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authorElena Pourmal <epourmal@hdfgroup.org>2010-05-15 04:10:53 (GMT)
committerElena Pourmal <epourmal@hdfgroup.org>2010-05-15 04:10:53 (GMT)
commitd7a89d6c7b67932c9c96e3ddc799605482391fdc (patch)
treeb13bee3e3b066b60f79cabf1876d0d35143cd8f1 /hl
parenta6698e571c3e08084e1b572ec29ce66c1d183214 (diff)
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[svn-r18818] Bug fix:
Fixed a bug in the H5DSdetach_scale function when 0 bytes were allocated after the last reference to a dim. scale was removed from the list of references in a VL element of the DIMENSION_LIST attribute; modified the function to comply with the Spec: DIMENSION_LIST attribute is deleted now when no dimension scales left attached. Platforms tested: jam with electric fence, amani amd linew
Diffstat (limited to 'hl')
-rw-r--r--hl/src/H5DS.c206
-rw-r--r--hl/test/Makefile.am2
-rw-r--r--hl/test/Makefile.in3
-rw-r--r--hl/test/test_ds.c147
4 files changed, 244 insertions, 114 deletions
diff --git a/hl/src/H5DS.c b/hl/src/H5DS.c
index 245a2c5..936afd1 100644
--- a/hl/src/H5DS.c
+++ b/hl/src/H5DS.c
@@ -620,9 +620,11 @@ out:
*
* Date: December 20, 2004
*
-* Comments:
+* Comments:
*
-* Modifications:
+* Modifications: Function didn't delete DIMENSION_LIST attribute, when
+* all dimension scales were detached from a dataset; added.
+* 2010/05/13 EIP
*
*-------------------------------------------------------------------------
*/
@@ -642,14 +644,15 @@ herr_t H5DSdetach_scale(hid_t did,
hid_t aid = -1; /* attribute ID */
int rank; /* rank of dataset */
ds_list_t *dsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */
- ds_list_t *dsbufn = NULL; /* array of attribute data in the DS pointing to the dataset */
- hsize_t *dims = NULL; /* dimension of the "REFERENCE_LIST" array */
+ hsize_t dims[1]; /* dimension of the "REFERENCE_LIST" array */
hobj_ref_t ref; /* reference to the DS */
hvl_t *buf = NULL; /* VL buffer to store in the attribute */
- unsigned i, j, jj;
- H5O_info_t oi1, oi2, oi3, oi4;
+ int i;
+ size_t j;
+ hssize_t ii;
+ H5O_info_t did_oi, dsid_oi, tmp_oi;
int found_dset = 0, found_ds = 0;
- H5I_type_t it1, it2;
+ int have_ds = 0;
htri_t is_scale;
/*-------------------------------------------------------------------------
@@ -657,32 +660,28 @@ herr_t H5DSdetach_scale(hid_t did,
*-------------------------------------------------------------------------
*/
- if ((is_scale = H5DSis_scale(did)) < 0)
+ /* check for valid types of identifiers */
+
+ if(H5I_DATASET!=H5Iget_type(did) || H5I_DATASET!=H5Iget_type(dsid))
+ return FAIL;
+
+ if((is_scale = H5DSis_scale(did)) < 0)
return FAIL;
/* the dataset cannot be a DS dataset */
- if ( is_scale == 1)
+ if( is_scale == 1)
return FAIL;
/* get info for the dataset in the parameter list */
- if(H5Oget_info(did, &oi1) < 0)
+ if(H5Oget_info(did, &did_oi) < 0)
return FAIL;
/* get info for the scale in the parameter list */
- if(H5Oget_info(dsid, &oi2) < 0)
+ if(H5Oget_info(dsid, &dsid_oi) < 0)
return FAIL;
/* same object, not valid */
- if(oi1.fileno == oi2.fileno && oi1.addr == oi2.addr)
- return FAIL;
-
- /* get ID type */
- if ((it1 = H5Iget_type(did)) < 0)
- return FAIL;
- if ((it2 = H5Iget_type(dsid)) < 0)
- return FAIL;
-
- if (H5I_DATASET!=it1 || H5I_DATASET!=it2)
+ if(did_oi.fileno == dsid_oi.fileno && did_oi.addr == dsid_oi.addr)
return FAIL;
@@ -761,46 +760,62 @@ herr_t H5DSdetach_scale(hid_t did,
if ((dsid_j = H5Rdereference(did,H5R_OBJECT,&ref)) < 0)
goto out;
- /* get info for DS in the parameter list */
- if(H5Oget_info(dsid, &oi1) < 0)
+ /* get info for this DS */
+ if(H5Oget_info(dsid_j, &tmp_oi) < 0)
goto out;
- /* get info for this DS */
- if(H5Oget_info(dsid_j, &oi2) < 0)
+ /* Close the dereferenced dataset */
+ if (H5Dclose(dsid_j) < 0)
goto out;
/* same object, reset */
- if(oi1.fileno == oi2.fileno && oi1.addr == oi2.addr)
+ if(dsid_oi.fileno == tmp_oi.fileno && dsid_oi.addr == tmp_oi.addr)
{
- size_t len;
-
- for(jj=j; jj<buf[idx].len-1; jj++)
- {
- ((hobj_ref_t *)buf[idx].p)[jj] = ((hobj_ref_t *)buf[idx].p)[jj+1];
+ /* If there are more than one reference in the VL element
+ and the reference we found is not the last one,
+ copy the last one to replace the found one since the order
+ of the references doesn't matter according to the spec;
+ reduce the size of the VL element by 1;
+ if the length of the element becomes 0, free the pointer
+ and reset to NULL */
+
+ size_t len = buf[idx].len;
+ if(j<len-1)
+ ((hobj_ref_t *)buf[idx].p)[j] = ((hobj_ref_t *)buf[idx].p)[len-1];
+ len = --buf[idx].len;
+ if(len == 0) {
+ free(buf[idx].p);
+ buf[idx].p = NULL;
}
-
- buf[idx].len--;
- len = buf[idx].len;
- buf[idx].p = realloc( buf[idx].p, len * sizeof(hobj_ref_t));
-
+ /* Since a reference to a dim. scale can be inserted only once,
+ we do not need to continue the search if it is found */
found_ds = 1;
-
- /* close the dereferenced dataset and break */
- if (H5Dclose(dsid_j) < 0)
- goto out;
break;
}
-
- /* close the dereferenced dataset */
- if (H5Dclose(dsid_j) < 0)
- goto out;
} /* j */
} /* if */
- /* write the attribute */
- if (H5Awrite(aid,tid,buf) < 0)
+ /* the scale must be present to continue */
+ if(found_ds == 0)
goto out;
+ /* Write the attribute, but check first, if we have any scales left,
+ because if not, we should delete the attribute according to the spec */
+ for(i=0; i < rank; i++) {
+ if(buf[i].len > 0) {
+ have_ds = 1;
+ break;
+ }
+ }
+ if(have_ds) {
+ if(H5Awrite(aid,tid,buf) < 0)
+ goto out;
+ }
+ else {
+ if(H5Adelete(did,DIMENSION_LIST) < 0)
+ goto out;
+ }
+
/* close */
if (H5Dvlen_reclaim(tid,sid,H5P_DEFAULT,buf) < 0)
goto out;
@@ -817,9 +832,6 @@ herr_t H5DSdetach_scale(hid_t did,
buf = NULL;
}
- /* the scale must be present */
- if(found_ds == 0)
- goto out;
/*-------------------------------------------------------------------------
* the "REFERENCE_LIST" array exists, update
@@ -849,41 +861,36 @@ herr_t H5DSdetach_scale(hid_t did,
if (H5Aread(aid,ntid,dsbuf) < 0)
goto out;
- for(i=0; i<nelmts; i++)
- {
- /* get the reference to the dataset */
- ref = dsbuf[i].ref;
-
- /* get the dataset id */
- if ((did_i = H5Rdereference(did,H5R_OBJECT,&ref)) < 0)
- goto out;
+ for(ii=0; ii<nelmts; ii++) {
+ /* First check if we have the same dimension index */
+ if((int)idx == dsbuf[ii].dim_idx) {
+ /* get the reference to the dataset */
+ ref = dsbuf[ii].ref;
- /* get info for dataset in the parameter list */
- if(H5Oget_info(did, &oi3) < 0)
- goto out;
-
- /* get info for this dataset */
- if(H5Oget_info(did_i, &oi4) < 0)
- goto out;
-
- /* same object, reset. we want to detach only for this DIM */
- if(oi3.fileno == oi4.fileno && oi3.addr == oi4.addr && (int)idx == dsbuf[i].dim_idx) {
- for(jj=i; jj<nelmts-1; jj++)
- dsbuf[jj] = dsbuf[jj+1];
- nelmts--;
- found_dset=1;
+ /* get the dataset id */
+ if ((did_i = H5Rdereference(did,H5R_OBJECT,&ref)) < 0)
+ goto out;
- /* close the dereferenced dataset and break */
- if (H5Dclose(did_i) < 0)
+ /* get info for this dataset */
+ if(H5Oget_info(did_i, &tmp_oi) < 0)
goto out;
- break;
- } /* if */
- /* close the dereferenced dataset */
- if (H5Dclose(did_i) < 0)
- goto out;
+ /* close the dereferenced dataset */
+ if(H5Dclose(did_i) < 0)
+ goto out;
- } /* i */
+ /* same object, reset. we want to detach only for this DIM */
+ if(did_oi.fileno == tmp_oi.fileno && did_oi.addr == tmp_oi.addr) {
+ /* if we found not the last one, copy the last one to replace
+ the one which is found */
+ if(i < nelmts-1)
+ dsbuf[ii] = dsbuf[nelmts-1];
+ nelmts--;
+ found_dset=1;
+ break;
+ } /* if */
+ } /* if we have the same dimension index */
+ } /* ii */
/* close space and attribute */
if (H5Sclose(sid) < 0)
@@ -915,19 +922,8 @@ herr_t H5DSdetach_scale(hid_t did,
if(nelmts)
{
/* create a new data space for the new references array */
- dims = (hsize_t*)malloc((size_t)nelmts * sizeof (hsize_t));
- if(dims == NULL)
- goto out;
dims[0] = nelmts;
- dsbufn = (ds_list_t*) malloc((size_t)nelmts * sizeof(ds_list_t));
- if(dsbufn == NULL)
- goto out;
-
- /* store the new information */
- for(i = 0; i < nelmts; i++)
- dsbufn[i] = dsbuf[i];
-
if((sid = H5Screate_simple(1, dims, NULL)) < 0)
goto out;
@@ -936,7 +932,7 @@ herr_t H5DSdetach_scale(hid_t did,
goto out;
/* write the new attribute with the new references */
- if(H5Awrite(aid, tid, dsbufn) < 0)
+ if(H5Awrite(aid, tid, dsbuf) < 0)
goto out;
/* close space and attribute */
@@ -955,16 +951,6 @@ herr_t H5DSdetach_scale(hid_t did,
free(dsbuf);
dsbuf=NULL;
}
- if (dsbufn)
- {
- free(dsbufn);
- dsbufn=NULL;
- }
- if (dims)
- {
- free(dims);
- dims=NULL;
- }
return SUCCEED;
@@ -982,18 +968,14 @@ out:
free(dsbuf);
dsbuf=NULL;
}
- if (dsbufn)
- {
- free(dsbufn);
- dsbufn=NULL;
- }
- if (dims)
- {
- free(dims);
- dims=NULL;
- }
if (buf)
{
+ /* Failure occured before H5Dvlen_reclaim was called;
+ free the pointers allocated when we read data in */
+ for(i=0; i<rank; i++) {
+ if(buf[i].p)
+ free(buf[i].p);
+ }
free(buf);
buf=NULL;
}
@@ -1218,7 +1200,7 @@ htri_t H5DSis_attached(hid_t did,
if (dsbuf == NULL)
goto out;
- if (H5Aread(aid,ntid,dsbuf) < 0)
+ if (H5Aread(aid,ntid,dsbuf) < 0)
goto out;
/*-------------------------------------------------------------------------
diff --git a/hl/test/Makefile.am b/hl/test/Makefile.am
index fc6e969..86e3318 100644
--- a/hl/test/Makefile.am
+++ b/hl/test/Makefile.am
@@ -46,6 +46,6 @@ endif
# Temporary files. These files are the ones created by running `make test'.
CHECK_CLEANFILES+=combine_tables[1-2].h5 test_ds[1-9].h5 test_image[1-3].h5 \
test_lite[1-2].h5 test_table.h5 test_packet_table.h5 \
- test_packet_compress.h5
+ test_packet_compress.h5 test_detach.h5
include $(top_srcdir)/config/conclude.am
diff --git a/hl/test/Makefile.in b/hl/test/Makefile.in
index a625c86..a68831e 100644
--- a/hl/test/Makefile.in
+++ b/hl/test/Makefile.in
@@ -383,7 +383,8 @@ TRACE = perl $(top_srcdir)/bin/trace
# Temporary files. These files are the ones created by running `make test'.
CHECK_CLEANFILES = *.chkexe *.chklog *.clog combine_tables[1-2].h5 \
test_ds[1-9].h5 test_image[1-3].h5 test_lite[1-2].h5 \
- test_table.h5 test_packet_table.h5 test_packet_compress.h5
+ test_table.h5 test_packet_table.h5 test_packet_compress.h5 \
+ test_detach.h5
# The tests depend on the hdf5, hdf5 test, and hdf5_hl libraries
LDADD = $(LIBH5_HL) $(LIBH5TEST) $(LIBHDF5)
diff --git a/hl/test/test_ds.c b/hl/test/test_ds.c
index d1705ec..2477bc0 100644
--- a/hl/test/test_ds.c
+++ b/hl/test/test_ds.c
@@ -71,6 +71,7 @@ static int test_long_scalenames(const char *fileext);
static int test_samelong_scalenames(const char *fileext);
static int test_float_scalenames(const char *fileext);
static int test_foreign_scaleattached(const char *fileforeign);
+static int test_detachscales(void);
static int test_simple(void);
static int test_errors(void);
@@ -136,6 +137,9 @@ static int read_data( const char* fname, int ndims, hsize_t *dims, float **buf )
#define FILE6 "test_ds8.h5"
#define FILE7 "test_ds9.h5"
+#define DIMENSION_LIST "DIMENSION_LIST"
+#define REFERENCE_LIST "REFERENCE_LIST"
+
/*-------------------------------------------------------------------------
* the main program
*-------------------------------------------------------------------------
@@ -169,6 +173,7 @@ int main(void)
nerrors += test_samelong_scalenames("2") < 0 ? 1 : 0;
nerrors += test_foreign_scaleattached(FOREIGN_FILE1) < 0 ? 1 : 0;
nerrors += test_foreign_scaleattached(FOREIGN_FILE2) < 0 ? 1 : 0;
+ nerrors += test_detachscales() < 0 ? 1 : 0;
/* the following tests have not been rewritten to match those above */
nerrors += test_simple() < 0 ?1:0;
@@ -1144,6 +1149,148 @@ herr_t test_cmp_scalename(hid_t fid, hid_t did, const char *name, const char *sc
return ret_value;
}
+static int test_detachscales(void)
+{
+ hid_t fid = -1;
+ hid_t did = -1;
+ hid_t dsid = -1;
+ int rank1 = 1;
+ int rank3 = 3;
+ hsize_t dims[] = {1,2,3}; /*some bogus numbers, not important for the test*/
+ int *buf = NULL;
+ char dname[10];
+ int i;
+
+ /* This tests creates two three dimensional datasets; then it creates
+ four integer datasets that are used as dim. scales; we will attach
+ and detach them to check that at the end there is no attributes
+ REFERENCE_LIST on a dimension scale and DIMENSION_LIST on a dataset */
+
+ TESTING2("test_detachscales");
+
+ if((fid = H5Fcreate("test_detach.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+
+ /* make datasets; they are three dimensional*/
+ for (i=0; i < 2; i++) {
+ sprintf(dname,"D%d", i);
+ if(H5LTmake_dataset_int(fid, dname, rank3, dims, buf) < 0)
+ goto out;
+ }
+ /* create datasets and make them dim. scales */
+
+ for (i=0; i < 4; i++) {
+ sprintf(dname, "DS%d", i);
+ if(H5LTmake_dataset_int(fid, dname, rank1, dims, buf) < 0)
+ goto out;
+ }
+ /* attach scales to the first dataset; first dimension will have
+ two scales attached */
+ if((did = H5Dopen2(fid, "D0", H5P_DEFAULT)) >= 0) {
+ for (i=0; i<4; i++) {
+ sprintf(dname, "DS%d", i);
+ if((dsid = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5DSattach_scale(did, dsid, (unsigned int) i%3) < 0)
+ goto out;
+ if(H5Dclose(dsid) < 0)
+ goto out;
+ }
+ if(H5Dclose(did) < 0)
+ goto out;
+ }
+ else
+ goto out;
+
+ /* attach scales to the second dataset */
+ if((did = H5Dopen2(fid, "D1", H5P_DEFAULT)) >= 0) {
+ for (i=0; i<3; i++) {
+ sprintf(dname, "DS%d", i);
+ if((dsid = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5DSattach_scale(did, dsid, (unsigned int) i) < 0)
+ goto out;
+ if(H5Dclose(dsid) < 0)
+ goto out;
+ }
+ if(H5Dclose(did) < 0)
+ goto out;
+ }
+ else
+ goto out;
+
+ /* detach DS0 from first dimension of D0 and D1; then check
+ that DS0 doesn't have attribute REFERENCE _LIST */
+
+ if((dsid = H5Dopen2(fid, "DS0", H5P_DEFAULT)) < 0)
+ goto out;
+
+ for (i=0; i<2; i++) {
+ sprintf(dname, "D%d", i);
+ if((did = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5DSdetach_scale(did, dsid, (unsigned int)0) < 0)
+ goto out;
+ if(H5Dclose(did) < 0)
+ goto out;
+ }
+ /* Check that attribute "REFERENCE_LIST" doesn't exist anymore */
+ if(H5Aexists(dsid, REFERENCE_LIST)!= 0)
+ goto out;
+ if(H5Dclose(dsid) < 0)
+ goto out;
+ /* Check that DS3 is the only dim. scale attached to the first
+ dimension of D0 */
+ if((did = H5Dopen2(fid, "D0", H5P_DEFAULT)) < 0)
+ goto out;
+ if((dsid = H5Dopen2(fid, "DS3", H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5DSis_attached(did, dsid, (unsigned int) 0) <= 0)
+ goto out;
+ if(H5Dclose(did) < 0)
+ goto out;
+ if(H5Dclose(dsid) < 0)
+ goto out;
+
+ /* Detach the rest of the scales DS3, DS1, DS2 from D0 and make
+ sure that attribute "DIMENSION_LIST" doesn't exist anymore */
+ if((did = H5Dopen2(fid, "D0", H5P_DEFAULT)) >= 0) {
+ for (i=1; i<4; i++) {
+ sprintf(dname, "DS%d", i);
+ if((dsid = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5DSdetach_scale(did, dsid, (unsigned int) i%3) < 0)
+ goto out;
+ if(H5Dclose(dsid) < 0)
+ goto out;
+ }
+ /* Check that attribute "REFERENCE_LIST" doesn't exist anymore */
+ if(H5Aexists(did, DIMENSION_LIST)!= 0)
+ goto out;
+ if(H5Dclose(did) < 0)
+ goto out;
+ }
+ else
+ goto out;
+
+
+ PASSED();
+
+ H5Fclose(fid);
+ return SUCCEED;
+
+out:
+ H5E_BEGIN_TRY {
+ H5Dclose(did);
+ H5Dclose(dsid);
+ H5Fclose(fid);
+ } H5E_END_TRY;
+
+ H5_FAILED();
+
+ return FAIL;
+}
+
static int test_char_attachscales(const char *fileext)
{
hid_t fid = -1;