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b58ab3cc1f80e876b7bddb6f120817b5ba84f5ef
hdf5/java/src-jni/jni/h5dImp.c
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Matt Landgithub-actions b58ab3cc1f Fix bad reads of nested cmpd/vlen types in JNI (#6413) 
* Fix H5DreadVL failing for pre-allocate cmpd-of-seq dsets

* Fix bad vlen of cmpd with null slot read

* Fix bad cmpd of cmpd read in java

`translate_rbuf`'s H5T_VLEN case had a similar bug where when `found_jList` was set to false due to an entyr in `ret_buf` being null, `ret_buf.add()` would be invoked on an array of objects without the list .add() method. This would occur whenever a read was invoked of a vlen sequence with a null (non-preallocated) entry. The pre-existing tests only tested the pre-allocated cases.

I removed the use of the `found_jList` flag, since it conflated the passing of an unallocated slot with `ret_buf` not being an array. Instead use `ret_buflen == 0` as the check to match the pattern in H5T_INTEGER and other branches.

The test for this fix is testH5Dread_vlen_of_compound_nullslot.

---

`translate_atomic_rebuf` had two issues related to handling of nested compounds. First, it discarded recursive returns, resulting in the construction of empty lists. Secondly, its member offset (`char_buf + i * typeSize + memb_offset`) was incorrect. In this case, `i` was the member index and `memberSize` was the entire cmpd size, so the offset would be erroneously large. It seems like this came from copying of the offset computation from `translate_rbuf`, which had to advance over entire  elements of compound data. This error was duplicated on the write side in `translate_atomic_wbuf`'s H5T_COMPOUND case (h5util.c:4611).

I changed `translate_atomic_rbuf` to capture the resultant object, and dropped the `i * typeSize` term in both routines.
The new test verifying the fix works is `testH5Dread_vlen_of_nested_compound`.

* Add exception checks

* Update NULL checks in translate_wbuf

* Correct potentially bad array length check

* Clang format

* Fix readVL/writeVL crash on malformed buffer

* Committing clang-format changes

* Add bufSize checks to wbuf/rbuf translation

* Remove vlen pre-allocation support

* Harden JNI buffer interface

* Handle opaque types as byte[] and document JNI buffer data model

Opaque elements were grouped with H5T_INTEGER in the nested-type
translation path, which boxed them as Integer/Long and rejected
arbitrary-sized opaque blobs. Treat H5T_OPAQUE like H5T_REFERENCE
(a byte[] per element) in translate_atomic_rbuf, translate_atomic_wbuf,
and h5validate_atomic_wbuf so nested opaque round-trips correctly.

Also add "Buffer data model" header comments on translate_rbuf() and
translate_wbuf() and note the reference/opaque byte[] leaves in the
H5.java javadocv.

* Initialize typeSize to fix -Werror=maybe-uninitialized

typeSize was assigned only inside the vl_data_class branch but read in
a second, separate vl_data_class branch, which gcc -O2 flags as
maybe-uninitialized under -Werror. Initialize it to 0 at declaration in
H5Aread/H5Awrite/H5Dread/H5Dwrite, matching the existing vl_array_len
pattern.

* Port nested cmpd/vlen tests to java/test and sync reference

The legacy java/test tree's JUnit-TestH5D.txt reference listed the new
nested compound/vlen tests, but the corresponding @Test methods existed
only in java/src-jni/test/TestH5D.java. Port the 10 tests and the
writeCompoundOfVlenDataset helper into java/test/TestH5D.java, remove
debug prints, and
regenerate the reference to match the actual JUnit output.

* Support nested vlen/compound datatypes in Java FFM compat layer

The FFM compatibility layer (java/hdf) lacked the vlen/compound read and
write support that the JNI interface gained, so the nested cmpd/vlen tests
ported into java/test (TestH5D) failed and leaked an id.

VLDataConverter now has recursive encodeValue/decodeValue helpers that pack
and unpack any member class (integer, float, fixed/vl string, nested
compound, and VLEN) in the native HDF5 in-memory layout. These are wired
into convertCompoundDatatype, readCompoundDatatype and convertRawDataToArrayList,
and a type-aware convertToHVLAuto handles top-level VLEN-of-compound writes.
Compound reads now reclaim VL memory, and type/count mismatches raise
IllegalArgumentException instead of silently corrupting data.

H5DwriteVL rejects an undersized buffer up front and routes VLEN writes
through convertToHVLAuto. The JUnit-TestH5D reference regains its trailing
blank line to match the actual JUnit output.

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2026-07-06 09:52:29 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the LICENSE file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#include <jni.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "hdf5.h"
#include "h5util.h"
#include "h5jni.h"
#include "h5dImp.h"
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
extern JavaVM *jvm;
typedef struct _cb_wrapper {
jobject visit_callback;
jobject op_data;
} cb_wrapper;
/********************/
/* Local Prototypes */
/********************/
static herr_t H5DreadVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid,
hid_t xfer_plist_id, jobjectArray buf);
static herr_t H5DreadVL_str(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid,
hid_t xfer_plist_id, jobjectArray buf);
static herr_t H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid,
hid_t xfer_plist_id, jobjectArray buf);
static herr_t H5DwriteVL_str(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid,
hid_t xfer_plist_id, jobjectArray buf);
/********************/
/* Local Macros */
/********************/
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Dcreate
* Signature: (JLjava/lang/String;JJJ)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Dcreate(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong type_id,
jlong space_id, jlong create_plist_id)
{
const char *dsetName = NULL;
hid_t dset_id = H5I_INVALID_HID;
UNUSED(clss);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dcreate: dataset name is NULL");
PIN_JAVA_STRING(ENVONLY, name, dsetName, NULL, "H5Dcreate: dataset name not pinned");
if ((dset_id = H5Dcreate2((hid_t)loc_id, dsetName, (hid_t)type_id, (hid_t)space_id, H5P_DEFAULT,
(hid_t)create_plist_id, H5P_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (dsetName)
UNPIN_JAVA_STRING(ENVONLY, name, dsetName);
return (jlong)dset_id;
} /* end Java_hdf_hdf5lib_H5__1H5Dcreate */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Dopen
* Signature: (JLjava/lang/String;)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Dopen(JNIEnv *env, jclass clss, jlong loc_id, jstring name)
{
const char *dsetName = NULL;
hid_t dset_id = H5I_INVALID_HID;
UNUSED(clss);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dopen: dataset name is NULL");
PIN_JAVA_STRING(ENVONLY, name, dsetName, NULL, "H5Dopen: dataset name not pinned");
if ((dset_id = H5Dopen2((hid_t)loc_id, dsetName, H5P_DEFAULT)))
H5_LIBRARY_ERROR(ENVONLY);
done:
if (dsetName)
UNPIN_JAVA_STRING(ENVONLY, name, dsetName);
return (jlong)dset_id;
} /* end Java_hdf_hdf5lib_H5__1H5Dopen */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Dget_space
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Dget_1space(JNIEnv *env, jclass clss, jlong dataset_id)
{
hid_t retVal = H5I_INVALID_HID;
UNUSED(clss);
if ((retVal = H5Dget_space((hid_t)dataset_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Dget_1space */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Dget_type
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Dget_1type(JNIEnv *env, jclass clss, jlong dataset_id)
{
hid_t retVal = H5I_INVALID_HID;
UNUSED(clss);
if ((retVal = H5Dget_type((hid_t)dataset_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Dget_1type */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Dget_create_plist
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Dget_1create_1plist(JNIEnv *env, jclass clss, jlong dataset_id)
{
hid_t retVal = H5I_INVALID_HID;
UNUSED(clss);
if ((retVal = H5Dget_create_plist((hid_t)dataset_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Dget_1create_1plist */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread
* Signature: (JJJJJ[BZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
jlong file_space_id, jlong xfer_plist_id, jbyteArray buf,
jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
jbyte *readBuf = NULL;
size_t typeSize = 0; // Only used by vl_data_class types
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, "H5Dread: read buffer is NULL");
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* For fixed-length data the byte buffer must cover the selection. */
if (!vl_data_class &&
h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jbyte),
"H5Dread") < 0)
goto done;
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 = calloc((size_t)vl_array_len, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread: failed to allocate raw VL read buffer");
}
else {
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, (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,
(size_t)vl_array_len * typeSize);
}
done:
if (readBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
if (vl_data_class) {
free(readBuf);
}
else {
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);
}
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite
* Signature: (JJJJJ[BZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jbyteArray buf,
jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
jbyte *writeBuf = NULL;
size_t typeSize = 0; // Only used by vl_data_class types
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, "H5Dwrite: write buffer is NULL");
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* For fixed-length data the byte buffer must cover the selection. */
if (!vl_data_class &&
h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jbyte),
"H5Dwrite") < 0)
goto done;
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 = calloc((size_t)vl_array_len, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dwrite: failed to allocate raw VL write buffer");
}
else {
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,
(size_t)vl_array_len * typeSize);
}
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 (vl_data_class) {
free(writeBuf);
}
else {
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);
}
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Dclose
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5__1H5Dclose(JNIEnv *env, jclass clss, jlong dataset_id)
{
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5Dclose((hid_t)dataset_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Dclose */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dget_storage_size
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Dget_1storage_1size(JNIEnv *env, jclass clss, jlong dataset_id)
{
hsize_t retVal = 0;
UNUSED(clss);
if (dataset_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dget_storage_size: not a dataset");
if (!(retVal = H5Dget_storage_size((hid_t)dataset_id)))
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Dget_1storage_1size */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dvlen_reclaim
* Signature: (JJJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dvlen_1reclaim(JNIEnv *env, jclass clss, jlong type_id, jlong space_id,
jlong xfer_plist_id, jbyteArray buf)
{
#ifndef H5_NO_DEPRECATED_SYMBOLS
jboolean vlenBufIsCopy;
jbyte *vlenBuf = NULL;
#endif
herr_t status = FAIL;
UNUSED(clss);
#ifdef H5_NO_DEPRECATED_SYMBOLS
UNUSED(type_id);
UNUSED(space_id);
UNUSED(xfer_plist_id);
UNUSED(buf);
H5_UNIMPLEMENTED(ENVONLY, "H5Dvlen_reclaim: not implemented");
#else
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dvlen_reclaim: buffer is NULL");
PIN_BYTE_ARRAY(ENVONLY, buf, vlenBuf, &vlenBufIsCopy, "H5Dvlen_reclaim: buffer not pinned");
if ((status = H5Dvlen_reclaim((hid_t)type_id, (hid_t)space_id, (hid_t)xfer_plist_id, vlenBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
#endif
done:
#ifndef H5_NO_DEPRECATED_SYMBOLS
if (vlenBuf)
UNPIN_BYTE_ARRAY(ENVONLY, buf, vlenBuf, (status < 0) ? JNI_ABORT : 0);
#endif
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dvlen_1reclaim */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_short
* Signature: (JJJJJ[SZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dread_1short(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jshortArray buf, jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
jshort *readBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_short: read buffer is NULL");
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jshort),
"H5Dread_short") < 0)
goto done;
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_short: read buffer not critically pinned");
}
else {
PIN_SHORT_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread_short: 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)
H5_LIBRARY_ERROR(ENVONLY);
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);
}
else {
UNPIN_SHORT_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1short */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite_short
* Signature: (JJJJJ[SZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1short(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jshortArray buf, jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
jshort *writeBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_short: write buffer is NULL");
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jshort),
"H5Dwrite_short") < 0)
goto done;
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_short: write buffer not critically pinned");
}
else {
PIN_SHORT_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite_short: 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);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
else {
UNPIN_SHORT_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1short */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_int
* Signature: (JJJJJ[IZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dread_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jintArray buf,
jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
jint *readBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_int: read buffer is NULL");
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jint),
"H5Dread_int") < 0)
goto done;
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_int: read buffer not critically pinned");
}
else {
PIN_INT_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread_int: 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)
H5_LIBRARY_ERROR(ENVONLY);
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);
}
else {
UNPIN_INT_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1int */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite_int
* Signature: (JJJJJ[IZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jintArray buf,
jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
jint *writeBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_int: write buffer is NULL");
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jint),
"H5Dwrite_int") < 0)
goto done;
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_int: write buffer not critically pinned");
}
else {
PIN_INT_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite_int: 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);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
else {
UNPIN_INT_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1int */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_long
* Signature: (JJJJJ[JZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dread_1long(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jlongArray buf, jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
jlong *readBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_long: read buffer is NULL");
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jlong),
"H5Dread_long") < 0)
goto done;
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_long: read buffer not critically pinned");
}
else {
PIN_LONG_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread_long: 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)
H5_LIBRARY_ERROR(ENVONLY);
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);
}
else {
UNPIN_LONG_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1long */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite_long
* Signature: (JJJJJ[JZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1long(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jlongArray buf, jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
jlong *writeBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_long: write buffer is NULL");
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jlong),
"H5Dwrite_long") < 0)
goto done;
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_long: write buffer not critically pinned");
}
else {
PIN_LONG_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite_long: 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);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
else {
UNPIN_LONG_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1long */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_float
* Signature: (JJJJJ[FZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dread_1float(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jfloatArray buf, jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
jfloat *readBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_float: read buffer is NULL");
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jfloat),
"H5Dread_float") < 0)
goto done;
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_float: read buffer not critically pinned");
}
else {
PIN_FLOAT_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread_float: 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)
H5_LIBRARY_ERROR(ENVONLY);
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);
}
else {
UNPIN_FLOAT_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1float */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite_float
* Signature: (JJJJJ[FZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1float(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jfloatArray buf, jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
jfloat *writeBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_float: write buffer is NULL");
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jfloat),
"H5Dwrite_float") < 0)
goto done;
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_float: write buffer not critically pinned");
}
else {
PIN_FLOAT_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite_float: 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);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
else {
UNPIN_FLOAT_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1float */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_double
* Signature: (JJJJJ[DZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dread_1double(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jdoubleArray buf, jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
jdouble *readBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_double: read buffer is NULL");
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jdouble),
"H5Dread_double") < 0)
goto done;
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_double: read buffer not critically pinned");
}
else {
PIN_DOUBLE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread_double: 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)
H5_LIBRARY_ERROR(ENVONLY);
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);
}
else {
UNPIN_DOUBLE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1double */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite_double
* Signature: (JJJJJ[DZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jdoubleArray buf, jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
jdouble *writeBuf = NULL;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_double: write buffer is NULL");
/* Verify the buffer is large enough for the selection. */
if (h5d_validate_raw_buf(env, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)dataset_id, ENVPTR->GetArrayLength(ENVONLY, buf), sizeof(jdouble),
"H5Dwrite_double") < 0)
goto done;
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_double: write buffer not critically pinned");
}
else {
PIN_DOUBLE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite_double: 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);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
else {
UNPIN_DOUBLE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1double */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_string
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dread_1string(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jobjectArray j_buf)
{
jstring jstr;
size_t str_len;
size_t pos;
jsize i, n;
char *c_buf = NULL;
char *cstr = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == j_buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_string: read buffer is NULL");
if ((n = ENVPTR->GetArrayLength(ENVONLY, j_buf)) <= 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_string: read buffer length <= 0");
}
/* The buffer must have one slot per selected point. */
if (h5d_validate_slot_buf(env, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)dataset_id, n,
"H5Dread_string") < 0)
goto done;
if (!(str_len = H5Tget_size((hid_t)mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (cstr = (char *)malloc(str_len + 1)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread_string: memory allocation failed");
if (NULL == (c_buf = (char *)malloc((size_t)n * str_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread_string: memory allocation failed");
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, c_buf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
for (i = 0, pos = 0; i < n; i++) {
memcpy(cstr, c_buf + pos, str_len);
cstr[str_len] = '\0';
if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, cstr))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_OUT_OF_MEMORY_ERROR(
ENVONLY, "H5Dread_string: out of memory - unable to construct string from UTF characters");
}
ENVPTR->SetObjectArrayElement(ENVONLY, j_buf, i, jstr);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
pos += str_len;
ENVPTR->DeleteLocalRef(ENVONLY, jstr);
} /* end for */
done:
if (c_buf)
free(c_buf);
if (cstr)
free(cstr);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1string */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite_string
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1string(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
jobjectArray j_buf)
{
const char *utf8 = NULL;
jstring obj;
size_t i, str_len;
jsize n;
char *c_buf = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == j_buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_string: write buffer is NULL");
if ((n = ENVPTR->GetArrayLength(ENVONLY, j_buf)) <= 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_string: write buffer length <= 0");
}
/* The buffer must have one slot per selected point. */
if (h5d_validate_slot_buf(env, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)dataset_id, n,
"H5Dwrite_string") < 0)
goto done;
if (!(str_len = H5Tget_size((hid_t)mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (c_buf = (char *)malloc((size_t)n * str_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dwrite_string: memory allocation failed");
for (i = 0; i < (size_t)n; i++) {
if (NULL == (obj = (jstring)ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)j_buf, (jsize)i))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
/*
* If the string object was NULL, skip it.
*/
memset(&c_buf[i * str_len], 0, str_len);
continue;
}
/*
* length = ENVPTR->GetStringUTFLength(ENVONLY, obj);
* CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
*/
PIN_JAVA_STRING(ENVONLY, obj, utf8, NULL, "H5Dwrite_string: string not pinned");
strncpy(&c_buf[i * str_len], utf8, str_len);
UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
utf8 = NULL;
ENVPTR->DeleteLocalRef(ENVONLY, obj);
} /* end for */
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, c_buf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (utf8)
UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
if (c_buf)
free(c_buf);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1string */
/*
* Class: hdf_hdf5lib_H5
* Method: H5DreadVL
* Signature: (JJJJJ[java/util/ArrayList;)I
*/
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)
{
void *readBuf = NULL;
size_t typeSize;
H5T_class_t type_class;
jsize vl_array_len;
hssize_t npoints;
htri_t vl_data_class;
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 ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: readBuf length < 0");
}
if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* The buffer must hold at least one slot per selected point; otherwise the
* H5Dread below would overrun the raw read buffer. */
if ((npoints = h5d_io_npoints(env, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)dataset_id)) < 0)
goto done;
if ((hssize_t)vl_array_len < npoints)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is smaller than the selection");
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (readBuf = calloc((size_t)vl_array_len, 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, readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
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, (size_t)vl_array_len * typeSize);
done:
if (readBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
if (is_variable) {
for (size_t i = 0; i < (size_t)vl_array_len; i++)
free(((char **)readBuf)[i]);
}
free(readBuf);
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5DreadVL */
/*
* Class: hdf_hdf5lib_H5
* Method: H5DwriteVL
* Signature: (JJJJJ[java/util/ArrayList;)I
*/
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)
{
void *writeBuf = NULL;
size_t typeSize;
H5T_class_t type_class;
jsize vl_array_len; // Only used by vl_data_class types
hssize_t npoints;
htri_t vl_data_class;
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 ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer length < 0");
}
if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Verify the buffer holds at least one element per selected point. */
if ((npoints = h5d_io_npoints(env, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)dataset_id)) < 0)
goto done;
if ((hssize_t)vl_array_len < npoints)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is smaller than the selection");
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Verify the buffer structure matches mem_type_id before converting it. */
if (h5validate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len) < 0)
goto done;
if (NULL == (writeBuf = calloc((size_t)vl_array_len, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer");
translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf,
(size_t)vl_array_len * typeSize);
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++)
free(((char **)writeBuf)[i]);
}
free(writeBuf);
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5DwriteVL */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_VLStrings
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dread_1VLStrings(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;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isCompound = 0;
htri_t isVlen = 0;
hid_t nested_tid = H5I_INVALID_HID;
bool isComposite = false;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVLStrings: read buffer is NULL");
/* The buffer must have one slot per selected point. */
if (h5d_validate_slot_buf(env, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)dataset_id,
ENVPTR->GetArrayLength(ENVONLY, buf), "H5Dread_VLStrings") < 0)
goto done;
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_COMPOUND) {
unsigned i;
int num_members;
if ((num_members = H5Tget_nmembers(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
for (i = 0; i < (unsigned)num_members; i++) {
if ((nested_tid = H5Tget_member_type((hid_t)mem_type_id, i)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((isCompound = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((isVlen = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
isComposite = isCompound || isVlen;
if (H5Tclose(nested_tid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
nested_tid = H5I_INVALID_HID;
}
}
else if (type_class == H5T_VLEN) {
isVlenStr = 1; /* Strings created by H5Tvlen_create(H5T_C_S1) */
}
if (!isStr || isComposite || isVlenStr) {
if ((status = H5DreadVL_asstr(env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, buf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else if (isStr) {
if ((status = H5DreadVL_str(env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, buf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
done:
if (nested_tid >= 0)
H5Tclose(nested_tid);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */
/*
* Helper method to read in a buffer of variable-length strings from an HDF5
* dataset. Each C-string is converted to a Java string and set in the output
* buffer in turn.
*/
static herr_t
H5DreadVL_str(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id,
jobjectArray buf)
{
jstring jstr;
jsize i, n;
char **strs = NULL;
herr_t status = FAIL;
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL_str: buf length < 0");
}
if (NULL == (strs = (char **)calloc((size_t)n, sizeof(char *))))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"H5DreadVL_str: failed to allocate variable length string read buffer");
if ((status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, strs)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/*
* When repeatedly reading a dataset with a large number of strs (e.g., 1,000,000 strings),
* H5Treclaim() may crash on Windows because the Java GC will not be able to collect
* free space in time. Instead, we use "H5free_memory(strs[i])" to free individual strings
* once done.
*/
for (i = 0; i < n; i++) {
if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, strs[i])))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetObjectArrayElement(ENVONLY, buf, i, jstr);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
H5free_memory(strs[i]);
strs[i] = NULL;
ENVPTR->DeleteLocalRef(ENVONLY, jstr);
} /* end for */
done:
if (strs) {
for (i = 0; i < n; i++) {
if (strs[i])
H5free_memory(strs[i]);
}
free(strs);
}
return status;
} /* end H5DreadVL_str */
/*
* Helper method to read in a buffer of variable-length (hvl_t)
* structures from an HDF5 dataset and convert each variable-length
* element's buffer into a Java string. Each string is then set
* in the output buffer in turn.
*/
static herr_t
H5DreadVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id,
jobjectArray buf)
{
H5T_class_t tclass;
jstring jstr;
h5str_t h5str;
bool close_mem_space = false;
size_t typeSize;
size_t i;
hid_t mem_space = mem_sid;
jsize n;
void *readBuf = NULL;
herr_t status = FAIL;
memset(&h5str, 0, sizeof(h5str_t));
if (mem_space == H5S_ALL) {
mem_space = file_sid;
if (mem_space == H5S_ALL) {
/*
* Retrieve a valid dataspace for H5Treclaim().
*/
if ((mem_space = H5Dget_space(did)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
close_mem_space = true;
if (H5Sselect_all(mem_space) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
}
/* Get size of string array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL_asstr: buf length < 0");
}
if (!(typeSize = H5Tget_size(tid)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (readBuf = calloc((size_t)n, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL_asstr: failed to allocate read buffer");
if ((status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Allocate a decent-sized initial string */
h5str_new(&h5str, 4 * typeSize);
if (!h5str.s)
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL_asstr: failed to allocate buffer");
if ((tclass = H5Tget_class(tid)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Convert each element to a char string */
for (i = 0; i < (size_t)n; i++) {
h5str.s[0] = '\0';
if (!h5str_sprintf(ENVONLY, &h5str, did, tid, &(((char *)readBuf)[i * typeSize]), 0))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetObjectArrayElement(ENVONLY, buf, (jsize)i, jstr);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->DeleteLocalRef(ENVONLY, jstr);
} /* end for */
done:
if (h5str.s)
h5str_free(&h5str);
if (readBuf) {
H5Treclaim(tid, mem_space, xfer_plist_id, readBuf);
free(readBuf);
}
if (close_mem_space)
H5Sclose(mem_space);
return status;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite_VLStrings
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings(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;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isCompound = 0;
htri_t isVlen = 0;
hid_t nested_tid = H5I_INVALID_HID;
bool isComposite = false;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVLStrings: write buffer is NULL");
/* The buffer must have one slot per selected point. */
if (h5d_validate_slot_buf(env, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)dataset_id,
ENVPTR->GetArrayLength(ENVONLY, buf), "H5Dwrite_VLStrings") < 0)
goto done;
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_COMPOUND) {
unsigned i;
int num_members;
if ((num_members = H5Tget_nmembers(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
for (i = 0; i < (unsigned)num_members; i++) {
if ((nested_tid = H5Tget_member_type((hid_t)mem_type_id, i)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((isCompound = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((isVlen = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
isComposite = isCompound || isVlen;
if (H5Tclose(nested_tid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
nested_tid = H5I_INVALID_HID;
}
}
else if (type_class == H5T_VLEN) {
isVlenStr = 1; /* Strings created by H5Tvlen_create(H5T_C_S1) */
}
if (!isStr || isComposite || isVlenStr) {
if ((status = H5DwriteVL_asstr(env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, buf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else if (isStr) {
if ((status = H5DwriteVL_str(env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, buf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
done:
if (nested_tid >= 0)
H5Tclose(nested_tid);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings */
/*
* Helper method to convert an array of Java strings into a buffer of C-strings.
* The buffer of C-strings is then written to the HDF5 dataset specified.
*/
static herr_t
H5DwriteVL_str(JNIEnv *env, hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id,
hid_t xfer_plist_id, jobjectArray buf)
{
const char *utf8 = NULL;
jstring obj;
jsize size;
jint i;
char **writeBuf = NULL;
herr_t status = FAIL;
if ((size = ENVPTR->GetArrayLength(ENVONLY, (jarray)buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL_str: buf length < 0");
}
if (NULL == (writeBuf = (char **)calloc((size_t)size + 1, sizeof(char *))))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"H5DwriteVL_str: failed to allocate variable length string write buffer");
for (i = 0; i < size; ++i) {
jsize length;
if (NULL == (obj = (jstring)ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, i))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
/*
* If the string object was NULL, skip it.
*/
writeBuf[i] = NULL;
continue;
}
length = ENVPTR->GetStringUTFLength(ENVONLY, obj);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
PIN_JAVA_STRING(ENVONLY, obj, utf8, NULL, "H5DwriteVL_str: string not pinned");
if (NULL == (writeBuf[i] = (char *)malloc((size_t)length + 1)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL_str: failed to allocate string buffer");
strncpy(writeBuf[i], utf8, (size_t)length + 1);
writeBuf[i][length] = '\0';
UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
utf8 = NULL;
ENVPTR->DeleteLocalRef(ENVONLY, obj);
} /* end for (i = 0; i < size; ++i) */
if ((status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, writeBuf)) <
0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (utf8)
UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
if (writeBuf) {
for (i = 0; i < size; i++) {
if (writeBuf[i])
free(writeBuf[i]);
}
free(writeBuf);
}
return status;
} /* end H5DwriteVL_str */
/*
* Helper method to convert an array of Java strings into a buffer of
* variable-length (hvl_t) elements. The buffer of variable-length
* elements is then written to the HDF5 dataset.
*/
static herr_t
H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id,
jobjectArray buf)
{
const char *utf8 = NULL;
jstring jstr = NULL;
bool close_mem_space = false;
size_t typeSize;
size_t i;
hid_t mem_space = mem_sid;
jsize n;
void *writeBuf = NULL;
herr_t status = FAIL;
if (mem_space == H5S_ALL) {
mem_space = file_sid;
if (mem_space == H5S_ALL) {
/*
* Retrieve a valid dataspace for H5Treclaim().
*/
if ((mem_space = H5Dget_space(did)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
close_mem_space = true;
if (H5Sselect_all(mem_space) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
}
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL_asstr: buf length < 0");
}
if (!(typeSize = H5Tget_size(tid)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (writeBuf = calloc((size_t)n, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL_asstr: failed to allocate write buffer");
for (i = 0; i < (size_t)n; ++i) {
if (NULL == (jstr = (jstring)ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
/*
* If the string object was NULL, skip it.
*/
memset(&(((char *)writeBuf)[i * typeSize]), 0, typeSize);
continue;
}
PIN_JAVA_STRING(ENVONLY, jstr, utf8, NULL, "H5DwriteVL_asstr: failed to pin string buffer");
/*
* 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, &utf8_copy, did, tid, &(((char *)writeBuf)[i * typeSize]), 0))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
free(utf8_copy);
UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
utf8 = NULL;
ENVPTR->DeleteLocalRef(ENVONLY, jstr);
} /* end for (i = 0; i < size; ++i) */
if ((status = H5Dwrite(did, tid, mem_sid, file_sid, xfer_plist_id, writeBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (utf8)
UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
if (writeBuf) {
H5Treclaim(tid, mem_space, xfer_plist_id, writeBuf);
free(writeBuf);
}
if (close_mem_space)
H5Sclose(mem_space);
return status;
} /* end H5DwriteVL_asstr */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_reg_ref
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref(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)
{
H5R_ref_t *ref_data = NULL;
h5str_t h5str;
jstring jstr;
jsize i, n;
herr_t status = FAIL;
UNUSED(clss);
memset(&h5str, 0, sizeof(h5str_t));
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_reg_ref: buf length < 0");
}
/* The buffer must have one slot per selected point. */
if (h5d_validate_slot_buf(env, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)dataset_id, n,
"H5Dread_reg_ref") < 0)
goto done;
if (NULL == (ref_data = (H5R_ref_t *)calloc(1, (size_t)n * sizeof(H5R_ref_t))))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread_reg_ref: failed to allocate read buffer");
if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
xfer_plist_id, ref_data)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
h5str_new(&h5str, 1024);
if (!h5str.s)
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread_reg_ref: failed to allocate buffer");
for (i = 0; i < n; i++) {
h5str.s[0] = '\0';
if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)dataset_id, (hid_t)mem_type_id, (void *)&ref_data[i], 0))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetObjectArrayElement(ENVONLY, buf, i, jstr);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->DeleteLocalRef(ENVONLY, jstr);
} /* end for */
done:
if (h5str.s)
h5str_free(&h5str);
if (ref_data)
free(ref_data);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Dcreate2
* Signature: (JLjava/lang/String;JJJJJ)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Dcreate2(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong type_id,
jlong space_id, jlong link_plist_id, jlong create_plist_id,
jlong access_plist_id)
{
const char *dsetName = NULL;
hid_t dset_id = H5I_INVALID_HID;
UNUSED(clss);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dcreate2: dataset name is NULL");
PIN_JAVA_STRING(ENVONLY, name, dsetName, NULL, "H5Dcreate2: dataset name not pinned");
if ((dset_id = H5Dcreate2((hid_t)loc_id, dsetName, (hid_t)type_id, (hid_t)space_id, (hid_t)link_plist_id,
(hid_t)create_plist_id, (hid_t)access_plist_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (dsetName)
UNPIN_JAVA_STRING(ENVONLY, name, dsetName);
return (jlong)dset_id;
} /* end Java_hdf_hdf5lib_H5__1H5Dcreate2 */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Dopen2
* Signature: (JLjava/lang/String;J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Dopen2(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong access_plist)
{
const char *dsetName = NULL;
hid_t dset_id = H5I_INVALID_HID;
UNUSED(clss);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dopen2: dataset name is NULL");
PIN_JAVA_STRING(ENVONLY, name, dsetName, NULL, "H5Dopen2: dataset name not pinned");
if ((dset_id = H5Dopen2((hid_t)loc_id, dsetName, (hid_t)access_plist)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (dsetName)
UNPIN_JAVA_STRING(ENVONLY, name, dsetName);
return (jlong)dset_id;
} /* end Java_hdf_hdf5lib_H5__1H5Dopen2 */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Dcreate_anon
* Signature: (JJJJJ)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Dcreate_1anon(JNIEnv *env, jclass clss, jlong loc_id, jlong type_id, jlong space_id,
jlong dcpl_id, jlong dapl_id)
{
hid_t dset_id = H5I_INVALID_HID;
UNUSED(clss);
if ((dset_id = H5Dcreate_anon((hid_t)loc_id, (hid_t)type_id, (hid_t)space_id, (hid_t)dcpl_id,
(hid_t)dapl_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)dset_id;
} /* end Java_hdf_hdf5lib_H5__1H5Dcreate_1anon */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dget_space_status
* Signature: (J)I;
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dget_1space_1status(JNIEnv *env, jclass clss, jlong loc_id)
{
H5D_space_status_t space_status = H5D_SPACE_STATUS_ERROR;
UNUSED(clss);
if (H5Dget_space_status((hid_t)loc_id, &space_status) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)space_status;
} /* end Java_hdf_hdf5lib_H5_H5Dget_1space_1status */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dget_access_plist
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Dget_1access_1plist(JNIEnv *env, jclass clss, jlong loc_id)
{
hid_t retVal = H5I_INVALID_HID;
UNUSED(clss);
if ((retVal = H5Dget_access_plist((hid_t)loc_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Dget_1access_1plist */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dget_offset
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Dget_1offset(JNIEnv *env, jclass clss, jlong loc_id)
{
haddr_t offset = HADDR_UNDEF;
UNUSED(clss);
if (HADDR_UNDEF == (offset = H5Dget_offset((hid_t)loc_id)))
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)offset;
} /* end Java_hdf_hdf5lib_H5_H5Dget_1offset */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dvlen_get_buf_size
* Signature: (JJJ)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size(JNIEnv *env, jclass clss, jlong dataset_id, jlong type_id,
jlong space_id)
{
hsize_t sz = 0;
UNUSED(clss);
if (H5Dvlen_get_buf_size((hid_t)dataset_id, (hid_t)type_id, (hid_t)space_id, &sz) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)sz;
} /* end Java_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size_1long */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dfill
* Signature: ([BJ[BJJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Dfill(JNIEnv *env, jclass clss, jbyteArray fill, jlong fill_type_id, jbyteArray buf,
jlong buf_type_id, jlong space_id)
{
jboolean isCopy1;
jboolean isCopy2;
herr_t status = FAIL;
jbyte *fillP = NULL;
jbyte *buffP = NULL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dfill: buffer is NULL");
PIN_BYTE_ARRAY(ENVONLY, buf, buffP, &isCopy2, "H5Dfill: buffer not pinned");
if (fill) {
PIN_BYTE_ARRAY(ENVONLY, fill, fillP, &isCopy1, "H5Dfill: fill buffer not pinned");
}
if ((status = H5Dfill((const void *)fillP, (hid_t)fill_type_id, (void *)buffP, (hid_t)buf_type_id,
(hid_t)space_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (fillP) {
UNPIN_BYTE_ARRAY(ENVONLY, fill, fillP, JNI_ABORT);
fillP = NULL;
}
done:
if (fillP)
UNPIN_BYTE_ARRAY(ENVONLY, fill, fillP, JNI_ABORT);
if (buffP)
UNPIN_BYTE_ARRAY(ENVONLY, buf, buffP, (status < 0) ? JNI_ABORT : 0);
} /* end Java_hdf_hdf5lib_H5_H5Dfill */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dset_extent
* Signature: (J[J)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Dset_1extent(JNIEnv *env, jclass clss, jlong loc_id, jlongArray buf)
{
jboolean isCopy;
hsize_t *dims = NULL;
herr_t status;
jsize rank;
jlong *dimsBuf = NULL;
int i = 0;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dset_extent: buffer is NULL");
if ((rank = ENVPTR->GetArrayLength(ENVONLY, buf)) <= 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dset_extent: buf length <= 0");
}
PIN_LONG_ARRAY(ENVONLY, buf, dimsBuf, &isCopy, "H5Dset_extent: buffer not pinned");
if (NULL == (dims = (hsize_t *)malloc((size_t)rank * sizeof(hsize_t))))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dset_extent: failed to allocate dataset dimension buffer");
for (i = 0; i < rank; i++)
dims[i] = (hsize_t)dimsBuf[i];
if ((status = H5Dset_extent((hid_t)loc_id, (hsize_t *)dims)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (dims)
free(dims);
if (dimsBuf)
UNPIN_LONG_ARRAY(ENVONLY, buf, dimsBuf, JNI_ABORT);
} /* end Java_hdf_hdf5lib_H5_H5Dset_1extent */
static herr_t
H5D_iterate_cb(void *elem, hid_t elem_id, unsigned ndim, const hsize_t *point, void *cb_data)
{
cb_wrapper *wrapper = (cb_wrapper *)cb_data;
jbyteArray elemArray;
jlongArray pointArray;
jmethodID mid;
jobject visit_callback = wrapper->visit_callback;
jclass cls;
JNIEnv *cbenv = NULL;
jint status = FAIL;
jsize size;
void *op_data = (void *)wrapper->op_data;
if (JVMPTR->AttachCurrentThread(JVMPAR, (void **)&cbenv, NULL) < 0) {
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_TRUE);
H5_JNI_FATAL_ERROR(CBENVONLY, "H5D_iterate_cb: failed to attach current thread to JVM");
}
if (NULL == (cls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
if (NULL == (mid = CBENVPTR->GetMethodID(CBENVONLY, cls, "callback",
"([BJI[JLhdf/hdf5lib/callbacks/H5D_iterate_t;)I")))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
if (NULL == elem)
H5_NULL_ARGUMENT_ERROR(CBENVONLY, "H5D_iterate_cb: element buffer is NULL");
if (NULL == point)
H5_NULL_ARGUMENT_ERROR(CBENVONLY, "H5D_iterate_cb: point is NULL");
if (!(size = (jsize)H5Tget_size(elem_id)))
H5_LIBRARY_ERROR(CBENVONLY);
if (NULL == (elemArray = CBENVPTR->NewByteArray(CBENVONLY, size)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
CBENVPTR->SetByteArrayRegion(CBENVONLY, elemArray, 0, size, (jbyte *)elem);
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
if (NULL == (pointArray = CBENVPTR->NewLongArray(CBENVONLY, 2)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
CBENVPTR->SetLongArrayRegion(CBENVONLY, pointArray, 0, 2, (const jlong *)point);
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
status = CBENVPTR->CallIntMethod(CBENVONLY, visit_callback, mid, (void *)elemArray, elem_id, ndim,
pointArray, op_data);
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
CBENVPTR->GetByteArrayRegion(CBENVONLY, elemArray, 0, size, (jbyte *)elem);
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
done:
if (cbenv)
JVMPTR->DetachCurrentThread(JVMPAR);
return (herr_t)status;
} /* end H5D_iterate_cb */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Diterate
* Signature: ([BJJLjava/lang/Object;Ljava/lang/Object;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Diterate(JNIEnv *env, jclass clss, jbyteArray buf, jlong buf_type, jlong space,
jobject callback_op, jobject op_data)
{
cb_wrapper wrapper = {callback_op, op_data};
jboolean isCopy;
jbyte *iterBuf = NULL;
herr_t status = FAIL;
UNUSED(clss);
ENVPTR->GetJavaVM(ENVONLY, &jvm);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == op_data)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Diterate: op_data is NULL");
if (NULL == callback_op)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Diterate: callback_op is NULL");
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Diterate: buffer is NULL");
PIN_BYTE_ARRAY(ENVONLY, buf, iterBuf, &isCopy, "H5Diterate: buffer not pinned");
if ((status = H5Diterate((void *)iterBuf, (hid_t)buf_type, (hid_t)space, (H5D_operator_t)H5D_iterate_cb,
(void *)&wrapper)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (iterBuf)
UNPIN_BYTE_ARRAY(ENVONLY, buf, iterBuf,
(status < 0) ? (JNI_ABORT) : ((isCopy == JNI_TRUE) ? 0 : JNI_ABORT));
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Diterate */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dflush
* Signature: (J)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Dflush(JNIEnv *env, jclass clss, jlong loc_id)
{
UNUSED(clss);
if (H5Dflush((hid_t)loc_id) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Drefresh
* Signature: (J)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Drefresh(JNIEnv *env, jclass clss, jlong loc_id)
{
UNUSED(clss);
if (H5Drefresh((hid_t)loc_id) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
}
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
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