diff options
Diffstat (limited to 'tools/h5ls/h5ls.c')
| -rw-r--r-- | tools/h5ls/h5ls.c | 300 |
1 files changed, 207 insertions, 93 deletions
diff --git a/tools/h5ls/h5ls.c b/tools/h5ls/h5ls.c index c856642..835af10 100644 --- a/tools/h5ls/h5ls.c +++ b/tools/h5ls/h5ls.c @@ -34,23 +34,24 @@ #define NAME_BUF_SIZE 2048 -/* Struct to keep track of external link targets visited */ -typedef struct elink_trav_t { +/* Struct to keep track of symbolic link targets visited */ +typedef struct symlink_trav_t { size_t nalloc; size_t nused; struct { + H5L_type_t type; char *file; char *path; } *objs; -} elink_trav_t; +} symlink_trav_t; /* Struct to pass through to visitors */ typedef struct { const char *fname; /* Filename */ hid_t fid; /* File ID */ hid_t gid; /* Group ID */ - hbool_t ext_target; /* Whether this is the target of an external link */ - elink_trav_t *elink_list; /* List of visited external links */ + hbool_t symlink_target; /* Whether this is the target of an symbolic link */ + symlink_trav_t *symlink_list; /* List of visited symbolic links */ int base_len; /* Length of base path name, if not root */ int name_start; /* # of leading characters to strip off path names on output */ }iter_t; @@ -64,6 +65,7 @@ static hbool_t label_g = FALSE; /* label compound values? */ static hbool_t string_g = FALSE; /* print 1-byte numbers as ASCII? */ static hbool_t fullname_g = FALSE; /* print full path names */ static hbool_t recursive_g = FALSE; /* recursive descent listing */ +static hbool_t follow_symlink_g = FALSE; /* follow symbolic links */ static hbool_t follow_elink_g = FALSE; /* follow external links */ static hbool_t grp_literal_g = FALSE; /* list group, not contents */ static hbool_t hexdump_g = FALSE; /* show data as raw hexadecimal */ @@ -111,30 +113,46 @@ usage (void) { fprintf(stderr, "\ usage: %s [OPTIONS] [OBJECTS...]\n\ - OPTIONS\n\ - -h, -?, --help Print a usage message and exit\n\ - -a, --address Print addresses for raw data\n\ - -d, --data Print the values of datasets\n\ - -e, --errors Show all HDF5 error reporting\n\ - -E, --external Allow traversal into external files\n\ - -f, --full Print full path names instead of base names\n\ - -g, --group Show information about a group, not its contents\n\ - -l, --label Label members of compound datasets\n\ - -r, --recursive List all groups recursively, avoiding cycles\n\ - -s, --string Print 1-byte integer datasets as ASCII\n\ - -S, --simple Use a machine-readable output format\n\ - -wN, --width=N Set the number of columns of output\n\ - -v, --verbose Generate more verbose output\n\ - -V, --version Print version number and exit\n\ - --vfd=DRIVER Use the specified virtual file driver\n\ - -x, --hexdump Show raw data in hexadecimal format\n\ + OPTIONS\n\ + -h, -?, --help Print a usage message and exit\n\ + -a, --address Print addresses for raw data\n\ + -d, --data Print the values of datasets\n\ + -e, --errors Show all HDF5 error reporting\n\ + --follow-symlinks Follow symbolic links (soft links and external links)\n\ + to display target object information.\n\ + Without this option, h5ls identifies a symbolic link\n\ + as a soft link or external link and prints the value\n\ + assigned to the symbolic link; it does not provide any\n\ + information regarding the target object or determine\n\ + whether the link is a dangling link.\n\ + -f, --full Print full path names instead of base names\n\ + -g, --group Show information about a group, not its contents\n\ + -l, --label Label members of compound datasets\n\ + -r, --recursive List all groups recursively, avoiding cycles\n\ + -s, --string Print 1-byte integer datasets as ASCII\n\ + -S, --simple Use a machine-readable output format\n\ + -wN, --width=N Set the number of columns of output\n\ + -v, --verbose Generate more verbose output\n\ + -V, --version Print version number and exit\n\ + --vfd=DRIVER Use the specified virtual file driver\n\ + -x, --hexdump Show raw data in hexadecimal format\n\ \n\ - OBJECTS\n\ - Each object consists of an HDF5 file name optionally followed by a\n\ - slash and an object name within the file (if no object is specified\n\ - within the file then the contents of the root group are displayed).\n\ - The file name may include a printf(3C) integer format such as\n\ - \"%%05d\" to open a file family.\n", + OBJECTS\n\ + Each object consists of an HDF5 file name optionally followed by a\n\ + slash and an object name within the file (if no object is specified\n\ + within the file then the contents of the root group are displayed).\n\ + The file name may include a printf(3C) integer format such as\n\ + \"%%05d\" to open a file family.\n\ +\n\ + Deprecated Options\n\ + The following options have been deprecated in HDF5. While they remain\n\ + available, they have been superseded as indicated and may be removed\n\ + from HDF5 in the future. Use the indicated replacement option in all\n\ + new work; where possible, existing scripts, et cetera, should also be\n\ + updated to use the replacement option.\n\ +\n\ + -E or --external Follow external links.\n\ + Replaced by --follow-symlinks.\n", h5tools_getprogname()); } @@ -469,6 +487,9 @@ display_precision(hid_t type, int ind) case H5T_NPAD: plsb_s = "unknown"; break; + default: + ; + break; } } if (H5Tget_offset(type)+prec<8*H5Tget_size(type)) { @@ -486,6 +507,9 @@ display_precision(hid_t type, int ind) case H5T_NPAD: pmsb_s = "unknown"; break; + default: + ; + break; } } if (plsb_s || pmsb_s) { @@ -646,6 +670,9 @@ display_float_type(hid_t type, int ind) case H5T_NORM_ERROR: norm_s = ", unknown normalization"; break; + default: + ; + break; } printf("\n%*s(significant for %lu bit%s at bit %lu%s)", ind, "", (unsigned long)msize, 1==msize?"":"s", (unsigned long)mpos, @@ -672,6 +699,9 @@ display_float_type(hid_t type, int ind) case H5T_NPAD: pad_s = "unknown"; break; + default: + ; + break; } printf("\n%*s(internal padding bits are %s)", ind, "", pad_s); } @@ -786,7 +816,7 @@ display_enum_type(hid_t type, int ind) /* Get the names and raw values of all members */ name = calloc(nmembs, sizeof(char*)); - value = calloc(nmembs, MAX(H5Tget_size(type), dst_size)); + value = (unsigned char *)calloc(nmembs, MAX(H5Tget_size(type), dst_size)); for (i=0; i<nmembs; i++) { name[i] = H5Tget_member_name(type, i); H5Tget_member_value(type, i, value+i*H5Tget_size(type)); @@ -889,6 +919,9 @@ display_string_type(hid_t type, int UNUSED ind) case H5T_STR_ERROR: pad_s = "unknown-format"; break; + default: + ; + break; } /* Character set */ @@ -917,6 +950,9 @@ display_string_type(hid_t type, int UNUSED ind) case H5T_CSET_ERROR: cset_s = "unknown-character-set"; break; + default: + ; + break; } if (H5Tis_variable_str(type)) { @@ -1054,7 +1090,7 @@ display_array_type(hid_t type, int ind) if (H5T_ARRAY!=H5Tget_class(type)) return FALSE; ndims = H5Tget_array_ndims(type); if (ndims) { - dims = malloc(ndims*sizeof(dims[0])); + dims = (hsize_t *)malloc(ndims*sizeof(dims[0])); H5Tget_array_dims2(type, dims); /* Print dimensions */ @@ -1701,7 +1737,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void iter_t *iter = (iter_t*)_iter; /* Print the link's name, either full name or base name */ - if(!iter->ext_target) + if(!iter->symlink_target) display_obj_name(stdout, iter, name, ""); /* Check object information */ @@ -1709,7 +1745,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void printf("Unknown type(%d)", (int)oinfo->type); obj_type = H5O_TYPE_UNKNOWN; } - if(iter->ext_target) + if(iter->symlink_target) fputc('{', stdout); if(obj_type >= 0 && dispatch_g[obj_type].name) fputs(dispatch_g[obj_type].name, stdout); @@ -1718,7 +1754,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void if(first_seen) { printf(", same as "); display_string(stdout, first_seen, TRUE); - if(!iter->ext_target) + if(!iter->symlink_target) printf("\n"); } /* end if */ else { @@ -1735,7 +1771,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void /* List the first line of information for the object. */ if(obj_type >= 0 && dispatch_g[obj_type].list1) (dispatch_g[obj_type].list1)(obj); - if(!iter->ext_target || (verbose_g > 0)) + if(!iter->symlink_target || (verbose_g > 0)) putchar('\n'); /* Show detailed information about the object, beginning with information @@ -1787,18 +1823,18 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void } /* end else */ done: - if(iter->ext_target) { + if(iter->symlink_target) { fputs("}\n", stdout); - iter->ext_target = FALSE; + iter->symlink_target = FALSE; } return 0; } /* end list_obj() */ /*------------------------------------------------------------------------- - * Function: elink_trav_add + * Function: symlink_visit_add * - * Purpose: Add an external link to visited data structure + * Purpose: Add an symbolic link to visited data structure * * Return: 0 on success, -1 on failure * @@ -1807,16 +1843,26 @@ done: * * Date: September 5, 2008 * + * Modified: + * Jonathan Kim + * - Renamed from elink_trav_add to symlink_visit_add for both soft and + * external links. (May 25, 2010) + * - Add type parameter to distingush between soft and external link for + * sure, which prevent from mixing up visited link when the target names + * are same between the soft and external link, as code marks with the + * target name. (May 25,2010) + * *------------------------------------------------------------------------- */ static herr_t -elink_trav_add(elink_trav_t *visited, const char *file, const char *path) +symlink_visit_add(symlink_trav_t *visited, H5L_type_t type, const char *file, const char *path) { size_t idx; /* Index of address to use */ void *tmp_ptr; /* Allocate space if necessary */ - if(visited->nused == visited->nalloc) { + if(visited->nused == visited->nalloc) + { visited->nalloc = MAX(1, visited->nalloc * 2); if(NULL == (tmp_ptr = HDrealloc(visited->objs, visited->nalloc * sizeof(visited->objs[0])))) return -1; @@ -1825,24 +1871,36 @@ elink_trav_add(elink_trav_t *visited, const char *file, const char *path) /* Append it */ idx = visited->nused++; - if(NULL == (visited->objs[idx].file = HDstrdup(file))) { - visited->nused--; - return -1; + + visited->objs[idx].type = type; + visited->objs[idx].file = NULL; + visited->objs[idx].path = NULL; + + if (type == H5L_TYPE_EXTERNAL) + { + if(NULL == (visited->objs[idx].file = HDstrdup(file))) + { + visited->nused--; + return -1; + } } - if(NULL == (visited->objs[idx].path = HDstrdup(path))) { + + if(NULL == (visited->objs[idx].path = HDstrdup(path))) + { visited->nused--; - HDfree (visited->objs[idx].file); + if (visited->objs[idx].file) + HDfree (visited->objs[idx].file); return -1; } return 0; -} /* end elink_trav_add() */ +} /* end symlink_visit_add() */ /*------------------------------------------------------------------------- - * Function: elink_trav_visited + * Function: symlink_is_visited * - * Purpose: Check if an external link has already been visited + * Purpose: Check if an symbolic link has already been visited * * Return: TRUE/FALSE * @@ -1851,22 +1909,41 @@ elink_trav_add(elink_trav_t *visited, const char *file, const char *path) * * Date: September 5, 2008 * + * Modified: + * Jonathan Kim + * - Renamed from elink_trav_visited to symlink_is_visited for both soft and + * external links. (May 25, 2010) + * - Add type parameter to distingush between soft and external link for + * sure, which prevent from mixing up visited link when the target names + * are same between the soft and external link, as code marks with the + * target name. (May 25,2010) + * *------------------------------------------------------------------------- */ static hbool_t -elink_trav_visited(elink_trav_t *visited, const char *file, const char *path) +symlink_is_visited(symlink_trav_t *visited, H5L_type_t type, const char *file, const char *path) { - size_t u; /* Local index variable */ + size_t u; /* Local index variable */ - /* Look for elink */ + /* Look for symlink */ for(u = 0; u < visited->nused; u++) - /* Check for elink value already in array */ - if(!HDstrcmp(visited->objs[u].file, file) && !HDstrcmp(visited->objs[u].path, path)) - return(TRUE); - - /* Didn't find elink */ + { + /* Check for symlink values already in array */ + /* check type and path pair to distingush between symbolic links */ + if ((visited->objs[u].type == type) && !HDstrcmp(visited->objs[u].path, path)) + { + /* if external link, file need to be matched as well */ + if (visited->objs[u].type == H5L_TYPE_EXTERNAL) + { + if (!HDstrcmp(visited->objs[u].file, file)) + return (TRUE); + } + return (TRUE); + } + } + /* Didn't find symlink */ return(FALSE); -} /* end elink_trav_visited() */ +} /* end symlink_is_visited() */ /*------------------------------------------------------------------------- @@ -1886,7 +1963,7 @@ elink_trav_visited(elink_trav_t *visited, const char *file, const char *path) static herr_t list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) { - char *buf; + char *buf=NULL; iter_t *iter = (iter_t*)_iter; /* Print the link's name, either full name or base name */ @@ -1894,18 +1971,52 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) switch(linfo->type) { case H5L_TYPE_SOFT: - if((buf = HDmalloc(linfo->u.val_size)) == NULL) + if((buf = (char*)HDmalloc(linfo->u.val_size)) == NULL) goto done; if(H5Lget_val(iter->fid, name, buf, linfo->u.val_size, H5P_DEFAULT) < 0) { - HDfree(buf); goto done; } /* end if */ HDfputs("Soft Link {", stdout); HDfputs(buf, stdout); - HDfree(buf); - HDfputs("}\n", stdout); + HDfputc('}', stdout); + if(follow_symlink_g) + { + hbool_t orig_grp_literal = grp_literal_g; + HDfputc(' ', stdout); + + /* Check if we have already seen this softlink */ + if(symlink_is_visited(iter->symlink_list, linfo->type, NULL, buf)) + { + HDfputs("{Already Visited}\n", stdout); + goto done; + } + + /* Add this link to the list of seen softlinks */ + if(symlink_visit_add(iter->symlink_list, linfo->type, NULL, buf) < 0) + goto done; + + /* Adjust user data to specify that we are operating on the + * target of an soft link */ + iter->symlink_target = TRUE; + + /* Prevent recursive listing of soft link target if + * recursive_g is off */ + if(!recursive_g) + grp_literal_g = TRUE; + /* Recurse through the soft link */ + if(visit_obj(iter->fid, name, iter) < 0) + { + grp_literal_g = orig_grp_literal; + goto done; + } + + grp_literal_g = orig_grp_literal; + } + else + HDfputc('\n', stdout); + break; case H5L_TYPE_EXTERNAL: @@ -1913,16 +2024,13 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) const char *filename; const char *path; - if((buf = HDmalloc(linfo->u.val_size)) == NULL) + if((buf = (char*)HDmalloc(linfo->u.val_size)) == NULL) goto done; - if(H5Lget_val(iter->fid, name, buf, linfo->u.val_size, H5P_DEFAULT) < 0) { - HDfree(buf); + if(H5Lget_val(iter->fid, name, buf, linfo->u.val_size, H5P_DEFAULT) < 0) goto done; - } /* end if */ - if(H5Lunpack_elink_val(buf, linfo->u.val_size, NULL, &filename, &path) < 0) { - HDfree(buf); + + if(H5Lunpack_elink_val(buf, linfo->u.val_size, NULL, &filename, &path) < 0) goto done; - } /* end if */ HDfputs("External Link {", stdout); HDfputs(filename, stdout); @@ -1933,27 +2041,28 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) HDfputc('}', stdout); /* Recurse through the external link */ - if(follow_elink_g) { + /* keep the follow_elink_g for backward compatibility with -E */ + if(follow_symlink_g || follow_elink_g) + { hbool_t orig_grp_literal = grp_literal_g; - HDfputc(' ', stdout); /* Check if we have already seen this elink */ - if(elink_trav_visited(iter->elink_list, filename, path)) { + if(symlink_is_visited(iter->symlink_list, linfo->type, filename, path)) + { HDfputs("{Already Visited}\n", stdout); - HDfree(buf); goto done; } /* Add this link to the list of seen elinks */ - if(elink_trav_add(iter->elink_list, filename, path) < 0) { - HDfree(buf); + if(symlink_visit_add(iter->symlink_list, linfo->type, filename, path) < 0) + { goto done; } /* Adjust user data to specify that we are operating on the * target of an external link */ - iter->ext_target = TRUE; + iter->symlink_target = TRUE; /* Prevent recursive listing of external link target if * recursive_g is off */ @@ -1962,7 +2071,6 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) /* Recurse through the external link */ if(visit_obj(iter->fid, name, iter) < 0) { - HDfree(buf); grp_literal_g = orig_grp_literal; goto done; } @@ -1972,7 +2080,6 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) else HDfputc('\n', stdout); - HDfree(buf); } break; @@ -1982,6 +2089,8 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) } /* end switch */ done: + if (buf) + HDfree(buf); return 0; } /* end list_lnk() */ @@ -2008,9 +2117,9 @@ visit_obj(hid_t file, const char *oname, iter_t *iter) /* Retrieve info for object to list */ if(H5Oget_info_by_name(file, oname, &oi, H5P_DEFAULT) < 0) { - if(iter->ext_target) { + if(iter->symlink_target) { HDfputs("{**NOT FOUND**}\n", stdout); - iter->ext_target = FALSE; + iter->symlink_target = FALSE; } else display_obj_name(stdout, iter, oname, "**NOT FOUND**"); @@ -2020,7 +2129,7 @@ visit_obj(hid_t file, const char *oname, iter_t *iter) /* Check for group iteration */ if(H5O_TYPE_GROUP == oi.type && !grp_literal_g) { /* Get ID for group */ - if(!iter->ext_target && (iter->gid = H5Gopen2(file, oname, H5P_DEFAULT)) < 0) { + if(!iter->symlink_target && (iter->gid = H5Gopen2(file, oname, H5P_DEFAULT)) < 0) { fprintf(stderr, "%s: unable to open '%s' as group\n", iter->fname, oname); return 0; /* Previously "continue", when this code was in main(). * We don't "continue" here in order to close the file @@ -2032,10 +2141,10 @@ visit_obj(hid_t file, const char *oname, iter_t *iter) iter->name_start = iter->base_len; /* Specified name is a group. List the complete contents of the group. */ - h5trav_visit(file, oname, (hbool_t) (display_root_g || iter->ext_target), recursive_g, list_obj, list_lnk, iter); + h5trav_visit(file, oname, (hbool_t) (display_root_g || iter->symlink_target), recursive_g, list_obj, list_lnk, iter); /* Close group */ - if(!iter->ext_target) + if(!iter->symlink_target) H5Gclose(iter->gid); } /* end if */ else { @@ -2211,6 +2320,8 @@ main(int argc, const char *argv[]) data_g = TRUE; } else if(!HDstrcmp(argv[argno], "--errors")) { show_errors_g = TRUE; + } else if(!HDstrcmp(argv[argno], "--follow-symlinks")) { + follow_symlink_g = TRUE; } else if(!HDstrcmp(argv[argno], "--external")) { follow_elink_g = TRUE; } else if(!HDstrcmp(argv[argno], "--full")) { @@ -2381,7 +2492,7 @@ main(int argc, const char *argv[]) while(argno < argc) { H5L_info_t li; iter_t iter; - elink_trav_t elink_list; + symlink_trav_t symlink_list; size_t u; fname = HDstrdup(argv[argno++]); @@ -2443,12 +2554,12 @@ main(int argc, const char *argv[]) iter.fname = fname; iter.fid = file; iter.gid = -1; - iter.ext_target = FALSE; - iter.elink_list = &elink_list; + iter.symlink_target = FALSE; + iter.symlink_list = &symlink_list; - /* Initialize list of visited external links */ - elink_list.nused = elink_list.nalloc = 0; - elink_list.objs = NULL; + /* Initialize list of visited symbolic links */ + symlink_list.nused = symlink_list.nalloc = 0; + symlink_list.objs = NULL; /* Check for root group as object name */ if(HDstrcmp(oname, root_name)) { @@ -2477,11 +2588,14 @@ main(int argc, const char *argv[]) if(x) HDfree(oname); - for(u=0; u < elink_list.nused; u++) { - HDfree(elink_list.objs[u].file); - HDfree(elink_list.objs[u].path); + for(u=0; u < symlink_list.nused; u++) + { + if (symlink_list.objs[u].type == H5L_TYPE_EXTERNAL) + HDfree(symlink_list.objs[u].file); + + HDfree(symlink_list.objs[u].path); } - HDfree(elink_list.objs); + HDfree(symlink_list.objs); } /* end while */ if (err_openfile) |