From 7a2dc4b860dd080199be81e84b84ebed550b634f Mon Sep 17 00:00:00 2001 From: jhendersonHDF Date: Thu, 15 Sep 2022 19:29:00 -0500 Subject: Cleanup some warnings in Java JNI code (#2034) (#2099) --- java/src/jni/h5aImp.c | 115 +++++++++++++++++++++++++++++--------------------- java/src/jni/h5dImp.c | 114 ++++++++++++++++++++++++++++--------------------- java/src/jni/h5rImp.c | 2 +- java/src/jni/h5util.c | 23 +++++----- 4 files changed, 146 insertions(+), 108 deletions(-) diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c index eeed806..0bc17d1 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 4b32af3..c7d7c5d 100644 --- a/java/src/jni/h5dImp.c +++ b/java/src/jni/h5dImp.c @@ -1078,8 +1078,7 @@ 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); @@ -1107,7 +1106,6 @@ 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); @@ -1127,7 +1125,7 @@ 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"); @@ -1135,8 +1133,10 @@ 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;"); @@ -1153,21 +1153,28 @@ 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); @@ -1178,8 +1185,8 @@ 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 = @@ -1189,8 +1196,8 @@ 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, @@ -1200,8 +1207,8 @@ 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); @@ -1210,8 +1217,8 @@ 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 = @@ -1226,8 +1233,8 @@ 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, @@ -1237,8 +1244,8 @@ 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, @@ -1252,14 +1259,19 @@ 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); @@ -1337,7 +1349,6 @@ 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); @@ -1353,7 +1364,7 @@ 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"); @@ -1361,7 +1372,7 @@ 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"); @@ -1371,6 +1382,8 @@ 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); @@ -1384,21 +1397,25 @@ 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; } */ @@ -1406,29 +1423,29 @@ 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; } @@ -1439,15 +1456,15 @@ 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; } @@ -1456,8 +1473,8 @@ 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; @@ -1468,6 +1485,9 @@ 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 54f4a01..763be05 100644 --- a/java/src/jni/h5rImp.c +++ b/java/src/jni/h5rImp.c @@ -312,7 +312,7 @@ 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 1e69428..5344d18 100644 --- a/java/src/jni/h5util.c +++ b/java/src/jni/h5util.c @@ -650,10 +650,8 @@ done: int h5str_sprint_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); @@ -661,8 +659,8 @@ h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *re H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); ret_value = SUCCEED; -done: +done: return ret_value; } /* h5str_sprint_reference */ @@ -2132,14 +2130,15 @@ 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; } @@ -2563,8 +2562,8 @@ 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 */ unsigned char *sm_buf = NULL; /* buffer for raw data */ @@ -2758,7 +2757,7 @@ 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 */ unsigned char *sm_buf = NULL; /* buffer for raw data */ hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */ -- cgit v0.12