diff options
Diffstat (limited to 'java/src/jni/h5aImp.c')
-rw-r--r-- | java/src/jni/h5aImp.c | 818 |
1 files changed, 682 insertions, 136 deletions
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c index 6bf86d0..32bae07 100644 --- a/java/src/jni/h5aImp.c +++ b/java/src/jni/h5aImp.c @@ -56,7 +56,7 @@ static herr_t H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *inf /* * Class: hdf_hdf5lib_H5 - * Method: H5Acreate + * Method: _H5Acreate * Signature: (JLjava/lang/String;JJJ)J */ JNIEXPORT jlong JNICALL @@ -86,7 +86,7 @@ done: /* * Class: hdf_hdf5lib_H5 - * Method: H5Aopen_name + * Method: _H5Aopen_name * Signature: (JLjava/lang/String;)J */ JNIEXPORT jlong JNICALL @@ -124,7 +124,7 @@ done: /* * Class: hdf_hdf5lib_H5 - * Method: H5Aopen_idx + * Method: _H5Aopen_idx * Signature: (JI)J */ JNIEXPORT jlong JNICALL @@ -158,7 +158,10 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t { jboolean readBufIsCopy; jbyte * readBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -166,18 +169,20 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread: read buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: variable length type not supported"); - - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (vl_data_class) { + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: variable length type not supported"); + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } if (isCriticalPinning) { PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, @@ -187,11 +192,17 @@ Java_hdf_hdf5lib_H5_H5Aread(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_t PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Aread: read buffer not pinned"); } - if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, readBuf)) < 0) + if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0) H5_LIBRARY_ERROR(ENVONLY); done: if (readBuf) { + if ((status >= 0) && vl_data_class) { + H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf); + if (sid >= 0) + H5Sclose(sid); + } + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); } @@ -214,7 +225,10 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_ { jboolean writeBufIsCopy; jbyte * writeBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -222,18 +236,18 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_ if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: variable length type not supported"); + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: variable length type not supported"); + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (isCriticalPinning) { PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, @@ -248,6 +262,9 @@ Java_hdf_hdf5lib_H5_H5Awrite(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_ done: if (writeBuf) { + if ((status >= 0) && vl_data_class) + H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); } @@ -270,7 +287,10 @@ Java_hdf_hdf5lib_H5_H5Aread_1short(JNIEnv *env, jclass clss, jlong attr_id, jlon { jboolean readBufIsCopy; jshort * readBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -278,18 +298,20 @@ Java_hdf_hdf5lib_H5_H5Aread_1short(JNIEnv *env, jclass clss, jlong attr_id, jlon if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_short: read buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_short: variable length type not supported"); - - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (vl_data_class) { + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_short: variable length type not supported"); + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } if (isCriticalPinning) { PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, @@ -304,6 +326,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1short(JNIEnv *env, jclass clss, jlong attr_id, jlon done: if (readBuf) { + if ((status >= 0) && vl_data_class) { + H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf); + if (sid >= 0) + H5Sclose(sid); + } + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); } @@ -326,7 +354,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1short(JNIEnv *env, jclass clss, jlong attr_id, jlo { jboolean writeBufIsCopy; jshort * writeBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -334,18 +365,18 @@ Java_hdf_hdf5lib_H5_H5Awrite_1short(JNIEnv *env, jclass clss, jlong attr_id, jlo if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: write buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: variable length type not supported"); + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_short: variable length type not supported"); + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (isCriticalPinning) { PIN_SHORT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, @@ -360,6 +391,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1short(JNIEnv *env, jclass clss, jlong attr_id, jlo done: if (writeBuf) { + if ((status >= 0) && vl_data_class) + H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); } @@ -381,27 +415,32 @@ Java_hdf_hdf5lib_H5_H5Aread_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong jboolean isCriticalPinning) { jboolean readBufIsCopy; - htri_t data_class; jint * readBuf = NULL; - herr_t status = FAIL; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; + herr_t status = FAIL; UNUSED(clss); if (buf == NULL) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_int: read buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_int: variable length type not supported"); - - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (vl_data_class) { + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_int: variable length type not supported"); + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } if (isCriticalPinning) { PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, @@ -416,6 +455,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong done: if (readBuf) { + if ((status >= 0) && vl_data_class) { + H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf); + if (sid >= 0) + H5Sclose(sid); + } + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); } @@ -438,7 +483,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong { jboolean writeBufIsCopy; jint * writeBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -446,18 +494,18 @@ Java_hdf_hdf5lib_H5_H5Awrite_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong if (buf == NULL) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: write buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: variable length type not supported"); + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_int: variable length type not supported"); + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (isCriticalPinning) { PIN_INT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, @@ -472,6 +520,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1int(JNIEnv *env, jclass clss, jlong attr_id, jlong done: if (writeBuf) { + if ((status >= 0) && vl_data_class) + H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); } @@ -494,7 +545,10 @@ Java_hdf_hdf5lib_H5_H5Aread_1long(JNIEnv *env, jclass clss, jlong attr_id, jlong { jboolean readBufIsCopy; jlong * readBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -502,18 +556,20 @@ Java_hdf_hdf5lib_H5_H5Aread_1long(JNIEnv *env, jclass clss, jlong attr_id, jlong if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_long: read buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_long: variable length type not supported"); - - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (vl_data_class) { + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_long: variable length type not supported"); + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } if (isCriticalPinning) { PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, @@ -528,6 +584,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1long(JNIEnv *env, jclass clss, jlong attr_id, jlong done: if (readBuf) { + if ((status >= 0) && vl_data_class) { + H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf); + if (sid >= 0) + H5Sclose(sid); + } + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); } @@ -550,7 +612,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1long(JNIEnv *env, jclass clss, jlong attr_id, jlon { jboolean writeBufIsCopy; jlong * writeBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -558,18 +623,18 @@ Java_hdf_hdf5lib_H5_H5Awrite_1long(JNIEnv *env, jclass clss, jlong attr_id, jlon if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: write buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: variable length type not supported"); + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_long: variable length type not supported"); + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (isCriticalPinning) { PIN_LONG_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, @@ -584,6 +649,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1long(JNIEnv *env, jclass clss, jlong attr_id, jlon done: if (writeBuf) { + if ((status >= 0) && vl_data_class) + H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); } @@ -606,7 +674,10 @@ Java_hdf_hdf5lib_H5_H5Aread_1float(JNIEnv *env, jclass clss, jlong attr_id, jlon { jboolean readBufIsCopy; jfloat * readBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -614,18 +685,20 @@ Java_hdf_hdf5lib_H5_H5Aread_1float(JNIEnv *env, jclass clss, jlong attr_id, jlon if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_float: read buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_float: variable length type not supported"); - - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (vl_data_class) { + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_float: variable length type not supported"); + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } if (isCriticalPinning) { PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, @@ -640,6 +713,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1float(JNIEnv *env, jclass clss, jlong attr_id, jlon done: if (readBuf) { + if ((status >= 0) && vl_data_class) { + H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf); + if (sid >= 0) + H5Sclose(sid); + } + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); } @@ -662,7 +741,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1float(JNIEnv *env, jclass clss, jlong attr_id, jlo { jboolean writeBufIsCopy; jfloat * writeBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -670,18 +752,18 @@ Java_hdf_hdf5lib_H5_H5Awrite_1float(JNIEnv *env, jclass clss, jlong attr_id, jlo if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: write buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: variable length type not supported"); + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_float: variable length type not supported"); + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (isCriticalPinning) { PIN_FLOAT_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, @@ -696,6 +778,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1float(JNIEnv *env, jclass clss, jlong attr_id, jlo done: if (writeBuf) { + if ((status >= 0) && vl_data_class) + H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); } @@ -718,7 +803,10 @@ Java_hdf_hdf5lib_H5_H5Aread_1double(JNIEnv *env, jclass clss, jlong attr_id, jlo { jboolean readBufIsCopy; jdouble *readBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -726,18 +814,20 @@ Java_hdf_hdf5lib_H5_H5Aread_1double(JNIEnv *env, jclass clss, jlong attr_id, jlo if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_double: read buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_double: variable length type not supported"); - - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (vl_data_class) { + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread_double: variable length type not supported"); + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } if (isCriticalPinning) { PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy, @@ -752,6 +842,12 @@ Java_hdf_hdf5lib_H5_H5Aread_1double(JNIEnv *env, jclass clss, jlong attr_id, jlo done: if (readBuf) { + if ((status >= 0) && vl_data_class) { + H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf); + if (sid >= 0) + H5Sclose(sid); + } + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); } @@ -774,7 +870,10 @@ Java_hdf_hdf5lib_H5_H5Awrite_1double(JNIEnv *env, jclass clss, jlong attr_id, jl { jboolean writeBufIsCopy; jdouble *writeBuf = NULL; - htri_t data_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; herr_t status = FAIL; UNUSED(clss); @@ -782,18 +881,17 @@ Java_hdf_hdf5lib_H5_H5Awrite_1double(JNIEnv *env, jclass clss, jlong attr_id, jl if (NULL == buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: write buffer is NULL"); - if ((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: variable length type not supported"); + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: buf length < 0"); + } - /* Recursively detect any vlen string in type (compound, array ...) */ - if ((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (data_class) - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite_double: variable length type not supported"); + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (isCriticalPinning) { PIN_DOUBLE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy, @@ -808,6 +906,9 @@ Java_hdf_hdf5lib_H5_H5Awrite_1double(JNIEnv *env, jclass clss, jlong attr_id, jl done: if (writeBuf) { + if ((status >= 0) && vl_data_class) + H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); + if (isCriticalPinning) { UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); } @@ -958,12 +1059,456 @@ done: /* * Class: hdf_hdf5lib_H5 * Method: H5AreadVL - * Signature: (JJ[Ljava/lang/String;)I + * Signature: (JJ[java/util/ArrayList;)I */ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) { H5T_class_t type_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; + herr_t status = FAIL; + jboolean readBufIsCopy; + jbyteArray *readBuf = NULL; + + UNUSED(clss); + + if (NULL == buf) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: read buffer is NULL"); + + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (vl_data_class) { + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + } + + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } + + if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (type_class == H5T_VLEN) { + size_t typeSize; + hid_t memb = H5I_INVALID_HID; + H5T_class_t vlClass; + size_t vlSize; + void * rawBuf = NULL; + jobject * jList = NULL; + + size_t i, j, x; + char * cp_vp = NULL; + + if (!(typeSize = H5Tget_size(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class((hid_t)memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AreadVL: failed to allocate raw VL read buffer"); + + if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)rawBuf)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + /* Cache class types */ + jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); + jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); + jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); + jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); + jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); + jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); + jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); + + jmethodID boolValueMid = + ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;"); + jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;"); + jmethodID shortValueMid = + ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;"); + jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;"); + jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;"); + jmethodID floatValueMid = + ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;"); + jmethodID doubleValueMid = + ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;"); + + // retrieve the java.util.List interface class + jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List"); + jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z"); + + /* Convert each element to a list */ + for (i = 0; i < (size_t)n; i++) { + // The list we're going to return: + if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + cp_vp = (char *)rawBuf + i * typeSize; + /* Get the number of sequence elements */ + jsize nelmts = ((hvl_t *)cp_vp)->len; + + jobject jobj = NULL; + for (j = 0; j < nelmts; j++) { + switch (vlClass) { + /* case H5T_BOOL: { + jboolean boolValue; + for (x = 0; x < (int)vlSize; x++) { + ((char *)&boolValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j*vlSize+x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } */ + case H5T_INTEGER: { + switch (vlSize) { + case sizeof(jbyte): { + jbyte byteValue; + for (x = 0; x < (int)vlSize; x++) { + ((char *)&byteValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x]; + } + + jobj = + ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jshort): { + jshort shortValue; + for (x = 0; x < (int)vlSize; x++) { + ((char *)&shortValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid, + shortValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jint): { + jint intValue; + for (x = 0; x < (int)vlSize; x++) { + ((char *)&intValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jlong): { + jlong longValue; + for (x = 0; x < (int)vlSize; x++) { + ((char *)&longValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x]; + } + + jobj = + ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + } + break; + } + case H5T_FLOAT: { + switch (vlSize) { + case sizeof(jfloat): { + jfloat floatValue; + for (x = 0; x < (int)vlSize; x++) { + ((char *)&floatValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid, + floatValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jdouble): { + jdouble doubleValue; + for (x = 0; x < (int)vlSize; x++) { + ((char *)&doubleValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x]; + } + + jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid, + doubleValue); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + } + break; + } + case H5T_REFERENCE: { + jboolean bb; + jbyte * barray = NULL; + if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, vlSize))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb, + "readVL reference: byte array not pinned"); + + for (x = 0; x < (int)vlSize; x++) { + barray[x] = ((jbyte *)((hvl_t *)cp_vp)->p)[j * vlSize + x]; + } + if (barray) + UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT); + break; + } + default: + H5_UNIMPLEMENTED(ENVONLY, "H5AreadVL: invalid class type"); + break; + } + + // Add it to the list + ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + } /* end for */ + + if (rawBuf) + HDfree(rawBuf); + } + else { + if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } + +done: + if (readBuf) { + if ((status >= 0) && vl_data_class) { + H5Treclaim(attr_id, sid, H5P_DEFAULT, readBuf); + if (sid >= 0) + H5Sclose(sid); + } + + UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0); + } + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5AreadVL */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5AwriteVL + * Signature: (JJ[java/util/ArrayList;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) +{ + H5T_class_t type_class; + hsize_t dims[H5S_MAX_RANK]; + hid_t sid = H5I_INVALID_HID; + jsize n; + htri_t vl_data_class; + herr_t status = FAIL; + jboolean writeBufIsCopy; + jbyteArray *writeBuf = NULL; + + UNUSED(clss); + + if (NULL == buf) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL"); + + /* Get size of data array */ + if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: readBuf length < 0"); + } + + dims[0] = (hsize_t)n; + if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (type_class == H5T_VLEN) { + size_t typeSize; + hid_t memb = H5I_INVALID_HID; + H5T_class_t vlClass; + size_t vlSize; + void * rawBuf = NULL; + jobject * jList = NULL; + + size_t i, j, x; + char * cp_vp = NULL; + + if (!(typeSize = H5Tget_size(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class((hid_t)memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate raw VL write buffer"); + + /* Cache class types */ + jclass cBool = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); + jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); + jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); + jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); + jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); + jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); + jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); + + jmethodID boolValueMid = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); + jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B"); + jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S"); + jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I"); + jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J"); + jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F"); + jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D"); + + /* Convert each list to a vlen element */ + for (i = 0; i < (size_t)n; i++) { + if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + // retrieve the java.util.List interface class + jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List"); + + // retrieve the toArray method and invoke it + jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;"); + if (mToArray == NULL) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray); + jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array); + + cp_vp = (char *)rawBuf + i * typeSize; + ((hvl_t *)cp_vp)->len = jnelmts; + + if (NULL == (((hvl_t *)cp_vp)->p = HDmalloc(jnelmts * vlSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate vlen ptr buffer"); + + jobject jobj = NULL; + for (j = 0; j < (int)jnelmts; j++) { + if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + switch (vlClass) { + /* case H5T_BOOL: { + jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid); + for (x = 0; x < (int)vlSize; x++) { + ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&boolValue)[x]; + } + break; + } */ + case H5T_INTEGER: { + switch (vlSize) { + case sizeof(jbyte): { + jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid); + for (x = 0; x < (int)vlSize; x++) { + ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&byteValue)[x]; + } + break; + } + case sizeof(jshort): { + jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid); + for (x = 0; x < (int)vlSize; x++) { + ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&shortValue)[x]; + } + break; + } + case sizeof(jint): { + jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid); + for (x = 0; x < (int)vlSize; x++) { + ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&intValue)[x]; + } + break; + } + case sizeof(jlong): { + jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid); + for (x = 0; x < (int)vlSize; x++) { + ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&longValue)[x]; + } + break; + } + } + break; + } + case H5T_FLOAT: { + switch (vlSize) { + case sizeof(jfloat): { + jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid); + for (x = 0; x < (int)vlSize; x++) { + ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&floatValue)[x]; + } + break; + } + case sizeof(jdouble): { + jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid); + for (x = 0; x < (int)vlSize; x++) { + ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&doubleValue)[x]; + } + break; + } + } + break; + } + case H5T_REFERENCE: { + jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0); + for (x = 0; x < (int)vlSize; x++) { + ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)barray)[x]; + } + ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0); + break; + } + default: + H5_UNIMPLEMENTED(ENVONLY, "H5AwriteVL: invalid class type"); + break; + } + ENVPTR->DeleteLocalRef(ENVONLY, jobj); + } + ENVPTR->DeleteLocalRef(ENVONLY, jList); + } /* end for (i = 0; i < n; i++) */ + + if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, rawBuf)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + if (rawBuf) + HDfree(rawBuf); + } + else { + PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5AwriteVL: write buffer not pinned"); + if ((status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, writeBuf)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } + +done: + if (writeBuf) { + if ((status >= 0) && vl_data_class) + H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); + + if (type_class != H5T_VLEN) + UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0); + } + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5AwriteVL */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Aread_VLStrings + * Signature: (JJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Aread_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, + jobjectArray buf) +{ + H5T_class_t type_class; htri_t isStr = 0; htri_t isVlenStr = 0; htri_t isComplex = 0; @@ -974,7 +1519,7 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem UNUSED(clss); if (NULL == buf) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: read buffer is NULL"); + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aread_VLStrings: read buffer is NULL"); if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1024,7 +1569,7 @@ done: H5Tclose(nested_tid); return (jint)status; -} /* end Java_hdf_hdf5lib_H5_H5Aread_1VL */ +} /* end Java_hdf_hdf5lib_H5_H5Aread_1VLStrings */ /* * Helper method to read in a buffer of variable-length strings from an HDF5 @@ -1160,11 +1705,12 @@ done: /* * Class: hdf_hdf5lib_H5 - * Method: H5AwriteVL + * Method: H5Awrite_VLStrings * Signature: (JJ[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL -Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) +Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, + jobjectArray buf) { H5T_class_t type_class; htri_t isStr = 0; @@ -1177,7 +1723,7 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me UNUSED(clss); if (NULL == buf) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: write buffer is NULL"); + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Awrite_VLStrings: write buffer is NULL"); if ((isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING)) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1227,7 +1773,7 @@ done: H5Tclose(nested_tid); return (jint)status; -} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VL */ +} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings */ /* * Helper method to convert an array of Java strings into a buffer of C-strings. @@ -1273,7 +1819,7 @@ H5AwriteVL_str(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) if (NULL == (writeBuf[i] = (char *)HDmalloc((size_t)length + 1))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL_str: failed to allocate string buffer"); - HDstrncpy(writeBuf[i], utf8, (size_t)length); + HDstrncpy(writeBuf[i], utf8, (size_t)length + 1); writeBuf[i][length] = '\0'; UNPIN_JAVA_STRING(ENVONLY, obj, utf8); @@ -1297,8 +1843,8 @@ done: HDfree(writeBuf); } - return (jint)status; -} + return status; +} /* end H5AwriteVL_str */ /* * Helper method to convert an array of Java strings into a buffer of @@ -1385,7 +1931,7 @@ done: H5Sclose(sid); return status; -} /* end H5AwriteVL_str */ +} /* end H5AwriteVL_asstr */ /* * Class: hdf_hdf5lib_H5 |