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https://github.com/HDFGroup/hdf5.git
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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
This commit is contained in:
Elena Pourmal
parent
a6698e571c
commit
d7a89d6c7b
206
hl/src/H5DS.c
206
hl/src/H5DS.c
@ -620,9 +620,11 @@ out:
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*
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* Date: December 20, 2004
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*
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* Comments:
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* Comments:
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*
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* Modifications:
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* Modifications: Function didn't delete DIMENSION_LIST attribute, when
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* all dimension scales were detached from a dataset; added.
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* 2010/05/13 EIP
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*
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*-------------------------------------------------------------------------
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*/
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@ -642,14 +644,15 @@ herr_t H5DSdetach_scale(hid_t did,
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hid_t aid = -1; /* attribute ID */
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int rank; /* rank of dataset */
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ds_list_t *dsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */
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ds_list_t *dsbufn = NULL; /* array of attribute data in the DS pointing to the dataset */
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hsize_t *dims = NULL; /* dimension of the "REFERENCE_LIST" array */
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hsize_t dims[1]; /* dimension of the "REFERENCE_LIST" array */
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hobj_ref_t ref; /* reference to the DS */
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hvl_t *buf = NULL; /* VL buffer to store in the attribute */
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unsigned i, j, jj;
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H5O_info_t oi1, oi2, oi3, oi4;
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int i;
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size_t j;
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hssize_t ii;
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H5O_info_t did_oi, dsid_oi, tmp_oi;
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int found_dset = 0, found_ds = 0;
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H5I_type_t it1, it2;
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int have_ds = 0;
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htri_t is_scale;
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/*-------------------------------------------------------------------------
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@ -657,32 +660,28 @@ herr_t H5DSdetach_scale(hid_t did,
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*-------------------------------------------------------------------------
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*/
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if ((is_scale = H5DSis_scale(did)) < 0)
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/* check for valid types of identifiers */
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if(H5I_DATASET!=H5Iget_type(did) || H5I_DATASET!=H5Iget_type(dsid))
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return FAIL;
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if((is_scale = H5DSis_scale(did)) < 0)
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return FAIL;
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/* the dataset cannot be a DS dataset */
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if ( is_scale == 1)
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if( is_scale == 1)
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return FAIL;
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/* get info for the dataset in the parameter list */
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if(H5Oget_info(did, &oi1) < 0)
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if(H5Oget_info(did, &did_oi) < 0)
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return FAIL;
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/* get info for the scale in the parameter list */
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if(H5Oget_info(dsid, &oi2) < 0)
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if(H5Oget_info(dsid, &dsid_oi) < 0)
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return FAIL;
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/* same object, not valid */
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if(oi1.fileno == oi2.fileno && oi1.addr == oi2.addr)
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return FAIL;
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/* get ID type */
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if ((it1 = H5Iget_type(did)) < 0)
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return FAIL;
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if ((it2 = H5Iget_type(dsid)) < 0)
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return FAIL;
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if (H5I_DATASET!=it1 || H5I_DATASET!=it2)
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if(did_oi.fileno == dsid_oi.fileno && did_oi.addr == dsid_oi.addr)
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return FAIL;
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@ -761,46 +760,62 @@ herr_t H5DSdetach_scale(hid_t did,
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if ((dsid_j = H5Rdereference(did,H5R_OBJECT,&ref)) < 0)
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goto out;
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/* get info for DS in the parameter list */
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if(H5Oget_info(dsid, &oi1) < 0)
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/* get info for this DS */
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if(H5Oget_info(dsid_j, &tmp_oi) < 0)
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goto out;
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/* get info for this DS */
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if(H5Oget_info(dsid_j, &oi2) < 0)
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/* Close the dereferenced dataset */
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if (H5Dclose(dsid_j) < 0)
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goto out;
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/* same object, reset */
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if(oi1.fileno == oi2.fileno && oi1.addr == oi2.addr)
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if(dsid_oi.fileno == tmp_oi.fileno && dsid_oi.addr == tmp_oi.addr)
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{
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size_t len;
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/* If there are more than one reference in the VL element
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and the reference we found is not the last one,
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copy the last one to replace the found one since the order
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of the references doesn't matter according to the spec;
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reduce the size of the VL element by 1;
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if the length of the element becomes 0, free the pointer
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and reset to NULL */
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for(jj=j; jj<buf[idx].len-1; jj++)
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{
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((hobj_ref_t *)buf[idx].p)[jj] = ((hobj_ref_t *)buf[idx].p)[jj+1];
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size_t len = buf[idx].len;
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if(j<len-1)
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((hobj_ref_t *)buf[idx].p)[j] = ((hobj_ref_t *)buf[idx].p)[len-1];
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len = --buf[idx].len;
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if(len == 0) {
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free(buf[idx].p);
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buf[idx].p = NULL;
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}
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buf[idx].len--;
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len = buf[idx].len;
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buf[idx].p = realloc( buf[idx].p, len * sizeof(hobj_ref_t));
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/* Since a reference to a dim. scale can be inserted only once,
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we do not need to continue the search if it is found */
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found_ds = 1;
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/* close the dereferenced dataset and break */
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if (H5Dclose(dsid_j) < 0)
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goto out;
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break;
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}
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/* close the dereferenced dataset */
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if (H5Dclose(dsid_j) < 0)
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goto out;
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} /* j */
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} /* if */
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/* write the attribute */
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if (H5Awrite(aid,tid,buf) < 0)
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/* the scale must be present to continue */
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if(found_ds == 0)
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goto out;
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/* Write the attribute, but check first, if we have any scales left,
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because if not, we should delete the attribute according to the spec */
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for(i=0; i < rank; i++) {
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if(buf[i].len > 0) {
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have_ds = 1;
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break;
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}
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}
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if(have_ds) {
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if(H5Awrite(aid,tid,buf) < 0)
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goto out;
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}
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else {
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if(H5Adelete(did,DIMENSION_LIST) < 0)
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goto out;
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}
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/* close */
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if (H5Dvlen_reclaim(tid,sid,H5P_DEFAULT,buf) < 0)
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goto out;
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@ -817,9 +832,6 @@ herr_t H5DSdetach_scale(hid_t did,
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buf = NULL;
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}
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/* the scale must be present */
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if(found_ds == 0)
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goto out;
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/*-------------------------------------------------------------------------
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* the "REFERENCE_LIST" array exists, update
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@ -849,41 +861,36 @@ herr_t H5DSdetach_scale(hid_t did,
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if (H5Aread(aid,ntid,dsbuf) < 0)
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goto out;
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for(i=0; i<nelmts; i++)
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{
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/* get the reference to the dataset */
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ref = dsbuf[i].ref;
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for(ii=0; ii<nelmts; ii++) {
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/* First check if we have the same dimension index */
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if((int)idx == dsbuf[ii].dim_idx) {
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/* get the reference to the dataset */
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ref = dsbuf[ii].ref;
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/* get the dataset id */
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if ((did_i = H5Rdereference(did,H5R_OBJECT,&ref)) < 0)
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goto out;
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/* get info for dataset in the parameter list */
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if(H5Oget_info(did, &oi3) < 0)
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goto out;
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/* get info for this dataset */
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if(H5Oget_info(did_i, &oi4) < 0)
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goto out;
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/* same object, reset. we want to detach only for this DIM */
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if(oi3.fileno == oi4.fileno && oi3.addr == oi4.addr && (int)idx == dsbuf[i].dim_idx) {
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for(jj=i; jj<nelmts-1; jj++)
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dsbuf[jj] = dsbuf[jj+1];
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nelmts--;
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found_dset=1;
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/* close the dereferenced dataset and break */
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if (H5Dclose(did_i) < 0)
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/* get the dataset id */
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if ((did_i = H5Rdereference(did,H5R_OBJECT,&ref)) < 0)
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goto out;
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break;
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} /* if */
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/* close the dereferenced dataset */
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if (H5Dclose(did_i) < 0)
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goto out;
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/* get info for this dataset */
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if(H5Oget_info(did_i, &tmp_oi) < 0)
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goto out;
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} /* i */
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/* close the dereferenced dataset */
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if(H5Dclose(did_i) < 0)
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goto out;
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/* same object, reset. we want to detach only for this DIM */
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if(did_oi.fileno == tmp_oi.fileno && did_oi.addr == tmp_oi.addr) {
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/* if we found not the last one, copy the last one to replace
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the one which is found */
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if(i < nelmts-1)
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dsbuf[ii] = dsbuf[nelmts-1];
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nelmts--;
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found_dset=1;
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break;
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} /* if */
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} /* if we have the same dimension index */
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} /* ii */
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/* close space and attribute */
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if (H5Sclose(sid) < 0)
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@ -915,19 +922,8 @@ herr_t H5DSdetach_scale(hid_t did,
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if(nelmts)
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{
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/* create a new data space for the new references array */
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dims = (hsize_t*)malloc((size_t)nelmts * sizeof (hsize_t));
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if(dims == NULL)
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goto out;
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dims[0] = nelmts;
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dsbufn = (ds_list_t*) malloc((size_t)nelmts * sizeof(ds_list_t));
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if(dsbufn == NULL)
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goto out;
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/* store the new information */
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for(i = 0; i < nelmts; i++)
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dsbufn[i] = dsbuf[i];
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if((sid = H5Screate_simple(1, dims, NULL)) < 0)
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goto out;
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@ -936,7 +932,7 @@ herr_t H5DSdetach_scale(hid_t did,
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goto out;
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/* write the new attribute with the new references */
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if(H5Awrite(aid, tid, dsbufn) < 0)
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if(H5Awrite(aid, tid, dsbuf) < 0)
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goto out;
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/* close space and attribute */
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@ -955,16 +951,6 @@ herr_t H5DSdetach_scale(hid_t did,
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free(dsbuf);
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dsbuf=NULL;
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}
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if (dsbufn)
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{
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free(dsbufn);
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dsbufn=NULL;
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}
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if (dims)
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{
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free(dims);
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dims=NULL;
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}
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return SUCCEED;
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@ -982,18 +968,14 @@ out:
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free(dsbuf);
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dsbuf=NULL;
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}
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if (dsbufn)
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{
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free(dsbufn);
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dsbufn=NULL;
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}
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if (dims)
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{
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free(dims);
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dims=NULL;
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}
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if (buf)
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{
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/* Failure occured before H5Dvlen_reclaim was called;
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free the pointers allocated when we read data in */
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for(i=0; i<rank; i++) {
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if(buf[i].p)
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free(buf[i].p);
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}
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free(buf);
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buf=NULL;
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}
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@ -1218,7 +1200,7 @@ htri_t H5DSis_attached(hid_t did,
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if (dsbuf == NULL)
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goto out;
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if (H5Aread(aid,ntid,dsbuf) < 0)
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if (H5Aread(aid,ntid,dsbuf) < 0)
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goto out;
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/*-------------------------------------------------------------------------
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@ -46,6 +46,6 @@ endif
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# Temporary files. These files are the ones created by running `make test'.
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CHECK_CLEANFILES+=combine_tables[1-2].h5 test_ds[1-9].h5 test_image[1-3].h5 \
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test_lite[1-2].h5 test_table.h5 test_packet_table.h5 \
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test_packet_compress.h5
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test_packet_compress.h5 test_detach.h5
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include $(top_srcdir)/config/conclude.am
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@ -383,7 +383,8 @@ TRACE = perl $(top_srcdir)/bin/trace
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# Temporary files. These files are the ones created by running `make test'.
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CHECK_CLEANFILES = *.chkexe *.chklog *.clog combine_tables[1-2].h5 \
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test_ds[1-9].h5 test_image[1-3].h5 test_lite[1-2].h5 \
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test_table.h5 test_packet_table.h5 test_packet_compress.h5
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test_table.h5 test_packet_table.h5 test_packet_compress.h5 \
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test_detach.h5
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# The tests depend on the hdf5, hdf5 test, and hdf5_hl libraries
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LDADD = $(LIBH5_HL) $(LIBH5TEST) $(LIBHDF5)
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@ -71,6 +71,7 @@ static int test_long_scalenames(const char *fileext);
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static int test_samelong_scalenames(const char *fileext);
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static int test_float_scalenames(const char *fileext);
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static int test_foreign_scaleattached(const char *fileforeign);
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static int test_detachscales(void);
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static int test_simple(void);
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static int test_errors(void);
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@ -136,6 +137,9 @@ static int read_data( const char* fname, int ndims, hsize_t *dims, float **buf )
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#define FILE6 "test_ds8.h5"
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#define FILE7 "test_ds9.h5"
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#define DIMENSION_LIST "DIMENSION_LIST"
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#define REFERENCE_LIST "REFERENCE_LIST"
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/*-------------------------------------------------------------------------
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* the main program
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*-------------------------------------------------------------------------
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@ -169,6 +173,7 @@ int main(void)
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nerrors += test_samelong_scalenames("2") < 0 ? 1 : 0;
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nerrors += test_foreign_scaleattached(FOREIGN_FILE1) < 0 ? 1 : 0;
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nerrors += test_foreign_scaleattached(FOREIGN_FILE2) < 0 ? 1 : 0;
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nerrors += test_detachscales() < 0 ? 1 : 0;
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/* the following tests have not been rewritten to match those above */
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nerrors += test_simple() < 0 ?1:0;
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@ -1144,6 +1149,148 @@ herr_t test_cmp_scalename(hid_t fid, hid_t did, const char *name, const char *sc
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return ret_value;
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}
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static int test_detachscales(void)
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{
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hid_t fid = -1;
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hid_t did = -1;
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hid_t dsid = -1;
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int rank1 = 1;
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int rank3 = 3;
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hsize_t dims[] = {1,2,3}; /*some bogus numbers, not important for the test*/
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int *buf = NULL;
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char dname[10];
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int i;
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/* This tests creates two three dimensional datasets; then it creates
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four integer datasets that are used as dim. scales; we will attach
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and detach them to check that at the end there is no attributes
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REFERENCE_LIST on a dimension scale and DIMENSION_LIST on a dataset */
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TESTING2("test_detachscales");
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if((fid = H5Fcreate("test_detach.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
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goto out;
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/* make datasets; they are three dimensional*/
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for (i=0; i < 2; i++) {
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sprintf(dname,"D%d", i);
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if(H5LTmake_dataset_int(fid, dname, rank3, dims, buf) < 0)
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goto out;
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}
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/* create datasets and make them dim. scales */
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for (i=0; i < 4; i++) {
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sprintf(dname, "DS%d", i);
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if(H5LTmake_dataset_int(fid, dname, rank1, dims, buf) < 0)
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goto out;
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}
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/* attach scales to the first dataset; first dimension will have
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two scales attached */
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if((did = H5Dopen2(fid, "D0", H5P_DEFAULT)) >= 0) {
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for (i=0; i<4; i++) {
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sprintf(dname, "DS%d", i);
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if((dsid = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0)
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goto out;
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if(H5DSattach_scale(did, dsid, (unsigned int) i%3) < 0)
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goto out;
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if(H5Dclose(dsid) < 0)
|
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goto out;
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}
|
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if(H5Dclose(did) < 0)
|
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goto out;
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}
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else
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goto out;
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|
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/* attach scales to the second dataset */
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if((did = H5Dopen2(fid, "D1", H5P_DEFAULT)) >= 0) {
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for (i=0; i<3; i++) {
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sprintf(dname, "DS%d", i);
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if((dsid = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0)
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goto out;
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if(H5DSattach_scale(did, dsid, (unsigned int) i) < 0)
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goto out;
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if(H5Dclose(dsid) < 0)
|
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goto out;
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}
|
||||
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;
|
||||
|
||||
@ -469,6 +469,13 @@ Bug Fixes since HDF5-1.8.0 release
|
||||
|
||||
High-Level APIs:
|
||||
------
|
||||
- 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.
|
||||
(EIP - 2010/05/14 -1822)
|
||||
- Fixed a bug where the H5TB API would forget the order of fields when
|
||||
added out of offset order. (NAF - 2009/10/27 - 1582)
|
||||
- H5DSis_attached failed to account for different platform types. Added a
|
||||
|
||||
Loading…
Reference in New Issue
Block a user