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hdf5/tools/lib/h5tools_utils.c
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jhendersonHDF 4883ee1ad8 Improve performance of h5trav interfaces for links to objects (#6400) 
For objects with multiple hard links, use hash table to map between
object tokens and pathnames during traversal to avoid linear scan over
all previous objects for each hard link seen

Use separate hash table for h5trav "table" interface to map between
object tokens and an index into the table of visited objects. This
facilitates quick lookups of objects when adding hard link name aliases
for h5repack processing
2026-07-08 15:53:10 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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 LICENSE file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Portions of this work are derived from _Obfuscated C and Other Mysteries_,
* by Don Libes, copyright (c) 1993 by John Wiley & Sons, Inc.
*/
#include "h5tools.h"
#include "h5tools_utils.h"
#include "H5private.h"
#include "h5trav.h"
#ifdef H5_HAVE_ROS3_VFD
#include "H5FDros3.h"
#endif
/* Global variables */
unsigned h5tools_nCols = 80;
static int h5tools_d_status = 0;
static const char *h5tools_progname = "h5tools";
/*
* The output functions need a temporary buffer to hold a piece of the
* dataset while it's being printed. This constant sets the limit on the
* size of that temporary buffer in bytes. For efficiency's sake, choose the
* largest value suitable for your machine (for testing use a small value).
*/
/* Maximum size used in a call to malloc for a dataset */
hsize_t H5TOOLS_MALLOCSIZE = (256 * 1024 * 1024); /* 256 MB */
/* size of hyperslab buffer when a dataset is bigger than H5TOOLS_MALLOCSIZE */
hsize_t H5TOOLS_BUFSIZE = (32 * 1024 * 1024); /* 32 MB */
/* ``parallel_print'' variables */
unsigned char g_Parallel = 0; /*0 for serial, 1 for parallel */
char outBuff[OUTBUFF_SIZE];
unsigned outBuffOffset;
FILE *overflow_file = NULL;
/* local functions */
static void init_table(hid_t fid, table_t **tbl);
#ifdef H5DUMP_DEBUG
static void dump_table(hid_t fid, char *tablename, table_t *table);
#endif /* H5DUMP_DEBUG */
static void add_obj(table_t *table, const H5O_token_t *obj_token, const char *objname, bool recorded);
/*-------------------------------------------------------------------------
* Function: parallel_print
*
* Purpose: wrapper for printf for use in parallel mode.
*-------------------------------------------------------------------------
*/
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 */ {
bytes_written = vsnprintf(outBuff + outBuffOffset, OUTBUFF_SIZE - outBuffOffset, format, ap);
va_end(ap);
va_start(ap, format);
if ((bytes_written < 0) || ((unsigned)bytes_written >= (OUTBUFF_SIZE - outBuffOffset))) {
/* Terminate the outbuff at the end of the previous output */
outBuff[outBuffOffset] = '\0';
overflow_file = tmpfile();
if (overflow_file == NULL)
fprintf(rawerrorstream,
"warning: could not create overflow file. Output may be truncated.\n");
else
bytes_written = vfprintf(overflow_file, format, ap);
}
else
outBuffOffset += (unsigned)bytes_written;
}
else
bytes_written = vfprintf(overflow_file, format, ap);
}
va_end(ap);
}
/*-------------------------------------------------------------------------
* Function: error_msg
*
* Purpose: Print a nicely formatted error message to stderr stream flushing
* the stdout stream first.
*
* Return: Nothing
*-------------------------------------------------------------------------
*/
void
error_msg(const char *fmt, ...)
{
va_list ap;
va_start(ap, fmt);
FLUSHSTREAM(rawattrstream);
FLUSHSTREAM(rawdatastream);
FLUSHSTREAM(rawoutstream);
fprintf(rawerrorstream, "%s error: ", h5tools_getprogname());
vfprintf(rawerrorstream, fmt, ap);
va_end(ap);
}
/*-------------------------------------------------------------------------
* Function: warn_msg
*
* Purpose: Print a nicely formatted warning message to stderr stream flushing
* the stdout stream first.
*
* Return: Nothing
*-------------------------------------------------------------------------
*/
void
warn_msg(const char *fmt, ...)
{
va_list ap;
va_start(ap, fmt);
FLUSHSTREAM(rawattrstream);
FLUSHSTREAM(rawdatastream);
FLUSHSTREAM(rawoutstream);
fprintf(rawerrorstream, "%s warning: ", h5tools_getprogname());
vfprintf(rawerrorstream, fmt, ap);
va_end(ap);
}
/*-------------------------------------------------------------------------
* Function: help_ref_msg
*
* Purpose: Print a message to refer help page
*
* Return: Nothing
*-------------------------------------------------------------------------
*/
void
help_ref_msg(FILE *output)
{
fprintf(output, "Try '-h' or '--help' for more information or ");
fprintf(output, "see the <%s> entry in the 'HDF5 Reference Manual'.\n", h5tools_getprogname());
}
/*-------------------------------------------------------------------------
* Function: parse_hsize_list
*
* Purpose: Parse a list of comma or space separated integers and return
* them in a list. The string being passed into this function
* should be at the start of the list you want to parse. You are
* responsible for freeing the array returned from here.
*
* Lists in the so-called "terse" syntax are separated by
* semicolons (;). The lists themselves can be separated by
* either commas (,) or white spaces.
*
* Return: <none>
*-------------------------------------------------------------------------
*/
void
parse_hsize_list(const char *h_list, subset_d *d)
{
hsize_t *p_list;
const char *ptr;
unsigned int size_count = 0;
unsigned int i = 0;
unsigned int last_digit = 0;
if (!h_list || !*h_list || *h_list == ';')
return;
H5TOOLS_START_DEBUG(" - h_list:%s", h_list);
/* count how many integers do we have */
for (ptr = h_list; ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
if (isdigit(*ptr)) {
if (!last_digit)
/* the last read character wasn't a digit */
size_count++;
last_digit = 1;
}
else
last_digit = 0;
if (size_count == 0) {
/* there aren't any integers to read */
H5TOOLS_ENDDEBUG("No integers to read");
return;
}
H5TOOLS_DEBUG("Number integers to read=%ld", size_count);
/* allocate an array for the integers in the list */
if ((p_list = (hsize_t *)calloc(size_count, sizeof(hsize_t))) == NULL)
H5TOOLS_INFO("Unable to allocate space for subset data");
for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
if (isdigit(*ptr)) {
/* we should have an integer now */
p_list[i++] = (hsize_t)strtoull(ptr, NULL, 0);
while (isdigit(*ptr))
/* scroll to end of integer */
ptr++;
}
d->data = p_list;
d->len = size_count;
H5TOOLS_ENDDEBUG(" ");
}
/*-------------------------------------------------------------------------
* Function: parse_subset_params
*
* Purpose: Parse the so-called "terse" syntax for specifying subsetting parameters.
*
* Return: Success: struct subset_t object
* Failure: NULL
*-------------------------------------------------------------------------
*/
struct subset_t *
parse_subset_params(const char *dset)
{
struct subset_t *s = NULL;
char *brace;
const char *q_dset;
H5TOOLS_START_DEBUG(" - dset:%s", dset);
/* if dset name is quoted wait till after second quote to look for subset brackets */
if (*dset == '"')
q_dset = strchr(dset, '"');
else
q_dset = dset;
if ((brace = strrchr(q_dset, '[')) != NULL) {
*brace++ = '\0';
s = (struct subset_t *)calloc(1, sizeof(struct subset_t));
parse_hsize_list(brace, &s->start);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
parse_hsize_list(brace, &s->stride);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
parse_hsize_list(brace, &s->count);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
parse_hsize_list(brace, &s->block);
}
H5TOOLS_ENDDEBUG(" ");
return s;
}
/*****************************************************************************
*
* Function: parse_tuple()
*
* Purpose:
*
* Create array of pointers to strings, identified as elements in a tuple
* of arbitrary length separated by provided character.
* ("tuple" because "nple" looks strange)
*
* * Receives pointer to start of tuple sequence string, '('.
* * Attempts to separate elements by token-character `sep`.
* * If the separator character is preceded by a backslash '\',
* the backslash is deleted and the separator is included in the
* element string as any other character.
* * To end an element with a backslash, escape the backslash, e.g.
* "(myelem\\,otherelem) -> {"myelem\", "otherelem"}
* * In all other cases, a backslash appearing not as part of "\\" or
* "\<sep>" digraph will be included berbatim.
* * Last two characters in the string MUST be ")\0".
*
* * Generates a copy of the input string `start`, (src..")\0"), replacing
* separators and close-paren with null characters.
* * This string is allocated at runtime and should be freed when done.
* * Generates array of char pointers, and directs start of each element
* (each pointer) into this copy.
* * Each tuple element points to the start of its string (substring)
* and ends with a null terminator.
* * This array is allocated at runtime and should be freed when done.
* * Reallocates and expands elements array during parsing.
* * Initially allocated for 2 (plus one null entry), and grows by
* powers of 2.
* * The final 'slot' in the element array (elements[nelements], e.g.)
* always points to NULL.
* * The number of elements found and stored are passed out through pointer
* to unsigned, `nelems`.
*
* Return:
*
* FAIL If malformed--does not look like a tuple "(...)"
* or major error was encountered while parsing.
* or
* SUCCEED String looks properly formed "(...)" and no major errors.
*
* Stores number of elements through pointer `nelems`.
* Stores list of pointers to char (first char in each element
* string) through pointer `ptrs_out`.
* NOTE: `ptrs_out[nelems] == NULL` should be true.
* NOTE: list is malloc'd by function, and should be freed
* when done.
* Stores "source string" for element pointers through `cpy_out`.
* NOTE: Each element substring is null-terminated.
* NOTE: There may be extra characters after the last element
* (past its null terminator), but is guaranteed to
* be null-terminated.
* NOTE: `cpy_out` string is malloc'd by function,
* and should be freed when done.
*
*****************************************************************************
*/
herr_t
parse_tuple(const char *start, int sep, char **cpy_out, unsigned *nelems, char ***ptrs_out)
{
char *elem_ptr = NULL;
char *dest_ptr = NULL;
unsigned elems_count = 0;
char **elems = NULL; /* more like *elems[], but compiler... */
char **elems_re = NULL; /* temporary pointer, for realloc */
char *cpy = NULL;
herr_t ret_value = SUCCEED;
unsigned init_slots = 2;
/*****************
* SANITY-CHECKS *
*****************/
/* must start with "("
*/
if (start[0] != '(') {
ret_value = FAIL;
goto done;
}
/* must end with ")"
*/
while (start[elems_count] != '\0') {
elems_count++;
}
if (start[elems_count - 1] != ')') {
ret_value = FAIL;
goto done;
}
elems_count = 0;
/***********
* PREPARE *
***********/
/* create list
*/
elems = (char **)malloc(sizeof(char *) * (init_slots + 1));
if (elems == NULL) {
ret_value = FAIL;
goto done;
} /* CANTALLOC */
/* create destination string
*/
start++; /* advance past opening paren '(' */
cpy = (char *)malloc(sizeof(char) * (strlen(start))); /* no +1; less '(' */
if (cpy == NULL) {
ret_value = FAIL;
goto done;
} /* CANTALLOC */
/* set pointers
*/
dest_ptr = cpy; /* start writing copy here */
elem_ptr = cpy; /* first element starts here */
elems[elems_count++] = elem_ptr; /* set first element pointer into list */
/*********
* PARSE *
*********/
while (*start != '\0') {
/* For each character in the source string...
*/
if (*start == '\\') {
/* Possibly an escape digraph.
*/
if ((*(start + 1) == '\\') || (*(start + 1) == sep)) {
/* Valid escape digraph of "\\" or "\<sep>".
*/
start++; /* advance past escape char '\' */
*(dest_ptr++) = *(start++); /* Copy subsequent char */
/* and advance pointers. */
}
else {
/* Not an accepted escape digraph.
* Copy backslash character.
*/
*(dest_ptr++) = *(start++);
}
}
else if (*start == sep) {
/* Non-escaped separator.
* Terminate elements substring in copy, record element, advance.
* Expand elements list if appropriate.
*/
*(dest_ptr++) = 0; /* Null-terminate elem substring in copy */
/* and advance pointer. */
start++; /* Advance src pointer past separator. */
elem_ptr = dest_ptr; /* Element pointer points to start of first */
/* character after null sep in copy. */
elems[elems_count++] = elem_ptr; /* Set elem pointer in list */
/* and increment count. */
/* Expand elements list, if necessary.
*/
if (elems_count == init_slots) {
init_slots *= 2;
elems_re = (char **)realloc(elems, sizeof(char *) * (init_slots + 1));
if (elems_re == NULL) {
/* CANTREALLOC */
ret_value = FAIL;
goto done;
}
elems = elems_re;
}
}
else if (*start == ')' && *(start + 1) == '\0') {
/* Found terminal, non-escaped close-paren. Last element.
* Write null terminator to copy.
* Advance source pointer to gently break from loop.
* Required to prevent ")" from always being added to last element.
*/
start++;
}
else {
/* Copy character into destination. Advance pointers.
*/
*(dest_ptr++) = *(start++);
}
}
*dest_ptr = '\0'; /* Null-terminate destination string. */
elems[elems_count] = NULL; /* Null-terminate elements list. */
/********************
* PASS BACK VALUES *
********************/
*ptrs_out = elems;
*nelems = elems_count;
*cpy_out = cpy;
done:
if (ret_value == FAIL) {
/* CLEANUP */
if (cpy)
free(cpy);
if (elems)
free(elems);
}
return ret_value;
} /* parse_tuple */
/*-------------------------------------------------------------------------
* Function: indentation
*
* Purpose: Print spaces for indentation
*
* Return: void
*-------------------------------------------------------------------------
*/
void
indentation(unsigned x)
{
if (x < h5tools_nCols) {
while (x-- > 0)
PRINTVALSTREAM(rawoutstream, " ");
}
else {
fprintf(rawerrorstream, "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
*-------------------------------------------------------------------------
*/
void
print_version(const char *progname)
{
PRINTSTREAM(rawoutstream, "%s: Version %u.%u.%u%s%s\n", progname, H5_VERS_MAJOR, H5_VERS_MINOR,
H5_VERS_RELEASE, ((const 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
*-------------------------------------------------------------------------
*/
static void
init_table(hid_t fid, table_t **tbl)
{
table_t *table = (table_t *)malloc(sizeof(table_t));
table->fid = fid;
table->size = 20;
table->nobjs = 0;
table->objs = (obj_t *)malloc(table->size * sizeof(obj_t));
*tbl = table;
}
/*-------------------------------------------------------------------------
* Function: free_table
*
* Purpose: free tables for shared groups, datasets,
* and committed types
*
* Return: void
*-------------------------------------------------------------------------
*/
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)
free(table->objs[u].objname);
free(table->objs);
free(table);
}
#ifdef H5DUMP_DEBUG
/*-------------------------------------------------------------------------
* Function: dump_table
*
* Purpose: display the contents of tables for debugging purposes
*
* Return: void
*-------------------------------------------------------------------------
*/
static void
dump_table(hid_t fid, char *tablename, table_t *table)
{
unsigned u;
char *obj_tok_str = NULL;
PRINTSTREAM(rawoutstream, "%s: # of entries = %d\n", tablename, table->nobjs);
for (u = 0; u < table->nobjs; u++) {
H5Otoken_to_str(fid, &table->objs[u].obj_token, &obj_tok_str);
PRINTSTREAM(rawoutstream, "%s %s %d %d\n", obj_tok_str, table->objs[u].objname,
table->objs[u].displayed, table->objs[u].recorded);
H5free_memory(obj_tok_str);
}
}
/*-------------------------------------------------------------------------
* Function: dump_tables
*
* Purpose: display the contents of tables for debugging purposes
*
* Return: void
*-------------------------------------------------------------------------
*/
void
dump_tables(find_objs_t *info)
{
dump_table(info->fid, "group_table", info->group_table);
dump_table(info->fid, "dset_table", info->dset_table);
dump_table(info->fid, "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
*-------------------------------------------------------------------------
*/
H5_ATTR_PURE obj_t *
search_obj(table_t *table, const H5O_token_t *obj_token)
{
unsigned u;
int token_cmp;
for (u = 0; u < table->nobjs; u++) {
if (H5Otoken_cmp(table->fid, &table->objs[u].obj_token, obj_token, &token_cmp) < 0)
return NULL;
if (!token_cmp)
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
*-------------------------------------------------------------------------
*/
static herr_t
find_objs_cb(const char *name, const H5O_info2_t *oinfo, bool already_seen,
const trav_seen_t H5_ATTR_UNUSED *visited_obj_info, 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 (!already_seen)
add_obj(info->group_table, &oinfo->token, name, true);
break;
case H5O_TYPE_DATASET:
if (!already_seen) {
hid_t dset = H5I_INVALID_HID;
/* Add the dataset to the list of objects */
add_obj(info->dset_table, &oinfo->token, 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_info2_t type_oinfo;
H5Oget_info3(type, &type_oinfo, H5O_INFO_BASIC);
if (search_obj(info->type_table, &type_oinfo.token) == NULL)
add_obj(info->type_table, &type_oinfo.token, name, false);
} /* end if */
H5Tclose(type);
H5Dclose(dset);
} /* end if */
else
ret_value = FAIL;
} /* end if */
break;
case H5O_TYPE_NAMED_DATATYPE:
if (!already_seen) {
obj_t *found_obj;
if ((found_obj = search_obj(info->type_table, &oinfo->token)) == NULL)
add_obj(info->type_table, &oinfo->token, name, true);
else {
/* Use latest version of name */
free(found_obj->objname);
found_obj->objname = strdup(name);
/* Mark named datatype as having valid name */
found_obj->recorded = true;
} /* end else */
} /* end if */
break;
case H5O_TYPE_MAP:
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default:
break;
} /* end switch */
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: init_objs
*
* Purpose: Initialize tables for groups, datasets & named datatypes
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*-------------------------------------------------------------------------
*/
herr_t
init_objs(hid_t fid, find_objs_t *info, table_t **group_table, table_t **dset_table, table_t **type_table)
{
herr_t ret_value = SUCCEED;
/* Initialize the tables */
init_table(fid, group_table);
init_table(fid, dset_table);
init_table(fid, 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 */
if ((ret_value = h5trav_visit(fid, "/", true, true, find_objs_cb, NULL, info, H5O_INFO_BASIC)) < 0)
H5TOOLS_GOTO_ERROR(FAIL, "finding shared objects failed");
done:
/* Release resources */
if (ret_value < 0) {
free_table(*group_table);
info->group_table = NULL;
free_table(*type_table);
info->type_table = NULL;
free_table(*dset_table);
info->dset_table = NULL;
}
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: add_obj
*
* Purpose: add a shared object to the table
* realloc the table if necessary
*
* Return: void
*-------------------------------------------------------------------------
*/
static void
add_obj(table_t *table, const H5O_token_t *obj_token, const char *objname, bool record)
{
size_t u;
/* See if we need to make table larger */
if (table->nobjs == table->size) {
table->size *= 2;
table->objs = (struct obj_t *)realloc(table->objs, table->size * sizeof(table->objs[0]));
} /* end if */
/* Increment number of objects in table */
u = table->nobjs++;
/* Set information about object */
memcpy(&table->objs[u].obj_token, obj_token, sizeof(H5O_token_t));
table->objs[u].objname = strdup(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.
*-------------------------------------------------------------------------
*/
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
*
* Parameters:
* - [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 : Succeed 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
*-------------------------------------------------------------------------*/
int
H5tools_get_symlink_info(hid_t file_id, const char *linkpath, h5tool_link_info_t *link_info,
bool get_obj_type)
{
htri_t l_ret;
H5O_info2_t trg_oinfo;
hid_t fapl = H5P_DEFAULT;
hid_t lapl = H5P_DEFAULT;
int ret_value = -1; /* init to fail */
/* init */
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* if path is root, return group type */
if (!strcmp(linkpath, "/")) {
link_info->trg_type = H5O_TYPE_GROUP;
H5TOOLS_GOTO_DONE(2);
}
/* 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);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* get info from link */
if (H5Lget_info2(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);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* given path is hard link (object) */
if (link_info->linfo.type == H5L_TYPE_HARD)
H5TOOLS_GOTO_DONE(2);
/* trg_path must be freed out of this function when finished using */
if ((link_info->trg_path = (char *)calloc(link_info->linfo.u.val_size, sizeof(char))) == NULL) {
if (link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to allocate buffer for <%s>\n", linkpath);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* 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);
H5TOOLS_GOTO_DONE(FAIL);
} /* 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) {
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
H5TOOLS_GOTO_DONE(FAIL);
if (H5Pset_fapl_sec2(fapl) < 0)
H5TOOLS_GOTO_DONE(FAIL);
if ((lapl = H5Pcreate(H5P_LINK_ACCESS)) < 0)
H5TOOLS_GOTO_DONE(FAIL);
if (H5Pset_elink_fapl(lapl, fapl) < 0)
H5TOOLS_GOTO_DONE(FAIL);
} /* 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) {
H5TOOLS_GOTO_DONE(0);
}
else if (l_ret < 0) { /* function failed */
H5TOOLS_GOTO_DONE(FAIL);
}
/* get target object info */
if (H5Oget_info_by_name3(file_id, linkpath, &trg_oinfo, H5O_INFO_BASIC, lapl) < 0) {
if (link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get object information for <%s>\n", linkpath);
H5TOOLS_GOTO_DONE(FAIL);
} /* 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);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* set target obj type to return */
memcpy(&link_info->obj_token, &trg_oinfo.token, sizeof(H5O_token_t));
link_info->trg_type = trg_oinfo.type;
link_info->fileno = trg_oinfo.fileno;
} /* end if */
else
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* succeed */
ret_value = 1;
done:
if (fapl != H5P_DEFAULT)
H5Pclose(fapl);
if (lapl != H5P_DEFAULT)
H5Pclose(lapl);
return ret_value;
} /* end H5tools_get_symlink_info() */
/*-------------------------------------------------------------------------
* Audience: Public
*
* 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;
}
H5_ATTR_PURE const char *
h5tools_getprogname(void)
{
return h5tools_progname;
}
H5_ATTR_PURE int
h5tools_getstatus(void)
{
return h5tools_d_status;
}
/*-----------------------------------------------------------
* PURPOSE :
* if environment variable H5TOOLS_BUFSIZE is set,
* update H5TOOLS_BUFSIZE and H5TOOLS_MALLOCSIZE from the env
* This can be called from each tools main() as part of initial act.
* Note: this is more of debugging purpose for now.
*/
int
h5tools_getenv_update_hyperslab_bufsize(void)
{
const char *env_str = NULL;
long hyperslab_bufsize_mb;
int ret_value = 1;
/* check if environment variable is set for the hyperslab buffer size */
if (NULL != (env_str = getenv("H5TOOLS_BUFSIZE"))) {
errno = 0;
hyperslab_bufsize_mb = strtol(env_str, (char **)NULL, 10);
if (errno != 0 || hyperslab_bufsize_mb <= 0)
H5TOOLS_GOTO_ERROR(FAIL, "hyperslab buffer size failed");
/* convert MB to byte */
H5TOOLS_BUFSIZE = (hsize_t)hyperslab_bufsize_mb * 1024 * 1024;
H5TOOLS_MALLOCSIZE = MAX(H5TOOLS_BUFSIZE, H5TOOLS_MALLOCSIZE);
}
done:
return ret_value;
}
#ifdef H5_HAVE_ROS3_VFD
/*----------------------------------------------------------------------------
*
* Function: h5tools_parse_ros3_fapl_tuple
*
* Purpose: A convenience function that parses a string containing a tuple
* of S3 VFD credential information and then passes the result to
* `h5tools_populate_ros3_fapl()` in order to setup a valid
* configuration for the S3 VFD.
*
* Return: SUCCEED/FAIL
*
*----------------------------------------------------------------------------
*/
herr_t
h5tools_parse_ros3_fapl_tuple(const char *tuple_str, int delim, H5FD_ros3_fapl_ext_t *fapl_config_out)
{
const char *ccred[4];
unsigned nelems = 0;
char *s3cred_src = NULL;
char **s3cred = NULL;
herr_t ret_value = SUCCEED;
/* Attempt to parse S3 credentials tuple */
if (parse_tuple(tuple_str, delim, &s3cred_src, &nelems, &s3cred) < 0)
H5TOOLS_GOTO_ERROR(FAIL, "failed to parse S3 VFD info tuple");
/* Sanity-check tuple count */
if (nelems != 3 && nelems != 4)
H5TOOLS_GOTO_ERROR(FAIL, "invalid S3 VFD credentials");
ccred[0] = (const char *)s3cred[0]; /* aws_region */
ccred[1] = (const char *)s3cred[1]; /* aws_access_key_id */
ccred[2] = (const char *)s3cred[2]; /* aws_secret_access_key */
if (nelems == 3) {
ccred[3] = "";
}
else {
ccred[3] = (const char *)s3cred[3]; /* aws_session_token */
}
if (FAIL == h5tools_populate_ros3_fapl(fapl_config_out, ccred, 4))
H5TOOLS_GOTO_ERROR(FAIL, "failed to populate S3 VFD FAPL config");
done:
if (s3cred)
free(s3cred);
if (s3cred_src)
free(s3cred_src);
return ret_value;
}
/*----------------------------------------------------------------------------
*
* Function: h5tools_populate_ros3_fapl()
*
* Purpose:
*
* Set the values of a ROS3 fapl configuration object.
*
* If the values pointer is NULL, sets fapl target `fa` to a default
* (valid, current-version, non-authenticating) fapl config.
*
* If `values` pointer is _not_ NULL, expects `values` to contain at least
* three non-null pointers to null-terminated strings, corresponding to:
* { aws_region,
* secret_id,
* secret_key,
* session_token (optional)
* }
* If all three (or four) strings are empty (""), the default fapl will be
* default. The aws_region and secret_id values must be both empty or both
* populated. Only secret_key is allowed to be empty (the empty string, "").
* All values are checked against overflow as defined in the ros3 vfd
* header file; if a value overruns the permitted space, FAIL is returned
* and the function aborts without resetting the fapl to values initially
* present.
*
* Return:
*
* FAIL if...
* * Read-Only S3 VFD is not enabled.
* * NULL fapl pointer: (NULL, {...} )
* * Warning: In all cases below, fapl will be set as "default"
* before error occurs.
* * NULL value strings: (&fa, {NULL?, NULL? NULL?, NULL?, ...})
* * Incomplete fapl info:
* * empty region, non-empty id, key either way, token either way
* * (&fa, token, {"", "...", "?", "?"})
* * non-empty region, empty id, key either way, token either way
* * (&fa, token, {"...", "", "?", "?"})
* * "non-empty key, token either way and either id or region empty
* * (&fa, token, {"", "", "...", "?")
* * (&fa, token, {"", "...", "...", "?")
* * (&fa, token, {"...", "", "...", "?")
* * Any string would overflow allowed space in fapl definition.
* or
* SUCCEED
* * Sets components in fapl_t pointer, copying strings as appropriate.
* * "Default" fapl (valid version, authenticate->False, empty strings)
* * `values` pointer is NULL
* * (&fa, token, NULL)
* * first four strings in `values` are empty ("")
* * (&fa, token, {"", "", "", "", ...})
* * Authenticating fapl
* * region, id, optional key and option session token provided
* * (&fa, token, {"...", "...", "", ""})
* * (&fa, token, {"...", "...", "...", ""})
* * (&fa, token, {"...", "...", "...", "..."})
*
* Return: SUCCEED/FAIL
*
*----------------------------------------------------------------------------
*/
herr_t
h5tools_populate_ros3_fapl(H5FD_ros3_fapl_ext_t *fa, const char **values, size_t num_values)
{
herr_t ret_value = SUCCEED;
H5TOOLS_START_DEBUG("");
if (fa == NULL)
H5TOOLS_GOTO_ERROR(FAIL, "ERROR: null pointer to fapl_t\n");
if (values && (num_values < 3))
H5TOOLS_GOTO_ERROR(FAIL, "ERROR: too few values (< 3) provided\n");
H5TOOLS_DEBUG(" preset fapl with default values\n");
fa->fa.version = H5FD_CURR_ROS3_FAPL_T_VERSION;
fa->fa.authenticate = false;
*(fa->fa.aws_region) = '\0';
*(fa->fa.secret_id) = '\0';
*(fa->fa.secret_key) = '\0';
*(fa->token) = '\0';
/* sanity-check supplied values */
if (values != NULL) {
if (values[0] == NULL)
H5TOOLS_GOTO_ERROR(FAIL, " ERROR: aws_region value cannot be NULL\n");
if (values[1] == NULL)
H5TOOLS_GOTO_ERROR(FAIL, " ERROR: secret_id value cannot be NULL\n");
if (values[2] == NULL)
H5TOOLS_GOTO_ERROR(FAIL, " ERROR: secret_key value cannot be NULL\n");
if ((num_values > 3) && (values[3] == NULL))
H5TOOLS_GOTO_ERROR(FAIL, " ERROR: token value cannot be NULL\n");
/* if region and ID are supplied (key optional), write to fapl...
* fail if value would overflow
*/
if (*values[0] != '\0' && *values[1] != '\0') {
if (strlen(values[0]) > H5FD_ROS3_MAX_REGION_LEN)
H5TOOLS_GOTO_ERROR(FAIL, " ERROR: aws_region value too long\n");
memcpy(fa->fa.aws_region, values[0], (strlen(values[0]) + 1));
H5TOOLS_DEBUG(" aws_region set\n");
if (strlen(values[1]) > H5FD_ROS3_MAX_SECRET_ID_LEN)
H5TOOLS_GOTO_ERROR(FAIL, " ERROR: secret_id value too long\n");
memcpy(fa->fa.secret_id, values[1], (strlen(values[1]) + 1));
H5TOOLS_DEBUG(" secret_id set\n");
if (strlen(values[2]) > H5FD_ROS3_MAX_SECRET_KEY_LEN)
H5TOOLS_GOTO_ERROR(FAIL, " ERROR: secret_key value too long\n");
memcpy(fa->fa.secret_key, values[2], (strlen(values[2]) + 1));
H5TOOLS_DEBUG(" secret_key set\n");
if (num_values > 3) {
if (strlen(values[3]) > H5FD_ROS3_MAX_SECRET_TOK_LEN)
H5TOOLS_GOTO_ERROR(FAIL, " ERROR: token value too long\n");
memcpy(fa->token, values[3], (strlen(values[3]) + 1));
H5TOOLS_DEBUG(" token set\n");
}
fa->fa.authenticate = true;
H5TOOLS_DEBUG(" set to authenticate\n");
}
else if (*values[0] != '\0' || *values[1] != '\0' || *values[2] != '\0' ||
((num_values > 3) && (*values[3] != '\0'))) {
H5TOOLS_GOTO_ERROR(FAIL, " ERROR: invalid assortment of empty/non-empty values\n");
}
} /* values != NULL */
done:
H5TOOLS_ENDDEBUG("");
return ret_value;
} /* h5tools_populate_ros3_fapl */
#endif /* H5_HAVE_ROS3_VFD */
#ifdef H5_HAVE_LIBHDFS
/*----------------------------------------------------------------------------
*
* Function: h5tools_parse_hdfs_fapl_tuple
*
* Purpose: A convenience function that parses a string containing a tuple
* of HDFS VFD configuration information.
*
* Return: SUCCEED/FAIL
*
*----------------------------------------------------------------------------
*/
herr_t
h5tools_parse_hdfs_fapl_tuple(const char *tuple_str, int delim, H5FD_hdfs_fapl_t *fapl_config_out)
{
unsigned long k = 0;
unsigned nelems = 0;
char *props_src = NULL;
char **props = NULL;
herr_t ret_value = SUCCEED;
/* Attempt to parse HDFS configuration tuple */
if (parse_tuple(tuple_str, delim, &props_src, &nelems, &props) < 0)
H5TOOLS_GOTO_ERROR(FAIL, "failed to parse HDFS VFD configuration tuple");
/* Sanity-check tuple count */
if (nelems != 5)
H5TOOLS_GOTO_ERROR(FAIL, "invalid HDFS VFD configuration");
/* Populate fapl configuration structure with given properties.
* WARNING: No error-checking is done on length of input strings...
* Silent overflow is possible, albeit unlikely.
*/
if (strncmp(props[0], "", 1)) {
strncpy(fapl_config_out->namenode_name, (const char *)props[0], strlen(props[0]));
}
if (strncmp(props[1], "", 1)) {
k = strtoul((const char *)props[1], NULL, 0);
if (errno == ERANGE)
H5TOOLS_GOTO_ERROR(FAIL, "supposed port number wasn't");
fapl_config_out->namenode_port = (int32_t)k;
}
if (strncmp(props[2], "", 1)) {
strncpy(fapl_config_out->kerberos_ticket_cache, (const char *)props[2], strlen(props[2]));
}
if (strncmp(props[3], "", 1)) {
strncpy(fapl_config_out->user_name, (const char *)props[3], strlen(props[3]));
}
if (strncmp(props[4], "", 1)) {
k = strtoul((const char *)props[4], NULL, 0);
if (errno == ERANGE)
H5TOOLS_GOTO_ERROR(FAIL, "supposed buffersize number wasn't");
fapl_config_out->stream_buffer_size = (int32_t)k;
}
done:
if (props)
free(props);
if (props_src)
free(props_src);
return ret_value;
}
#endif /* H5_HAVE_LIBHDFS */
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