mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-12-27 08:01:04 +08:00
3dc1e6dd38
h5diff issues "unable to read attribute" error message when comparing two files
Description:
h5diff did not handle attributes of variable length strings correctly. It created the wrong memory type if one but not both compared attributes are of the variable strings type. It ended in H5Aread() failure.
Solution:
We decided to treat the case when one type is variable length string and the other is not as incomparable. That bypassed the above error. We still need to figure out the proper way, if possible, to compare variable string with non-variable string types.
Tested: h5committested plus tested in Swallow (OS X 10.8).
607 lines
21 KiB
C
607 lines
21 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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#include <stdlib.h>
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#include <string.h>
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#include "H5private.h"
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#include "h5diff.h"
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#include "h5diff_common.h"
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#include "h5tools.h"
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#include "h5tools_utils.h"
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static int check_n_input( const char* );
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static int check_p_input( const char* );
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static int check_d_input( const char* );
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/*
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* Command-line options: The user can specify short or long-named
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* parameters.
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*/
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static const char *s_opts = "hVrv:qn:d:p:Nc";
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static struct long_options l_opts[] = {
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{ "help", no_arg, 'h' },
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{ "version", no_arg, 'V' },
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{ "report", no_arg, 'r' },
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{ "verbose", optional_arg, 'v' },
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{ "quiet", no_arg, 'q' },
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{ "count", require_arg, 'n' },
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{ "delta", require_arg, 'd' },
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{ "relative", require_arg, 'p' },
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{ "nan", no_arg, 'N' },
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{ "compare", no_arg, 'c' },
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{ "use-system-epsilon", no_arg, 'e' },
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{ "follow-symlinks", no_arg, 'l' },
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{ "no-dangling-links", no_arg, 'x' },
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{ "exclude-path", require_arg, 'E' },
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{ NULL, 0, '\0' }
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};
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/*-------------------------------------------------------------------------
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* Function: check_options
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*
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* Purpose: parse command line input
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*
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*-------------------------------------------------------------------------
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*/
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static void check_options(diff_opt_t* options)
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{
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/*--------------------------------------------------------------
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* check for mutually exclusive options
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*--------------------------------------------------------------*/
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/* check between -d , -p, --use-system-epsilon.
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* These options are mutually exclusive.
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*/
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if ((options->d + options->p + options->use_system_epsilon) > 1)
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{
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printf("%s error: -d, -p and --use-system-epsilon options are mutually-exclusive;\n", PROGRAMNAME);
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printf("use no more than one.\n");
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printf("Try '-h' or '--help' option for more information or see the %s entry in the 'HDF5 Reference Manual'.\n", PROGRAMNAME);
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h5diff_exit(EXIT_FAILURE);
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}
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}
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/*-------------------------------------------------------------------------
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* Function: parse_command_line
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*
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* Purpose: parse command line input
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*
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*-------------------------------------------------------------------------
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*/
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void parse_command_line(int argc,
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const char* argv[],
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const char** fname1,
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const char** fname2,
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const char** objname1,
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const char** objname2,
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diff_opt_t* options)
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{
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int i;
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int opt;
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struct exclude_path_list *exclude_head, *exclude_prev, *exclude_node;
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/* process the command-line */
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memset(options, 0, sizeof (diff_opt_t));
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/* assume equal contents initially */
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options->contents = 1;
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/* NaNs are handled by default */
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options->do_nans = 1;
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/* not Listing objects that are not comparable */
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options->m_list_not_cmp = 0;
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/* initially no not-comparable. */
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/**this is bad in mixing option with results**/
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options->not_cmp=0;
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/* init for exclude-path option */
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exclude_head = NULL;
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/* parse command line options */
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while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF)
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{
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switch ((char)opt)
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{
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default:
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usage();
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h5diff_exit(EXIT_FAILURE);
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case 'h':
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usage();
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h5diff_exit(EXIT_SUCCESS);
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case 'V':
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print_version(h5tools_getprogname());
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h5diff_exit(EXIT_SUCCESS);
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case 'v':
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options->m_verbose = 1;
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/* This for loop is for handling style like
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* -v, -v1, --verbose, --verbose=1.
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*/
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for (i = 1; i < argc; i++)
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{
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/*
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* short opt
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*/
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if (!strcmp (argv[i], "-v")) /* no arg */
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{
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opt_ind--;
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options->m_verbose_level = 0;
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break;
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}
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else if (!strncmp (argv[i], "-v", (size_t)2))
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{
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options->m_verbose_level = atoi(&argv[i][2]);
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break;
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}
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/*
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* long opt
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*/
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if (!strcmp (argv[i], "--verbose")) /* no arg */
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{
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options->m_verbose_level = 0;
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break;
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}
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else if ( !strncmp (argv[i], "--verbose", (size_t)9) && argv[i][9]=='=')
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{
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options->m_verbose_level = atoi(&argv[i][10]);
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break;
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}
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}
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break;
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case 'q':
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/* use quiet mode; supress the message "0 differences found" */
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options->m_quiet = 1;
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break;
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case 'r':
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options->m_report = 1;
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break;
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case 'l':
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options->follow_links = TRUE;
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break;
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case 'x':
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options->no_dangle_links = 1;
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break;
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case 'E':
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options->exclude_path = 1;
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/* create linked list of excluding objects */
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if( (exclude_node = (struct exclude_path_list*) HDmalloc(sizeof(struct exclude_path_list))) == NULL)
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{
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printf("Error: lack of memory!\n");
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h5diff_exit(EXIT_FAILURE);
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}
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/* init */
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exclude_node->obj_path = (char*)opt_arg;
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exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN;
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exclude_prev = exclude_head;
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if (NULL == exclude_head)
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{
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exclude_head = exclude_node;
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exclude_head->next = NULL;
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}
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else
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{
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while(NULL != exclude_prev->next)
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exclude_prev=exclude_prev->next;
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exclude_node->next = NULL;
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exclude_prev->next = exclude_node;
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}
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break;
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case 'd':
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options->d=1;
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if ( check_d_input( opt_arg )==-1)
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{
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printf("<-d %s> is not a valid option\n", opt_arg );
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usage();
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h5diff_exit(EXIT_FAILURE);
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}
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options->delta = atof( opt_arg );
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/* -d 0 is the same as default */
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if (options->delta == 0)
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options->d=0;
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break;
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case 'p':
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options->p=1;
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if ( check_p_input( opt_arg )==-1)
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{
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printf("<-p %s> is not a valid option\n", opt_arg );
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usage();
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h5diff_exit(EXIT_FAILURE);
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}
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options->percent = atof( opt_arg );
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/* -p 0 is the same as default */
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if (options->percent == 0)
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options->p = 0;
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break;
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case 'n':
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options->n=1;
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if ( check_n_input( opt_arg )==-1)
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{
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printf("<-n %s> is not a valid option\n", opt_arg );
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usage();
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h5diff_exit(EXIT_FAILURE);
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}
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options->count = atol( opt_arg );
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break;
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case 'N':
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options->do_nans = 0;
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break;
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case 'c':
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options->m_list_not_cmp = 1;
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break;
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case 'e':
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options->use_system_epsilon = 1;
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break;
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}
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}
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/* check options */
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check_options(options);
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/* if exclude-path option is used, keep the exclude path list */
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if (options->exclude_path)
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options->exclude = exclude_head;
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/* check for file names to be processed */
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if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL)
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{
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error_msg("missing file names\n");
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usage();
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h5diff_exit(EXIT_FAILURE);
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}
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*fname1 = argv[ opt_ind ];
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*fname2 = argv[ opt_ind + 1 ];
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*objname1 = argv[ opt_ind + 2 ];
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if ( *objname1 == NULL )
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{
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*objname2 = NULL;
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return;
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}
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if ( argv[ opt_ind + 3 ] != NULL)
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{
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*objname2 = argv[ opt_ind + 3 ];
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}
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else
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{
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*objname2 = *objname1;
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}
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}
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/*-------------------------------------------------------------------------
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* Function: print_info
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*
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* Purpose: print several information messages after h5diff call
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*
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*-------------------------------------------------------------------------
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*/
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void print_info(diff_opt_t* options)
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{
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if (options->m_quiet || options->err_stat )
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return;
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if (options->cmn_objs==0)
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{
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printf("No common objects found. Files are not comparable.\n");
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if (!options->m_verbose)
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printf("Use -v for a list of objects.\n");
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}
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if (options->not_cmp==1)
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{
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if ( options->m_list_not_cmp == 0 )
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{
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printf("--------------------------------\n");
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printf("Some objects are not comparable\n");
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printf("--------------------------------\n");
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if (options->m_verbose)
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printf("Use -c for a list of objects without details of differences.\n");
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else
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printf("Use -c for a list of objects.\n");
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}
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}
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}
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/*-------------------------------------------------------------------------
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* Function: check_n_input
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*
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* Purpose: check for valid input
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*
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* Return: 1 for ok, -1 for fail
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*
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* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
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*
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* Date: May 9, 2003
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*
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* Comments:
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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static int
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check_n_input( const char *str )
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{
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unsigned i;
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char c;
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for ( i = 0; i < strlen(str); i++)
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{
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c = str[i];
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if ( i==0 )
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{
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if ( c < 49 || c > 57 ) /* ascii values between 1 and 9 */
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return -1;
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}
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else
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if ( c < 48 || c > 57 ) /* 0 also */
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return -1;
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}
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return 1;
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}
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/*-------------------------------------------------------------------------
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* Function: check_p_input
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*
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* Purpose: check for a valid p option input
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*
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* Return: 1 for ok, -1 for fail
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*
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* Date: May 9, 2003
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*
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* Comments:
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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static int
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check_p_input( const char *str )
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{
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double x;
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/*
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the atof return value on a hexadecimal input is different
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on some systems; we do a character check for this
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*/
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if (strlen(str)>2 && str[0]=='0' && str[1]=='x')
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return -1;
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x=atof(str);
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if (x<0)
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return -1;
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return 1;
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}
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/*-------------------------------------------------------------------------
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* Function: check_d_input
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*
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* Purpose: check for a valid d option input
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*
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* Return: 1 for ok, -1 for fail
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*
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* Date: November 11, 2007
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*
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* Comments:
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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static int
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check_d_input( const char *str )
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{
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double x;
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/*
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the atof return value on a hexadecimal input is different
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on some systems; we do a character check for this
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*/
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if (strlen(str)>2 && str[0]=='0' && str[1]=='x')
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return -1;
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x=atof(str);
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if (x <0)
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return -1;
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return 1;
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}
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/*-------------------------------------------------------------------------
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* Function: usage
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*
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* Purpose: print a usage message
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*
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* Return: void
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*
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*-------------------------------------------------------------------------
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*/
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void usage(void)
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{
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printf("usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] \n");
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printf(" file1 File name of the first HDF5 file\n");
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printf(" file2 File name of the second HDF5 file\n");
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printf(" [obj1] Name of an HDF5 object, in absolute path\n");
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printf(" [obj2] Name of an HDF5 object, in absolute path\n");
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printf("\n");
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printf(" OPTIONS\n");
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printf(" -h, --help\n");
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printf(" Print a usage message and exit.\n");
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printf(" -V, --version\n");
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printf(" Print version number and exit.\n");
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printf(" -r, --report\n");
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printf(" Report mode. Print differences.\n");
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printf(" -v --verbose\n");
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printf(" Verbose mode. Print differences information and list of objects.\n");
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printf(" -vN --verbose=N\n");
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printf(" Verbose mode with level. Print differences and list of objects.\n");
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printf(" Level of detail depends on value of N:\n");
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printf(" 0 : Identical to '-v' or '--verbose'.\n");
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printf(" 1 : All level 0 information plus one-line attribute\n");
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printf(" status summary.\n");
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printf(" 2 : All level 1 information plus extended attribute\n");
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printf(" status report.\n");
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printf(" -q, --quiet\n");
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printf(" Quiet mode. Do not produce output.\n");
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printf(" --follow-symlinks\n");
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printf(" Follow symbolic links (soft links and external links and compare the)\n");
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printf(" links' target objects.\n");
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printf(" If symbolic link(s) with the same name exist in the files being\n");
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printf(" compared, then determine whether the target of each link is an existing\n");
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printf(" object (dataset, group, or named datatype) or the link is a dangling\n");
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printf(" link (a soft or external link pointing to a target object that does\n");
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printf(" not yet exist).\n");
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printf(" - If both symbolic links are dangling links, they are treated as being\n");
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printf(" the same; by default, h5diff returns an exit code of 0.\n");
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printf(" If, however, --no-dangling-links is used with --follow-symlinks,\n");
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printf(" this situation is treated as an error and h5diff returns an\n");
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printf(" exit code of 2.\n");
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printf(" - If only one of the two links is a dangling link,they are treated as\n");
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printf(" being different and h5diff returns an exit code of 1.\n");
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printf(" If, however, --no-dangling-links is used with --follow-symlinks,\n");
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printf(" this situation is treated as an error and h5diff returns an\n");
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printf(" exit code of 2.\n");
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printf(" - If both symbolic links point to existing objects, h5diff compares the\n");
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printf(" two objects.\n");
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printf(" If any symbolic link specified in the call to h5diff does not exist,\n");
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printf(" h5diff treats it as an error and returns an exit code of 2.\n");
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printf(" --no-dangling-links\n");
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printf(" Must be used with --follow-symlinks option; otherwise, h5diff shows\n");
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printf(" error message and returns an exit code of 2.\n");
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printf(" Check for any symbolic links (soft links or external links) that do not\n");
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printf(" resolve to an existing object (dataset, group, or named datatype).\n");
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printf(" If any dangling link is found, this situation is treated as an error\n");
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printf(" and h5diff returns an exit code of 2.\n");
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printf(" -c, --compare\n");
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printf(" List objects that are not comparable\n");
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printf(" -N, --nan\n");
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printf(" Avoid NaNs detection\n");
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printf(" -n C, --count=C\n");
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printf(" Print differences up to C. C must be a positive integer.\n");
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printf(" -d D, --delta=D\n");
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printf(" Print difference if (|a-b| > D). D must be a positive number.\n");
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printf(" Can not use with '-p' or '--use-system-epsilon'.\n");
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printf(" -p R, --relative=R\n");
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printf(" Print difference if (|(a-b)/b| > R). R must be a positive number.\n");
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printf(" Can not use with '-d' or '--use-system-epsilon'.\n");
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printf(" --use-system-epsilon\n");
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printf(" Print difference if (|a-b| > EPSILON), EPSILON is system defined value.\n");
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printf(" If the system epsilon is not defined,one of the following predefined\n");
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printf(" values will be used:\n");
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printf(" FLT_EPSILON = 1.19209E-07 for floating-point type\n");
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printf(" DBL_EPSILON = 2.22045E-16 for double precision type\n");
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printf(" Can not use with '-p' or '-d'.\n");
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printf(" --exclude-path \"path\" \n");
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printf(" Exclude the specified path to an object when comparing files or groups.\n");
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printf(" If a group is excluded, all member objects will also be excluded.\n");
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printf(" The specified path is excluded wherever it occurs.\n");
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printf(" This flexibility enables the same option to exclude either objects that\n");
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printf(" exist only in one file or common objects that are known to differ.\n");
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printf("\n");
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printf(" When comparing files, \"path\" is the absolute path to the excluded;\n");
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printf(" object; when comparing groups, \"path\" is similar to the relative\n");
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printf(" path from the group to the excluded object. This \"path\" can be\n");
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printf(" taken from the first section of the output of the --verbose option.\n");
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printf(" For example, if you are comparing the group /groupA in two files and\n");
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printf(" you want to exclude /groupA/groupB/groupC in both files, the exclude\n");
|
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printf(" option would read as follows:\n");
|
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printf(" --exclude-path \"/groupB/groupC\"\n");
|
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printf("\n");
|
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printf(" If there are multiple paths to an object, only the specified path(s)\n");
|
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printf(" will be excluded; the comparison will include any path not explicitly\n");
|
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printf(" excluded.\n");
|
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printf(" This option can be used repeatedly to exclude multiple paths.\n");
|
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printf("\n");
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|
|
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printf(" Modes of output:\n");
|
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printf(" Default mode: print the number of differences found and where they occured\n");
|
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printf(" -r Report mode: print the above plus the differences\n");
|
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printf(" -v Verbose mode: print the above plus a list of objects and warnings\n");
|
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printf(" -q Quiet mode: do not print output\n");
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|
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printf("\n");
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|
|
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printf(" File comparison:\n");
|
|
printf(" If no objects [obj1[ obj2]] are specified, the h5diff comparison proceeds as\n");
|
|
printf(" a comparison of the two files' root groups. That is, h5diff first compares\n");
|
|
printf(" the names of root group members, generates a report of root group objects\n");
|
|
printf(" that appear in only one file or in both files, and recursively compares\n");
|
|
printf(" common objects.\n");
|
|
printf("\n");
|
|
|
|
printf(" Object comparison:\n");
|
|
printf(" 1) Groups \n");
|
|
printf(" First compares the names of member objects (relative path, from the\n");
|
|
printf(" specified group) and generates a report of objects that appear in only\n");
|
|
printf(" one group or in both groups. Common objects are then compared recursively.\n");
|
|
printf(" 2) Datasets \n");
|
|
printf(" Array rank and dimensions, datatypes, and data values are compared.\n");
|
|
printf(" 3) Datatypes \n");
|
|
printf(" The comparison is based on the return value of H5Tequal.\n");
|
|
printf(" 4) Symbolic links \n");
|
|
printf(" The paths to the target objects are compared.\n");
|
|
printf(" (The option --follow-symlinks overrides the default behavior when\n");
|
|
printf(" symbolic links are compared.).\n");
|
|
printf("\n");
|
|
|
|
printf(" Exit code:\n");
|
|
printf(" 0 if no differences, 1 if differences found, 2 if error\n");
|
|
printf("\n");
|
|
printf(" Examples of use:\n");
|
|
printf(" 1) h5diff file1 file2 /g1/dset1 /g1/dset2\n");
|
|
printf(" Compares object '/g1/dset1' in file1 with '/g1/dset2' in file2\n");
|
|
printf("\n");
|
|
printf(" 2) h5diff file1 file2 /g1/dset1\n");
|
|
printf(" Compares object '/g1/dset1' in both files\n");
|
|
printf("\n");
|
|
printf(" 3) h5diff file1 file2\n");
|
|
printf(" Compares all objects in both files\n");
|
|
printf("\n");
|
|
printf(" Notes:\n");
|
|
printf(" file1 and file2 can be the same file.\n");
|
|
printf(" Use h5diff file1 file1 /g1/dset1 /g1/dset2 to compare\n");
|
|
printf(" '/g1/dset1' and '/g1/dset2' in the same file\n");
|
|
printf("\n");
|
|
}
|