CMake.git - CMake is a cross-platform, open-source build system generator.

	Commit message (Collapse)	Author	Age	Files	Lines
*	ENH: Create CTestCustom.cmake instead of CTestCustom.ctest. Create the old ↵	Brad King	2007-08-31	1	-41/+3
\| \| \| \|	file to include the new one for compatibility. This should prevent the long delays of CTest traversing the whole tree looking for CTestCustom.ctest files.
*	ENH: fix warnings on windows paths	Bill Hoffman	2006-10-27	1	-6/+6
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*	ENH: try to get rid of clock skew warning	Bill Hoffman	2006-07-25	1	-0/+1
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*	ENH: supress xcode warning	Bill Hoffman	2006-04-21	1	-1/+1
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*	ENH: add ignore for xcode	Bill Hoffman	2006-04-20	1	-0/+1
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*	ENH: Some ctest custom fixes	Andy Cedilnik	2006-04-10	1	-9/+9
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*	ENH: try to get rid of warning on HP	Bill Hoffman	2006-03-23	1	-1/+1
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*	ENH: add more warning stuff	Bill Hoffman	2006-03-18	1	-0/+1
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*	ENH: cleaner code coverage	Ken Martin	2005-09-15	1	-0/+6
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*	ENH: coverage cleanup for non XCode builds	Ken Martin	2005-09-13	1	-0/+8
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*	COMP: shut up warning	Ken Martin	2005-06-29	1	-1/+1
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*	ENH: mods to warning excludes based on new locaiton of curl	Ken Martin	2005-06-27	1	-0/+1
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*	ENH: shut up buggy gcc stl header	Ken Martin	2005-06-03	1	-1/+2
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*	COMP: suppress warnings in 3rd party libs	Ken Martin	2005-06-01	1	-0/+2
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*	ENH: shut up some warning on SGI	Ken Martin	2005-05-31	1	-1/+3
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*	ENH: shut up warning in 3rd party packages	Ken Martin	2005-03-31	1	-0/+3
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*	ENH: add supp for xlc linking on darwin	Ken Martin	2005-02-16	1	-0/+1
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*	COMP: add a warning ignore for gcc 3.4.2	Bill Hoffman	2005-02-16	1	-0/+1
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*	ENH: added supp for Curl coding style	Ken Martin	2005-02-14	1	-0/+1
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*	ENH: added custom supp for cmake	Ken Martin	2004-11-10	1	-0/+12

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5repack.h" #include "h5diff.h" #include "h5tools.h" /*------------------------------------------------------------------------- * local functions *------------------------------------------------------------------------- */ static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt); static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options, trav_table_t *travt, hid_t fidout); static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, hid_t fid_out, void *ref_out, trav_table_t *travt); /*------------------------------------------------------------------------- * Function: do_copy_refobjs * * Purpose: duplicate all referenced HDF5 objects in the file * and create hard links * * Return: 0, ok, -1 no * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: December, 10, 2003 * *------------------------------------------------------------------------- */ int do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { hid_t grp_in = (-1); /* read group ID */ hid_t grp_out = (-1); /* write group ID */ hid_t dset_in = (-1); /* read dataset ID */ hid_t dset_out = (-1); /* write dataset ID */ hid_t type_in = (-1); /* named type ID */ hid_t dcpl_id = (-1); /* dataset creation property list ID */ hid_t space_id = (-1); /* space ID */ hid_t ftype_id = (-1); /* file data type ID */ hid_t mtype_id = (-1); /* memory data type ID */ size_t msize; /* memory size of memory type */ hsize_t nelmts; /* number of elements in dataset */ int rank; /* rank of dataset */ hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ unsigned int i, j; int k; named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes copied */ /*------------------------------------------------------------------------- * browse *------------------------------------------------------------------------- */ for(i = 0; i < travt->nobjs; i++) { switch(travt->objs[i].type) { /*------------------------------------------------------------------------- * H5TRAV_TYPE_GROUP *------------------------------------------------------------------------- */ case H5TRAV_TYPE_GROUP: /*------------------------------------------------------------------------- * copy referenced objects in attributes *------------------------------------------------------------------------- */ if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) goto error; if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) goto error; if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0) goto error; if(H5Gclose(grp_out) < 0) goto error; if(H5Gclose(grp_in) < 0) goto error; /*------------------------------------------------------------------------- * check for hard links *------------------------------------------------------------------------- */ if(travt->objs[i].nlinks) for(j = 0; j < travt->objs[i].nlinks; j++) H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); break; /*------------------------------------------------------------------------- * H5TRAV_TYPE_DATASET *------------------------------------------------------------------------- */ case H5TRAV_TYPE_DATASET: if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) goto error; if((space_id = H5Dget_space(dset_in)) < 0) goto error; if((ftype_id = H5Dget_type(dset_in)) < 0) goto error; if((dcpl_id = H5Dget_create_plist(dset_in)) < 0) goto error; if((rank = H5Sget_simple_extent_ndims(space_id)) < 0) goto error; if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) goto error; nelmts = 1; for(k = 0; k < rank; k++) nelmts *= dims[k]; if((mtype_id = h5tools_get_native_type(ftype_id)) < 0) goto error; if((msize = H5Tget_size(mtype_id)) == 0) goto error; /*------------------------------------------------------------------------- * check if the dataset creation property list has filters that * are not registered in the current configuration * 1) the external filters GZIP and SZIP might not be available * 2) the internal filters might be turned off *------------------------------------------------------------------------- */ if(h5tools_canreadf(NULL, dcpl_id) == 1) { /*------------------------------------------------------------------------- * test for a valid output dataset *------------------------------------------------------------------------- */ dset_out = FAIL; /*------------------------------------------------------------------------- * object references are a special case * we cannot just copy the buffers, but instead we recreate the reference *------------------------------------------------------------------------- */ if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { hid_t refobj_id; hobj_ref_t *refbuf = NULL; /* buffer for object references */ hobj_ref_t *buf = NULL; const char* refname; unsigned u; /*------------------------------------------------------------------------- * read to memory *------------------------------------------------------------------------- */ if(nelmts) { buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf==NULL) { printf("cannot read into memory\n" ); goto error; } /* end if */ if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) goto error; refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize); if(refbuf == NULL){ printf("cannot allocate memory\n" ); goto error; } /* end if */ for(u = 0; u < nelmts; u++) { H5E_BEGIN_TRY { if((refobj_id = H5Rdereference(dset_in, H5R_OBJECT, &buf[u])) < 0) continue; } H5E_END_TRY; /* get the name. a valid name could only occur * in the second traversal of the file */ if((refname = MapIdToName(refobj_id, travt)) != NULL) { /* create the reference, -1 parameter for objects */ if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, -1) < 0) goto error; if(options->verbose) { printf(FORMAT_OBJ,"dset",travt->objs[i].name ); printf("object <%s> object reference created to <%s>\n", travt->objs[i].name, refname); } } /*refname*/ H5Oclose(refobj_id); } /* u */ } /*nelmts*/ /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) goto error; if(nelmts) if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) goto error; if(buf) HDfree(buf); if(refbuf) HDfree(refbuf); /*------------------------------------------------------ * copy attrs *----------------------------------------------------*/ if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) goto error; } /*H5T_STD_REF_OBJ*/ /*------------------------------------------------------------------------- * dataset region references *------------------------------------------------------------------------- */ else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { hid_t refobj_id; hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */ hdset_reg_ref_t *buf = NULL; /* output buffer */ const char* refname; unsigned u; /*------------------------------------------------------------------------- * read input to memory *------------------------------------------------------------------------- */ if(nelmts) { buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf == NULL) { printf("cannot read into memory\n"); goto error; } /* end if */ if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) goto error; /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ if(refbuf == NULL) { printf("cannot allocate memory\n"); goto error; } /* end if */ for(u = 0; u < nelmts; u++) { H5E_BEGIN_TRY { if((refobj_id = H5Rdereference(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) continue; } H5E_END_TRY; /* get the name. a valid name could only occur * in the second traversal of the file */ if((refname = MapIdToName(refobj_id, travt)) != NULL) { hid_t region_id; /* region id of the referenced dataset */ if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) goto error; /* create the reference, we need the space_id */ if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0) goto error; if(H5Sclose(region_id) < 0) goto error; if(options->verbose) { printf(FORMAT_OBJ,"dset",travt->objs[i].name ); printf("object <%s> region reference created to <%s>\n", travt->objs[i].name, refname); } } /*refname*/ H5Oclose(refobj_id); } /* u */ } /*nelmts*/ /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) goto error; if(nelmts) if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) goto error; if(buf) HDfree(buf); if(refbuf) HDfree(refbuf); /*----------------------------------------------------- * copy attrs *----------------------------------------------------*/ if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) goto error; } /* H5T_STD_REF_DSETREG */ /*------------------------------------------------------------------------- * not references, open previously created object in 1st traversal *------------------------------------------------------------------------- */ else { if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) goto error; } /* end else */ HDassert(dset_out != FAIL); /*------------------------------------------------------------------------- * copy referenced objects in attributes *------------------------------------------------------------------------- */ if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0) goto error; /*------------------------------------------------------------------------- * check for hard links *------------------------------------------------------------------------- */ if(travt->objs[i].nlinks) for(j = 0; j < travt->objs[i].nlinks; j++) H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); if(H5Dclose(dset_out) < 0) goto error; } /*can_read*/ /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ if(H5Tclose(ftype_id) < 0) goto error; if(H5Tclose(mtype_id) < 0) goto error; if(H5Pclose(dcpl_id) < 0) goto error; if(H5Sclose(space_id) < 0) goto error; if(H5Dclose(dset_in) < 0) goto error; break; /*------------------------------------------------------------------------- * H5TRAV_TYPE_NAMED_DATATYPE *------------------------------------------------------------------------- */ case H5TRAV_TYPE_NAMED_DATATYPE: if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) goto error; if(H5Tclose(type_in) < 0) goto error; break; /*------------------------------------------------------------------------- * H5TRAV_TYPE_LINK *------------------------------------------------------------------------- */ case H5TRAV_TYPE_LINK: /*nothing to do */ break; case H5TRAV_TYPE_UNKNOWN: case H5TRAV_TYPE_UDLINK: goto error; default: break; } /* end switch */ } /* end for */ /* Finalize (link) the stack of named datatypes (if any) * This function is paired with copy_named_datatype() which is called * in copy_attr(), so need to free. */ named_datatype_free(&named_dt_head, 0); return 0; error: H5E_BEGIN_TRY { H5Gclose(grp_in); H5Gclose(grp_out); H5Pclose(dcpl_id); H5Sclose(space_id); H5Dclose(dset_in); H5Dclose(dset_out); H5Tclose(ftype_id); H5Tclose(mtype_id); H5Tclose(type_in); named_datatype_free(&named_dt_head, 0); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: copy_refs_attr * * Purpose: duplicate all referenced HDF5 located in attributes * relative to LOC_IN, which is obtained either from * loc_id = H5Gopen2(fid, name, H5P_DEFAULT); * loc_id = H5Dopen2(fid, name, H5P_DEFAULT); * loc_id = H5Topen2(fid, name, H5P_DEFAULT); * * Return: 0, ok, -1 no * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Modifier: xcao@hdfgroup.org, 9/12/2011 * Update values of references(object and region) for the following types: * 1) References, * 2) ARRAY of reference, * 3) VLEN of references. * 4) COMPOUND of references. * This function does not handle references in other complicated structures, * such as references in nested compound datatypes. * * Date: October, 28, 2003 * *------------------------------------------------------------------------- */ static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options, trav_table_t *travt, hid_t fidout /* for saving references */ ) { hid_t attr_id = -1; /* attr ID */ hid_t attr_out = -1; /* attr ID */ hid_t space_id = -1; /* space ID */ hid_t ftype_id = -1; /* file data type ID */ hid_t mtype_id = -1; /* memory data type ID */ size_t msize; /* memory size of type */ hsize_t nelmts; /* number of elements in dataset */ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ char name[255]; H5O_info_t oinfo; /* Object info */ unsigned u, i, j; int rank; H5T_class_t type_class = -1; hbool_t is_ref=0, is_ref_vlen=0, is_ref_array=0, is_ref_comp=0; void *refbuf = NULL; void *buf = NULL; const char* refname; int *ref_comp_index = NULL; size_t *ref_comp_size = NULL; int ref_comp_field_n = 0; if(H5Oget_info(loc_in, &oinfo) < 0) goto error; for(u = 0; u < (unsigned)oinfo.num_attrs; u++) { is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0; /* open attribute */ if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; /* get the file datatype */ if((ftype_id = H5Aget_type(attr_id)) < 0) goto error; type_class = H5Tget_class(ftype_id); if((mtype_id = h5tools_get_native_type(ftype_id)) < 0) goto error; if((msize = H5Tget_size(mtype_id)) == 0) goto error; is_ref = (type_class == H5T_REFERENCE); if (type_class == H5T_VLEN ) { hid_t base_type = -1; base_type = H5Tget_super(ftype_id); is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE); msize = H5Tget_size(base_type); H5Tclose(base_type); } if (type_class == H5T_ARRAY ) { hid_t base_type = -1; base_type = H5Tget_super(ftype_id); is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE); msize = H5Tget_size(base_type); H5Tclose(base_type); } if (type_class == H5T_COMPOUND) { int nmembers = H5Tget_nmembers(ftype_id) ; if (nmembers < 1) goto error; ref_comp_index = (int *)HDmalloc(nmembers*sizeof (int)); ref_comp_size = (size_t *)HDmalloc(nmembers*sizeof(ref_comp_size)); ref_comp_field_n = 0; for (i=0; i<(unsigned)nmembers; i++) { hid_t mtid = H5Tget_member_type( ftype_id, i ); if ((H5Tget_class(mtid)==H5T_REFERENCE)) { ref_comp_index[ref_comp_field_n] = i; ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid); ref_comp_field_n++; } H5Tclose(mtid); } /* if compound don't contain reference type member, free the above * mallocs. Otherwise there can be memory leaks by the 'continue' * statement below. */ if (!ref_comp_field_n) { if (ref_comp_index) { HDfree(ref_comp_index); ref_comp_index = NULL; } if (ref_comp_size) { HDfree(ref_comp_size); ref_comp_size = NULL; } } } is_ref_comp = (ref_comp_field_n > 0); if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) { H5Tclose(mtype_id); H5Tclose(ftype_id); H5Aclose(attr_id); continue; } /* get name */ if(H5Aget_name(attr_id, 255, name) < 0) goto error; /* get the dataspace handle */ if((space_id = H5Aget_space(attr_id)) < 0) goto error; /* get dimensions */ if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) goto error; /*------------------------------------------------------------------------- * elements *------------------------------------------------------------------------- */ nelmts = 1; for(j = 0; j < (unsigned)rank; j++) nelmts *= dims[j]; if (is_ref_array) { unsigned array_rank = 0; hsize_t array_size = 1; hsize_t array_dims[H5S_MAX_RANK]; hid_t base_type = -1; base_type = H5Tget_super(ftype_id); msize = H5Tget_size(base_type); H5Tclose(base_type); array_rank = H5Tget_array_ndims(mtype_id); H5Tget_array_dims2(mtype_id, array_dims); for(j = 0; j <array_rank; j++) array_size *= array_dims[j]; nelmts *= array_size; } if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; if (nelmts>0) { /* handle object references */ if((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE==msize)) { buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf == NULL) { printf("cannot read into memory\n"); goto error; } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) goto error; refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize); if(refbuf == NULL) { printf( "cannot allocate memory\n" ); goto error; } /* end if */ for(i = 0; i < (unsigned)nelmts; i++) { if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt)<0) continue; if(options->verbose) printf("object <%s> reference created to <%s>\n", name, refname); } /* k */ }/*H5T_STD_REF_OBJ*/ /* handle region references */ else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) { buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf == NULL) { printf( "cannot read into memory\n" ); goto error; } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) goto error; /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ if(refbuf == NULL) { printf( "cannot allocate memory\n" ); goto error; } /* end if */ for(i = 0; i < (unsigned)nelmts; i++) { if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt)<0) continue; if(options->verbose) printf("object <%s> region reference created to <%s>\n", name, refname); } } /* H5T_STD_REF_DSETREG */ else if (is_ref_vlen) { /* handle VLEN of references */ buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t))); refbuf = buf; /* reuse the read buffer for write */ if(buf == NULL) { printf( "cannot read into memory\n" ); goto error; } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) goto error; if (H5R_OBJ_REF_BUF_SIZE==msize) { hobj_ref_t ref_out; for (i=0; i<(unsigned)nelmts; i++) { hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p; for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0) continue; HDmemcpy(&(ptr[j]), &ref_out, msize); } } /* for (i=0; i<nelems; i++) */ } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) { hdset_reg_ref_t ref_out; for (i=0; i<(unsigned)nelmts; i++) { hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p; for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0) continue; HDmemcpy(&(ptr[j]), &ref_out, msize); } } /* for (i=0; i<nelems; i++) */ } } /* else if (is_ref_vlen) */ else if (is_ref_comp) { /* handle ref fields in a compound */ buf = HDmalloc((unsigned)(nelmts * msize)); refbuf = buf; /* reuse the read buffer for write */ if(buf == NULL) { printf( "cannot read into memory\n" ); goto error; } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) goto error; for (i=0; i<(unsigned)nelmts; i++) { for (j=0; j<(unsigned)ref_comp_field_n; j++) { if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) { int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]); hobj_ref_t ref_out; if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) continue; HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); } /* if */ else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) { int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]); hdset_reg_ref_t ref_out; if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) continue; HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); } /* else if */ } /* j */ } /* i */ } /* else if (is_ref_comp) */ if(H5Awrite(attr_out, mtype_id, refbuf) < 0) goto error; if (is_ref_vlen && buf) H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf); } /* if (nelmts) */ if (refbuf == buf) refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */ if(buf) { HDfree(buf); buf = NULL; } if(refbuf) { HDfree(refbuf); refbuf = NULL; } if (ref_comp_index) { HDfree(ref_comp_index); ref_comp_index = NULL; } if (ref_comp_size) { HDfree(ref_comp_size); ref_comp_size = NULL; } if(H5Aclose(attr_out) < 0) goto error; /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ if(H5Tclose(ftype_id) < 0) goto error; if(H5Tclose(mtype_id) < 0) goto error; if(H5Sclose(space_id) < 0) goto error; if(H5Aclose(attr_id) < 0) goto error; } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */ return 0; error: if(refbuf) HDfree(refbuf); if(buf) HDfree(buf); if (ref_comp_index) HDfree(ref_comp_index); if (ref_comp_size) HDfree(ref_comp_size); H5E_BEGIN_TRY { H5Tclose(ftype_id); H5Tclose(mtype_id); H5Sclose(space_id); H5Aclose(attr_id); H5Aclose(attr_out); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: MapIdToName * * Purpose: map a ID from a reference to a dataset name * *------------------------------------------------------------------------- */ static const char* MapIdToName(hid_t refobj_id, trav_table_t *travt) { unsigned int u; const char* ret = NULL; /* linear search */ for(u = 0; u < travt->nobjs; u++) { if(travt->objs[u].type == H5O_TYPE_DATASET || travt->objs[u].type == H5O_TYPE_GROUP || travt->objs[u].type == H5O_TYPE_NAMED_DATATYPE) { H5O_info_t ref_oinfo; /* Stat for the refobj id */ /* obtain information to identify the referenced object uniquely */ if(H5Oget_info(refobj_id, &ref_oinfo) < 0) goto out; if(ref_oinfo.addr == travt->objs[u].objno) { ret = travt->objs[u].name; goto out; } /* end if */ } /* end if */ } /* u */ out: return ret; } /*------------------------------------------------------------------------- * Function: Update_Ref_value * * Purpose: Update a reference value * * Programmer: xcao@hdfgroup.org 9/12/2011 * *------------------------------------------------------------------------- */ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, hid_t fid_out, void *ref_out, trav_table_t *travt) { herr_t ret = -1; const char* ref_obj_name; hid_t space_id=-1, ref_obj_id=-1; ref_obj_id = H5Rdereference(obj_id, ref_type, ref_in); if (ref_obj_id<0) goto done; ref_obj_name = MapIdToName(ref_obj_id, travt); if (ref_obj_name == NULL) goto done; if (ref_type == H5R_DATASET_REGION) { space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in); if (space_id < 0) goto done; } ret = H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id); if (ret < 0) goto done; ret = 0; done: H5E_BEGIN_TRY { H5Sclose(space_id); H5Oclose(ref_obj_id); } H5E_END_TRY; return ret; }