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Revert "1.12 eliminate unnecessary errors in the error stack (#1880)" (#1935)

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This reverts commit f699768133.
This commit is contained in:
Larry Knox
2022-07-26 14:30:04 -05:00
committed by GitHub
parent 6eaa59d2f8
commit d0739f13c1
38 changed files with 7360 additions and 607 deletions
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java/src/hdf/hdf5lib/H5.java
+42 -8
View File
@@ -1242,6 +1242,10 @@ public class H5 implements java.io.Serializable {
log.trace("H5Aread_string type");
status = H5Aread_string(attr_id, mem_type_id, (String[])obj);
}
else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
log.trace("H5AreadVL type");
status = H5AreadVL(attr_id, mem_type_id, (Object[])obj);
}
else {
// Create a data buffer to hold the data into a Java Array
HDFArray theArray = new HDFArray(obj);
@@ -1788,6 +1792,10 @@ public class H5 implements java.io.Serializable {
log.trace("H5Dwrite_string type");
status = H5Awrite_string(attr_id, mem_type_id, (String[])obj);
}
else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
log.trace("H5AwriteVL type");
status = H5AwriteVL(attr_id, mem_type_id, (Object[])obj);
}
else {
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.byteify();
@@ -2772,6 +2780,11 @@ public class H5 implements java.io.Serializable {
status = H5Dread_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
(String[])obj);
}
else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
log.trace("H5DreadVL type");
status =
H5DreadVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[])obj);
}
else {
// Create a data buffer to hold the data into a Java Array
HDFArray theArray = new HDFArray(obj);
@@ -3450,6 +3463,11 @@ public class H5 implements java.io.Serializable {
status = H5Dwrite_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
(String[])obj);
}
else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
log.trace("H5DwriteVL type");
status = H5DwriteVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
(Object[])obj);
}
else {
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.byteify();
@@ -9356,9 +9374,8 @@ public class H5 implements java.io.Serializable {
byte[] buf = theArray.emptyBytes();
int status = H5Pget_fill_value(plist_id, type_id, buf);
if (status >= 0) {
if (status >= 0)
obj = theArray.arrayify(buf);
}
return status;
}
@@ -11018,8 +11035,6 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Rdestroy(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
// Info //
/**
* H5Rget_type retrieves the type of a reference.
*
@@ -11076,8 +11091,6 @@ public class H5 implements java.io.Serializable {
public synchronized static native byte[] H5Rcopy(byte[] src_ref_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
// Dereference //
/**
* H5Ropen_object opens that object and returns an identifier.
* The object opened with this function should be closed when it is no longer needed
@@ -11224,8 +11237,6 @@ public class H5 implements java.io.Serializable {
public synchronized static native int H5Rget_obj_type3(byte[] ref_ptr, long rapl_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
// Get name //
/**
* H5Rget_file_name retrieves the file name for the object, region or attribute reference pointed to.
*
@@ -11399,6 +11410,29 @@ public class H5 implements java.io.Serializable {
long size)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Rget_name_string retrieves a name for the object identified by ref.
*
* @param loc_id
* IN: Identifier for the dataset containing the reference or for the group that dataset is in.
* @param ref_type
* IN: Type of reference.
* @param ref
* IN: An object or dataset region reference.
*
* @return Returns the name if successful, returning null if no name is associated with
* the identifier.
*
* @exception HDF5LibraryException
* Error from the HDF-5 Library.
* @exception NullPointerException
* size is null.
* @exception IllegalArgumentException
* Argument is illegal.
**/
public synchronized static native String H5Rget_name_string(long loc_id, int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Rget_obj_type Given a reference to an object ref, H5Rget_obj_type returns the type of the object
* pointed to.
java/src/hdf/hdf5lib/HDF5Constants.java
+48 -17
View File
@@ -16,7 +16,7 @@ package hdf.hdf5lib;
import hdf.hdf5lib.structs.H5O_token_t;
/**
* /** This class contains C constants and enumerated types of HDF5 library. The
* This class contains C constants and enumerated types of HDF5 library. The
* values of these constants are obtained from the library by calling J2C(int
* jconstant), where jconstant is any of the private constants which start their
* name with "JH5" need to be converted.
@@ -62,31 +62,62 @@ public class HDF5Constants {
public static final int H5_ITER_NATIVE = H5_ITER_NATIVE();
/** Common iteration orders, Number of iteration orders */
public static final int H5_ITER_N = H5_ITER_N();
/** */
/** The version of the H5AC_cache_config_t in use */
public static final int H5AC_CURR_CACHE_CONFIG_VERSION = H5AC_CURR_CACHE_CONFIG_VERSION();
/** */
/** The maximum length of the trace file path */
public static final int H5AC_MAX_TRACE_FILE_NAME_LEN = H5AC_MAX_TRACE_FILE_NAME_LEN();
/** */
/**
* When metadata_write_strategy is set to this value, only process
* zero is allowed to write dirty metadata to disk. All other
* processes must retain dirty metadata until they are informed at
* a sync point that the dirty metadata in question has been written
* to disk.
*/
public static final int H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY =
H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY();
/** */
/**
* In the distributed metadata write strategy, process zero still makes
* the decisions as to what entries should be flushed, but the actual
* flushes are distributed across the processes in the computation to
* the extent possible.
*/
public static final int H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED =
H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED();
/** */
/** Don't attempt to increase the size of the cache automatically */
public static final int H5C_incr_off = H5C_incr_off();
/** */
/**
* Attempt to increase the size of the cache
* whenever the average hit rate over the last epoch drops
* below the value supplied in the lower_hr_threshold
* field
*/
public static final int H5C_incr_threshold = H5C_incr_threshold();
/** */
/** Don't perform flash increases in the size of the cache */
public static final int H5C_flash_incr_off = H5C_flash_incr_off();
/** */
/** increase the current maximum cache size by x * flash_multiple less any free space in the cache */
public static final int H5C_flash_incr_add_space = H5C_flash_incr_add_space();
/** */
/** Don't attempt to decrease the size of the cache automatically */
public static final int H5C_decr_off = H5C_decr_off();
/** */
/**
* Attempt to decrease the size of the cache
* whenever the average hit rate over the last epoch rises
* above the value supplied in the upper_hr_threshold
* field
*/
public static final int H5C_decr_threshold = H5C_decr_threshold();
/** */
/**
* At the end of each epoch, search the cache for
* entries that have not been accessed for at least the number
* of epochs specified in the epochs_before_eviction field, and
* evict these entries
*/
public static final int H5C_decr_age_out = H5C_decr_age_out();
/** */
/**
* Same as age_out, but we only
* attempt to reduce the cache size when the hit rate observed
* over the last epoch exceeds the value provided in the
* upper_hr_threshold field
*/
public static final int H5C_decr_age_out_with_threshold = H5C_decr_age_out_with_threshold();
/** */
public static final int H5D_CHUNK_IDX_BTREE = H5D_CHUNK_IDX_BTREE();
@@ -910,11 +941,11 @@ public class HDF5Constants {
/** */
public static final int H5R_MAXTYPE = H5R_MAXTYPE();
/** */
public static final int H5R_REF_BUF_SIZE = H5R_REF_BUF_SIZE();
public static final int H5R_DSET_REG_REF_BUF_SIZE = H5R_DSET_REG_REF_BUF_SIZE();
/** */
public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE();
/** */
public static final int H5R_DSET_REG_REF_BUF_SIZE = H5R_DSET_REG_REF_BUF_SIZE();
public static final int H5R_REF_BUF_SIZE = H5R_REF_BUF_SIZE();
/** */
public static final int H5R_OBJECT = H5R_OBJECT();
/** */
@@ -2393,11 +2424,11 @@ public class HDF5Constants {
private static native final int H5R_MAXTYPE();
private static native final int H5R_REF_BUF_SIZE();
private static native final int H5R_DSET_REG_REF_BUF_SIZE();
private static native final int H5R_OBJ_REF_BUF_SIZE();
private static native final int H5R_DSET_REG_REF_BUF_SIZE();
private static native final int H5R_REF_BUF_SIZE();
private static native final int H5R_OBJECT();
java/src/jni/h5aImp.c
+682 -136
View File
@@ -56,7 +56,7 @@ static herr_t H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *inf
/*
* Class: hdf_hdf5lib_H5
* Method: H5Acreate
* Method: _H5Acreate
* Signature: (JLjava/lang/String;JJJ)J
*/
JNIEXPORT jlong JNICALL
@@ -86,7 +86,7 @@ done:
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aopen_name
* Method: _H5Aopen_name
* Signature: (JLjava/lang/String;)J
*/
JNIEXPORT jlong JNICALL
@@ -124,7 +124,7 @@ done:
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aopen_idx
* Method: _H5Aopen_idx
* Signature: (JI)J
*/
JNIEXPORT jlong JNICALL
@@ -158,7 +158,10 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t
{
jboolean readBufIsCopy;
jbyte * readBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -166,18 +169,20 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread: read buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: variable length type not supported");
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, "H5Aread: readBuf length < 0");
}
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: variable length type not supported");
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -187,11 +192,17 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t
PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Aread: read buffer not pinned");
}
if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, readBuf)) < 0)
if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
if (sid >= 0)
H5Sclose(sid);
}
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -214,7 +225,10 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_
{
jboolean writeBufIsCopy;
jbyte * writeBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -222,19 +236,19 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: variable length type not supported");
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite: write buffer not critically pinned");
@@ -248,6 +262,9 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -270,7 +287,10 @@ Java_hdf_hdf5lib_H5_H5Aread_1short(JNIEnv *env, jclass clss, jlong attr_id, jlon
{
jboolean readBufIsCopy;
jshort * readBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -278,18 +298,20 @@ Java_hdf_hdf5lib_H5_H5Aread_1short(JNIEnv *env, jclass clss, jlong attr_id, jlon
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_short: read buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_short: variable length type not supported");
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, "H5Aread: readBuf length < 0");
}
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_short: variable length type not supported");
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -304,6 +326,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1short(JNIEnv *env, jclass clss, jlong attr_id, jlon
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
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);
}
@@ -326,7 +354,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1short(JNIEnv *env, jclass clss, jlong attr_id, jlo
{
jboolean writeBufIsCopy;
jshort * writeBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -334,19 +365,19 @@ Java_hdf_hdf5lib_H5_H5Awrite_1short(JNIEnv *env, jclass clss, jlong attr_id, jlo
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: write buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: variable length type not supported");
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_short: write buffer not critically pinned");
@@ -360,6 +391,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1short(JNIEnv *env, jclass clss, jlong attr_id, jlo
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -381,27 +415,32 @@ Java_hdf_hdf5lib_H5_H5Aread_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong
jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
htri_t data_class;
jint * readBuf = NULL;
herr_t status = FAIL;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
if (buf == NULL)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_int: read buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_int: variable length type not supported");
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, "H5Aread: readBuf length < 0");
}
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_int: variable length type not supported");
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -416,6 +455,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
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);
}
@@ -438,7 +483,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong
{
jboolean writeBufIsCopy;
jint * writeBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -446,19 +494,19 @@ Java_hdf_hdf5lib_H5_H5Awrite_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong
if (buf == NULL)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: write buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: variable length type not supported");
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_int: write buffer not critically pinned");
@@ -472,6 +520,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -494,7 +545,10 @@ Java_hdf_hdf5lib_H5_H5Aread_1long(JNIEnv *env, jclass clss, jlong attr_id, jlong
{
jboolean readBufIsCopy;
jlong * readBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -502,18 +556,20 @@ Java_hdf_hdf5lib_H5_H5Aread_1long(JNIEnv *env, jclass clss, jlong attr_id, jlong
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_long: read buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_long: variable length type not supported");
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, "H5Aread: readBuf length < 0");
}
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_long: variable length type not supported");
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -528,6 +584,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1long(JNIEnv *env, jclass clss, jlong attr_id, jlong
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
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);
}
@@ -550,7 +612,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1long(JNIEnv *env, jclass clss, jlong attr_id, jlon
{
jboolean writeBufIsCopy;
jlong * writeBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -558,19 +623,19 @@ Java_hdf_hdf5lib_H5_H5Awrite_1long(JNIEnv *env, jclass clss, jlong attr_id, jlon
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: write buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: variable length type not supported");
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_long: write buffer not critically pinned");
@@ -584,6 +649,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1long(JNIEnv *env, jclass clss, jlong attr_id, jlon
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -606,7 +674,10 @@ Java_hdf_hdf5lib_H5_H5Aread_1float(JNIEnv *env, jclass clss, jlong attr_id, jlon
{
jboolean readBufIsCopy;
jfloat * readBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -614,18 +685,20 @@ Java_hdf_hdf5lib_H5_H5Aread_1float(JNIEnv *env, jclass clss, jlong attr_id, jlon
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_float: read buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_float: variable length type not supported");
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, "H5Aread: readBuf length < 0");
}
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_float: variable length type not supported");
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -640,6 +713,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1float(JNIEnv *env, jclass clss, jlong attr_id, jlon
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
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);
}
@@ -662,7 +741,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1float(JNIEnv *env, jclass clss, jlong attr_id, jlo
{
jboolean writeBufIsCopy;
jfloat * writeBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -670,19 +752,19 @@ Java_hdf_hdf5lib_H5_H5Awrite_1float(JNIEnv *env, jclass clss, jlong attr_id, jlo
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: write buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: variable length type not supported");
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_float: write buffer not critically pinned");
@@ -696,6 +778,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1float(JNIEnv *env, jclass clss, jlong attr_id, jlo
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -718,7 +803,10 @@ Java_hdf_hdf5lib_H5_H5Aread_1double(JNIEnv *env, jclass clss, jlong attr_id, jlo
{
jboolean readBufIsCopy;
jdouble *readBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -726,18 +814,20 @@ Java_hdf_hdf5lib_H5_H5Aread_1double(JNIEnv *env, jclass clss, jlong attr_id, jlo
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_double: read buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_double: variable length type not supported");
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, "H5Aread: readBuf length < 0");
}
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_double: variable length type not supported");
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -752,6 +842,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1double(JNIEnv *env, jclass clss, jlong attr_id, jlo
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
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);
}
@@ -774,7 +870,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1double(JNIEnv *env, jclass clss, jlong attr_id, jl
{
jboolean writeBufIsCopy;
jdouble *writeBuf = NULL;
htri_t data_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -782,19 +881,18 @@ Java_hdf_hdf5lib_H5_H5Awrite_1double(JNIEnv *env, jclass clss, jlong attr_id, jl
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: write buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: buf length < 0");
}
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: variable length type not supported");
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_double: write buffer not critically pinned");
@@ -808,6 +906,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1double(JNIEnv *env, jclass clss, jlong attr_id, jl
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -958,10 +1059,454 @@ done:
/*
* Class: hdf_hdf5lib_H5
* Method: H5AreadVL
* Signature: (JJ[Ljava/lang/String;)I
* Signature: (JJ[java/util/ArrayList;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
H5T_class_t type_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean readBufIsCopy;
jbyteArray *readBuf = NULL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: read buffer is NULL");
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (vl_data_class) {
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
}
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_VLEN) {
size_t typeSize;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
void * rawBuf = NULL;
jobject * jList = NULL;
size_t i, j, x;
char * cp_vp = NULL;
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++) {
// The list we're going to return:
if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
cp_vp = (char *)rawBuf + i * typeSize;
/* Get the number of sequence elements */
jsize nelmts = ((hvl_t *)cp_vp)->len;
jobject jobj = NULL;
for (j = 0; j < nelmts; j++) {
switch (vlClass) {
/* case H5T_BOOL: {
jboolean boolValue;
for (x = 0; x < (int)vlSize; x++) {
((char *)&boolValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j*vlSize+x];
}
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 < (int)vlSize; x++) {
((char *)&byteValue)[x] = ((char *)((hvl_t *)cp_vp)->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 < (int)vlSize; x++) {
((char *)&shortValue)[x] = ((char *)((hvl_t *)cp_vp)->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 < (int)vlSize; x++) {
((char *)&intValue)[x] = ((char *)((hvl_t *)cp_vp)->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 < (int)vlSize; x++) {
((char *)&longValue)[x] = ((char *)((hvl_t *)cp_vp)->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 < (int)vlSize; x++) {
((char *)&floatValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
floatValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jdouble): {
jdouble doubleValue;
for (x = 0; x < (int)vlSize; x++) {
((char *)&doubleValue)[x] = ((char *)((hvl_t *)cp_vp)->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;
if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, vlSize)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
"readVL reference: byte array not pinned");
for (x = 0; x < (int)vlSize; x++) {
barray[x] = ((jbyte *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
}
if (barray)
UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "H5AreadVL: invalid class type");
break;
}
// Add it to the list
ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
} /* end for */
if (rawBuf)
HDfree(rawBuf);
}
else {
if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
done:
if (readBuf) {
if ((status >= 0) && vl_data_class) {
H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
if (sid >= 0)
H5Sclose(sid);
}
UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5AreadVL */
/*
* Class: hdf_hdf5lib_H5
* Method: H5AwriteVL
* Signature: (JJ[java/util/ArrayList;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
H5T_class_t type_class;
hsize_t dims[H5S_MAX_RANK];
hid_t sid = H5I_INVALID_HID;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean writeBufIsCopy;
jbyteArray *writeBuf = NULL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL");
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: readBuf length < 0");
}
dims[0] = (hsize_t)n;
if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_VLEN) {
size_t typeSize;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
void * rawBuf = NULL;
jobject * jList = NULL;
size_t i, j, x;
char * cp_vp = NULL;
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++) {
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);
cp_vp = (char *)rawBuf + i * typeSize;
((hvl_t *)cp_vp)->len = jnelmts;
if (NULL == (((hvl_t *)cp_vp)->p = HDmalloc(jnelmts * vlSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate vlen ptr buffer");
jobject jobj = NULL;
for (j = 0; j < (int)jnelmts; j++) {
if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
switch (vlClass) {
/* case H5T_BOOL: {
jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&boolValue)[x];
}
break;
} */
case H5T_INTEGER: {
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&byteValue)[x];
}
break;
}
case sizeof(jshort): {
jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&shortValue)[x];
}
break;
}
case sizeof(jint): {
jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&intValue)[x];
}
break;
}
case sizeof(jlong): {
jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&longValue)[x];
}
break;
}
}
break;
}
case H5T_FLOAT: {
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&floatValue)[x];
}
break;
}
case sizeof(jdouble): {
jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&doubleValue)[x];
}
break;
}
}
break;
}
case H5T_REFERENCE: {
jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)barray)[x];
}
ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "H5AwriteVL: invalid class type");
break;
}
ENVPTR->DeleteLocalRef(ENVONLY, jobj);
}
ENVPTR->DeleteLocalRef(ENVONLY, jList);
} /* end for (i = 0; i < n; i++) */
if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, rawBuf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (rawBuf)
HDfree(rawBuf);
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5AwriteVL: write buffer not pinned");
if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
if (type_class != H5T_VLEN)
UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5AwriteVL */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aread_VLStrings
* Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Aread_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id,
jobjectArray buf)
{
H5T_class_t type_class;
htri_t isStr = 0;
@@ -974,7 +1519,7 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: read buffer is NULL");
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_VLStrings: read buffer is NULL");
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -1024,7 +1569,7 @@ done:
H5Tclose(nested_tid);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Aread_1VL */
} /* end Java_hdf_hdf5lib_H5_H5Aread_1VLStrings */
/*
* Helper method to read in a buffer of variable-length strings from an HDF5
@@ -1160,11 +1705,12 @@ done:
/*
* Class: hdf_hdf5lib_H5
* Method: H5AwriteVL
* Method: H5Awrite_VLStrings
* Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id,
jobjectArray buf)
{
H5T_class_t type_class;
htri_t isStr = 0;
@@ -1177,7 +1723,7 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL");
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_VLStrings: write buffer is NULL");
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -1227,7 +1773,7 @@ done:
H5Tclose(nested_tid);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VL */
} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings */
/*
* Helper method to convert an array of Java strings into a buffer of C-strings.
@@ -1273,7 +1819,7 @@ H5AwriteVL_str(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
if (NULL == (writeBuf[i] = (char *)HDmalloc((size_t)length + 1)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL_str: failed to allocate string buffer");
HDstrncpy(writeBuf[i], utf8, (size_t)length);
HDstrncpy(writeBuf[i], utf8, (size_t)length + 1);
writeBuf[i][length] = '\0';
UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
@@ -1297,8 +1843,8 @@ done:
HDfree(writeBuf);
}
return (jint)status;
}
return status;
} /* end H5AwriteVL_str */
/*
* Helper method to convert an array of Java strings into a buffer of
@@ -1385,7 +1931,7 @@ done:
H5Sclose(sid);
return status;
} /* end H5AwriteVL_str */
} /* end H5AwriteVL_asstr */
/*
* Class: hdf_hdf5lib_H5
java/src/jni/h5aImp.h
+9 -9
View File
@@ -22,7 +22,7 @@ extern "C" {
/*
* Class: hdf_hdf5lib_H5
* Method: H5Acreate
* Method: _H5Acreate
* Signature: (JLjava/lang/String;JJJ)J
*/
JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Acreate(JNIEnv *, jclass, jlong, jstring, jlong, jlong,
@@ -30,14 +30,14 @@ JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Acreate(JNIEnv *, jclass, jlong,
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aopen_name
* Method: _H5Aopen_name
* Signature: (JLjava/lang/String;)J
*/
JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Aopen_1name(JNIEnv *, jclass, jlong, jstring);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aopen_idx
* Method: _H5Aopen_idx
* Signature: (JI)J
*/
JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Aopen_1idx(JNIEnv *, jclass, jlong, jint);
@@ -137,14 +137,14 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Awrite_1double(JNIEnv *, jclass, jl
/*
* Class: hdf_hdf5lib_H5
* Method: H5AreadVL
* Signature: (JJ[Ljava/lang/String;)I
* Signature: (JJ[Ljava/util/ArrayList;)I
*/
JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *, jclass, jlong, jlong, jobjectArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5AwriteVL
* Signature: (JJ[Ljava/lang/String;)I
* Signature: (JJ[Ljava/util/ArrayList;)I
*/
JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *, jclass, jlong, jlong, jobjectArray);
@@ -185,14 +185,14 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref(JNIEnv *, jclass, j
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aget_space
* Method: _H5Aget_space
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Aget_1space(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aget_type
* Method: _H5Aget_type
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Aget_1type(JNIEnv *, jclass, jlong);
@@ -220,7 +220,7 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Adelete(JNIEnv *, jclass, jlong, js
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aclose
* Method: _H5Aclose
* Signature: (J)I
*/
JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5__1H5Aclose(JNIEnv *, jclass, jlong);
@@ -350,7 +350,7 @@ JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Aopen_1by_1name(JNIEnv *, jclass
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aget_create_plist
* Method: _H5Aget_create_plist
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Aget_1create_1plist(JNIEnv *, jclass, jlong);
java/src/jni/h5dImp.c
+587 -240
View File
@@ -183,28 +183,24 @@ Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong me
jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
htri_t data_class;
jbyte * readBuf = NULL;
herr_t status = FAIL;
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 ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: variable length type not supported");
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread: read buffer not critically pinned");
@@ -219,6 +215,9 @@ Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong me
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);
}
@@ -241,28 +240,24 @@ Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong m
jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
htri_t data_class;
jbyte * writeBuf = NULL;
herr_t status = FAIL;
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 ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: variable length type not supported");
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite: write buffer not critically pinned");
@@ -277,6 +272,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong m
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);
}
@@ -383,7 +381,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1short(JNIEnv *env, jclass clss, jlong dataset_id, j
{
jboolean readBufIsCopy;
jshort * readBuf = NULL;
htri_t data_class;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -391,19 +389,15 @@ Java_hdf_hdf5lib_H5_H5Dread_1short(JNIEnv *env, jclass clss, jlong dataset_id, j
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_short: read buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_short: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_short: variable length type not supported");
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_short: read buffer not critically pinned");
@@ -418,6 +412,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1short(JNIEnv *env, jclass clss, jlong dataset_id, j
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);
}
@@ -441,7 +438,7 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1short(JNIEnv *env, jclass clss, jlong dataset_id,
{
jboolean writeBufIsCopy;
jshort * writeBuf = NULL;
htri_t data_class;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -449,19 +446,15 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1short(JNIEnv *env, jclass clss, jlong dataset_id,
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_short: write buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_short: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_short: variable length type not supported");
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_short: write buffer not critically pinned");
@@ -476,6 +469,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1short(JNIEnv *env, jclass clss, jlong dataset_id,
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);
}
@@ -498,28 +494,24 @@ Java_hdf_hdf5lib_H5_H5Dread_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlo
jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
htri_t data_class;
jint * readBuf = NULL;
herr_t status = FAIL;
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");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_int: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_int: variable length type not supported");
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_int: read buffer not critically pinned");
@@ -534,6 +526,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlo
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);
}
@@ -556,28 +551,24 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1int(JNIEnv *env, jclass clss, jlong dataset_id, jl
jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
htri_t data_class;
jint * writeBuf = NULL;
herr_t status = FAIL;
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");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_int: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_int: variable length type not supported");
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_int: write buffer not critically pinned");
@@ -592,6 +583,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1int(JNIEnv *env, jclass clss, jlong dataset_id, jl
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);
}
@@ -614,28 +608,24 @@ Java_hdf_hdf5lib_H5_H5Dread_1long(JNIEnv *env, jclass clss, jlong dataset_id, jl
jlongArray buf, jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
htri_t data_class;
jlong * readBuf = NULL;
herr_t status = FAIL;
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");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* 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 (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_long: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_long: variable length type not supported");
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_long: read buffer not critically pinned");
@@ -650,6 +640,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1long(JNIEnv *env, jclass clss, jlong dataset_id, jl
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);
}
@@ -672,28 +665,24 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1long(JNIEnv *env, jclass clss, jlong dataset_id, j
jlongArray buf, jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
htri_t data_class;
jlong * writeBuf = NULL;
herr_t status = FAIL;
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");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* Get size of data array */
if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_long: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_long: variable length type not supported");
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_long: write buffer not critically pinned");
@@ -708,6 +697,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1long(JNIEnv *env, jclass clss, jlong dataset_id, j
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);
}
@@ -730,28 +722,24 @@ Java_hdf_hdf5lib_H5_H5Dread_1float(JNIEnv *env, jclass clss, jlong dataset_id, j
jfloatArray buf, jboolean isCriticalPinning)
{
jboolean readBufIsCopy;
htri_t data_class;
jfloat * readBuf = NULL;
herr_t status = FAIL;
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");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* Get size of data array */
if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_float: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_float: variable length type not supported");
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_float: read buffer not critically pinned");
@@ -766,6 +754,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1float(JNIEnv *env, jclass clss, jlong dataset_id, j
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);
}
@@ -788,27 +779,23 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1float(JNIEnv *env, jclass clss, jlong dataset_id,
jfloatArray buf, jboolean isCriticalPinning)
{
jboolean writeBufIsCopy;
htri_t data_class;
jfloat * writeBuf = NULL;
herr_t status = FAIL;
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 ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_float: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_float: variable length type not supported");
/* 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 (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
@@ -824,6 +811,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1float(JNIEnv *env, jclass clss, jlong dataset_id,
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);
}
@@ -847,7 +837,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1double(JNIEnv *env, jclass clss, jlong dataset_id,
{
jboolean readBufIsCopy;
jdouble *readBuf = NULL;
htri_t data_class;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -855,19 +845,15 @@ Java_hdf_hdf5lib_H5_H5Dread_1double(JNIEnv *env, jclass clss, jlong dataset_id,
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_double: read buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
/* Get size of data array */
if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_double: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_double: variable length type not supported");
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_double: read buffer not critically pinned");
@@ -882,6 +868,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1double(JNIEnv *env, jclass clss, jlong dataset_id,
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);
}
@@ -905,7 +894,7 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *env, jclass clss, jlong dataset_id,
{
jboolean writeBufIsCopy;
jdouble *writeBuf = NULL;
htri_t data_class;
htri_t vl_data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -913,19 +902,14 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *env, jclass clss, jlong dataset_id,
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_double: write buffer is NULL");
if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_double: buf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_double: variable length type not supported");
/* Recursively detect any vlen string in type (compound, array ...) */
if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (data_class)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_double: variable length type not supported");
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_double: write buffer not critically pinned");
@@ -940,6 +924,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *env, jclass clss, jlong dataset_id,
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);
}
@@ -1094,11 +1081,443 @@ done:
/*
* Class: hdf_hdf5lib_H5
* Method: H5DreadVL
* Signature: (JJJJJ[Ljava/lang/String;)I
* 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)
{
H5T_class_t type_class;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean readBufIsCopy;
jbyteArray *readBuf = NULL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL");
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: readBuf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_VLEN) {
size_t typeSize;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
void * rawBuf = NULL;
jobject * jList = NULL;
size_t i, j, x;
char * cp_vp = NULL;
if (!(typeSize = H5Tget_size(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if (!(memb = H5Tget_super(mem_type_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!(vlSize = H5Tget_size(memb)))
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer");
if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)rawBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Cache class types */
jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
jmethodID boolValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
jmethodID shortValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
jmethodID floatValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
jmethodID doubleValueMid =
ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
// retrieve the java.util.List interface class
jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z");
/* Convert each element to a list */
for (i = 0; i < (size_t)n; i++) {
// The list we're going to return:
if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
cp_vp = (char *)rawBuf + i * typeSize;
/* Get the number of sequence elements */
jsize nelmts = ((hvl_t *)cp_vp)->len;
jobject jobj = NULL;
for (j = 0; j < nelmts; j++) {
switch (vlClass) {
/*case H5T_BOOL: {
jboolean boolValue;
for (x = 0; x < (int)vlSize; x++) {
((char *)&boolValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j*vlSize+x];
}
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 < (int)vlSize; x++) {
((char *)&byteValue)[x] = ((char *)((hvl_t *)cp_vp)->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 < (int)vlSize; x++) {
((char *)&shortValue)[x] = ((char *)((hvl_t *)cp_vp)->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 < (int)vlSize; x++) {
((char *)&intValue)[x] = ((char *)((hvl_t *)cp_vp)->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 < (int)vlSize; x++) {
((char *)&longValue)[x] = ((char *)((hvl_t *)cp_vp)->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 < (int)vlSize; x++) {
((char *)&floatValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
}
jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
floatValue);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case sizeof(jdouble): {
jdouble doubleValue;
for (x = 0; x < (int)vlSize; x++) {
((char *)&doubleValue)[x] = ((char *)((hvl_t *)cp_vp)->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;
if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, vlSize)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
"readVL reference: byte array not pinned");
for (x = 0; x < (int)vlSize; x++) {
barray[x] = ((jbyte *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
}
if (barray)
UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "H5DreadVL: invalid class type");
break;
}
// Add it to the list
ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
} /* end for */
if (rawBuf)
HDfree(rawBuf);
}
else {
if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
done:
if (readBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
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)
{
H5T_class_t type_class;
jsize n;
htri_t vl_data_class;
herr_t status = FAIL;
jboolean writeBufIsCopy;
jbyteArray *writeBuf = NULL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL");
/* Get size of data array */
if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: readBuf length < 0");
}
if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (type_class == H5T_VLEN) {
size_t typeSize;
hid_t memb = H5I_INVALID_HID;
H5T_class_t vlClass;
size_t vlSize;
void * rawBuf = NULL;
jobject * jList = NULL;
size_t i, j, x;
char * cp_vp = NULL;
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++) {
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);
cp_vp = (char *)rawBuf + i * typeSize;
((hvl_t *)cp_vp)->len = jnelmts;
if (NULL == (((hvl_t *)cp_vp)->p = HDmalloc(jnelmts * vlSize)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate vlen ptr buffer");
jobject jobj = NULL;
for (j = 0; j < (int)jnelmts; j++) {
if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
switch (vlClass) {
/* case H5T_BOOL: {
jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&boolValue)[x];
}
break;
} */
case H5T_INTEGER: {
switch (vlSize) {
case sizeof(jbyte): {
jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&byteValue)[x];
}
break;
}
case sizeof(jshort): {
jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&shortValue)[x];
}
break;
}
case sizeof(jint): {
jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&intValue)[x];
}
break;
}
case sizeof(jlong): {
jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&longValue)[x];
}
break;
}
}
break;
}
case H5T_FLOAT: {
switch (vlSize) {
case sizeof(jfloat): {
jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&floatValue)[x];
}
break;
}
case sizeof(jdouble): {
jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&doubleValue)[x];
}
break;
}
}
break;
}
case H5T_REFERENCE: {
jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
for (x = 0; x < (int)vlSize; x++) {
((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)barray)[x];
}
ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
break;
}
default:
H5_UNIMPLEMENTED(ENVONLY, "H5DwriteVL: invalid class type");
break;
}
ENVPTR->DeleteLocalRef(ENVONLY, jobj);
}
ENVPTR->DeleteLocalRef(ENVONLY, jList);
} /* end for (i = 0; i < n; i++) */
if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, rawBuf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (rawBuf)
HDfree(rawBuf);
}
else {
PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5DwriteVL: write buffer not pinned");
if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, writeBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
done:
if (writeBuf) {
if ((status >= 0) && vl_data_class)
H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
if (type_class != H5T_VLEN)
UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
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;
@@ -1111,7 +1530,7 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL");
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVLStrings: read buffer is NULL");
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -1163,7 +1582,7 @@ done:
H5Tclose(nested_tid);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1VL */
} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */
/*
* Helper method to read in a buffer of variable-length strings from an HDF5
@@ -1315,54 +1734,15 @@ done:
return status;
}
/**
* Read VLEN data into array of arrays.
* Object[] buf contains VL arrays of data points
* Currently only deal with variable length of atomic data types
*/
/* old version */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_VLStrings
* Method: H5Dwrite_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)
{
htri_t isVlenStr = 0;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_VLStrings: read buffer is NULL");
if ((isVlenStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isVlenStr) {
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)
H5_LIBRARY_ERROR(ENVONLY);
}
else
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_VLStrings: datatype is not variable length String");
done:
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */
/*
* Class: hdf_hdf5lib_H5
* Method: H5DwriteVL
* Signature: (JJJJJ[Ljava/lang/String;)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)
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;
@@ -1375,7 +1755,7 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL");
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVLStrings: write buffer is NULL");
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -1427,7 +1807,7 @@ done:
H5Tclose(nested_tid);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1VL */
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings */
/*
* Helper method to convert an array of Java strings into a buffer of C-strings.
@@ -1440,7 +1820,7 @@ H5DwriteVL_str(JNIEnv *env, hid_t dataset_id, hid_t mem_type_id, hid_t mem_space
const char *utf8 = NULL;
jstring obj;
jsize size;
jsize i;
jint i;
char ** writeBuf = NULL;
herr_t status = FAIL;
@@ -1512,7 +1892,7 @@ H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_si
jobjectArray buf)
{
const char *utf8 = NULL;
jstring obj = NULL;
jstring jstr = NULL;
hbool_t close_mem_space = FALSE;
size_t typeSize;
size_t i;
@@ -1549,7 +1929,7 @@ H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_si
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL_asstr: failed to allocate write buffer");
for (i = 0; i < (size_t)n; ++i) {
if (NULL == (obj = (jstring)ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) {
if (NULL == (jstr = (jstring)ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
/*
@@ -1560,11 +1940,11 @@ H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_si
}
/*
* length = ENVPTR->GetStringUTFLength(ENVONLY, obj);
* length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
* CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
*/
PIN_JAVA_STRING(ENVONLY, obj, utf8, NULL, "H5DwriteVL_asstr: failed to pin string buffer");
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
@@ -1574,10 +1954,10 @@ H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_si
if (!h5str_convert(ENVONLY, (char **)&utf8, did, tid, &(((char *)writeBuf)[i * typeSize]), 0))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
utf8 = NULL;
ENVPTR->DeleteLocalRef(ENVONLY, obj);
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)
@@ -1585,7 +1965,7 @@ H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_si
done:
if (utf8)
UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
if (writeBuf) {
H5Treclaim(tid, mem_space, xfer_plist_id, writeBuf);
HDfree(writeBuf);
@@ -1596,39 +1976,6 @@ done:
return status;
} /* end H5DwriteVL_asstr */
/*
* 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)
{
htri_t isVlenStr = 0;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_VLStrings: write buffer is NULL");
if ((isVlenStr = H5Tis_variable_str((hid_t)mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (isVlenStr) {
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)
H5_LIBRARY_ERROR(ENVONLY);
} /* end if */
else
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_VLStrings: datatype is not variable length String");
done:
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dread_reg_ref
java/src/jni/h5dImp.h
+2 -2
View File
@@ -177,7 +177,7 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *, jclass, jl
/*
* Class: hdf_hdf5lib_H5
* Method: H5DreadVL
* Signature: (JJJJJ[Ljava/lang/String;)I
* Signature: (JJJJJ[Ljava/util/ArrayList;)I
*/
JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *, jclass, jlong, jlong, jlong, jlong, jlong,
jobjectArray);
@@ -185,7 +185,7 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *, jclass, jlong, jl
/*
* Class: hdf_hdf5lib_H5
* Method: H5DwriteVL
* Signature: (JJJJJ[Ljava/lang/String;)I
* Signature: (JJJJJ[Ljava/util/ArrayList;)I
*/
JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *, jclass, jlong, jlong, jlong, jlong, jlong,
jobjectArray);
java/src/jni/h5rImp.c
+61
View File
@@ -877,6 +877,67 @@ done:
return ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Rget_1name */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Rget_name_string
* Signature: (JI[B)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Rget_1name_1string(JNIEnv *env, jclass clss, jlong loc_id, jint ref_type,
jbyteArray ref)
{
jboolean isCopy;
jstring str;
jsize refBufLen;
jbyte * refBuf = NULL;
char * aName = NULL;
ssize_t buf_size = -1;
jlong ret_val = -1;
UNUSED(clss);
if (NULL == ref)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rget_name: reference buffer is NULL");
if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, ref)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Rget_name: ref array length < 0");
}
if ((H5R_OBJECT == ref_type) && (refBufLen != H5R_OBJ_REF_BUF_SIZE))
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Rget_name: reference input array length != H5R_OBJ_REF_BUF_SIZE");
else if ((H5R_DATASET_REGION == ref_type) && (refBufLen != H5R_DSET_REG_REF_BUF_SIZE))
H5_BAD_ARGUMENT_ERROR(
ENVONLY, "H5Rget_name: region reference input array length != H5R_DSET_REG_REF_BUF_SIZE");
else if ((H5R_OBJECT != ref_type) && (H5R_DATASET_REGION != ref_type))
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Rget_name: unknown reference type");
PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_name: reference buffer not pinned");
/* Get the length of the name */
if ((buf_size = H5Rget_name((hid_t)loc_id, (H5R_type_t)ref_type, refBuf, NULL, 0)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (aName = HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rget_name: failed to allocate referenced object name buffer");
if ((ret_val = (jlong)H5Rget_name((hid_t)loc_id, (H5R_type_t)ref_type, refBuf, aName,
(size_t)buf_size + 1)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
aName[(size_t)buf_size] = '\0';
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, aName)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
done:
if (aName)
HDfree(aName);
if (refBuf)
UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, JNI_ABORT);
return str;
} /* end Java_hdf_hdf5lib_H5_H5Rget_1name_1string */
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
java/src/jni/h5rImp.h
+7
View File
@@ -170,6 +170,13 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Rget_1obj_1type2(JNIEnv *, jclass,
JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Rget_1name(JNIEnv *, jclass, jlong, jint, jbyteArray,
jobjectArray, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Rget_name_string
* Signature: (JI[B)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL Java_hdf_hdf5lib_H5_H5Rget_1name_1string(JNIEnv *, jclass, jlong, jint, jbyteArray);
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
java/src/jni/h5util.c
+322 -125
View File
@@ -52,6 +52,7 @@ void * edata;
/* Local Prototypes */
/********************/
int h5str_old_region_dataset(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_buf, int expand_data);
int h5str_region_dataset(JNIEnv *env, h5str_t *out_str, H5R_ref_t *ref_vp, int expand_data);
static int h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj,
@@ -63,7 +64,6 @@ static int h5str_is_zero(const void *_mem, size_t size);
static hid_t h5str_get_native_type(hid_t type);
static hid_t h5str_get_little_endian_type(hid_t type);
static hid_t h5str_get_big_endian_type(hid_t type);
static htri_t h5str_detect_vlen(hid_t tid);
static htri_t h5str_detect_vlen_str(hid_t tid);
static int h5str_dump_simple_data(JNIEnv *env, FILE *stream, hid_t container, hid_t type, void *_mem,
hsize_t nelmts);
@@ -641,6 +641,33 @@ done:
return retVal;
} /* end h5str_convert */
/*-------------------------------------------------------------------------
* Function: h5str_sprint_old_reference
*
* Purpose: Object reference -- show the name of the 1.10 referenced object.
*
* Return: SUCCEED or FAIL
*-------------------------------------------------------------------------
*/
int
h5str_sprint_old_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *ref_buf)
{
hid_t region = H5I_INVALID_HID;
char ref_name[1024];
int ret_value = FAIL;
if ((H5Rget_name(region_obj, H5R_DATASET_REGION, ref_buf, (char *)ref_name, 1024)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!h5str_append(out_str, ref_name))
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
ret_value = SUCCEED;
done:
return ret_value;
} /* h5str_sprint_reference */
/*-------------------------------------------------------------------------
* Function: h5str_sprint_reference
*
@@ -704,6 +731,48 @@ done:
return ret_value;
} /* h5str_sprint_reference */
int
h5str_old_region_dataset(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_buf, int expand_data)
{
H5S_sel_type region_type = H5S_SEL_ERROR;
hid_t region_obj = H5I_INVALID_HID;
hid_t region_sid = H5I_INVALID_HID;
int ret_value = FAIL;
if ((region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, ref_buf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((region_sid = H5Rget_region(container, H5R_DATASET_REGION, ref_buf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (expand_data == 0)
if (h5str_sprint_old_reference(ENVONLY, out_str, region_obj, ref_buf) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if ((region_type = H5Sget_select_type(region_sid)) > H5S_SEL_ERROR) {
if (H5S_SEL_POINTS == region_type) {
if (h5str_dump_region_points(ENVONLY, out_str, region_sid, region_obj, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else if (H5S_SEL_HYPERSLABS == region_type) {
if (h5str_dump_region_blocks(ENVONLY, out_str, region_sid, region_obj, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
}
ret_value = SUCCEED;
done:
if (region_sid >= 0)
if (H5Sclose(region_sid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (region_obj >= 0)
if (H5Dclose(region_obj) < 0)
H5_LIBRARY_ERROR(ENVONLY);
return ret_value;
}
int
h5str_region_dataset(JNIEnv *env, h5str_t *out_str, H5R_ref_t *ref_vp, int expand_data)
{
@@ -1106,125 +1175,217 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
}
case H5T_REFERENCE: {
/* H5T_STD_REF */
hid_t new_obj_id = H5I_INVALID_HID;
H5O_type_t obj_type = -1; /* Object type */
H5R_type_t ref_type; /* Reference type */
if (H5R_DSET_REG_REF_BUF_SIZE == typeSize) {
if (h5str_old_region_dataset(ENVONLY, out_str, container, cptr, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else if (H5R_OBJ_REF_BUF_SIZE == typeSize) {
H5O_info2_t oi;
hid_t obj = H5I_INVALID_HID;
char * obj_tok_str = NULL;
H5R_ref_t *ref_vp = (H5R_ref_t *)cptr;
/*
* Object references -- show the type and OID of the referenced
* object.
*/
ref_type = H5Rget_type(ref_vp);
if (!h5str_is_zero(ref_vp, H5Tget_size(H5T_STD_REF))) {
switch (ref_type) {
case H5R_OBJECT1:
if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_DATASET:
if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
if (NULL == (this_str = (char *)HDmalloc(64)))
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
case H5O_TYPE_GROUP:
case H5O_TYPE_NAMED_DATATYPE:
case H5O_TYPE_MAP:
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default: {
/* Object references -- show the type and OID of the referenced object. */
H5O_info2_t oi;
char * obj_tok_str = NULL;
if ((new_obj_id = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >=
0) {
H5Oget_info3(new_obj_id, &oi, H5O_INFO_BASIC);
H5Otoken_to_str(new_obj_id, &oi.token, &obj_tok_str);
if (H5Dclose(new_obj_id) < 0)
if ((obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, cptr)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Oget_info3(obj, &oi, H5O_INFO_ALL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Print object data and close object */
H5Otoken_to_str(obj, &oi.token, &obj_tok_str);
switch (oi.type) {
case H5O_TYPE_GROUP:
if (HDsprintf(this_str, "%s %s", H5_TOOLS_GROUP, obj_tok_str) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
break;
case H5O_TYPE_DATASET:
if (HDsprintf(this_str, "%s %s", H5_TOOLS_DATASET, obj_tok_str) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
break;
case H5O_TYPE_NAMED_DATATYPE:
if (HDsprintf(this_str, "%s %s", H5_TOOLS_DATATYPE, obj_tok_str) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
break;
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default:
if (HDsprintf(this_str, "%u-%s", (unsigned)oi.type, obj_tok_str) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
break;
}
if (obj_tok_str) {
H5free_memory(obj_tok_str);
obj_tok_str = NULL;
}
if (H5Oclose(obj) < 0)
H5_LIBRARY_ERROR(ENVONLY);
obj = H5I_INVALID_HID;
}
else {
/* H5T_STD_REF */
hid_t new_obj_id = H5I_INVALID_HID;
H5O_type_t obj_type = -1; /* Object type */
H5R_type_t ref_type; /* Reference type */
H5R_ref_t *ref_vp = (H5R_ref_t *)cptr;
ref_type = H5Rget_type(ref_vp);
if (!h5str_is_zero(ref_vp, H5Tget_size(H5T_STD_REF))) {
switch (ref_type) {
case H5R_OBJECT1:
if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_DATASET:
if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
case H5O_TYPE_GROUP:
case H5O_TYPE_NAMED_DATATYPE:
case H5O_TYPE_MAP:
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default: {
/* Object references -- show the type and
* OID of the referenced object. */
H5O_info2_t oi;
char * obj_tok_str = NULL;
if ((new_obj_id = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >=
0) {
H5Oget_info3(new_obj_id, &oi, H5O_INFO_BASIC);
H5Otoken_to_str(new_obj_id, &oi.token, &obj_tok_str);
if (H5Dclose(new_obj_id) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
else
H5_LIBRARY_ERROR(ENVONLY);
}
else
H5_LIBRARY_ERROR(ENVONLY);
size_t this_len = 14;
if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(
ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsnprintf(this_str, this_len, "%u-", (unsigned)oi.type) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
if (!h5str_append(out_str, this_str))
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
HDfree(this_str);
this_str = NULL;
/* Print OID */
{
char *token_str;
H5Otoken_to_str(tid, &oi.token, &token_str);
size_t that_len = 64 + strlen(token_str) + 1;
if (NULL == (this_str = HDmalloc(that_len)))
size_t this_len = 14;
if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(
ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (HDsnprintf(this_str, that_len, "%lu:%s", oi.fileno, token_str) <
0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
switch (oi.type) {
case H5O_TYPE_GROUP:
if (HDsnprintf(this_str, this_len, "%s ", H5_TOOLS_GROUP) < 0)
H5_JNI_FATAL_ERROR(ENVONLY,
"h5str_sprintf: HDsnprintf failure");
break;
H5free_memory(token_str);
}
} break;
} /* end switch */
}
else
H5_LIBRARY_ERROR(ENVONLY);
break;
case H5R_DATASET_REGION1:
if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
case H5R_OBJECT2:
if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_GROUP:
break;
case H5O_TYPE_DATASET:
if (HDsnprintf(this_str, this_len, "%s ", H5_TOOLS_DATASET) <
0)
H5_JNI_FATAL_ERROR(ENVONLY,
"h5str_sprintf: HDsnprintf failure");
break;
case H5O_TYPE_DATASET:
if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
case H5O_TYPE_NAMED_DATATYPE:
if (HDsnprintf(this_str, this_len, "%s ", H5_TOOLS_DATATYPE) <
0)
H5_JNI_FATAL_ERROR(ENVONLY,
"h5str_sprintf: HDsnprintf failure");
break;
case H5O_TYPE_NAMED_DATATYPE:
break;
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default:
if (HDsnprintf(this_str, this_len, "%u-", (unsigned)oi.type) <
0)
H5_JNI_FATAL_ERROR(ENVONLY,
"h5str_sprintf: HDsnprintf failure");
break;
} /* end switch */
if (!h5str_append(out_str, this_str))
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
HDfree(this_str);
this_str = NULL;
case H5O_TYPE_MAP:
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default:
break;
} /* end switch */
}
else
H5_ASSERTION_ERROR(ENVONLY, "h5str_sprintf: H5R_OBJECT2 failed");
break;
case H5R_DATASET_REGION2:
if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
case H5R_ATTR:
if ((new_obj_id = H5Ropen_attr(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
if (h5str_dump_region_attribute(ENVONLY, out_str, new_obj_id) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (H5Aclose(new_obj_id) < 0)
/* Print OID */
{
char *token_str;
H5Otoken_to_str(tid, &oi.token, &token_str);
size_t that_len = 64 + strlen(token_str) + 1;
if (NULL == (this_str = HDmalloc(that_len)))
H5_OUT_OF_MEMORY_ERROR(
ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
if (HDsnprintf(this_str, that_len, "%lu:%s", oi.fileno,
token_str) < 0)
H5_JNI_FATAL_ERROR(ENVONLY,
"h5str_sprintf: HDsnprintf failure");
H5free_memory(token_str);
}
} break;
} /* end switch */
}
else
H5_LIBRARY_ERROR(ENVONLY);
}
break;
case H5R_BADTYPE:
case H5R_MAXTYPE:
default:
break;
} /* end switch */
}
break;
case H5R_DATASET_REGION1:
if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
case H5R_OBJECT2:
if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_GROUP:
break;
if (H5Rdestroy(ref_vp) < 0)
H5_LIBRARY_ERROR(ENVONLY);
case H5O_TYPE_DATASET:
if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
case H5O_TYPE_NAMED_DATATYPE:
break;
case H5O_TYPE_MAP:
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default:
break;
} /* end switch */
}
else
H5_ASSERTION_ERROR(ENVONLY, "h5str_sprintf: H5R_OBJECT2 failed");
break;
case H5R_DATASET_REGION2:
if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
case H5R_ATTR:
if ((new_obj_id = H5Ropen_attr(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
if (h5str_dump_region_attribute(ENVONLY, out_str, new_obj_id) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (H5Aclose(new_obj_id) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
break;
case H5R_BADTYPE:
case H5R_MAXTYPE:
default:
break;
} /* end switch */
}
if (H5Rdestroy(ref_vp) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
break;
}
@@ -1761,7 +1922,7 @@ h5str_is_zero(const void *_mem, size_t size)
* Negative value: error occurred
*-------------------------------------------------------------------------
*/
static htri_t
htri_t
h5str_detect_vlen(hid_t tid)
{
htri_t ret = FAIL;
@@ -3118,29 +3279,65 @@ done:
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: H5Tdetect_variable_str
*
* Purpose: Recursive check for variable length string of a datatype.
*
* Return: TRUE : type contains any variable length string
* FALSE : type doesn't contain any variable length string
* Negative value: failed
*-------------------------------------------------------------------------
*/
htri_t
H5Tdetect_variable_str(hid_t tid)
{
htri_t ret_val = 0;
H5T_class_t tclass = -1;
htri_t ret = FALSE;
if (H5Tget_class(tid) == H5T_COMPOUND) {
unsigned i;
unsigned nm = (unsigned)H5Tget_nmembers(tid);
for (i = 0; i < nm; i++) {
htri_t status = 0;
hid_t mtid = 0;
if ((mtid = H5Tget_member_type(tid, i)) < 0)
return FAIL; /* exit immediately on error */
if ((status = H5Tdetect_variable_str(mtid)) < 0)
return status; /* exit immediately on error */
ret_val |= status;
ret = H5Tis_variable_str(tid);
if ((ret == TRUE) || (ret < 0))
goto done;
tclass = H5Tget_class(tid);
if (tclass == H5T_ARRAY || tclass == H5T_VLEN) {
hid_t btid = H5Tget_super(tid);
if (btid < 0) {
ret = (htri_t)btid;
goto done;
}
ret = H5Tdetect_variable_str(btid);
if ((ret == TRUE) || (ret < 0)) {
H5Tclose(btid);
goto done;
}
}
else if (tclass == H5T_COMPOUND) {
unsigned nmembs;
int snmembs = H5Tget_nmembers(tid);
unsigned u;
if (snmembs < 0) {
ret = FAIL;
goto done;
}
nmembs = (unsigned)snmembs;
for (u = 0; u < nmembs; u++) {
hid_t mtid = H5Tget_member_type(tid, u);
ret = H5Tdetect_variable_str(mtid);
if ((ret == TRUE) || (ret < 0)) {
H5Tclose(mtid);
goto done;
}
H5Tclose(mtid);
} /* end for */
} /* end if */
else
ret_val = H5Tis_variable_str(tid);
}
}
return ret_val;
done:
return ret;
} /* end H5Tdetect_variable_str */
static int
java/src/jni/h5util.h
+2
View File
@@ -39,8 +39,10 @@ extern void h5str_new(h5str_t *str, size_t len);
extern void h5str_free(h5str_t *str);
extern void h5str_resize(h5str_t *str, size_t new_len);
extern char * h5str_append(h5str_t *str, const char *cstr);
extern htri_t h5str_detect_vlen(hid_t tid);
extern size_t h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_buf,
size_t out_buf_offset);
extern int h5str_sprint_old_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *ref_buf);
extern int h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, void *ref_p);
extern size_t h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf,
int expand_data);
java/src/jni/nativeData.c
+1 -2
View File
@@ -46,8 +46,7 @@ extern "C" {
/* returns int [] */
JNIEXPORT jintArray JNICALL
Java_hdf_hdf5lib_HDFNativeData_byteToInt___3B(JNIEnv *env, jclass clss,
jbyteArray bdata) /* IN: array of bytes */
Java_hdf_hdf5lib_HDFNativeData_byteToInt___3B(JNIEnv *env, jclass clss, jbyteArray bdata)
{
jintArray rarray = NULL;
jboolean bb;