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Switch test for nc_inq_unlimdim and nc_inq_unlimdims to use the same …
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…ordering as

the rest of the dimension queries.  Correct error in library where types used
in sub-group variables but that were added to the file after the sub-group was
created weren't available for sub-group variables to use.  Start cleaning up
test suite and un-commenting tests that were commented out (got up to
nc_test4/tst_fills2.c, alphabetically) before running into an error in HDF5.
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@qkoziol
qkoziol committed Dec 16, 2013
1 parent 11e6343 commit 0d42ac7
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3 changes: 3 additions & 0 deletions RELEASE_NOTES.md
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Expand Up @@ -7,6 +7,9 @@ Recent releases include references to Jira issue identifiers for more informatio
## 4.3.1 Released TBD


* Corrected behavior of nc_inq_unlimdim and nv_inq_unlimdims to report dimids
in same order as nc_inq_dimids

* Addressed an issue reported by Jeff Whitaker regarding `nc_inq_nvars` returning an incorrect number of dimensions (this issue was introduced in 4.3.1-rc5). Integrated a test contributed by Jeff Whitaker.

### 4.3.1-rc5 Released 2013-12-06
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289 changes: 210 additions & 79 deletions libsrc4/nc4file.c
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,24 @@ extern int num_spaces;
#define DIMENSION_LIST "DIMENSION_LIST"
#define NAME "NAME"

/* Struct to track information about objects in a group, for nc4_rec_read_metadata() */
typedef struct NC4_rec_read_metadata_obj_info
{
hid_t oid; /* HDF5 object ID */
char oname[NC_MAX_NAME + 1]; /* Name of object */
H5G_stat_t statbuf; /* Information about the object */
struct NC4_rec_read_metadata_obj_info *next; /* Pointer to next node in list */
} NC4_rec_read_metadata_obj_info_t;

/* User data struct for call to H5Literate() in nc4_rec_read_metadata() */
/* Tracks the groups, named datatypes and datasets in the group, for later use */
typedef struct NC4_rec_read_metadata_ud
{
NC4_rec_read_metadata_obj_info_t *types_head, *types_tail; /* Pointers to head & tail of list of named datatypes */
NC4_rec_read_metadata_obj_info_t *dsets_head, *dsets_tail; /* Pointers to head & tail of list of datasets */
NC4_rec_read_metadata_obj_info_t *grps_head, *grps_tail; /* Pointers to head & tail of list of groups */
} NC4_rec_read_metadata_ud_t;

/* Forward */
static int NC4_enddef(int ncid);
static int nc4_rec_read_metadata(NC_GRP_INFO_T *grp);
Expand Down Expand Up @@ -1675,6 +1693,11 @@ read_grp_atts(NC_GRP_INFO_T *grp)
num_obj = H5Aget_num_attrs(grp->hdf_grpid);
for (i = 0; i < num_obj; i++)
{
/* Close an attribute from previous loop iteration */
/* (Should be from 'continue' statement, below) */
if (attid && H5Aclose(attid) < 0)
BAIL(NC_EHDFERR);

if ((attid = H5Aopen_idx(grp->hdf_grpid, (unsigned int)i)) < 0)
BAIL(NC_EATTMETA);
if (H5Aget_name(attid, NC_MAX_NAME + 1, obj_name) < 0)
Expand Down Expand Up @@ -1717,9 +1740,6 @@ read_grp_atts(NC_GRP_INFO_T *grp)
if (type)
att->class = type->class;
}
if (H5Aclose(attid) < 0)
BAIL(NC_EATTMETA);
attid = 0;
}

exit:
Expand Down Expand Up @@ -1784,111 +1804,120 @@ read_dataset(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
return retval;
}

static int
nc4_iter_list_add(NC4_rec_read_metadata_obj_info_t **head,
NC4_rec_read_metadata_obj_info_t **tail,
NC4_rec_read_metadata_obj_info_t *oinfo)
{
if (*tail)
{
assert(*head);
(*tail)->next = oinfo;
*tail = oinfo;
}
else
{
assert(NULL == *head);
*head = *tail = oinfo;
}

return (NC_NOERR);
}

static int
nc4_rec_read_metadata_cb(hid_t grpid, const char *name, const H5L_info_t *info,
void *_op_data)
{
hid_t oid=-1;
H5G_stat_t statbuf;
char oname[NC_MAX_NAME + 1];
NC_GRP_INFO_T *grp = (NC_GRP_INFO_T *) (_op_data);
NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info;

/* Open this critter. */
if ((oid = H5Oopen(grpid, name, H5P_DEFAULT)) < 0)
return H5_ITER_ERROR;
NC4_rec_read_metadata_ud_t *udata = (NC4_rec_read_metadata_ud_t *)_op_data; /* Pointer to user data for callback */
NC4_rec_read_metadata_obj_info_t *oinfo; /* Pointer to info for object */
int retval = H5_ITER_CONT;

/* Allocate memory for the object's info */
if (!(oinfo = calloc(1, sizeof(NC4_rec_read_metadata_obj_info_t))))
return NC_ENOMEM;

/* Open this critter. */
if ((oinfo->oid = H5Oopen(grpid, name, H5P_DEFAULT)) < 0)
return H5_ITER_ERROR;

/* Get more info about the object.*/
if (H5Gget_objinfo(oid, ".", 1, &statbuf) < 0)
return H5_ITER_ERROR;
/* Get info about the object.*/
if (H5Gget_objinfo(oinfo->oid, ".", 1, &oinfo->statbuf) < 0)
return H5_ITER_ERROR;

strncpy(oname, name, NC_MAX_NAME);
strncpy(oinfo->oname, name, NC_MAX_NAME);

/* Deal with objects. */
switch(statbuf.type)
{
case H5G_GROUP:
{
NC_GRP_INFO_T *child_grp;

LOG((3, "found group %s", oname));
/* Add object to list, for later */
switch(oinfo->statbuf.type)
{
case H5G_GROUP:
LOG((3, "found group %s", oinfo->oname));
if (nc4_iter_list_add(&udata->grps_head, &udata->grps_tail, oinfo))
BAIL(H5_ITER_ERROR);
break;

/* Add group to file's hierarchy */
if (nc4_grp_list_add(&(grp->children), h5->next_nc_grpid++,
grp, grp->nc4_info->controller, oname, &child_grp))
return H5_ITER_ERROR;
case H5G_DATASET:
LOG((3, "found dataset %s", oinfo->oname));
if (nc4_iter_list_add(&udata->dsets_head, &udata->dsets_tail, oinfo))
BAIL(H5_ITER_ERROR);
break;

/* Recursively read the child group's metadata */
if (nc4_rec_read_metadata(child_grp))
return H5_ITER_ERROR;
}
break;
case H5G_TYPE:
LOG((3, "found datatype %s", oinfo->oname));
if (nc4_iter_list_add(&udata->types_head, &udata->types_tail, oinfo))
BAIL(H5_ITER_ERROR);
break;

case H5G_DATASET:
{
int retval = NC_NOERR;

LOG((3, "found dataset %s", oname));

/* Learn all about this dataset, which may be a dimscale
* (i.e. dimension metadata), or real data. */
if ((retval = read_dataset(grp, oid, oname, &statbuf)))
{
/* Allow NC_EBADTYPID to transparently skip over datasets
* which have a datatype that netCDF-4 doesn't undertand
* (currently), but break out of iteration for other
* errors.
*/
if(NC_EBADTYPID != retval)
return H5_ITER_ERROR;
}
}
break;
default:
LOG((0, "Unknown object class %d in %s!", oinfo->statbuf.type, __func__));
BAIL(H5_ITER_ERROR);
}

case H5G_TYPE:
LOG((3, "found datatype %s", oname));
if (read_type(grp, oid, oname))
return H5_ITER_ERROR;
break;
exit:
if (retval)
{
if (oinfo)
{
if (oinfo->oid > 0 && H5Oclose(oinfo->oid) < 0)
BAIL2(H5_ITER_ERROR);
free(oinfo);
}
}

default:
LOG((0, "Unknown object class %d in %s!", statbuf.type, __func__));
}

/* Close the object */
if (H5Oclose(oid) < 0)
return H5_ITER_ERROR;

return (H5_ITER_CONT);
return (retval);
}

static int
nc4_rec_read_metadata(NC_GRP_INFO_T *grp)
{
NC4_rec_read_metadata_ud_t udata; /* User data for iteration */
NC4_rec_read_metadata_obj_info_t *oinfo; /* Pointer to info for object */
hsize_t idx=0;
int retval;
hid_t pid = 0;
unsigned crt_order_flags = 0;
H5_index_t iter_index;
int retval = NC_NOERR; /* everything worked! */

assert(grp && grp->name);
LOG((3, "%s: grp->name %s", __func__, grp->name));

/* Portably initialize user data for iteration */
memset(&udata, 0, sizeof(udata));

/* Open this HDF5 group and retain its grpid. It will remain open
* with HDF5 until this file is nc_closed. */
if (!grp->hdf_grpid)
{
if (grp->parent)
{
if ((grp->hdf_grpid = H5Gopen2(grp->parent->hdf_grpid,
if ((grp->hdf_grpid = H5Gopen2(grp->parent->hdf_grpid,
grp->name, H5P_DEFAULT)) < 0)
return NC_EHDFERR;
BAIL(NC_EHDFERR);
}
else
{
if ((grp->hdf_grpid = H5Gopen2(grp->nc4_info->hdfid,
"/", H5P_DEFAULT)) < 0)
return NC_EHDFERR;
BAIL(NC_EHDFERR);
}
}
assert(grp->hdf_grpid > 0);
Expand All @@ -1897,7 +1926,7 @@ nc4_rec_read_metadata(NC_GRP_INFO_T *grp)
pid = H5Gget_create_plist(grp->hdf_grpid);
H5Pget_link_creation_order(pid, &crt_order_flags);
if (H5Pclose(pid) < 0)
return NC_EHDFERR;
BAIL(NC_EHDFERR);

/* Set the iteration index to use */
if (crt_order_flags & H5P_CRT_ORDER_TRACKED)
Expand All @@ -1908,23 +1937,125 @@ nc4_rec_read_metadata(NC_GRP_INFO_T *grp)

/* Without creation ordering, file must be read-only. */
if (!h5->no_write)
return NC_ECANTWRITE;
BAIL(NC_ECANTWRITE);

iter_index = H5_INDEX_NAME;
}

/* Iterate over links in this group, processing all the objects
* and recursively handling the types encountered
/* Iterate over links in this group, building lists for the types,
* datasets and groups encountered
*/
if (H5Literate(grp->hdf_grpid, iter_index, H5_ITER_INC, &idx,
nc4_rec_read_metadata_cb, (void *)grp) < 0)
return NC_EHDFERR;
nc4_rec_read_metadata_cb, (void *)&udata) < 0)
BAIL(NC_EHDFERR);

/* Process the types, datasets and groups found */
/* (Make certain it's in this order, so that the types are available for
* future datasets & child groups)
*/
for (oinfo = udata.types_head; oinfo; oinfo = udata.types_head)
{
/* Process the named datatype */
if ((retval = read_type(grp, oinfo->oid, oinfo->oname)))
BAIL(retval);

/* Close the object */
if (H5Oclose(oinfo->oid) < 0)
BAIL(NC_EHDFERR);

/* Advance to next node, free current node */
udata.types_head = oinfo->next;
free(oinfo);
}
for (oinfo = udata.dsets_head; oinfo; oinfo = udata.dsets_head)
{
/* Learn all about this dataset, which may be a dimscale
* (i.e. dimension metadata), or real data. */
if ((retval = read_dataset(grp, oinfo->oid, oinfo->oname, &oinfo->statbuf)))
{
/* Allow NC_EBADTYPID to transparently skip over datasets
* which have a datatype that netCDF-4 doesn't undertand
* (currently), but break out of iteration for other
* errors.
*/
if(NC_EBADTYPID != retval)
BAIL(retval);
else
retval = NC_NOERR;
}

/* Close the object */
if (H5Oclose(oinfo->oid) < 0)
BAIL(NC_EHDFERR);

/* Advance to next node, free current node */
udata.dsets_head = oinfo->next;
free(oinfo);
}
for (oinfo = udata.grps_head; oinfo; oinfo = udata.grps_head)
{
NC_GRP_INFO_T *child_grp;
NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info;

/* Add group to file's hierarchy */
if ((retval = nc4_grp_list_add(&(grp->children), h5->next_nc_grpid++,
grp, grp->nc4_info->controller, oinfo->oname, &child_grp)))
BAIL(retval);

/* Recursively read the child group's metadata */
if ((retval = nc4_rec_read_metadata(child_grp)))
BAIL(retval);

/* Close the object */
if (H5Oclose(oinfo->oid) < 0)
BAIL(NC_EHDFERR);

/* Advance to next node, free current node */
udata.grps_head = oinfo->next;
free(oinfo);
}

/* Scan the group for global (i.e. group-level) attributes. */
if ((retval = read_grp_atts(grp)))
return retval;
BAIL(retval);

return NC_NOERR; /* everything worked! */
exit:
/* Clean up local information on error, if anything remains */
if (retval)
{
for (oinfo = udata.types_head; oinfo; oinfo = udata.types_head)
{
/* Close the object */
if (H5Oclose(oinfo->oid) < 0)
BAIL(NC_EHDFERR);

/* Advance to next node, free current node */
udata.types_head = oinfo->next;
free(oinfo);
}
for (oinfo = udata.dsets_head; oinfo; oinfo = udata.dsets_head)
{
/* Close the object */
if (H5Oclose(oinfo->oid) < 0)
BAIL(NC_EHDFERR);

/* Advance to next node, free current node */
udata.dsets_head = oinfo->next;
free(oinfo);
}
for (oinfo = udata.grps_head; oinfo; oinfo = udata.grps_head)
{
/* Close the object */
if (H5Oclose(oinfo->oid) < 0)
BAIL(NC_EHDFERR);

/* Advance to next node, free current node */
udata.grps_head = oinfo->next;
free(oinfo);
}
}

return retval;
}

/* Open a netcdf-4 file. Things have already been kicked off in
Expand Down
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