/*
* Class: hdf_hdf5lib_H5
* Method: H5Eget_msg
* Signature: (J[I)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Eget_1msg
(JNIEnv *env, jclass cls, jlong msg_id, jintArray error_msg_type_list)
{
char *namePtr;
jstring str = NULL;
jboolean isCopy;
ssize_t buf_size;
jint *theArray;
H5E_type_t error_msg_type;
if (msg_id < 0) {
h5badArgument(env, "H5Eget_msg: invalid argument");
} /* end if */
else if (error_msg_type_list == NULL) {
h5nullArgument(env, "H5Eget_msg: error_msg_type_list is NULL");
} /* end if */
else {
/* get the length of the name */
buf_size = H5Eget_msg((hid_t)msg_id, NULL, NULL, 0);
if ((buf_size < 0) || (buf_size == 0)) {
h5JNIFatalError(env, "H5Eget_msg: Invalid message");
} /* end if */
else {
buf_size++; /* add extra space for the null terminator */
namePtr = (char*)HDmalloc(sizeof(char) * (size_t)buf_size);
if (namePtr == NULL) {
h5outOfMemory(env, "H5Eget_msg: malloc failed");
} /* end if */
else {
theArray = (jint*)ENVPTR->GetIntArrayElements(ENVPAR error_msg_type_list, &isCopy);
if (theArray == NULL) {
HDfree(namePtr);
h5JNIFatalError(env, "H5Eget_msg: error_msg_type_list not pinned");
} /* end if */
else {
buf_size = H5Eget_msg((hid_t)msg_id, &error_msg_type, (char *)namePtr, (size_t)buf_size);
if (buf_size < 0) {
HDfree(namePtr);
ENVPTR->ReleaseIntArrayElements(ENVPAR error_msg_type_list, theArray, JNI_ABORT);
h5libraryError(env);
} /* end if */
else {
theArray[0] = error_msg_type;
ENVPTR->ReleaseIntArrayElements(ENVPAR error_msg_type_list, theArray, 0);
str = ENVPTR->NewStringUTF(ENVPAR namePtr);
HDfree(namePtr);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
} /* end else */
return str;
} /* end Java_hdf_hdf5lib_H5_H5Eget_1msg */
herr_t
H5AreadVL_str
(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
{
char **strs;
jstring jstr;
jint i;
jint n;
hid_t sid;
hsize_t dims[H5S_MAX_RANK];
herr_t status = -1;
n = ENVPTR->GetArrayLength(ENVPAR buf);
strs =(char**)HDcalloc((size_t)n, sizeof(char*));
if (strs == NULL) {
h5JNIFatalError(env, "H5AreadVL_str: failed to allocate buff for read variable length strings");
} /* end if */
else {
status = H5Aread(aid, tid, strs);
if (status < 0) {
dims[0] = (hsize_t)n;
sid = H5Screate_simple(1, dims, NULL);
H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
H5Sclose(sid);
HDfree(strs);
h5JNIFatalError(env, "H5AreadVL_str: failed to read variable length strings");
} /* end if */
else {
for (i=0; i < n; i++) {
jstr = ENVPTR->NewStringUTF(ENVPAR strs[i]);
ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
H5free_memory (strs[i]);
} /* end for */
/*
for repeatedly reading a dataset with a large number of strs (e.g., 1,000,000 strings,
H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect
free space in time. Instead, use "H5free_memory(strs[i])" above to free individual strings
after it is done.
H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs);
*/
HDfree(strs);
} /* end else */
} /* end else */
return status;
} /* end H5AreadVL_str */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Rdereference
* Signature: (JJI[B)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Rdereference(JNIEnv *env, jclass clss, jlong dataset, jlong access_list, jint ref_type, jbyteArray ref)
{
jboolean isCopy;
jbyte *refP;
hid_t retVal = -1;
if (ref == NULL) {
h5nullArgument( env, "H5Rdereference: ref is NULL");
} /* end if */
else if ((ref_type == H5R_OBJECT) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_OBJ_REF_BUF_SIZE) {
h5badArgument( env, "H5Rdereference: obj ref input array != H5R_OBJ_REF_BUF_SIZE");
} /* end else if */
else if ((ref_type == H5R_DATASET_REGION) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) {
h5badArgument( env, "H5Rdereference: region ref input array != H5R_DSET_REG_REF_BUF_SIZE");
} /* end else if */
else {
refP = (jbyte*)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy);
if (refP == NULL) {
h5JNIFatalError(env, "H5Rderefernce: ref not pinned");
} /* end if */
else {
retVal = H5Rdereference2((hid_t)dataset, (hid_t)access_list, (H5R_type_t)ref_type, refP);
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
if (retVal < 0)
h5libraryError(env);
} /* end else */
} /* end else */
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Rdereference */
/*
* Class: hdf_hdf5lib_H5
* Method: H5get_libversion
* Signature: ([I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5get_1libversion
(JNIEnv *env, jclass clss, jintArray libversion)
{
unsigned *theArray = NULL;
herr_t status = -1;
jboolean isCopy;
if (libversion == NULL) {
h5nullArgument(env, "H5get_version: libversion is NULL");
} /* end if */
else {
theArray = (unsigned*)ENVPTR->GetIntArrayElements(ENVPAR libversion, &isCopy);
if (theArray == NULL) {
h5JNIFatalError( env, "H5get_libversion: input not pinned");
} /* end if */
else {
status = H5get_libversion(&(theArray[0]), &(theArray[1]), &(theArray[2]));
if (status < 0) {
ENVPTR->ReleaseIntArrayElements(ENVPAR libversion, (jint*)theArray, JNI_ABORT);
h5libraryError(env);
} /* end if */
ENVPTR->ReleaseIntArrayElements(ENVPAR libversion, (jint*)theArray,0);
} /* end else */
} /* end else */
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5get_1libversion */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aread
* Signature: (JJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Aread
(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf)
{
herr_t status = -1;
jbyte *byteP;
jboolean isCopy;
if (buf == NULL) {
h5nullArgument( env,"H5Aread: buf is NULL");
} /* end if */
else {
byteP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy);
if (byteP == NULL) {
h5JNIFatalError( env,"H5Aread: buf is not pinned");
} /* end if */
else {
status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP);
if (status < 0) {
ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT);
h5libraryError(env);
} /* end if */
else {
ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, 0);
} /* end else */
} /* end else */
} /* end else */
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Aread */
/*
* Class: hdf_hdf5lib_H5
* Method: H5G_obj_t H5Rget_obj_type
* Signature: (JI[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Rget_1obj_1type(JNIEnv *env, jclass clss, jlong loc_id, jint ref_type, jbyteArray ref)
{
int retVal =-1;
jboolean isCopy;
jbyte *refP;
H5O_type_t object_info;
if (ref == NULL) {
h5nullArgument( env, "H5Rget_object_type: ref is NULL");
} /* end if */
else {
refP = (jbyte*)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy);
if (refP == NULL) {
h5JNIFatalError(env, "H5Rget_object_type: ref not pinned");
} /* end if */
else {
retVal = H5Rget_obj_type2((hid_t)loc_id, (H5R_type_t)ref_type, refP, &object_info);
if(retVal >= 0)
retVal = object_info;
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
if (retVal < 0)
h5libraryError(env);
} /* end else */
} /* end else */
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Rget_1obj_1type */
/*
* Class: hdf_hdf5lib_H5
* Method: int H5Rget_obj_type2
* Signature: (JI[B[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Rget_1obj_1type2(JNIEnv *env, jclass clss, jlong loc_id, jint ref_type, jbyteArray ref, jintArray ref_obj)
{
jint status;
jboolean isCopy;
jbyte *refP;
jint *ref_objP;
int retVal = -1;
if (ref == NULL) {
h5nullArgument( env, "H5Rget_object_type: ref is NULL");
} /* end if */
else if (ref_obj == NULL) {
h5nullArgument( env, "H5Rget_object_type: ref_obj is NULL");
} /* end else if */
else {
refP = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy);
if (refP == NULL) {
h5JNIFatalError(env, "H5Rget_object_type: ref not pinned");
} /* end if */
else {
ref_objP = (jint *)ENVPTR->GetIntArrayElements(ENVPAR ref_obj, &isCopy);
if (ref_objP == NULL) {
ENVPTR->ReleaseByteArrayElements(ENVPAR ref,refP,0);
h5JNIFatalError(env, "H5Rget_object_type: ref_obj not pinned");
} /* end if */
else {
status = H5Rget_obj_type2((hid_t)loc_id, (H5R_type_t)ref_type, refP, (H5O_type_t*)ref_objP);
retVal = ref_objP[0];
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
if (status < 0) {
ENVPTR->ReleaseIntArrayElements(ENVPAR ref_obj,ref_objP, JNI_ABORT);
h5libraryError(env);
} /* end if */
else {
ENVPTR->ReleaseIntArrayElements(ENVPAR ref_obj, ref_objP, 0);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Rget_1obj_1type2 */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Rget_name
* Signature: (JI[B[Ljava/lang/String;J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Rget_1name(JNIEnv *env, jclass clss, jlong loc_id, jint ref_type, jbyteArray ref, jobjectArray name, jlong size)
{
jlong ret_val = -1;
jbyte *refP;
jboolean isCopy;
char *aName = NULL;
jstring str;
size_t bs;
bs = (size_t)size;
if (bs <= 0) {
h5badArgument(env, "H5Rget_name: size <= 0");
} /* end if */
else if (ref == NULL) {
h5nullArgument(env, "H5Rget_name: ref is NULL");
} /* end else if */
else {
if ((ref_type == H5R_OBJECT) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_OBJ_REF_BUF_SIZE) {
h5badArgument(env, "H5Rget_name: obj ref input array != H5R_OBJ_REF_BUF_SIZE");
} /* end if */
else if ((ref_type == H5R_DATASET_REGION)
&& ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) {
h5badArgument(env, "H5Rget_name: region ref input array != H5R_DSET_REG_REF_BUF_SIZE");
} /* end else if */
else {
refP = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy);
if (refP == NULL) {
h5JNIFatalError(env, "H5Rget_name: ref not pinned");
} /* end if */
else {
aName = (char*)HDmalloc(sizeof(char)*bs);
if (aName == NULL) {
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
h5outOfMemory(env, "H5Rget_name: malloc failed");
} /* end if */
else {
ret_val = (jlong)H5Rget_name((hid_t)loc_id, (H5R_type_t)ref_type, refP, aName, bs) ;
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
if (ret_val < 0) {
HDfree(aName);
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR aName);
ENVPTR->SetObjectArrayElement(ENVPAR name, 0, str);
HDfree(aName);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
} /* end else */
return ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Rget_1name */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aget_name_by_idx
* Signature: (JLjava/lang/String;IIJJ)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Aget_1name_1by_1idx
(JNIEnv *env, jclass clss, jlong loc_id, jstring obj_name, jint idx_type, jint order, jlong n, jlong lapl_id)
{
size_t buf_size;
char *aValue;
jlong status_size;
jstring str = NULL;
const char *aName;
PIN_JAVA_STRING(obj_name, aName);
if (aName != NULL) {
/* get the length of the attribute name */
status_size = H5Aget_name_by_idx((hid_t)loc_id, aName, (H5_index_t)idx_type,
(H5_iter_order_t) order, (hsize_t) n, (char*)NULL, (size_t)0, (hid_t)lapl_id);
if(status_size < 0) {
UNPIN_JAVA_STRING(obj_name, aName);
h5libraryError(env);
} /* end if */
else {
buf_size = (size_t)status_size + 1;/* add extra space for the null terminator */
aValue = (char*)HDmalloc(sizeof(char) * buf_size);
if (aValue == NULL) {
UNPIN_JAVA_STRING(obj_name, aName);
h5outOfMemory(env, "H5Aget_name_by_idx: malloc failed ");
} /* end if */
else {
status_size = H5Aget_name_by_idx((hid_t)loc_id, aName, (H5_index_t)idx_type,
(H5_iter_order_t) order, (hsize_t) n, (char*)aValue, (size_t)buf_size, (hid_t)lapl_id);
UNPIN_JAVA_STRING(obj_name, aName);
if (status_size < 0) {
HDfree(aValue);
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR aValue);
HDfree(aValue);
if (str == NULL) {
/* exception -- fatal JNI error */
h5JNIFatalError(env, "H5Aget_name_by_idx: return string not created");
} /* end if */
} /* end else */
} /* end else */
} /* end else */
}
return str;
} /* end Java_hdf_hdf5lib_H5_H5Aget_1name_1by_1idx */
herr_t
H5AwriteVL_str
(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
{
herr_t status = -1;
char **wdata;
jsize size;
jint i;
size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf);
wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*));
if (!wdata) {
h5JNIFatalError(env, "H5AwriteVL_str: cannot allocate buffer");
} /* end if */
else {
HDmemset(wdata, 0, (size_t)size * sizeof(char*));
for (i = 0; i < size; ++i) {
jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray) buf, i);
if (obj != 0) {
jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj);
const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
if (utf8) {
wdata[i] = (char*)HDmalloc((size_t)length + 1);
if (wdata[i]) {
HDmemset(wdata[i], 0, ((size_t)length + 1));
HDstrncpy(wdata[i], utf8, (size_t)length);
} /* end if */
} /* end if */
ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
ENVPTR->DeleteLocalRef(ENVPAR obj);
} /* end if */
} /* end for (i = 0; i < size; ++i) */
status = H5Awrite((hid_t)aid, (hid_t)tid, wdata);
for (i = 0; i < size; i++) {
if(wdata[i]) {
HDfree(wdata[i]);
} /* end if */
} /* end for */
HDfree(wdata);
if (status < 0)
h5libraryError(env);
} /* end else */
return (jint)status;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Rcreate
* Signature: ([BJLjava/lang/String;IJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Rcreate(JNIEnv *env, jclass clss, jbyteArray ref, jlong loc_id, jstring name, jint ref_type, jlong space_id)
{
const char *rName;
herr_t status = -1;
jbyte *refP;
jboolean isCopy2;
PIN_JAVA_STRING(name, rName, -1);
if (ref == NULL) {
UNPIN_JAVA_STRING(name, rName);
h5nullArgument( env, "H5Rcreate: ref is NULL");
} /* end if */
else {
if ((ref_type == H5R_OBJECT) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_OBJ_REF_BUF_SIZE) {
UNPIN_JAVA_STRING(name, rName);
h5badArgument( env, "H5Rcreate: ref input array != H5R_OBJ_REF_BUF_SIZE");
} /* end if */
else if ((ref_type == H5R_DATASET_REGION) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) {
UNPIN_JAVA_STRING(name, rName);
h5badArgument( env, "H5Rcreate: region ref input array != H5R_DSET_REG_REF_BUF_SIZE");
} /* end else if */
else if ((ref_type != H5R_OBJECT) && (ref_type != H5R_DATASET_REGION)) {
UNPIN_JAVA_STRING(name, rName);
h5badArgument( env, "H5Rcreate: ref_type unknown type ");
} /* end else if */
else {
refP = (jbyte*)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy2);
if (refP == NULL) {
UNPIN_JAVA_STRING(name, rName);
h5JNIFatalError(env, "H5Rcreate: ref not pinned");
} /* end if */
else {
status = H5Rcreate(refP, (hid_t)loc_id, rName, (H5R_type_t)ref_type, (hid_t)space_id);
UNPIN_JAVA_STRING(name, rName);
if (status < 0) {
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
h5libraryError(env);
} /* end if */
else {
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, 0);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Rcreate */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Lget_name_by_idx
* Signature: (JLjava/lang/String;IIJJ)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Lget_1name_1by_1idx
(JNIEnv *env, jclass clss, jlong loc_id, jstring name,
jint index_field, jint order, jlong link_n, jlong access_id)
{
jlong status_size;
jstring str = NULL;
size_t buf_size;
const char *lName;
char *lValue;
PIN_JAVA_STRING(name, lName);
if (lName != NULL) {
/* get the length of the link name */
status_size = H5Lget_name_by_idx((hid_t)loc_id, lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (char*)NULL, (size_t)0, H5P_DEFAULT);
if(status_size < 0) {
h5libraryError(env);
} /* end if */
else {
buf_size = (size_t)status_size + 1;/* add extra space for the null terminator */
lValue = (char*)HDmalloc(sizeof(char) * buf_size);
if (lValue == NULL) {
h5outOfMemory(env, "H5Lget_name_by_idx: malloc failed ");
} /* end if */
else {
status_size = H5Lget_name_by_idx((hid_t)loc_id, lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (char*)lValue, (size_t)buf_size, (hid_t)access_id);
if (status_size < 0) {
HDfree(lValue);
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR lValue);
HDfree(lValue);
if (str == NULL)
h5JNIFatalError(env, "H5Lget_name_by_idx: return string not created");
} /* end else */
} /* end else */
} /* end else */
UNPIN_JAVA_STRING(name, lName);
}
return str;
} /* end Java_hdf_hdf5lib_H5_H5Lget_1name_1by_1idx */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Oget_comment_by_name
* Signature: (JLjava/lang/String;J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Oget_1comment_1by_1name
(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong access_id)
{
char *oComment;
const char *oName;
ssize_t buf_size;
ssize_t status;
jstring str = NULL;
PIN_JAVA_STRING(name, oName);
if (oName != NULL) {
/* get the length of the comment */
buf_size = H5Oget_comment_by_name((hid_t)loc_id, oName, NULL, 0, (hid_t)access_id);
if (buf_size < 0) {
h5badArgument( env, "H5Oget_comment_by_name: buf_size < 0");
} /* end if */
else if (buf_size > 0) {
buf_size++; /* add extra space for the null terminator */
oComment = (char *)HDmalloc(sizeof(char) * (size_t)buf_size);
if (oComment == NULL) {
h5outOfMemory( env, "H5Oget_comment_by_name: malloc failed");
} /* end if */
else {
status = H5Oget_comment_by_name((hid_t)loc_id, oName, oComment, (size_t)buf_size, (hid_t)access_id);
if (status < 0) {
h5libraryError(env);
} /* end if */
else {
/* may throw OutOfMemoryError */
str = ENVPTR->NewStringUTF(ENVPAR oComment);
if (str == NULL) {
h5JNIFatalError( env, "H5Oget_comment_by_name: return string not allocated");
} /* end if */
} /* end else */
HDfree(oComment);
}
} /* end if */
UNPIN_JAVA_STRING(name, oName);
}
return (jstring)str;
} /* end Java_hdf_hdf5lib_H5_H5Oget_1comment_1by_1name */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Oget_comment
* Signature: (J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Oget_1comment
(JNIEnv *env, jclass clss, jlong loc_id)
{
char *oComment;
ssize_t buf_size;
ssize_t status;
jstring str = NULL;
/* get the length of the comment */
buf_size = H5Oget_comment((hid_t)loc_id, NULL, 0);
if (buf_size < 0) {
h5badArgument( env, "H5Oget_comment: buf_size < 0");
} /* end if */
else if (buf_size > 0) {
buf_size++; /* add extra space for the null terminator */
oComment = (char *)HDmalloc(sizeof(char) * (size_t)buf_size);
if (oComment == NULL) {
/* exception -- out of memory */
h5outOfMemory( env, "H5Oget_comment: malloc failed");
} /* end if */
else {
status = H5Oget_comment((hid_t)loc_id, oComment, (size_t)buf_size);
if (status < 0) {
h5libraryError(env);
} /* end if */
else {
/* may throw OutOfMemoryError */
str = ENVPTR->NewStringUTF(ENVPAR oComment);
if (str == NULL) {
h5JNIFatalError( env, "H5Oget_comment: return string not allocated");
} /* end if */
} /* end else */
HDfree(oComment);
}
} /* end else if */
return (jstring)str;
} /* end Java_hdf_hdf5lib_H5_H5Oget_1comment */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Lget_value
* Signature: (JLjava/lang/String;[Ljava/lang/String;J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Lget_1value
(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jobjectArray link_value, jlong access_id)
{
size_t buf_size;
herr_t status;
H5L_info_t infobuf;
const char *lName;
char *lValue;
const char *file_name;
const char *obj_name;
jstring str;
infobuf.type = -1;
PIN_JAVA_STRING(name, lName);
if (lName != NULL) {
/* get the length of the link val */
status = H5Lget_info((hid_t)loc_id, lName, &infobuf, H5P_DEFAULT);
if(status < 0) {
h5libraryError(env);
} /* end if */
else {
buf_size = infobuf.u.val_size + 1;/* add extra space for the null terminator */
if(infobuf.type == H5L_TYPE_HARD) {
h5JNIFatalError(env, "H5Lget_val: link is hard type");
} /* end if */
else {
lValue = (char*)HDmalloc(sizeof(char) * buf_size);
if (lValue == NULL) {
h5outOfMemory(env, "H5Lget_val: malloc failed");
} /* end if */
else {
status = H5Lget_val((hid_t)loc_id, lName, (void*)lValue, buf_size, (hid_t)access_id);
if (status < 0) {
h5libraryError(env);
} /* end if */
else if(infobuf.type == H5L_TYPE_EXTERNAL) {
status = H5Lunpack_elink_val(lValue, (size_t)infobuf.u.val_size, (unsigned*)NULL, &file_name, &obj_name);
if (status < 0) {
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR obj_name);
if (str == NULL) {
h5JNIFatalError(env, "H5Lget_val: return string not created");
} /* end if */
else {
ENVPTR->SetObjectArrayElement(ENVPAR link_value, 0, str);
str = ENVPTR->NewStringUTF(ENVPAR file_name);
if (str == NULL) {
h5JNIFatalError(env, "H5Lget_val: return string not created");
} /* end if */
else {
ENVPTR->SetObjectArrayElement(ENVPAR link_value, 1, str);
} /* end else */
} /* end else */
} /* end else */
} /* end else if */
else {
str = ENVPTR->NewStringUTF(ENVPAR lValue);
if (str == NULL) {
/* exception -- fatal JNI error */
h5JNIFatalError(env, "H5Lget_val: return string not created");
} /* end if */
else {
ENVPTR->SetObjectArrayElement(ENVPAR link_value, 0, str);
} /* end else */
} /* end else */
HDfree(lValue);
} /* end else */
} /* end else */
} /* end else */
UNPIN_JAVA_STRING(name, lName);
}
return infobuf.type;
} /* end Java_hdf_hdf5lib_H5_H5Lget_1val */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Lget_value_by_idx
* Signature: (JLjava/lang/String;IIJ[Ljava/lang/String;J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Lget_1value_1by_1idx
(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jint index_field, jint order,
jlong link_n, jobjectArray link_value, jlong access_id)
{
herr_t status;
size_t buf_size;
H5L_info_t infobuf;
const char *lName;
void *lValue;
const char *file_name;
const char *obj_name;
jstring str;
infobuf.type = -1;
PIN_JAVA_STRING(name, lName);
if (lName != NULL) {
/* get the length of the link valuee */
status = H5Lget_info_by_idx((hid_t)loc_id, lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, &infobuf, (hid_t)access_id);
if(status < 0) {
h5libraryError(env);
} /* end if */
else {
buf_size = infobuf.u.val_size;
if(buf_size == 0) {
h5libraryError(env);
} /* end if */
else {
lValue = (void*)HDmalloc(buf_size);
if (lValue == NULL) {
h5outOfMemory(env, "H5Lget_val_by_idx: malloc failed ");
} /* end if */
else {
status = H5Lget_val_by_idx((hid_t)loc_id, lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (void*)lValue, (size_t)buf_size, (hid_t)access_id);
if (status < 0) {
h5libraryError(env);
} /* end if */
else if(infobuf.type == H5L_TYPE_EXTERNAL) {
status = H5Lunpack_elink_val((char*)lValue, (size_t)infobuf.u.val_size, (unsigned*)NULL, (const char**)&file_name, (const char**)&obj_name);
if (status < 0) {
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR obj_name);
if (str == NULL) {
h5JNIFatalError(env, "H5Lget_val_by_idx: return string not created");
} /* end if */
else {
ENVPTR->SetObjectArrayElement(ENVPAR link_value, 0, str);
str = ENVPTR->NewStringUTF(ENVPAR file_name);
if (str == NULL) {
h5JNIFatalError(env, "H5Lget_val_by_idx: return string not created");
} /* end if */
else {
ENVPTR->SetObjectArrayElement(ENVPAR link_value, 1, str);
} /* end else */
} /* end else */
} /* end else */
} /* end else if */
else {
str = ENVPTR->NewStringUTF(ENVPAR (char *)lValue);
if (str == NULL) {
h5JNIFatalError(env, "H5Lget_val_by_idx: return string not created");
} /* end if */
else {
ENVPTR->SetObjectArrayElement(ENVPAR link_value, 0, str);
} /* end else */
} /* end else */
HDfree(lValue);
} /* end else */
} /* end else */
} /* end else */
UNPIN_JAVA_STRING(name, lName);
}
return infobuf.type;
} /* end Java_hdf_hdf5lib_H5_H5Lget_1val_1by_1idx */
herr_t
H5AreadVL_asstr
(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
{
jint i;
jint n;
hid_t sid;
jstring jstr;
h5str_t h5str;
hvl_t *rdata;
hsize_t dims[H5S_MAX_RANK];
size_t size;
size_t max_len = 0;
herr_t status = -1;
/* Get size of string array */
n = ENVPTR->GetArrayLength(ENVPAR buf);
/* we will need to read n number of hvl_t structures */
rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
if (rdata == NULL) {
h5JNIFatalError(env, "H5AreadVL_asstr: failed to allocate buff for read");
} /* end if */
else {
status = H5Aread(aid, tid, rdata);
if (status < 0) {
dims[0] = (hsize_t)n;
sid = H5Screate_simple(1, dims, NULL);
H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata);
H5Sclose(sid);
HDfree(rdata);
h5JNIFatalError(env, "H5AreadVL_asstr: failed to read data");
} /* end if */
else {
/* calculate the largest size of all the hvl_t structures read */
max_len = 1;
for (i=0; i < n; i++) {
if ((rdata + i)->len > max_len)
max_len = (rdata + i)->len;
}
/* create one malloc to hold largest element */
size = H5Tget_size(tid) * max_len;
HDmemset(&h5str, 0, sizeof(h5str_t));
h5str_new(&h5str, 4 * size);
if (h5str.s == NULL) {
dims[0] = (hsize_t)n;
sid = H5Screate_simple(1, dims, NULL);
H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata);
H5Sclose(sid);
HDfree(rdata);
h5JNIFatalError(env, "H5AreadVL_asstr: failed to allocate buf");
} /* end if */
else {
H5T_class_t tclass = H5Tget_class(tid);
/* convert each element to char string */
for (i=0; i < n; i++) {
h5str.s[0] = '\0';
h5str_vlsprintf(&h5str, aid, tid, rdata+i, 0);
jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
} /* end for */
h5str_free(&h5str);
dims[0] = (hsize_t)n;
sid = H5Screate_simple(1, dims, NULL);
H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata);
H5Sclose(sid);
HDfree(rdata);
} /* end else */
} /* end else */
} /* end else */
return status;
}
