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authorAllen Byrne <50328838+byrnHDF@users.noreply.github.com>2023-08-21 22:13:03 (GMT)
committerGitHub <noreply@github.com>2023-08-21 22:13:03 (GMT)
commitceef4a9ebd055f9ec0378a97ec2ce9421cdec866 (patch)
tree887ab50783fb357f8c5f9fe0dee1d6ba5dc536a5 /java/src
parent89b4afd4b317c5131cbc8607c99d21b369d050eb (diff)
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Merge/update CMake, presets,java and tools (#3393)
Diffstat (limited to 'java/src')
-rw-r--r--java/src/Makefile.am2
-rw-r--r--java/src/hdf/hdf5lib/H5.java5
-rw-r--r--java/src/jni/CMakeLists.txt4
-rw-r--r--java/src/jni/h5aImp.c597
-rw-r--r--java/src/jni/h5dImp.c561
-rw-r--r--java/src/jni/h5util.c882
-rw-r--r--java/src/jni/h5util.h5
7 files changed, 1179 insertions, 877 deletions
diff --git a/java/src/Makefile.am b/java/src/Makefile.am
index 67d21f8..35232ff 100644
--- a/java/src/Makefile.am
+++ b/java/src/Makefile.am
@@ -36,7 +36,7 @@ jarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
hdf5_javadir = $(libdir)
pkgpath = hdf/hdf5lib
-CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.33.jar:$$CLASSPATH
+CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$$CLASSPATH
AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 90c4575..78ce2a0 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -57,6 +57,9 @@ import hdf.hdf5lib.structs.H5O_info_t;
import hdf.hdf5lib.structs.H5O_native_info_t;
import hdf.hdf5lib.structs.H5O_token_t;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* @page HDF5LIB HDF5 Java API Package
* This class is the Java interface for the HDF5 library.
@@ -257,7 +260,7 @@ public class H5 implements java.io.Serializable {
*/
private static final long serialVersionUID = 6129888282117053288L;
- private final static org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(H5.class);
+ private final static Logger log = LoggerFactory.getLogger(H5.class);
/**
* @ingroup JH5
diff --git a/java/src/jni/CMakeLists.txt b/java/src/jni/CMakeLists.txt
index ab306ef..fc11c1b 100644
--- a/java/src/jni/CMakeLists.txt
+++ b/java/src/jni/CMakeLists.txt
@@ -78,7 +78,7 @@ set (CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON)
########### JNI libraries always must be built shared ###############
add_library (${HDF5_JAVA_JNI_LIB_TARGET} SHARED ${HDF5_JAVA_JNI_CSRCS} ${HDF5_JAVA_JNI_CHDRS})
target_include_directories (${HDF5_JAVA_JNI_LIB_TARGET}
- PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};${HDF5_JAVA_JNI_SOURCE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
+ PRIVATE "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};${HDF5_JAVA_JNI_SOURCE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
)
target_compile_options(${HDF5_JAVA_JNI_LIB_TARGET} PRIVATE "${HDF5_CMAKE_C_FLAGS}")
TARGET_C_PROPERTIES (${HDF5_JAVA_JNI_LIB_TARGET} SHARED)
@@ -106,7 +106,7 @@ if (HDF5_EXPORTED_TARGETS)
${HDF5_EXPORTED_TARGETS}
LIBRARY DESTINATION ${HDF5_INSTALL_LIB_DIR} COMPONENT libraries
ARCHIVE DESTINATION ${HDF5_INSTALL_LIB_DIR} COMPONENT libraries
- RUNTIME DESTINATION ${HDF5_INSTALL_LIB_DIR} COMPONENT libraries
+ RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT libraries
FRAMEWORK DESTINATION ${HDF5_INSTALL_FWRK_DIR} COMPONENT libraries
INCLUDES DESTINATION include
)
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index 4b531a6..00c39da 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -155,13 +155,15 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf,
jboolean isCriticalPinning)
{
- jboolean readBufIsCopy;
- jbyte *readBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ jboolean readBufIsCopy;
+ jbyte *readBuf = NULL;
+ hsize_t dims[H5S_MAX_RANK];
+ hid_t sid = H5I_INVALID_HID;
+ size_t typeSize;
+ H5T_class_t type_class;
+ jsize vl_array_len = 0; // Only used by vl_data_class types
+ htri_t vl_data_class;
+ herr_t status = FAIL;
UNUSED(clss);
@@ -173,40 +175,58 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t
if (vl_data_class) {
/* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
- }
- dims[0] = (hsize_t)n;
- if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
+ if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
- }
- if (isCriticalPinning) {
- PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
- "H5Aread: read buffer not critically pinned");
+ if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Aread: failed to allocate raw VL read buffer");
}
else {
- PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Aread: read buffer not pinned");
+ if (isCriticalPinning) {
+ PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
+ "H5Aread: read buffer not critically pinned");
+ }
+ else {
+ PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Aread: read buffer not pinned");
+ }
}
if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (vl_data_class) {
+ if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf);
+ }
+
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
+ dims[0] = (hsize_t)vl_array_len;
+ if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
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);
+ }
}
}
@@ -222,38 +242,52 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf,
jboolean isCriticalPinning)
{
- jboolean writeBufIsCopy;
- jbyte *writeBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ jboolean writeBufIsCopy;
+ jbyte *writeBuf = NULL;
+ hsize_t dims[H5S_MAX_RANK];
+ hid_t sid = H5I_INVALID_HID;
+ size_t typeSize;
+ H5T_class_t type_class;
+ jsize vl_array_len = 0; // Only used by vl_data_class types
+ htri_t vl_data_class;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer is NULL");
- /* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
- }
-
- dims[0] = (hsize_t)n;
- if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if (isCriticalPinning) {
- PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
- "H5Awrite: write buffer not critically pinned");
+ if (vl_data_class) {
+ /* Get size of data array */
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer length < 0");
+ }
+
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Awrite: failed to allocate raw VL write buffer");
}
else {
- PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Awrite: write buffer not pinned");
+ if (isCriticalPinning) {
+ PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
+ "H5Awrite: write buffer not critically pinned");
+ }
+ else {
+ PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Awrite: write buffer not pinned");
+ }
+ }
+
+ if (vl_data_class) {
+ if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
}
if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0)
@@ -261,14 +295,24 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
+ if ((status >= 0) && vl_data_class) {
+ dims[0] = (hsize_t)vl_array_len;
+ if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
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);
+ }
}
}
@@ -1063,13 +1107,15 @@ done:
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
- H5T_class_t type_class;
+ jbyte *readBuf = NULL;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
- jsize n = 0;
+ size_t typeSize;
+ H5T_class_t type_class;
+ jsize vl_array_len;
htri_t vl_data_class;
- herr_t status = FAIL;
- jbyteArray *readBuf = NULL;
+ herr_t status = FAIL;
+ htri_t is_variable = 0;
UNUSED(clss);
@@ -1078,228 +1124,42 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ /* Get size of data array */
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
- if (vl_data_class) {
- /* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: readBuf length < 0");
- }
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
- dims[0] = (hsize_t)n;
- if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
+ if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Aread: failed to allocate raw VL read buffer");
+ if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if (type_class == H5T_VLEN) {
- size_t typeSize;
- hid_t memb = H5I_INVALID_HID;
- H5T_class_t vlClass;
- size_t vlSize;
- void *rawBuf = NULL;
- jobjectArray jList = NULL;
-
- size_t i, j, x;
-
- if (!(typeSize = H5Tget_size(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (!(memb = H5Tget_super(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
- if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!(vlSize = H5Tget_size(memb)))
- H5_LIBRARY_ERROR(ENVONLY);
- if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AreadVL: failed to allocate raw VL read buffer");
-
- if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)rawBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- /* Cache class types */
- /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
- jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
- jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
- jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
- jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
- jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
- jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
- /*
- jmethodID boolValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
- */
- jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
- jmethodID shortValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
- jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
- jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
- jmethodID floatValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
- jmethodID doubleValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
-
- // retrieve the java.util.List interface class
- jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
- jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z");
-
- /* Convert each element to a list */
- for (i = 0; i < (size_t)n; i++) {
- hvl_t vl_elem;
-
- // The list we're going to return:
- if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- /* Get the number of sequence elements */
- HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
-
- jsize nelmts = (jsize)vl_elem.len;
- if (vl_elem.len != (size_t)nelmts)
- H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadVL: overflow of number of VL elements");
- if (nelmts < 0)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: number of VL elements < 0");
-
- jobject jobj = NULL;
- for (j = 0; j < (size_t)nelmts; j++) {
- switch (vlClass) {
- /* case H5T_BOOL: {
- jboolean boolValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- } */
- case H5T_INTEGER: {
- switch (vlSize) {
- case sizeof(jbyte): {
- jbyte byteValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj =
- ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jshort): {
- jshort shortValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
- shortValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jint): {
- jint intValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jlong): {
- jlong longValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj =
- ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- }
- break;
- }
- case H5T_FLOAT: {
- switch (vlSize) {
- case sizeof(jfloat): {
- jfloat floatValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
- (double)floatValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jdouble): {
- jdouble doubleValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
- doubleValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- }
- break;
- }
- case H5T_REFERENCE: {
- jboolean bb;
- jbyte *barray = NULL;
-
- jsize byteArraySize = (jsize)vlSize;
- if (vlSize != (size_t)byteArraySize)
- H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadVL: overflow of byteArraySize");
-
- if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
- "readVL reference: byte array not pinned");
-
- for (x = 0; x < vlSize; x++) {
- barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x];
- }
- if (barray)
- UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
- break;
- }
- default:
- H5_UNIMPLEMENTED(ENVONLY, "H5AreadVL: invalid class type");
- break;
- }
-
- // Add it to the list
- ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- } /* end for */
-
- if (rawBuf)
- HDfree(rawBuf);
- }
- else {
- if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
+ translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf);
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
+ dims[0] = (hsize_t)vl_array_len;
+ if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
+
if (sid >= 0)
H5Sclose(sid);
}
-
- UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
+ if (is_variable) {
+ for (size_t i = 0; i < (size_t)vl_array_len; i++)
+ HDfree(((char **)readBuf)[i]);
+ }
+ HDfree(readBuf);
}
return (jint)status;
@@ -1313,205 +1173,61 @@ done:
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
- H5T_class_t type_class;
+ jbyte *writeBuf = NULL;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
- jsize n;
+ size_t typeSize;
+ H5T_class_t type_class;
+ jsize vl_array_len;
htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean writeBufIsCopy;
- jbyteArray writeBuf = NULL;
+ herr_t status = FAIL;
+ htri_t is_variable = 0;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
/* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: readBuf length < 0");
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer length < 0");
}
-
- dims[0] = (hsize_t)n;
- if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
+ if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Awrite: failed to allocate raw VL write buffer");
+
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if (type_class == H5T_VLEN) {
- size_t typeSize;
- hid_t memb = H5I_INVALID_HID;
- H5T_class_t vlClass;
- size_t vlSize;
- void *rawBuf = NULL;
- jobjectArray jList = NULL;
-
- size_t i, j, x;
- if (!(typeSize = H5Tget_size(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (!(memb = H5Tget_super(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
- if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!(vlSize = H5Tget_size(memb)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate raw VL write buffer");
-
- /* Cache class types */
- /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
- jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
- jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
- jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
- jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
- jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
- jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
- /* jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */
- jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
- jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
- jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
- jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J");
- jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F");
- jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D");
-
- /* Convert each list to a vlen element */
- for (i = 0; i < (size_t)n; i++) {
- hvl_t vl_elem;
-
- if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- // retrieve the java.util.List interface class
- jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
-
- // retrieve the toArray method and invoke it
- jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;");
- if (mToArray == NULL)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
- jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
-
- if (jnelmts < 0)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: number of VL elements < 0");
-
- HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
- vl_elem.len = (size_t)jnelmts;
-
- if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate vlen ptr buffer");
-
- jobject jobj = NULL;
- for (j = 0; j < (size_t)jnelmts; j++) {
- if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- switch (vlClass) {
- /* case H5T_BOOL: {
- jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
- }
- break;
- } */
- case H5T_INTEGER: {
- switch (vlSize) {
- case sizeof(jbyte): {
- jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x];
- }
- break;
- }
- case sizeof(jshort): {
- jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x];
- }
- break;
- }
- case sizeof(jint): {
- jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x];
- }
- break;
- }
- case sizeof(jlong): {
- jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
- }
- break;
- }
- }
- break;
- }
- case H5T_FLOAT: {
- switch (vlSize) {
- case sizeof(jfloat): {
- jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x];
- }
- break;
- }
- case sizeof(jdouble): {
- jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
- }
- break;
- }
- }
- break;
- }
- case H5T_REFERENCE: {
- jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
- }
- ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
- break;
- }
- default:
- H5_UNIMPLEMENTED(ENVONLY, "H5AwriteVL: invalid class type");
- break;
- }
- ENVPTR->DeleteLocalRef(ENVONLY, jobj);
- }
-
- HDmemcpy((char *)rawBuf + i * typeSize, &vl_elem, sizeof(hvl_t));
-
- ENVPTR->DeleteLocalRef(ENVONLY, jList);
- } /* end for (i = 0; i < n; i++) */
-
- if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, rawBuf)) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
- if (rawBuf)
- HDfree(rawBuf);
- }
- else {
- PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5AwriteVL: write buffer not pinned");
- if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
+ if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
+ if ((status >= 0) && vl_data_class) {
+ dims[0] = (hsize_t)vl_array_len;
+ if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
+ }
+ if (is_variable) {
+ for (size_t i = 0; i < (size_t)vl_array_len; i++)
+ HDfree(((char **)writeBuf)[i]);
+ }
- if (type_class != H5T_VLEN)
- UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
+ HDfree(writeBuf);
}
return (jint)status;
@@ -1914,21 +1630,24 @@ H5AwriteVL_asstr(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
continue;
}
- /*
- * length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
- * CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- */
-
PIN_JAVA_STRING(ENVONLY, jstr, utf8, NULL, "H5AwriteVL_asstr: failed to pin string buffer");
/*
- * TODO: If the string isn't a copy, we should probably make
- * one before destroying it with h5str_convert.
+ * Make a copy of the string since h5str_convert uses strtok.
*/
+ char *utf8_copy = NULL;
- if (!h5str_convert(ENVONLY, (char **)&utf8, aid, tid, &(((char *)writeBuf)[i * typeSize]), 0))
+ jsize length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+ if (NULL == (utf8_copy = HDstrndup(utf8, (size_t)length)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (!h5str_convert(ENVONLY, &utf8_copy, aid, tid, &(((char *)writeBuf)[i * typeSize]), 0))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ free(utf8_copy);
+
UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
utf8 = NULL;
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index c8dc0c3..de7fb21 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -181,47 +181,71 @@ Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong me
jlong file_space_id, jlong xfer_plist_id, jbyteArray buf,
jboolean isCriticalPinning)
{
- jboolean readBufIsCopy;
- jbyte *readBuf = NULL;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ jboolean readBufIsCopy;
+ jbyte *readBuf = NULL;
+ size_t typeSize;
+ H5T_class_t type_class;
+ jsize vl_array_len; // Only used by vl_data_class types
+ htri_t vl_data_class;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread: read buffer is NULL");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
- }
-
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if (isCriticalPinning) {
- PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
- "H5Dread: read buffer not critically pinned");
+ if (vl_data_class) {
+ /* Get size of data array */
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
+ }
+
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread: failed to allocate raw VL read buffer");
}
else {
- PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread: read buffer not pinned");
+ if (isCriticalPinning) {
+ PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
+ "H5Dread: read buffer not critically pinned");
+ }
+ else {
+ PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread: read buffer not pinned");
+ }
}
if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
- (hid_t)xfer_plist_id, readBuf)) < 0)
+ (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (vl_data_class) {
+ if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf);
+ }
+
done:
if (readBuf) {
if ((status >= 0) && vl_data_class)
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);
+ }
}
}
@@ -238,31 +262,50 @@ Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong m
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jbyteArray buf,
jboolean isCriticalPinning)
{
- jboolean writeBufIsCopy;
- jbyte *writeBuf = NULL;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ jboolean writeBufIsCopy;
+ jbyte *writeBuf = NULL;
+ size_t typeSize;
+ H5T_class_t type_class;
+ jsize vl_array_len; // Only used by vl_data_class types
+ htri_t vl_data_class;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer is NULL");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
- }
-
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if (isCriticalPinning) {
- PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
- "H5Dwrite: write buffer not critically pinned");
+ if (vl_data_class) {
+ /* Get size of data array */
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer length < 0");
+ }
+
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dwrite: failed to allocate raw VL write buffer");
}
else {
- PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite: write buffer not pinned");
+ if (isCriticalPinning) {
+ PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
+ "H5Dwrite: write buffer not critically pinned");
+ }
+ else {
+ PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite: write buffer not pinned");
+ }
+ }
+
+ if (vl_data_class) {
+ if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
}
if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
@@ -274,11 +317,16 @@ done:
if ((status >= 0) && vl_data_class)
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);
+ }
}
}
@@ -1086,234 +1134,52 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
{
+ jbyte *readBuf = NULL;
+ size_t typeSize;
H5T_class_t type_class;
- jsize n;
+ jsize vl_array_len;
htri_t vl_data_class;
- herr_t status = FAIL;
- jbyteArray *readBuf = NULL;
+ herr_t status = FAIL;
+ htri_t is_variable = 0;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
/* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: readBuf length < 0");
}
-
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
- if (type_class == H5T_VLEN) {
- size_t typeSize;
- hid_t memb = H5I_INVALID_HID;
- H5T_class_t vlClass;
- size_t vlSize;
- void *rawBuf = NULL;
- jobjectArray jList = NULL;
-
- size_t i, j, x;
-
- if (!(typeSize = H5Tget_size(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (!(memb = H5Tget_super(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
- if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!(vlSize = H5Tget_size(memb)))
- H5_LIBRARY_ERROR(ENVONLY);
- if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer");
-
- if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
- (hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)rawBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
+ if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer");
- /* Cache class types */
- /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
- jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
- jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
- jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
- jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
- jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
- jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
- /*
- jmethodID boolValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
- */
- jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
- jmethodID shortValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
- jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
- jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
- jmethodID floatValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
- jmethodID doubleValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
-
- // retrieve the java.util.List interface class
- jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
- jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z");
-
- /* Convert each element to a list */
- for (i = 0; i < (size_t)n; i++) {
- hvl_t vl_elem;
-
- // The list we're going to return:
- if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- /* Get the number of sequence elements */
- HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
-
- jsize nelmts = (jsize)vl_elem.len;
- if (vl_elem.len != (size_t)nelmts)
- H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of number of VL elements");
- if (nelmts < 0)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: number of VL elements < 0");
-
- jobject jobj = NULL;
- for (j = 0; j < (size_t)nelmts; j++) {
- switch (vlClass) {
- /*case H5T_BOOL: {
- jboolean boolValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- } */
- case H5T_INTEGER: {
- switch (vlSize) {
- case sizeof(jbyte): {
- jbyte byteValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj =
- ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jshort): {
- jshort shortValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
- shortValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jint): {
- jint intValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jlong): {
- jlong longValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj =
- ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- }
- break;
- }
- case H5T_FLOAT: {
- switch (vlSize) {
- case sizeof(jfloat): {
- jfloat floatValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
- (double)floatValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jdouble): {
- jdouble doubleValue;
- for (x = 0; x < vlSize; x++) {
- ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
- doubleValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- }
- break;
- }
- case H5T_REFERENCE: {
- jboolean bb;
- jbyte *barray = NULL;
-
- jsize byteArraySize = (jsize)vlSize;
- if (vlSize != (size_t)byteArraySize)
- H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of byteArraySize");
-
- if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
- "readVL reference: byte array not pinned");
-
- for (x = 0; x < vlSize; x++) {
- barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x];
- }
- if (barray)
- UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
- break;
- }
- default:
- H5_UNIMPLEMENTED(ENVONLY, "H5DreadVL: invalid class type");
- break;
- }
-
- // Add it to the list
- ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- } /* end for */
+ if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
+ (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
- if (rawBuf)
- HDfree(rawBuf);
- }
- else {
- if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
- (hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
+ translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf);
done:
if (readBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
- UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
+ if (is_variable) {
+ for (size_t i = 0; i < (size_t)vl_array_len; i++)
+ HDfree(((char **)readBuf)[i]);
+ }
+ HDfree(readBuf);
}
return (jint)status;
@@ -1328,201 +1194,55 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
{
+ jbyte *writeBuf = NULL;
+ size_t typeSize;
H5T_class_t type_class;
- jsize n;
+ jsize vl_array_len; // Only used by vl_data_class types
htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean writeBufIsCopy;
- jbyteArray writeBuf = NULL;
+ herr_t status = FAIL;
+ htri_t is_variable = 0;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
/* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: readBuf length < 0");
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer length < 0");
}
-
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
- if (type_class == H5T_VLEN) {
- size_t typeSize;
- hid_t memb = H5I_INVALID_HID;
- H5T_class_t vlClass;
- size_t vlSize;
- void *rawBuf = NULL;
- jobjectArray jList = NULL;
-
- size_t i, j, x;
-
- if (!(typeSize = H5Tget_size(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (!(memb = H5Tget_super(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
- if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!(vlSize = H5Tget_size(memb)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer");
-
- /* Cache class types */
- /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
- jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
- jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
- jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
- jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
- jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
- jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
- /* jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */
- jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
- jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
- jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
- jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J");
- jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F");
- jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D");
-
- /* Convert each list to a vlen element */
- for (i = 0; i < (size_t)n; i++) {
- hvl_t vl_elem;
-
- if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- // retrieve the java.util.List interface class
- jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
-
- // retrieve the toArray method and invoke it
- jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;");
- if (mToArray == NULL)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
- jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
-
- if (jnelmts < 0)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: number of VL elements < 0");
-
- HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
- vl_elem.len = (size_t)jnelmts;
-
- if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate vlen ptr buffer");
-
- jobject jobj = NULL;
- for (j = 0; j < (size_t)jnelmts; j++) {
- if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- switch (vlClass) {
- /* case H5T_BOOL: {
- jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
- }
- break;
- } */
- case H5T_INTEGER: {
- switch (vlSize) {
- case sizeof(jbyte): {
- jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x];
- }
- break;
- }
- case sizeof(jshort): {
- jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x];
- }
- break;
- }
- case sizeof(jint): {
- jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x];
- }
- break;
- }
- case sizeof(jlong): {
- jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
- }
- break;
- }
- }
- break;
- }
- case H5T_FLOAT: {
- switch (vlSize) {
- case sizeof(jfloat): {
- jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x];
- }
- break;
- }
- case sizeof(jdouble): {
- jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
- }
- break;
- }
- }
- break;
- }
- case H5T_REFERENCE: {
- jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
- for (x = 0; x < vlSize; x++) {
- ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
- }
- ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
- break;
- }
- default:
- H5_UNIMPLEMENTED(ENVONLY, "H5DwriteVL: invalid class type");
- break;
- }
- ENVPTR->DeleteLocalRef(ENVONLY, jobj);
- }
- HDmemcpy((char *)rawBuf + i * typeSize, &vl_elem, sizeof(hvl_t));
+ if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer");
- ENVPTR->DeleteLocalRef(ENVONLY, jList);
- } /* end for (i = 0; i < n; i++) */
+ if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
- if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
- (hid_t)file_space_id, (hid_t)xfer_plist_id, rawBuf)) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
- if (rawBuf)
- HDfree(rawBuf);
- }
- else {
- PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5DwriteVL: write buffer not pinned");
- if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
- (hid_t)file_space_id, (hid_t)xfer_plist_id, writeBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
+ if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
+ (hid_t)xfer_plist_id, writeBuf)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
+ if (is_variable) {
+ for (size_t i = 0; i < (size_t)vl_array_len; i++)
+ HDfree(((char **)writeBuf)[i]);
+ }
- if (type_class != H5T_VLEN)
- UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
+ HDfree(writeBuf);
}
return (jint)status;
@@ -1958,21 +1678,24 @@ H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_si
continue;
}
- /*
- * length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
- * CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- */
-
PIN_JAVA_STRING(ENVONLY, jstr, utf8, NULL, "H5DwriteVL_asstr: failed to pin string buffer");
/*
- * TODO: If the string isn't a copy, we should probably make
- * one before destroying it with h5str_convert.
+ * Make a copy of the string since h5str_convert uses strtok.
*/
+ char *utf8_copy = NULL;
+
+ jsize length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+ if (NULL == (utf8_copy = HDstrndup(utf8, (size_t)length)))
+ H5_LIBRARY_ERROR(ENVONLY);
- if (!h5str_convert(ENVONLY, (char **)&utf8, did, tid, &(((char *)writeBuf)[i * typeSize]), 0))
+ if (!h5str_convert(ENVONLY, &utf8_copy, did, tid, &(((char *)writeBuf)[i * typeSize]), 0))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ HDfree(utf8_copy);
+
UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
utf8 = NULL;
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 06087a7..152f019 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -77,6 +77,9 @@ static int render_bin_output_region_data_points(FILE *stream, hid_t region_sp
hsize_t *ptdata);
static int render_bin_output_region_points(FILE *stream, hid_t region_space, hid_t region_id,
hid_t container);
+jobject translate_atomic_rbuf(JNIEnv *env, jlong mem_type_id, H5T_class_t type_class, void *raw_buf);
+void translate_atomic_wbuf(JNIEnv *env, jobject in_obj, jlong mem_type_id, H5T_class_t type_class,
+ void *raw_buf);
/* Strings for output */
#define H5_TOOLS_GROUP "GROUP"
@@ -435,40 +438,43 @@ h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_
break;
case H5T_ENUM: {
- void *value = NULL;
+ void *value = NULL;
+ unsigned char tmp_uchar = 0;
+ unsigned short tmp_ushort = 0;
+ unsigned int tmp_uint = 0;
+#if H5_SIZEOF_LONG != H5_SIZEOF_INT
+ unsigned long tmp_ulong = 0;
+#endif
+#if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG
+ unsigned long long tmp_ullong = 0;
+#endif
token = HDstrtok(this_str, delimiter);
switch (typeSize) {
case sizeof(char): {
- unsigned char tmp_uchar = 0;
- value = &tmp_uchar;
+ value = &tmp_uchar;
break;
}
case sizeof(short): {
- unsigned short tmp_ushort = 0;
- value = &tmp_ushort;
+ value = &tmp_ushort;
break;
}
#if H5_SIZEOF_LONG != H5_SIZEOF_INT
case sizeof(long): {
- unsigned long tmp_ulong = 0;
- value = &tmp_ulong;
+ value = &tmp_ulong;
break;
}
#endif
#if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG
case sizeof(long long): {
- unsigned long long tmp_ullong = 0;
- value = &tmp_ullong;
+ value = &tmp_ullong;
break;
}
#endif
-
default: {
- unsigned int tmp_uint = 0;
- value = &tmp_uint;
+ value = &tmp_uint;
break;
}
}
@@ -3426,10 +3432,8 @@ Java_hdf_hdf5lib_H5_H5AreadComplex(JNIEnv *env, jclass clss, jlong attr_id, jlon
size = (((H5Tget_size(mem_type_id)) > (H5Tget_size(p_type))) ? (H5Tget_size(mem_type_id))
: (H5Tget_size(p_type)));
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) <= 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) <= 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadComplex: read buffer length <= 0");
- }
if (NULL == (readBuf = (char *)HDmalloc((size_t)n * size)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AreadComplex: failed to allocate read buffer");
@@ -4042,6 +4046,854 @@ done:
H5Aclose(attr_id);
} /* end Java_hdf_hdf5lib_H5_H5export_1attribute */
+jobject
+translate_atomic_rbuf(JNIEnv *env, jlong mem_type_id, H5T_class_t type_class, void *raw_buf)
+{
+ jobject jobj = NULL;
+ hid_t memb = H5I_INVALID_HID;
+ jobjectArray jList = NULL;
+ H5T_class_t vlClass;
+ size_t vlSize;
+ size_t i;
+ size_t typeSize;
+ // raw_buf is normally bytes except when used for variable length strings
+ char *char_buf = (char *)raw_buf;
+
+ /* retrieve the java.util.ArrayList interface class */
+ jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList");
+ jmethodID arrListMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "<init>", "(I)V");
+
+ /* Cache class types */
+ /* jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
+ jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
+ jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
+ jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
+ jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
+ jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
+ jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
+ /*jobjectArray
+ jmethodID boolValueMid =
+ ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
+ */
+ jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
+ jmethodID shortValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
+ jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
+ jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
+ jmethodID floatValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
+ jmethodID doubleValueMid =
+ ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
+
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ switch (type_class) {
+ case H5T_VLEN: {
+ if (!(memb = H5Tget_super(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if ((vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert element to a list */
+ hvl_t vl_elem;
+
+ /* Get the number of sequence elements */
+ memcpy(&vl_elem, char_buf, sizeof(hvl_t));
+ jsize nelmts = (jsize)vl_elem.len;
+ if (vl_elem.len != (size_t)nelmts)
+ H5_JNI_FATAL_ERROR(ENVONLY, "translate_atomic_rbuf: overflow of number of VL elements");
+
+ if (nelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_atomic_rbuf: number of VL elements < 0");
+
+ /* The list we're going to return: */
+ if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate list read buffer");
+
+ translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)nelmts, vl_elem.p);
+ jobj = jList;
+ break;
+ } /* H5T_VLEN */
+ case H5T_COMPOUND: {
+ int nmembs = H5Tget_nmembers(mem_type_id);
+
+ /* The list we're going to return: */
+ if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate list read buffer");
+
+ /* Convert each element to a compound object */
+ for (i = 0; i < (size_t)nmembs; i++) {
+ H5T_class_t memb_vlClass;
+ size_t memb_vlSize;
+ size_t memb_offset;
+
+ if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)i)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)i);
+ if ((memb_vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(memb_vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ translate_atomic_rbuf(ENVONLY, memb, memb_vlClass, char_buf + i * typeSize + memb_offset);
+ H5Tclose(memb);
+ }
+ jobj = jList;
+ break;
+ } /* H5T_COMPOUND */
+ case H5T_ARRAY: {
+ void *objBuf = NULL;
+ size_t typeCount;
+
+ if (!(memb = H5Tget_super(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if ((vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ typeCount = typeSize / vlSize;
+
+ if (NULL == (objBuf = HDmalloc(typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate buffer");
+
+ /* Convert each element */
+ /* Get the object element */
+ memcpy((char *)objBuf, char_buf, typeSize);
+
+ /* The list we're going to return: */
+ if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate list read buffer");
+
+ translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)typeCount, objBuf);
+ jobj = jList;
+
+ if (objBuf)
+ HDfree(objBuf);
+
+ break;
+ } /* H5T_ARRAY */
+ case H5T_ENUM:
+ case H5T_BITFIELD:
+ case H5T_OPAQUE:
+ case H5T_INTEGER: {
+ /* Convert each element */
+ switch (typeSize) {
+ case sizeof(jbyte): {
+ jbyte byteValue;
+ HDmemcpy(((char *)&byteValue), char_buf, typeSize);
+
+ if (NULL ==
+ (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ case sizeof(jshort): {
+ jshort shortValue;
+ HDmemcpy(((char *)&shortValue), char_buf, typeSize);
+
+ if (NULL ==
+ (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid, shortValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ case sizeof(jint): {
+ jint intValue;
+
+ HDmemcpy(((char *)&intValue), char_buf, typeSize);
+
+ if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ case sizeof(jlong): {
+ jlong longValue;
+ HDmemcpy(((char *)&longValue), char_buf, typeSize);
+
+ if (NULL ==
+ (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ }
+ break;
+ } /* H5T_INTEGER */
+ case H5T_FLOAT: {
+ /* Convert each element to a list */
+ switch (typeSize) {
+ case sizeof(jfloat): {
+ jfloat floatValue;
+ HDmemcpy(((char *)&floatValue), char_buf, typeSize);
+
+ if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
+ (double)floatValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ case sizeof(jdouble): {
+ jdouble doubleValue;
+ HDmemcpy(((char *)&doubleValue), char_buf, typeSize);
+
+ if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
+ doubleValue)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ }
+ }
+ break;
+ } /* H5T_FLOAT */
+ case H5T_REFERENCE: {
+ /* Convert each element to a list */
+ jboolean bb;
+ jbyte *barray = NULL;
+
+ jsize byteArraySize = (jsize)typeSize;
+ if (typeSize != (size_t)byteArraySize)
+ H5_JNI_FATAL_ERROR(ENVONLY, "translate_atomic_rbuf: overflow of byteArraySize");
+
+ if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+ PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
+ "translate_atomic_rbuf reference: byte array not pinned");
+
+ HDmemcpy(barray, ((jbyte *)raw_buf), typeSize);
+ if (barray)
+ UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
+
+ break;
+ } /* H5T_REFERENCE */
+ case H5T_STRING: {
+ htri_t is_variable = 0;
+
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert each element */
+ if (is_variable) {
+ char **var_str_buf = (char **)raw_buf;
+ if (NULL == (jobj = ENVPTR->NewStringUTF(ENVONLY, *var_str_buf))) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: out of memory - unable to "
+ "construct string from UTF characters");
+ }
+ }
+ else {
+ if (NULL == (jobj = ENVPTR->NewStringUTF(ENVONLY, char_buf))) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: out of memory - unable to "
+ "construct string from UTF characters");
+ }
+ }
+
+ break;
+ } /* H5T_STRING */
+ default:
+ H5_UNIMPLEMENTED(ENVONLY, "translate_atomic_rbuf: invalid class type");
+ break;
+ } /* switch(type_class) */
+
+done:
+
+ return jobj;
+}
+
+void
+translate_atomic_wbuf(JNIEnv *env, jobject in_obj, jlong mem_type_id, H5T_class_t type_class, void *raw_buf)
+{
+ hid_t memb = H5I_INVALID_HID;
+ H5T_class_t vlClass;
+ size_t vlSize;
+ size_t i;
+ size_t typeSize;
+ // raw_buf is normally bytes except when used for variable length strings
+ char *char_buf = (char *)raw_buf;
+
+ /* retrieve the java.util.ArrayList interface class */
+ jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList");
+ /* retrieve the toArray method */
+ jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, arrCList, "toArray", "()[Ljava/lang/Object;");
+
+ /* Cache class types */
+ jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
+ jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
+ jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
+ jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
+ jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
+ jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
+
+ jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
+ jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
+ jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
+ jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J");
+ jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F");
+ jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D");
+
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ switch (type_class) {
+ case H5T_VLEN: {
+ if (!(memb = H5Tget_super(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert element to a vlen element */
+ hvl_t vl_elem;
+
+ jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, in_obj);
+
+ if (jnelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_atomic_wbuf: number of VL elements < 0");
+
+ vl_elem.len = (size_t)jnelmts;
+
+ if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_wbuf: failed to allocate vlen ptr buffer");
+
+ translate_wbuf(ENVONLY, (jobjectArray)in_obj, memb, vlClass, (jsize)jnelmts, vl_elem.p);
+
+ HDmemcpy(char_buf, &vl_elem, sizeof(hvl_t));
+ break;
+ } /* H5T_VLEN */
+ case H5T_COMPOUND: {
+ /* Convert each compound element */
+ int nmembs = H5Tget_nmembers(mem_type_id);
+
+ /* invoke the toArray method */
+ if (mToArray == NULL)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, in_obj, mToArray);
+ jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
+
+ if (jnelmts != nmembs)
+ H5_BAD_ARGUMENT_ERROR(
+ ENVONLY, "translate_atomic_wbuf: number of elements not equal to number of members");
+
+ /* Convert each compound object to an element */
+ for (i = 0; i < (size_t)nmembs; i++) {
+ H5T_class_t memb_vlClass;
+ size_t memb_vlSize;
+ size_t memb_offset;
+
+ if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)i)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)i);
+ if ((memb_vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(memb_vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ jobject arr_obj = ENVPTR->GetObjectArrayElement(ENVONLY, array, (jsize)i);
+ translate_atomic_wbuf(ENVONLY, arr_obj, memb, memb_vlClass,
+ char_buf + i * typeSize + memb_offset);
+ ENVPTR->DeleteLocalRef(ENVONLY, arr_obj);
+ H5Tclose(memb);
+ }
+ break;
+ } /* H5T_COMPOUND */
+ case H5T_ARRAY: {
+ void *objBuf = NULL;
+
+ if (!(memb = H5Tget_super(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if ((vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert each array element */
+ /* invoke the toArray method */
+ if (mToArray == NULL)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, in_obj, mToArray);
+ jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
+
+ if (jnelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_atomic_wbuf: number of array elements < 0");
+
+ if (NULL == (objBuf = HDmalloc((size_t)jnelmts * vlSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_wbuf: failed to allocate buffer");
+
+ translate_wbuf(ENVONLY, array, memb, vlClass, (jsize)jnelmts, objBuf);
+
+ HDmemcpy(char_buf, (char *)objBuf, vlSize * (size_t)jnelmts);
+ break;
+ } /* H5T_ARRAY */
+ case H5T_ENUM:
+ case H5T_BITFIELD:
+ case H5T_OPAQUE:
+ case H5T_INTEGER: {
+ /* Convert each element */
+ switch (typeSize) {
+ case sizeof(jbyte): {
+ jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, in_obj, byteValueMid);
+ HDmemcpy(char_buf, ((char *)&byteValue), typeSize);
+ break;
+ }
+ case sizeof(jshort): {
+ jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, in_obj, shortValueMid);
+ HDmemcpy(char_buf, ((char *)&shortValue), typeSize);
+ break;
+ }
+ case sizeof(jint): {
+ jint intValue = ENVPTR->CallIntMethod(ENVONLY, in_obj, intValueMid);
+ HDmemcpy(char_buf, ((char *)&intValue), typeSize);
+ break;
+ }
+ case sizeof(jlong): {
+ jlong longValue = ENVPTR->CallLongMethod(ENVONLY, in_obj, longValueMid);
+ HDmemcpy(char_buf, ((char *)&longValue), typeSize);
+ break;
+ }
+ }
+ break;
+ } /* H5T_INTEGER */
+ case H5T_FLOAT: {
+ /* Convert each element */
+ switch (typeSize) {
+ case sizeof(jfloat): {
+ jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, in_obj, floatValueMid);
+ HDmemcpy(char_buf, ((char *)&floatValue), typeSize);
+ break;
+ }
+ case sizeof(jdouble): {
+ jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, in_obj, doubleValueMid);
+ HDmemcpy(char_buf, ((char *)&doubleValue), typeSize);
+ break;
+ }
+ }
+ break;
+ } /* H5T_FLOAT */
+ case H5T_REFERENCE: {
+ /* Convert each array element */
+ jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, in_obj, 0);
+ HDmemcpy(char_buf, ((char *)barray), typeSize);
+ ENVPTR->ReleaseByteArrayElements(ENVONLY, in_obj, barray, 0);
+ break;
+ } /* H5T_REFERENCE */
+ case H5T_STRING: {
+ htri_t is_variable = 0;
+
+ if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert each pointer element */
+ jsize length;
+ const char *utf8 = NULL;
+
+ HDmemset(char_buf, 0, typeSize);
+ if (NULL != in_obj) {
+ PIN_JAVA_STRING(ENVONLY, in_obj, utf8, NULL, "translate_atomic_wbuf jobj not pinned");
+ length = ENVPTR->GetStringUTFLength(ENVONLY, in_obj);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ if (is_variable) {
+ char *new_buf = (char *)calloc(1, (size_t)(length + 1));
+ HDmemcpy(((char *)new_buf), utf8, (size_t)length);
+ HDmemcpy(char_buf, &new_buf, typeSize);
+ }
+ else {
+ HDmemcpy(char_buf, utf8, (size_t)length);
+ }
+ UNPIN_JAVA_STRING(ENVONLY, in_obj, utf8);
+ utf8 = NULL;
+ }
+ break;
+ } /* H5T_STRING */
+ default:
+ H5_UNIMPLEMENTED(ENVONLY, "translate_atomic_wbuf: invalid class type");
+ break;
+ } /* switch(type_class) */
+
+done:
+
+ return;
+}
+
+void
+translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, jsize count,
+ void *raw_buf)
+{
+ hid_t memb = H5I_INVALID_HID;
+ int ret_buflen = -1;
+ jboolean found_jList = JNI_TRUE;
+ jobjectArray jList = NULL;
+ jobject jobj = NULL;
+ H5T_class_t vlClass;
+ size_t vlSize;
+ size_t i, x;
+ size_t typeSize;
+ // raw_buf is normally bytes except when used for variable length strings
+ char *char_buf = (char *)raw_buf;
+
+ /* retrieve the java.util.ArrayList interface class */
+ jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList");
+ jmethodID arrListMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "<init>", "(I)V");
+ jmethodID arrAddMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "add", "(Ljava/lang/Object;)Z");
+
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ ret_buflen = ENVPTR->GetArrayLength(ENVONLY, ret_buf);
+ if (ret_buflen < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "ret_buflen: Array length cannot be negative");
+
+ switch (type_class) {
+ case H5T_VLEN: {
+ if (!(memb = H5Tget_super(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if ((vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert each element to a list */
+ for (i = 0; i < (size_t)count; i++) {
+ hvl_t vl_elem;
+
+ found_jList = JNI_TRUE;
+ jList = NULL;
+
+ /* Get the number of sequence elements */
+ HDmemcpy(&vl_elem, char_buf + i * sizeof(hvl_t), sizeof(hvl_t));
+ jsize nelmts = (jsize)vl_elem.len;
+ if (vl_elem.len != (size_t)nelmts)
+ H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: overflow of number of VL elements");
+
+ if (nelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_rbuf: number of VL elements < 0");
+
+ /* The list we're going to return: */
+ if (i < (size_t)ret_buflen) {
+ jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i);
+ }
+ if (NULL == jList) {
+ found_jList = JNI_FALSE;
+ if (NULL ==
+ (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY,
+ "translate_rbuf: failed to allocate list read buffer");
+ }
+
+ translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)nelmts, vl_elem.p);
+ if (found_jList == JNI_FALSE) {
+ jboolean addResult =
+ ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, (jobject)jList);
+ if (!addResult)
+ H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: cannot add VL element");
+ }
+ else {
+ ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, (jsize)i, (jobject)jList);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ }
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ }
+ break;
+ } /* H5T_VLEN */
+ case H5T_COMPOUND: {
+ /* Convert each compound element to a list */
+ for (i = 0; i < (size_t)count; i++) {
+ found_jList = JNI_TRUE;
+ jList = NULL;
+
+ /* The list we're going to return: */
+ if (i < (size_t)ret_buflen) {
+ jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i);
+ }
+ if (NULL == jList) {
+ found_jList = JNI_FALSE;
+ if (NULL ==
+ (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY,
+ "translate_rbuf: failed to allocate list read buffer");
+ }
+ int nmembs = H5Tget_nmembers(mem_type_id);
+ /* Convert each element to a list */
+ for (x = 0; x < (size_t)nmembs; x++) {
+ H5T_class_t memb_vlClass;
+ size_t memb_vlSize;
+ size_t memb_offset;
+
+ if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)x)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)x);
+
+ if ((memb_vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(memb_vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ jobj = translate_atomic_rbuf(ENVONLY, memb, memb_vlClass,
+ char_buf + i * typeSize + memb_offset);
+ if (jobj) {
+ if (found_jList == JNI_FALSE)
+ ENVPTR->CallBooleanMethod(ENVONLY, jList, arrAddMethod, (jobject)jobj);
+ else
+ ENVPTR->SetObjectArrayElement(ENVONLY, jList, (jsize)i, (jobject)jobj);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ ENVPTR->DeleteLocalRef(ENVONLY, jobj);
+ }
+
+ H5Tclose(memb);
+ }
+ if (ret_buflen == 0)
+ ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList);
+ else
+ ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, (jsize)i, jList);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ }
+ break;
+ } /* H5T_COMPOUND */
+ case H5T_ARRAY: {
+ void *objBuf = NULL;
+ size_t typeCount;
+
+ if (!(memb = H5Tget_super(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if ((vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ typeCount = typeSize / vlSize;
+
+ if (NULL == (objBuf = HDmalloc(typeSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_rbuf: failed to allocate buffer");
+
+ /* Convert each element to a list */
+ for (i = 0; i < (size_t)count; i++) {
+ found_jList = JNI_TRUE;
+ jList = NULL;
+
+ /* Get the object element */
+ HDmemcpy((char *)objBuf, char_buf + i * typeSize, typeSize);
+
+ /* The list we're going to return: */
+ if (i < (size_t)ret_buflen) {
+ if (NULL ==
+ (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i)))
+ found_jList = JNI_FALSE;
+ }
+ if (NULL == jList) {
+ if (NULL ==
+ (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY,
+ "translate_rbuf: failed to allocate list read buffer");
+ }
+
+ translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)typeCount, objBuf);
+ if (found_jList == JNI_FALSE)
+ ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList);
+ else
+ ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, (jsize)i, jList);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ }
+
+ if (objBuf)
+ HDfree(objBuf);
+
+ break;
+ } /* H5T_ARRAY */
+ case H5T_ENUM:
+ case H5T_BITFIELD:
+ case H5T_OPAQUE:
+ case H5T_INTEGER:
+ case H5T_FLOAT:
+ case H5T_REFERENCE:
+ case H5T_STRING: {
+ /* Convert each element to a list */
+ for (i = 0; i < (size_t)count; i++) {
+ jobj = translate_atomic_rbuf(ENVONLY, mem_type_id, type_class, char_buf + i * typeSize);
+ if (jobj) {
+ if (ret_buflen == 0)
+ ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, (jobject)jobj);
+ else
+ ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, (jsize)i, (jobject)jobj);
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ ENVPTR->DeleteLocalRef(ENVONLY, jobj);
+ }
+ }
+ break;
+ }
+ default:
+ H5_UNIMPLEMENTED(ENVONLY, "translate_rbuf: invalid class type");
+ break;
+ } /* switch(type_class) */
+
+done:
+
+ return;
+}
+
+void
+translate_wbuf(JNIEnv *env, jobjectArray in_buf, jlong mem_type_id, H5T_class_t type_class, jsize count,
+ void *raw_buf)
+{
+ hid_t memb = H5I_INVALID_HID;
+ jobjectArray jList = NULL;
+ jobject jobj = NULL;
+ H5T_class_t vlClass;
+ size_t vlSize;
+ size_t i, x;
+ size_t typeSize;
+ // raw_buf is normally bytes except when used for variable length strings
+ char *char_buf = (char *)raw_buf;
+
+ /* retrieve the java.util.ArrayList interface class */
+ jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList");
+ /* retrieve the toArray method */
+ jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, arrCList, "toArray", "()[Ljava/lang/Object;");
+
+ if (!(typeSize = H5Tget_size(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ switch (type_class) {
+ case H5T_VLEN: {
+ if (!(memb = H5Tget_super(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert each list to a vlen element */
+ for (i = 0; i < (size_t)count; i++) {
+ hvl_t vl_elem;
+
+ if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+ /* invoke the toArray method */
+ if (mToArray == NULL)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
+ jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
+
+ if (jnelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_wbuf: number of VL elements < 0");
+
+ vl_elem.len = (size_t)jnelmts;
+
+ if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
+ H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_wbuf: failed to allocate vlen ptr buffer");
+
+ translate_wbuf(ENVONLY, array, memb, vlClass, (jsize)jnelmts, vl_elem.p);
+
+ HDmemcpy(char_buf + i * sizeof(hvl_t), &vl_elem, sizeof(hvl_t));
+
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ } /* end for (i = 0; i < count; i++) */
+ break;
+ } /* H5T_VLEN */
+ case H5T_COMPOUND: {
+ /* Convert each list to a compound element */
+ for (i = 0; i < (size_t)count; i++) {
+ if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+ int nmembs = H5Tget_nmembers(mem_type_id);
+
+ /* invoke the toArray method */
+ if (mToArray == NULL)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
+ jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
+
+ if (jnelmts != nmembs)
+ H5_BAD_ARGUMENT_ERROR(
+ ENVONLY, "translate_wbuf: number of elements not equal to number of members");
+
+ /* Convert each compound object to an element */
+ for (x = 0; x < (size_t)nmembs; x++) {
+ H5T_class_t memb_vlClass;
+ size_t memb_vlSize;
+ size_t memb_offset;
+
+ if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)x)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)x);
+
+ if ((memb_vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(memb_vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ jobject arr_obj = ENVPTR->GetObjectArrayElement(ENVONLY, array, (jsize)x);
+ translate_atomic_wbuf(ENVONLY, arr_obj, memb, memb_vlClass,
+ char_buf + i * typeSize + memb_offset);
+ ENVPTR->DeleteLocalRef(ENVONLY, arr_obj);
+ H5Tclose(memb);
+ }
+
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ } /* end for (i = 0; i < count; i++) */
+ break;
+ } /* H5T_COMPOUND */
+ case H5T_ARRAY: {
+ if (!(memb = H5Tget_super(mem_type_id)))
+ H5_LIBRARY_ERROR(ENVONLY);
+ if ((vlClass = H5Tget_class(memb)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ if (!(vlSize = H5Tget_size(memb)))
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ /* Convert each list to an array element */
+ for (i = 0; i < (size_t)count; i++) {
+ if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+ /* invoke the toArray method */
+ if (mToArray == NULL)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
+ jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
+
+ if (jnelmts < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_wbuf: number of array elements < 0");
+
+ translate_wbuf(ENVONLY, array, memb, vlClass, jnelmts,
+ char_buf + i * vlSize * (size_t)jnelmts);
+
+ ENVPTR->DeleteLocalRef(ENVONLY, jList);
+ } /* end for (i = 0; i < count; i++) */
+ break;
+ } /* H5T_ARRAY */
+ case H5T_ENUM:
+ case H5T_BITFIELD:
+ case H5T_OPAQUE:
+ case H5T_INTEGER:
+ case H5T_FLOAT:
+ case H5T_REFERENCE:
+ case H5T_STRING: {
+ /* Convert each list to an array element */
+ for (i = 0; i < (size_t)count; i++) {
+ if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i)))
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ translate_atomic_wbuf(ENVONLY, jobj, mem_type_id, type_class, char_buf + i * typeSize);
+ ENVPTR->DeleteLocalRef(ENVONLY, jobj);
+ }
+ break;
+ }
+ default:
+ H5_UNIMPLEMENTED(ENVONLY, "translate_wbuf: invalid class type");
+ break;
+ } /* switch(type_class) */
+
+done:
+
+ return;
+}
+
#ifdef __cplusplus
}
#endif
diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h
index fa0a061..d8ecef9 100644
--- a/java/src/jni/h5util.h
+++ b/java/src/jni/h5util.h
@@ -51,6 +51,11 @@ extern int h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr, int b
extern htri_t H5Tdetect_variable_str(hid_t tid);
+extern void translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class,
+ jsize count, void *raw_buf);
+extern void translate_wbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class,
+ jsize count, void *raw_buf);
+
/*
* Symbols used to format the output of h5str_sprintf and
* to interpret the input to h5str_convert.
generated by cgit v0.12 at 2024-07-01 02:13:33 (GMT)