hdf5/tools/lib/h5tools_utils.c
Jonathan Kim 4147de8d02 [svn-r20294] Purpose:
Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the 
    different set of attributes (different number and names)

Description:
    Previously h5diff compared attributes correctly only when two objects have 
    the same number of attributes and attribute names are identical.
    This fix covers all other cases.
    Also didn't display useful information about attribute difference.
    This fixes both issues.

     
Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
2011-03-22 10:47:07 -05:00

870 lines
24 KiB
C
Raw Blame History

This file contains invisible Unicode characters

This file contains invisible Unicode characters that are indistinguishable to humans but may be processed differently by a computer. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Bill Wendling <wendling@ncsa.uiuc.edu>
* Tuesday, 6. March 2001
*/
/*
* Portions of this work are derived from _Obfuscated C and Other Mysteries_,
* by Don Libes, copyright (c) 1993 by John Wiley & Sons, Inc.
*/
#include <ctype.h>
#include <stdarg.h>
#include <stdio.h>
#include <stdlib.h>
#include "h5tools_utils.h"
#include "H5private.h"
#include "h5trav.h"
/* global variables */
int nCols = 80;
/* ``get_option'' variables */
int opt_err = 1; /*get_option prints errors if this is on */
int opt_ind = 1; /*token pointer */
const char *opt_arg; /*flag argument (or value) */
static int h5tools_d_status = 0;
static const char *h5tools_progname = "h5tools";
/* ``parallel_print'' variables */
unsigned char g_Parallel = 0; /*0 for serial, 1 for parallel */
char outBuff[OUTBUFF_SIZE];
int outBuffOffset;
FILE* overflow_file = NULL;
/* local functions */
static void init_table(table_t **tbl);
#ifdef H5DUMP_DEBUG
static void dump_table(char* tablename, table_t *table);
#endif /* H5DUMP_DEBUG */
static void add_obj(table_t *table, haddr_t objno, const char *objname, hbool_t recorded);
/*-------------------------------------------------------------------------
* Function: parallel_print
*
* Purpose: wrapper for printf for use in parallel mode.
*
* Programmer: Leon Arber
*
* Date: December 1, 2004
*
*-------------------------------------------------------------------------
*/
void parallel_print(const char* format, ...)
{
int bytes_written;
va_list ap;
va_start(ap, format);
if(!g_Parallel)
vprintf(format, ap);
else
{
if(overflow_file == NULL) /*no overflow has occurred yet */
{
#if 0
printf("calling HDvsnprintf: OUTBUFF_SIZE=%ld, outBuffOffset=%ld, ", (long)OUTBUFF_SIZE, (long)outBuffOffset);
#endif
bytes_written = HDvsnprintf(outBuff+outBuffOffset, OUTBUFF_SIZE-outBuffOffset, format, ap);
#if 0
printf("bytes_written=%ld\n", (long)bytes_written);
#endif
va_end(ap);
va_start(ap, format);
#if 0
printf("Result: bytes_written=%ld, OUTBUFF_SIZE-outBuffOffset=%ld\n", (long)bytes_written, (long)OUTBUFF_SIZE-outBuffOffset);
#endif
if ((bytes_written < 0) ||
#ifdef H5_VSNPRINTF_WORKS
(bytes_written >= (OUTBUFF_SIZE-outBuffOffset))
#else
((bytes_written+1) == (OUTBUFF_SIZE-outBuffOffset))
#endif
)
{
/* Terminate the outbuff at the end of the previous output */
outBuff[outBuffOffset] = '\0';
overflow_file = HDtmpfile();
if(overflow_file == NULL)
fprintf(stderr, "warning: could not create overflow file. Output may be truncated.\n");
else
bytes_written = HDvfprintf(overflow_file, format, ap);
}
else
outBuffOffset += bytes_written;
}
else
bytes_written = HDvfprintf(overflow_file, format, ap);
}
va_end(ap);
}
/*-------------------------------------------------------------------------
* Function: error_msg
*
* Purpose: Print a nicely formatted error message to stderr flushing the
* stdout stream first.
*
* Return: Nothing
*
* Programmer: Bill Wendling
* Tuesday, 20. February 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
error_msg(const char *fmt, ...)
{
va_list ap;
va_start(ap, fmt);
HDfflush(stdout);
HDfprintf(stderr, "%s error: ", h5tools_getprogname());
HDvfprintf(stderr, fmt, ap);
va_end(ap);
}
/*-------------------------------------------------------------------------
* Function: warn_msg
*
* Purpose: Print a nicely formatted warning message to stderr flushing
* the stdout stream first.
*
* Return: Nothing
*
* Programmer: Bill Wendling
* Tuesday, 20. February 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
warn_msg(const char *fmt, ...)
{
va_list ap;
va_start(ap, fmt);
HDfflush(stdout);
HDfprintf(stderr, "%s warning: ", h5tools_getprogname());
HDvfprintf(stderr, fmt, ap);
va_end(ap);
}
/*-------------------------------------------------------------------------
* Function: get_option
*
* Purpose: Determine the command-line options a user specified. We can
* accept both short and long type command-lines.
*
* Return: Success: The short valued "name" of the command line
* parameter or EOF if there are no more
* parameters to process.
*
* Failure: A question mark.
*
* Programmer: Bill Wendling
* Friday, 5. January 2001
*
* Modifications: Pedro Vicente
* October, 27 2008
* Wilcard "*" argument type
*
*-------------------------------------------------------------------------
*/
int
get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts)
{
static int sp = 1; /* character index in current token */
int opt_opt = '?'; /* option character passed back to user */
if (sp == 1) {
/* check for more flag-like tokens */
if (opt_ind >= argc || argv[opt_ind][0] != '-' || argv[opt_ind][1] == '\0') {
return EOF;
} else if (HDstrcmp(argv[opt_ind], "--") == 0) {
opt_ind++;
return EOF;
}
}
if (sp == 1 && argv[opt_ind][0] == '-' && argv[opt_ind][1] == '-') {
/* long command line option */
const char *arg = &argv[opt_ind][2];
int i;
for (i = 0; l_opts && l_opts[i].name; i++) {
size_t len = HDstrlen(l_opts[i].name);
if (HDstrncmp(arg, l_opts[i].name, len) == 0) {
/* we've found a matching long command line flag */
opt_opt = l_opts[i].shortval;
if (l_opts[i].has_arg != no_arg) {
if (arg[len] == '=') {
opt_arg = &arg[len + 1];
}
else if (l_opts[i].has_arg != optional_arg) {
if (opt_ind < (argc - 1))
if (argv[opt_ind + 1][0] != '-')
opt_arg = argv[++opt_ind];
} else if (l_opts[i].has_arg == require_arg) {
if (opt_err)
HDfprintf(stderr,
"%s: option required for \"--%s\" flag\n",
argv[0], arg);
opt_opt = '?';
}
} else {
if (arg[len] == '=') {
if (opt_err)
HDfprintf(stderr,
"%s: no option required for \"%s\" flag\n",
argv[0], arg);
opt_opt = '?';
}
opt_arg = NULL;
}
break;
}
}
if (l_opts[i].name == NULL) {
/* exhausted all of the l_opts we have and still didn't match */
if (opt_err)
HDfprintf(stderr, "%s: unknown option \"%s\"\n", argv[0], arg);
opt_opt = '?';
}
opt_ind++;
sp = 1;
} else {
register char *cp; /* pointer into current token */
/* short command line option */
opt_opt = argv[opt_ind][sp];
if (opt_opt == ':' || (cp = strchr(opts, opt_opt)) == 0) {
if (opt_err)
HDfprintf(stderr, "%s: unknown option \"%c\"\n",
argv[0], opt_opt);
/* if no chars left in this token, move to next token */
if (argv[opt_ind][++sp] == '\0') {
opt_ind++;
sp = 1;
}
return '?';
}
if (*++cp == ':') {
/* if a value is expected, get it */
if (argv[opt_ind][sp + 1] != '\0') {
/* flag value is rest of current token */
opt_arg = &argv[opt_ind++][sp + 1];
} else if (++opt_ind >= argc) {
if (opt_err)
HDfprintf(stderr,
"%s: value expected for option \"%c\"\n",
argv[0], opt_opt);
opt_opt = '?';
} else {
/* flag value is next token */
opt_arg = argv[opt_ind++];
}
sp = 1;
}
/* wildcard argument */
else if (*cp == '*')
{
/* check the next argument */
opt_ind++;
/* we do have an extra argument, check if not last */
if ( argv[opt_ind][0] != '-' && (opt_ind+1) < argc )
{
opt_arg = argv[opt_ind++];
}
else
{
opt_arg = NULL;
}
}
else
{
/* set up to look at next char in token, next time */
if (argv[opt_ind][++sp] == '\0') {
/* no more in current token, so setup next token */
opt_ind++;
sp = 1;
}
opt_arg = NULL;
}
}
/* return the current flag character found */
return opt_opt;
}
/*-------------------------------------------------------------------------
* Function: indentation
*
* Purpose: Print spaces for indentation
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
indentation(int x)
{
if (x < nCols) {
while (x-- > 0)
printf(" ");
} else {
HDfprintf(stderr, "error: the indentation exceeds the number of cols.\n");
exit(1);
}
}
/*-------------------------------------------------------------------------
* Function: print_version
*
* Purpose: Print the program name and the version information which is
* defined the same as the HDF5 library version.
*
* Return: void
*
* Programmer: unknown
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
print_version(const char *progname)
{
printf("%s: Version %u.%u.%u%s%s\n",
progname, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE,
((char *)H5_VERS_SUBRELEASE)[0] ? "-" : "", H5_VERS_SUBRELEASE);
}
/*-------------------------------------------------------------------------
* Function: init_table
*
* Purpose: allocate and initialize tables for shared groups, datasets,
* and committed types
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
init_table(table_t **tbl)
{
table_t *table = (table_t *)HDmalloc(sizeof(table_t));
table->size = 20;
table->nobjs = 0;
table->objs = (obj_t *)HDmalloc(table->size * sizeof(obj_t));
*tbl = table;
}
/*-------------------------------------------------------------------------
* Function: free_table
*
* Purpose: free tables for shared groups, datasets,
* and committed types
*
* Return: void
*
* Programmer: Paul Harten
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
free_table(table_t *table)
{
unsigned u; /* Local index value */
/* Free the names for the objects in the table */
for(u = 0; u < table->nobjs; u++)
if(table->objs[u].objname)
HDfree(table->objs[u].objname);
HDfree(table->objs);
}
#ifdef H5DUMP_DEBUG
/*-------------------------------------------------------------------------
* Function: dump_table
*
* Purpose: display the contents of tables for debugging purposes
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_table(char* tablename, table_t *table)
{
unsigned u;
printf("%s: # of entries = %d\n", tablename,table->nobjs);
for (u = 0; u < table->nobjs; u++)
HDfprintf(stdout,"%a %s %d %d\n", table->objs[u].objno,
table->objs[u].objname,
table->objs[u].displayed, table->objs[u].recorded);
}
/*-------------------------------------------------------------------------
* Function: dump_tables
*
* Purpose: display the contents of tables for debugging purposes
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
dump_tables(find_objs_t *info)
{
dump_table("group_table", info->group_table);
dump_table("dset_table", info->dset_table);
dump_table("type_table", info->type_table);
}
#endif /* H5DUMP_DEBUG */
/*-------------------------------------------------------------------------
* Function: search_obj
*
* Purpose: search the object specified by objno in the table
*
* Return: Success: an integer, the location of the object
*
* Failure: FAIL if object is not found
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
obj_t *
search_obj(table_t *table, haddr_t objno)
{
unsigned u;
for(u = 0; u < table->nobjs; u++)
if(table->objs[u].objno == objno)
return &(table->objs[u]);
return NULL;
}
/*-------------------------------------------------------------------------
* Function: find_objs_cb
*
* Purpose: Callback to find objects, committed types and store them in tables
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
find_objs_cb(const char *name, const H5O_info_t *oinfo, const char *already_seen,
void *op_data)
{
find_objs_t *info = (find_objs_t*)op_data;
herr_t ret_value = 0;
switch(oinfo->type) {
case H5O_TYPE_GROUP:
if(NULL == already_seen)
add_obj(info->group_table, oinfo->addr, name, TRUE);
break;
case H5O_TYPE_DATASET:
if(NULL == already_seen) {
hid_t dset;
/* Add the dataset to the list of objects */
add_obj(info->dset_table, oinfo->addr, name, TRUE);
/* Check for a dataset that uses a named datatype */
if((dset = H5Dopen2(info->fid, name, H5P_DEFAULT)) >= 0) {
hid_t type = H5Dget_type(dset);
if(H5Tcommitted(type) > 0) {
H5O_info_t type_oinfo;
H5Oget_info(type, &type_oinfo);
if(search_obj(info->type_table, type_oinfo.addr) == NULL)
add_obj(info->type_table, type_oinfo.addr, name, FALSE);
} /* end if */
H5Tclose(type);
H5Dclose(dset);
} /* end if */
else
ret_value = FAIL;
} /* end if */
break;
case H5O_TYPE_NAMED_DATATYPE:
if(NULL == already_seen) {
obj_t *found_obj;
if((found_obj = search_obj(info->type_table, oinfo->addr)) == NULL)
add_obj(info->type_table, oinfo->addr, name, TRUE);
else {
/* Use latest version of name */
HDfree(found_obj->objname);
found_obj->objname = HDstrdup(name);
/* Mark named datatype as having valid name */
found_obj->recorded = TRUE;
} /* end else */
} /* end if */
break;
default:
break;
} /* end switch */
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: init_objs
*
* Purpose: Initialize tables for groups, datasets & named datatypes
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
init_objs(hid_t fid, find_objs_t *info, table_t **group_table,
table_t **dset_table, table_t **type_table)
{
/* Initialize the tables */
init_table(group_table);
init_table(dset_table);
init_table(type_table);
/* Init the find_objs_t */
info->fid = fid;
info->group_table = *group_table;
info->type_table = *type_table;
info->dset_table = *dset_table;
/* Find all shared objects */
return(h5trav_visit(fid, "/", TRUE, TRUE, find_objs_cb, NULL, info));
}
/*-------------------------------------------------------------------------
* Function: add_obj
*
* Purpose: add a shared object to the table
* realloc the table if necessary
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
add_obj(table_t *table, haddr_t objno, const char *objname, hbool_t record)
{
unsigned u;
/* See if we need to make table larger */
if(table->nobjs == table->size) {
table->size *= 2;
table->objs = (struct obj_t *)HDrealloc(table->objs, table->size * sizeof(table->objs[0]));
} /* end if */
/* Increment number of objects in table */
u = table->nobjs++;
/* Set information about object */
table->objs[u].objno = objno;
table->objs[u].objname = HDstrdup(objname);
table->objs[u].recorded = record;
table->objs[u].displayed = 0;
}
#ifndef H5_HAVE_TMPFILE
/*-------------------------------------------------------------------------
* Function: tmpfile
*
* Purpose: provide tmpfile() function when it is not supported by the
* system. Always return NULL for now.
*
* Return: a stream description when succeeds.
* NULL if fails.
*
* Programmer: Albert Cheng, 2005/8/9
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
FILE *
tmpfile(void)
{
return NULL;
}
#endif
/*-------------------------------------------------------------------------
* Function: H5tools_get_symlink_info
*
* Purpose: Get symbolic link (soft, external) info and its target object type
(dataset, group, named datatype) and path, if exist
*
* Patameters:
* - [IN] fileid : link file id
* - [IN] linkpath : link path
* - [OUT] link_info: returning target object info (h5tool_link_info_t)
*
* Return:
* 2 : given pathname is object
* 1 : Succed to get link info.
* 0 : Detected as a dangling link
* -1 : H5 API failed.
*
* NOTE:
* link_info->trg_path must be freed out of this function
*
* Programmer: Jonathan Kim
*
* Date: Feb 8, 2010
*-------------------------------------------------------------------------*/
int
H5tools_get_symlink_info(hid_t file_id, const char * linkpath, h5tool_link_info_t *link_info,
hbool_t get_obj_type)
{
htri_t l_ret;
H5O_info_t trg_oinfo;
hid_t fapl = H5P_DEFAULT;
hid_t lapl = H5P_DEFAULT;
int ret = -1; /* init to fail */
/* init */
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* if path is root, return group type */
if(!HDstrcmp(linkpath,"/"))
{
link_info->trg_type = H5O_TYPE_GROUP;
ret = 2;
goto out;
}
/* check if link itself exist */
if(H5Lexists(file_id, linkpath, H5P_DEFAULT) <= 0) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: link <%s> doesn't exist \n",linkpath);
goto out;
} /* end if */
/* get info from link */
if(H5Lget_info(file_id, linkpath, &(link_info->linfo), H5P_DEFAULT) < 0) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get link info from <%s>\n",linkpath);
goto out;
} /* end if */
/* given path is hard link (object) */
if(link_info->linfo.type == H5L_TYPE_HARD) {
ret = 2;
goto out;
} /* end if */
/* trg_path must be freed out of this function when finished using */
link_info->trg_path = (char*)HDcalloc(link_info->linfo.u.val_size, sizeof(char));
HDassert(link_info->trg_path);
/* get link value */
if(H5Lget_val(file_id, linkpath, (void *)link_info->trg_path, link_info->linfo.u.val_size, H5P_DEFAULT) < 0) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get link value from <%s>\n",linkpath);
goto out;
} /* end if */
/*-----------------------------------------------------
* if link type is external link use different lapl to
* follow object in other file
*/
if(link_info->linfo.type == H5L_TYPE_EXTERNAL) {
fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_sec2(fapl);
lapl = H5Pcreate(H5P_LINK_ACCESS);
H5Pset_elink_fapl(lapl, fapl);
} /* end if */
/* Check for retrieving object info */
if(get_obj_type) {
/*--------------------------------------------------------------
* if link's target object exist, get type
*/
/* check if target object exist */
l_ret = H5Oexists_by_name(file_id, linkpath, lapl);
/* detect dangling link */
if(l_ret == FALSE) {
ret = 0;
goto out;
} /* end if */
/* function failed */
else if(l_ret < 0)
goto out;
/* get target object info */
if(H5Oget_info_by_name(file_id, linkpath, &trg_oinfo, lapl) < 0) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get object information for <%s>\n", linkpath);
goto out;
} /* end if */
/* check unknown type */
if(trg_oinfo.type < H5O_TYPE_GROUP || trg_oinfo.type >=H5O_TYPE_NTYPES) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: target object of <%s> is unknown type\n", linkpath);
goto out;
} /* end if */
/* set target obj type to return */
link_info->trg_type = trg_oinfo.type;
} /* end if */
else
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* succeed */
ret = 1;
out:
if(fapl != H5P_DEFAULT)
H5Pclose(fapl);
if(lapl != H5P_DEFAULT)
H5Pclose(lapl);
return ret;
} /* end H5tools_get_symlink_info() */
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Initialize the name and operation status of the H5 Tools library
* Description:
* These are utility functions to set/get the program name and operation status.
*-------------------------------------------------------------------------
*/
void h5tools_setprogname(const char *Progname)
{
h5tools_progname = Progname;
}
void h5tools_setstatus(int D_status)
{
h5tools_d_status = D_status;
}
const char*h5tools_getprogname(void)
{
return h5tools_progname;
}
int h5tools_getstatus(void)
{
return h5tools_d_status;
}