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authorAllen Byrne <50328838+byrnHDF@users.noreply.github.com>2023-08-29 21:28:52 (GMT)
committerGitHub <noreply@github.com>2023-08-29 21:28:52 (GMT)
commit1dec26ca327c615e9f34e981102998d3256010da (patch)
treee4a93205afd734852d0d3137f6e711e8bfd9dbd6
parent6129233f4e5c892623e0533b13de3b987af436ea (diff)
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Sync Java changes - particularly VL handling (#3442)
Diffstat
-rw-r--r--java/src/jni/h5aImp.c597
-rw-r--r--java/src/jni/h5dImp.c561
-rw-r--r--java/src/jni/h5util.c891
-rw-r--r--java/src/jni/h5util.h5
-rw-r--r--java/test/TestH5A.java436
-rw-r--r--java/test/TestH5D.java819
-rw-r--r--java/test/testfiles/JUnit-TestH5A.txt5
-rw-r--r--java/test/testfiles/JUnit-TestH5D.txt8
8 files changed, 2384 insertions, 938 deletions
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index d69ab95..2058d61 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -155,13 +155,15 @@ 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 = 0; // Only used by vl_data_class types
+ htri_t vl_data_class;
+ herr_t status = FAIL;
UNUSED(clss);
@@ -173,40 +175,58 @@ 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) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0)
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);
+
H5Dvlen_reclaim(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);
+ }
}
}
@@ -222,38 +242,52 @@ 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 = 0; // 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)
@@ -261,14 +295,24 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
+ 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);
+
H5Dvlen_reclaim(attr_id, sid, 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);
+ }
}
}
@@ -1063,13 +1107,15 @@ 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;
+ jbyte *readBuf = NULL;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
- jsize n = 0;
+ size_t typeSize;
+ H5T_class_t type_class;
+ jsize vl_array_len;
htri_t vl_data_class;
- herr_t status = FAIL;
- jbyteArray *readBuf = NULL;
+ herr_t status = FAIL;
+ htri_t is_variable = 0;
UNUSED(clss);
@@ -1078,228 +1124,42 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ /* Get size of data array */
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
+ if ((is_variable = H5Tis_variable_str(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");
- }
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
- dims[0] = (hsize_t)n;
- if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
+ if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Aread: failed to allocate raw VL read buffer");
+ if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 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);
- }
+ 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);
+
H5Dvlen_reclaim(attr_id, sid, H5P_DEFAULT, readBuf);
+
if (sid >= 0)
H5Sclose(sid);
}
-
- UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
+ if (is_variable) {
+ for (size_t i = 0; i < (size_t)vl_array_len; i++)
+ HDfree(((char **)readBuf)[i]);
+ }
+ HDfree(readBuf);
}
return (jint)status;
@@ -1313,205 +1173,61 @@ 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;
+ jbyte *writeBuf = NULL;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
- jsize n;
+ size_t typeSize;
+ H5T_class_t type_class;
+ jsize vl_array_len;
htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean writeBufIsCopy;
- jbyteArray writeBuf = NULL;
+ herr_t status = FAIL;
+ htri_t is_variable = 0;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
/* 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, "H5AwriteVL: readBuf length < 0");
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer length < 0");
}
-
- dims[0] = (hsize_t)n;
- if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 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");
+
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);
+ translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
- 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);
- }
+ 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)
+ 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);
+
H5Dvlen_reclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
+ }
+ if (is_variable) {
+ for (size_t i = 0; i < (size_t)vl_array_len; i++)
+ HDfree(((char **)writeBuf)[i]);
+ }
- if (type_class != H5T_VLEN)
- UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
+ HDfree(writeBuf);
}
return (jint)status;
@@ -1914,21 +1630,24 @@ H5AwriteVL_asstr(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
continue;
}
- /*
- * length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
- * CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- */
-
PIN_JAVA_STRING(ENVONLY, jstr, utf8, NULL, "H5AwriteVL_asstr: failed to pin string buffer");
/*
- * TODO: If the string isn't a copy, we should probably make
- * one before destroying it with h5str_convert.
+ * Make a copy of the string since h5str_convert uses strtok.
*/
+ char *utf8_copy = NULL;
- if (!h5str_convert(ENVONLY, (char **)&utf8, aid, tid, &(((char *)writeBuf)[i * typeSize]), 0))
+ jsize length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+ if (NULL == (utf8_copy = HDstrndup(utf8, (size_t)length)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (!h5str_convert(ENVONLY, &utf8_copy, aid, tid, &(((char *)writeBuf)[i * typeSize]), 0))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ free(utf8_copy);
+
UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
utf8 = NULL;
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index f0ba4ac..3dc4b98 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -181,47 +181,71 @@ 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)
H5Dvlen_reclaim(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);
+ }
}
}
@@ -238,31 +262,50 @@ 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,
@@ -274,11 +317,16 @@ done:
if ((status >= 0) && vl_data_class)
H5Dvlen_reclaim(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);
+ }
}
}
@@ -1074,234 +1122,52 @@ 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)
{
+ jbyte *readBuf = NULL;
+ size_t typeSize;
H5T_class_t type_class;
- jsize n;
+ jsize vl_array_len;
htri_t vl_data_class;
- herr_t status = FAIL;
- jbyteArray *readBuf = NULL;
+ herr_t status = FAIL;
+ htri_t is_variable = 0;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
/* 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, "H5DreadVL: readBuf length < 0");
}
-
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ if (!(typeSize = H5Tget_size(mem_type_id)))
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);
+ if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read 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->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 ((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);
+ if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
- 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);
- }
+ translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf);
done:
if (readBuf) {
if ((status >= 0) && vl_data_class)
H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
- UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
+ if (is_variable) {
+ for (size_t i = 0; i < (size_t)vl_array_len; i++)
+ HDfree(((char **)readBuf)[i]);
+ }
+ HDfree(readBuf);
}
return (jint)status;
@@ -1316,201 +1182,55 @@ 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)
{
+ jbyte *writeBuf = NULL;
+ size_t typeSize;
H5T_class_t type_class;
- jsize n;
+ jsize vl_array_len; // Only used by vl_data_class types
htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean writeBufIsCopy;
- jbyteArray writeBuf = NULL;
+ herr_t status = FAIL;
+ htri_t is_variable = 0;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
/* 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, "H5DwriteVL: readBuf length < 0");
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer length < 0");
}
-
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ if (!(typeSize = H5Tget_size(mem_type_id)))
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));
+ if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer");
- ENVPTR->DeleteLocalRef(ENVONLY, jList);
- } /* end for (i = 0; i < n; i++) */
+ if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
- 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);
+ translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
- 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);
- }
+ 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)
H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
+ if (is_variable) {
+ for (size_t i = 0; i < (size_t)vl_array_len; i++)
+ HDfree(((char **)writeBuf)[i]);
+ }
- if (type_class != H5T_VLEN)
- UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
+ HDfree(writeBuf);
}
return (jint)status;
@@ -1946,21 +1666,24 @@ H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_si
continue;
}
- /*
- * length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
- * CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- */
-
PIN_JAVA_STRING(ENVONLY, jstr, utf8, NULL, "H5DwriteVL_asstr: failed to pin string buffer");
/*
- * TODO: If the string isn't a copy, we should probably make
- * one before destroying it with h5str_convert.
+ * Make a copy of the string since h5str_convert uses strtok.
*/
+ char *utf8_copy = NULL;
+
+ jsize length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+ if (NULL == (utf8_copy = HDstrndup(utf8, (size_t)length)))
+ H5_LIBRARY_ERROR(ENVONLY);
- if (!h5str_convert(ENVONLY, (char **)&utf8, did, tid, &(((char *)writeBuf)[i * typeSize]), 0))
+ if (!h5str_convert(ENVONLY, &utf8_copy, did, tid, &(((char *)writeBuf)[i * typeSize]), 0))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ HDfree(utf8_copy);
+
UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
utf8 = NULL;
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 6a6dde4..5e32125 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -75,6 +75,9 @@ static int render_bin_output_region_data_points(FILE *stream, hid_t region_sp
hsize_t *ptdata);
static int render_bin_output_region_points(FILE *stream, hid_t region_space, hid_t region_id,
hid_t container);
+jobject translate_atomic_rbuf(JNIEnv *env, jlong mem_type_id, H5T_class_t type_class, void *raw_buf);
+void translate_atomic_wbuf(JNIEnv *env, jobject in_obj, jlong mem_type_id, H5T_class_t type_class,
+ void *raw_buf);
/* Strings for output */
#define H5_TOOLS_GROUP "GROUP"
@@ -433,40 +436,43 @@ h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_
break;
case H5T_ENUM: {
- void *value = NULL;
+ void *value = NULL;
+ unsigned char tmp_uchar = 0;
+ unsigned short tmp_ushort = 0;
+ unsigned int tmp_uint = 0;
+#if H5_SIZEOF_LONG != H5_SIZEOF_INT
+ unsigned long tmp_ulong = 0;
+#endif
+#if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG
+ unsigned long long tmp_ullong = 0;
+#endif
token = HDstrtok(this_str, delimiter);
switch (typeSize) {
case sizeof(char): {
- unsigned char tmp_uchar = 0;
- value = &tmp_uchar;
+ value = &tmp_uchar;
break;
}
case sizeof(short): {
- unsigned short tmp_ushort = 0;
- value = &tmp_ushort;
+ value = &tmp_ushort;
break;
}
#if H5_SIZEOF_LONG != H5_SIZEOF_INT
case sizeof(long): {
- unsigned long tmp_ulong = 0;
- value = &tmp_ulong;
+ value = &tmp_ulong;
break;
}
#endif
#if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG
case sizeof(long long): {
- unsigned long long tmp_ullong = 0;
- value = &tmp_ullong;
+ value = &tmp_ullong;
break;
}
#endif
-
default: {
- unsigned int tmp_uint = 0;
- value = &tmp_uint;
+ value = &tmp_uint;
break;
}
}
@@ -3010,10 +3016,8 @@ Java_hdf_hdf5lib_H5_H5AreadComplex(JNIEnv *env, jclass clss, jlong attr_id, jlon
size = (((H5Tget_size(mem_type_id)) > (H5Tget_size(p_type))) ? (H5Tget_size(mem_type_id))
: (H5Tget_size(p_type)));
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) <= 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) <= 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadComplex: read buffer length <= 0");
- }
if (NULL == (readBuf = (char *)HDmalloc((size_t)n * size)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AreadComplex: failed to allocate read buffer");
@@ -3646,7 +3650,7 @@ done:
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5export_1attribute(JNIEnv *env, jclass clss, jstring file_export_name, jlong dset_id,
- jstring object_path, jint binary_order)
+ jstring attribute_name, jint binary_order)
{
const char *file_export = NULL;
const char *object_name = NULL;
@@ -3660,10 +3664,11 @@ Java_hdf_hdf5lib_H5_H5export_1attribute(JNIEnv *env, jclass clss, jstring file_e
if (NULL == file_export_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_export_name is NULL");
- if (NULL == object_path)
+ if (NULL == attribute_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: object_path is NULL");
- PIN_JAVA_STRING(ENVONLY, object_path, object_name, &isCopy, "H5export_dataset: object_path not pinned");
+ PIN_JAVA_STRING(ENVONLY, attribute_name, object_name, &isCopy,
+ "H5export_dataset: object_path not pinned");
if ((attr_id = H5Aopen(dset_id, object_name, H5P_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -3688,11 +3693,859 @@ done:
if (file_export)
UNPIN_JAVA_STRING(ENVONLY, file_export_name, file_export);
if (object_name)
- UNPIN_JAVA_STRING(ENVONLY, object_path, object_name);
+ UNPIN_JAVA_STRING(ENVONLY, attribute_name, object_name);
if (attr_id >= 0)
H5Aclose(attr_id);
} /* end Java_hdf_hdf5lib_H5_H5export_1attribute */
+jobject
+translate_atomic_rbuf(JNIEnv *env, jlong mem_type_id, H5T_class_t type_class, void *raw_buf)
+{
+ jobject jobj = NULL;
+ hid_t memb = H5I_INVALID_HID;
+ jobjectArray jList = NULL;
+ H5T_class_t vlClass;
+ size_t vlSize;
+ size_t i;
+ size_t typeSize;
+ // raw_buf is normally bytes except when used for variable length strings
+ char *char_buf = (char *)raw_buf;
+
+ /* retrieve the java.util.ArrayList interface class */
+ jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList");
+ jmethodID arrListMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "<init>", "(I)V");
+
+ /* 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 (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ switch (type_class) {
+ case 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 element to a list */
+ hvl_t vl_elem;
+
+ /* Get the number of sequence elements */
+ memcpy(&vl_elem, char_buf, sizeof(hvl_t));
+ jsize nelmts = (jsize)vl_elem.len;
+ if (vl_elem.len != (size_t)nelmts)
+ H5_JNI_FATAL_ERROR(ENVONLY, "translate_atomic_rbuf: overflow of number of VL elements");
+
+ if (nelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_atomic_rbuf: number of VL elements < 0");
+
+ /* The list we're going to return: */
+ if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate list read buffer");
+
+ translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)nelmts, vl_elem.p);
+ jobj = jList;
+ break;
+ } /* H5T_VLEN */
+ case H5T_COMPOUND: {
+ int nmembs = H5Tget_nmembers(mem_type_id);
+
+ /* The list we're going to return: */
+ if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate list read buffer");
+
+ /* Convert each element to a compound object */
+ for (i = 0; i < (size_t)nmembs; i++) {
+ H5T_class_t memb_vlClass;
+ size_t memb_vlSize;
+ size_t memb_offset;
+
+ if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)i)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)i);
+ if ((memb_vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(memb_vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ translate_atomic_rbuf(ENVONLY, memb, memb_vlClass, char_buf + i * typeSize + memb_offset);
+ H5Tclose(memb);
+ }
+ jobj = jList;
+ break;
+ } /* H5T_COMPOUND */
+ case H5T_ARRAY: {
+ void *objBuf = NULL;
+ size_t typeCount;
+
+ 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);
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ typeCount = typeSize / vlSize;
+
+ if (NULL == (objBuf = HDmalloc(typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate buffer");
+
+ /* Convert each element */
+ /* Get the object element */
+ memcpy((char *)objBuf, char_buf, typeSize);
+
+ /* The list we're going to return: */
+ if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate list read buffer");
+
+ translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)typeCount, objBuf);
+ jobj = jList;
+
+ if (objBuf)
+ HDfree(objBuf);
+
+ break;
+ } /* H5T_ARRAY */
+ case H5T_ENUM:
+ case H5T_BITFIELD:
+ case H5T_OPAQUE:
+ case H5T_INTEGER: {
+ /* Convert each element */
+ switch (typeSize) {
+ case sizeof(jbyte): {
+ jbyte byteValue;
+ HDmemcpy(((char *)&byteValue), char_buf, typeSize);
+
+ if (NULL ==
+ (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ case sizeof(jshort): {
+ jshort shortValue;
+ HDmemcpy(((char *)&shortValue), char_buf, typeSize);
+
+ if (NULL ==
+ (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid, shortValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ case sizeof(jint): {
+ jint intValue;
+
+ HDmemcpy(((char *)&intValue), char_buf, typeSize);
+
+ if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ case sizeof(jlong): {
+ jlong longValue;
+ HDmemcpy(((char *)&longValue), char_buf, typeSize);
+
+ if (NULL ==
+ (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ }
+ break;
+ } /* H5T_INTEGER */
+ case H5T_FLOAT: {
+ /* Convert each element to a list */
+ switch (typeSize) {
+ case sizeof(jfloat): {
+ jfloat floatValue;
+ HDmemcpy(((char *)&floatValue), char_buf, typeSize);
+
+ if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
+ (double)floatValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ case sizeof(jdouble): {
+ jdouble doubleValue;
+ HDmemcpy(((char *)&doubleValue), char_buf, typeSize);
+
+ if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
+ doubleValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ }
+ break;
+ } /* H5T_FLOAT */
+ case H5T_REFERENCE: {
+ /* Convert each element to a list */
+ jboolean bb;
+ jbyte *barray = NULL;
+
+ jsize byteArraySize = (jsize)typeSize;
+ if (typeSize != (size_t)byteArraySize)
+ H5_JNI_FATAL_ERROR(ENVONLY, "translate_atomic_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_atomic_rbuf reference: byte array not pinned");
+
+ HDmemcpy(barray, ((jbyte *)raw_buf), typeSize);
+ if (barray)
+ UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
+
+ break;
+ } /* H5T_REFERENCE */
+ case H5T_STRING: {
+ htri_t is_variable = 0;
+
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert each element */
+ if (is_variable) {
+ char **var_str_buf = (char **)raw_buf;
+ if (NULL == (jobj = ENVPTR->NewStringUTF(ENVONLY, *var_str_buf))) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: out of memory - unable to "
+ "construct string from UTF characters");
+ }
+ }
+ else {
+ if (NULL == (jobj = ENVPTR->NewStringUTF(ENVONLY, char_buf))) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: out of memory - unable to "
+ "construct string from UTF characters");
+ }
+ }
+
+ break;
+ } /* H5T_STRING */
+ default:
+ H5_UNIMPLEMENTED(ENVONLY, "translate_atomic_rbuf: invalid class type");
+ break;
+ } /* switch(type_class) */
+
+done:
+
+ return jobj;
+}
+
+void
+translate_atomic_wbuf(JNIEnv *env, jobject in_obj, jlong mem_type_id, H5T_class_t type_class, void *raw_buf)
+{
+ hid_t memb = H5I_INVALID_HID;
+ H5T_class_t vlClass;
+ size_t vlSize;
+ size_t i;
+ size_t typeSize;
+ // raw_buf is normally bytes except when used for variable length strings
+ char *char_buf = (char *)raw_buf;
+
+ /* 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 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 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 (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ switch (type_class) {
+ case 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 element to a vlen element */
+ hvl_t vl_elem;
+
+ jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, in_obj);
+
+ if (jnelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_atomic_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_atomic_wbuf: failed to allocate vlen ptr buffer");
+
+ translate_wbuf(ENVONLY, (jobjectArray)in_obj, memb, vlClass, (jsize)jnelmts, vl_elem.p);
+
+ HDmemcpy(char_buf, &vl_elem, sizeof(hvl_t));
+ break;
+ } /* H5T_VLEN */
+ case H5T_COMPOUND: {
+ /* Convert each compound element */
+ int nmembs = H5Tget_nmembers(mem_type_id);
+
+ /* invoke the toArray method */
+ if (mToArray == NULL)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, in_obj, mToArray);
+ jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
+
+ if (jnelmts != nmembs)
+ H5_BAD_ARGUMENT_ERROR(
+ ENVONLY, "translate_atomic_wbuf: number of elements not equal to number of members");
+
+ /* Convert each compound object to an element */
+ for (i = 0; i < (size_t)nmembs; i++) {
+ H5T_class_t memb_vlClass;
+ size_t memb_vlSize;
+ size_t memb_offset;
+
+ if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)i)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)i);
+ if ((memb_vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(memb_vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ jobject arr_obj = ENVPTR->GetObjectArrayElement(ENVONLY, array, (jsize)i);
+ translate_atomic_wbuf(ENVONLY, arr_obj, memb, memb_vlClass,
+ char_buf + i * typeSize + memb_offset);
+ ENVPTR->DeleteLocalRef(ENVONLY, arr_obj);
+ H5Tclose(memb);
+ }
+ break;
+ } /* H5T_COMPOUND */
+ case H5T_ARRAY: {
+ void *objBuf = NULL;
+
+ 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 array element */
+ /* invoke the toArray method */
+ if (mToArray == NULL)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, in_obj, mToArray);
+ jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
+
+ if (jnelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_atomic_wbuf: number of array elements < 0");
+
+ if (NULL == (objBuf = HDmalloc((size_t)jnelmts * vlSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_wbuf: failed to allocate buffer");
+
+ translate_wbuf(ENVONLY, array, memb, vlClass, (jsize)jnelmts, objBuf);
+
+ HDmemcpy(char_buf, (char *)objBuf, vlSize * (size_t)jnelmts);
+ break;
+ } /* H5T_ARRAY */
+ case H5T_ENUM:
+ case H5T_BITFIELD:
+ case H5T_OPAQUE:
+ case H5T_INTEGER: {
+ /* Convert each element */
+ switch (typeSize) {
+ case sizeof(jbyte): {
+ jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, in_obj, byteValueMid);
+ HDmemcpy(char_buf, ((char *)&byteValue), typeSize);
+ break;
+ }
+ case sizeof(jshort): {
+ jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, in_obj, shortValueMid);
+ HDmemcpy(char_buf, ((char *)&shortValue), typeSize);
+ break;
+ }
+ case sizeof(jint): {
+ jint intValue = ENVPTR->CallIntMethod(ENVONLY, in_obj, intValueMid);
+ HDmemcpy(char_buf, ((char *)&intValue), typeSize);
+ break;
+ }
+ case sizeof(jlong): {
+ jlong longValue = ENVPTR->CallLongMethod(ENVONLY, in_obj, longValueMid);
+ HDmemcpy(char_buf, ((char *)&longValue), typeSize);
+ break;
+ }
+ }
+ break;
+ } /* H5T_INTEGER */
+ case H5T_FLOAT: {
+ /* Convert each element */
+ switch (typeSize) {
+ case sizeof(jfloat): {
+ jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, in_obj, floatValueMid);
+ HDmemcpy(char_buf, ((char *)&floatValue), typeSize);
+ break;
+ }
+ case sizeof(jdouble): {
+ jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, in_obj, doubleValueMid);
+ HDmemcpy(char_buf, ((char *)&doubleValue), typeSize);
+ break;
+ }
+ }
+ break;
+ } /* H5T_FLOAT */
+ case H5T_REFERENCE: {
+ /* Convert each array element */
+ jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, in_obj, 0);
+ HDmemcpy(char_buf, ((char *)barray), typeSize);
+ ENVPTR->ReleaseByteArrayElements(ENVONLY, in_obj, barray, 0);
+ break;
+ } /* H5T_REFERENCE */
+ case H5T_STRING: {
+ htri_t is_variable = 0;
+
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert each pointer element */
+ jsize length;
+ const char *utf8 = NULL;
+
+ HDmemset(char_buf, 0, typeSize);
+ if (NULL != in_obj) {
+ PIN_JAVA_STRING(ENVONLY, in_obj, utf8, NULL, "translate_atomic_wbuf jobj not pinned");
+ length = ENVPTR->GetStringUTFLength(ENVONLY, in_obj);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ if (is_variable) {
+ char *new_buf = (char *)calloc(1, (size_t)(length + 1));
+ HDmemcpy(((char *)new_buf), utf8, (size_t)length);
+ HDmemcpy(char_buf, &new_buf, typeSize);
+ }
+ else {
+ HDmemcpy(char_buf, utf8, (size_t)length);
+ }
+ UNPIN_JAVA_STRING(ENVONLY, in_obj, utf8);
+ utf8 = NULL;
+ }
+ break;
+ } /* H5T_STRING */
+ default:
+ H5_UNIMPLEMENTED(ENVONLY, "translate_atomic_wbuf: invalid class type");
+ break;
+ } /* switch(type_class) */
+
+done:
+
+ return;
+}
+
+void
+translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, jsize count,
+ void *raw_buf)
+{
+ hid_t memb = H5I_INVALID_HID;
+ int ret_buflen = -1;
+ jboolean found_jList = JNI_TRUE;
+ jobjectArray jList = NULL;
+ jobject jobj = NULL;
+ H5T_class_t vlClass;
+ size_t vlSize;
+ size_t i, x;
+ size_t typeSize;
+ // raw_buf is normally bytes except when used for variable length strings
+ char *char_buf = (char *)raw_buf;
+
+ /* 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");
+
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ ret_buflen = ENVPTR->GetArrayLength(ENVONLY, ret_buf);
+ if (ret_buflen < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "ret_buflen: Array length cannot be negative");
+
+ switch (type_class) {
+ case 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;
+
+ found_jList = JNI_TRUE;
+ jList = NULL;
+
+ /* Get the number of sequence elements */
+ HDmemcpy(&vl_elem, char_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 (i < (size_t)ret_buflen) {
+ jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i);
+ }
+ if (NULL == jList) {
+ 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");
+ }
+
+ translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)nelmts, vl_elem.p);
+ if (found_jList == JNI_FALSE) {
+ jboolean addResult =
+ ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, (jobject)jList);
+ if (!addResult)
+ H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: cannot add VL element");
+ }
+ else {
+ ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, (jsize)i, (jobject)jList);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ }
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ }
+ break;
+ } /* H5T_VLEN */
+ case H5T_COMPOUND: {
+ /* Convert each compound element to a list */
+ for (i = 0; i < (size_t)count; i++) {
+ found_jList = JNI_TRUE;
+ jList = NULL;
+
+ /* The list we're going to return: */
+ if (i < (size_t)ret_buflen) {
+ jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i);
+ }
+ if (NULL == jList) {
+ 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");
+ }
+ int nmembs = H5Tget_nmembers(mem_type_id);
+ /* Convert each element to a list */
+ for (x = 0; x < (size_t)nmembs; x++) {
+ H5T_class_t memb_vlClass;
+ size_t memb_vlSize;
+ size_t memb_offset;
+
+ if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)x)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)x);
+
+ if ((memb_vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(memb_vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ jobj = translate_atomic_rbuf(ENVONLY, memb, memb_vlClass,
+ char_buf + i * typeSize + memb_offset);
+ if (jobj) {
+ if (found_jList == JNI_FALSE)
+ ENVPTR->CallBooleanMethod(ENVONLY, jList, arrAddMethod, (jobject)jobj);
+ else
+ ENVPTR->SetObjectArrayElement(ENVONLY, jList, (jsize)i, (jobject)jobj);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ ENVPTR->DeleteLocalRef(ENVONLY, jobj);
+ }
+
+ H5Tclose(memb);
+ }
+ if (ret_buflen == 0)
+ ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList);
+ else
+ ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, (jsize)i, jList);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ }
+ break;
+ } /* H5T_COMPOUND */
+ case H5T_ARRAY: {
+ void *objBuf = NULL;
+ size_t typeCount;
+
+ 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);
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ typeCount = typeSize / vlSize;
+
+ if (NULL == (objBuf = HDmalloc(typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_rbuf: failed to allocate buffer");
+
+ /* Convert each element to a list */
+ for (i = 0; i < (size_t)count; i++) {
+ found_jList = JNI_TRUE;
+ jList = NULL;
+
+ /* Get the object element */
+ HDmemcpy((char *)objBuf, char_buf + i * typeSize, typeSize);
+
+ /* The list we're going to return: */
+ if (i < (size_t)ret_buflen) {
+ if (NULL ==
+ (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i)))
+ found_jList = JNI_FALSE;
+ }
+ if (NULL == jList) {
+ if (NULL ==
+ (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY,
+ "translate_rbuf: failed to allocate list read buffer");
+ }
+
+ translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)typeCount, objBuf);
+ if (found_jList == JNI_FALSE)
+ ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList);
+ else
+ ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, (jsize)i, jList);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ }
+
+ if (objBuf)
+ HDfree(objBuf);
+
+ break;
+ } /* H5T_ARRAY */
+ case H5T_ENUM:
+ case H5T_BITFIELD:
+ case H5T_OPAQUE:
+ case H5T_INTEGER:
+ case H5T_FLOAT:
+ case H5T_REFERENCE:
+ case H5T_STRING: {
+ /* Convert each element to a list */
+ for (i = 0; i < (size_t)count; i++) {
+ jobj = translate_atomic_rbuf(ENVONLY, mem_type_id, type_class, char_buf + i * typeSize);
+ if (jobj) {
+ if (ret_buflen == 0)
+ ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, (jobject)jobj);
+ else
+ ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, (jsize)i, (jobject)jobj);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ ENVPTR->DeleteLocalRef(ENVONLY, jobj);
+ }
+ }
+ break;
+ }
+ default:
+ H5_UNIMPLEMENTED(ENVONLY, "translate_rbuf: invalid class type");
+ break;
+ } /* switch(type_class) */
+
+done:
+
+ return;
+}
+
+void
+translate_wbuf(JNIEnv *env, jobjectArray in_buf, jlong mem_type_id, H5T_class_t type_class, jsize count,
+ void *raw_buf)
+{
+ hid_t memb = H5I_INVALID_HID;
+ jobjectArray jList = NULL;
+ jobject jobj = NULL;
+ H5T_class_t vlClass;
+ size_t vlSize;
+ size_t i, x;
+ size_t typeSize;
+ // raw_buf is normally bytes except when used for variable length strings
+ char *char_buf = (char *)raw_buf;
+
+ /* 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;");
+
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ switch (type_class) {
+ case 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");
+
+ translate_wbuf(ENVONLY, array, memb, vlClass, (jsize)jnelmts, vl_elem.p);
+
+ HDmemcpy(char_buf + i * sizeof(hvl_t), &vl_elem, sizeof(hvl_t));
+
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ } /* end for (i = 0; i < count; i++) */
+ break;
+ } /* H5T_VLEN */
+ case H5T_COMPOUND: {
+ /* Convert each list to a compound element */
+ for (i = 0; i < (size_t)count; i++) {
+ if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+ int nmembs = H5Tget_nmembers(mem_type_id);
+
+ /* 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 != nmembs)
+ H5_BAD_ARGUMENT_ERROR(
+ ENVONLY, "translate_wbuf: number of elements not equal to number of members");
+
+ /* Convert each compound object to an element */
+ for (x = 0; x < (size_t)nmembs; x++) {
+ H5T_class_t memb_vlClass;
+ size_t memb_vlSize;
+ size_t memb_offset;
+
+ if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)x)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)x);
+
+ if ((memb_vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(memb_vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ jobject arr_obj = ENVPTR->GetObjectArrayElement(ENVONLY, array, (jsize)x);
+ translate_atomic_wbuf(ENVONLY, arr_obj, memb, memb_vlClass,
+ char_buf + i * typeSize + memb_offset);
+ ENVPTR->DeleteLocalRef(ENVONLY, arr_obj);
+ H5Tclose(memb);
+ }
+
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ } /* end for (i = 0; i < count; i++) */
+ break;
+ } /* H5T_COMPOUND */
+ case 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);
+
+ /* Convert each list to an array element */
+ for (i = 0; i < (size_t)count; i++) {
+ 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 array elements < 0");
+
+ translate_wbuf(ENVONLY, array, memb, vlClass, jnelmts,
+ char_buf + i * vlSize * (size_t)jnelmts);
+
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ } /* end for (i = 0; i < count; i++) */
+ break;
+ } /* H5T_ARRAY */
+ case H5T_ENUM:
+ case H5T_BITFIELD:
+ case H5T_OPAQUE:
+ case H5T_INTEGER:
+ case H5T_FLOAT:
+ case H5T_REFERENCE:
+ case H5T_STRING: {
+ /* Convert each list to an array element */
+ for (i = 0; i < (size_t)count; i++) {
+ if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ translate_atomic_wbuf(ENVONLY, jobj, mem_type_id, type_class, char_buf + i * typeSize);
+ ENVPTR->DeleteLocalRef(ENVONLY, jobj);
+ }
+ break;
+ }
+ default:
+ H5_UNIMPLEMENTED(ENVONLY, "translate_wbuf: invalid class type");
+ break;
+ } /* switch(type_class) */
+
+done:
+
+ return;
+}
+
#ifdef __cplusplus
}
#endif
diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h
index 1d76823..e09d94b 100644
--- a/java/src/jni/h5util.h
+++ b/java/src/jni/h5util.h
@@ -50,6 +50,11 @@ 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 void translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class,
+ jsize count, void *raw_buf);
+extern void translate_wbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class,
+ jsize count, void *raw_buf);
+
/*
* Symbols used to format the output of h5str_sprintf and
* to interpret the input to h5str_convert.
diff --git a/java/test/TestH5A.java b/java/test/TestH5A.java
index 2633fde..0d38914 100644
--- a/java/test/TestH5A.java
+++ b/java/test/TestH5A.java
@@ -46,6 +46,7 @@ public class TestH5A {
private static final int DIM_Y = 6;
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5dsid = HDF5Constants.H5I_INVALID_HID;
+ long H5atid = HDF5Constants.H5I_INVALID_HID;
long H5did = HDF5Constants.H5I_INVALID_HID;
long[] H5dims = {DIM_X, DIM_Y};
long type_id = HDF5Constants.H5I_INVALID_HID;
@@ -133,8 +134,12 @@ public class TestH5A {
}
catch (Exception ex) {
}
-
- _deleteFile(H5_FILE);
+ if (H5atid > 0)
+ try {
+ H5.H5Tclose(H5atid);
+ }
+ catch (Exception ex) {
+ }
if (type_id > 0)
try {
@@ -154,6 +159,8 @@ public class TestH5A {
}
catch (Exception ex) {
}
+
+ _deleteFile(H5_FILE);
System.out.println();
}
@@ -1066,7 +1073,7 @@ public class TestH5A {
HDF5Constants.H5P_DEFAULT);
assertTrue("testH5Awrite_readVL: ", attr_id >= 0);
- H5.H5Awrite_VLStrings(attr_id, atype_id, str_data);
+ H5.H5AwriteVL(attr_id, atype_id, str_data);
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
@@ -1078,7 +1085,7 @@ public class TestH5A {
strs[j] = "";
}
try {
- H5.H5Aread_VLStrings(attr_id, atype_id, strs);
+ H5.H5AreadVL(attr_id, atype_id, strs);
}
catch (Exception ex) {
ex.printStackTrace();
@@ -1495,9 +1502,8 @@ public class TestH5A {
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];
@@ -1570,4 +1576,422 @@ 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) {
+ }
+ if (atype_int_id > 0)
+ try {
+ H5.H5Tclose(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.H5AwriteVL(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.H5AreadVL(attr_int_id, base_atype_int_id, base_vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ ArrayList<ArrayList<Integer>> vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[0];
+ assertTrue("vl_readbuf 0 exists", vl_readbuf != null);
+ ArrayList<Integer> vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(0));
+ /*
+ * System.out.println(); System.out.println("vl_readbuf: " + vl_readbuf);
+ * System.out.println("vl_readbuf_int: " + vl_readbuf_int);
+ */
+ assertTrue("testHADVLwrVL:" + vl_readbuf_int.get(0),
+ vl_int_data[0].get(0).equals(vl_readbuf_int.get(0)));
+
+ vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[1];
+ vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(1));
+ /*
+ * System.out.println("vl_readbuf: " + vl_readbuf); System.out.println("vl_readbuf_int: " +
+ * vl_readbuf_int);
+ */
+ assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(1),
+ vl_int_data[1].get(1).equals(vl_readbuf_int.get(1)));
+
+ vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[2];
+ vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(2));
+ /*
+ * System.out.println("vl_readbuf: " + vl_readbuf); System.out.println("vl_readbuf_int: " +
+ * vl_readbuf_int);
+ */
+ assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(2),
+ vl_int_data[2].get(2).equals(vl_readbuf_int.get(2)));
+
+ vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[3];
+ vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(3));
+ /*
+ * System.out.println("vl_readbuf: " + vl_readbuf); System.out.println("vl_readbuf_int: " +
+ * vl_readbuf_int);
+ */
+ assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(3),
+ vl_int_data[3].get(3).equals(vl_readbuf_int.get(3)));
+ }
+ 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) {
+ }
+ }
+ }
+
+ @Test
+ public void testH5AArraywr()
+ {
+ String att_int_name = "ArrayIntdata";
+ long att_int_id = HDF5Constants.H5I_INVALID_HID;
+ long atype_int_id = HDF5Constants.H5I_INVALID_HID;
+ long aspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] dims = {4};
+ long lsize = 1;
+
+ ArrayList[] arr_int_data = new ArrayList[4];
+ try {
+ // Write Integer data
+ arr_int_data[0] = new ArrayList<Integer>(Arrays.asList(1, 2, 3, 4));
+ arr_int_data[1] = new ArrayList<Integer>(Arrays.asList(2, 3, 4, 5));
+ arr_int_data[2] = new ArrayList<Integer>(Arrays.asList(4, 5, 6, 7));
+ arr_int_data[3] = new ArrayList<Integer>(Arrays.asList(7, 8, 9, 10));
+ Class dataClass = arr_int_data.getClass();
+ assertTrue("testH5AArraywr.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ atype_int_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_U32LE, 1, dims);
+ assertTrue("testH5AArraywr.H5Tarray_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.testH5AArraywr: " + err);
+ }
+
+ try {
+ aspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(aspace_id > 0);
+ att_int_id = H5.H5Acreate(H5did, att_int_name, atype_int_id, aspace_id,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5AVLwr: ", att_int_id >= 0);
+
+ H5.H5AwriteVL(att_int_id, atype_int_id, arr_int_data);
+ }
+ catch (Exception err) {
+ if (att_int_id > 0)
+ try {
+ H5.H5Aclose(att_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) {
+ }
+ }
+
+ H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+
+ for (int j = 0; j < dims.length; j++)
+ lsize *= dims[j];
+
+ // Read Integer data
+ ArrayList[] arr_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ arr_readbuf[j] = new ArrayList<Integer>();
+
+ try {
+ H5.H5AreadVL(att_int_id, atype_int_id, arr_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5AVLwr:" + arr_readbuf[0].get(0),
+ arr_int_data[0].get(0).equals(arr_readbuf[0].get(0)));
+ assertTrue("testH5AVLwr:" + arr_readbuf[1].get(0),
+ arr_int_data[1].get(0).equals(arr_readbuf[1].get(0)));
+ assertTrue("testH5AVLwr:" + arr_readbuf[2].get(0),
+ arr_int_data[2].get(0).equals(arr_readbuf[2].get(0)));
+ assertTrue("testH5AVLwr:" + arr_readbuf[3].get(0),
+ arr_int_data[3].get(0).equals(arr_readbuf[3].get(0)));
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.testH5AArraywr: " + err);
+ }
+ finally {
+ if (att_int_id > 0)
+ try {
+ H5.H5Aclose(att_int_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_int_id > 0)
+ try {
+ H5.H5Tclose(atype_int_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+ }
+
+ @Test
+ public void testH5AArray_string_buffer() throws Throwable
+ {
+ String att_str_name = "ArrayStringdata";
+ long att_str_id = HDF5Constants.H5I_INVALID_HID;
+ long atype_str_id = HDF5Constants.H5I_INVALID_HID;
+ long aspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] strdims = {4};
+ long[] dims = {6};
+ long lsize = 1;
+
+ String[] str_data0 = {"Parting", "is such", "sweet", "sorrow."};
+ String[] str_data1 = {"Testing", "one", "two", "three."};
+ String[] str_data2 = {"Dog,", "man's", "best", "friend."};
+ String[] str_data3 = {"Diamonds", "are", "a", "girls!"};
+ String[] str_data4 = {"S A", "T U R", "D A Y", "night"};
+ String[] str_data5 = {"That's", "all", "folks", "!!!"};
+
+ ArrayList[] arr_str_data = new ArrayList[6];
+ arr_str_data[0] = new ArrayList<String>(Arrays.asList(str_data0));
+ arr_str_data[1] = new ArrayList<String>(Arrays.asList(str_data1));
+ arr_str_data[2] = new ArrayList<String>(Arrays.asList(str_data2));
+ arr_str_data[3] = new ArrayList<String>(Arrays.asList(str_data3));
+ arr_str_data[4] = new ArrayList<String>(Arrays.asList(str_data4));
+ arr_str_data[5] = new ArrayList<String>(Arrays.asList(str_data5));
+
+ try {
+ H5atid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("testH5AArray_string_buffer.H5.H5Tcopy: " + err);
+ }
+ assertTrue("testH5AArray_string_buffer.H5Tcopy: ", H5atid >= 0);
+ try {
+ H5.H5Tset_size(H5atid, HDF5Constants.H5T_VARIABLE);
+ assertTrue("testH5AArray_string_buffer.H5Tis_variable_str", H5.H5Tis_variable_str(H5atid));
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("testH5DArray_string_buffer.H5Tset_size: " + err);
+ }
+ try {
+ atype_str_id = H5.H5Tarray_create(H5atid, 1, strdims);
+ assertTrue("testH5AArray_string_buffer.H5Tarray_create: ", atype_str_id >= 0);
+ }
+ catch (Exception err) {
+ if (atype_str_id > 0)
+ try {
+ H5.H5Tclose(atype_str_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("testH5AArray_string_buffer: " + err);
+ }
+
+ try {
+ aspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(aspace_id > 0);
+ att_str_id = H5.H5Acreate(H5did, att_str_name, atype_str_id, aspace_id, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5AArray_string_buffer: ", att_str_id >= 0);
+
+ H5.H5AwriteVL(att_str_id, atype_str_id, arr_str_data);
+ }
+ catch (Exception err) {
+ if (att_str_id > 0)
+ try {
+ H5.H5Dclose(att_str_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_str_id > 0)
+ try {
+ H5.H5Tclose(atype_str_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("testH5AArray_string_buffer: " + 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];
+
+ ArrayList[] arr_readbuf = new ArrayList[6];
+ for (int j = 0; j < lsize; j++)
+ arr_readbuf[j] = new ArrayList<String>();
+
+ try {
+ H5.H5AreadVL(att_str_id, atype_str_id, arr_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ finally {
+ if (att_str_id > 0)
+ try {
+ H5.H5Aclose(att_str_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_str_id > 0)
+ try {
+ H5.H5Tclose(atype_str_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+ assertTrue("testH5AArray_string_buffer:" + arr_readbuf[0].get(0),
+ arr_str_data[0].get(0).equals(arr_readbuf[0].get(0)));
+ assertTrue("testH5AArray_string_buffer:" + arr_readbuf[1].get(0),
+ arr_str_data[1].get(0).equals(arr_readbuf[1].get(0)));
+ assertTrue("testH5AArray_string_buffer:" + arr_readbuf[2].get(0),
+ arr_str_data[2].get(0).equals(arr_readbuf[2].get(0)));
+ assertTrue("testH5AArray_string_buffer:" + arr_readbuf[3].get(0),
+ arr_str_data[3].get(0).equals(arr_readbuf[3].get(0)));
+ }
}
diff --git a/java/test/TestH5D.java b/java/test/TestH5D.java
index f7e5702..eacaabf 100644
--- a/java/test/TestH5D.java
+++ b/java/test/TestH5D.java
@@ -31,6 +31,7 @@ import hdf.hdf5lib.exceptions.HDF5LibraryException;
import org.junit.After;
import org.junit.Before;
+import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;
@@ -157,7 +158,7 @@ public class TestH5D {
assertTrue("TestH5D._createDataset.H5Dcreate: ", H5did >= 0);
}
- private final void _createVLDataset(long fid, long dsid, String name, long dapl)
+ private final void _createVLStrDataset(String name, long dapl)
{
try {
H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
@@ -166,24 +167,24 @@ public class TestH5D {
err.printStackTrace();
fail("H5.H5Tcopy: " + err);
}
- assertTrue("TestH5D._createVLDataset.H5Tcopy: ", H5dtid >= 0);
+ assertTrue("TestH5D._createVLStrDataset.H5Tcopy: ", H5dtid >= 0);
try {
H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE);
- assertTrue("TestH5D._createVLDataset.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid));
+ assertTrue("TestH5D._createVLStrDataset.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Tset_size: " + err);
}
try {
- H5did = H5.H5Dcreate(fid, name, H5dtid, dsid, HDF5Constants.H5P_DEFAULT,
+ H5did = H5.H5Dcreate(H5fid, name, H5dtid, H5dsid, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
- assertTrue("TestH5D._createVLDataset.H5Dcreate: ", H5did >= 0);
+ assertTrue("TestH5D._createVLStrDataset.H5Dcreate: ", H5did >= 0);
}
private final void _closeH5file() throws HDF5LibraryException
@@ -934,7 +935,7 @@ public class TestH5D {
buf_data[(indx * DIM_Y) + jndx] == 126);
}
- @Test
+ @Ignore
public void testH5Dvlen_get_buf_size()
{
String[] str_data = {"Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.",
@@ -945,12 +946,12 @@ public class TestH5D {
for (int idx = 0; idx < str_data.length; idx++)
str_data_bytes += str_data[idx].length() + 1; // Account for terminating null
- _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
+ _createVLStrDataset("dset", HDF5Constants.H5P_DEFAULT);
try {
if ((H5did >= 0) && (H5dtid >= 0))
- H5.H5Dwrite_VLStrings(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
- HDF5Constants.H5P_DEFAULT, str_data);
+ H5.H5DwriteVL(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, str_data);
}
catch (Exception e) {
e.printStackTrace();
@@ -964,26 +965,122 @@ public class TestH5D {
assertTrue("H5Dvlen_get_buf_size " + vl_size + " == " + str_data_bytes, vl_size == str_data_bytes);
}
- @Test
- public void testH5Dvlen_read_default_buffer() throws Throwable
+ @Ignore
+ public void testH5Dvlen_string_buffer() throws Throwable
{
- String[] str_data = {"Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.",
- "Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!",
- "S A", "T U R", "D A Y", "night", "That's", "all", "folks", "!!!"};
- byte[] read_data = new byte[512];
+ String dset_str_name = "VLStringdata";
+ long dset_str_id = HDF5Constants.H5I_INVALID_HID;
+ long dtype_str_id = HDF5Constants.H5I_INVALID_HID;
+ long dspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] dims = {64};
+ long lsize = 1;
- _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
+ String[] str_data0 = {"Parting", "is such", "sweet", "sorrow."};
+ String[] str_data1 = {"Testing", "one", "two", "three."};
+ String[] str_data2 = {"Dog,", "man's", "best", "friend."};
+ String[] str_data3 = {"Diamonds", "are", "a", "girls!"};
+ String[] str_data4 = {"S A", "T U R", "D A Y", "night"};
+ String[] str_data5 = {"That's", "all", "folks", "!!!"};
+
+ ArrayList[] vl_str_data = new ArrayList[6];
+ vl_str_data[0] = new ArrayList<String>(Arrays.asList(str_data0));
+ vl_str_data[1] = new ArrayList<String>(Arrays.asList(str_data1));
+ vl_str_data[2] = new ArrayList<String>(Arrays.asList(str_data2));
+ vl_str_data[3] = new ArrayList<String>(Arrays.asList(str_data3));
+ vl_str_data[4] = new ArrayList<String>(Arrays.asList(str_data4));
+ vl_str_data[5] = new ArrayList<String>(Arrays.asList(str_data5));
try {
- H5.H5Dwrite_VLStrings(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
- HDF5Constants.H5P_DEFAULT, str_data);
+ H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
}
- catch (Exception e) {
- e.printStackTrace();
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("testH5Dvlen_string_buffer.H5.H5Tcopy: " + err);
+ }
+ assertTrue("testH5Dvlen_string_buffer.H5Tcopy: ", H5dtid >= 0);
+ try {
+ H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE);
+ assertTrue("testH5Dvlen_string_buffer.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid));
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("testH5Dvlen_string_buffer.H5Tset_size: " + err);
+ }
+ try {
+ dtype_str_id = H5.H5Tvlen_create(H5dtid);
+ assertTrue("testH5Dvlen_string_buffer.H5Tvlen_create: ", dtype_str_id >= 0);
+ }
+ catch (Exception err) {
+ if (dtype_str_id > 0)
+ try {
+ H5.H5Tclose(dtype_str_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("testH5Dvlen_string_buffer: " + err);
+ }
+
+ try {
+ dspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(dspace_id > 0);
+ dset_str_id =
+ H5.H5Dcreate(H5fid, dset_str_name, dtype_str_id, dspace_id, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5Dvlen_string_buffer: ", dset_str_id >= 0);
+
+ H5.H5DwriteVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_str_data);
+ }
+ catch (Exception err) {
+ if (dset_str_id > 0)
+ try {
+ H5.H5Dclose(dset_str_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_str_id > 0)
+ try {
+ H5.H5Tclose(dtype_str_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("testH5Dvlen_string_buffer: " + err);
+ }
+ finally {
+ if (dspace_id > 0)
+ try {
+ H5.H5Sclose(dspace_id);
+ }
+ catch (Exception ex) {
+ }
}
- H5.H5Dread(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT,
- read_data);
+ H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+
+ for (int j = 0; j < dims.length; j++)
+ lsize *= dims[j];
+
+ ArrayList[] vl_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ vl_readbuf[j] = new ArrayList<String>();
+
+ try {
+ H5.H5DreadVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[0].get(0),
+ vl_str_data[0].get(0).equals(vl_readbuf[0].get(0)));
+ assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[1].get(0),
+ vl_str_data[1].get(0).equals(vl_readbuf[1].get(0)));
+ assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[2].get(0),
+ vl_str_data[2].get(0).equals(vl_readbuf[2].get(0)));
+ assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[3].get(0),
+ vl_str_data[3].get(0).equals(vl_readbuf[3].get(0)));
}
@Test
@@ -994,20 +1091,21 @@ public class TestH5D {
"S A", "T U R", "D A Y", "night", "That's", "all", "folks", "!!!"};
String[] str_rdata = new String[DIM_X * DIM_Y];
- _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
+ _createVLStrDataset("dset", HDF5Constants.H5P_DEFAULT);
try {
if ((H5did >= 0) && (H5dtid >= 0))
- H5.H5Dwrite_VLStrings(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
- HDF5Constants.H5P_DEFAULT, str_wdata);
+ H5.H5DwriteVL(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, str_wdata);
}
catch (Exception e) {
e.printStackTrace();
}
+
try {
if ((H5did >= 0) && (H5dtid >= 0))
- H5.H5Dread_VLStrings(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
- HDF5Constants.H5P_DEFAULT, str_rdata);
+ H5.H5DreadVL(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, str_rdata);
}
catch (Exception e) {
e.printStackTrace();
@@ -1153,51 +1251,50 @@ 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];
+ ArrayList[] vl_int_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
- vl_readbuf[j] = new ArrayList<Integer>();
+ vl_int_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);
+ HDF5Constants.H5P_DEFAULT, vl_int_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)));
+ assertTrue("testH5DVLwr:" + vl_int_readbuf[0].get(0),
+ vl_int_data[0].get(0).equals(vl_int_readbuf[0].get(0)));
+ assertTrue("testH5DVLwr:" + vl_int_readbuf[1].get(0),
+ vl_int_data[1].get(0).equals(vl_int_readbuf[1].get(0)));
+ assertTrue("testH5DVLwr:" + vl_int_readbuf[2].get(0),
+ vl_int_data[2].get(0).equals(vl_int_readbuf[2].get(0)));
+ assertTrue("testH5DVLwr:" + vl_int_readbuf[3].get(0),
+ vl_int_data[3].get(0).equals(vl_int_readbuf[3].get(0)));
// Read Double data
- vl_readbuf = new ArrayList[4];
+ ArrayList[] vl_dbl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
- vl_readbuf[j] = new ArrayList<Double>();
+ vl_dbl_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);
+ HDF5Constants.H5P_DEFAULT, vl_dbl_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)));
+ assertTrue("testH5DVLwr:" + vl_dbl_readbuf[0].get(0),
+ vl_dbl_data[0].get(0).equals(vl_dbl_readbuf[0].get(0)));
+ assertTrue("testH5DVLwr:" + vl_dbl_readbuf[1].get(0),
+ vl_dbl_data[1].get(0).equals(vl_dbl_readbuf[1].get(0)));
+ assertTrue("testH5DVLwr:" + vl_dbl_readbuf[2].get(0),
+ vl_dbl_data[2].get(0).equals(vl_dbl_readbuf[2].get(0)));
+ assertTrue("testH5DVLwr:" + vl_dbl_readbuf[3].get(0),
+ vl_dbl_data[3].get(0).equals(vl_dbl_readbuf[3].get(0)));
}
catch (Throwable err) {
err.printStackTrace();
@@ -1230,4 +1327,624 @@ 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.H5DwriteVL(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.H5DreadVL(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<ArrayList<Integer>> vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[0];
+ assertTrue("vl_readbuf 0 exists", vl_readbuf != null);
+ ArrayList<Integer> vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(0));
+ /*
+ * System.out.println(); System.out.println("vl_readbuf: " + vl_readbuf);
+ * System.out.println("vl_readbuf_int: " + vl_readbuf_int);
+ */
+ assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(0),
+ vl_int_data[0].get(0).equals(vl_readbuf_int.get(0)));
+
+ vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[1];
+ vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(1));
+ /*
+ * System.out.println("vl_readbuf: " + vl_readbuf); System.out.println("vl_readbuf_int: " +
+ * vl_readbuf_int);
+ */
+ assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(1),
+ vl_int_data[1].get(1).equals(vl_readbuf_int.get(1)));
+
+ vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[2];
+ vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(2));
+ /*
+ * System.out.println("vl_readbuf: " + vl_readbuf); System.out.println("vl_readbuf_int: " +
+ * vl_readbuf_int);
+ */
+ assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(2),
+ vl_int_data[2].get(2).equals(vl_readbuf_int.get(2)));
+
+ vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[3];
+ vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(3));
+ /*
+ * System.out.println("vl_readbuf: " + vl_readbuf); System.out.println("vl_readbuf_int: " +
+ * vl_readbuf_int);
+ */
+ assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(3),
+ vl_int_data[3].get(3).equals(vl_readbuf_int.get(3)));
+ }
+ 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) {
+ }
+ }
+ }
+
+ @Test
+ public void testH5DArraywr()
+ {
+ String dset_int_name = "ArrayIntdata";
+ long dset_int_id = HDF5Constants.H5I_INVALID_HID;
+ long dtype_int_id = HDF5Constants.H5I_INVALID_HID;
+ long dspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] dims = {4};
+ long lsize = 1;
+
+ ArrayList[] arr_int_data = new ArrayList[4];
+ try {
+ // Write Integer data
+ arr_int_data[0] = new ArrayList<Integer>(Arrays.asList(1, 2, 3, 4));
+ arr_int_data[1] = new ArrayList<Integer>(Arrays.asList(2, 3, 4, 5));
+ arr_int_data[2] = new ArrayList<Integer>(Arrays.asList(4, 5, 6, 7));
+ arr_int_data[3] = new ArrayList<Integer>(Arrays.asList(7, 8, 9, 10));
+ Class dataClass = arr_int_data.getClass();
+ assertTrue("testH5DArraywr.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ dtype_int_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_U32LE, 1, dims);
+ assertTrue("testH5DArraywr.H5Tarray_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.testH5DArraywr: " + 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, arr_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) {
+ }
+ }
+
+ H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+
+ for (int j = 0; j < dims.length; j++)
+ lsize *= dims[j];
+
+ // Read Integer data
+ ArrayList[] arr_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ arr_readbuf[j] = new ArrayList<Integer>();
+
+ try {
+ H5.H5DreadVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, arr_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5DVLwr:" + arr_readbuf[0].get(0),
+ arr_int_data[0].get(0).equals(arr_readbuf[0].get(0)));
+ assertTrue("testH5DVLwr:" + arr_readbuf[1].get(0),
+ arr_int_data[1].get(0).equals(arr_readbuf[1].get(0)));
+ assertTrue("testH5DVLwr:" + arr_readbuf[2].get(0),
+ arr_int_data[2].get(0).equals(arr_readbuf[2].get(0)));
+ assertTrue("testH5DVLwr:" + arr_readbuf[3].get(0),
+ arr_int_data[3].get(0).equals(arr_readbuf[3].get(0)));
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.testH5DArraywr: " + 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) {
+ }
+ }
+ }
+
+ @Test
+ public void testH5DArray_string_buffer() throws Throwable
+ {
+ String dset_str_name = "ArrayStringdata";
+ long dset_str_id = HDF5Constants.H5I_INVALID_HID;
+ long dtype_str_id = HDF5Constants.H5I_INVALID_HID;
+ long dspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] strdims = {4};
+ long[] dims = {6};
+ long lsize = 1;
+
+ String[] str_data0 = {"Parting", "is such", "sweet", "sorrow."};
+ String[] str_data1 = {"Testing", "one", "two", "three."};
+ String[] str_data2 = {"Dog,", "man's", "best", "friend."};
+ String[] str_data3 = {"Diamonds", "are", "a", "girls!"};
+ String[] str_data4 = {"S A", "T U R", "D A Y", "night"};
+ String[] str_data5 = {"That's", "all", "folks", "!!!"};
+
+ ArrayList[] arr_str_data = new ArrayList[6];
+ arr_str_data[0] = new ArrayList<String>(Arrays.asList(str_data0));
+ arr_str_data[1] = new ArrayList<String>(Arrays.asList(str_data1));
+ arr_str_data[2] = new ArrayList<String>(Arrays.asList(str_data2));
+ arr_str_data[3] = new ArrayList<String>(Arrays.asList(str_data3));
+ arr_str_data[4] = new ArrayList<String>(Arrays.asList(str_data4));
+ arr_str_data[5] = new ArrayList<String>(Arrays.asList(str_data5));
+
+ try {
+ H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("testH5DArray_string_buffer.H5.H5Tcopy: " + err);
+ }
+ assertTrue("testH5DArray_string_buffer.H5Tcopy: ", H5dtid >= 0);
+ try {
+ H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE);
+ assertTrue("testH5DArray_string_buffer.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid));
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("testH5DArray_string_buffer.H5Tset_size: " + err);
+ }
+ try {
+ dtype_str_id = H5.H5Tarray_create(H5dtid, 1, strdims);
+ assertTrue("testH5DArray_string_buffer.H5Tarray_create: ", dtype_str_id >= 0);
+ }
+ catch (Exception err) {
+ if (dtype_str_id > 0)
+ try {
+ H5.H5Tclose(dtype_str_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("testH5DArray_string_buffer: " + err);
+ }
+
+ try {
+ dspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(dspace_id > 0);
+ dset_str_id =
+ H5.H5Dcreate(H5fid, dset_str_name, dtype_str_id, dspace_id, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5DArray_string_buffer: ", dset_str_id >= 0);
+
+ H5.H5DwriteVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, arr_str_data);
+ }
+ catch (Exception err) {
+ if (dset_str_id > 0)
+ try {
+ H5.H5Dclose(dset_str_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_str_id > 0)
+ try {
+ H5.H5Tclose(dtype_str_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("testH5DArray_string_buffer: " + 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];
+
+ ArrayList[] arr_readbuf = new ArrayList[6];
+ for (int j = 0; j < lsize; j++)
+ arr_readbuf[j] = new ArrayList<String>();
+
+ try {
+ H5.H5DreadVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, arr_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ finally {
+ if (dset_str_id > 0)
+ try {
+ H5.H5Dclose(dset_str_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_str_id > 0)
+ try {
+ H5.H5Tclose(dtype_str_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+ assertTrue("testH5DArray_string_buffer:" + arr_readbuf[0].get(0),
+ arr_str_data[0].get(0).equals(arr_readbuf[0].get(0)));
+ assertTrue("testH5DArray_string_buffer:" + arr_readbuf[1].get(0),
+ arr_str_data[1].get(0).equals(arr_readbuf[1].get(0)));
+ assertTrue("testH5DArray_string_buffer:" + arr_readbuf[2].get(0),
+ arr_str_data[2].get(0).equals(arr_readbuf[2].get(0)));
+ assertTrue("testH5DArray_string_buffer:" + arr_readbuf[3].get(0),
+ arr_str_data[3].get(0).equals(arr_readbuf[3].get(0)));
+ }
+
+ @Test
+ public void testH5DArrayenum_rw()
+ {
+ String dset_enum_name = "ArrayEnumdata";
+ long dset_enum_id = HDF5Constants.H5I_INVALID_HID;
+ long dtype_enum_id = HDF5Constants.H5I_INVALID_HID;
+ long dtype_arr_enum_id = HDF5Constants.H5I_INVALID_HID;
+ long dspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] dims = {4};
+ long lsize = 1;
+ String enum_type = "Enum_type";
+ byte[] enum_val = new byte[1];
+ String enum_name = null;
+
+ // Create a enumerate datatype
+ try {
+ dtype_enum_id = H5.H5Tcreate(HDF5Constants.H5T_ENUM, (long)1);
+ assertTrue("testH5DArrayenum_wr.H5Tarray_create: ", dtype_enum_id >= 0);
+ }
+ catch (Throwable err) {
+ if (dtype_enum_id > 0)
+ try {
+ H5.H5Tclose(dtype_enum_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("testH5DArrayenum_rw:H5Tcreate " + err);
+ }
+
+ try {
+ enum_val[0] = 10;
+ H5.H5Tenum_insert(dtype_enum_id, "RED", enum_val);
+ enum_val[0] = 11;
+ H5.H5Tenum_insert(dtype_enum_id, "GREEN", enum_val);
+ enum_val[0] = 12;
+ H5.H5Tenum_insert(dtype_enum_id, "BLUE", enum_val);
+ enum_val[0] = 13;
+ H5.H5Tenum_insert(dtype_enum_id, "ORANGE", enum_val);
+ enum_val[0] = 14;
+ H5.H5Tenum_insert(dtype_enum_id, "YELLOW", enum_val);
+
+ // Query member number and member index by member name, for enumeration type.
+ assertTrue("Can't get member number", H5.H5Tget_nmembers(dtype_enum_id) == 5);
+ assertTrue("Can't get correct index number",
+ H5.H5Tget_member_index(dtype_enum_id, "ORANGE") == 3);
+
+ // Commit enumeration datatype and close it */
+ H5.H5Tcommit(H5fid, enum_type, dtype_enum_id, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+
+ H5.H5Tclose(dtype_enum_id);
+
+ // Open the dataytpe for query
+ dtype_enum_id = H5.H5Topen(H5fid, enum_type, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5DArrayenum_rw:H5Tcreate", dtype_enum_id >= 0);
+
+ // Query member number and member index by member name, for enumeration type
+ assertTrue("Can't get member number", H5.H5Tget_nmembers(dtype_enum_id) == 5);
+ assertTrue("Can't get correct index number",
+ H5.H5Tget_member_index(dtype_enum_id, "ORANGE") == 3);
+
+ // Query member value by member name, for enumeration type
+ H5.H5Tenum_valueof(dtype_enum_id, "ORANGE", enum_val);
+ assertTrue("Incorrect value for enum member", enum_val[0] == 13);
+
+ // Query member value by member index, for enumeration type
+ H5.H5Tget_member_value(dtype_enum_id, 2, enum_val);
+ assertTrue("Incorrect value for enum member", enum_val[0] == 12);
+
+ // Query member name by member value, for enumeration type
+ enum_val[0] = 14;
+ enum_name = H5.H5Tenum_nameof(dtype_enum_id, enum_val, 16);
+ assertTrue("Incorrect name for enum member", enum_name.compareTo("YELLOW") == 0);
+
+ ArrayList[] arr_enum_data = new ArrayList[4];
+ try {
+ // Write Integer data
+ arr_enum_data[0] = new ArrayList<Integer>(Arrays.asList(10, 11, 12, 13));
+ arr_enum_data[1] = new ArrayList<Integer>(Arrays.asList(11, 12, 13, 14));
+ arr_enum_data[2] = new ArrayList<Integer>(Arrays.asList(12, 13, 14, 10));
+ arr_enum_data[3] = new ArrayList<Integer>(Arrays.asList(13, 14, 10, 11));
+ Class dataClass = arr_enum_data.getClass();
+ assertTrue("testH5DArrayenum_wr.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ dtype_arr_enum_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_U32LE, 1, dims);
+ assertTrue("testH5DArrayenum_wr.H5Tarray_create: ", dtype_arr_enum_id >= 0);
+ }
+ catch (Exception err) {
+ if (dtype_arr_enum_id > 0)
+ try {
+ H5.H5Tclose(dtype_arr_enum_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5DArrayenum_wr: " + err);
+ }
+
+ dspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(dspace_id > 0);
+ dset_enum_id = H5.H5Dcreate(H5fid, dset_enum_name, dtype_arr_enum_id, dspace_id,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5DVLwr: ", dset_enum_id >= 0);
+
+ H5.H5DwriteVL(dset_enum_id, dtype_arr_enum_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, arr_enum_data);
+ }
+ catch (Throwable err) {
+ if (dset_enum_id > 0)
+ try {
+ H5.H5Dclose(dset_enum_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_enum_id > 0)
+ try {
+ H5.H5Tclose(dtype_enum_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_arr_enum_id > 0)
+ try {
+ H5.H5Tclose(dtype_arr_enum_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("testH5DArrayenum_rw:query " + 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[] arr_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ arr_readbuf[j] = new ArrayList<Integer>();
+
+ try {
+ H5.H5DreadVL(dset_enum_id, dtype_arr_enum_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, arr_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[0].get(0),
+ arr_enum_data[0].get(0).equals(arr_readbuf[0].get(0)));
+ assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[1].get(0),
+ arr_enum_data[1].get(0).equals(arr_readbuf[1].get(0)));
+ assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[2].get(0),
+ arr_enum_data[2].get(0).equals(arr_readbuf[2].get(0)));
+ assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[3].get(0),
+ arr_enum_data[3].get(0).equals(arr_readbuf[3].get(0)));
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.testH5DArrayenum_wr: " + err);
+ }
+ finally {
+ if (dset_enum_id > 0)
+ try {
+ H5.H5Dclose(dset_enum_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_enum_id > 0)
+ try {
+ H5.H5Tclose(dtype_enum_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_arr_enum_id > 0)
+ try {
+ H5.H5Tclose(dtype_arr_enum_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+ }
}
diff --git a/java/test/testfiles/JUnit-TestH5A.txt b/java/test/testfiles/JUnit-TestH5A.txt
index efdd4a2..f31c86c 100644
--- a/java/test/testfiles/JUnit-TestH5A.txt
+++ b/java/test/testfiles/JUnit-TestH5A.txt
@@ -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
@@ -22,14 +23,16 @@ JUnit version 4.11
.testH5Adelete_by_idx_order
.testH5Arename_by_name
.testH5Acreate2_invalidobject
+.testH5AArraywr
.testH5Acreate2
.testH5Aiterate_by_name
.testH5Adelete_by_idx_null
.testH5Adelete_by_idx_invalidobject
.testH5Awrite_readVL
+.testH5AArray_string_buffer
.testH5Aget_info1
Time: XXXX
-OK (29 tests)
+OK (32 tests)
diff --git a/java/test/testfiles/JUnit-TestH5D.txt b/java/test/testfiles/JUnit-TestH5D.txt
index 288e6d0..4c30621 100644
--- a/java/test/testfiles/JUnit-TestH5D.txt
+++ b/java/test/testfiles/JUnit-TestH5D.txt
@@ -1,5 +1,8 @@
JUnit version 4.11
+.testH5DArrayenum_rw
+.testH5DVLwrVL
.testH5Dget_storage_size
+.testH5DArraywr
.testH5Diterate_write
.testH5Dcreate
.testH5Dget_offset
@@ -12,15 +15,14 @@ JUnit version 4.11
.testH5Dget_storage_size_empty
.testH5Diterate
.testH5Dget_access_plist
-.testH5Dvlen_get_buf_size
.testH5Dget_space_closed
+.testH5DArray_string_buffer
.testH5Dget_space_status
.testH5Dvlen_write_read
.testH5Dget_space
.testH5Dget_type_closed
-.testH5Dvlen_read_default_buffer
Time: XXXX
-OK (20 tests)
+OK (22 tests)
generated by cgit v0.12 at 2024-06-28 23:59:18 (GMT)