diff options
| -rw-r--r-- | tools/h5repack/h5repack.h | 62 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 132 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_refs.c | 76 | ||||
| -rw-r--r-- | tools/h5repack/testh5repack_filters.c | 160 | ||||
| -rw-r--r-- | tools/h5repack/testh5repack_main.c | 29 | ||||
| -rw-r--r-- | tools/lib/h5diff.c | 6 | ||||
| -rw-r--r-- | tools/lib/h5trav.c | 133 | ||||
| -rw-r--r-- | tools/lib/h5trav.h | 29 | ||||
| -rw-r--r-- | tools/lib/h5trav_table.c | 76 |
9 files changed, 474 insertions, 229 deletions
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h index 546ae3a..a372a6f 100644 --- a/tools/h5repack/h5repack.h +++ b/tools/h5repack/h5repack.h @@ -134,52 +134,39 @@ void print_objlist(const char *filename, int do_copy_file(hid_t fidin, hid_t fidout, - int nobjects, - trav_info_t *info, + trav_table_t *travt, pack_opt_t *options); int copy_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options, - int nobjects, /* number of objects */ - trav_info_t *travi, /* array of object names */ - hid_t fidout /*for saving references */ + trav_table_t *travt, + hid_t fidout /* for saving references */ ); - -void read_info(const char *filename,pack_opt_t *options); - - -void close_obj(H5G_obj_t obj_type, hid_t obj_id); - const char* MapIdToName(hid_t refobj_id, - int nobjects, /* number of objects */ - trav_info_t *travi, /* array of object names */ + trav_table_t *travt, pack_opt_t *options) /* repack options */; - - int do_copy_refobjs(hid_t fidin, hid_t fidout, - int nobjects, /* number of objects */ - trav_info_t *travi, /* array of object names */ + trav_table_t *travt, pack_opt_t *options); /* repack options */ int do_copy_refobjs_inattr(hid_t loc_in, hid_t loc_out, pack_opt_t *options, - int nobjects, /* number of objects */ - trav_info_t *travi, /* array of object names */ + trav_table_t *travt, hid_t fidout /* for saving references */ ); +void read_info(const char *filename,pack_opt_t *options); +void close_obj(H5G_obj_t obj_type, hid_t obj_id); /*------------------------------------------------------------------------- * options table *------------------------------------------------------------------------- */ - - int options_table_init( pack_opttbl_t **tbl ); int options_table_free( pack_opttbl_t *table ); int options_add_chunk ( obj_list_t *obj_list, @@ -194,9 +181,6 @@ int options_add_comp ( obj_list_t *obj_list, pack_info_t* options_get_object( const char *path, pack_opttbl_t *table); - - - /*------------------------------------------------------------------------- * parse functions *------------------------------------------------------------------------- @@ -217,46 +201,36 @@ int parse_number(char *str); *------------------------------------------------------------------------- */ - -#define FNAME1 "testcopy.h5" -#define FNAME1OUT "testcopyout.h5" -#define FNAME2 "testfilters.h5" -#define FNAME2OUT "testfiltersout.h5" - - - -#define FNAME1 "testcopy.h5" -#define FNAME1OUT "testcopyout.h5" -#define FNAME2 "testfilters.h5" -#define FNAME2OUT "testfiltersout.h5" - +#define FNAME1 "test1.h5" +#define FNAME1OUT "test1out.h5" +#define FNAME2 "test2.h5" +#define FNAME2OUT "test2out.h5" +#define FNAME3 "test3.h5" +#define FNAME3OUT "test3out.h5" +#define FNAME4 "test4.h5" +#define FNAME4OUT "test4out.h5" int make_testfiles(void); - int make_all_objects(hid_t fid); - +int make_attributes(hid_t fid); +int make_special_objects(hid_t loc_id); int make_attr(hid_t fid); - int write_dset( hid_t loc_id, int rank, hsize_t *dims, const char *dset_name, hid_t type_id, void *buf ); - int write_attr(hid_t loc_id, int rank, hsize_t *dims, const char *attr_name, hid_t type_id, void *buf); - - void write_attr_in(hid_t loc_id, const char* dset_name, /* for saving reference to dataset*/ hid_t fid, /* for reference create */ int make_diffs /* flag to modify data buffers */); - void write_dset_in(hid_t loc_id, const char* dset_name, /* for saving reference to dataset*/ hid_t file_id, diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index f7d5016..2afc94b 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -37,10 +37,10 @@ int copy_file(const char* fnamein, const char* fnameout, pack_opt_t *options) { - hid_t fidin; - hid_t fidout; - int nobjects; - trav_info_t *travi=NULL; + hid_t fidin; + hid_t fidout; + int nobjects=0; + trav_table_t *travt=NULL; /*------------------------------------------------------------------------- * open the files @@ -67,65 +67,66 @@ int copy_file(const char* fnamein, printf("Making file <%s>...\n",fnameout); -/*------------------------------------------------------------------------- - * get the number of objects in the file - *------------------------------------------------------------------------- - */ + /* init table */ + trav_table_init(&travt); - if ((nobjects = h5trav_getinfo(fidin, NULL ))<0) { - printf("h5repack: <%s>: Could not obtain object list\n", fnamein ); - return -1; - } + /* get the list of objects in the file */ + if (h5trav_gettable(fidin,travt)<0) + goto out; -/*------------------------------------------------------------------------- - * get the list of objects in the file - *------------------------------------------------------------------------- - */ - - if ((travi = (trav_info_t*) malloc( nobjects * sizeof(trav_info_t)))==NULL){ - printf("h5repack: <%s>: Could not allocate object list\n", fnamein ); - return -1; - } - if (h5trav_getinfo(fidin, travi )<0) { - printf("h5repack: <%s>: Could not obtain object list\n", fnamein ); - return -1; - } +#if defined (H5_REPACK_DEBUG) + h5trav_printtable(travt); +#endif /*------------------------------------------------------------------------- * do the copy *------------------------------------------------------------------------- */ - if(do_copy_file(fidin,fidout,nobjects,travi,options)<0) { + if(do_copy_file(fidin,fidout,travt,options)<0) { printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); - return -1; + goto out; } /*------------------------------------------------------------------------- * do the copy of referenced objects + * and create hard links *------------------------------------------------------------------------- */ - if(do_copy_refobjs(fidin,fidout,nobjects,travi,options)<0) { + if(do_copy_refobjs(fidin,fidout,travt,options)<0) { printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); - return -1; + goto out; } -#if defined (H5_REPACK_DEBUG) - h5trav_printinfo(nobjects,travi); -#endif - + /* free table */ + trav_table_free(travt); /*------------------------------------------------------------------------- - * free + * close *------------------------------------------------------------------------- */ + H5Fclose(fidin); H5Fclose(fidout); - h5trav_freeinfo(travi,nobjects); return 0; + +/*------------------------------------------------------------------------- + * out + *------------------------------------------------------------------------- + */ + +out: + H5E_BEGIN_TRY { + H5Fclose(fidin); + H5Fclose(fidout); + trav_table_free(travt); + } H5E_END_TRY; + + return -1; } + /*------------------------------------------------------------------------- * Function: do_copy_file * @@ -142,8 +143,7 @@ int copy_file(const char* fnamein, int do_copy_file(hid_t fidin, hid_t fidout, - int nobjects, /* number of objects */ - trav_info_t *travi, /* array of object names */ + trav_table_t *travt, pack_opt_t *options) /* repack options */ { hid_t grp_in; /* group ID */ @@ -168,10 +168,10 @@ int do_copy_file(hid_t fidin, *------------------------------------------------------------------------- */ - for ( i = 0; i < nobjects; i++) + for ( i = 0; i < travt->nobjs; i++) { - switch ( travi[i].type ) + switch ( travt->objs[i].type ) { /*------------------------------------------------------------------------- * H5G_GROUP @@ -179,19 +179,19 @@ int do_copy_file(hid_t fidin, */ case H5G_GROUP: if (options->verbose) - printf(" %-10s %s\n", "group",travi[i].name ); + printf(" %-10s %s\n", "group",travt->objs[i].name ); - if ((grp_out=H5Gcreate(fidout,travi[i].name, 0))<0) + if ((grp_out=H5Gcreate(fidout,travt->objs[i].name, 0))<0) goto error; - if((grp_in = H5Gopen (fidin,travi[i].name))<0) + if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0) goto error; -/*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(grp_in,grp_out,options,nobjects,travi,fidout)<0) + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(grp_in,grp_out,options,travt,fidout)<0) goto error; if (H5Gclose(grp_out)<0) @@ -199,6 +199,7 @@ int do_copy_file(hid_t fidin, if (H5Gclose(grp_in)<0) goto error; + break; /*------------------------------------------------------------------------- @@ -207,9 +208,9 @@ int do_copy_file(hid_t fidin, */ case H5G_DATASET: if (options->verbose) - printf(" %-10s %s\n", "dataset",travi[i].name ); + printf(" %-10s %s\n", "dataset",travt->objs[i].name ); - if ((dset_in=H5Dopen(fidin,travi[i].name))<0) + if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) goto error; if ((space_id=H5Dget_space(dset_in))<0) goto error; @@ -256,7 +257,7 @@ int do_copy_file(hid_t fidin, * create/write dataset/close *------------------------------------------------------------------------- */ - if ((dset_out=H5Dcreate(fidout,travi[i].name,ftype_id,space_id,dcpl_id))<0) + if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,ftype_id,space_id,dcpl_id))<0) goto error; if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0) goto error; @@ -264,8 +265,8 @@ int do_copy_file(hid_t fidin, /*------------------------------------------------------------------------- * copy attrs *------------------------------------------------------------------------- - */ - if (copy_attr(dset_in,dset_out,options,nobjects,travi,fidout)<0) + */ + if (copy_attr(dset_in,dset_out,options,travt,fidout)<0) goto error; /*close */ @@ -274,6 +275,7 @@ int do_copy_file(hid_t fidin, if (buf) free(buf); + }/*H5T_STD_REF_OBJ*/ @@ -293,8 +295,6 @@ int do_copy_file(hid_t fidin, goto error; if (H5Dclose(dset_in)<0) goto error; - - break; @@ -304,20 +304,20 @@ int do_copy_file(hid_t fidin, */ case H5G_TYPE: - if ((type_in = H5Topen (fidin,travi[i].name))<0) + if ((type_in = H5Topen (fidin,travt->objs[i].name))<0) goto error; if ((type_out = H5Tcopy(type_in))<0) goto error; - if ((H5Tcommit(fidout,travi[i].name,type_out))<0) + if ((H5Tcommit(fidout,travt->objs[i].name,type_out))<0) goto error; /*------------------------------------------------------------------------- * copy attrs *------------------------------------------------------------------------- */ - if (copy_attr(type_in,type_out,options,nobjects,travi,fidout)<0) + if (copy_attr(type_in,type_out,options,travt,fidout)<0) goto error; if (H5Tclose(type_in)<0) @@ -326,7 +326,7 @@ int do_copy_file(hid_t fidin, goto error; if (options->verbose) - printf(" %-10s %s\n","datatype",travi[i].name ); + printf(" %-10s %s\n","datatype",travt->objs[i].name ); break; @@ -343,32 +343,32 @@ int do_copy_file(hid_t fidin, H5G_stat_t statbuf; char *targbuf=NULL; - if (H5Gget_objinfo(fidin,travi[i].name,FALSE,&statbuf)<0) + if (H5Gget_objinfo(fidin,travt->objs[i].name,FALSE,&statbuf)<0) goto error; targbuf = malloc(statbuf.linklen); - if (H5Gget_linkval(fidin,travi[i].name,statbuf.linklen,targbuf)<0) + if (H5Gget_linkval(fidin,travt->objs[i].name,statbuf.linklen,targbuf)<0) goto error; if (H5Glink(fidout, H5G_LINK_SOFT, targbuf, /* current name of object */ - travi[i].name /* new name of object */ + travt->objs[i].name /* new name of object */ )<0) goto error; free(targbuf); if (options->verbose) - printf(" %-10s %s\n","link",travi[i].name ); + printf(" %-10s %s\n","link",travt->objs[i].name ); } break; default: if (options->verbose) - printf(" %-10s %s\n","User defined object",travi[i].name); + printf(" %-10s %s\n","User defined object",travt->objs[i].name); break; } } @@ -389,7 +389,7 @@ int do_copy_file(hid_t fidin, if ((grp_in = H5Gopen(fidin,"/"))<0) goto error; - if (copy_attr(grp_in,grp_out,options,nobjects,travi,fidout)<0) + if (copy_attr(grp_in,grp_out,options,travt,fidout)<0) goto error; if (H5Gclose(grp_out)<0) @@ -439,8 +439,7 @@ error: int copy_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options, - int nobjects, /* number of objects */ - trav_info_t *travi, /* array of object names */ + trav_table_t *travt, hid_t fidout /* for saving references */ ) { @@ -577,4 +576,3 @@ error: return -1; } - diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c index cd5fe80..81bafab 100644 --- a/tools/h5repack/h5repack_refs.c +++ b/tools/h5repack/h5repack_refs.c @@ -24,6 +24,7 @@ * Function: do_copy_refobjs * * Purpose: duplicate all referenced HDF5 objects in the file + * and create hard links * * Return: 0, ok, -1 no * @@ -36,8 +37,7 @@ int do_copy_refobjs(hid_t fidin, hid_t fidout, - int nobjects, /* number of objects */ - trav_info_t *travi, /* array of object names */ + trav_table_t *travt, pack_opt_t *options) /* repack options */ { hid_t grp_in; /* group ID */ @@ -62,22 +62,32 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ - for ( i = 0; i < nobjects; i++) + for ( i = 0; i < travt->nobjs; i++) { - switch ( travi[i].type ) + switch ( travt->objs[i].type ) { /*------------------------------------------------------------------------- * H5G_GROUP *------------------------------------------------------------------------- */ case H5G_GROUP: - - if((grp_in = H5Gopen (fidin,travi[i].name))<0) - goto error; + + /*------------------------------------------------------------------------- + * check for hard links + *------------------------------------------------------------------------- + */ - if (H5Gclose(grp_in)<0) - goto error; + if (travt->objs[i].nlinks) + { + for ( j=0; j<travt->objs[i].nlinks; j++) + { + H5Glink(fidout, + H5G_LINK_HARD, + travt->objs[i].name, + travt->objs[i].links[j].new_name); + } + } break; @@ -87,7 +97,7 @@ int do_copy_refobjs(hid_t fidin, */ case H5G_DATASET: - if ((dset_in=H5Dopen(fidin,travi[i].name))<0) + if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) goto error; if ((space_id=H5Dget_space(dset_in))<0) goto error; @@ -149,14 +159,14 @@ int do_copy_refobjs(hid_t fidin, /* get the name. a valid name could only occur in the second traversal of the file */ - if ((refname=MapIdToName(refobj_id,nobjects,travi,options))!=NULL) + if ((refname=MapIdToName(refobj_id,travt,options))!=NULL) { /* create the reference */ if (H5Rcreate(&refbuf[j],fidout,refname,H5R_OBJECT,-1)<0) goto error; if (options->verbose) - printf("object <%s> reference created to <%s>\n",travi[i].name,refname); + printf("object <%s> reference created to <%s>\n",travt->objs[i].name,refname); } close_obj(obj_type,refobj_id); }/* j */ @@ -167,7 +177,7 @@ int do_copy_refobjs(hid_t fidin, * create/write dataset/close *------------------------------------------------------------------------- */ - if ((dset_out=H5Dcreate(fidout,travi[i].name,ftype_id,space_id,dcpl_id))<0) + if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,ftype_id,space_id,dcpl_id))<0) goto error; if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0) goto error; @@ -185,7 +195,7 @@ int do_copy_refobjs(hid_t fidin, else { - if ((dset_out=H5Dopen(fidout,travi[i].name))<0) + if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0) goto error; } @@ -194,8 +204,24 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ - if (do_copy_refobjs_inattr(dset_in,dset_out,options,nobjects,travi,fidout)<0) + if (do_copy_refobjs_inattr(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++) + { + H5Glink(fidout, + H5G_LINK_HARD, + travt->objs[i].name, + travt->objs[i].links[j].new_name); + } + } /*------------------------------------------------------------------------- @@ -225,7 +251,7 @@ int do_copy_refobjs(hid_t fidin, */ case H5G_TYPE: - if ((type_in = H5Topen (fidin,travi[i].name))<0) + if ((type_in = H5Topen (fidin,travt->objs[i].name))<0) goto error; if (H5Tclose(type_in)<0) @@ -267,7 +293,7 @@ int do_copy_refobjs(hid_t fidin, if ((grp_in = H5Gopen(fidin,"/"))<0) goto error; - if (do_copy_refobjs_inattr(grp_in,grp_out,options,nobjects,travi,fidout)<0) + if (do_copy_refobjs_inattr(grp_in,grp_out,options,travt,fidout)<0) goto error; if (H5Gclose(grp_out)<0) @@ -314,8 +340,7 @@ error: int do_copy_refobjs_inattr(hid_t loc_in, hid_t loc_out, pack_opt_t *options, - int nobjects, /* number of objects */ - trav_info_t *travi, /* array of object names */ + trav_table_t *travt, hid_t fidout /* for saving references */ ) { @@ -414,7 +439,7 @@ int do_copy_refobjs_inattr(hid_t loc_in, /* get the name. a valid name could only occur in the second traversal of the file */ - if ((refname=MapIdToName(refobj_id,nobjects,travi,options))!=NULL) + if ((refname=MapIdToName(refobj_id,travt,options))!=NULL) { /* create the reference */ if (H5Rcreate(&refbuf[i],fidout,refname,H5R_OBJECT,-1)<0) @@ -506,8 +531,7 @@ static void close_obj(H5G_obj_t obj_type, hid_t obj_id) */ const char* MapIdToName(hid_t refobj_id, - int nobjects, /* number of objects */ - trav_info_t *travi, /* array of object names */ + trav_table_t *travt, pack_opt_t *options) /* repack options */ { hid_t id; @@ -521,9 +545,9 @@ const char* MapIdToName(hid_t refobj_id, } - for ( i=0; i<nobjects; i++) + for ( i=0; i<travt->nobjs; i++) { - switch ( travi[i].type ) + switch ( travt->objs[i].type ) { /*------------------------------------------------------------------------- @@ -543,7 +567,7 @@ const char* MapIdToName(hid_t refobj_id, case H5G_DATASET: - if ((id = H5Dopen(fid,travi[i].name))<0) + if ((id = H5Dopen(fid,travt->objs[i].name))<0) { assert(0); return NULL; @@ -558,7 +582,7 @@ const char* MapIdToName(hid_t refobj_id, if (id==refobj_id) { H5Fclose(fid); - return travi[i].name; + return travt->objs[i].name; } diff --git a/tools/h5repack/testh5repack_filters.c b/tools/h5repack/testh5repack_filters.c index 36abc06..dd72813 100644 --- a/tools/h5repack/testh5repack_filters.c +++ b/tools/h5repack/testh5repack_filters.c @@ -22,12 +22,6 @@ * * Purpose: make a dataset using DEFLATE (GZIP) compression in FID * - * Return: Success: zero - * Failure: 1 - * - * Programmer: Pedro Vicente <pvn@ncsa.uiuc.edu> - * September, 19, 2003 - * *------------------------------------------------------------------------- */ static int @@ -82,12 +76,6 @@ error: * * Purpose: make a dataset using SZIP compression in FID * - * Return: Success: zero - * Failure: 1 - * - * Programmer: Pedro Vicente <pvn@ncsa.uiuc.edu> - * September, 19, 2003 - * *------------------------------------------------------------------------- */ static int @@ -152,12 +140,6 @@ error: * Purpose: make a test file with all types of HDF5 objects, * datatypes and filters * - * Return: Success: zero - * Failure: 1 - * - * Programmer: Pedro Vicente <pvn@ncsa.uiuc.edu> - * September, 19, 2003 - * *------------------------------------------------------------------------- */ int make_testfiles(void) @@ -167,23 +149,35 @@ int make_testfiles(void) TESTING(" generating datasets"); - /* create a file for the copy test */ + /* create a file for general copy test */ if((fid = H5Fcreate(FNAME1,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0) TEST_ERROR; - nerrors += make_all_objects(fid); + /* close */ + if(H5Fclose(fid)<0) + TEST_ERROR; + /* create a file for attributes copy test */ + if((fid = H5Fcreate(FNAME2,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0) + TEST_ERROR; + nerrors += make_attributes(fid); /* close */ if(H5Fclose(fid)<0) TEST_ERROR; + /* create a file for special items test */ + if((fid = H5Fcreate(FNAME3,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0) + TEST_ERROR; + nerrors += make_special_objects(fid); + /* close */ + if(H5Fclose(fid)<0) + TEST_ERROR; + /* create a file for the filters test */ - if((fid = H5Fcreate(FNAME2,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0) + if((fid = H5Fcreate(FNAME4,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0) TEST_ERROR; - nerrors += make_deflate(fid); nerrors += make_szip(fid); - /* close */ if(H5Fclose(fid)<0) TEST_ERROR; @@ -199,20 +193,11 @@ error: } - - - /*------------------------------------------------------------------------- * Function: make_all_objects * * Purpose: make a test file with all types of HDF5 objects, datatypes * - * Return: Success: zero - * Failure: 1 - * - * Programmer: Pedro Vicente <pvn@ncsa.uiuc.edu> - * September, 19, 2003 - * *------------------------------------------------------------------------- */ int make_all_objects(hid_t fid) @@ -267,22 +252,63 @@ int make_all_objects(hid_t fid) H5Glink(fid, H5G_LINK_SOFT, "dset", "link"); /*------------------------------------------------------------------------- - * write a series of attributes on the dataset, group, and root group + * write a series of datasetes on the group, and root group *------------------------------------------------------------------------- */ - write_attr_in(dset_id,"dset_ref",fid,0); - write_attr_in(group_id,"dset_ref",fid,0); - write_attr_in(root_id,"dset_ref",fid,0); + write_dset_in(root_id,"dset_ref",fid,0); + write_dset_in(group_id,"dset_ref",fid,0); + + + /* Close */ + H5Dclose(dset_id); + H5Gclose(group_id); + H5Gclose(root_id); + + return 0; + +} + /*------------------------------------------------------------------------- - * write a series of datasetes on the group, and root group + * Function: make_attributes + * + * Purpose: make a test file with all types of attributes + * + *------------------------------------------------------------------------- + */ +int make_attributes(hid_t fid) +{ + hid_t dset_id; + hid_t group_id; + hid_t root_id; + hid_t space_id; + hsize_t dims[1]={2}; + +/*------------------------------------------------------------------------- + * H5G_DATASET *------------------------------------------------------------------------- */ - write_dset_in(root_id,"dset_ref",fid,0); - write_dset_in(group_id,"dset_ref",fid,0); + space_id = H5Screate_simple(1,dims,NULL); + dset_id = H5Dcreate(fid,"dset",H5T_NATIVE_INT,space_id,H5P_DEFAULT); + H5Sclose(space_id); + +/*------------------------------------------------------------------------- + * H5G_GROUP + *------------------------------------------------------------------------- + */ + group_id = H5Gcreate(fid,"g1",0); + root_id = H5Gopen(fid, "/"); + +/*------------------------------------------------------------------------- + * write a series of attributes on the dataset, group, and root group + *------------------------------------------------------------------------- + */ + write_attr_in(dset_id,"dset",fid,0); + write_attr_in(group_id,"dset",fid,0); + write_attr_in(root_id,"dset",fid,0); /* Close */ H5Dclose(dset_id); @@ -293,3 +319,59 @@ int make_all_objects(hid_t fid) } + + +/*------------------------------------------------------------------------- + * Function: make_special_objects + * + * Purpose: make a test file with non common items + * + *------------------------------------------------------------------------- + */ +int make_special_objects(hid_t loc_id) +{ + hid_t group1_id; + hid_t group2_id; + hid_t group3_id; + hsize_t dims[1]={2}; + int buf[2]= {1,2}; + + +/*------------------------------------------------------------------------- + * create a dataset and some hard links to it + *------------------------------------------------------------------------- + */ + + if (write_dset(loc_id,1,dims,"dset",H5T_NATIVE_INT,buf)<0) + return -1; + if (H5Glink(loc_id, H5G_LINK_HARD, "dset", "link1 to dset")<0) + return -1; + if (H5Glink(loc_id, H5G_LINK_HARD, "dset", "link2 to dset")<0) + return -1; + if (H5Glink(loc_id, H5G_LINK_HARD, "dset", "link3 to dset")<0) + return -1; + +/*------------------------------------------------------------------------- + * create a group and some hard links to it + *------------------------------------------------------------------------- + */ + + if ((group1_id = H5Gcreate(loc_id,"g1",0))<0) + return -1; + if ((group2_id = H5Gcreate(group1_id,"g2",0))<0) + return -1; + if ((group3_id = H5Gcreate(group2_id,"g3",0))<0) + return -1; + if (H5Glink(loc_id, H5G_LINK_HARD, "g1", "link1 to g1")<0) + return -1; + if (H5Glink(loc_id, H5G_LINK_HARD, "g1", "link2 to g1")<0) + return -1; + + + H5Gclose(group1_id); + H5Gclose(group2_id); + + return 0; + +} + diff --git a/tools/h5repack/testh5repack_main.c b/tools/h5repack/testh5repack_main.c index 0acd632..83b9b77 100644 --- a/tools/h5repack/testh5repack_main.c +++ b/tools/h5repack/testh5repack_main.c @@ -42,7 +42,6 @@ test_copy(void) memset(&diff_options, 0, sizeof (diff_opt_t)); TESTING(" copy with no filters"); - if (h5repack_init (&pack_options, 0)<0) TEST_ERROR; if (h5repack(FNAME1,FNAME1OUT,&pack_options)<0) @@ -51,8 +50,30 @@ test_copy(void) TEST_ERROR; if (h5diff(FNAME1,FNAME1OUT,NULL,NULL,&diff_options) == 1) TEST_ERROR; + PASSED(); + + TESTING(" copy of attributes"); + if (h5repack_init (&pack_options, 0)<0) + TEST_ERROR; + if (h5repack(FNAME2,FNAME2OUT,&pack_options)<0) + TEST_ERROR; + if (h5repack_end (&pack_options)<0) + TEST_ERROR; + if (h5diff(FNAME2,FNAME2OUT,NULL,NULL,&diff_options) == 1) + TEST_ERROR; + PASSED(); + + TESTING(" copy of hardlinks"); + if (h5repack_init (&pack_options, 0)<0) + TEST_ERROR; + if (h5repack(FNAME3,FNAME3OUT,&pack_options)<0) + TEST_ERROR; + if (h5repack_end (&pack_options)<0) + TEST_ERROR; + if (h5diff(FNAME3,FNAME3OUT,NULL,NULL,&diff_options) == 1) + TEST_ERROR; + PASSED(); - PASSED(); return 0; error: @@ -97,11 +118,11 @@ test_filter_deflate(void) TEST_ERROR; if (h5repack_addchunk("dset_gzip:5x4",&pack_options)<0) TEST_ERROR; - if (h5repack(FNAME2,FNAME2OUT,&pack_options)<0) + if (h5repack(FNAME4,FNAME4OUT,&pack_options)<0) TEST_ERROR; if (h5repack_end (&pack_options)<0) TEST_ERROR; - if (h5diff(FNAME2,FNAME2OUT,NULL,NULL,&diff_options) == 1) + if (h5diff(FNAME4,FNAME4OUT,NULL,NULL,&diff_options) == 1) TEST_ERROR; PASSED(); diff --git a/tools/lib/h5diff.c b/tools/lib/h5diff.c index 3b59b0e..eeabd8c 100644 --- a/tools/lib/h5diff.c +++ b/tools/lib/h5diff.c @@ -239,7 +239,7 @@ int diff_match( hid_t file1_id, { c1 = (table->objs[i].flags[0]) ? 'x' : ' '; c2 = (table->objs[i].flags[1]) ? 'x' : ' '; - printf("%5c %6c %-15s\n", c1, c2, table->objs[i].objname); + printf("%5c %6c %-15s\n", c1, c2, table->objs[i].name); } printf("\n"); } @@ -254,9 +254,9 @@ int diff_match( hid_t file1_id, { if ( table->objs[i].flags[0] && table->objs[i].flags[1] ) nfound+=diff( file1_id, - table->objs[i].objname, + table->objs[i].name, file2_id, - table->objs[i].objname, + table->objs[i].name, options, table->objs[i].type ); } diff --git a/tools/lib/h5trav.c b/tools/lib/h5trav.c index fc64fc7..e065e28 100644 --- a/tools/lib/h5trav.c +++ b/tools/lib/h5trav.c @@ -25,7 +25,7 @@ int traverse( hid_t loc_id, trav_info_t *info, int *idx ); -herr_t get_nobjects( hid_t loc_id, +herr_t get_nnames( hid_t loc_id, const char *group_name ); herr_t get_name_type( hid_t loc_id, @@ -40,7 +40,7 @@ herr_t get_name_type( hid_t loc_id, * Purpose: get an array of "trav_info_t" , containing the name and type of * objects in the file * - * Return: number of objects in file + * Return: number of object names in file * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * @@ -53,19 +53,46 @@ int h5trav_getinfo( hid_t file_id, trav_info_t *info ) { trav_table_t *table=NULL; - int nobjects=0; + int nnames=0; /* init table */ trav_table_init( &table ); /* iterate starting on the root group */ - if (( nobjects = traverse( file_id, "/", table, info, &nobjects )) < 0 ) + if (( nnames = traverse( file_id, "/", table, info, &nnames )) < 0 ) return -1; /* free table */ trav_table_free( table ); - return nobjects; + return nnames; + +} + + +/*------------------------------------------------------------------------- + * Function: h5trav_gettable + * + * Purpose: get the trav_table_t struct + * + * Return: 0, -1 on error + * + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * + * Date: December 17, 2003 + * + *------------------------------------------------------------------------- + */ + +int h5trav_gettable(hid_t fid, trav_table_t *travt) +{ + int nnames=0; + + /* iterate starting on the root group */ + if (( nnames = traverse(fid,"/",travt,NULL,&nnames))<0) + return -1; + + return 0; } @@ -131,7 +158,7 @@ void h5trav_freeinfo( trav_info_t *info, int nobjs ) /*------------------------------------------------------------------------- - * Function: count_objects + * Function: count_names * * Purpose: operator function * @@ -146,7 +173,7 @@ void h5trav_freeinfo( trav_info_t *info, int nobjs ) *------------------------------------------------------------------------- */ -static herr_t count_objects( hid_t loc_id, const char *name, void *op_data) +static herr_t count_names( hid_t loc_id, const char *name, void *op_data) { H5G_stat_t statbuf; @@ -161,9 +188,9 @@ static herr_t count_objects( hid_t loc_id, const char *name, void *op_data) } /*------------------------------------------------------------------------- - * Function: get_nobjects + * Function: get_nnames * - * Purpose: Counts the number of objects in the group GROUP_NAME + * Purpose: Counts the number of names in the group GROUP_NAME * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * @@ -181,12 +208,12 @@ static herr_t count_objects( hid_t loc_id, const char *name, void *op_data) *------------------------------------------------------------------------- */ -herr_t get_nobjects( hid_t loc_id, const char *group_name ) +herr_t get_nnames( hid_t loc_id, const char *group_name ) { int nobjs = 0; - if ( H5Giterate( loc_id, group_name, NULL, count_objects, (void *)&nobjs ) < 0 ) + if ( H5Giterate( loc_id, group_name, NULL, count_names, (void *)&nobjs ) < 0 ) return -1; return nobjs; @@ -287,17 +314,18 @@ int traverse( hid_t loc_id, char *name=NULL; H5G_obj_t type; - int nobjs; - int i; + int n_names; char *path=NULL; H5G_stat_t statbuf; int inserted_objs=0; - int j; + int i, j; + - if (( nobjs = get_nobjects( loc_id, group_name )) < 0 ) + /* get the number of names */ + if (( n_names = get_nnames( loc_id, group_name )) < 0 ) return -1; - for ( i = 0; i < nobjs; i++) + for ( i = 0; i < n_names; i++) { if (get_name_type( loc_id, group_name, i, &name, &type ) < 0 ) @@ -365,8 +393,9 @@ int traverse( hid_t loc_id, else { #if defined (H5_TRAV_DEBUG) - printf("%s %s\n", "HARDLINK", table->objs[j].objname); + printf("<%s> HARDLINK to <%s>\n", path, table->objs[j].name); #endif + trav_table_addlink(table,j,path); } } @@ -404,11 +433,11 @@ int traverse( hid_t loc_id, else { #if defined (H5_TRAV_DEBUG) - printf("%s %s\n", "HARDLINK", table->objs[j].objname); + printf("<%s> HARDLINK to <%s>\n", path, table->objs[j].name); #endif - } - - } + trav_table_addlink(table,j,path); + } /* displayed==1 */ + } /* nlink>1 */ break; @@ -442,7 +471,10 @@ int traverse( hid_t loc_id, /* increment */ inserted_objs++; - + + /* add object to table */ + trav_table_add(statbuf.objno, path, H5G_LINK, table ); + break; @@ -471,9 +503,9 @@ int traverse( hid_t loc_id, /*------------------------------------------------------------------------- - * Function: diff_list + * Function: h5trav_printinfo * - * Purpose: print list of objects in file + * Purpose: print list of names in file * * Return: void * @@ -481,10 +513,6 @@ int traverse( hid_t loc_id, * * Date: May 9, 2003 * - * Comments: - * - * Modifications: - * *------------------------------------------------------------------------- */ void h5trav_printinfo(int nobjs, trav_info_t *travi) @@ -515,3 +543,52 @@ void h5trav_printinfo(int nobjs, trav_info_t *travi) +/*------------------------------------------------------------------------- + * Function: h5trav_printtable + * + * Purpose: print list of objects in file + * + * Return: void + * + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * + * Date: May 9, 2003 + * + *------------------------------------------------------------------------- + */ +void h5trav_printtable(trav_table_t *table) +{ + int i, j; + + for ( i = 0; i < table->nobjs; i++) + { + switch ( table->objs[i].type ) + { + case H5G_GROUP: + printf(" %-10s %s\n", "group", table->objs[i].name ); + break; + case H5G_DATASET: + printf(" %-10s %s\n", "dataset", table->objs[i].name ); + break; + case H5G_TYPE: + printf(" %-10s %s\n", "datatype", table->objs[i].name ); + break; + case H5G_LINK: + printf(" %-10s %s\n", "link", table->objs[i].name ); + break; + default: + printf(" %-10s %s\n", "User defined object", table->objs[i].name ); + break; + } + + if (table->objs[i].nlinks) + { + for ( j=0; j<table->objs[i].nlinks; j++) + { + printf(" %-10s %s\n", " hardlink", table->objs[i].links[j] ); + } + } + + } +} + diff --git a/tools/lib/h5trav.h b/tools/lib/h5trav.h index 1f826bb..cedbc54 100644 --- a/tools/lib/h5trav.h +++ b/tools/lib/h5trav.h @@ -40,16 +40,28 @@ typedef struct trav_info_t { /*------------------------------------------------------------------------- + * keep record of hard link information + *------------------------------------------------------------------------- + */ +typedef struct trav_link_t { + char *new_name; +} trav_link_t; + + +/*------------------------------------------------------------------------- * struct to store basic info needed for the h5trav table traversal algorythm *------------------------------------------------------------------------- */ typedef struct trav_obj_t { - haddr_t objno; - unsigned flags[2]; - char *objname; - int displayed; - H5G_obj_t type; + haddr_t objno; /* object number from H5Gget_objinfo */ + unsigned flags[2]; /* h5diff.object is present or not in both files*/ + char *name; /* name */ + int displayed; /* hard link already traversed once */ + H5G_obj_t type; /* type of object */ + trav_link_t *links; /* array of possible link names */ + int sizelinks; /* size of links array */ + int nlinks; /* number of links */ } trav_obj_t; @@ -78,7 +90,7 @@ int h5trav_getinfo( hid_t file_id, trav_info_t *info ); int h5trav_getindex( const char *obj, int nobjs, trav_info_t *info ); void h5trav_freeinfo( trav_info_t *info, int nobjs ); void h5trav_printinfo(int nobjs, trav_info_t *info); - +int h5trav_gettable(hid_t fid, trav_table_t *travt); #ifdef __cplusplus @@ -107,6 +119,11 @@ void trav_table_addflags(unsigned *flags, H5G_obj_t type, trav_table_t *table); +void h5trav_printtable(trav_table_t *table); + +void trav_table_addlink(trav_table_t *table, + int j /* the object index */, + char *path ); #endif /* H5TRAV_H__ */ diff --git a/tools/lib/h5trav_table.c b/tools/lib/h5trav_table.c index bbbe2d6..0071559 100644 --- a/tools/lib/h5trav_table.c +++ b/tools/lib/h5trav_table.c @@ -57,7 +57,7 @@ int trav_table_search(haddr_t objno, trav_table_t *table ) */ void trav_table_add(haddr_t objno, - char *objname, + char *name, H5G_obj_t type, trav_table_t *table) { @@ -73,16 +73,21 @@ void trav_table_add(haddr_t objno, table->objs[i].flags[0] = table->objs[i].flags[1] = 0; table->objs[i].displayed = 0; table->objs[i].type = H5G_UNKNOWN; - table->objs[i].objname = NULL; + table->objs[i].name = NULL; + table->objs[i].links = NULL; + table->objs[i].nlinks = 0; + table->objs[i].sizelinks = 0; } } i = table->nobjs++; table->objs[i].objno = objno; table->objs[i].flags[0] = table->objs[i].flags[1] = 0; - HDfree(table->objs[i].objname); - table->objs[i].objname = (char *)HDstrdup(objname); + HDfree(table->objs[i].name); + table->objs[i].name = (char *)HDstrdup(name); table->objs[i].type = type; + table->objs[i].links = NULL; + table->objs[i].nlinks = 0; } @@ -101,7 +106,7 @@ void trav_table_add(haddr_t objno, */ void trav_table_addflags(unsigned *flags, - char *objname, + char *name, H5G_obj_t type, trav_table_t *table) { @@ -117,7 +122,10 @@ void trav_table_addflags(unsigned *flags, table->objs[i].flags[0] = table->objs[i].flags[1] = 0; table->objs[i].displayed = 0; table->objs[i].type = H5G_UNKNOWN; - table->objs[i].objname = NULL; + table->objs[i].name = NULL; + table->objs[i].links = NULL; + table->objs[i].nlinks = 0; + table->objs[i].sizelinks = 0; } } @@ -125,9 +133,11 @@ void trav_table_addflags(unsigned *flags, table->objs[i].objno = 0; table->objs[i].flags[0] = flags[0]; table->objs[i].flags[1] = flags[1]; - HDfree(table->objs[i].objname); - table->objs[i].objname = (char *)HDstrdup(objname); + HDfree(table->objs[i].name); + table->objs[i].name = (char *)HDstrdup(name); table->objs[i].type = type; + table->objs[i].links = NULL; + table->objs[i].nlinks = 0; } @@ -160,7 +170,10 @@ void trav_table_init( trav_table_t **tbl ) table->objs[i].flags[0] = table->objs[i].flags[1] = 0; table->objs[i].displayed = 0; table->objs[i].type = H5G_UNKNOWN; - table->objs[i].objname = NULL; + table->objs[i].name = NULL; + table->objs[i].links = NULL; + table->objs[i].nlinks = 0; + table->objs[i].sizelinks = 0; } *tbl = table; @@ -184,14 +197,53 @@ void trav_table_init( trav_table_t **tbl ) void trav_table_free( trav_table_t *table ) { - int i; + int i, j; for ( i = 0; i < table->nobjs; i++) - HDfree( table->objs[i].objname ); - + { + HDfree( table->objs[i].name ); + if (table->objs[i].nlinks) + { + for ( j=0; j<table->objs[i].nlinks; j++) + HDfree( table->objs[i].links[j].new_name ); + + HDfree(table->objs[i].links); + } + } HDfree(table->objs); HDfree(table); } +/*------------------------------------------------------------------------- + * Function: trav_table_addlink + * + * Purpose: Add a hardlink name to the object + * + * Return: void + * + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * + * Date: December 17, 2003 + * + *------------------------------------------------------------------------- + */ + +void trav_table_addlink(trav_table_t *table, + int j /* the object index */, + char *path ) +{ + int k; + /* store the link information */ + if (table->objs[j].nlinks == table->objs[j].sizelinks) { + table->objs[j].sizelinks += 2; + table->objs[j].links = + (trav_link_t*)HDrealloc(table->objs[j].links, + table->objs[j].sizelinks * sizeof(trav_link_t)); + } + k = table->objs[j].nlinks++; + table->objs[j].links[k].new_name = (char*)HDstrdup(path); +} + + |