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-rw-r--r--java/src/jni/h5aImp.c115
-rw-r--r--java/src/jni/h5dImp.c114
-rw-r--r--java/src/jni/h5rImp.c110
-rw-r--r--java/src/jni/h5util.c101
4 files changed, 278 insertions, 162 deletions
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index b139239..e5e8462 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -1067,10 +1067,9 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
H5T_class_t type_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
- jsize n;
+ jsize n = 0;
htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean readBufIsCopy;
+ herr_t status = FAIL;
jbyteArray *readBuf = NULL;
UNUSED(clss);
@@ -1104,7 +1103,6 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
jobject *jList = NULL;
size_t i, j, x;
- char *cp_vp = NULL;
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
@@ -1123,7 +1121,7 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
H5_LIBRARY_ERROR(ENVONLY);
/* Cache class types */
- jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
+ /* 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");
@@ -1131,8 +1129,10 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
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;");
@@ -1149,21 +1149,28 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
/* 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);
- cp_vp = (char *)rawBuf + i * typeSize;
/* Get the number of sequence elements */
- jsize nelmts = ((hvl_t *)cp_vp)->len;
+ 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 < nelmts; j++) {
+ for (j = 0; j < (size_t)nelmts; j++) {
switch (vlClass) {
/* case H5T_BOOL: {
jboolean boolValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&boolValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j*vlSize+x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
@@ -1174,8 +1181,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&byteValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj =
@@ -1185,8 +1192,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
}
case sizeof(jshort): {
jshort shortValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&shortValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
@@ -1196,8 +1203,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
}
case sizeof(jint): {
jint intValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&intValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
@@ -1206,8 +1213,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
}
case sizeof(jlong): {
jlong longValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&longValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj =
@@ -1222,8 +1229,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&floatValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
@@ -1233,8 +1240,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
}
case sizeof(jdouble): {
jdouble doubleValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&doubleValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
@@ -1248,14 +1255,19 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
case H5T_REFERENCE: {
jboolean bb;
jbyte *barray = NULL;
- if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, vlSize)))
+
+ 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 < (int)vlSize; x++) {
- barray[x] = ((jbyte *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ 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);
@@ -1340,7 +1352,6 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
jobject *jList = NULL;
size_t i, j, x;
- char *cp_vp = NULL;
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
@@ -1356,7 +1367,7 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
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 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");
@@ -1364,7 +1375,7 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
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 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");
@@ -1374,6 +1385,8 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
/* 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);
@@ -1387,22 +1400,25 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
- cp_vp = (char *)rawBuf + i * typeSize;
- ((hvl_t *)cp_vp)->len = jnelmts;
+ if (jnelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: number of VL elements < 0");
- if (NULL == (((hvl_t *)cp_vp)->p = HDmalloc(jnelmts * vlSize)))
+ 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 < (int)jnelmts; j++) {
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&boolValue)[x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
}
break;
} */
@@ -1410,29 +1426,29 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&byteValue)[x];
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&shortValue)[x];
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&intValue)[x];
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&longValue)[x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
}
break;
}
@@ -1443,15 +1459,15 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&floatValue)[x];
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&doubleValue)[x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
}
break;
}
@@ -1460,8 +1476,8 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
}
case H5T_REFERENCE: {
jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)barray)[x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
}
ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
break;
@@ -1472,6 +1488,9 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
}
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++) */
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index 244d13c..e6e9a76 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -1090,8 +1090,7 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
H5T_class_t type_class;
jsize n;
htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean readBufIsCopy;
+ herr_t status = FAIL;
jbyteArray *readBuf = NULL;
UNUSED(clss);
@@ -1119,7 +1118,6 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
jobject *jList = NULL;
size_t i, j, x;
- char *cp_vp = NULL;
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
@@ -1139,7 +1137,7 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
H5_LIBRARY_ERROR(ENVONLY);
/* Cache class types */
- jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
+ /* 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");
@@ -1147,8 +1145,10 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
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;");
@@ -1165,21 +1165,28 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
/* 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);
- cp_vp = (char *)rawBuf + i * typeSize;
/* Get the number of sequence elements */
- jsize nelmts = ((hvl_t *)cp_vp)->len;
+ 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 < nelmts; j++) {
+ for (j = 0; j < (size_t)nelmts; j++) {
switch (vlClass) {
/*case H5T_BOOL: {
jboolean boolValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&boolValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j*vlSize+x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
@@ -1190,8 +1197,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&byteValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj =
@@ -1201,8 +1208,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
}
case sizeof(jshort): {
jshort shortValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&shortValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
@@ -1212,8 +1219,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
}
case sizeof(jint): {
jint intValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&intValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
@@ -1222,8 +1229,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
}
case sizeof(jlong): {
jlong longValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&longValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj =
@@ -1238,8 +1245,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&floatValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
@@ -1249,8 +1256,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
}
case sizeof(jdouble): {
jdouble doubleValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&doubleValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
@@ -1264,14 +1271,19 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
case H5T_REFERENCE: {
jboolean bb;
jbyte *barray = NULL;
- if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, vlSize)))
+
+ 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 < (int)vlSize; x++) {
- barray[x] = ((jbyte *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+ 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);
@@ -1349,7 +1361,6 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
jobject *jList = NULL;
size_t i, j, x;
- char *cp_vp = NULL;
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
@@ -1365,7 +1376,7 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
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 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");
@@ -1373,7 +1384,7 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
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 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");
@@ -1383,6 +1394,8 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
/* 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);
@@ -1396,21 +1409,25 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
- cp_vp = (char *)rawBuf + i * typeSize;
- ((hvl_t *)cp_vp)->len = jnelmts;
+ 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 == (((hvl_t *)cp_vp)->p = HDmalloc(jnelmts * vlSize)))
+ 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 < (int)jnelmts; j++) {
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&boolValue)[x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
}
break;
} */
@@ -1418,29 +1435,29 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&byteValue)[x];
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&shortValue)[x];
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&intValue)[x];
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&longValue)[x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
}
break;
}
@@ -1451,15 +1468,15 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&floatValue)[x];
+ 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 < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&doubleValue)[x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
}
break;
}
@@ -1468,8 +1485,8 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
}
case H5T_REFERENCE: {
jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)barray)[x];
+ for (x = 0; x < vlSize; x++) {
+ ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
}
ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
break;
@@ -1480,6 +1497,9 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
}
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++) */
diff --git a/java/src/jni/h5rImp.c b/java/src/jni/h5rImp.c
index 527c801..1bdb381 100644
--- a/java/src/jni/h5rImp.c
+++ b/java/src/jni/h5rImp.c
@@ -51,9 +51,13 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1object(JNIEnv *env, jclass clss, jlong loc_id, js
if (NULL == (refBuf = HDcalloc(1, H5R_REF_BUF_SIZE)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rcreate_object: failed to allocate reference buffer");
- if ((status = H5Rcreate_object((hid_t)loc_id, refName, (hid_t)aid, (const H5R_ref_t *)refBuf)) < 0)
+ H5R_ref_t loc_ref;
+ if ((status = H5Rcreate_object((hid_t)loc_id, refName, (hid_t)aid, &loc_ref)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(refBuf, &loc_ref, H5R_REF_BUF_SIZE);
+
if (NULL == (ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
@@ -93,10 +97,13 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1region(JNIEnv *env, jclass clss, jlong loc_id, js
if (NULL == (refBuf = HDcalloc(1, H5R_REF_BUF_SIZE)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rcreate_region: failed to allocate reference buffer");
- if ((status = H5Rcreate_region((hid_t)loc_id, refName, space_id, (hid_t)aid, (const H5R_ref_t *)refBuf)) <
- 0)
+ H5R_ref_t loc_ref;
+ if ((status = H5Rcreate_region((hid_t)loc_id, refName, space_id, (hid_t)aid, &loc_ref)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(refBuf, &loc_ref, H5R_REF_BUF_SIZE);
+
if (NULL == (ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
@@ -141,10 +148,13 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1attr(JNIEnv *env, jclass clss, jlong loc_id, jstr
if (NULL == (refBuf = HDcalloc(1, H5R_REF_BUF_SIZE)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rcreate_attr: failed to allocate reference buffer");
- if ((status = H5Rcreate_attr((hid_t)loc_id, refName, attrName, (hid_t)aid, (const H5R_ref_t *)refBuf)) <
- 0)
+ H5R_ref_t loc_ref;
+ if ((status = H5Rcreate_attr((hid_t)loc_id, refName, attrName, (hid_t)aid, &loc_ref)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(refBuf, &loc_ref, H5R_REF_BUF_SIZE);
+
if (NULL == (ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
@@ -187,7 +197,12 @@ Java_hdf_hdf5lib_H5_H5Rdestroy(JNIEnv *env, jclass clss, jbyteArray ref)
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rdestroy: reference buffer not pinned");
- if ((status = H5Rdestroy((const H5R_ref_t *)refBuf)) < 0)
+ H5R_ref_t loc_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref, refBuf, H5R_REF_BUF_SIZE);
+
+ if ((status = H5Rdestroy(&loc_ref)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
@@ -220,7 +235,12 @@ Java_hdf_hdf5lib_H5_H5Rget_1type(JNIEnv *env, jclass clss, jbyteArray ref)
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_type: reference buffer not pinned");
- if ((ref_type = H5Rget_type((const H5R_ref_t *)refBuf)) < 0)
+ H5R_ref_t loc_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref, refBuf, H5R_REF_BUF_SIZE);
+
+ if ((ref_type = H5Rget_type(&loc_ref)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
@@ -267,7 +287,13 @@ Java_hdf_hdf5lib_H5_H5Requal(JNIEnv *env, jclass clss, jbyteArray ref1, jbyteArr
PIN_BYTE_ARRAY(ENVONLY, ref2, refBuf2, &isCopy, "H5Requal: reference2 buffer not pinned");
- if ((bval = H5Requal((const H5R_ref_t *)refBuf1, (const H5R_ref_t *)refBuf2)) < 0)
+ H5R_ref_t loc_ref1, loc_ref2;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref1, refBuf1, H5R_REF_BUF_SIZE);
+ HDmemcpy(&loc_ref2, refBuf2, H5R_REF_BUF_SIZE);
+
+ if ((bval = H5Requal(&loc_ref1, &loc_ref2)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
status = bval;
@@ -312,9 +338,17 @@ Java_hdf_hdf5lib_H5_H5Rcopy(JNIEnv *env, jclass clss, jbyteArray src_ref)
if (NULL == (dst_refBuf = HDcalloc(1, H5R_REF_BUF_SIZE)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rcreate_attr: failed to allocate dst reference buffer");
- if ((status = H5Rcopy((const H5R_ref_t *)src_refBuf, (const H5R_ref_t *)dst_refBuf)) < 0)
+ H5R_ref_t loc_src_ref, loc_dst_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_src_ref, src_refBuf, H5R_REF_BUF_SIZE);
+ HDmemcpy(&loc_dst_ref, dst_refBuf, H5R_REF_BUF_SIZE);
+
+ if ((status = H5Rcopy(&loc_src_ref, &loc_dst_ref)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ HDmemcpy(dst_refBuf, &loc_dst_ref, H5R_REF_BUF_SIZE);
+
if (NULL == (dst_ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
@@ -355,7 +389,12 @@ Java_hdf_hdf5lib_H5__1H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref,
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Ropen_object: reference buffer not pinned");
- if ((retVal = H5Ropen_object((const H5R_ref_t *)refBuf, (hid_t)rapl_id, (hid_t)oapl_id)) < 0)
+ H5R_ref_t loc_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref, refBuf, H5R_REF_BUF_SIZE);
+
+ if ((retVal = H5Ropen_object(&loc_ref, (hid_t)rapl_id, (hid_t)oapl_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
@@ -390,7 +429,12 @@ Java_hdf_hdf5lib_H5__1H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref,
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Ropen_region: reference buffer not pinned");
- if ((retVal = H5Ropen_region((const H5R_ref_t *)refBuf, (hid_t)rapl_id, (hid_t)oapl_id)) < 0)
+ H5R_ref_t loc_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref, refBuf, H5R_REF_BUF_SIZE);
+
+ if ((retVal = H5Ropen_region(&loc_ref, (hid_t)rapl_id, (hid_t)oapl_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
@@ -425,7 +469,12 @@ Java_hdf_hdf5lib_H5__1H5Ropen_1attr(JNIEnv *env, jclass clss, jbyteArray ref, jl
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Ropen_attr: reference buffer not pinned");
- if ((retVal = H5Ropen_attr((const H5R_ref_t *)refBuf, (hid_t)rapl_id, (hid_t)aapl_id)) < 0)
+ H5R_ref_t loc_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref, refBuf, H5R_REF_BUF_SIZE);
+
+ if ((retVal = H5Ropen_attr(&loc_ref, (hid_t)rapl_id, (hid_t)aapl_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
@@ -455,7 +504,12 @@ Java_hdf_hdf5lib_H5_H5Rget_1obj_1type3(JNIEnv *env, jclass clss, jbyteArray ref,
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_obj_type3: reference buffer not pinned");
- if ((retVal = H5Rget_obj_type3((const H5R_ref_t *)refBuf, (hid_t)rapl_id, &object_info)) < 0)
+ H5R_ref_t loc_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref, refBuf, H5R_REF_BUF_SIZE);
+
+ if ((retVal = H5Rget_obj_type3(&loc_ref, (hid_t)rapl_id, &object_info)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (retVal >= 0)
@@ -490,14 +544,19 @@ Java_hdf_hdf5lib_H5_H5Rget_1file_1name(JNIEnv *env, jclass clss, jbyteArray ref)
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_file_name: reference buffer not pinned");
+ H5R_ref_t loc_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref, refBuf, H5R_REF_BUF_SIZE);
+
/* Get the length of the name */
- if ((buf_size = H5Rget_file_name((const H5R_ref_t *)refBuf, NULL, 0)) < 0)
+ if ((buf_size = H5Rget_file_name(&loc_ref, NULL, 0)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (namePtr = HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rget_file_name: malloc failed");
- if ((check_size = H5Rget_file_name((const H5R_ref_t *)refBuf, namePtr, (size_t)buf_size + 1)) < 0)
+ if ((check_size = H5Rget_file_name(&loc_ref, namePtr, (size_t)buf_size + 1)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
namePtr[buf_size] = '\0';
@@ -535,15 +594,19 @@ Java_hdf_hdf5lib_H5_H5Rget_1obj_1name(JNIEnv *env, jclass clss, jbyteArray ref,
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_obj_name: reference buffer not pinned");
+ H5R_ref_t loc_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref, refBuf, H5R_REF_BUF_SIZE);
+
/* Get the length of the name */
- if ((buf_size = H5Rget_obj_name((const H5R_ref_t *)refBuf, (hid_t)rapl_id, NULL, 0)) < 0)
+ if ((buf_size = H5Rget_obj_name(&loc_ref, (hid_t)rapl_id, NULL, 0)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (namePtr = HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rget_obj_name: malloc failed");
- if ((check_size =
- H5Rget_obj_name((const H5R_ref_t *)refBuf, (hid_t)rapl_id, namePtr, (size_t)buf_size + 1)) < 0)
+ if ((check_size = H5Rget_obj_name(&loc_ref, (hid_t)rapl_id, namePtr, (size_t)buf_size + 1)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
namePtr[buf_size] = '\0';
@@ -581,14 +644,19 @@ Java_hdf_hdf5lib_H5_H5Rget_1attr_1name(JNIEnv *env, jclass clss, jbyteArray ref)
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_attr_name: reference buffer not pinned");
+ H5R_ref_t loc_ref;
+
+ HDcompile_assert(H5R_REF_BUF_SIZE <= sizeof(H5R_ref_t));
+ HDmemcpy(&loc_ref, refBuf, H5R_REF_BUF_SIZE);
+
/* Get the length of the name */
- if ((buf_size = H5Rget_attr_name((const H5R_ref_t *)refBuf, NULL, 0)) < 0)
+ if ((buf_size = H5Rget_attr_name(&loc_ref, NULL, 0)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (namePtr = HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rget_attr_name: malloc failed");
- if ((check_size = H5Rget_attr_name((const H5R_ref_t *)refBuf, namePtr, (size_t)buf_size + 1)) < 0)
+ if ((check_size = H5Rget_attr_name(&loc_ref, namePtr, (size_t)buf_size + 1)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
namePtr[buf_size] = '\0';
@@ -887,7 +955,7 @@ Java_hdf_hdf5lib_H5_H5Rget_1name_1string(JNIEnv *env, jclass clss, jlong loc_id,
jbyteArray ref)
{
jboolean isCopy;
- jstring str;
+ jstring str = NULL;
jsize refBufLen;
jbyte *refBuf = NULL;
char *aName = NULL;
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 31eb320..e8417b6 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -652,10 +652,8 @@ done:
int
h5str_sprint_old_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *ref_buf)
{
- hid_t region = H5I_INVALID_HID;
- char ref_name[1024];
-
- int ret_value = FAIL;
+ char ref_name[1024];
+ int ret_value = FAIL;
if ((H5Rget_name(region_obj, H5R_DATASET_REGION, ref_buf, (char *)ref_name, 1024)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -663,8 +661,8 @@ h5str_sprint_old_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
ret_value = SUCCEED;
-done:
+done:
return ret_value;
} /* h5str_sprint_reference */
@@ -686,9 +684,9 @@ h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, void *ref_p)
int ret_value = FAIL;
buf_size = H5Rget_file_name(ref_vp, NULL, 0);
- if (buf_size) {
+ if (buf_size > 0) {
ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1);
- if (H5Rget_file_name(ref_vp, ref_name, buf_size + 1) >= 0) {
+ if (H5Rget_file_name(ref_vp, ref_name, (size_t)buf_size + 1) >= 0) {
ref_name[buf_size] = '\0';
if (!h5str_append(out_str, ref_name))
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
@@ -698,9 +696,9 @@ h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, void *ref_p)
}
buf_size = H5Rget_obj_name(ref_vp, H5P_DEFAULT, NULL, 0);
- if (buf_size) {
+ if (buf_size > 0) {
ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1);
- if (H5Rget_obj_name(ref_vp, H5P_DEFAULT, ref_name, buf_size + 1) >= 0) {
+ if (H5Rget_obj_name(ref_vp, H5P_DEFAULT, ref_name, (size_t)buf_size + 1) >= 0) {
ref_name[buf_size] = '\0';
if (!h5str_append(out_str, ref_name))
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
@@ -711,9 +709,9 @@ h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, void *ref_p)
if (H5Rget_type(ref_vp) == H5R_ATTR) {
buf_size = H5Rget_attr_name(ref_vp, NULL, 0);
- if (buf_size) {
+ if (buf_size > 0) {
ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1);
- if (H5Rget_attr_name(ref_vp, ref_name, buf_size + 1) >= 0) {
+ if (H5Rget_attr_name(ref_vp, ref_name, (size_t)buf_size + 1) >= 0) {
ref_name[buf_size] = '\0';
if (!h5str_append(out_str, ref_name))
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
@@ -1240,16 +1238,18 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
H5O_type_t obj_type = -1; /* Object type */
H5R_type_t ref_type; /* Reference type */
- H5R_ref_t *ref_vp = (H5R_ref_t *)cptr;
+ H5R_ref_t loc_ref;
- ref_type = H5Rget_type(ref_vp);
- if (!h5str_is_zero(ref_vp, H5Tget_size(H5T_STD_REF))) {
+ HDmemcpy(&loc_ref, cptr, sizeof(H5R_ref_t));
+
+ ref_type = H5Rget_type(&loc_ref);
+ if (!h5str_is_zero(&loc_ref, H5Tget_size(H5T_STD_REF))) {
switch (ref_type) {
case H5R_OBJECT1:
- if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
+ if (H5Rget_obj_type3(&loc_ref, H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_DATASET:
- if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
+ if (h5str_region_dataset(ENVONLY, out_str, &loc_ref, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
@@ -1263,8 +1263,8 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
* OID of the referenced object. */
H5O_info2_t oi;
char *obj_tok_str = NULL;
- if ((new_obj_id = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >=
- 0) {
+ if ((new_obj_id =
+ H5Ropen_object(&loc_ref, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
H5Oget_info3(new_obj_id, &oi, H5O_INFO_BASIC);
H5Otoken_to_str(new_obj_id, &oi.token, &obj_tok_str);
if (H5Dclose(new_obj_id) < 0)
@@ -1337,17 +1337,17 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
H5_LIBRARY_ERROR(ENVONLY);
break;
case H5R_DATASET_REGION1:
- if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
+ if (h5str_region_dataset(ENVONLY, out_str, &loc_ref, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
case H5R_OBJECT2:
- if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
+ if (H5Rget_obj_type3(&loc_ref, H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_GROUP:
break;
case H5O_TYPE_DATASET:
- if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
+ if (h5str_region_dataset(ENVONLY, out_str, &loc_ref, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
@@ -1365,11 +1365,11 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
H5_ASSERTION_ERROR(ENVONLY, "h5str_sprintf: H5R_OBJECT2 failed");
break;
case H5R_DATASET_REGION2:
- if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
+ if (h5str_region_dataset(ENVONLY, out_str, &loc_ref, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
case H5R_ATTR:
- if ((new_obj_id = H5Ropen_attr(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ if ((new_obj_id = H5Ropen_attr(&loc_ref, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
if (h5str_dump_region_attribute(ENVONLY, out_str, new_obj_id) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (H5Aclose(new_obj_id) < 0)
@@ -1383,7 +1383,7 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
} /* end switch */
}
- if (H5Rdestroy(ref_vp) < 0)
+ if (H5Rdestroy(&loc_ref) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
@@ -2395,14 +2395,15 @@ h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hs
}
for (block_index = 0; block_index < block_nelmts; block_index++) {
- mem = ((unsigned char *)_mem) + block_index * size;
+ hvl_t vl_elem;
+
+ HDmemcpy(&vl_elem, ((unsigned char *)_mem) + block_index * size, sizeof(hvl_t));
/* Get the number of sequence elements */
- nelmts = ((hvl_t *)mem)->len;
+ nelmts = vl_elem.len;
/* dump the array element */
- if (h5str_render_bin_output(stream, container, memb, ((char *)(((hvl_t *)mem)->p)), nelmts) <
- 0) {
+ if (h5str_render_bin_output(stream, container, memb, ((char *)(vl_elem.p)), nelmts) < 0) {
ret_value = FAIL;
break;
}
@@ -2420,11 +2421,14 @@ h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hs
/* Region data */
for (block_index = 0; block_index < block_nelmts; block_index++) {
- mem = ((unsigned char *)_mem) + block_index * size;
- if ((region_id = H5Ropen_object((H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ H5R_ref_t loc_ref;
+
+ HDmemcpy(&loc_ref, ((unsigned char *)_mem) + block_index * size, sizeof(H5R_ref_t));
+
+ if ((region_id = H5Ropen_object(&loc_ref, H5P_DEFAULT, H5P_DEFAULT)) < 0)
continue;
- if ((region_space = H5Ropen_region((H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
- if (!h5str_is_zero(mem, H5Tget_size(H5T_STD_REF))) {
+ if ((region_space = H5Ropen_region(&loc_ref, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ if (!h5str_is_zero(&loc_ref, H5Tget_size(H5T_STD_REF))) {
region_type = H5Sget_select_type(region_space);
if (region_type == H5S_SEL_POINTS)
ret_value =
@@ -2849,7 +2853,7 @@ h5str_dump_region_attribute(JNIEnv *env, h5str_t *str, hid_t region_id)
H5Sget_simple_extent_dims(region_space, total_size, NULL);
p_nelmts = 1;
- for (i = 0; i < sndims; i++)
+ for (i = 0; i < (size_t)sndims; i++)
p_nelmts *= total_size[i];
if ((atype = H5Aget_type(region_id)) < 0) {
@@ -2924,8 +2928,8 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
int carry; /* counter carry value */
/* Print info */
- hsize_t p_nelmts; /* total selected elmts */
- size_t p_type_nbytes; /* size of memory type */
+ hssize_t p_nelmts; /* total selected elmts */
+ size_t p_type_nbytes; /* size of memory type */
/* Stripmine info */
void *sm_buf = NULL; /* buffer for raw data */
@@ -2962,7 +2966,9 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) {
- p_nelmts = H5Sget_simple_extent_npoints(f_space);
+ if ((p_nelmts = H5Sget_simple_extent_npoints(f_space)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
if (NULL ==
(sm_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
@@ -2972,11 +2978,11 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
H5_LIBRARY_ERROR(ENVONLY);
if (binary_order == 99) {
- if (h5str_dump_simple_data(ENVONLY, stream, dset, H5T_STD_REF, sm_buf, p_nelmts) < 0)
+ if (h5str_dump_simple_data(ENVONLY, stream, dset, H5T_STD_REF, sm_buf, (size_t)p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
- if (h5str_render_bin_output(stream, dset, H5T_STD_REF, sm_buf, p_nelmts) < 0)
+ if (h5str_render_bin_output(stream, dset, H5T_STD_REF, sm_buf, (size_t)p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
}
@@ -3058,7 +3064,7 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
HDmemset(hs_offset, 0, sizeof hs_offset);
HDmemset(zero, 0, sizeof zero);
- for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) {
+ for (elmtno = 0; elmtno < (hsize_t)p_nelmts; elmtno += hs_nelmts) {
/* Calculate the hyperslab size */
if (ndims > 0) {
for (i = 0, hs_nelmts = 1; i < (size_t)ndims; i++) {
@@ -3145,7 +3151,7 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
int ndims; /* rank of dataspace */
unsigned i; /* counters */
hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/
- hsize_t p_nelmts; /* total selected elmts */
+ hssize_t p_nelmts; /* total selected elmts */
void *sm_buf = NULL; /* buffer for raw data */
hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */
@@ -3173,7 +3179,9 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
H5_LIBRARY_ERROR(ENVONLY);
if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) {
- p_nelmts = H5Sget_simple_extent_npoints(f_space);
+ if ((p_nelmts = H5Sget_simple_extent_npoints(f_space)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
if (NULL ==
(sm_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
@@ -3183,11 +3191,11 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
H5_LIBRARY_ERROR(ENVONLY);
if (binary_order == 99) {
- if (h5str_dump_simple_data(ENVONLY, stream, attr_id, H5T_STD_REF, sm_buf, p_nelmts) < 0)
+ if (h5str_dump_simple_data(ENVONLY, stream, attr_id, H5T_STD_REF, sm_buf, (size_t)p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
- if (h5str_render_bin_output(stream, attr_id, H5T_STD_REF, sm_buf, p_nelmts) < 0)
+ if (h5str_render_bin_output(stream, attr_id, H5T_STD_REF, sm_buf, (size_t)p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
}
@@ -3238,7 +3246,7 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
if (h5str_detect_vlen(p_type) != 0)
vl_data = 1;
- alloc_size = p_nelmts * H5Tget_size(p_type);
+ alloc_size = (size_t)p_nelmts * H5Tget_size(p_type);
if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)alloc_size)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
@@ -3247,11 +3255,12 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
H5_LIBRARY_ERROR(ENVONLY);
if (binary_order == 99) {
- if (h5str_dump_simple_data(ENVONLY, stream, attr_id, p_type, sm_buf, p_nelmts) < 0)
+ if (h5str_dump_simple_data(ENVONLY, stream, attr_id, p_type, sm_buf, (size_t)p_nelmts) <
+ 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
- if (h5str_render_bin_output(stream, attr_id, p_type, sm_buf, p_nelmts) < 0)
+ if (h5str_render_bin_output(stream, attr_id, p_type, sm_buf, (size_t)p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
generated by cgit v0.12 at 2024-10-30 09:25:01 (GMT)