread(env, clss, attr_id, mem_type_id, (jbyteArray)buf, JNI_TRUE);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5AreadVL */
@ -1314,206 +1125,9 @@ done:
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
H5T_class_t type_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean writeBufIsCopy;
jbyteArray writeBuf = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL");
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: readBuf length < 0");
}
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_VLEN) {
size_t typeSize;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
void *rawBuf = NULL;
jobjectArray jList = NULL;
size_t i, j, x;
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (!(memb = H5Tget_super(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate raw VL write buffer");
/* Cache class types */
/* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
/* jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */
jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J");
jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F");
jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D");
/* Convert each list to a vlen element */
for (i = 0; i < (size_t)n; i++) {
hvl_t vl_elem;
if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
// retrieve the java.util.List interface class
jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
// retrieve the toArray method and invoke it
jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;");
if (mToArray == NULL)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
if (jnelmts < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: number of VL elements < 0");
HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
vl_elem.len = (size_t)jnelmts;
if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate vlen ptr buffer");
jobject jobj = NULL;
for (j = 0; j < (size_t)jnelmts; j++) {
if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
switch (vlClass) {
/* case H5T_BOOL: {
jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
}
break;
} */
case H5T_INTEGER: {
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x];
}
break;
}
case sizeof(jshort): {
jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x];
}
break;
}
case sizeof(jint): {
jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x];
}
break;
}
case sizeof(jlong): {
jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
}
break;
}
}
break;
}
case H5T_FLOAT: {
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x];
}
break;
}
case sizeof(jdouble): {
jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
}
break;
}
}
break;
}
case H5T_REFERENCE: {
jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
}
ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "H5AwriteVL: invalid class type");
break;
}
ENVPTR->DeleteLocalRef(ENVONLY, jobj);
}
HDmemcpy((char *)rawBuf + i * typeSize, &vl_elem, sizeof(hvl_t));
ENVPTR->DeleteLocalRef(ENVONLY, jList);
} /* end for (i = 0; i < n; i++) */
if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, rawBuf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (rawBuf)
HDfree(rawBuf);
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5AwriteVL: write buffer not pinned");
if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
if (type_class != H5T_VLEN)
UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
status = Java_hdf_hdf5lib_H5_H5Awrite(env, clss, attr_id, mem_type_id, (jbyteArray)buf, JNI_TRUE);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5AwriteVL */

547
java/src/jni/h5dImp.c
View File

@ -182,47 +182,71 @@ Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong me
jlong file_space_id, jlong xfer_plist_id, jbyteArray buf,
jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
jbyte *readBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean readBufIsCopy;
jbyte *readBuf = NULL;
size_t typeSize;
H5T_class_t type_class;
jsize vl_array_len; // Only used by vl_data_class types
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread: read buffer is NULL");
/* Get size of data array */
if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread: read buffer not critically pinned");
if (vl_data_class) {
/* Get size of data array */
if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
}
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread: failed to allocate raw VL read buffer");
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread: read buffer not pinned");
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread: read buffer not critically pinned");
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread: read buffer not pinned");
}
}
if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)xfer_plist_id, readBuf)) < 0)
(hid_t)xfer_plist_id, (void *)readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (vl_data_class) {
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf);
}
done:
if (readBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
if (vl_data_class) {
HDfree(readBuf);
}
else {
UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
else {
UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
}
}
@ -239,31 +263,50 @@ Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong m
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jbyteArray buf,
jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
jbyte *writeBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean writeBufIsCopy;
jbyte *writeBuf = NULL;
size_t typeSize;
H5T_class_t type_class;
jsize vl_array_len; // Only used by vl_data_class types
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer is NULL");
/* Get size of data array */
if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite: write buffer not critically pinned");
if (vl_data_class) {
/* Get size of data array */
if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer length < 0");
}
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dwrite: failed to allocate raw VL write buffer");
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite: write buffer not pinned");
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite: write buffer not critically pinned");
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite: write buffer not pinned");
}
}
if (vl_data_class) {
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
}
if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
@ -275,11 +318,16 @@ done:
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
if (vl_data_class) {
HDfree(writeBuf);
}
else {
UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
else {
UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
}
}
@ -1087,235 +1135,10 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
{
H5T_class_t type_class;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
jbyteArray *readBuf = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL");
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: readBuf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_VLEN) {
size_t typeSize;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
void *rawBuf = NULL;
jobjectArray jList = NULL;
size_t i, j, x;
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (!(memb = H5Tget_super(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer");
if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)rawBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Cache class types */
/* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
/*
jmethodID boolValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
*/
jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
jmethodID shortValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
jmethodID floatValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
jmethodID doubleValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
// retrieve the java.util.List interface class
jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z");
/* Convert each element to a list */
for (i = 0; i < (size_t)n; i++) {
hvl_t vl_elem;
// The list we're going to return:
if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
/* Get the number of sequence elements */
HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
jsize nelmts = (jsize)vl_elem.len;
if (vl_elem.len != (size_t)nelmts)
H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of number of VL elements");
if (nelmts < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: number of VL elements < 0");
jobject jobj = NULL;
for (j = 0; j < (size_t)nelmts; j++) {
switch (vlClass) {
/*case H5T_BOOL: {
jboolean boolValue;
for (x = 0; x < vlSize; x++) {
((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
} */
case H5T_INTEGER: {
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue;
for (x = 0; x < vlSize; x++) {
((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj =
ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jshort): {
jshort shortValue;
for (x = 0; x < vlSize; x++) {
((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
shortValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jint): {
jint intValue;
for (x = 0; x < vlSize; x++) {
((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jlong): {
jlong longValue;
for (x = 0; x < vlSize; x++) {
((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj =
ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
}
break;
}
case H5T_FLOAT: {
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue;
for (x = 0; x < vlSize; x++) {
((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
(double)floatValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jdouble): {
jdouble doubleValue;
for (x = 0; x < vlSize; x++) {
((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
doubleValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
}
break;
}
case H5T_REFERENCE: {
jboolean bb;
jbyte *barray = NULL;
jsize byteArraySize = (jsize)vlSize;
if (vlSize != (size_t)byteArraySize)
H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of byteArraySize");
if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
"readVL reference: byte array not pinned");
for (x = 0; x < vlSize; x++) {
barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x];
}
if (barray)
UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "H5DreadVL: invalid class type");
break;
}
// Add it to the list
ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
} /* end for */
if (rawBuf)
HDfree(rawBuf);
}
else {
if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
done:
if (readBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
status = Java_hdf_hdf5lib_H5_H5Dread(env, clss, dataset_id, mem_type_id, mem_space_id, file_space_id,
xfer_plist_id, (jbyteArray)buf, JNI_TRUE);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5DreadVL */
@ -1329,202 +1152,10 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
{
H5T_class_t type_class;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean writeBufIsCopy;
jbyteArray writeBuf = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL");
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: readBuf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_VLEN) {
size_t typeSize;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
void *rawBuf = NULL;
jobjectArray jList = NULL;
size_t i, j, x;
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (!(memb = H5Tget_super(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer");
/* Cache class types */
/* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
/* jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */
jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J");
jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F");
jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D");
/* Convert each list to a vlen element */
for (i = 0; i < (size_t)n; i++) {
hvl_t vl_elem;
if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
// retrieve the java.util.List interface class
jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
// retrieve the toArray method and invoke it
jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;");
if (mToArray == NULL)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
if (jnelmts < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: number of VL elements < 0");
HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
vl_elem.len = (size_t)jnelmts;
if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate vlen ptr buffer");
jobject jobj = NULL;
for (j = 0; j < (size_t)jnelmts; j++) {
if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
switch (vlClass) {
/* case H5T_BOOL: {
jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
}
break;
} */
case H5T_INTEGER: {
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x];
}
break;
}
case sizeof(jshort): {
jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x];
}
break;
}
case sizeof(jint): {
jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x];
}
break;
}
case sizeof(jlong): {
jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
}
break;
}
}
break;
}
case H5T_FLOAT: {
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x];
}
break;
}
case sizeof(jdouble): {
jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
}
break;
}
}
break;
}
case H5T_REFERENCE: {
jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
}
ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "H5DwriteVL: invalid class type");
break;
}
ENVPTR->DeleteLocalRef(ENVONLY, jobj);
}
HDmemcpy((char *)rawBuf + i * typeSize, &vl_elem, sizeof(hvl_t));
ENVPTR->DeleteLocalRef(ENVONLY, jList);
} /* end for (i = 0; i < n; i++) */
if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, rawBuf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (rawBuf)
HDfree(rawBuf);
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5DwriteVL: write buffer not pinned");
if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, writeBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
if (type_class != H5T_VLEN)
UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
status = Java_hdf_hdf5lib_H5_H5Dwrite(env, clss, dataset_id, mem_type_id, mem_space_id, file_space_id,
xfer_plist_id, (jbyteArray)buf, JNI_TRUE);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5DwriteVL */

4
java/src/jni/h5fImp.c
View File

@ -742,7 +742,7 @@ Java_hdf_hdf5lib_H5_H5Fset_1dset_1no_1attrs_1hint(JNIEnv *env, jclass clss, jlon
done:
return;
}
} /* end Java_hdf_hdf5lib_H5_H5Fset_1dset_1no_1attrs_1hint */
/*
* Class: hdf_hdf5lib_H5
@ -765,7 +765,7 @@ Java_hdf_hdf5lib_H5_H5Fget_1dset_1no_1attrs_1hint(JNIEnv *env, jclass clss, jlon
done:
return bval;
}
} /* end Java_hdf_hdf5lib_H5_H5Fget_1dset_1no_1attrs_1hint */
/*
* Class: hdf_hdf5lib_H5

4
java/src/jni/h5tImp.c
View File

@ -1688,7 +1688,7 @@ Java_hdf_hdf5lib_H5_H5Tflush(JNIEnv *env, jclass clss, jlong loc_id)
done:
return;
}
} /* end Java_hdf_hdf5lib_H5_H5Tflush */
/*
* Class: hdf_hdf5lib_H5
@ -1705,7 +1705,7 @@ Java_hdf_hdf5lib_H5_H5Trefresh(JNIEnv *env, jclass clss, jlong loc_id)
done:
return;
}
} /* end Java_hdf_hdf5lib_H5_H5Trefresh */
#ifdef __cplusplus
} /* end extern "C" */

545
java/src/jni/h5util.c
View File

@ -4043,6 +4043,551 @@ done:
H5Aclose(attr_id);
} /* end Java_hdf_hdf5lib_H5_H5export_1attribute */
herr_t
translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, jsize count,
jbyte *raw_buf)
{
herr_t status = FAIL;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
jobjectArray jList = NULL;
size_t i, j, x;
/* retrieve the java.util.ArrayList interface class */
jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList");
jmethodID arrListMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "<init>", "(I)V");
jmethodID arrAddMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "add", "(Ljava/lang/Object;)Z");
/* Cache class types */
/* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
/*jobjectArray
jmethodID boolValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
*/
jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
jmethodID shortValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
jmethodID floatValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
jmethodID doubleValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
if (type_class == H5T_VLEN) {
if (!(memb = H5Tget_super(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((vlClass = H5Tget_class(memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
/* Convert each element to a list */
for (i = 0; i < (size_t)count; i++) {
hvl_t vl_elem;
jboolean found_jList = JNI_TRUE;
/* Get the number of sequence elements */
HDmemcpy(&vl_elem, (char *)raw_buf + i * sizeof(hvl_t), sizeof(hvl_t));
jsize nelmts = (jsize)vl_elem.len;
if (vl_elem.len != (size_t)nelmts)
H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: overflow of number of VL elements");
if (nelmts < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_rbuf: number of VL elements < 0");
/* The list we're going to return: */
if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i))) {
found_jList = JNI_FALSE;
if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_rbuf: failed to allocate list read buffer");
}
if ((vlClass == H5T_ARRAY) || (vlClass == H5T_COMPOUND) || (vlClass == H5T_VLEN))
translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)nelmts, vl_elem.p);
else {
jobject jobj = NULL;
for (j = 0; j < (size_t)nelmts; j++) {
switch (vlClass) {
/*case H5T_BOOL: {
jboolean boolValue;
for (x = 0; x < vlSize; x++) {
((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
} */
case H5T_INTEGER: {
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue;
for (x = 0; x < vlSize; x++) {
((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid,
byteValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jshort): {
jshort shortValue;
for (x = 0; x < vlSize; x++) {
((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
shortValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jint): {
jint intValue;
for (x = 0; x < vlSize; x++) {
((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj =
ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
break;
}
case sizeof(jlong): {
jlong longValue;
for (x = 0; x < vlSize; x++) {
((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid,
longValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
}
break;
}
case H5T_FLOAT: {
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue;
for (x = 0; x < vlSize; x++) {
((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
(double)floatValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jdouble): {
jdouble doubleValue;
for (x = 0; x < vlSize; x++) {
((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
doubleValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
}
break;
}
case H5T_REFERENCE: {
jboolean bb;
jbyte *barray = NULL;
jsize byteArraySize = (jsize)vlSize;
if (vlSize != (size_t)byteArraySize)
H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: overflow of byteArraySize");
if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
"read(translate_buf) reference: byte array not pinned");
for (x = 0; x < vlSize; x++) {
barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x];
}
if (barray)
UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "translate_rbuf: invalid class type");
break;
}
/* Add it to the list */
if (jobj) {
ENVPTR->CallBooleanMethod(ENVONLY, jList, arrAddMethod, jobj);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
ENVPTR->DeleteLocalRef(ENVONLY, jobj);
}
}
if (!found_jList) {
ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
ENVPTR->DeleteLocalRef(ENVONLY, jList);
}
}
}
}
else if (type_class == H5T_COMPOUND) {
int nmembs = H5Tget_nmembers(mem_type_id);
void *objBuf = NULL;
size_t offset;
if (nmembs < 0)
goto done;
/* Convert each element to a list */
for (i = 0; i < (size_t)nmembs; i++) {
jboolean found_jList = JNI_TRUE;
if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)i)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
offset = H5Tget_member_offset(mem_type_id, (unsigned int)i);
if ((vlClass = H5Tget_class(memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
/* Get the object element */
HDmemcpy(&objBuf, (char *)raw_buf + offset, vlSize);
/* The list we're going to return: */
if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i))) {
found_jList = JNI_FALSE;
if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_rbuf: failed to allocate list read buffer");
}
if ((vlClass == H5T_ARRAY) || (vlClass == H5T_COMPOUND) || (vlClass == H5T_VLEN))
translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)1, objBuf);
else {
jobject jobj = NULL;
switch (vlClass) {
/*case H5T_BOOL: {
jboolean boolValue;
for (x = 0; x < vlSize; x++) {
((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
} */
case H5T_INTEGER: {
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue;
for (x = 0; x < vlSize; x++) {
((char *)&byteValue)[x] = ((char *)objBuf)[vlSize + x];
}
jobj =
ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jshort): {
jshort shortValue;
for (x = 0; x < vlSize; x++) {
((char *)&shortValue)[x] = ((char *)objBuf)[vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
shortValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jint): {
jint intValue;
for (x = 0; x < vlSize; x++) {
((char *)&intValue)[x] = ((char *)objBuf)[vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jlong): {
jlong longValue;
for (x = 0; x < vlSize; x++) {
((char *)&longValue)[x] = ((char *)objBuf)[vlSize + x];
}
jobj =
ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
}
break;
}
case H5T_FLOAT: {
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue;
for (x = 0; x < vlSize; x++) {
((char *)&floatValue)[x] = ((char *)objBuf)[vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
(double)floatValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jdouble): {
jdouble doubleValue;
for (x = 0; x < vlSize; x++) {
((char *)&doubleValue)[x] = ((char *)objBuf)[vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
doubleValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
}
break;
}
case H5T_REFERENCE: {
jboolean bb;
jbyte *barray = NULL;
jsize byteArraySize = (jsize)vlSize;
if (vlSize != (size_t)byteArraySize)
H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: overflow of byteArraySize");
if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
"translate_rbuf reference: byte array not pinned");
for (x = 0; x < vlSize; x++) {
barray[x] = ((jbyte *)objBuf)[vlSize + x];
}
if (barray)
UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "translate_rbuf: invalid class type");
break;
}
/* Add it to the list */
if (jobj) {
ENVPTR->CallBooleanMethod(ENVONLY, jList, arrAddMethod, jobj);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
ENVPTR->DeleteLocalRef(ENVONLY, jobj);
}
}
if (!found_jList) {
ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
ENVPTR->DeleteLocalRef(ENVONLY, jList);
}
}
H5Tclose(memb);
}
else if (type_class == H5T_ARRAY) {
if (!(memb = H5Tget_super(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((vlClass = H5Tget_class(memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
// TODO
H5_UNIMPLEMENTED(ENVONLY, "translate_rbuf: invalid H5T_ARRAY type");
}
done:
return (jint)status;
}
herr_t
translate_wbuf(JNIEnv *env, jobjectArray in_buf, jlong mem_type_id, H5T_class_t type_class, jsize count,
jbyte *raw_buf)
{
herr_t status = FAIL;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
jobjectArray jList = NULL;
size_t i, j, x;
/* retrieve the java.util.ArrayList interface class */
jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList");
/* retrieve the toArray method */
jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, arrCList, "toArray", "()[Ljava/lang/Object;");
/* Cache class types */
/* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
/* jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */
jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J");
jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F");
jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D");
if (type_class == H5T_VLEN) {
if (!(memb = H5Tget_super(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
/* Convert each list to a vlen element */
for (i = 0; i < (size_t)count; i++) {
hvl_t vl_elem;
if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
/* invoke the toArray method */
if (mToArray == NULL)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
if (jnelmts < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_wbuf: number of VL elements < 0");
vl_elem.len = (size_t)jnelmts;
if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_wbuf: failed to allocate vlen ptr buffer");
if ((vlClass == H5T_ARRAY) || (vlClass == H5T_COMPOUND) || (vlClass == H5T_VLEN))
translate_wbuf(ENVONLY, (jobjectArray)array, memb, vlClass, (jsize)jnelmts, vl_elem.p);
else {
jobject jobj = NULL;
for (j = 0; j < (size_t)jnelmts; j++) {
if (NULL ==
(jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
switch (vlClass) {
/* case H5T_BOOL: {
jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
}
break;
} */
case H5T_INTEGER: {
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x];
}
break;
}
case sizeof(jshort): {
jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x];
}
break;
}
case sizeof(jint): {
jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x];
}
break;
}
case sizeof(jlong): {
jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
}
break;
}
}
break;
}
case H5T_FLOAT: {
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x];
}
break;
}
case sizeof(jdouble): {
jdouble doubleValue =
ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
}
break;
}
}
break;
}
case H5T_REFERENCE: {
jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
for (x = 0; x < vlSize; x++) {
((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
}
ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "translate_wbuf: invalid class type");
break;
}
ENVPTR->DeleteLocalRef(ENVONLY, jobj);
}
}
HDmemcpy((char *)raw_buf + i * sizeof(hvl_t), &vl_elem, sizeof(hvl_t));
ENVPTR->DeleteLocalRef(ENVONLY, jList);
} /* end for (i = 0; i < count; i++) */
}
else if (type_class == H5T_COMPOUND) {
// TODO
H5_UNIMPLEMENTED(ENVONLY, "translate_wbuf: invalid H5T_COMPOUND type");
}
else if (type_class == H5T_ARRAY) {
if (!(memb = H5Tget_super(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((vlClass = H5Tget_class(memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
// TODO
H5_UNIMPLEMENTED(ENVONLY, "translate_wbuf: invalid H5T_ARRAY type");
}
done:
return (jint)status;
}
#ifdef __cplusplus
}
#endif

5
java/src/jni/h5util.h
View File

@ -52,6 +52,11 @@ extern int h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr, int b
extern htri_t H5Tdetect_variable_str(hid_t tid);
extern herr_t translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class,
jsize count, jbyte *raw_buf);
extern herr_t translate_wbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class,
jsize count, jbyte *raw_buf);
/*
* Symbols used to format the output of h5str_sprintf and
* to interpret the input to h5str_convert.

161
java/test/TestH5A.java
View File

@ -1415,7 +1415,7 @@ public class TestH5A {
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AVLwr: ", attr_int_id >= 0);
H5.H5AwriteVL(attr_int_id, atype_int_id, vl_int_data);
H5.H5Awrite(attr_int_id, atype_int_id, vl_int_data);
}
catch (Exception err) {
if (attr_int_id > 0)
@ -1472,7 +1472,7 @@ public class TestH5A {
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AVLwr: ", attr_dbl_id >= 0);
H5.H5AwriteVL(attr_dbl_id, atype_dbl_id, vl_dbl_data);
H5.H5Awrite(attr_dbl_id, atype_dbl_id, vl_dbl_data);
}
catch (Exception err) {
if (attr_dbl_id > 0)
@ -1511,7 +1511,7 @@ public class TestH5A {
vl_readbuf[j] = new ArrayList<Integer>();
try {
H5.H5AreadVL(attr_int_id, atype_int_id, vl_readbuf);
H5.H5Aread(attr_int_id, atype_int_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
@ -1531,7 +1531,7 @@ public class TestH5A {
vl_readbuf[j] = new ArrayList<Double>();
try {
H5.H5AreadVL(attr_dbl_id, atype_dbl_id, vl_readbuf);
H5.H5Aread(attr_dbl_id, atype_dbl_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
@ -1576,4 +1576,157 @@ public class TestH5A {
}
}
}
@Test
public void testH5AVLwrVL()
{
String attr_int_name = "VLIntdata";
long attr_int_id = HDF5Constants.H5I_INVALID_HID;
long atype_int_id = HDF5Constants.H5I_INVALID_HID;
long base_atype_int_id = HDF5Constants.H5I_INVALID_HID;
long aspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
ArrayList[] base_vl_int_data = new ArrayList[4];
ArrayList[] vl_int_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("testH5AVLwrVL.getClass: " + dataClass, dataClass.isArray());
// Write VL data
base_vl_int_data[0] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[0].add(vl_int_data[0]);
base_vl_int_data[1] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[1].add(vl_int_data[0]);
base_vl_int_data[1].add(vl_int_data[1]);
base_vl_int_data[2] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[2].add(vl_int_data[0]);
base_vl_int_data[2].add(vl_int_data[1]);
base_vl_int_data[2].add(vl_int_data[2]);
base_vl_int_data[3] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[3].add(vl_int_data[0]);
base_vl_int_data[3].add(vl_int_data[1]);
base_vl_int_data[3].add(vl_int_data[2]);
base_vl_int_data[3].add(vl_int_data[3]);
try {
atype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
assertTrue("testH5AVLwr.H5Tvlen_create: ", atype_int_id >= 0);
base_atype_int_id = H5.H5Tvlen_create(atype_int_id);
assertTrue("testH5AVLwrVL.H5Tvlen_create: ", base_atype_int_id >= 0);
}
catch (Exception err) {
if (base_atype_int_id > 0)
try {
H5.H5Tclose(base_atype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwrVL: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_int_id = H5.H5Acreate(H5did, attr_int_name, base_atype_int_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AVLwrVL: ", attr_int_id >= 0);
H5.H5Awrite(attr_int_id, base_atype_int_id, base_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.testH5AVLwrVL: " + 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[] base_vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
base_vl_readbuf[j] = new ArrayList<ArrayList<Integer>>();
try {
H5.H5Aread(attr_int_id, base_atype_int_id, base_vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
ArrayList vl_readbuf = (ArrayList)base_vl_readbuf[0];
assertTrue("vl_readbuf exists", vl_readbuf != null);
assertTrue("vl_readbuf has size " + vl_readbuf.size(), vl_readbuf.size() > 0);
ArrayList vl_readbuf_int = (ArrayList)vl_readbuf.get(0);
assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(0),
vl_int_data[0].get(0).equals(vl_readbuf_int.get(0)));
vl_readbuf = (ArrayList)base_vl_readbuf[1];
vl_readbuf_int = (ArrayList)vl_readbuf.get(1);
assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(0),
vl_int_data[1].get(0).equals(vl_readbuf_int.get(0)));
vl_readbuf = (ArrayList)base_vl_readbuf[2];
vl_readbuf_int = (ArrayList)vl_readbuf.get(2);
assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(0),
vl_int_data[2].get(0).equals(vl_readbuf_int.get(0)));
vl_readbuf = (ArrayList)base_vl_readbuf[3];
vl_readbuf_int = (ArrayList)vl_readbuf.get(3);
assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(0),
vl_int_data[3].get(0).equals(vl_readbuf_int.get(0)));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5AVLwrVL: " + err);
}
finally {
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) {
}
if (base_atype_int_id > 0)
try {
H5.H5Tclose(base_atype_int_id);
}
catch (Exception ex) {
}
}
}
}

181
java/test/TestH5D.java
View File

@ -1064,8 +1064,8 @@ public class TestH5D {
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);
H5.H5Dwrite(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)
@ -1123,8 +1123,8 @@ public class TestH5D {
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);
H5.H5Dwrite(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)
@ -1153,9 +1153,8 @@ public class TestH5D {
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
for (int j = 0; j < dims.length; j++) {
for (int j = 0; j < dims.length; j++)
lsize *= dims[j];
}
// Read Integer data
ArrayList[] vl_readbuf = new ArrayList[4];
@ -1163,8 +1162,8 @@ public class TestH5D {
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);
H5.H5Dread(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
@ -1184,8 +1183,8 @@ public class TestH5D {
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);
H5.H5Dread(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
@ -1230,4 +1229,166 @@ public class TestH5D {
}
}
}
@Test
public void testH5DVLwrVL()
{
String dset_int_name = "VLIntdata";
long dset_int_id = HDF5Constants.H5I_INVALID_HID;
long dtype_int_id = HDF5Constants.H5I_INVALID_HID;
long base_dtype_int_id = HDF5Constants.H5I_INVALID_HID;
long dspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
ArrayList[] base_vl_int_data = new ArrayList[4];
ArrayList[] vl_int_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("testH5DVLwrVL.getClass: " + dataClass, dataClass.isArray());
// Write VL data
base_vl_int_data[0] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[0].add(vl_int_data[0]);
base_vl_int_data[1] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[1].add(vl_int_data[0]);
base_vl_int_data[1].add(vl_int_data[1]);
base_vl_int_data[2] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[2].add(vl_int_data[0]);
base_vl_int_data[2].add(vl_int_data[1]);
base_vl_int_data[2].add(vl_int_data[2]);
base_vl_int_data[3] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[3].add(vl_int_data[0]);
base_vl_int_data[3].add(vl_int_data[1]);
base_vl_int_data[3].add(vl_int_data[2]);
base_vl_int_data[3].add(vl_int_data[3]);
try {
dtype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
assertTrue("testH5DVLwrVL.H5Tvlen_create: ", dtype_int_id >= 0);
base_dtype_int_id = H5.H5Tvlen_create(dtype_int_id);
assertTrue("testH5DVLwrVL.H5Tvlen_create: ", base_dtype_int_id >= 0);
}
catch (Exception err) {
if (base_dtype_int_id > 0)
try {
H5.H5Tclose(base_dtype_int_id);
}
catch (Exception ex) {
}
if (dtype_int_id > 0)
try {
H5.H5Tclose(dtype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5DVLwrVL: " + err);
}
try {
dspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(dspace_id > 0);
dset_int_id = H5.H5Dcreate(H5fid, dset_int_name, base_dtype_int_id, dspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
assertTrue("testH5DVLwrVL: ", dset_int_id >= 0);
H5.H5Dwrite(dset_int_id, base_dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, base_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.testH5DVLwrVL: " + 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[] base_vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
base_vl_readbuf[j] = new ArrayList<ArrayList<Integer>>();
try {
H5.H5Dread(dset_int_id, base_dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, base_vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
ArrayList vl_readbuf = (ArrayList)base_vl_readbuf[0];
assertTrue("vl_readbuf exists", vl_readbuf != null);
assertTrue("vl_readbuf has size " + vl_readbuf.size(), vl_readbuf.size() > 0);
ArrayList vl_readbuf_int = (ArrayList)vl_readbuf.get(0);
assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(0),
vl_int_data[0].get(0).equals(vl_readbuf_int.get(0)));
vl_readbuf = (ArrayList)base_vl_readbuf[1];
vl_readbuf_int = (ArrayList)vl_readbuf.get(1);
assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(0),
vl_int_data[1].get(0).equals(vl_readbuf_int.get(0)));
vl_readbuf = (ArrayList)base_vl_readbuf[2];
vl_readbuf_int = (ArrayList)vl_readbuf.get(2);
assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(0),
vl_int_data[2].get(0).equals(vl_readbuf_int.get(0)));
vl_readbuf = (ArrayList)base_vl_readbuf[3];
vl_readbuf_int = (ArrayList)vl_readbuf.get(3);
assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(0),
vl_int_data[3].get(0).equals(vl_readbuf_int.get(0)));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5DVLwrVL: " + err);
}
finally {
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) {
}
if (base_dtype_int_id > 0)
try {
H5.H5Tclose(base_dtype_int_id);
}
catch (Exception ex) {
}
}
}
}

24
java/test/TestH5R.java
View File

@ -600,7 +600,7 @@ public class TestH5R {
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLattr_ref: ", attr_obj_id >= 0);
H5.H5AwriteVL(attr_obj_id, atype_obj_id, vl_obj_data);
H5.H5Awrite(attr_obj_id, atype_obj_id, vl_obj_data);
}
catch (Exception err) {
if (attr_obj_id > 0)
@ -657,7 +657,7 @@ public class TestH5R {
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLattr_ref: ", attr_reg_id >= 0);
H5.H5AwriteVL(attr_reg_id, atype_reg_id, vl_reg_data);
H5.H5Awrite(attr_reg_id, atype_reg_id, vl_reg_data);
}
catch (Exception err) {
if (attr_reg_id > 0)
@ -696,7 +696,7 @@ public class TestH5R {
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5AreadVL(attr_obj_id, atype_obj_id, vl_readbuf);
H5.H5Aread(attr_obj_id, atype_obj_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
@ -716,7 +716,7 @@ public class TestH5R {
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5AreadVL(attr_reg_id, atype_reg_id, vl_readbuf);
H5.H5Aread(attr_reg_id, atype_reg_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
@ -831,8 +831,8 @@ public class TestH5R {
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);
H5.H5Dwrite(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)
@ -890,8 +890,8 @@ public class TestH5R {
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);
H5.H5Dwrite(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)
@ -930,8 +930,8 @@ public class TestH5R {
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);
H5.H5Dread(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
@ -951,8 +951,8 @@ public class TestH5R {
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);
H5.H5Dread(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();

3
java/test/testfiles/JUnit-TestH5A.txt
View File

@ -11,6 +11,7 @@ JUnit version 4.11
.testH5Aget_info_by_name
.testH5Aget_create_plist
.testH5Adelete_by_name
.testH5AVLwrVL
.testH5Aopen_by_name
.testH5Aget_info
.testH5Aget_name
@ -31,5 +32,5 @@ JUnit version 4.11
Time: XXXX
OK (29 tests)
OK (30 tests)

3
java/test/testfiles/JUnit-TestH5D.txt
View File

@ -1,4 +1,5 @@
JUnit version 4.11
.testH5DVLwrVL
.testH5Dget_storage_size
.testH5Diterate_write
.testH5Dcreate
@ -22,5 +23,5 @@ JUnit version 4.11
Time: XXXX
OK (20 tests)
OK (21 tests)

9
release_docs/RELEASE.txt
View File

@ -183,7 +183,14 @@ Bug Fixes since HDF5-1.13.2 release
Java Library
------------
-
- Improve variable-length datatype handling in JNI.
The existing JNI read-write functions could handle variable-length datatypes
that were simple variable-length datatype with an atomic sub-datatype. More
complex combinations could not be handled. Reworked the JNI read-write functions
to recursively inspect datatypes for variable-length sub-datatypes.
(ADB - 2022/10/12, HDFFV-8701,10375)
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