diff options
Diffstat (limited to 'java')
-rw-r--r-- | java/src/jni/h5aImp.c | 115 | ||||
-rw-r--r-- | java/src/jni/h5dImp.c | 114 | ||||
-rw-r--r-- | java/src/jni/h5rImp.c | 110 | ||||
-rw-r--r-- | java/src/jni/h5util.c | 101 |
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 38eed3b..4140a9e 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); } |