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authorAllen Byrne <50328838+byrnHDF@users.noreply.github.com>2022-07-18 17:23:37 (GMT)
committerGitHub <noreply@github.com>2022-07-18 17:23:37 (GMT)
commitf6997681335f0b5fe2e8904f9108a71c5200fb2d (patch)
treeedc5aabdcae1035ce6e888bde550e15b1ad2e878 /java
parent7f9a5f0b6e58e9c04a18ea83ff0400f95294c6ac (diff)
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1.12 eliminate unnecessary errors in the error stack (#1880)
* Eliminate unnecessary error output * Fix merge typo * fix format * Fix object address to tokens * Fix conflict
Diffstat (limited to 'java')
-rw-r--r--java/src/hdf/hdf5lib/H5.java50
-rw-r--r--java/src/hdf/hdf5lib/HDF5Constants.java65
-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/h5rImp.c61
-rw-r--r--java/src/jni/h5rImp.h7
-rw-r--r--java/src/jni/h5util.c461
-rw-r--r--java/src/jni/h5util.h2
-rw-r--r--java/src/jni/nativeData.c3
-rw-r--r--java/test/TestH5A.java243
-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
17 files changed, 560 insertions, 2679 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 25a1f8d..133cd2c 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -1242,10 +1242,6 @@ 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);
@@ -1792,10 +1788,6 @@ 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();
@@ -2780,11 +2772,6 @@ 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);
@@ -3463,11 +3450,6 @@ 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();
@@ -9374,8 +9356,9 @@ public class H5 implements java.io.Serializable {
byte[] buf = theArray.emptyBytes();
int status = H5Pget_fill_value(plist_id, type_id, buf);
- if (status >= 0)
+ if (status >= 0) {
obj = theArray.arrayify(buf);
+ }
return status;
}
@@ -11035,6 +11018,8 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Rdestroy(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+ // Info //
+
/**
* H5Rget_type retrieves the type of a reference.
*
@@ -11091,6 +11076,8 @@ public class H5 implements java.io.Serializable {
public synchronized static native byte[] H5Rcopy(byte[] src_ref_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+ // Dereference //
+
/**
* H5Ropen_object opens that object and returns an identifier.
* The object opened with this function should be closed when it is no longer needed
@@ -11237,6 +11224,8 @@ public class H5 implements java.io.Serializable {
public synchronized static native int H5Rget_obj_type3(byte[] ref_ptr, long rapl_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+ // Get name //
+
/**
* H5Rget_file_name retrieves the file name for the object, region or attribute reference pointed to.
*
@@ -11411,29 +11400,6 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
- * H5Rget_name_string retrieves a name for the object identified by ref.
- *
- * @param loc_id
- * IN: Identifier for the dataset containing the reference or for the group that dataset is in.
- * @param ref_type
- * IN: Type of reference.
- * @param ref
- * IN: An object or dataset region reference.
- *
- * @return Returns the name if successful, returning null if no name is associated with
- * the identifier.
- *
- * @exception HDF5LibraryException
- * Error from the HDF-5 Library.
- * @exception NullPointerException
- * size is null.
- * @exception IllegalArgumentException
- * Argument is illegal.
- **/
- public synchronized static native String H5Rget_name_string(long loc_id, int ref_type, byte[] ref)
- throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
-
- /**
* H5Rget_obj_type Given a reference to an object ref, H5Rget_obj_type returns the type of the object
* pointed to.
*
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 2f5ec91..1b85c1f 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -16,7 +16,7 @@ package hdf.hdf5lib;
import hdf.hdf5lib.structs.H5O_token_t;
/**
- * This class contains C constants and enumerated types of HDF5 library. The
+ * /** This class contains C constants and enumerated types of HDF5 library. The
* values of these constants are obtained from the library by calling J2C(int
* jconstant), where jconstant is any of the private constants which start their
* name with "JH5" need to be converted.
@@ -62,62 +62,31 @@ public class HDF5Constants {
public static final int H5_ITER_NATIVE = H5_ITER_NATIVE();
/** Common iteration orders, Number of iteration orders */
public static final int H5_ITER_N = H5_ITER_N();
- /** The version of the H5AC_cache_config_t in use */
+ /** */
public static final int H5AC_CURR_CACHE_CONFIG_VERSION = H5AC_CURR_CACHE_CONFIG_VERSION();
- /** The maximum length of the trace file path */
+ /** */
public static final int H5AC_MAX_TRACE_FILE_NAME_LEN = H5AC_MAX_TRACE_FILE_NAME_LEN();
- /**
- * When metadata_write_strategy is set to this value, only process
- * zero is allowed to write dirty metadata to disk. All other
- * processes must retain dirty metadata until they are informed at
- * a sync point that the dirty metadata in question has been written
- * to disk.
- */
+ /** */
public static final int H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY =
H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY();
- /**
- * In the distributed metadata write strategy, process zero still makes
- * the decisions as to what entries should be flushed, but the actual
- * flushes are distributed across the processes in the computation to
- * the extent possible.
- */
+ /** */
public static final int H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED =
H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED();
- /** Don't attempt to increase the size of the cache automatically */
+ /** */
public static final int H5C_incr_off = H5C_incr_off();
- /**
- * Attempt to increase the size of the cache
- * whenever the average hit rate over the last epoch drops
- * below the value supplied in the lower_hr_threshold
- * field
- */
+ /** */
public static final int H5C_incr_threshold = H5C_incr_threshold();
- /** Don't perform flash increases in the size of the cache */
+ /** */
public static final int H5C_flash_incr_off = H5C_flash_incr_off();
- /** increase the current maximum cache size by x * flash_multiple less any free space in the cache */
+ /** */
public static final int H5C_flash_incr_add_space = H5C_flash_incr_add_space();
- /** Don't attempt to decrease the size of the cache automatically */
+ /** */
public static final int H5C_decr_off = H5C_decr_off();
- /**
- * Attempt to decrease the size of the cache
- * whenever the average hit rate over the last epoch rises
- * above the value supplied in the upper_hr_threshold
- * field
- */
+ /** */
public static final int H5C_decr_threshold = H5C_decr_threshold();
- /**
- * At the end of each epoch, search the cache for
- * entries that have not been accessed for at least the number
- * of epochs specified in the epochs_before_eviction field, and
- * evict these entries
- */
+ /** */
public static final int H5C_decr_age_out = H5C_decr_age_out();
- /**
- * Same as age_out, but we only
- * attempt to reduce the cache size when the hit rate observed
- * over the last epoch exceeds the value provided in the
- * upper_hr_threshold field
- */
+ /** */
public static final int H5C_decr_age_out_with_threshold = H5C_decr_age_out_with_threshold();
/** */
public static final int H5D_CHUNK_IDX_BTREE = H5D_CHUNK_IDX_BTREE();
@@ -941,11 +910,11 @@ public class HDF5Constants {
/** */
public static final int H5R_MAXTYPE = H5R_MAXTYPE();
/** */
- public static final int H5R_DSET_REG_REF_BUF_SIZE = H5R_DSET_REG_REF_BUF_SIZE();
+ public static final int H5R_REF_BUF_SIZE = H5R_REF_BUF_SIZE();
/** */
public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE();
/** */
- public static final int H5R_REF_BUF_SIZE = H5R_REF_BUF_SIZE();
+ public static final int H5R_DSET_REG_REF_BUF_SIZE = H5R_DSET_REG_REF_BUF_SIZE();
/** */
public static final int H5R_OBJECT = H5R_OBJECT();
/** */
@@ -2424,11 +2393,11 @@ public class HDF5Constants {
private static native final int H5R_MAXTYPE();
- private static native final int H5R_DSET_REG_REF_BUF_SIZE();
+ private static native final int H5R_REF_BUF_SIZE();
private static native final int H5R_OBJ_REF_BUF_SIZE();
- private static native final int H5R_REF_BUF_SIZE();
+ private static native final int H5R_DSET_REG_REF_BUF_SIZE();
private static native final int H5R_OBJECT();
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index 32bae07..6bf86d0 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
@@ -158,10 +158,7 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t
{
jboolean readBufIsCopy;
jbyte * readBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -169,20 +166,18 @@ 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 ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 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);
- }
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: variable length type not supported");
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -192,17 +187,11 @@ 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, (void *)readBuf)) < 0)
+ if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, readBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class) {
- H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
- if (sid >= 0)
- H5Sclose(sid);
- }
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -225,10 +214,7 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_
{
jboolean writeBufIsCopy;
jbyte * writeBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -236,19 +222,19 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer is NULL");
- /* 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)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: variable length type not supported");
+
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite: write buffer not critically pinned");
@@ -262,9 +248,6 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -287,10 +270,7 @@ Java_hdf_hdf5lib_H5_H5Aread_1short(JNIEnv *env, jclass clss, jlong attr_id, jlon
{
jboolean readBufIsCopy;
jshort * readBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -298,20 +278,18 @@ 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 ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 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);
- }
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_short: variable length type not supported");
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -326,12 +304,6 @@ Java_hdf_hdf5lib_H5_H5Aread_1short(JNIEnv *env, jclass clss, jlong attr_id, jlon
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class) {
- H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
- if (sid >= 0)
- H5Sclose(sid);
- }
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -354,10 +326,7 @@ Java_hdf_hdf5lib_H5_H5Awrite_1short(JNIEnv *env, jclass clss, jlong attr_id, jlo
{
jboolean writeBufIsCopy;
jshort * writeBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -365,19 +334,19 @@ Java_hdf_hdf5lib_H5_H5Awrite_1short(JNIEnv *env, jclass clss, jlong attr_id, jlo
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: write buffer is NULL");
- /* 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)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: variable length type not supported");
+
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_short: write buffer not critically pinned");
@@ -391,9 +360,6 @@ Java_hdf_hdf5lib_H5_H5Awrite_1short(JNIEnv *env, jclass clss, jlong attr_id, jlo
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -415,32 +381,27 @@ 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;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ herr_t status = FAIL;
UNUSED(clss);
if (buf == NULL)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_int: read buffer is NULL");
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 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);
- }
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_int: variable length type not supported");
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -455,12 +416,6 @@ Java_hdf_hdf5lib_H5_H5Aread_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class) {
- H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
- if (sid >= 0)
- H5Sclose(sid);
- }
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -483,10 +438,7 @@ Java_hdf_hdf5lib_H5_H5Awrite_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong
{
jboolean writeBufIsCopy;
jint * writeBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -494,19 +446,19 @@ Java_hdf_hdf5lib_H5_H5Awrite_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong
if (buf == NULL)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: write buffer is NULL");
- /* 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)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: variable length type not supported");
+
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_int: write buffer not critically pinned");
@@ -520,9 +472,6 @@ Java_hdf_hdf5lib_H5_H5Awrite_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -545,10 +494,7 @@ Java_hdf_hdf5lib_H5_H5Aread_1long(JNIEnv *env, jclass clss, jlong attr_id, jlong
{
jboolean readBufIsCopy;
jlong * readBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -556,20 +502,18 @@ 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 ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 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);
- }
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_long: variable length type not supported");
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -584,12 +528,6 @@ Java_hdf_hdf5lib_H5_H5Aread_1long(JNIEnv *env, jclass clss, jlong attr_id, jlong
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class) {
- H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
- if (sid >= 0)
- H5Sclose(sid);
- }
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -612,10 +550,7 @@ Java_hdf_hdf5lib_H5_H5Awrite_1long(JNIEnv *env, jclass clss, jlong attr_id, jlon
{
jboolean writeBufIsCopy;
jlong * writeBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -623,19 +558,19 @@ Java_hdf_hdf5lib_H5_H5Awrite_1long(JNIEnv *env, jclass clss, jlong attr_id, jlon
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: write buffer is NULL");
- /* 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)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: variable length type not supported");
+
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_long: write buffer not critically pinned");
@@ -649,9 +584,6 @@ Java_hdf_hdf5lib_H5_H5Awrite_1long(JNIEnv *env, jclass clss, jlong attr_id, jlon
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -674,10 +606,7 @@ Java_hdf_hdf5lib_H5_H5Aread_1float(JNIEnv *env, jclass clss, jlong attr_id, jlon
{
jboolean readBufIsCopy;
jfloat * readBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -685,20 +614,18 @@ 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 ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 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);
- }
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_float: variable length type not supported");
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -713,12 +640,6 @@ Java_hdf_hdf5lib_H5_H5Aread_1float(JNIEnv *env, jclass clss, jlong attr_id, jlon
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class) {
- H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
- if (sid >= 0)
- H5Sclose(sid);
- }
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -741,10 +662,7 @@ Java_hdf_hdf5lib_H5_H5Awrite_1float(JNIEnv *env, jclass clss, jlong attr_id, jlo
{
jboolean writeBufIsCopy;
jfloat * writeBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -752,19 +670,19 @@ Java_hdf_hdf5lib_H5_H5Awrite_1float(JNIEnv *env, jclass clss, jlong attr_id, jlo
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: write buffer is NULL");
- /* 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)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: variable length type not supported");
+
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_float: write buffer not critically pinned");
@@ -778,9 +696,6 @@ Java_hdf_hdf5lib_H5_H5Awrite_1float(JNIEnv *env, jclass clss, jlong attr_id, jlo
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -803,10 +718,7 @@ Java_hdf_hdf5lib_H5_H5Aread_1double(JNIEnv *env, jclass clss, jlong attr_id, jlo
{
jboolean readBufIsCopy;
jdouble *readBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -814,20 +726,18 @@ 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 ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 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);
- }
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_double: variable length type not supported");
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
@@ -842,12 +752,6 @@ Java_hdf_hdf5lib_H5_H5Aread_1double(JNIEnv *env, jclass clss, jlong attr_id, jlo
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class) {
- H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
- if (sid >= 0)
- H5Sclose(sid);
- }
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -870,10 +774,7 @@ Java_hdf_hdf5lib_H5_H5Awrite_1double(JNIEnv *env, jclass clss, jlong attr_id, jl
{
jboolean writeBufIsCopy;
jdouble *writeBuf = NULL;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -881,18 +782,19 @@ 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 ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: buf length < 0");
- }
-
- dims[0] = (hsize_t)n;
- if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: variable length type not supported");
+
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Awrite_double: write buffer not critically pinned");
@@ -906,9 +808,6 @@ Java_hdf_hdf5lib_H5_H5Awrite_1double(JNIEnv *env, jclass clss, jlong attr_id, jl
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -1059,454 +958,10 @@ done:
/*
* Class: hdf_hdf5lib_H5
* Method: H5AreadVL
- * Signature: (JJ[java/util/ArrayList;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
-{
- H5T_class_t type_class;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean readBufIsCopy;
- jbyteArray *readBuf = NULL;
-
- UNUSED(clss);
-
- if (NULL == buf)
- H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: read buffer is NULL");
-
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (vl_data_class) {
- /* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
- }
-
- dims[0] = (hsize_t)n;
- if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
-
- if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (type_class == H5T_VLEN) {
- size_t typeSize;
- hid_t memb = H5I_INVALID_HID;
- H5T_class_t vlClass;
- size_t vlSize;
- void * rawBuf = NULL;
- jobject * jList = NULL;
-
- size_t i, j, x;
- char * cp_vp = NULL;
-
- if (!(typeSize = H5Tget_size(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (!(memb = H5Tget_super(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
- if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!(vlSize = H5Tget_size(memb)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AreadVL: failed to allocate raw VL read buffer");
-
- if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)rawBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- /* Cache class types */
- jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
- jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
- jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
- jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
- jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
- jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
- jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
- jmethodID boolValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
- jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
- jmethodID shortValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
- jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
- jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
- jmethodID floatValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
- jmethodID doubleValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
-
- // retrieve the java.util.List interface class
- jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
- jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z");
-
- /* Convert each element to a list */
- for (i = 0; i < (size_t)n; i++) {
- // The list we're going to return:
- if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- cp_vp = (char *)rawBuf + i * typeSize;
- /* Get the number of sequence elements */
- jsize nelmts = ((hvl_t *)cp_vp)->len;
-
- jobject jobj = NULL;
- for (j = 0; j < nelmts; j++) {
- switch (vlClass) {
- /* case H5T_BOOL: {
- jboolean boolValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&boolValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j*vlSize+x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- } */
- case H5T_INTEGER: {
- switch (vlSize) {
- case sizeof(jbyte): {
- jbyte byteValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&byteValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj =
- ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jshort): {
- jshort shortValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&shortValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
- shortValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jint): {
- jint intValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&intValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jlong): {
- jlong longValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&longValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj =
- ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- }
- break;
- }
- case H5T_FLOAT: {
- switch (vlSize) {
- case sizeof(jfloat): {
- jfloat floatValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&floatValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
- floatValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jdouble): {
- jdouble doubleValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&doubleValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
- doubleValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- }
- break;
- }
- case H5T_REFERENCE: {
- jboolean bb;
- jbyte * barray = NULL;
- if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, vlSize)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
- "readVL reference: byte array not pinned");
-
- for (x = 0; x < (int)vlSize; x++) {
- barray[x] = ((jbyte *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
- if (barray)
- UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
- break;
- }
- default:
- H5_UNIMPLEMENTED(ENVONLY, "H5AreadVL: invalid class type");
- break;
- }
-
- // Add it to the list
- ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- } /* end for */
-
- if (rawBuf)
- HDfree(rawBuf);
- }
- else {
- if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
-
-done:
- if (readBuf) {
- if ((status >= 0) && vl_data_class) {
- H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf);
- if (sid >= 0)
- H5Sclose(sid);
- }
-
- UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
- }
-
- return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5AreadVL */
-
-/*
- * Class: hdf_hdf5lib_H5
- * Method: H5AwriteVL
- * Signature: (JJ[java/util/ArrayList;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
-{
- H5T_class_t type_class;
- hsize_t dims[H5S_MAX_RANK];
- hid_t sid = H5I_INVALID_HID;
- jsize n;
- htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean writeBufIsCopy;
- jbyteArray *writeBuf = NULL;
-
- UNUSED(clss);
-
- if (NULL == buf)
- H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL");
-
- /* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: readBuf length < 0");
- }
-
- dims[0] = (hsize_t)n;
- if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (type_class == H5T_VLEN) {
- size_t typeSize;
- hid_t memb = H5I_INVALID_HID;
- H5T_class_t vlClass;
- size_t vlSize;
- void * rawBuf = NULL;
- jobject * jList = NULL;
-
- size_t i, j, x;
- char * cp_vp = NULL;
-
- if (!(typeSize = H5Tget_size(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (!(memb = H5Tget_super(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
- if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!(vlSize = H5Tget_size(memb)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate raw VL write buffer");
-
- /* Cache class types */
- jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
- jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
- jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
- jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
- jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
- jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
- jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
- jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z");
- jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
- jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
- jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
- jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J");
- jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F");
- jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D");
-
- /* Convert each list to a vlen element */
- for (i = 0; i < (size_t)n; i++) {
- if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- // retrieve the java.util.List interface class
- jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
-
- // retrieve the toArray method and invoke it
- jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;");
- if (mToArray == NULL)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
- jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
-
- cp_vp = (char *)rawBuf + i * typeSize;
- ((hvl_t *)cp_vp)->len = jnelmts;
-
- if (NULL == (((hvl_t *)cp_vp)->p = HDmalloc(jnelmts * vlSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate vlen ptr buffer");
-
- jobject jobj = NULL;
- for (j = 0; j < (int)jnelmts; j++) {
- if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- switch (vlClass) {
- /* case H5T_BOOL: {
- jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&boolValue)[x];
- }
- break;
- } */
- case H5T_INTEGER: {
- switch (vlSize) {
- case sizeof(jbyte): {
- jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&byteValue)[x];
- }
- break;
- }
- case sizeof(jshort): {
- jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&shortValue)[x];
- }
- break;
- }
- case sizeof(jint): {
- jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&intValue)[x];
- }
- break;
- }
- case sizeof(jlong): {
- jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&longValue)[x];
- }
- break;
- }
- }
- break;
- }
- case H5T_FLOAT: {
- switch (vlSize) {
- case sizeof(jfloat): {
- jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&floatValue)[x];
- }
- break;
- }
- case sizeof(jdouble): {
- jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&doubleValue)[x];
- }
- break;
- }
- }
- break;
- }
- case H5T_REFERENCE: {
- jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)barray)[x];
- }
- ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
- break;
- }
- default:
- H5_UNIMPLEMENTED(ENVONLY, "H5AwriteVL: invalid class type");
- break;
- }
- ENVPTR->DeleteLocalRef(ENVONLY, jobj);
- }
- ENVPTR->DeleteLocalRef(ENVONLY, jList);
- } /* end for (i = 0; i < n; i++) */
-
- if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, rawBuf)) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- if (rawBuf)
- HDfree(rawBuf);
- }
- else {
- PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5AwriteVL: write buffer not pinned");
- if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
-
-done:
- if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf);
-
- if (type_class != H5T_VLEN)
- UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
- }
-
- return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5AwriteVL */
-
-/*
- * Class: hdf_hdf5lib_H5
- * Method: H5Aread_VLStrings
* Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5Aread_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id,
- jobjectArray buf)
+Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
H5T_class_t type_class;
htri_t isStr = 0;
@@ -1519,7 +974,7 @@ Java_hdf_hdf5lib_H5_H5Aread_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id,
UNUSED(clss);
if (NULL == buf)
- H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_VLStrings: read buffer is NULL");
+ H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: read buffer is NULL");
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -1569,7 +1024,7 @@ done:
H5Tclose(nested_tid);
return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5Aread_1VLStrings */
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1VL */
/*
* Helper method to read in a buffer of variable-length strings from an HDF5
@@ -1705,12 +1160,11 @@ done:
/*
* Class: hdf_hdf5lib_H5
- * Method: H5Awrite_VLStrings
+ * Method: H5AwriteVL
* Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id,
- jobjectArray buf)
+Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
{
H5T_class_t type_class;
htri_t isStr = 0;
@@ -1723,7 +1177,7 @@ Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id,
UNUSED(clss);
if (NULL == buf)
- H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_VLStrings: write buffer is NULL");
+ H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL");
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -1773,7 +1227,7 @@ done:
H5Tclose(nested_tid);
return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings */
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VL */
/*
* Helper method to convert an array of Java strings into a buffer of C-strings.
@@ -1819,7 +1273,7 @@ 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 + 1);
+ HDstrncpy(writeBuf[i], utf8, (size_t)length);
writeBuf[i][length] = '\0';
UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
@@ -1843,8 +1297,8 @@ done:
HDfree(writeBuf);
}
- return status;
-} /* end H5AwriteVL_str */
+ return (jint)status;
+}
/*
* Helper method to convert an array of Java strings into a buffer of
@@ -1931,7 +1385,7 @@ done:
H5Sclose(sid);
return status;
-} /* end H5AwriteVL_asstr */
+} /* end H5AwriteVL_str */
/*
* Class: hdf_hdf5lib_H5
diff --git a/java/src/jni/h5aImp.h b/java/src/jni/h5aImp.h
index 094f990..aee0e40 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/util/ArrayList;)I
+ * Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *, jclass, jlong, jlong, jobjectArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5AwriteVL
- * Signature: (JJ[Ljava/util/ArrayList;)I
+ * Signature: (JJ[Ljava/lang/String;)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 a20bb6c..73b252a 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -183,24 +183,28 @@ 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;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread: read buffer is NULL");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
- }
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: variable length type not supported");
+
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread: read buffer not critically pinned");
@@ -215,9 +219,6 @@ Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong me
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -240,24 +241,28 @@ 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;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer is NULL");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
- }
+ if ((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");
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: variable length type not supported");
+
if (isCriticalPinning) {
PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite: write buffer not critically pinned");
@@ -272,9 +277,6 @@ Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong m
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -381,7 +383,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1short(JNIEnv *env, jclass clss, jlong dataset_id, j
{
jboolean readBufIsCopy;
jshort * readBuf = NULL;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -389,15 +391,19 @@ 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");
- /* 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 ((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");
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_short: variable length type not supported");
+
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_short: read buffer not critically pinned");
@@ -412,9 +418,6 @@ Java_hdf_hdf5lib_H5_H5Dread_1short(JNIEnv *env, jclass clss, jlong dataset_id, j
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -438,7 +441,7 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1short(JNIEnv *env, jclass clss, jlong dataset_id,
{
jboolean writeBufIsCopy;
jshort * writeBuf = NULL;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -446,15 +449,19 @@ 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");
- /* 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 ((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");
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_short: variable length type not supported");
+
if (isCriticalPinning) {
PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_short: write buffer not critically pinned");
@@ -469,9 +476,6 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1short(JNIEnv *env, jclass clss, jlong dataset_id,
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -494,24 +498,28 @@ 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;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_int: read buffer is NULL");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
- }
+ if ((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");
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_int: variable length type not supported");
+
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_int: read buffer not critically pinned");
@@ -526,9 +534,6 @@ Java_hdf_hdf5lib_H5_H5Dread_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlo
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -551,24 +556,28 @@ 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;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_int: write buffer is NULL");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
- }
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_int: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_int: variable length type not supported");
+
if (isCriticalPinning) {
PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_int: write buffer not critically pinned");
@@ -583,9 +592,6 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1int(JNIEnv *env, jclass clss, jlong dataset_id, jl
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -608,24 +614,28 @@ 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;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_long: read buffer is NULL");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
- }
+ if ((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");
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_long: variable length type not supported");
+
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_long: read buffer not critically pinned");
@@ -640,9 +650,6 @@ Java_hdf_hdf5lib_H5_H5Dread_1long(JNIEnv *env, jclass clss, jlong dataset_id, jl
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -665,24 +672,28 @@ 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;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_long: write buffer is NULL");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
- }
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_long: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_long: variable length type not supported");
+
if (isCriticalPinning) {
PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_long: write buffer not critically pinned");
@@ -697,9 +708,6 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1long(JNIEnv *env, jclass clss, jlong dataset_id, j
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -722,24 +730,28 @@ 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;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_float: read buffer is NULL");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
- }
+ 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");
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_float: variable length type not supported");
+
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_float: read buffer not critically pinned");
@@ -754,9 +766,6 @@ Java_hdf_hdf5lib_H5_H5Dread_1float(JNIEnv *env, jclass clss, jlong dataset_id, j
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -779,23 +788,27 @@ 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;
- htri_t vl_data_class;
- herr_t status = FAIL;
+ herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_float: write buffer is NULL");
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
- /* 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 (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_float: variable length type not supported");
+
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_float: variable length type not supported");
if (isCriticalPinning) {
PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
@@ -811,9 +824,6 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1float(JNIEnv *env, jclass clss, jlong dataset_id,
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -837,7 +847,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1double(JNIEnv *env, jclass clss, jlong dataset_id,
{
jboolean readBufIsCopy;
jdouble *readBuf = NULL;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -845,15 +855,19 @@ 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");
- /* Get size of data array */
- if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
- }
+ if ((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");
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_double: variable length type not supported");
+
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
"H5Dread_double: read buffer not critically pinned");
@@ -868,9 +882,6 @@ Java_hdf_hdf5lib_H5_H5Dread_1double(JNIEnv *env, jclass clss, jlong dataset_id,
done:
if (readBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -894,7 +905,7 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *env, jclass clss, jlong dataset_id,
{
jboolean writeBufIsCopy;
jdouble *writeBuf = NULL;
- htri_t vl_data_class;
+ htri_t data_class;
herr_t status = FAIL;
UNUSED(clss);
@@ -902,14 +913,19 @@ 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 (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_double: buf length < 0");
- }
+ 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 ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+ /* Recursively detect any vlen string in type (compound, array ...) */
+ if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
+ if (data_class)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite_double: variable length type not supported");
+
if (isCriticalPinning) {
PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
"H5Dwrite_double: write buffer not critically pinned");
@@ -924,9 +940,6 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *env, jclass clss, jlong dataset_id,
done:
if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
-
if (isCriticalPinning) {
UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
}
@@ -1081,445 +1094,13 @@ done:
/*
* Class: hdf_hdf5lib_H5
* Method: H5DreadVL
- * Signature: (JJJJJ[java/util/ArrayList;)I
+ * Signature: (JJJJJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
{
H5T_class_t type_class;
- jsize n;
- htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean readBufIsCopy;
- jbyteArray *readBuf = NULL;
-
- UNUSED(clss);
-
- if (NULL == buf)
- H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL");
-
- /* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: readBuf length < 0");
- }
-
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (type_class == H5T_VLEN) {
- size_t typeSize;
- hid_t memb = H5I_INVALID_HID;
- H5T_class_t vlClass;
- size_t vlSize;
- void * rawBuf = NULL;
- jobject * jList = NULL;
-
- size_t i, j, x;
- char * cp_vp = NULL;
-
- if (!(typeSize = H5Tget_size(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (!(memb = H5Tget_super(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
- if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!(vlSize = H5Tget_size(memb)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer");
-
- if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
- (hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)rawBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- /* Cache class types */
- jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
- jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
- jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
- jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
- jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
- jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
- jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
- jmethodID boolValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
- jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
- jmethodID shortValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
- jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
- jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
- jmethodID floatValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
- jmethodID doubleValueMid =
- ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
-
- // retrieve the java.util.List interface class
- jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
- jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z");
-
- /* Convert each element to a list */
- for (i = 0; i < (size_t)n; i++) {
- // The list we're going to return:
- if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- cp_vp = (char *)rawBuf + i * typeSize;
- /* Get the number of sequence elements */
- jsize nelmts = ((hvl_t *)cp_vp)->len;
-
- jobject jobj = NULL;
- for (j = 0; j < nelmts; j++) {
- switch (vlClass) {
- /*case H5T_BOOL: {
- jboolean boolValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&boolValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j*vlSize+x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- } */
- case H5T_INTEGER: {
- switch (vlSize) {
- case sizeof(jbyte): {
- jbyte byteValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&byteValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj =
- ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jshort): {
- jshort shortValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&shortValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
- shortValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jint): {
- jint intValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&intValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jlong): {
- jlong longValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&longValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj =
- ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- }
- break;
- }
- case H5T_FLOAT: {
- switch (vlSize) {
- case sizeof(jfloat): {
- jfloat floatValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&floatValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
- floatValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- case sizeof(jdouble): {
- jdouble doubleValue;
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)&doubleValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
-
- jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
- doubleValue);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- }
- }
- break;
- }
- case H5T_REFERENCE: {
- jboolean bb;
- jbyte * barray = NULL;
- if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, vlSize)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
- "readVL reference: byte array not pinned");
-
- for (x = 0; x < (int)vlSize; x++) {
- barray[x] = ((jbyte *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
- }
- if (barray)
- UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
- break;
- }
- default:
- H5_UNIMPLEMENTED(ENVONLY, "H5DreadVL: invalid class type");
- break;
- }
-
- // Add it to the list
- ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj);
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- } /* end for */
-
- if (rawBuf)
- HDfree(rawBuf);
- }
- else {
- if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
- (hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
-
-done:
- if (readBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
- UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
- }
-
- return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5DreadVL */
-
-/*
- * Class: hdf_hdf5lib_H5
- * Method: H5DwriteVL
- * Signature: (JJJJJ[java/util/ArrayList;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
- jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
-{
- H5T_class_t type_class;
- jsize n;
- htri_t vl_data_class;
- herr_t status = FAIL;
- jboolean writeBufIsCopy;
- jbyteArray *writeBuf = NULL;
-
- UNUSED(clss);
-
- if (NULL == buf)
- H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL");
-
- /* Get size of data array */
- if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: readBuf length < 0");
- }
-
- if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (type_class == H5T_VLEN) {
- size_t typeSize;
- hid_t memb = H5I_INVALID_HID;
- H5T_class_t vlClass;
- size_t vlSize;
- void * rawBuf = NULL;
- jobject * jList = NULL;
-
- size_t i, j, x;
- char * cp_vp = NULL;
-
- if (!(typeSize = H5Tget_size(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (!(memb = H5Tget_super(mem_type_id)))
- H5_LIBRARY_ERROR(ENVONLY);
- if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!(vlSize = H5Tget_size(memb)))
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer");
-
- /* Cache class types */
- jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
- jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
- jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
- jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
- jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
- jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
- jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
- jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z");
- jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
- jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
- jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
- jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J");
- jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F");
- jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D");
-
- /* Convert each list to a vlen element */
- for (i = 0; i < (size_t)n; i++) {
- if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- // retrieve the java.util.List interface class
- jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
-
- // retrieve the toArray method and invoke it
- jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;");
- if (mToArray == NULL)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
- jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
-
- cp_vp = (char *)rawBuf + i * typeSize;
- ((hvl_t *)cp_vp)->len = jnelmts;
-
- if (NULL == (((hvl_t *)cp_vp)->p = HDmalloc(jnelmts * vlSize)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate vlen ptr buffer");
- jobject jobj = NULL;
- for (j = 0; j < (int)jnelmts; j++) {
- if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- switch (vlClass) {
- /* case H5T_BOOL: {
- jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&boolValue)[x];
- }
- break;
- } */
- case H5T_INTEGER: {
- switch (vlSize) {
- case sizeof(jbyte): {
- jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&byteValue)[x];
- }
- break;
- }
- case sizeof(jshort): {
- jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&shortValue)[x];
- }
- break;
- }
- case sizeof(jint): {
- jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&intValue)[x];
- }
- break;
- }
- case sizeof(jlong): {
- jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&longValue)[x];
- }
- break;
- }
- }
- break;
- }
- case H5T_FLOAT: {
- switch (vlSize) {
- case sizeof(jfloat): {
- jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&floatValue)[x];
- }
- break;
- }
- case sizeof(jdouble): {
- jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&doubleValue)[x];
- }
- break;
- }
- }
- break;
- }
- case H5T_REFERENCE: {
- jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
- for (x = 0; x < (int)vlSize; x++) {
- ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)barray)[x];
- }
- ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
- break;
- }
- default:
- H5_UNIMPLEMENTED(ENVONLY, "H5DwriteVL: invalid class type");
- break;
- }
- ENVPTR->DeleteLocalRef(ENVONLY, jobj);
- }
- ENVPTR->DeleteLocalRef(ENVONLY, jList);
- } /* end for (i = 0; i < n; i++) */
-
- if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
- (hid_t)file_space_id, (hid_t)xfer_plist_id, rawBuf)) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- if (rawBuf)
- HDfree(rawBuf);
- }
- else {
- PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5DwriteVL: write buffer not pinned");
- if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
- (hid_t)file_space_id, (hid_t)xfer_plist_id, writeBuf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
-
-done:
- if (writeBuf) {
- if ((status >= 0) && vl_data_class)
- H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
-
- if (type_class != H5T_VLEN)
- UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
- }
-
- return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5DwriteVL */
-
-/*
- * Class: hdf_hdf5lib_H5
- * Method: H5Dread_VLStrings
- * Signature: (JJJJJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5Dread_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
- jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
- jobjectArray buf)
-{
- H5T_class_t type_class;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isComplex = 0;
@@ -1530,7 +1111,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_i
UNUSED(clss);
if (NULL == buf)
- H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVLStrings: read buffer is NULL");
+ H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL");
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -1582,7 +1163,7 @@ done:
H5Tclose(nested_tid);
return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1VL */
/*
* Helper method to read in a buffer of variable-length strings from an HDF5
@@ -1734,15 +1315,54 @@ 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: H5Dwrite_VLStrings
+ * Method: H5Dread_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)
+Java_hdf_hdf5lib_H5_H5Dread_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
+ jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id,
+ jobjectArray buf)
+{
+ htri_t isVlenStr = 0;
+ herr_t status = FAIL;
+
+ UNUSED(clss);
+
+ if (NULL == buf)
+ H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread_VLStrings: read buffer is NULL");
+
+ if ((isVlenStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ if (isVlenStr) {
+ if ((status = H5DreadVL_str(env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
+ (hid_t)file_space_id, (hid_t)xfer_plist_id, buf)) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ }
+ else
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread_VLStrings: datatype is not variable length String");
+
+done:
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5DwriteVL
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
+ jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
{
H5T_class_t type_class;
htri_t isStr = 0;
@@ -1755,7 +1375,7 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_
UNUSED(clss);
if (NULL == buf)
- H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVLStrings: write buffer is NULL");
+ H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL");
if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@@ -1807,7 +1427,7 @@ done:
H5Tclose(nested_tid);
return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings */
+} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1VL */
/*
* Helper method to convert an array of Java strings into a buffer of C-strings.
@@ -1820,7 +1440,7 @@ 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;
- jint i;
+ jsize i;
char ** writeBuf = NULL;
herr_t status = FAIL;
@@ -1892,7 +1512,7 @@ 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 jstr = NULL;
+ jstring obj = NULL;
hbool_t close_mem_space = FALSE;
size_t typeSize;
size_t i;
@@ -1929,7 +1549,7 @@ 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 == (jstr = (jstring)ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) {
+ if (NULL == (obj = (jstring)ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
/*
@@ -1940,11 +1560,11 @@ H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_si
}
/*
- * length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
+ * length = ENVPTR->GetStringUTFLength(ENVONLY, obj);
* CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
*/
- PIN_JAVA_STRING(ENVONLY, jstr, utf8, NULL, "H5DwriteVL_asstr: failed to pin string buffer");
+ PIN_JAVA_STRING(ENVONLY, obj, utf8, NULL, "H5DwriteVL_asstr: failed to pin string buffer");
/*
* TODO: If the string isn't a copy, we should probably make
@@ -1954,10 +1574,10 @@ 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, jstr, utf8);
+ UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
utf8 = NULL;
- ENVPTR->DeleteLocalRef(ENVONLY, jstr);
+ ENVPTR->DeleteLocalRef(ENVONLY, obj);
} /* end for (i = 0; i < size; ++i) */
if ((status = H5Dwrite(did, tid, mem_sid, file_sid, xfer_plist_id, writeBuf)) < 0)
@@ -1965,7 +1585,7 @@ 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, jstr, utf8);
+ UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
if (writeBuf) {
H5Treclaim(tid, mem_space, xfer_plist_id, writeBuf);
HDfree(writeBuf);
@@ -1978,6 +1598,39 @@ 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 f79cc2c..e339dad 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/util/ArrayList;)I
+ * Signature: (JJJJJ[Ljava/lang/String;)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/util/ArrayList;)I
+ * Signature: (JJJJJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *, jclass, jlong, jlong, jlong, jlong, jlong,
jobjectArray);
diff --git a/java/src/jni/h5rImp.c b/java/src/jni/h5rImp.c
index 58b5522..9fe0701 100644
--- a/java/src/jni/h5rImp.c
+++ b/java/src/jni/h5rImp.c
@@ -877,67 +877,6 @@ done:
return ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Rget_1name */
-/*
- * Class: hdf_hdf5lib_H5
- * Method: H5Rget_name_string
- * Signature: (JI[B)Ljava/lang/String;
- */
-JNIEXPORT jstring JNICALL
-Java_hdf_hdf5lib_H5_H5Rget_1name_1string(JNIEnv *env, jclass clss, jlong loc_id, jint ref_type,
- jbyteArray ref)
-{
- jboolean isCopy;
- jstring str;
- jsize refBufLen;
- jbyte * refBuf = NULL;
- char * aName = NULL;
- ssize_t buf_size = -1;
- jlong ret_val = -1;
-
- UNUSED(clss);
-
- if (NULL == ref)
- H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rget_name: reference buffer is NULL");
-
- if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, ref)) < 0) {
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Rget_name: ref array length < 0");
- }
-
- if ((H5R_OBJECT == ref_type) && (refBufLen != H5R_OBJ_REF_BUF_SIZE))
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Rget_name: reference input array length != H5R_OBJ_REF_BUF_SIZE");
- else if ((H5R_DATASET_REGION == ref_type) && (refBufLen != H5R_DSET_REG_REF_BUF_SIZE))
- H5_BAD_ARGUMENT_ERROR(
- ENVONLY, "H5Rget_name: region reference input array length != H5R_DSET_REG_REF_BUF_SIZE");
- else if ((H5R_OBJECT != ref_type) && (H5R_DATASET_REGION != ref_type))
- H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Rget_name: unknown reference type");
-
- PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_name: reference buffer not pinned");
-
- /* Get the length of the name */
- if ((buf_size = H5Rget_name((hid_t)loc_id, (H5R_type_t)ref_type, refBuf, NULL, 0)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (NULL == (aName = HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
- H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rget_name: failed to allocate referenced object name buffer");
-
- if ((ret_val = (jlong)H5Rget_name((hid_t)loc_id, (H5R_type_t)ref_type, refBuf, aName,
- (size_t)buf_size + 1)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- aName[(size_t)buf_size] = '\0';
-
- if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, aName)))
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
-done:
- if (aName)
- HDfree(aName);
- if (refBuf)
- UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, JNI_ABORT);
-
- return str;
-} /* end Java_hdf_hdf5lib_H5_H5Rget_1name_1string */
-
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
diff --git a/java/src/jni/h5rImp.h b/java/src/jni/h5rImp.h
index 5865495..ffd7737 100644
--- a/java/src/jni/h5rImp.h
+++ b/java/src/jni/h5rImp.h
@@ -170,13 +170,6 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Rget_1obj_1type2(JNIEnv *, jclass,
JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Rget_1name(JNIEnv *, jclass, jlong, jint, jbyteArray,
jobjectArray, jlong);
-/*
- * Class: hdf_hdf5lib_H5
- * Method: H5Rget_name_string
- * Signature: (JI[B)Ljava/lang/String;
- */
-JNIEXPORT jstring JNICALL Java_hdf_hdf5lib_H5_H5Rget_1name_1string(JNIEnv *, jclass, jlong, jint, jbyteArray);
-
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index a1a1eda..2de5d87 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -52,7 +52,6 @@ void * edata;
/* Local Prototypes */
/********************/
-int h5str_old_region_dataset(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_buf, int expand_data);
int h5str_region_dataset(JNIEnv *env, h5str_t *out_str, H5R_ref_t *ref_vp, int expand_data);
static int h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj,
@@ -64,6 +63,7 @@ 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);
@@ -642,33 +642,6 @@ done:
} /* end h5str_convert */
/*-------------------------------------------------------------------------
- * Function: h5str_sprint_old_reference
- *
- * Purpose: Object reference -- show the name of the 1.10 referenced object.
- *
- * Return: SUCCEED or FAIL
- *-------------------------------------------------------------------------
- */
-int
-h5str_sprint_old_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *ref_buf)
-{
- hid_t region = H5I_INVALID_HID;
- char ref_name[1024];
-
- int ret_value = FAIL;
-
- if ((H5Rget_name(region_obj, H5R_DATASET_REGION, ref_buf, (char *)ref_name, 1024)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (!h5str_append(out_str, ref_name))
- H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
-
- ret_value = SUCCEED;
-done:
-
- return ret_value;
-} /* h5str_sprint_reference */
-
-/*-------------------------------------------------------------------------
* Function: h5str_sprint_reference
*
* Purpose: Object reference -- show the name of the referenced object.
@@ -732,48 +705,6 @@ done:
} /* h5str_sprint_reference */
int
-h5str_old_region_dataset(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_buf, int expand_data)
-{
- H5S_sel_type region_type = H5S_SEL_ERROR;
- hid_t region_obj = H5I_INVALID_HID;
- hid_t region_sid = H5I_INVALID_HID;
-
- int ret_value = FAIL;
-
- if ((region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, ref_buf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if ((region_sid = H5Rget_region(container, H5R_DATASET_REGION, ref_buf)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (expand_data == 0)
- if (h5str_sprint_old_reference(ENVONLY, out_str, region_obj, ref_buf) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
- if ((region_type = H5Sget_select_type(region_sid)) > H5S_SEL_ERROR) {
- if (H5S_SEL_POINTS == region_type) {
- if (h5str_dump_region_points(ENVONLY, out_str, region_sid, region_obj, expand_data) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- else if (H5S_SEL_HYPERSLABS == region_type) {
- if (h5str_dump_region_blocks(ENVONLY, out_str, region_sid, region_obj, expand_data) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- }
-
- ret_value = SUCCEED;
-done:
- if (region_sid >= 0)
- if (H5Sclose(region_sid) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- if (region_obj >= 0)
- if (H5Dclose(region_obj) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- return ret_value;
-}
-
-int
h5str_region_dataset(JNIEnv *env, h5str_t *out_str, H5R_ref_t *ref_vp, int expand_data)
{
hid_t new_obj_id = H5I_INVALID_HID;
@@ -1175,217 +1106,125 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
}
case H5T_REFERENCE: {
- if (H5R_DSET_REG_REF_BUF_SIZE == typeSize) {
- if (h5str_old_region_dataset(ENVONLY, out_str, container, cptr, expand_data) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- }
- else if (H5R_OBJ_REF_BUF_SIZE == typeSize) {
- H5O_info2_t oi;
- hid_t obj = H5I_INVALID_HID;
- char * obj_tok_str = NULL;
-
- /*
- * Object references -- show the type and OID of the referenced
- * object.
- */
-
- if (NULL == (this_str = (char *)HDmalloc(64)))
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
-
- if ((obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, cptr)) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- if (H5Oget_info3(obj, &oi, H5O_INFO_ALL) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
-
- /* Print object data and close object */
- H5Otoken_to_str(obj, &oi.token, &obj_tok_str);
-
- switch (oi.type) {
- case H5O_TYPE_GROUP:
- if (HDsprintf(this_str, "%s %s", H5_TOOLS_GROUP, obj_tok_str) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ /* H5T_STD_REF */
+ hid_t new_obj_id = H5I_INVALID_HID;
+ H5O_type_t obj_type = -1; /* Object type */
+ H5R_type_t ref_type; /* Reference type */
+
+ H5R_ref_t *ref_vp = (H5R_ref_t *)cptr;
+
+ ref_type = H5Rget_type(ref_vp);
+ if (!h5str_is_zero(ref_vp, H5Tget_size(H5T_STD_REF))) {
+ switch (ref_type) {
+ case H5R_OBJECT1:
+ if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
+ switch (obj_type) {
+ case H5O_TYPE_DATASET:
+ if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+
+ case H5O_TYPE_GROUP:
+ case H5O_TYPE_NAMED_DATATYPE:
+ case H5O_TYPE_MAP:
+ case H5O_TYPE_UNKNOWN:
+ case H5O_TYPE_NTYPES:
+ default: {
+ /* Object references -- show the type and OID of the referenced object. */
+ H5O_info2_t oi;
+ char * obj_tok_str = NULL;
+ if ((new_obj_id = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >=
+ 0) {
+ H5Oget_info3(new_obj_id, &oi, H5O_INFO_BASIC);
+ H5Otoken_to_str(new_obj_id, &oi.token, &obj_tok_str);
+ if (H5Dclose(new_obj_id) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ }
+ else
+ H5_LIBRARY_ERROR(ENVONLY);
+
+ size_t this_len = 14;
+ if (NULL == (this_str = (char *)HDmalloc(this_len)))
+ H5_OUT_OF_MEMORY_ERROR(
+ ENVONLY, "h5str_sprintf: failed to allocate string buffer");
+ if (HDsnprintf(this_str, this_len, "%u-", (unsigned)oi.type) < 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
+ if (!h5str_append(out_str, this_str))
+ H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
+ HDfree(this_str);
+ this_str = NULL;
+
+ /* Print OID */
+ {
+ char *token_str;
+
+ H5Otoken_to_str(tid, &oi.token, &token_str);
+
+ size_t that_len = 64 + strlen(token_str) + 1;
+ if (NULL == (this_str = HDmalloc(that_len)))
+ H5_OUT_OF_MEMORY_ERROR(
+ ENVONLY, "h5str_sprintf: failed to allocate string buffer");
+ if (HDsnprintf(this_str, that_len, "%lu:%s", oi.fileno, token_str) <
+ 0)
+ H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
+
+ H5free_memory(token_str);
+ }
+ } break;
+ } /* end switch */
+ }
+ else
+ H5_LIBRARY_ERROR(ENVONLY);
break;
-
- case H5O_TYPE_DATASET:
- if (HDsprintf(this_str, "%s %s", H5_TOOLS_DATASET, obj_tok_str) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ case H5R_DATASET_REGION1:
+ if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
-
- case H5O_TYPE_NAMED_DATATYPE:
- if (HDsprintf(this_str, "%s %s", H5_TOOLS_DATATYPE, obj_tok_str) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
+ case H5R_OBJECT2:
+ if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
+ switch (obj_type) {
+ case H5O_TYPE_GROUP:
+ break;
+
+ case H5O_TYPE_DATASET:
+ if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+
+ case H5O_TYPE_NAMED_DATATYPE:
+ break;
+
+ case H5O_TYPE_MAP:
+ case H5O_TYPE_UNKNOWN:
+ case H5O_TYPE_NTYPES:
+ default:
+ break;
+ } /* end switch */
+ }
+ else
+ H5_ASSERTION_ERROR(ENVONLY, "h5str_sprintf: H5R_OBJECT2 failed");
break;
-
- case H5O_TYPE_UNKNOWN:
- case H5O_TYPE_NTYPES:
+ case H5R_DATASET_REGION2:
+ if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ break;
+ case H5R_ATTR:
+ if ((new_obj_id = H5Ropen_attr(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ if (h5str_dump_region_attribute(ENVONLY, out_str, new_obj_id) < 0)
+ CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+ if (H5Aclose(new_obj_id) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
+ }
+ break;
+ case H5R_BADTYPE:
+ case H5R_MAXTYPE:
default:
- if (HDsprintf(this_str, "%u-%s", (unsigned)oi.type, obj_tok_str) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
break;
- }
-
- if (obj_tok_str) {
- H5free_memory(obj_tok_str);
- obj_tok_str = NULL;
- }
-
- if (H5Oclose(obj) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- obj = H5I_INVALID_HID;
+ } /* end switch */
}
- else {
- /* H5T_STD_REF */
- hid_t new_obj_id = H5I_INVALID_HID;
- H5O_type_t obj_type = -1; /* Object type */
- H5R_type_t ref_type; /* Reference type */
-
- H5R_ref_t *ref_vp = (H5R_ref_t *)cptr;
-
- ref_type = H5Rget_type(ref_vp);
- if (!h5str_is_zero(ref_vp, H5Tget_size(H5T_STD_REF))) {
- switch (ref_type) {
- case H5R_OBJECT1:
- if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
- switch (obj_type) {
- case H5O_TYPE_DATASET:
- if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
-
- case H5O_TYPE_GROUP:
- case H5O_TYPE_NAMED_DATATYPE:
- case H5O_TYPE_MAP:
- case H5O_TYPE_UNKNOWN:
- case H5O_TYPE_NTYPES:
- default: {
- /* Object references -- show the type and
- * OID of the referenced object. */
- H5O_info2_t oi;
- char * obj_tok_str = NULL;
- if ((new_obj_id = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >=
- 0) {
- H5Oget_info3(new_obj_id, &oi, H5O_INFO_BASIC);
- H5Otoken_to_str(new_obj_id, &oi.token, &obj_tok_str);
- if (H5Dclose(new_obj_id) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
- else
- H5_LIBRARY_ERROR(ENVONLY);
-
- size_t this_len = 14;
- if (NULL == (this_str = (char *)HDmalloc(this_len)))
- H5_OUT_OF_MEMORY_ERROR(
- ENVONLY, "h5str_sprintf: failed to allocate string buffer");
- switch (oi.type) {
- case H5O_TYPE_GROUP:
- if (HDsnprintf(this_str, this_len, "%s ", H5_TOOLS_GROUP) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY,
- "h5str_sprintf: HDsnprintf failure");
- break;
-
- case H5O_TYPE_DATASET:
- if (HDsnprintf(this_str, this_len, "%s ", H5_TOOLS_DATASET) <
- 0)
- H5_JNI_FATAL_ERROR(ENVONLY,
- "h5str_sprintf: HDsnprintf failure");
- break;
-
- case H5O_TYPE_NAMED_DATATYPE:
- if (HDsnprintf(this_str, this_len, "%s ", H5_TOOLS_DATATYPE) <
- 0)
- H5_JNI_FATAL_ERROR(ENVONLY,
- "h5str_sprintf: HDsnprintf failure");
- break;
-
- case H5O_TYPE_UNKNOWN:
- case H5O_TYPE_NTYPES:
- default:
- if (HDsnprintf(this_str, this_len, "%u-", (unsigned)oi.type) <
- 0)
- H5_JNI_FATAL_ERROR(ENVONLY,
- "h5str_sprintf: HDsnprintf failure");
- break;
- } /* end switch */
- if (!h5str_append(out_str, this_str))
- H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
- HDfree(this_str);
- this_str = NULL;
-
- /* Print OID */
- {
- char *token_str;
-
- H5Otoken_to_str(tid, &oi.token, &token_str);
-
- size_t that_len = 64 + strlen(token_str) + 1;
- if (NULL == (this_str = HDmalloc(that_len)))
- H5_OUT_OF_MEMORY_ERROR(
- ENVONLY,
- "h5str_sprintf: failed to allocate string buffer");
- if (HDsnprintf(this_str, that_len, "%lu:%s", oi.fileno,
- token_str) < 0)
- H5_JNI_FATAL_ERROR(ENVONLY,
- "h5str_sprintf: HDsnprintf failure");
-
- H5free_memory(token_str);
- }
- } break;
- } /* end switch */
- }
- else
- H5_LIBRARY_ERROR(ENVONLY);
- break;
- case H5R_DATASET_REGION1:
- if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- case H5R_OBJECT2:
- if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
- switch (obj_type) {
- case H5O_TYPE_GROUP:
- break;
-
- case H5O_TYPE_DATASET:
- if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
-
- case H5O_TYPE_NAMED_DATATYPE:
- break;
-
- case H5O_TYPE_MAP:
- case H5O_TYPE_UNKNOWN:
- case H5O_TYPE_NTYPES:
- default:
- break;
- } /* end switch */
- }
- else
- H5_ASSERTION_ERROR(ENVONLY, "h5str_sprintf: H5R_OBJECT2 failed");
- break;
- case H5R_DATASET_REGION2:
- if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- break;
- case H5R_ATTR:
- if ((new_obj_id = H5Ropen_attr(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
- if (h5str_dump_region_attribute(ENVONLY, out_str, new_obj_id) < 0)
- CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
- if (H5Aclose(new_obj_id) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
- break;
- case H5R_BADTYPE:
- case H5R_MAXTYPE:
- default:
- break;
- } /* end switch */
- }
- if (H5Rdestroy(ref_vp) < 0)
- H5_LIBRARY_ERROR(ENVONLY);
- }
+ if (H5Rdestroy(ref_vp) < 0)
+ H5_LIBRARY_ERROR(ENVONLY);
break;
}
@@ -1922,7 +1761,7 @@ h5str_is_zero(const void *_mem, size_t size)
* Negative value: error occurred
*-------------------------------------------------------------------------
*/
-htri_t
+static htri_t
h5str_detect_vlen(hid_t tid)
{
htri_t ret = FAIL;
@@ -3279,65 +3118,29 @@ 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)
{
- 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;
- }
+ 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;
H5Tclose(mtid);
- }
- }
+ } /* end for */
+ } /* end if */
+ else
+ ret_val = H5Tis_variable_str(tid);
-done:
- return ret;
+ return ret_val;
} /* end H5Tdetect_variable_str */
static int
diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h
index 3146c06..6c568e1 100644
--- a/java/src/jni/h5util.h
+++ b/java/src/jni/h5util.h
@@ -39,10 +39,8 @@ extern void h5str_new(h5str_t *str, size_t len);
extern void h5str_free(h5str_t *str);
extern void h5str_resize(h5str_t *str, size_t new_len);
extern char * h5str_append(h5str_t *str, const char *cstr);
-extern htri_t h5str_detect_vlen(hid_t tid);
extern size_t h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_buf,
size_t out_buf_offset);
-extern int h5str_sprint_old_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *ref_buf);
extern int h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, void *ref_p);
extern size_t h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf,
int expand_data);
diff --git a/java/src/jni/nativeData.c b/java/src/jni/nativeData.c
index ac9168b..9e63f4f 100644
--- a/java/src/jni/nativeData.c
+++ b/java/src/jni/nativeData.c
@@ -46,7 +46,8 @@ extern "C" {
/* returns int [] */
JNIEXPORT jintArray JNICALL
-Java_hdf_hdf5lib_HDFNativeData_byteToInt___3B(JNIEnv *env, jclass clss, jbyteArray bdata)
+Java_hdf_hdf5lib_HDFNativeData_byteToInt___3B(JNIEnv *env, jclass clss,
+ jbyteArray bdata) /* IN: array of bytes */
{
jintArray rarray = NULL;
jboolean bb;
diff --git a/java/test/TestH5A.java b/java/test/TestH5A.java
index 96ce5b5..fed13ce 100644
--- a/java/test/TestH5A.java
+++ b/java/test/TestH5A.java
@@ -20,8 +20,6 @@ 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;
@@ -639,8 +637,9 @@ public class TestH5A {
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_INC, 0, lapl_id);
assertNotNull(attr_info);
- assertTrue("Corder ", attr_info.corder ==
- 0); // should equal 0 as this is the order of 1st attribute created.
+ assertTrue("Corder ",
+ attr_info.corder ==
+ 0); // should equal 0 as this is the order of 1st attribute created.
assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr_id));
// Verify info for 2nd attribute, in increasing creation order
@@ -654,29 +653,33 @@ public class TestH5A {
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_DEC, 0, lapl_id);
assertNotNull(attr_info);
- assertTrue("Corder", attr_info.corder ==
- 1); // should equal 1 as this is the order of 2nd attribute created.
+ assertTrue("Corder",
+ attr_info.corder ==
+ 1); // should equal 1 as this is the order of 2nd attribute created.
// verify info for 1st attribute, in decreasing creation order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_DEC, 1, lapl_id);
assertNotNull(attr_info);
- assertTrue("Corder", attr_info.corder ==
- 0); // should equal 0 as this is the order of 1st attribute created.
+ assertTrue("Corder",
+ attr_info.corder ==
+ 0); // should equal 0 as this is the order of 1st attribute created.
// verify info for 1st attribute, in increasing name order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_NAME,
HDF5Constants.H5_ITER_INC, 1, lapl_id);
assertNotNull(attr_info);
- assertTrue("Corder", attr_info.corder ==
- 0); // should equal 0 as this is the order of 1st attribute created.
+ assertTrue("Corder",
+ attr_info.corder ==
+ 0); // should equal 0 as this is the order of 1st attribute created.
// verify info for 2nd attribute, in decreasing name order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_NAME,
HDF5Constants.H5_ITER_DEC, 1, lapl_id);
assertNotNull(attr_info);
- assertTrue("Corder", attr_info.corder ==
- 1); // should equal 1 as this is the order of 2nd attribute created.
+ assertTrue("Corder",
+ attr_info.corder ==
+ 1); // should equal 1 as this is the order of 2nd attribute created.
}
catch (Throwable err) {
err.printStackTrace();
@@ -1072,7 +1075,7 @@ public class TestH5A {
HDF5Constants.H5P_DEFAULT);
assertTrue("testH5Awrite_readVL: ", attr_id >= 0);
- H5.H5Awrite_VLStrings(attr_id, atype_id, str_data);
+ H5.H5AwriteVL(attr_id, atype_id, str_data);
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
@@ -1084,7 +1087,7 @@ public class TestH5A {
strs[j] = "";
}
try {
- H5.H5Aread_VLStrings(attr_id, atype_id, strs);
+ H5.H5AreadVL(attr_id, atype_id, strs);
}
catch (Exception ex) {
ex.printStackTrace();
@@ -1159,12 +1162,12 @@ 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);
}
@@ -1368,212 +1371,4 @@ 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 f7e5702..4bab1a9 100644
--- a/java/test/TestH5D.java
+++ b/java/test/TestH5D.java
@@ -17,9 +17,6 @@ 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;
@@ -964,8 +961,8 @@ public class TestH5D {
assertTrue("H5Dvlen_get_buf_size " + vl_size + " == " + str_data_bytes, vl_size == str_data_bytes);
}
- @Test
- public void testH5Dvlen_read_default_buffer() throws Throwable
+ @Test(expected = IllegalArgumentException.class)
+ public void testH5Dvlen_read_invalid_buffer() throws Throwable
{
String[] str_data = {"Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.",
"Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!",
@@ -1016,218 +1013,4 @@ 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 dd8634b..4e610bc 100644
--- a/java/test/TestH5R.java
+++ b/java/test/TestH5R.java
@@ -19,9 +19,6 @@ 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;
@@ -531,470 +528,4 @@ public class TestH5R {
byte[] ref = null;
H5.H5Rget_attr_name(ref);
}
-
- @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 efdd4a2..2026d21 100644
--- a/java/test/testfiles/JUnit-TestH5A.txt
+++ b/java/test/testfiles/JUnit-TestH5A.txt
@@ -6,7 +6,6 @@ JUnit version 4.11
.testH5Aiterate
.testH5Aopen_by_idx
.testH5Aopen_invalidname
-.testH5AVLwr
.testH5Aopen
.testH5Aget_info_by_name
.testH5Aget_create_plist
@@ -31,5 +30,5 @@ JUnit version 4.11
Time: XXXX
-OK (29 tests)
+OK (28 tests)
diff --git a/java/test/testfiles/JUnit-TestH5D.txt b/java/test/testfiles/JUnit-TestH5D.txt
index 288e6d0..987655b 100644
--- a/java/test/testfiles/JUnit-TestH5D.txt
+++ b/java/test/testfiles/JUnit-TestH5D.txt
@@ -4,7 +4,6 @@ JUnit version 4.11
.testH5Dcreate
.testH5Dget_offset
.testH5Dget_type
-.testH5DVLwr
.testH5Dfill
.testH5Dopen
.testH5Dcreate_anon
@@ -12,15 +11,15 @@ 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 (20 tests)
+OK (19 tests)
diff --git a/java/test/testfiles/JUnit-TestH5R.txt b/java/test/testfiles/JUnit-TestH5R.txt
index 2420d62..a96fbb4 100644
--- a/java/test/testfiles/JUnit-TestH5R.txt
+++ b/java/test/testfiles/JUnit-TestH5R.txt
@@ -4,8 +4,6 @@ JUnit version 4.11
.testH5Ropen_region_Nullref
.testH5Requal_Nullref1
.testH5Requal_Nullref2
-.testH5RVLdset_ref
-.testH5RVLattr_ref
.testH5Rget_object
.testH5Rget_obj_type3_Nullref
.testH5Ropen_object_Nullref
@@ -26,5 +24,5 @@ JUnit version 4.11
Time: XXXX
-OK (24 tests)
+OK (22 tests)