int main(){
hid_t fprop;
hid_t fid;
hid_t vol_id = H5VL_memvol_init();
herr_t status;
hid_t g1, g2;
hid_t plist;
char name[1024];
fprop = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_vol(fprop, vol_id, &fprop);
fid = H5Fcreate("test", H5F_ACC_TRUNC, H5P_DEFAULT, fprop);
H5VLget_plugin_name(fid, name, 1024);
printf ("Using VOL %s\n", name);
g1 = H5Gcreate2(fid, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(g1);
g2 = H5Gcreate2(fid, "g2", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
g1 = H5Gcreate2(g2, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(g1);
H5Gclose(g2);
// is this allowed?
//g3 = H5Gcreate2(fid, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//H5Gclose(g3);
printf("Testing additional functions\n");
g1 = H5Gopen2(fid, "g1", H5P_DEFAULT );
plist = H5Gget_create_plist(g1);
H5G_info_t group_info;
H5Gget_info(g1, & group_info );
H5Gget_info_by_idx(fid, "g1", H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, 0, & group_info, H5P_DEFAULT ) ;
H5Gget_info_by_idx(fid, "g1", H5_INDEX_NAME, H5_ITER_NATIVE, 0, & group_info, H5P_DEFAULT ) ;
H5Gget_info_by_name(fid, "g1", & group_info, H5P_DEFAULT);
H5Pclose(plist);
status = H5Gclose(g1);
g1 = H5Gopen2(fid, "g2", H5P_DEFAULT );
H5Gclose(g1);
//g1 = H5Gopen2(fid, "INVALID", H5P_DEFAULT );
//H5Gclose(g1);
g1 = H5Gcreate_anon( fid, H5P_DEFAULT, H5P_DEFAULT );
H5Gclose(g1);
H5Fclose(fid);
H5VL_memvol_finalize();
printf("Status: %d\n", status);
return 0;
}
/*-------------------------------------------------------------------------
* Function: group_stats
*
* Purpose: Gather statistics about the group
*
* Return: Success: 0
*
* Failure: -1
*
* Programmer: Quincey Koziol
* Tuesday, August 16, 2005
*
* Modifications: Refactored code from the walk_function
* EIP, Wednesday, August 16, 2006
*
* Vailin Choi 12 July 2007
* 1. Gathered storage info for btree and heap
* (groups and attributes)
* 2. Gathered info for attributes
*
* Vailin Choi 14 July 2007
* Cast "num_objs" and "num_attrs" to size_t
* Due to the -Mbounds problem for the pgi-32 bit compiler on indexing
*
*-------------------------------------------------------------------------
*/
static herr_t
group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
{
H5G_info_t ginfo; /* Group information */
unsigned bin; /* "bin" the number of objects falls in */
herr_t ret;
/* Gather statistics about this type of object */
iter->uniq_groups++;
/* Get object header information */
iter->group_ohdr_info.total_size += oi->hdr.space.total;
iter->group_ohdr_info.free_size += oi->hdr.space.free;
/* Get group information */
ret = H5Gget_info_by_name(iter->fid, name, &ginfo, H5P_DEFAULT);
HDassert(ret >= 0);
/* Update link stats */
if(ginfo.nlinks < SIZE_SMALL_GROUPS)
(iter->num_small_groups[(size_t)ginfo.nlinks])++;
if(ginfo.nlinks > iter->max_fanout)
iter->max_fanout = ginfo.nlinks;
/* Add group count to proper bin */
bin = ceil_log10((unsigned long)ginfo.nlinks);
if((bin + 1) > iter->group_nbins) {
/* Allocate more storage for info about dataset's datatype */
iter->group_bins = (unsigned long *)HDrealloc(iter->group_bins, (bin + 1) * sizeof(unsigned long));
HDassert(iter->group_bins);
/* Initialize counts for intermediate bins */
while(iter->group_nbins < bin)
iter->group_bins[iter->group_nbins++] = 0;
iter->group_nbins++;
/* Initialize count for new bin */
iter->group_bins[bin] = 1;
} /* end if */
else
(iter->group_bins[bin])++;
/* Update group metadata info */
iter->groups_btree_storage_size += oi->meta_size.obj.index_size;
iter->groups_heap_storage_size += oi->meta_size.obj.heap_size;
/* Update attribute metadata info */
ret = attribute_stats(iter, oi);
HDassert(ret >= 0);
return 0;
} /* end group_stats() */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Gget_info_by_name
* Signature: (JLjava/lang/String;J)Lhdf/hdf5lib/structs/H5G_info_t;
*/
JNIEXPORT jobject JNICALL
Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1name(JNIEnv *env, jclass cls, jlong loc_id, jstring name, jlong lapl_id)
{
herr_t ret_val = -1;
const char *gName;
H5G_info_t group_info;
PIN_JAVA_STRING(name, gName, NULL);
ret_val = H5Gget_info_by_name((hid_t)loc_id, gName, &group_info, (hid_t)lapl_id);
UNPIN_JAVA_STRING(name, gName);
if (ret_val < 0) {
h5libraryError(env);
return NULL;
} /* end if */
return create_H5G_info_t(env, group_info);
} /* end Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1name */
std::vector<std::string> fast5_get_multi_read_groups(fast5_file& fh)
{
std::vector<std::string> out;
size_t buffer_size = 0;
char* buffer = NULL;
// get the number of groups in the root group
H5G_info_t group_info;
int ret = H5Gget_info_by_name(fh.hdf5_file, "/", &group_info, H5P_DEFAULT);
if(ret < 0) {
fprintf(stderr, "error getting group info\n");
exit(EXIT_FAILURE);
}
for(size_t group_idx = 0; group_idx < group_info.nlinks; ++group_idx) {
// retrieve the size of this group name
ssize_t size = H5Lget_name_by_idx(fh.hdf5_file, "/", H5_INDEX_NAME, H5_ITER_INC, group_idx, NULL, 0, H5P_DEFAULT);
if(size < 0) {
fprintf(stderr, "error getting group name size\n");
exit(EXIT_FAILURE);
}
size += 1; // for null terminator
if(size > buffer_size) {
buffer = (char*)realloc(buffer, size);
buffer_size = size;
}
// copy the group name
H5Lget_name_by_idx(fh.hdf5_file, "/", H5_INDEX_NAME, H5_ITER_INC, group_idx, buffer, buffer_size, H5P_DEFAULT);
buffer[size] = '\0';
out.push_back(buffer);
}
free(buffer);
buffer = NULL;
buffer_size = 0;
return out;
}
med_err _MEDchecknSublinkFunc(med_idt id,const char *lname, const H5L_info_t *linfo, med_bool *data) {
med_err _ret=-1;
H5O_info_t oinfo;
H5G_info_t _group_info;
#ifdef _DEBUG_
SSCRUTE(lname);
#endif
if (!strcmp(lname,".")) return 0;
switch ( (*linfo).type ) {
case H5L_TYPE_SOFT:
oinfo.type=H5G_LINK;
break;
case H5L_TYPE_HARD:
if ( H5Oget_info_by_name( id, lname, &oinfo, H5P_DEFAULT ) <0) {
MED_ERR_(_ret,MED_ERR_CALL,MED_ERR_API,"H5Oget_info_by_name");
SSCRUTE(lname);
}
break;
case H5L_TYPE_EXTERNAL:
case H5L_TYPE_ERROR:
default:
MED_ERR_(_ret,MED_ERR_UNRECOGNIZED,MED_ERR_HDFTYPE,lname);
ISCRUTE_int((*linfo).type);
goto ERROR;
break;
}
switch ( oinfo.type ) {
case H5G_GROUP:
if ( H5Gget_info_by_name(id, lname, &_group_info, H5P_DEFAULT ) < 0 ){
MED_ERR_(_ret,MED_ERR_ACCESS,MED_ERR_GROUP, MED_ERR_NAME_MSG );
SSCRUTE(lname);goto ERROR;
}
if ( _group_info.nlinks > 1 ) {
*data=MED_TRUE;
MED_ERR_(_ret,MED_ERR_INVALID,MED_ERR_GROUP,lname);
ISCRUTE_size(_group_info.nlinks);goto ERROR;
}
/* SSCRUTE(lname); */
/* ISCRUTE(*data); */
/* ISCRUTE(_group_info.nlinks); */
break;
case H5G_DATASET:
case H5G_LINK:
MED_ERR_(_ret,MED_ERR_INVALID,MED_ERR_HDFTYPE,lname);
goto ERROR;
break;
case H5G_TYPE:
default:
MED_ERR_(_ret,MED_ERR_UNRECOGNIZED,MED_ERR_HDFTYPE,lname);
goto ERROR;
}
_ret = 0;
ERROR:
return _ret;
}
