From 9c61f7b1e1cfb65cd562febfbb7ad49e8785825c Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue, 25 Oct 2022 23:33:30 -0500 Subject: JNI: Improve varlen datatype handling in H5A/H5D read/write functions (#2156) * Improve JNI VL datatype read/write to handle complex combinations * Implement VL of VL JNI writes and reads * Add Java VLofVL test for attributtes * Changes to address review issues * Fix H5Aread vl blocks --- java/src/jni/h5aImp.c | 572 ++++++---------------------------- java/src/jni/h5dImp.c | 547 ++++++-------------------------- java/src/jni/h5fImp.c | 4 +- java/src/jni/h5tImp.c | 4 +- java/src/jni/h5util.c | 545 ++++++++++++++++++++++++++++++++ java/src/jni/h5util.h | 5 + java/test/TestH5A.java | 161 +++++++++- java/test/TestH5D.java | 181 ++++++++++- java/test/TestH5R.java | 24 +- java/test/testfiles/JUnit-TestH5A.txt | 3 +- java/test/testfiles/JUnit-TestH5D.txt | 3 +- release_docs/RELEASE.txt | 9 +- 12 files changed, 1088 insertions(+), 970 deletions(-) diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c index 086fea8..4665376 100644 --- a/java/src/jni/h5aImp.c +++ b/java/src/jni/h5aImp.c @@ -156,13 +156,15 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf, jboolean isCriticalPinning) { - jboolean readBufIsCopy; - jbyte *readBuf = NULL; - hsize_t dims[H5S_MAX_RANK]; - hid_t sid = H5I_INVALID_HID; - jsize n; - htri_t vl_data_class; - herr_t status = FAIL; + jboolean readBufIsCopy; + jbyte *readBuf = NULL; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + size_t typeSize; + H5T_class_t type_class; + jsize vl_array_len; // Only used by vl_data_class types + htri_t vl_data_class; + herr_t status = FAIL; UNUSED(clss); @@ -174,40 +176,60 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t if (vl_data_class) { /* Get size of data array */ - if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); } - dims[0] = (hsize_t)n; - if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + if (!(typeSize = H5Tget_size(mem_type_id))) H5_LIBRARY_ERROR(ENVONLY); - } - if (isCriticalPinning) { - PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, - "H5Aread: read buffer not critically pinned"); + if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Aread: failed to allocate raw VL read buffer"); } else { - PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Aread: read buffer not pinned"); + if (isCriticalPinning) { + PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, + "H5Aread: read buffer not critically pinned"); + } + else { + PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Aread: read buffer not pinned"); + } } if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0) H5_LIBRARY_ERROR(ENVONLY); + if (vl_data_class) { + if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf); + } + done: if (readBuf) { if ((status >= 0) && vl_data_class) { + dims[0] = (hsize_t)vl_array_len; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf); + if (sid >= 0) H5Sclose(sid); } - if (isCriticalPinning) { - UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); + if (vl_data_class) { + HDfree(readBuf); } else { - UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); + if (isCriticalPinning) { + UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); + } + else { + UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); + } } } @@ -223,38 +245,52 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf, jboolean isCriticalPinning) { - jboolean writeBufIsCopy; - jbyte *writeBuf = NULL; - hsize_t dims[H5S_MAX_RANK]; - hid_t sid = H5I_INVALID_HID; - jsize n; - htri_t vl_data_class; - herr_t status = FAIL; + jboolean writeBufIsCopy; + jbyte *writeBuf = NULL; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + size_t typeSize; + H5T_class_t type_class; + jsize vl_array_len; // Only used by vl_data_class types + htri_t vl_data_class; + herr_t status = FAIL; UNUSED(clss); if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer is NULL"); - /* Get size of data array */ - if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { - CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); - } - - dims[0] = (hsize_t)n; - if ((sid = H5Screate_simple(1, dims, NULL)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (isCriticalPinning) { - PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, - "H5Awrite: write buffer not critically pinned"); + if (vl_data_class) { + /* Get size of data array */ + if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer length < 0"); + } + + if (!(typeSize = H5Tget_size(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Awrite: failed to allocate raw VL write buffer"); } else { - PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Awrite: write buffer not pinned"); + if (isCriticalPinning) { + PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, + "H5Awrite: write buffer not critically pinned"); + } + else { + PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Awrite: write buffer not pinned"); + } + } + + if (vl_data_class) { + if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf); } if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0) @@ -262,14 +298,24 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_ done: if (writeBuf) { - if ((status >= 0) && vl_data_class) + if ((status >= 0) && vl_data_class) { + dims[0] = (hsize_t)vl_array_len; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); + } - if (isCriticalPinning) { - UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); + if (vl_data_class) { + HDfree(writeBuf); } else { - UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); + if (isCriticalPinning) { + UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); + } + else { + UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); + } } } @@ -1064,244 +1110,9 @@ done: JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) { - H5T_class_t type_class; - hsize_t dims[H5S_MAX_RANK]; - hid_t sid = H5I_INVALID_HID; - jsize n = 0; - htri_t vl_data_class; - herr_t status = FAIL; - jbyteArray *readBuf = NULL; - - UNUSED(clss); - - if (NULL == buf) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: read buffer is NULL"); - - if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if (vl_data_class) { - /* Get size of data array */ - if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { - CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: readBuf length < 0"); - } - - dims[0] = (hsize_t)n; - if ((sid = H5Screate_simple(1, dims, NULL)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - } - - if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (type_class == H5T_VLEN) { - size_t typeSize; - hid_t memb = H5I_INVALID_HID; - H5T_class_t vlClass; - size_t vlSize; - void *rawBuf = NULL; - jobjectArray jList = NULL; - - size_t i, j, x; - - if (!(typeSize = H5Tget_size(mem_type_id))) - H5_LIBRARY_ERROR(ENVONLY); - - if (!(memb = H5Tget_super(mem_type_id))) - H5_LIBRARY_ERROR(ENVONLY); - if ((vlClass = H5Tget_class((hid_t)memb)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (!(vlSize = H5Tget_size(memb))) - H5_LIBRARY_ERROR(ENVONLY); - - if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AreadVL: failed to allocate raw VL read buffer"); + herr_t status = FAIL; - if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)rawBuf)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - /* Cache class types */ - /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */ - jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); - jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); - jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); - jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); - jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); - jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); - - /* - jmethodID boolValueMid = - ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;"); - */ - jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;"); - jmethodID shortValueMid = - ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;"); - jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;"); - jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;"); - jmethodID floatValueMid = - ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;"); - jmethodID doubleValueMid = - ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;"); - - // retrieve the java.util.List interface class - jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List"); - jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z"); - - /* Convert each element to a list */ - for (i = 0; i < (size_t)n; i++) { - hvl_t vl_elem; - - // The list we're going to return: - if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - /* Get the number of sequence elements */ - HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t)); - - jsize nelmts = (jsize)vl_elem.len; - if (vl_elem.len != (size_t)nelmts) - H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadVL: overflow of number of VL elements"); - if (nelmts < 0) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: number of VL elements < 0"); - - jobject jobj = NULL; - for (j = 0; j < (size_t)nelmts; j++) { - switch (vlClass) { - /* case H5T_BOOL: { - jboolean boolValue; - for (x = 0; x < vlSize; x++) { - ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } */ - case H5T_INTEGER: { - switch (vlSize) { - case sizeof(jbyte): { - jbyte byteValue; - for (x = 0; x < vlSize; x++) { - ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = - ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jshort): { - jshort shortValue; - for (x = 0; x < vlSize; x++) { - ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid, - shortValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jint): { - jint intValue; - for (x = 0; x < vlSize; x++) { - ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jlong): { - jlong longValue; - for (x = 0; x < vlSize; x++) { - ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = - ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - } - break; - } - case H5T_FLOAT: { - switch (vlSize) { - case sizeof(jfloat): { - jfloat floatValue; - for (x = 0; x < vlSize; x++) { - ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid, - (double)floatValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jdouble): { - jdouble doubleValue; - for (x = 0; x < vlSize; x++) { - ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid, - doubleValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - } - break; - } - case H5T_REFERENCE: { - jboolean bb; - jbyte *barray = NULL; - - jsize byteArraySize = (jsize)vlSize; - if (vlSize != (size_t)byteArraySize) - H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadVL: overflow of byteArraySize"); - - if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb, - "readVL reference: byte array not pinned"); - - for (x = 0; x < vlSize; x++) { - barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x]; - } - if (barray) - UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT); - break; - } - default: - H5_UNIMPLEMENTED(ENVONLY, "H5AreadVL: invalid class type"); - break; - } - - // Add it to the list - ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } - } /* end for */ - - if (rawBuf) - HDfree(rawBuf); - } - else { - if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - } - -done: - if (readBuf) { - if ((status >= 0) && vl_data_class) { - H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf); - if (sid >= 0) - H5Sclose(sid); - } - - UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); - } + status = Java_hdf_hdf5lib_H5_H5Aread(env, clss, attr_id, mem_type_id, (jbyteArray)buf, JNI_TRUE); return (jint)status; } /* end Java_hdf_hdf5lib_H5_H5AreadVL */ @@ -1314,206 +1125,9 @@ done: JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) { - H5T_class_t type_class; - hsize_t dims[H5S_MAX_RANK]; - hid_t sid = H5I_INVALID_HID; - jsize n; - htri_t vl_data_class; - herr_t status = FAIL; - jboolean writeBufIsCopy; - jbyteArray writeBuf = NULL; - - UNUSED(clss); - - if (NULL == buf) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL"); - - /* Get size of data array */ - if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { - CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: readBuf length < 0"); - } + herr_t status = FAIL; - dims[0] = (hsize_t)n; - if ((sid = H5Screate_simple(1, dims, NULL)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (type_class == H5T_VLEN) { - size_t typeSize; - hid_t memb = H5I_INVALID_HID; - H5T_class_t vlClass; - size_t vlSize; - void *rawBuf = NULL; - jobjectArray jList = NULL; - - size_t i, j, x; - - if (!(typeSize = H5Tget_size(mem_type_id))) - H5_LIBRARY_ERROR(ENVONLY); - - if (!(memb = H5Tget_super(mem_type_id))) - H5_LIBRARY_ERROR(ENVONLY); - if ((vlClass = H5Tget_class((hid_t)memb)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (!(vlSize = H5Tget_size(memb))) - H5_LIBRARY_ERROR(ENVONLY); - - if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate raw VL write buffer"); - - /* Cache class types */ - /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */ - jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); - jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); - jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); - jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); - jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); - jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); - - /* jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */ - jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B"); - jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S"); - jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I"); - jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J"); - jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F"); - jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D"); - - /* Convert each list to a vlen element */ - for (i = 0; i < (size_t)n; i++) { - hvl_t vl_elem; - - if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - // retrieve the java.util.List interface class - jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List"); - - // retrieve the toArray method and invoke it - jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;"); - if (mToArray == NULL) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray); - jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array); - - if (jnelmts < 0) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: number of VL elements < 0"); - - HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t)); - vl_elem.len = (size_t)jnelmts; - - if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate vlen ptr buffer"); - - jobject jobj = NULL; - for (j = 0; j < (size_t)jnelmts; j++) { - if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - switch (vlClass) { - /* case H5T_BOOL: { - jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x]; - } - break; - } */ - case H5T_INTEGER: { - switch (vlSize) { - case sizeof(jbyte): { - jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x]; - } - break; - } - case sizeof(jshort): { - jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x]; - } - break; - } - case sizeof(jint): { - jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x]; - } - break; - } - case sizeof(jlong): { - jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x]; - } - break; - } - } - break; - } - case H5T_FLOAT: { - switch (vlSize) { - case sizeof(jfloat): { - jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x]; - } - break; - } - case sizeof(jdouble): { - jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x]; - } - break; - } - } - break; - } - case H5T_REFERENCE: { - jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x]; - } - ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0); - break; - } - default: - H5_UNIMPLEMENTED(ENVONLY, "H5AwriteVL: invalid class type"); - break; - } - ENVPTR->DeleteLocalRef(ENVONLY, jobj); - } - - HDmemcpy((char *)rawBuf + i * typeSize, &vl_elem, sizeof(hvl_t)); - - ENVPTR->DeleteLocalRef(ENVONLY, jList); - } /* end for (i = 0; i < n; i++) */ - - if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, rawBuf)) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - if (rawBuf) - HDfree(rawBuf); - } - else { - PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5AwriteVL: write buffer not pinned"); - if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - } - -done: - if (writeBuf) { - if ((status >= 0) && vl_data_class) - H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); - - if (type_class != H5T_VLEN) - UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); - } + status = Java_hdf_hdf5lib_H5_H5Awrite(env, clss, attr_id, mem_type_id, (jbyteArray)buf, JNI_TRUE); return (jint)status; } /* end Java_hdf_hdf5lib_H5_H5AwriteVL */ diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c index 59775e3..0f97522 100644 --- a/java/src/jni/h5dImp.c +++ b/java/src/jni/h5dImp.c @@ -182,47 +182,71 @@ Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong me jlong file_space_id, jlong xfer_plist_id, jbyteArray buf, jboolean isCriticalPinning) { - jboolean readBufIsCopy; - jbyte *readBuf = NULL; - htri_t vl_data_class; - herr_t status = FAIL; + jboolean readBufIsCopy; + jbyte *readBuf = NULL; + size_t typeSize; + H5T_class_t type_class; + jsize vl_array_len; // Only used by vl_data_class types + htri_t vl_data_class; + herr_t status = FAIL; UNUSED(clss); if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread: read buffer is NULL"); - /* Get size of data array */ - if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) { - CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0"); - } - if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (isCriticalPinning) { - PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, - "H5Dread: read buffer not critically pinned"); + if (vl_data_class) { + /* Get size of data array */ + if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0"); + } + + if (!(typeSize = H5Tget_size(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread: failed to allocate raw VL read buffer"); } else { - PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread: read buffer not pinned"); + if (isCriticalPinning) { + PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, + "H5Dread: read buffer not critically pinned"); + } + else { + PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread: read buffer not pinned"); + } } if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, - (hid_t)xfer_plist_id, readBuf)) < 0) + (hid_t)xfer_plist_id, (void *)readBuf)) < 0) H5_LIBRARY_ERROR(ENVONLY); + if (vl_data_class) { + if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf); + } + done: if (readBuf) { if ((status >= 0) && vl_data_class) H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf); - if (isCriticalPinning) { - UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); + if (vl_data_class) { + HDfree(readBuf); } else { - UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); + if (isCriticalPinning) { + UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); + } + else { + UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); + } } } @@ -239,31 +263,50 @@ Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong m jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jbyteArray buf, jboolean isCriticalPinning) { - jboolean writeBufIsCopy; - jbyte *writeBuf = NULL; - htri_t vl_data_class; - herr_t status = FAIL; + jboolean writeBufIsCopy; + jbyte *writeBuf = NULL; + size_t typeSize; + H5T_class_t type_class; + jsize vl_array_len; // Only used by vl_data_class types + htri_t vl_data_class; + herr_t status = FAIL; UNUSED(clss); if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer is NULL"); - /* Get size of data array */ - if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) { - CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0"); - } - if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (isCriticalPinning) { - PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, - "H5Dwrite: write buffer not critically pinned"); + if (vl_data_class) { + /* Get size of data array */ + if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer length < 0"); + } + + if (!(typeSize = H5Tget_size(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dwrite: failed to allocate raw VL write buffer"); } else { - PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite: write buffer not pinned"); + if (isCriticalPinning) { + PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, + "H5Dwrite: write buffer not critically pinned"); + } + else { + PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite: write buffer not pinned"); + } + } + + if (vl_data_class) { + if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf); } if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, @@ -275,11 +318,16 @@ done: if ((status >= 0) && vl_data_class) H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf); - if (isCriticalPinning) { - UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); + if (vl_data_class) { + HDfree(writeBuf); } else { - UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); + if (isCriticalPinning) { + UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); + } + else { + UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); + } } } @@ -1087,235 +1135,10 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf) { - H5T_class_t type_class; - jsize n; - htri_t vl_data_class; - herr_t status = FAIL; - jbyteArray *readBuf = NULL; - - UNUSED(clss); - - if (NULL == buf) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL"); - - /* Get size of data array */ - if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { - CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: readBuf length < 0"); - } - - if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (type_class == H5T_VLEN) { - size_t typeSize; - hid_t memb = H5I_INVALID_HID; - H5T_class_t vlClass; - size_t vlSize; - void *rawBuf = NULL; - jobjectArray jList = NULL; - - size_t i, j, x; - - if (!(typeSize = H5Tget_size(mem_type_id))) - H5_LIBRARY_ERROR(ENVONLY); - - if (!(memb = H5Tget_super(mem_type_id))) - H5_LIBRARY_ERROR(ENVONLY); - if ((vlClass = H5Tget_class((hid_t)memb)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (!(vlSize = H5Tget_size(memb))) - H5_LIBRARY_ERROR(ENVONLY); - - if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer"); - - if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, - (hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)rawBuf)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - /* Cache class types */ - /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */ - jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); - jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); - jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); - jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); - jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); - jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); - - /* - jmethodID boolValueMid = - ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;"); - */ - jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;"); - jmethodID shortValueMid = - ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;"); - jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;"); - jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;"); - jmethodID floatValueMid = - ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;"); - jmethodID doubleValueMid = - ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;"); - - // retrieve the java.util.List interface class - jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List"); - jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z"); - - /* Convert each element to a list */ - for (i = 0; i < (size_t)n; i++) { - hvl_t vl_elem; - - // The list we're going to return: - if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - /* Get the number of sequence elements */ - HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t)); - - jsize nelmts = (jsize)vl_elem.len; - if (vl_elem.len != (size_t)nelmts) - H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of number of VL elements"); - if (nelmts < 0) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: number of VL elements < 0"); - - jobject jobj = NULL; - for (j = 0; j < (size_t)nelmts; j++) { - switch (vlClass) { - /*case H5T_BOOL: { - jboolean boolValue; - for (x = 0; x < vlSize; x++) { - ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } */ - case H5T_INTEGER: { - switch (vlSize) { - case sizeof(jbyte): { - jbyte byteValue; - for (x = 0; x < vlSize; x++) { - ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = - ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jshort): { - jshort shortValue; - for (x = 0; x < vlSize; x++) { - ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid, - shortValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jint): { - jint intValue; - for (x = 0; x < vlSize; x++) { - ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jlong): { - jlong longValue; - for (x = 0; x < vlSize; x++) { - ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = - ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - } - break; - } - case H5T_FLOAT: { - switch (vlSize) { - case sizeof(jfloat): { - jfloat floatValue; - for (x = 0; x < vlSize; x++) { - ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid, - (double)floatValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jdouble): { - jdouble doubleValue; - for (x = 0; x < vlSize; x++) { - ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; - } - - jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid, - doubleValue); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - } - break; - } - case H5T_REFERENCE: { - jboolean bb; - jbyte *barray = NULL; - - jsize byteArraySize = (jsize)vlSize; - if (vlSize != (size_t)byteArraySize) - H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of byteArraySize"); - - if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb, - "readVL reference: byte array not pinned"); - - for (x = 0; x < vlSize; x++) { - barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x]; - } - if (barray) - UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT); - break; - } - default: - H5_UNIMPLEMENTED(ENVONLY, "H5DreadVL: invalid class type"); - break; - } - - // Add it to the list - ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj); - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } - } /* end for */ - - if (rawBuf) - HDfree(rawBuf); - } - else { - if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, - (hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)readBuf)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - } - -done: - if (readBuf) { - if ((status >= 0) && vl_data_class) - H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf); + herr_t status = FAIL; - UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); - } + status = Java_hdf_hdf5lib_H5_H5Dread(env, clss, dataset_id, mem_type_id, mem_space_id, file_space_id, + xfer_plist_id, (jbyteArray)buf, JNI_TRUE); return (jint)status; } /* end Java_hdf_hdf5lib_H5_H5DreadVL */ @@ -1329,202 +1152,10 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf) { - H5T_class_t type_class; - jsize n; - htri_t vl_data_class; - herr_t status = FAIL; - jboolean writeBufIsCopy; - jbyteArray writeBuf = NULL; - - UNUSED(clss); - - if (NULL == buf) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL"); - - /* Get size of data array */ - if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { - CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: readBuf length < 0"); - } - - if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (type_class == H5T_VLEN) { - size_t typeSize; - hid_t memb = H5I_INVALID_HID; - H5T_class_t vlClass; - size_t vlSize; - void *rawBuf = NULL; - jobjectArray jList = NULL; - - size_t i, j, x; - - if (!(typeSize = H5Tget_size(mem_type_id))) - H5_LIBRARY_ERROR(ENVONLY); - - if (!(memb = H5Tget_super(mem_type_id))) - H5_LIBRARY_ERROR(ENVONLY); - if ((vlClass = H5Tget_class((hid_t)memb)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (!(vlSize = H5Tget_size(memb))) - H5_LIBRARY_ERROR(ENVONLY); - - if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer"); - - /* Cache class types */ - /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */ - jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); - jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); - jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); - jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); - jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); - jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); - - /* jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */ - jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B"); - jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S"); - jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I"); - jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J"); - jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F"); - jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D"); - - /* Convert each list to a vlen element */ - for (i = 0; i < (size_t)n; i++) { - hvl_t vl_elem; - - if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - // retrieve the java.util.List interface class - jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List"); - - // retrieve the toArray method and invoke it - jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;"); - if (mToArray == NULL) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray); - jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array); - - if (jnelmts < 0) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: number of VL elements < 0"); - - HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t)); - vl_elem.len = (size_t)jnelmts; - - if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate vlen ptr buffer"); - - jobject jobj = NULL; - for (j = 0; j < (size_t)jnelmts; j++) { - if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - switch (vlClass) { - /* case H5T_BOOL: { - jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x]; - } - break; - } */ - case H5T_INTEGER: { - switch (vlSize) { - case sizeof(jbyte): { - jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x]; - } - break; - } - case sizeof(jshort): { - jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x]; - } - break; - } - case sizeof(jint): { - jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x]; - } - break; - } - case sizeof(jlong): { - jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x]; - } - break; - } - } - break; - } - case H5T_FLOAT: { - switch (vlSize) { - case sizeof(jfloat): { - jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x]; - } - break; - } - case sizeof(jdouble): { - jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x]; - } - break; - } - } - break; - } - case H5T_REFERENCE: { - jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0); - for (x = 0; x < vlSize; x++) { - ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x]; - } - ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0); - break; - } - default: - H5_UNIMPLEMENTED(ENVONLY, "H5DwriteVL: invalid class type"); - break; - } - ENVPTR->DeleteLocalRef(ENVONLY, jobj); - } - - HDmemcpy((char *)rawBuf + i * typeSize, &vl_elem, sizeof(hvl_t)); - - ENVPTR->DeleteLocalRef(ENVONLY, jList); - } /* end for (i = 0; i < n; i++) */ - - if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, - (hid_t)file_space_id, (hid_t)xfer_plist_id, rawBuf)) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - if (rawBuf) - HDfree(rawBuf); - } - else { - PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5DwriteVL: write buffer not pinned"); - if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, - (hid_t)file_space_id, (hid_t)xfer_plist_id, writeBuf)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - } - -done: - if (writeBuf) { - if ((status >= 0) && vl_data_class) - H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf); + herr_t status = FAIL; - if (type_class != H5T_VLEN) - UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); - } + status = Java_hdf_hdf5lib_H5_H5Dwrite(env, clss, dataset_id, mem_type_id, mem_space_id, file_space_id, + xfer_plist_id, (jbyteArray)buf, JNI_TRUE); return (jint)status; } /* end Java_hdf_hdf5lib_H5_H5DwriteVL */ diff --git a/java/src/jni/h5fImp.c b/java/src/jni/h5fImp.c index 2d2b0f2..5ff1db1 100644 --- a/java/src/jni/h5fImp.c +++ b/java/src/jni/h5fImp.c @@ -742,7 +742,7 @@ Java_hdf_hdf5lib_H5_H5Fset_1dset_1no_1attrs_1hint(JNIEnv *env, jclass clss, jlon done: return; -} +} /* end Java_hdf_hdf5lib_H5_H5Fset_1dset_1no_1attrs_1hint */ /* * Class: hdf_hdf5lib_H5 @@ -765,7 +765,7 @@ Java_hdf_hdf5lib_H5_H5Fget_1dset_1no_1attrs_1hint(JNIEnv *env, jclass clss, jlon done: return bval; -} +} /* end Java_hdf_hdf5lib_H5_H5Fget_1dset_1no_1attrs_1hint */ /* * Class: hdf_hdf5lib_H5 diff --git a/java/src/jni/h5tImp.c b/java/src/jni/h5tImp.c index 5a1d398..c0161f9 100644 --- a/java/src/jni/h5tImp.c +++ b/java/src/jni/h5tImp.c @@ -1688,7 +1688,7 @@ Java_hdf_hdf5lib_H5_H5Tflush(JNIEnv *env, jclass clss, jlong loc_id) done: return; -} +} /* end Java_hdf_hdf5lib_H5_H5Tflush */ /* * Class: hdf_hdf5lib_H5 @@ -1705,7 +1705,7 @@ Java_hdf_hdf5lib_H5_H5Trefresh(JNIEnv *env, jclass clss, jlong loc_id) done: return; -} +} /* end Java_hdf_hdf5lib_H5_H5Trefresh */ #ifdef __cplusplus } /* end extern "C" */ diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c index 37d0194..265213e 100644 --- a/java/src/jni/h5util.c +++ b/java/src/jni/h5util.c @@ -4043,6 +4043,551 @@ done: H5Aclose(attr_id); } /* end Java_hdf_hdf5lib_H5_H5export_1attribute */ +herr_t +translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, jsize count, + jbyte *raw_buf) +{ + herr_t status = FAIL; + hid_t memb = H5I_INVALID_HID; + H5T_class_t vlClass; + size_t vlSize; + jobjectArray jList = NULL; + size_t i, j, x; + + /* retrieve the java.util.ArrayList interface class */ + jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList"); + jmethodID arrListMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "", "(I)V"); + jmethodID arrAddMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "add", "(Ljava/lang/Object;)Z"); + + /* Cache class types */ + /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */ + jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); + jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); + jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); + jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); + jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); + jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); + /*jobjectArray + jmethodID boolValueMid = + ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;"); + */ + jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;"); + jmethodID shortValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;"); + jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;"); + jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;"); + jmethodID floatValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;"); + jmethodID doubleValueMid = + ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;"); + + if (type_class == H5T_VLEN) { + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + /* Convert each element to a list */ + for (i = 0; i < (size_t)count; i++) { + hvl_t vl_elem; + jboolean found_jList = JNI_TRUE; + + /* Get the number of sequence elements */ + HDmemcpy(&vl_elem, (char *)raw_buf + i * sizeof(hvl_t), sizeof(hvl_t)); + jsize nelmts = (jsize)vl_elem.len; + if (vl_elem.len != (size_t)nelmts) + H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: overflow of number of VL elements"); + + if (nelmts < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_rbuf: number of VL elements < 0"); + + /* The list we're going to return: */ + if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i))) { + found_jList = JNI_FALSE; + if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_rbuf: failed to allocate list read buffer"); + } + + if ((vlClass == H5T_ARRAY) || (vlClass == H5T_COMPOUND) || (vlClass == H5T_VLEN)) + translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)nelmts, vl_elem.p); + else { + jobject jobj = NULL; + for (j = 0; j < (size_t)nelmts; j++) { + switch (vlClass) { + /*case H5T_BOOL: { + jboolean boolValue; + for (x = 0; x < vlSize; x++) { + ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } */ + case H5T_INTEGER: { + switch (vlSize) { + case sizeof(jbyte): { + jbyte byteValue; + for (x = 0; x < vlSize; x++) { + ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; + } + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, + byteValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jshort): { + jshort shortValue; + for (x = 0; x < vlSize; x++) { + ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; + } + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid, + shortValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jint): { + jint intValue; + for (x = 0; x < vlSize; x++) { + ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; + } + jobj = + ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + break; + } + case sizeof(jlong): { + jlong longValue; + for (x = 0; x < vlSize; x++) { + ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; + } + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, + longValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + } + break; + } + case H5T_FLOAT: { + switch (vlSize) { + case sizeof(jfloat): { + jfloat floatValue; + for (x = 0; x < vlSize; x++) { + ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; + } + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid, + (double)floatValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jdouble): { + jdouble doubleValue; + for (x = 0; x < vlSize; x++) { + ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x]; + } + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid, + doubleValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + } + break; + } + case H5T_REFERENCE: { + jboolean bb; + jbyte *barray = NULL; + jsize byteArraySize = (jsize)vlSize; + + if (vlSize != (size_t)byteArraySize) + H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: overflow of byteArraySize"); + + if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb, + "read(translate_buf) reference: byte array not pinned"); + for (x = 0; x < vlSize; x++) { + barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x]; + } + if (barray) + UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT); + + break; + } + default: + H5_UNIMPLEMENTED(ENVONLY, "translate_rbuf: invalid class type"); + break; + } + /* Add it to the list */ + if (jobj) { + ENVPTR->CallBooleanMethod(ENVONLY, jList, arrAddMethod, jobj); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + + ENVPTR->DeleteLocalRef(ENVONLY, jobj); + } + } + if (!found_jList) { + ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + ENVPTR->DeleteLocalRef(ENVONLY, jList); + } + } + } + } + else if (type_class == H5T_COMPOUND) { + int nmembs = H5Tget_nmembers(mem_type_id); + void *objBuf = NULL; + size_t offset; + + if (nmembs < 0) + goto done; + + /* Convert each element to a list */ + for (i = 0; i < (size_t)nmembs; i++) { + jboolean found_jList = JNI_TRUE; + + if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)i)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + offset = H5Tget_member_offset(mem_type_id, (unsigned int)i); + + if ((vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + /* Get the object element */ + HDmemcpy(&objBuf, (char *)raw_buf + offset, vlSize); + + /* The list we're going to return: */ + if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i))) { + found_jList = JNI_FALSE; + if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_rbuf: failed to allocate list read buffer"); + } + + if ((vlClass == H5T_ARRAY) || (vlClass == H5T_COMPOUND) || (vlClass == H5T_VLEN)) + translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)1, objBuf); + else { + jobject jobj = NULL; + switch (vlClass) { + /*case H5T_BOOL: { + jboolean boolValue; + for (x = 0; x < vlSize; x++) { + ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } */ + case H5T_INTEGER: { + switch (vlSize) { + case sizeof(jbyte): { + jbyte byteValue; + for (x = 0; x < vlSize; x++) { + ((char *)&byteValue)[x] = ((char *)objBuf)[vlSize + x]; + } + + jobj = + ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jshort): { + jshort shortValue; + for (x = 0; x < vlSize; x++) { + ((char *)&shortValue)[x] = ((char *)objBuf)[vlSize + x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid, + shortValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jint): { + jint intValue; + for (x = 0; x < vlSize; x++) { + ((char *)&intValue)[x] = ((char *)objBuf)[vlSize + x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jlong): { + jlong longValue; + for (x = 0; x < vlSize; x++) { + ((char *)&longValue)[x] = ((char *)objBuf)[vlSize + x]; + } + + jobj = + ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + } + break; + } + case H5T_FLOAT: { + switch (vlSize) { + case sizeof(jfloat): { + jfloat floatValue; + for (x = 0; x < vlSize; x++) { + ((char *)&floatValue)[x] = ((char *)objBuf)[vlSize + x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid, + (double)floatValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jdouble): { + jdouble doubleValue; + for (x = 0; x < vlSize; x++) { + ((char *)&doubleValue)[x] = ((char *)objBuf)[vlSize + x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid, + doubleValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + } + break; + } + case H5T_REFERENCE: { + jboolean bb; + jbyte *barray = NULL; + + jsize byteArraySize = (jsize)vlSize; + if (vlSize != (size_t)byteArraySize) + H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: overflow of byteArraySize"); + + if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb, + "translate_rbuf reference: byte array not pinned"); + + for (x = 0; x < vlSize; x++) { + barray[x] = ((jbyte *)objBuf)[vlSize + x]; + } + if (barray) + UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT); + break; + } + default: + H5_UNIMPLEMENTED(ENVONLY, "translate_rbuf: invalid class type"); + break; + } + /* Add it to the list */ + if (jobj) { + ENVPTR->CallBooleanMethod(ENVONLY, jList, arrAddMethod, jobj); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + + ENVPTR->DeleteLocalRef(ENVONLY, jobj); + } + } + if (!found_jList) { + ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + ENVPTR->DeleteLocalRef(ENVONLY, jList); + } + } + H5Tclose(memb); + } + else if (type_class == H5T_ARRAY) { + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + // TODO + H5_UNIMPLEMENTED(ENVONLY, "translate_rbuf: invalid H5T_ARRAY type"); + } + +done: + + return (jint)status; +} + +herr_t +translate_wbuf(JNIEnv *env, jobjectArray in_buf, jlong mem_type_id, H5T_class_t type_class, jsize count, + jbyte *raw_buf) +{ + herr_t status = FAIL; + hid_t memb = H5I_INVALID_HID; + H5T_class_t vlClass; + size_t vlSize; + jobjectArray jList = NULL; + size_t i, j, x; + + /* retrieve the java.util.ArrayList interface class */ + jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList"); + /* retrieve the toArray method */ + jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, arrCList, "toArray", "()[Ljava/lang/Object;"); + + /* Cache class types */ + /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */ + jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); + jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); + jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); + jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); + jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); + jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); + + /* jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */ + jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B"); + jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S"); + jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I"); + jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J"); + jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F"); + jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D"); + + if (type_class == H5T_VLEN) { + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class((hid_t)memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + /* Convert each list to a vlen element */ + for (i = 0; i < (size_t)count; i++) { + hvl_t vl_elem; + + if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + /* invoke the toArray method */ + if (mToArray == NULL) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray); + jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array); + + if (jnelmts < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_wbuf: number of VL elements < 0"); + + vl_elem.len = (size_t)jnelmts; + + if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_wbuf: failed to allocate vlen ptr buffer"); + + if ((vlClass == H5T_ARRAY) || (vlClass == H5T_COMPOUND) || (vlClass == H5T_VLEN)) + translate_wbuf(ENVONLY, (jobjectArray)array, memb, vlClass, (jsize)jnelmts, vl_elem.p); + else { + jobject jobj = NULL; + for (j = 0; j < (size_t)jnelmts; j++) { + if (NULL == + (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + switch (vlClass) { + /* case H5T_BOOL: { + jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid); + for (x = 0; x < vlSize; x++) { + ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x]; + } + break; + } */ + case H5T_INTEGER: { + switch (vlSize) { + case sizeof(jbyte): { + jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid); + for (x = 0; x < vlSize; x++) { + ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x]; + } + break; + } + case sizeof(jshort): { + jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid); + for (x = 0; x < vlSize; x++) { + ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x]; + } + break; + } + case sizeof(jint): { + jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid); + for (x = 0; x < vlSize; x++) { + ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x]; + } + break; + } + case sizeof(jlong): { + jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid); + for (x = 0; x < vlSize; x++) { + ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x]; + } + break; + } + } + break; + } + case H5T_FLOAT: { + switch (vlSize) { + case sizeof(jfloat): { + jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid); + for (x = 0; x < vlSize; x++) { + ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x]; + } + break; + } + case sizeof(jdouble): { + jdouble doubleValue = + ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid); + for (x = 0; x < vlSize; x++) { + ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x]; + } + break; + } + } + break; + } + case H5T_REFERENCE: { + jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0); + for (x = 0; x < vlSize; x++) { + ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x]; + } + ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0); + break; + } + default: + H5_UNIMPLEMENTED(ENVONLY, "translate_wbuf: invalid class type"); + break; + } + ENVPTR->DeleteLocalRef(ENVONLY, jobj); + } + } + + HDmemcpy((char *)raw_buf + i * sizeof(hvl_t), &vl_elem, sizeof(hvl_t)); + + ENVPTR->DeleteLocalRef(ENVONLY, jList); + } /* end for (i = 0; i < count; i++) */ + } + else if (type_class == H5T_COMPOUND) { + // TODO + H5_UNIMPLEMENTED(ENVONLY, "translate_wbuf: invalid H5T_COMPOUND type"); + } + else if (type_class == H5T_ARRAY) { + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + // TODO + H5_UNIMPLEMENTED(ENVONLY, "translate_wbuf: invalid H5T_ARRAY type"); + } + +done: + + return (jint)status; +} + #ifdef __cplusplus } #endif diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h index 24c1116..5b9da13 100644 --- a/java/src/jni/h5util.h +++ b/java/src/jni/h5util.h @@ -52,6 +52,11 @@ extern int h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr, int b extern htri_t H5Tdetect_variable_str(hid_t tid); +extern herr_t translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, + jsize count, jbyte *raw_buf); +extern herr_t translate_wbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, + jsize count, jbyte *raw_buf); + /* * Symbols used to format the output of h5str_sprintf and * to interpret the input to h5str_convert. diff --git a/java/test/TestH5A.java b/java/test/TestH5A.java index 4437ec7..095691e 100644 --- a/java/test/TestH5A.java +++ b/java/test/TestH5A.java @@ -1415,7 +1415,7 @@ public class TestH5A { HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5AVLwr: ", attr_int_id >= 0); - H5.H5AwriteVL(attr_int_id, atype_int_id, vl_int_data); + H5.H5Awrite(attr_int_id, atype_int_id, vl_int_data); } catch (Exception err) { if (attr_int_id > 0) @@ -1472,7 +1472,7 @@ public class TestH5A { HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5AVLwr: ", attr_dbl_id >= 0); - H5.H5AwriteVL(attr_dbl_id, atype_dbl_id, vl_dbl_data); + H5.H5Awrite(attr_dbl_id, atype_dbl_id, vl_dbl_data); } catch (Exception err) { if (attr_dbl_id > 0) @@ -1511,7 +1511,7 @@ public class TestH5A { vl_readbuf[j] = new ArrayList(); try { - H5.H5AreadVL(attr_int_id, atype_int_id, vl_readbuf); + H5.H5Aread(attr_int_id, atype_int_id, vl_readbuf); } catch (Exception ex) { ex.printStackTrace(); @@ -1531,7 +1531,7 @@ public class TestH5A { vl_readbuf[j] = new ArrayList(); try { - H5.H5AreadVL(attr_dbl_id, atype_dbl_id, vl_readbuf); + H5.H5Aread(attr_dbl_id, atype_dbl_id, vl_readbuf); } catch (Exception ex) { ex.printStackTrace(); @@ -1576,4 +1576,157 @@ public class TestH5A { } } } + + @Test + public void testH5AVLwrVL() + { + String attr_int_name = "VLIntdata"; + long attr_int_id = HDF5Constants.H5I_INVALID_HID; + long atype_int_id = HDF5Constants.H5I_INVALID_HID; + long base_atype_int_id = HDF5Constants.H5I_INVALID_HID; + long aspace_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {4}; + long lsize = 1; + + ArrayList[] base_vl_int_data = new ArrayList[4]; + ArrayList[] vl_int_data = new ArrayList[4]; + try { + // Write Integer data + vl_int_data[0] = new ArrayList(Arrays.asList(1)); + vl_int_data[1] = new ArrayList(Arrays.asList(2, 3)); + vl_int_data[2] = new ArrayList(Arrays.asList(4, 5, 6)); + vl_int_data[3] = new ArrayList(Arrays.asList(7, 8, 9, 10)); + Class dataClass = vl_int_data.getClass(); + assertTrue("testH5AVLwrVL.getClass: " + dataClass, dataClass.isArray()); + + // Write VL data + base_vl_int_data[0] = new ArrayList>(); + base_vl_int_data[0].add(vl_int_data[0]); + base_vl_int_data[1] = new ArrayList>(); + base_vl_int_data[1].add(vl_int_data[0]); + base_vl_int_data[1].add(vl_int_data[1]); + base_vl_int_data[2] = new ArrayList>(); + base_vl_int_data[2].add(vl_int_data[0]); + base_vl_int_data[2].add(vl_int_data[1]); + base_vl_int_data[2].add(vl_int_data[2]); + base_vl_int_data[3] = new ArrayList>(); + base_vl_int_data[3].add(vl_int_data[0]); + base_vl_int_data[3].add(vl_int_data[1]); + base_vl_int_data[3].add(vl_int_data[2]); + base_vl_int_data[3].add(vl_int_data[3]); + + try { + atype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE); + assertTrue("testH5AVLwr.H5Tvlen_create: ", atype_int_id >= 0); + base_atype_int_id = H5.H5Tvlen_create(atype_int_id); + assertTrue("testH5AVLwrVL.H5Tvlen_create: ", base_atype_int_id >= 0); + } + catch (Exception err) { + if (base_atype_int_id > 0) + try { + H5.H5Tclose(base_atype_int_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("H5.testH5AVLwrVL: " + err); + } + + try { + aspace_id = H5.H5Screate_simple(1, dims, null); + assertTrue(aspace_id > 0); + attr_int_id = H5.H5Acreate(H5did, attr_int_name, base_atype_int_id, aspace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + assertTrue("testH5AVLwrVL: ", attr_int_id >= 0); + + H5.H5Awrite(attr_int_id, base_atype_int_id, base_vl_int_data); + } + catch (Exception err) { + if (attr_int_id > 0) + try { + H5.H5Aclose(attr_int_id); + } + catch (Exception ex) { + } + if (atype_int_id > 0) + try { + H5.H5Tclose(atype_int_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("H5.testH5AVLwrVL: " + err); + } + finally { + if (aspace_id > 0) + try { + H5.H5Sclose(aspace_id); + } + catch (Exception ex) { + } + } + + H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); + + for (int j = 0; j < dims.length; j++) + lsize *= dims[j]; + + // Read Integer data + ArrayList[] base_vl_readbuf = new ArrayList[4]; + for (int j = 0; j < lsize; j++) + base_vl_readbuf[j] = new ArrayList>(); + + try { + H5.H5Aread(attr_int_id, base_atype_int_id, base_vl_readbuf); + } + catch (Exception ex) { + ex.printStackTrace(); + } + ArrayList vl_readbuf = (ArrayList)base_vl_readbuf[0]; + assertTrue("vl_readbuf exists", vl_readbuf != null); + assertTrue("vl_readbuf has size " + vl_readbuf.size(), vl_readbuf.size() > 0); + ArrayList vl_readbuf_int = (ArrayList)vl_readbuf.get(0); + assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(0), + vl_int_data[0].get(0).equals(vl_readbuf_int.get(0))); + + vl_readbuf = (ArrayList)base_vl_readbuf[1]; + vl_readbuf_int = (ArrayList)vl_readbuf.get(1); + assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(0), + vl_int_data[1].get(0).equals(vl_readbuf_int.get(0))); + + vl_readbuf = (ArrayList)base_vl_readbuf[2]; + vl_readbuf_int = (ArrayList)vl_readbuf.get(2); + assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(0), + vl_int_data[2].get(0).equals(vl_readbuf_int.get(0))); + + vl_readbuf = (ArrayList)base_vl_readbuf[3]; + vl_readbuf_int = (ArrayList)vl_readbuf.get(3); + assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(0), + vl_int_data[3].get(0).equals(vl_readbuf_int.get(0))); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.testH5AVLwrVL: " + err); + } + finally { + if (attr_int_id > 0) + try { + H5.H5Aclose(attr_int_id); + } + catch (Exception ex) { + } + if (atype_int_id > 0) + try { + H5.H5Tclose(atype_int_id); + } + catch (Exception ex) { + } + if (base_atype_int_id > 0) + try { + H5.H5Tclose(base_atype_int_id); + } + catch (Exception ex) { + } + } + } } diff --git a/java/test/TestH5D.java b/java/test/TestH5D.java index f7e5702..ec9caa3 100644 --- a/java/test/TestH5D.java +++ b/java/test/TestH5D.java @@ -1064,8 +1064,8 @@ public class TestH5D { HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5DVLwr: ", dset_int_id >= 0); - H5.H5DwriteVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_int_data); + H5.H5Dwrite(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_int_data); } catch (Exception err) { if (dset_int_id > 0) @@ -1123,8 +1123,8 @@ public class TestH5D { HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5DVLwr: ", dset_dbl_id >= 0); - H5.H5DwriteVL(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_dbl_data); + H5.H5Dwrite(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_dbl_data); } catch (Exception err) { if (dset_dbl_id > 0) @@ -1153,9 +1153,8 @@ public class TestH5D { H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); - for (int j = 0; j < dims.length; j++) { + for (int j = 0; j < dims.length; j++) lsize *= dims[j]; - } // Read Integer data ArrayList[] vl_readbuf = new ArrayList[4]; @@ -1163,8 +1162,8 @@ public class TestH5D { vl_readbuf[j] = new ArrayList(); try { - H5.H5DreadVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_readbuf); + H5.H5Dread(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_readbuf); } catch (Exception ex) { ex.printStackTrace(); @@ -1184,8 +1183,8 @@ public class TestH5D { vl_readbuf[j] = new ArrayList(); try { - H5.H5DreadVL(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_readbuf); + H5.H5Dread(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_readbuf); } catch (Exception ex) { ex.printStackTrace(); @@ -1230,4 +1229,166 @@ public class TestH5D { } } } + + @Test + public void testH5DVLwrVL() + { + String dset_int_name = "VLIntdata"; + long dset_int_id = HDF5Constants.H5I_INVALID_HID; + long dtype_int_id = HDF5Constants.H5I_INVALID_HID; + long base_dtype_int_id = HDF5Constants.H5I_INVALID_HID; + long dspace_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {4}; + long lsize = 1; + + ArrayList[] base_vl_int_data = new ArrayList[4]; + ArrayList[] vl_int_data = new ArrayList[4]; + try { + // Write Integer data + vl_int_data[0] = new ArrayList(Arrays.asList(1)); + vl_int_data[1] = new ArrayList(Arrays.asList(2, 3)); + vl_int_data[2] = new ArrayList(Arrays.asList(4, 5, 6)); + vl_int_data[3] = new ArrayList(Arrays.asList(7, 8, 9, 10)); + Class dataClass = vl_int_data.getClass(); + assertTrue("testH5DVLwrVL.getClass: " + dataClass, dataClass.isArray()); + + // Write VL data + base_vl_int_data[0] = new ArrayList>(); + base_vl_int_data[0].add(vl_int_data[0]); + base_vl_int_data[1] = new ArrayList>(); + base_vl_int_data[1].add(vl_int_data[0]); + base_vl_int_data[1].add(vl_int_data[1]); + base_vl_int_data[2] = new ArrayList>(); + base_vl_int_data[2].add(vl_int_data[0]); + base_vl_int_data[2].add(vl_int_data[1]); + base_vl_int_data[2].add(vl_int_data[2]); + base_vl_int_data[3] = new ArrayList>(); + base_vl_int_data[3].add(vl_int_data[0]); + base_vl_int_data[3].add(vl_int_data[1]); + base_vl_int_data[3].add(vl_int_data[2]); + base_vl_int_data[3].add(vl_int_data[3]); + + try { + dtype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE); + assertTrue("testH5DVLwrVL.H5Tvlen_create: ", dtype_int_id >= 0); + base_dtype_int_id = H5.H5Tvlen_create(dtype_int_id); + assertTrue("testH5DVLwrVL.H5Tvlen_create: ", base_dtype_int_id >= 0); + } + catch (Exception err) { + if (base_dtype_int_id > 0) + try { + H5.H5Tclose(base_dtype_int_id); + } + catch (Exception ex) { + } + if (dtype_int_id > 0) + try { + H5.H5Tclose(dtype_int_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("H5.testH5DVLwrVL: " + err); + } + + try { + dspace_id = H5.H5Screate_simple(1, dims, null); + assertTrue(dspace_id > 0); + dset_int_id = H5.H5Dcreate(H5fid, dset_int_name, base_dtype_int_id, dspace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + assertTrue("testH5DVLwrVL: ", dset_int_id >= 0); + + H5.H5Dwrite(dset_int_id, base_dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, base_vl_int_data); + } + catch (Exception err) { + if (dset_int_id > 0) + try { + H5.H5Dclose(dset_int_id); + } + catch (Exception ex) { + } + if (dtype_int_id > 0) + try { + H5.H5Tclose(dtype_int_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("H5.testH5DVLwrVL: " + err); + } + finally { + if (dspace_id > 0) + try { + H5.H5Sclose(dspace_id); + } + catch (Exception ex) { + } + } + + H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); + + for (int j = 0; j < dims.length; j++) + lsize *= dims[j]; + + // Read Integer data + ArrayList[] base_vl_readbuf = new ArrayList[4]; + for (int j = 0; j < lsize; j++) + base_vl_readbuf[j] = new ArrayList>(); + + try { + H5.H5Dread(dset_int_id, base_dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, base_vl_readbuf); + } + catch (Exception ex) { + ex.printStackTrace(); + } + ArrayList vl_readbuf = (ArrayList)base_vl_readbuf[0]; + assertTrue("vl_readbuf exists", vl_readbuf != null); + assertTrue("vl_readbuf has size " + vl_readbuf.size(), vl_readbuf.size() > 0); + ArrayList vl_readbuf_int = (ArrayList)vl_readbuf.get(0); + assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(0), + vl_int_data[0].get(0).equals(vl_readbuf_int.get(0))); + + vl_readbuf = (ArrayList)base_vl_readbuf[1]; + vl_readbuf_int = (ArrayList)vl_readbuf.get(1); + assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(0), + vl_int_data[1].get(0).equals(vl_readbuf_int.get(0))); + + vl_readbuf = (ArrayList)base_vl_readbuf[2]; + vl_readbuf_int = (ArrayList)vl_readbuf.get(2); + assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(0), + vl_int_data[2].get(0).equals(vl_readbuf_int.get(0))); + + vl_readbuf = (ArrayList)base_vl_readbuf[3]; + vl_readbuf_int = (ArrayList)vl_readbuf.get(3); + assertTrue("testH5DVLwrVL:" + vl_readbuf_int.get(0), + vl_int_data[3].get(0).equals(vl_readbuf_int.get(0))); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.testH5DVLwrVL: " + err); + } + finally { + if (dset_int_id > 0) + try { + H5.H5Dclose(dset_int_id); + } + catch (Exception ex) { + } + if (dtype_int_id > 0) + try { + H5.H5Tclose(dtype_int_id); + } + catch (Exception ex) { + } + if (base_dtype_int_id > 0) + try { + H5.H5Tclose(base_dtype_int_id); + } + catch (Exception ex) { + } + } + } } diff --git a/java/test/TestH5R.java b/java/test/TestH5R.java index 221a71e..1dcf992 100644 --- a/java/test/TestH5R.java +++ b/java/test/TestH5R.java @@ -600,7 +600,7 @@ public class TestH5R { HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5RVLattr_ref: ", attr_obj_id >= 0); - H5.H5AwriteVL(attr_obj_id, atype_obj_id, vl_obj_data); + H5.H5Awrite(attr_obj_id, atype_obj_id, vl_obj_data); } catch (Exception err) { if (attr_obj_id > 0) @@ -657,7 +657,7 @@ public class TestH5R { HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5RVLattr_ref: ", attr_reg_id >= 0); - H5.H5AwriteVL(attr_reg_id, atype_reg_id, vl_reg_data); + H5.H5Awrite(attr_reg_id, atype_reg_id, vl_reg_data); } catch (Exception err) { if (attr_reg_id > 0) @@ -696,7 +696,7 @@ public class TestH5R { vl_readbuf[j] = new ArrayList(); try { - H5.H5AreadVL(attr_obj_id, atype_obj_id, vl_readbuf); + H5.H5Aread(attr_obj_id, atype_obj_id, vl_readbuf); } catch (Exception ex) { ex.printStackTrace(); @@ -716,7 +716,7 @@ public class TestH5R { vl_readbuf[j] = new ArrayList(); try { - H5.H5AreadVL(attr_reg_id, atype_reg_id, vl_readbuf); + H5.H5Aread(attr_reg_id, atype_reg_id, vl_readbuf); } catch (Exception ex) { ex.printStackTrace(); @@ -831,8 +831,8 @@ public class TestH5R { HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5RVLdset_ref: ", dset_obj_id >= 0); - H5.H5DwriteVL(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_obj_data); + H5.H5Dwrite(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_obj_data); } catch (Exception err) { if (dset_obj_id > 0) @@ -890,8 +890,8 @@ public class TestH5R { HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5RVLdset_ref: ", dset_reg_id >= 0); - H5.H5DwriteVL(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_reg_data); + H5.H5Dwrite(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_reg_data); } catch (Exception err) { if (dset_reg_id > 0) @@ -930,8 +930,8 @@ public class TestH5R { vl_readbuf[j] = new ArrayList(); try { - H5.H5DreadVL(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_readbuf); + H5.H5Dread(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_readbuf); } catch (Exception ex) { ex.printStackTrace(); @@ -951,8 +951,8 @@ public class TestH5R { vl_readbuf[j] = new ArrayList(); try { - H5.H5DreadVL(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_readbuf); + H5.H5Dread(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_readbuf); } catch (Exception ex) { ex.printStackTrace(); diff --git a/java/test/testfiles/JUnit-TestH5A.txt b/java/test/testfiles/JUnit-TestH5A.txt index efdd4a2..edd493c 100644 --- a/java/test/testfiles/JUnit-TestH5A.txt +++ b/java/test/testfiles/JUnit-TestH5A.txt @@ -11,6 +11,7 @@ JUnit version 4.11 .testH5Aget_info_by_name .testH5Aget_create_plist .testH5Adelete_by_name +.testH5AVLwrVL .testH5Aopen_by_name .testH5Aget_info .testH5Aget_name @@ -31,5 +32,5 @@ JUnit version 4.11 Time: XXXX -OK (29 tests) +OK (30 tests) diff --git a/java/test/testfiles/JUnit-TestH5D.txt b/java/test/testfiles/JUnit-TestH5D.txt index 288e6d0..cdeaed3 100644 --- a/java/test/testfiles/JUnit-TestH5D.txt +++ b/java/test/testfiles/JUnit-TestH5D.txt @@ -1,4 +1,5 @@ JUnit version 4.11 +.testH5DVLwrVL .testH5Dget_storage_size .testH5Diterate_write .testH5Dcreate @@ -22,5 +23,5 @@ JUnit version 4.11 Time: XXXX -OK (20 tests) +OK (21 tests) diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 9e72697..df70ea1 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -183,7 +183,14 @@ Bug Fixes since HDF5-1.13.2 release Java Library ------------ - - + - Improve variable-length datatype handling in JNI. + + The existing JNI read-write functions could handle variable-length datatypes + that were simple variable-length datatype with an atomic sub-datatype. More + complex combinations could not be handled. Reworked the JNI read-write functions + to recursively inspect datatypes for variable-length sub-datatypes. + + (ADB - 2022/10/12, HDFFV-8701,10375) Configuration -- cgit v0.12