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-rw-r--r--java/src/hdf/hdf5lib/H5.java22
-rw-r--r--java/src/hdf/hdf5lib/HDF5Constants.java12
-rw-r--r--java/src/jni/h5aImp.c818
-rw-r--r--java/src/jni/h5aImp.h18
-rw-r--r--java/src/jni/h5dImp.c805
-rw-r--r--java/src/jni/h5dImp.h4
-rw-r--r--java/src/jni/h5util.c243
-rw-r--r--java/src/jni/h5util.h1
8 files changed, 1453 insertions, 470 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index b95495a..e96cf06 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -246,7 +246,7 @@ public class H5 implements java.io.Serializable {
*
* Make sure to update the versions number when a different library is used.
*/
- public final static int LIB_VERSION[] = {1, 10, 9};
+ public final static int LIB_VERSION[] = {1, 10, 10};
/**
* add system property to load library by path
@@ -1267,6 +1267,10 @@ 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);
@@ -1813,6 +1817,10 @@ 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();
@@ -2797,6 +2805,11 @@ 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);
@@ -3472,6 +3485,11 @@ 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();
@@ -6468,7 +6486,7 @@ public class H5 implements java.io.Serializable {
/**
* H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and
- *relative name.
+ * relative name.
*
* @param loc_id
* IN: File or group identifier specifying location of group in which object is located
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 7c02af9..bcf3eab 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -81,7 +81,8 @@ public class HDF5Constants {
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
+ /**
+ * 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
@@ -93,19 +94,22 @@ public class HDF5Constants {
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
+ /**
+ * 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
+ /**
+ * 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
+ /**
+ * 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
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index f06075c..065022d 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -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");
-
- /* Recursively detect any vlen string in type (compound, array ...) */
- if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
+ if (vl_data_class) {
+ /* Get size of data array */
+ if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
+ }
- 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) {
+ H5Dvlen_reclaim(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);
@@ -222,18 +236,18 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: variable length type not supported");
+ /* 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)
+ 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");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
@@ -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)
+ H5Dvlen_reclaim(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");
-
- /* Recursively detect any vlen string in type (compound, array ...) */
- if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
+ if (vl_data_class) {
+ /* Get size of data array */
+ if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
+ }
- 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) {
+ H5Dvlen_reclaim(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);
@@ -334,18 +365,18 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: variable length type not supported");
+ /* 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)
+ 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");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
@@ -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)
+ H5Dvlen_reclaim(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");
-
- /* Recursively detect any vlen string in type (compound, array ...) */
- if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
+ if (vl_data_class) {
+ /* Get size of data array */
+ if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
+ }
- 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) {
+ H5Dvlen_reclaim(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);
@@ -446,18 +494,18 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: variable length type not supported");
+ /* 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)
+ 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");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
@@ -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)
+ H5Dvlen_reclaim(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");
-
- /* Recursively detect any vlen string in type (compound, array ...) */
- if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
+ if (vl_data_class) {
+ /* Get size of data array */
+ if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
+ }
- 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) {
+ H5Dvlen_reclaim(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);
@@ -558,18 +623,18 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: variable length type not supported");
+ /* 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)
+ 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");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
@@ -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)
+ H5Dvlen_reclaim(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");
-
- /* Recursively detect any vlen string in type (compound, array ...) */
- if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
+ if (vl_data_class) {
+ /* Get size of data array */
+ if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
+ }
- 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) {
+ H5Dvlen_reclaim(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);
@@ -670,18 +752,18 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: variable length type not supported");
+ /* 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)
+ 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");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
@@ -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)
+ H5Dvlen_reclaim(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");
-
- /* Recursively detect any vlen string in type (compound, array ...) */
- if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
+ if (vl_data_class) {
+ /* Get size of data array */
+ if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
+ }
- 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) {
+ H5Dvlen_reclaim(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);
@@ -782,18 +881,17 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: variable length type not supported");
+ if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: buf length < 0");
+ }
- /* Recursively detect any vlen string in type (compound, array ...) */
- if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 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");
+ if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
@@ -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)
+ H5Dvlen_reclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -958,12 +1059,456 @@ 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) {
+ H5Dvlen_reclaim(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)
+ H5Dvlen_reclaim(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;
htri_t isVlenStr = 0;
htri_t isComplex = 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
diff --git a/java/src/jni/h5aImp.h b/java/src/jni/h5aImp.h
index aee0e40..094f990 100644
--- a/java/src/jni/h5aImp.h
+++ b/java/src/jni/h5aImp.h
@@ -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);
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index 24263a5..136d82f 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: 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");
+ }
- /* 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, "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)
+ H5Dvlen_reclaim(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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: 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");
+ }
- /* 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, "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)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -371,7 +369,7 @@ 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);
@@ -379,19 +377,15 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_short: 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");
+ }
- /* 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, "H5Dread_short: variable length type not supported");
-
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_short: read buffer not critically pinned");
@@ -406,6 +400,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1short(JNIEnv *env, jclass clss, jlong dataset_id, j
done:
if (readBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -429,7 +426,7 @@ 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);
@@ -437,19 +434,15 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_short: 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");
+ }
- /* 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, "H5Dwrite_short: variable length type not supported");
-
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_short: write buffer not critically pinned");
@@ -464,6 +457,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1short(JNIEnv *env, jclass clss, jlong dataset_id,
done:
if (writeBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -486,28 +482,24 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_int: 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");
+ }
- /* 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, "H5Dread_int: variable length type not supported");
-
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_int: read buffer not critically pinned");
@@ -522,6 +514,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlo
done:
if (readBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -544,28 +539,24 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_int: 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");
+ }
- /* 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, "H5Dwrite_int: variable length type not supported");
-
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_int: write buffer not critically pinned");
@@ -580,6 +571,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1int(JNIEnv *env, jclass clss, jlong dataset_id, jl
done:
if (writeBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -602,28 +596,24 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_long: 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");
+ }
- /* 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, "H5Dread_long: variable length type not supported");
-
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_long: read buffer not critically pinned");
@@ -638,6 +628,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1long(JNIEnv *env, jclass clss, jlong dataset_id, jl
done:
if (readBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -660,28 +653,24 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_long: 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, "H5Aread: readBuf length < 0");
+ }
- /* 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, "H5Dwrite_long: variable length type not supported");
-
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_long: write buffer not critically pinned");
@@ -696,6 +685,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1long(JNIEnv *env, jclass clss, jlong dataset_id, j
done:
if (writeBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -718,28 +710,24 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_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, "H5Aread: readBuf length < 0");
+ }
- /* 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, "H5Dread_float: variable length type not supported");
-
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_float: read buffer not critically pinned");
@@ -754,6 +742,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1float(JNIEnv *env, jclass clss, jlong dataset_id, j
done:
if (readBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -776,27 +767,23 @@ 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)
- 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)
+ 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");
+ /* 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,
@@ -812,6 +799,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1float(JNIEnv *env, jclass clss, jlong dataset_id,
done:
if (writeBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -835,7 +825,7 @@ 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);
@@ -843,19 +833,15 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_double: 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, "H5Aread: readBuf length < 0");
+ }
- /* 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, "H5Dread_double: variable length type not supported");
-
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_double: read buffer not critically pinned");
@@ -870,6 +856,9 @@ Java_hdf_hdf5lib_H5_H5Dread_1double(JNIEnv *env, jclass clss, jlong dataset_id,
done:
if (readBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -893,7 +882,7 @@ 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);
@@ -901,19 +890,14 @@ 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)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (data_class)
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_double: variable length type not supported");
+ if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_double: buf length < 0");
+ }
- /* 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, "H5Dwrite_double: variable length type not supported");
-
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_double: write buffer not critically pinned");
@@ -928,6 +912,9 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *env, jclass clss, jlong dataset_id,
done:
if (writeBuf) {
+ if ((status >= 0) && vl_data_class)
+ H5Dvlen_reclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
+
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -1082,13 +1069,445 @@ 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)
+ H5Dvlen_reclaim(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)
+ H5Dvlen_reclaim(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;
htri_t isVlenStr = 0;
htri_t isComplex = 0;
@@ -1099,7 +1518,7 @@ 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);
@@ -1151,7 +1570,7 @@ 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
@@ -1303,54 +1722,15 @@ 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
- * 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
+ * Method: H5Dwrite_VLStrings
* 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;
@@ -1363,7 +1743,7 @@ 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);
@@ -1415,7 +1795,7 @@ 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.
@@ -1428,7 +1808,7 @@ 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;
@@ -1500,7 +1880,7 @@ 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;
@@ -1537,7 +1917,7 @@ 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);
/*
@@ -1548,11 +1928,11 @@ 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
@@ -1562,10 +1942,10 @@ 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)
@@ -1573,7 +1953,7 @@ 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) {
H5Dvlen_reclaim(tid, mem_space, xfer_plist_id, writeBuf);
HDfree(writeBuf);
@@ -1586,39 +1966,6 @@ done:
/*
* 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
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
diff --git a/java/src/jni/h5dImp.h b/java/src/jni/h5dImp.h
index e339dad..f79cc2c 100644
--- a/java/src/jni/h5dImp.h
+++ b/java/src/jni/h5dImp.h
@@ -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);
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 4568880..7de5a05 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -62,7 +62,6 @@ 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);
@@ -210,10 +209,10 @@ h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_
/* Build default formats for long long types */
if (!fmt_llong[0]) {
- if (HDsprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure");
- if (HDsprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure");
+ if (HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%%sd", H5_PRINTF_LL_WIDTH) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsnprintf failure");
+ if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%%su", H5_PRINTF_LL_WIDTH) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsnprintf failure");
} /* end if */
switch (tclass) {
@@ -651,9 +650,8 @@ done:
int
h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *ref_buf)
{
- hid_t region = H5I_INVALID_HID;
- char ref_name[1024];
- const char *path;
+ hid_t region = H5I_INVALID_HID;
+ char ref_name[1024];
int ret_value = FAIL;
@@ -756,11 +754,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
HDmemcpy(&tmp_float, cptr, sizeof(float));
- if (NULL == (this_str = (char *)HDmalloc(25)))
+ size_t this_len = 25;
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%g", tmp_float) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%g", tmp_float) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
break;
}
@@ -770,11 +769,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
HDmemcpy(&tmp_double, cptr, sizeof(double));
- if (NULL == (this_str = (char *)HDmalloc(25)))
+ size_t this_len = 25;
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%g", tmp_double) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%g", tmp_double) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
break;
}
@@ -784,11 +784,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
HDmemcpy(&tmp_ldouble, cptr, sizeof(long double));
- if (NULL == (this_str = (char *)HDmalloc(27)))
+ size_t this_len = 27;
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%Lg", tmp_ldouble) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%Lg", tmp_ldouble) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
break;
}
@@ -850,25 +851,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
unsigned char tmp_uchar = 0;
char tmp_char = 0;
+ size_t this_len = 7;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_uchar, cptr, sizeof(unsigned char));
- if (NULL == (this_str = (char *)HDmalloc(7)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%hhu", tmp_uchar) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%hhu", tmp_uchar) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
else {
HDmemcpy(&tmp_char, cptr, sizeof(char));
- if (NULL == (this_str = (char *)HDmalloc(7)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%hhd", tmp_char) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%hhd", tmp_char) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
break;
@@ -878,25 +880,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
unsigned short tmp_ushort = 0;
short tmp_short = 0;
+ size_t this_len = 9;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short));
- if (NULL == (this_str = (char *)HDmalloc(9)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%hu", tmp_ushort) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%hu", tmp_ushort) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
else {
HDmemcpy(&tmp_short, cptr, sizeof(short));
- if (NULL == (this_str = (char *)HDmalloc(9)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%hd", tmp_short) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%hd", tmp_short) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
break;
@@ -906,25 +909,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
unsigned int tmp_uint = 0;
int tmp_int = 0;
+ size_t this_len = 14;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_uint, cptr, sizeof(unsigned int));
- if (NULL == (this_str = (char *)HDmalloc(14)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%u", tmp_uint) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%u", tmp_uint) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
else {
HDmemcpy(&tmp_int, cptr, sizeof(int));
- if (NULL == (this_str = (char *)HDmalloc(14)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%d", tmp_int) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%d", tmp_int) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
break;
@@ -934,25 +938,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
unsigned long tmp_ulong = 0;
long tmp_long = 0;
+ size_t this_len = 23;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_ulong, cptr, sizeof(unsigned long));
- if (NULL == (this_str = (char *)HDmalloc(23)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%lu", tmp_ulong) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%lu", tmp_ulong) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
else {
HDmemcpy(&tmp_long, cptr, sizeof(long));
- if (NULL == (this_str = (char *)HDmalloc(23)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, "%ld", tmp_long) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%ld", tmp_long) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
break;
@@ -963,25 +968,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
unsigned long long tmp_ullong = 0;
long long tmp_llong = 0;
+ size_t this_len = 25;
if (H5T_SGN_NONE == nsign) {
HDmemcpy(&tmp_ullong, cptr, sizeof(unsigned long long));
- if (NULL == (this_str = (char *)HDmalloc(25)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, fmt_ullong, tmp_ullong) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, fmt_ullong, tmp_ullong) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
else {
HDmemcpy(&tmp_llong, cptr, sizeof(long long));
- if (NULL == (this_str = (char *)HDmalloc(25)))
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY,
"h5str_sprintf: failed to allocate string buffer");
- if (HDsprintf(this_str, fmt_llong, tmp_llong) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, fmt_llong, tmp_llong) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
break;
@@ -1041,17 +1047,18 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
else {
size_t i;
- if (NULL == (this_str = (char *)HDmalloc(4 * (typeSize + 1))))
+ size_t this_len = 4 * (typeSize + 1);
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (1 == typeSize) {
- if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%#02x", ucptr[0]) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
else {
for (i = 0; i < typeSize; i++)
- if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%s%02x", i ? ":" : "", ucptr[i]) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
}
@@ -1088,8 +1095,29 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
H5_LIBRARY_ERROR(ENVONLY);
/* Print object data and close object */
- if (HDsprintf(this_str, "%u-%llu", (unsigned)oi.type, oi.addr) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ switch (oi.type) {
+ case H5O_TYPE_GROUP:
+ if (HDsprintf(this_str, "%s %llu", H5_TOOLS_GROUP, oi.addr) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ break;
+
+ case H5O_TYPE_DATASET:
+ if (HDsprintf(this_str, "%s %llu", H5_TOOLS_DATASET, oi.addr) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ break;
+
+ case H5O_TYPE_NAMED_DATATYPE:
+ if (HDsprintf(this_str, "%s %llu", H5_TOOLS_DATATYPE, oi.addr) < 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-%llu", (unsigned)oi.type, oi.addr) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ break;
+ } /* end switch */
if (H5Oclose(obj) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -1189,17 +1217,18 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
/* All other types get printed as hexadecimal */
- if (NULL == (this_str = (char *)HDmalloc(4 * (typeSize + 1))))
+ size_t this_len = 4 * (typeSize + 1);
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
if (1 == typeSize) {
- if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%#02x", ucptr[0]) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
else {
for (i = 0; i < typeSize; i++)
- if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ if (HDsnprintf(this_str, this_len, "%s%02x", i ? ":" : "", ucptr[i]) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
}
break;
@@ -1230,7 +1259,7 @@ done:
* This is a special case subfunction to print the data in a region reference of type blocks.
*
* Return:
- * The function returns FAIL if there was an error, otherwise SUCEED
+ * The function returns FAIL if there was an error, otherwise SUCCEED
*-------------------------------------------------------------------------
*/
static int
@@ -1401,8 +1430,9 @@ h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t re
for (j = 0; j < ndims; j++) {
tmp_str[0] = '\0';
- if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)ptdata[i * 2 * ndims + j]) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure");
+ if (HDsnprintf(tmp_str, sizeof(tmp_str), "%s%lu", j ? "," : "(",
+ (unsigned long)ptdata[i * 2 * ndims + j]) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsnprintf failure");
if (!h5str_append(str, tmp_str))
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
@@ -1411,9 +1441,9 @@ h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t re
for (j = 0; j < ndims; j++) {
tmp_str[0] = '\0';
- if (HDsprintf(tmp_str, "%s%lu", j ? "," : ")-(",
- (unsigned long)ptdata[i * 2 * ndims + j + ndims]) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure");
+ if (HDsnprintf(tmp_str, sizeof(tmp_str), "%s%lu", j ? "," : ")-(",
+ (unsigned long)ptdata[i * 2 * ndims + j + ndims]) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsnprintf failure");
if (!h5str_append(str, tmp_str))
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
@@ -1578,8 +1608,9 @@ h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t re
for (j = 0; j < ndims; j++) {
tmp_str[0] = '\0';
- if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)(ptdata[i * ndims + j])) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsprintf failure");
+ if (HDsnprintf(tmp_str, sizeof(tmp_str), "%s%lu", j ? "," : "(",
+ (unsigned long)(ptdata[i * ndims + j])) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsnprintf failure");
if (!h5str_append(str, tmp_str))
H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
@@ -1628,7 +1659,7 @@ 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;
@@ -1653,7 +1684,7 @@ done:
* Purpose: Recursive check for variable length string of a datatype.
*
* Return:
- * TRUE : type conatains any variable length string
+ * TRUE : type contains any variable length string
* FALSE : type doesn't contain any variable length string
* Negative value: error occur
*
@@ -2187,7 +2218,7 @@ done:
* This is a special case subfunction to print the data in a region reference of type blocks.
*
* Return:
- * The function returns FAIL if there was an error, otherwise SUCEED
+ * The function returns FAIL if there was an error, otherwise SUCCEED
*
*-------------------------------------------------------------------------
*/
@@ -2838,29 +2869,65 @@ 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;
-
- 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;
+ H5T_class_t tclass = -1;
+ htri_t ret = FALSE;
+
+ 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
diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h
index b7f12bd..9517630 100644
--- a/java/src/jni/h5util.h
+++ b/java/src/jni/h5util.h
@@ -39,6 +39,7 @@ 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_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *ref_buf);
generated by cgit v0.12 at 2024-07-17 03:42:35 (GMT)