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authorAllen Byrne <50328838+byrnHDF@users.noreply.github.com>2022-07-12 15:47:06 (GMT)
committerGitHub <noreply@github.com>2022-07-12 15:47:06 (GMT)
commitddb0c502ede9d46c43ef0cecee5cb1fc03c5f6b5 (patch)
tree16fe614a360f7a724dc2b5398eec74fd34547066
parentd0bbd4e8abf64810c7cda15018d8fcce2999f11d (diff)
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1 10 HDFFV-11310 implement JNI VL support for primitive types (#1858)
* HDFFV-11310 - implement vlen read/write for atomic types. * HDFFV-11310 - VL read/write function for primitive types * Add read/write VL option * fix function name typo * remove debugging prints * Remove more debugging code * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Fix unreleased allocations, fix debug * Fix format * Fix formatting * Correct typo
Diffstat
-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
-rw-r--r--java/test/TestH5A.java259
-rw-r--r--java/test/TestH5D.java221
-rw-r--r--java/test/TestH5R.java469
-rw-r--r--java/test/testfiles/JUnit-TestH5A.txt3
-rw-r--r--java/test/testfiles/JUnit-TestH5D.txt5
-rw-r--r--java/test/testfiles/JUnit-TestH5R.txt4
-rw-r--r--release_docs/RELEASE.txt33
15 files changed, 2415 insertions, 502 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);
diff --git a/java/test/TestH5A.java b/java/test/TestH5A.java
index 113196a..52731b3 100644
--- a/java/test/TestH5A.java
+++ b/java/test/TestH5A.java
@@ -20,6 +20,8 @@ import static org.junit.Assert.fail;
import java.io.File;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
@@ -249,9 +251,8 @@ public class TestH5A {
// Opening the existing attribute, obj_name(Created by H5ACreate2)
// by index, attached to an object identifier.
- attribute_id =
- H5.H5Aopen_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0,
- HDF5Constants.H5P_DEFAULT, lapl_id);
+ attribute_id = H5.H5Aopen_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
+ HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT, lapl_id);
assertTrue("testH5Aopen_by_idx: H5Aopen_by_idx", attribute_id >= 0);
@@ -313,9 +314,9 @@ public class TestH5A {
boolean bool_val = false;
try {
- attribute_id =
- H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT,
- HDF5Constants.H5P_DEFAULT, lapl_id);
+ attribute_id = H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
+ lapl_id);
assertTrue("testH5Acreate_by_name: H5Acreate_by_name", attribute_id >= 0);
// Check if the name of attribute attached to the object specified
@@ -433,9 +434,9 @@ public class TestH5A {
long attribute_id = HDF5Constants.H5I_INVALID_HID;
try {
- attribute_id =
- H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT,
- HDF5Constants.H5P_DEFAULT, lapl_id);
+ attribute_id = H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
+ lapl_id);
assertTrue("testH5Aget_name: H5Acreate_by_name ", attribute_id > 0);
ret_name = H5.H5Aget_name(attribute_id);
assertEquals(ret_name, attr_name);
@@ -539,7 +540,7 @@ public class TestH5A {
try {
attr_id = H5.H5Acreate(H5did, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT,
- HDF5Constants.H5P_DEFAULT);
+ HDF5Constants.H5P_DEFAULT);
attribute_id = H5.H5Aopen(H5did, "dset", HDF5Constants.H5P_DEFAULT);
// Calling H5Aget_info with attribute_id returned from H5Aopen.
attr_info = H5.H5Aget_info(attribute_id);
@@ -580,7 +581,7 @@ public class TestH5A {
try {
attr_id = H5.H5Acreate(H5did, ".", type_id, space_id, HDF5Constants.H5P_DEFAULT,
- HDF5Constants.H5P_DEFAULT);
+ HDF5Constants.H5P_DEFAULT);
attribute_id = H5.H5Aopen_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER, order, 0,
HDF5Constants.H5P_DEFAULT, lapl_id);
// Calling H5Aget_info with attribute_id returned from
@@ -623,7 +624,7 @@ public class TestH5A {
try {
attr_id = H5.H5Acreate(H5did, "dset1", type_id, space_id, HDF5Constants.H5P_DEFAULT,
- HDF5Constants.H5P_DEFAULT);
+ HDF5Constants.H5P_DEFAULT);
attr2_id = H5.H5Acreate(H5did, "dataset2", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
@@ -700,7 +701,7 @@ public class TestH5A {
try {
attr_id = H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id,
- HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr_info = H5.H5Aget_info_by_name(H5fid, obj_name, attr_name, lapl_id);
assertNotNull(attr_info);
}
@@ -1064,7 +1065,7 @@ public class TestH5A {
HDF5Constants.H5P_DEFAULT);
assertTrue("testH5Awrite_readVL: ", attr_id >= 0);
- H5.H5AwriteVL(attr_id, atype_id, str_data);
+ H5.H5Awrite_VLStrings(attr_id, atype_id, str_data);
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
@@ -1076,7 +1077,7 @@ public class TestH5A {
strs[j] = "";
}
try {
- H5.H5AreadVL(attr_id, atype_id, strs);
+ H5.H5Aread_VLStrings(attr_id, atype_id, strs);
}
catch (Exception ex) {
ex.printStackTrace();
@@ -1151,12 +1152,12 @@ public class TestH5A {
fail("H5.H5Acreate: " + err);
}
- /* Close the property list, and get the attribute's property list */
+ // Close the property list, and get the attribute's property list
H5.H5Pclose(plist_id);
plist_id = H5.H5Aget_create_plist(attribute_id);
assertTrue(plist_id > 0);
- /* Get the character encoding and ensure that it is the default (ASCII) */
+ // Get the character encoding and ensure that it is the default (ASCII)
try {
char_encoding = H5.H5Pget_char_encoding(plist_id);
}
@@ -1213,13 +1214,13 @@ public class TestH5A {
}
try {
attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id,
- HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id,
- HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id,
- HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr4_id = H5.H5Acreate_by_name(H5fid, ".", "attribute4", type_id, space_id,
- HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
H5A_iterate_cb iter_cb = new H5A_iter_callback();
try {
H5.H5Aiterate(H5fid, HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0L, iter_cb,
@@ -1306,13 +1307,13 @@ public class TestH5A {
}
try {
attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute4", type_id, space_id,
- HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id,
- HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id,
- HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr4_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id,
- HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
H5A_iterate_cb iter_cb = new H5A_iter_callback();
try {
H5.H5Aiterate_by_name(H5fid, ".", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0L,
@@ -1360,4 +1361,212 @@ public class TestH5A {
}
}
}
+
+ @Test
+ public void testH5AVLwr()
+ {
+ String attr_int_name = "VLIntdata";
+ String attr_dbl_name = "VLDbldata";
+ long attr_int_id = HDF5Constants.H5I_INVALID_HID;
+ long attr_dbl_id = HDF5Constants.H5I_INVALID_HID;
+ long atype_int_id = HDF5Constants.H5I_INVALID_HID;
+ long atype_dbl_id = HDF5Constants.H5I_INVALID_HID;
+ long aspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] dims = {4};
+ long lsize = 1;
+
+ ArrayList[] vl_int_data = new ArrayList[4];
+ ArrayList[] vl_dbl_data = new ArrayList[4];
+ try {
+ // Write Integer data
+ vl_int_data[0] = new ArrayList<Integer>(Arrays.asList(1));
+ vl_int_data[1] = new ArrayList<Integer>(Arrays.asList(2, 3));
+ vl_int_data[2] = new ArrayList<Integer>(Arrays.asList(4, 5, 6));
+ vl_int_data[3] = new ArrayList<Integer>(Arrays.asList(7, 8, 9, 10));
+ Class dataClass = vl_int_data.getClass();
+ assertTrue("testH5AVLwr.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ atype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
+ assertTrue("testH5AVLwr.H5Tvlen_create: ", atype_int_id >= 0);
+ }
+ catch (Exception err) {
+ if (atype_int_id > 0)
+ try {
+ H5.H5Tclose(atype_int_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5AVLwr: " + err);
+ }
+
+ try {
+ aspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(aspace_id > 0);
+ attr_int_id = H5.H5Acreate(H5did, attr_int_name, atype_int_id, aspace_id,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5AVLwr: ", attr_int_id >= 0);
+
+ H5.H5AwriteVL(attr_int_id, atype_int_id, vl_int_data);
+ }
+ catch (Exception err) {
+ if (attr_int_id > 0)
+ try {
+ H5.H5Aclose(attr_int_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_int_id > 0)
+ try {
+ H5.H5Tclose(atype_int_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5AVLwr: " + err);
+ }
+ finally {
+ if (aspace_id > 0)
+ try {
+ H5.H5Sclose(aspace_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+
+ // Write Double data
+ vl_dbl_data[0] = new ArrayList<Double>(Arrays.asList(1.1));
+ vl_dbl_data[1] = new ArrayList<Double>(Arrays.asList(2.2, 3.3));
+ vl_dbl_data[2] = new ArrayList<Double>(Arrays.asList(4.4, 5.5, 6.6));
+ vl_dbl_data[3] = new ArrayList<Double>(Arrays.asList(7.7, 8.8, 9.9, 10.0));
+ dataClass = vl_dbl_data.getClass();
+ assertTrue("testH5AVLwr.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ atype_dbl_id = H5.H5Tvlen_create(HDF5Constants.H5T_NATIVE_DOUBLE);
+ assertTrue("testH5AVLwr.H5Tvlen_create: ", atype_dbl_id >= 0);
+ }
+ catch (Exception err) {
+ if (atype_dbl_id > 0)
+ try {
+ H5.H5Tclose(atype_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5AVLwr: " + err);
+ }
+
+ try {
+ aspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(aspace_id > 0);
+ attr_dbl_id = H5.H5Acreate(H5did, attr_dbl_name, atype_dbl_id, aspace_id,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5AVLwr: ", attr_dbl_id >= 0);
+
+ H5.H5AwriteVL(attr_dbl_id, atype_dbl_id, vl_dbl_data);
+ }
+ catch (Exception err) {
+ if (attr_dbl_id > 0)
+ try {
+ H5.H5Aclose(attr_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_dbl_id > 0)
+ try {
+ H5.H5Tclose(atype_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5AVLwr: " + err);
+ }
+ finally {
+ if (aspace_id > 0)
+ try {
+ H5.H5Sclose(aspace_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+
+ H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+
+ for (int j = 0; j < dims.length; j++) {
+ lsize *= dims[j];
+ }
+
+ // Read Integer data
+ ArrayList[] vl_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ vl_readbuf[j] = new ArrayList<Integer>();
+
+ try {
+ H5.H5AreadVL(attr_int_id, atype_int_id, vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5AVLwr:" + vl_readbuf[0].get(0),
+ vl_int_data[0].get(0).equals(vl_readbuf[0].get(0)));
+ assertTrue("testH5AVLwr:" + vl_readbuf[1].get(0),
+ vl_int_data[1].get(0).equals(vl_readbuf[1].get(0)));
+ assertTrue("testH5AVLwr:" + vl_readbuf[2].get(0),
+ vl_int_data[2].get(0).equals(vl_readbuf[2].get(0)));
+ assertTrue("testH5AVLwr:" + vl_readbuf[3].get(0),
+ vl_int_data[3].get(0).equals(vl_readbuf[3].get(0)));
+
+ // Read Double data
+ vl_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ vl_readbuf[j] = new ArrayList<Double>();
+
+ try {
+ H5.H5AreadVL(attr_dbl_id, atype_dbl_id, vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5AVLwr:" + vl_readbuf[0].get(0),
+ vl_dbl_data[0].get(0).equals(vl_readbuf[0].get(0)));
+ assertTrue("testH5AVLwr:" + vl_readbuf[1].get(0),
+ vl_dbl_data[1].get(0).equals(vl_readbuf[1].get(0)));
+ assertTrue("testH5AVLwr:" + vl_readbuf[2].get(0),
+ vl_dbl_data[2].get(0).equals(vl_readbuf[2].get(0)));
+ assertTrue("testH5AVLwr:" + vl_readbuf[3].get(0),
+ vl_dbl_data[3].get(0).equals(vl_readbuf[3].get(0)));
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.testH5AVLwr: " + err);
+ }
+ finally {
+ if (attr_dbl_id > 0)
+ try {
+ H5.H5Aclose(attr_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ if (attr_int_id > 0)
+ try {
+ H5.H5Aclose(attr_int_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_dbl_id > 0)
+ try {
+ H5.H5Tclose(atype_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_int_id > 0)
+ try {
+ H5.H5Tclose(atype_int_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+ }
}
diff --git a/java/test/TestH5D.java b/java/test/TestH5D.java
index 4bab1a9..f7e5702 100644
--- a/java/test/TestH5D.java
+++ b/java/test/TestH5D.java
@@ -17,6 +17,9 @@ import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
@@ -961,8 +964,8 @@ public class TestH5D {
assertTrue("H5Dvlen_get_buf_size " + vl_size + " == " + str_data_bytes, vl_size == str_data_bytes);
}
- @Test(expected = IllegalArgumentException.class)
- public void testH5Dvlen_read_invalid_buffer() throws Throwable
+ @Test
+ public void testH5Dvlen_read_default_buffer() throws Throwable
{
String[] str_data = {"Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.",
"Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!",
@@ -1013,4 +1016,218 @@ public class TestH5D {
assertTrue("testH5Dvlen_write_read " + str_wdata[v] + " == " + str_rdata[v],
str_wdata[v] == str_wdata[v]);
}
+
+ @Test
+ public void testH5DVLwr()
+ {
+ String dset_int_name = "VLIntdata";
+ String dset_dbl_name = "VLDbldata";
+ long dset_int_id = HDF5Constants.H5I_INVALID_HID;
+ long dset_dbl_id = HDF5Constants.H5I_INVALID_HID;
+ long dtype_int_id = HDF5Constants.H5I_INVALID_HID;
+ long dtype_dbl_id = HDF5Constants.H5I_INVALID_HID;
+ long dspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] dims = {4};
+ long lsize = 1;
+
+ ArrayList[] vl_int_data = new ArrayList[4];
+ ArrayList[] vl_dbl_data = new ArrayList[4];
+ try {
+ // Write Integer data
+ vl_int_data[0] = new ArrayList<Integer>(Arrays.asList(1));
+ vl_int_data[1] = new ArrayList<Integer>(Arrays.asList(2, 3));
+ vl_int_data[2] = new ArrayList<Integer>(Arrays.asList(4, 5, 6));
+ vl_int_data[3] = new ArrayList<Integer>(Arrays.asList(7, 8, 9, 10));
+ Class dataClass = vl_int_data.getClass();
+ assertTrue("testH5DVLwr.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ dtype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
+ assertTrue("testH5DVLwr.H5Tvlen_create: ", dtype_int_id >= 0);
+ }
+ catch (Exception err) {
+ if (dtype_int_id > 0)
+ try {
+ H5.H5Tclose(dtype_int_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5DVLwr: " + err);
+ }
+
+ try {
+ dspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(dspace_id > 0);
+ dset_int_id =
+ H5.H5Dcreate(H5fid, dset_int_name, dtype_int_id, dspace_id, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5DVLwr: ", dset_int_id >= 0);
+
+ H5.H5DwriteVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_int_data);
+ }
+ catch (Exception err) {
+ if (dset_int_id > 0)
+ try {
+ H5.H5Dclose(dset_int_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_int_id > 0)
+ try {
+ H5.H5Tclose(dtype_int_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5DVLwr: " + err);
+ }
+ finally {
+ if (dspace_id > 0)
+ try {
+ H5.H5Sclose(dspace_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+
+ // Write Double data
+ vl_dbl_data[0] = new ArrayList<Double>(Arrays.asList(1.1));
+ vl_dbl_data[1] = new ArrayList<Double>(Arrays.asList(2.2, 3.3));
+ vl_dbl_data[2] = new ArrayList<Double>(Arrays.asList(4.4, 5.5, 6.6));
+ vl_dbl_data[3] = new ArrayList<Double>(Arrays.asList(7.7, 8.8, 9.9, 10.0));
+ dataClass = vl_dbl_data.getClass();
+ assertTrue("testH5DVLwr.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ dtype_dbl_id = H5.H5Tvlen_create(HDF5Constants.H5T_NATIVE_DOUBLE);
+ assertTrue("testH5DVLwr.H5Tvlen_create: ", dtype_dbl_id >= 0);
+ }
+ catch (Exception err) {
+ if (dtype_dbl_id > 0)
+ try {
+ H5.H5Tclose(dtype_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5DVLwr: " + err);
+ }
+
+ try {
+ dspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(dspace_id > 0);
+ dset_dbl_id =
+ H5.H5Dcreate(H5fid, dset_dbl_name, dtype_dbl_id, dspace_id, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5DVLwr: ", dset_dbl_id >= 0);
+
+ H5.H5DwriteVL(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_dbl_data);
+ }
+ catch (Exception err) {
+ if (dset_dbl_id > 0)
+ try {
+ H5.H5Dclose(dset_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_dbl_id > 0)
+ try {
+ H5.H5Tclose(dtype_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5DVLwr: " + err);
+ }
+ finally {
+ if (dspace_id > 0)
+ try {
+ H5.H5Sclose(dspace_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+
+ H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+
+ for (int j = 0; j < dims.length; j++) {
+ lsize *= dims[j];
+ }
+
+ // Read Integer data
+ ArrayList[] vl_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ vl_readbuf[j] = new ArrayList<Integer>();
+
+ try {
+ H5.H5DreadVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5DVLwr:" + vl_readbuf[0].get(0),
+ vl_int_data[0].get(0).equals(vl_readbuf[0].get(0)));
+ assertTrue("testH5DVLwr:" + vl_readbuf[1].get(0),
+ vl_int_data[1].get(0).equals(vl_readbuf[1].get(0)));
+ assertTrue("testH5DVLwr:" + vl_readbuf[2].get(0),
+ vl_int_data[2].get(0).equals(vl_readbuf[2].get(0)));
+ assertTrue("testH5DVLwr:" + vl_readbuf[3].get(0),
+ vl_int_data[3].get(0).equals(vl_readbuf[3].get(0)));
+
+ // Read Double data
+ vl_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ vl_readbuf[j] = new ArrayList<Double>();
+
+ try {
+ H5.H5DreadVL(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5DVLwr:" + vl_readbuf[0].get(0),
+ vl_dbl_data[0].get(0).equals(vl_readbuf[0].get(0)));
+ assertTrue("testH5DVLwr:" + vl_readbuf[1].get(0),
+ vl_dbl_data[1].get(0).equals(vl_readbuf[1].get(0)));
+ assertTrue("testH5DVLwr:" + vl_readbuf[2].get(0),
+ vl_dbl_data[2].get(0).equals(vl_readbuf[2].get(0)));
+ assertTrue("testH5DVLwr:" + vl_readbuf[3].get(0),
+ vl_dbl_data[3].get(0).equals(vl_readbuf[3].get(0)));
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.testH5DVLwr: " + err);
+ }
+ finally {
+ if (dset_dbl_id > 0)
+ try {
+ H5.H5Dclose(dset_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dset_int_id > 0)
+ try {
+ H5.H5Dclose(dset_int_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_dbl_id > 0)
+ try {
+ H5.H5Tclose(dtype_dbl_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_int_id > 0)
+ try {
+ H5.H5Tclose(dtype_int_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+ }
}
diff --git a/java/test/TestH5R.java b/java/test/TestH5R.java
index a8e7387..54ff9c2 100644
--- a/java/test/TestH5R.java
+++ b/java/test/TestH5R.java
@@ -19,6 +19,9 @@ import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
@@ -407,4 +410,470 @@ public class TestH5R {
ref2 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
H5.H5Rdereference(H5gid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, ref1);
}
+
+ @Test
+ public void testH5RVLattr_ref()
+ {
+ String attr_obj_name = "VLObjRefdata";
+ String attr_reg_name = "VLRegRefdata";
+ long attr_obj_id = HDF5Constants.H5I_INVALID_HID;
+ long attr_reg_id = HDF5Constants.H5I_INVALID_HID;
+ long atype_obj_id = HDF5Constants.H5I_INVALID_HID;
+ long atype_reg_id = HDF5Constants.H5I_INVALID_HID;
+ long aspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] dims = {4};
+ long lsize = 1;
+ byte[] ref1 = null;
+ byte[] ref2 = null;
+ byte[] ref3 = null;
+ byte[] ref4 = null;
+
+ try {
+ // Create reference on dataset
+ ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid);
+ assertNotNull(ref1);
+ ref2 = H5.H5Rcreate(H5gid, "dset2", HDF5Constants.H5R_DATASET_REGION, H5dsid);
+ assertNotNull(ref2);
+ ref3 = H5.H5Rcreate(H5gid, "/dset", HDF5Constants.H5R_OBJECT, -1);
+ assertNotNull(ref3);
+
+ // Create reference on group
+ ref4 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
+ assertNotNull(ref3);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("testH5RVLattr_ref: " + err);
+ }
+
+ ArrayList[] vl_obj_data = new ArrayList[4];
+ ArrayList[] vl_reg_data = new ArrayList[4];
+ try {
+ // Write Object Reference data
+ vl_obj_data[0] = new ArrayList<byte[]>(Arrays.asList(ref3));
+ vl_obj_data[1] = new ArrayList<byte[]>(Arrays.asList(ref3, ref4));
+ vl_obj_data[2] = new ArrayList<byte[]>(Arrays.asList(ref3, ref3, ref3));
+ vl_obj_data[3] = new ArrayList<byte[]>(Arrays.asList(ref4, ref4, ref4, ref4));
+ Class dataClass = vl_obj_data.getClass();
+ assertTrue("testH5RVLattr_ref.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ atype_obj_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_OBJ);
+ assertTrue("testH5RVLattr_ref.H5Tvlen_create: ", atype_obj_id >= 0);
+ }
+ catch (Exception err) {
+ if (atype_obj_id > 0)
+ try {
+ H5.H5Tclose(atype_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5RVLattr_ref: " + err);
+ }
+
+ try {
+ aspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(aspace_id > 0);
+ attr_obj_id = H5.H5Acreate(H5did, attr_obj_name, atype_obj_id, aspace_id,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5RVLattr_ref: ", attr_obj_id >= 0);
+
+ H5.H5AwriteVL(attr_obj_id, atype_obj_id, vl_obj_data);
+ }
+ catch (Exception err) {
+ if (attr_obj_id > 0)
+ try {
+ H5.H5Aclose(attr_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_obj_id > 0)
+ try {
+ H5.H5Tclose(atype_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5RVLattr_ref: " + err);
+ }
+ finally {
+ if (aspace_id > 0)
+ try {
+ H5.H5Sclose(aspace_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+
+ // Write Region Reference data
+ vl_reg_data[0] = new ArrayList<byte[]>(Arrays.asList(ref1));
+ vl_reg_data[1] = new ArrayList<byte[]>(Arrays.asList(ref1, ref2));
+ vl_reg_data[2] = new ArrayList<byte[]>(Arrays.asList(ref1, ref1, ref1));
+ vl_reg_data[3] = new ArrayList<byte[]>(Arrays.asList(ref2, ref2, ref2, ref2));
+ dataClass = vl_reg_data.getClass();
+ assertTrue("testH5RVLattr_ref.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ atype_reg_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_DSETREG);
+ assertTrue("testH5RVLattr_ref.H5Tvlen_create: ", atype_reg_id >= 0);
+ }
+ catch (Exception err) {
+ if (atype_reg_id > 0)
+ try {
+ H5.H5Tclose(atype_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5RVLattr_ref: " + err);
+ }
+
+ try {
+ aspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(aspace_id > 0);
+ attr_reg_id = H5.H5Acreate(H5did, attr_reg_name, atype_reg_id, aspace_id,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5RVLattr_ref: ", attr_reg_id >= 0);
+
+ H5.H5AwriteVL(attr_reg_id, atype_reg_id, vl_reg_data);
+ }
+ catch (Exception err) {
+ if (attr_reg_id > 0)
+ try {
+ H5.H5Aclose(attr_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_reg_id > 0)
+ try {
+ H5.H5Tclose(atype_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5RVLattr_ref: " + err);
+ }
+ finally {
+ if (aspace_id > 0)
+ try {
+ H5.H5Sclose(aspace_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+
+ H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+
+ for (int j = 0; j < dims.length; j++) {
+ lsize *= dims[j];
+ }
+
+ // Read Object Reference data
+ ArrayList[] vl_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ vl_readbuf[j] = new ArrayList<byte[]>();
+
+ try {
+ H5.H5AreadVL(attr_obj_id, atype_obj_id, vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
+ ((byte[])vl_obj_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
+ assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
+ ((byte[])vl_obj_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
+ assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
+ ((byte[])vl_obj_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
+ assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
+ ((byte[])vl_obj_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
+
+ // Read Region Reference data
+ vl_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ vl_readbuf[j] = new ArrayList<byte[]>();
+
+ try {
+ H5.H5AreadVL(attr_reg_id, atype_reg_id, vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
+ ((byte[])vl_reg_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
+ assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
+ ((byte[])vl_reg_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
+ assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
+ ((byte[])vl_reg_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
+ assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
+ ((byte[])vl_reg_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.testH5RVLattr_ref: " + err);
+ }
+ finally {
+ if (attr_reg_id > 0)
+ try {
+ H5.H5Aclose(attr_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ if (attr_obj_id > 0)
+ try {
+ H5.H5Aclose(attr_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_reg_id > 0)
+ try {
+ H5.H5Tclose(atype_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ if (atype_obj_id > 0)
+ try {
+ H5.H5Tclose(atype_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+ }
+
+ @Test
+ public void testH5RVLdset_ref()
+ {
+ String dset_obj_name = "VLObjRefdata";
+ String dset_reg_name = "VLRegRefdata";
+ long dset_obj_id = HDF5Constants.H5I_INVALID_HID;
+ long dset_reg_id = HDF5Constants.H5I_INVALID_HID;
+ long dtype_obj_id = HDF5Constants.H5I_INVALID_HID;
+ long dtype_reg_id = HDF5Constants.H5I_INVALID_HID;
+ long dspace_id = HDF5Constants.H5I_INVALID_HID;
+ long[] dims = {4};
+ long lsize = 1;
+ byte[] ref1 = null;
+ byte[] ref2 = null;
+ byte[] ref3 = null;
+ byte[] ref4 = null;
+
+ try {
+ // Create reference on dataset
+ ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid);
+ assertNotNull(ref1);
+ ref2 = H5.H5Rcreate(H5gid, "dset2", HDF5Constants.H5R_DATASET_REGION, H5dsid);
+ assertNotNull(ref2);
+ ref3 = H5.H5Rcreate(H5gid, "/dset", HDF5Constants.H5R_OBJECT, -1);
+ assertNotNull(ref3);
+
+ // Create reference on group
+ ref4 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
+ assertNotNull(ref3);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("testH5RVLattr_ref: " + err);
+ }
+
+ ArrayList[] vl_obj_data = new ArrayList[4];
+ ArrayList[] vl_reg_data = new ArrayList[4];
+ try {
+ // Write Object Reference data
+ vl_obj_data[0] = new ArrayList<byte[]>(Arrays.asList(ref3));
+ vl_obj_data[1] = new ArrayList<byte[]>(Arrays.asList(ref3, ref4));
+ vl_obj_data[2] = new ArrayList<byte[]>(Arrays.asList(ref3, ref3, ref3));
+ vl_obj_data[3] = new ArrayList<byte[]>(Arrays.asList(ref4, ref4, ref4, ref4));
+ Class dataClass = vl_obj_data.getClass();
+ assertTrue("testH5RVLdset_ref.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ dtype_obj_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_OBJ);
+ assertTrue("testH5RVLdset_ref.H5Tvlen_create: ", dtype_obj_id >= 0);
+ }
+ catch (Exception err) {
+ if (dtype_obj_id > 0)
+ try {
+ H5.H5Tclose(dtype_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5RVLdset_ref: " + err);
+ }
+
+ try {
+ dspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(dspace_id > 0);
+ dset_obj_id =
+ H5.H5Dcreate(H5fid, dset_obj_name, dtype_obj_id, dspace_id, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5RVLdset_ref: ", dset_obj_id >= 0);
+
+ H5.H5DwriteVL(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_obj_data);
+ }
+ catch (Exception err) {
+ if (dset_obj_id > 0)
+ try {
+ H5.H5Dclose(dset_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_obj_id > 0)
+ try {
+ H5.H5Tclose(dtype_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5RVLdset_ref: " + err);
+ }
+ finally {
+ if (dspace_id > 0)
+ try {
+ H5.H5Sclose(dspace_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+
+ // Write Region Reference data
+ vl_reg_data[0] = new ArrayList<byte[]>(Arrays.asList(ref1));
+ vl_reg_data[1] = new ArrayList<byte[]>(Arrays.asList(ref1, ref2));
+ vl_reg_data[2] = new ArrayList<byte[]>(Arrays.asList(ref1, ref1, ref1));
+ vl_reg_data[3] = new ArrayList<byte[]>(Arrays.asList(ref2, ref2, ref2, ref2));
+ dataClass = vl_reg_data.getClass();
+ assertTrue("testH5RVLdset_ref.getClass: " + dataClass, dataClass.isArray());
+
+ try {
+ dtype_reg_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_DSETREG);
+ assertTrue("testH5RVLdset_ref.H5Tvlen_create: ", dtype_reg_id >= 0);
+ }
+ catch (Exception err) {
+ if (dtype_reg_id > 0)
+ try {
+ H5.H5Tclose(dtype_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5RVLdset_ref: " + err);
+ }
+
+ try {
+ dspace_id = H5.H5Screate_simple(1, dims, null);
+ assertTrue(dspace_id > 0);
+ dset_reg_id =
+ H5.H5Dcreate(H5fid, dset_reg_name, dtype_reg_id, dspace_id, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ assertTrue("testH5RVLdset_ref: ", dset_reg_id >= 0);
+
+ H5.H5DwriteVL(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_reg_data);
+ }
+ catch (Exception err) {
+ if (dset_reg_id > 0)
+ try {
+ H5.H5Dclose(dset_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_reg_id > 0)
+ try {
+ H5.H5Tclose(dtype_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ err.printStackTrace();
+ fail("H5.testH5RVLdset_ref: " + err);
+ }
+ finally {
+ if (dspace_id > 0)
+ try {
+ H5.H5Sclose(dspace_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+
+ H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+
+ for (int j = 0; j < dims.length; j++) {
+ lsize *= dims[j];
+ }
+
+ // Read Object Reference data
+ ArrayList[] vl_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ vl_readbuf[j] = new ArrayList<byte[]>();
+
+ try {
+ H5.H5DreadVL(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
+ ((byte[])vl_obj_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
+ assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
+ ((byte[])vl_obj_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
+ assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
+ ((byte[])vl_obj_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
+ assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
+ ((byte[])vl_obj_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
+
+ // Read Region Reference data
+ vl_readbuf = new ArrayList[4];
+ for (int j = 0; j < lsize; j++)
+ vl_readbuf[j] = new ArrayList<byte[]>();
+
+ try {
+ H5.H5DreadVL(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+ HDF5Constants.H5P_DEFAULT, vl_readbuf);
+ }
+ catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
+ ((byte[])vl_reg_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
+ assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
+ ((byte[])vl_reg_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
+ assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
+ ((byte[])vl_reg_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
+ assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
+ ((byte[])vl_reg_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.testH5RVLdset_ref: " + err);
+ }
+ finally {
+ if (dset_reg_id > 0)
+ try {
+ H5.H5Dclose(dset_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dset_obj_id > 0)
+ try {
+ H5.H5Dclose(dset_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_reg_id > 0)
+ try {
+ H5.H5Tclose(dtype_reg_id);
+ }
+ catch (Exception ex) {
+ }
+ if (dtype_obj_id > 0)
+ try {
+ H5.H5Tclose(dtype_obj_id);
+ }
+ catch (Exception ex) {
+ }
+ }
+ }
}
diff --git a/java/test/testfiles/JUnit-TestH5A.txt b/java/test/testfiles/JUnit-TestH5A.txt
index 2026d21..efdd4a2 100644
--- a/java/test/testfiles/JUnit-TestH5A.txt
+++ b/java/test/testfiles/JUnit-TestH5A.txt
@@ -6,6 +6,7 @@ JUnit version 4.11
.testH5Aiterate
.testH5Aopen_by_idx
.testH5Aopen_invalidname
+.testH5AVLwr
.testH5Aopen
.testH5Aget_info_by_name
.testH5Aget_create_plist
@@ -30,5 +31,5 @@ JUnit version 4.11
Time: XXXX
-OK (28 tests)
+OK (29 tests)
diff --git a/java/test/testfiles/JUnit-TestH5D.txt b/java/test/testfiles/JUnit-TestH5D.txt
index 987655b..288e6d0 100644
--- a/java/test/testfiles/JUnit-TestH5D.txt
+++ b/java/test/testfiles/JUnit-TestH5D.txt
@@ -4,6 +4,7 @@ JUnit version 4.11
.testH5Dcreate
.testH5Dget_offset
.testH5Dget_type
+.testH5DVLwr
.testH5Dfill
.testH5Dopen
.testH5Dcreate_anon
@@ -11,15 +12,15 @@ JUnit version 4.11
.testH5Dget_storage_size_empty
.testH5Diterate
.testH5Dget_access_plist
-.testH5Dvlen_read_invalid_buffer
.testH5Dvlen_get_buf_size
.testH5Dget_space_closed
.testH5Dget_space_status
.testH5Dvlen_write_read
.testH5Dget_space
.testH5Dget_type_closed
+.testH5Dvlen_read_default_buffer
Time: XXXX
-OK (19 tests)
+OK (20 tests)
diff --git a/java/test/testfiles/JUnit-TestH5R.txt b/java/test/testfiles/JUnit-TestH5R.txt
index 150df54..ecdd322 100644
--- a/java/test/testfiles/JUnit-TestH5R.txt
+++ b/java/test/testfiles/JUnit-TestH5R.txt
@@ -2,6 +2,8 @@ JUnit version 4.11
.testH5Rgetregion_Nullreference
.testH5Rget_obj_type2_Invalidreftype
.testH5Rdereference
+.testH5RVLdset_ref
+.testH5RVLattr_ref
.testH5Rget_name
.testH5Rcreate_Invalidreftype
.testH5Rget_name_NULLreference
@@ -19,5 +21,5 @@ JUnit version 4.11
Time: XXXX
-OK (17 tests)
+OK (19 tests)
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 85ccf45..eb94be8 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -74,7 +74,38 @@ New Features
Java Library:
-------------
- -
+ - Added reference support to H5A and H5D read write vlen JNI functions.
+
+ Added the implementation to handle VL references as an Array of Lists
+ of byte arrays.
+
+ The JNI wrappers translate the Array of Lists to/from the hvl_t vlen
+ structures. The wrappers use the specified datatype arguments for the
+ List type translation, it is expected that the Java type is correct.
+
+ (ADB - 2022/07/11, HDFFV-11318)
+
+ - H5A and H5D read write vlen JNI functions were incorrect.
+
+ Corrected the vlen function implementations for the basic primitive types.
+ The VLStrings functions now correctly use the implementation that had been
+ the VL functions. (VLStrings functions did not have an implementation.)
+ The new VL functions implementation now expect an Array of Lists between
+ Java and the JNI wrapper.
+
+ The JNI wrappers translate the Array of Lists to/from the hvl_t vlen
+ structures. The wrappers use the specified datatype arguments for the
+ List type translation, it is expected that the Java type is correct.
+
+ (ADB - 2022/07/07, HDFFV-11310)
+
+ - H5A and H5D read write JNI functions had flawed vlen datatype check.
+
+ Adapted tools function for JNI utils file. This reduced multiple calls
+ to a single check and variable. The variable can then be used to call
+ the H5Treclaim function. Adjusted existing test and added new test.
+
+ (ADB - 2022/06/22)
Tools:
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