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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#include "ctx.h"
#include "caps.h"
#include "mem.h"
#include "except.h"
#include "status.h"
#include "sra-sort.h"
#include <kapp/main.h>
#include <kapp/args.h>
#include <vdb/manager.h>
#include <vdb/vdb-priv.h>
#include <kdb/manager.h>
#include <kfg/config.h>
#include <kfs/directory.h>
#include <klib/printf.h>
#include <klib/text.h>
#include <klib/out.h>
#include <klib/log.h>
#include <klib/rc.h>
#include <strtol.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#ifdef _WIN32
#include <process.h>
#else
#include <unistd.h>
#endif
FILE_ENTRY ( sra-sort );
/* this goes away in vdb-3 */
const char UsageDefaultName [] = "sra-sort";
rc_t CC UsageSummary ( const char *prog_name )
{
return KOutMsg ( "Usage: %s [options] src-object dst-object\n"
" %s [options] src-object [src-object...] dst-dir\n"
"\n"
, prog_name
, prog_name
);
}
#define OPT_IGNORE_FAILURE "ignore-failure"
#define OPT_FORCE "force"
#define OPT_MEM_LIMIT "mem-limit"
#define OPT_MAP_FILE_BSIZE "map-file-bsize"
#define OPT_MAX_IDX_IDS "max-idx-ids"
#define OPT_MAX_REF_IDX_IDS "max-ref-idx-ids"
#define OPT_MAX_LARGE_IDX_IDS "max-large-idx-ids"
#define OPT_TEMP_DIR "tempdir"
#define OPT_MMAP_DIR "mmapdir"
#define OPT_UNSORTED_OLD_NEW "unsorted-old-new"
#define OPT_COLUMN_MD5 "column-md5"
#define OPT_NO_COLUMN_CHECKSUM "no-column-checksum"
#define OPT_BLOB_CRC32 "blob-crc32"
#define OPT_BLOB_MD5 "blob-md5"
#define OPT_NO_BLOB_CHECKSUM "no-blob-checksum"
#define OPT_KEEP_IDX_FILES "keep-idx-files"
#define OPT_IDX_CONSISTENCY_CHECK "idx-cc"
static const char *hlp_ignore_failure [] = { "ignore failure when sorting multiple objects",
"i.e. continue in spite of previous errors", NULL };
static const char *hlp_force [] = { "force overwrite of existing destination", NULL };
static const char *hlp_mem_limit [] = { "sets limit on dynamic memory usage", NULL };
static const char *hlp_map_file_bsize [] = { "sets id map-file cache size", NULL };
static const char *hlp_max_idx_ids [] = { "sets number of join-index ids to process at a time", NULL };
static const char *hlp_max_ref_idx_ids [] = { "sets number of join-index ids to process within REFERENCE table", NULL };
static const char *hlp_max_large_idx_ids [] = { "sets number of rows to process with large columns", NULL };
static const char *hlp_temp_dir [] = { "sets a specific directory to use for temporary files", NULL };
static const char *hlp_mmap_dir [] = { "sets a specific directory to use for memory-mapped buffers", NULL };
static const char *hlp_unsorted_old_new [] = { "write old=>new index in unsorted order", NULL };
static const char *hlp_column_md5 [] = { "generate md5sum compatible checksum files for each column [default]", NULL };
static const char *hlp_no_column_checksum [] = { "disable generation of column checksums", NULL };
static const char *hlp_blob_crc32 [] = { "generate CRC32 checksums for each blob [default]", NULL };
static const char *hlp_blob_md5 [] = { "generate MD5 checksums for each blob", NULL };
static const char *hlp_no_blob_checksum [] = { "disable generation of blob checksums", NULL };
#if _DEBUGGING
static const char *hlp_keep_idx_files [] = { "keep temporary index files for debugging", NULL };
static const char *hlp_idx_consistency_check [] = { "run consistency check on index files", NULL };
#endif
static OptDef options [] =
{
/* 1. long-name
2. list of single character short names
3. help-gen function
4. list of help strings, NULL terminated
5. max count
6. option requires value
7. option is required
*/
{ OPT_IGNORE_FAILURE, "i", NULL, hlp_ignore_failure, 1, false, false }
, { OPT_FORCE, "f", NULL, hlp_force, 1, false, false }
, { OPT_MEM_LIMIT, NULL, NULL, hlp_mem_limit, 1, true, false }
, { OPT_MAP_FILE_BSIZE, NULL, NULL, hlp_map_file_bsize, 1, true, false }
, { OPT_MAX_IDX_IDS, NULL, NULL, hlp_max_idx_ids, 1, true, false }
, { OPT_MAX_REF_IDX_IDS, NULL, NULL, hlp_max_ref_idx_ids, 1, true, false }
, { OPT_MAX_LARGE_IDX_IDS, NULL, NULL, hlp_max_large_idx_ids, 1, true, false }
, { OPT_TEMP_DIR, NULL, NULL, hlp_temp_dir, 1, true, false }
, { OPT_MMAP_DIR, NULL, NULL, hlp_mmap_dir, 1, true, false }
, { OPT_UNSORTED_OLD_NEW, NULL, NULL, hlp_unsorted_old_new, 1, false, false }
, { OPT_COLUMN_MD5, NULL, NULL, hlp_column_md5, 1, false, false }
, { OPT_NO_COLUMN_CHECKSUM, NULL, NULL, hlp_no_column_checksum, 1, false, false }
, { OPT_BLOB_CRC32, NULL, NULL, hlp_blob_crc32, 1, false, false }
, { OPT_BLOB_MD5, NULL, NULL, hlp_blob_md5, 1, false, false }
, { OPT_NO_BLOB_CHECKSUM, NULL, NULL, hlp_no_blob_checksum, 1, false, false }
#if _DEBUGGING
, { OPT_KEEP_IDX_FILES, NULL, NULL, hlp_keep_idx_files, 1, false, false }
, { OPT_IDX_CONSISTENCY_CHECK, NULL, NULL, hlp_idx_consistency_check, 1, false, false }
#endif
};
static const char *option_params [] =
{
NULL
, NULL
, "bytes"
, "cache-size"
, "num-ids"
, "num-ids"
, "num-ids"
, "path-to-tmp"
, "path-to-mmaps"
, NULL
, NULL
, NULL
, NULL
, NULL
, NULL
#if _DEBUGGING
, NULL
, NULL
#endif
};
rc_t CC Usage ( const Args *args )
{
uint32_t i;
const char *progname, *fullpath;
rc_t rc = ArgsProgram ( args, & fullpath, & progname );
if ( rc != 0 )
progname = fullpath = UsageDefaultName;
UsageSummary ( progname );
KOutMsg ( "Options:\n" );
for ( i = 0; i < sizeof options / sizeof options [ 0 ]; ++ i )
{
HelpOptionLine ( options [ i ] . aliases, options [ i ] . name,
option_params [ i ], options [ i ] . help );
}
HelpOptionsStandard ();
HelpVersion ( fullpath, KAppVersion () );
return 0;
}
static
const char *ArgsGetOptStr ( Args *self, const ctx_t *ctx, const char *optname, uint32_t *count )
{
rc_t rc;
const char *val = NULL;
uint32_t dummy;
if ( count == NULL )
count = & dummy;
rc = ArgsOptionCount ( self, optname, count );
if ( rc == 0 && * count != 0 )
{
rc = ArgsOptionValue ( self, optname, 0, (const void **)& val );
if ( rc != 0 )
INTERNAL_ERROR ( rc, "failed to retrieve '%s' parameter", optname );
}
return val;
}
static
uint64_t ArgsGetOptU64 ( Args *self, const ctx_t *ctx, const char *optname, uint32_t *count )
{
rc_t rc;
uint64_t val = 0;
uint32_t dummy;
if ( count == NULL )
count = & dummy;
rc = ArgsOptionCount ( self, optname, count );
if ( rc == 0 && * count != 0 )
{
const char *str;
rc = ArgsOptionValue ( self, optname, 0, (const void **)& str );
if ( rc != 0 )
INTERNAL_ERROR ( rc, "failed to retrieve '%s' parameter", optname );
else
{
char *end;
val = strtou64 ( str, & end, 0 );
if ( end [ 0 ] != 0 )
{
rc = RC ( rcExe, rcArgv, rcParsing, rcParam, rcIncorrect );
ERROR ( rc, "bad '%s' parameter: '%s'", optname, str );
}
}
}
return val;
}
static
bool ArgsGetOptBool ( Args *self, const ctx_t *ctx, const char *optname, uint32_t *count )
{
rc_t rc;
bool val = false;
uint32_t dummy;
if ( count == NULL )
count = & dummy;
rc = ArgsOptionCount ( self, optname, count );
if ( rc == 0 && * count != 0 )
val = true;
return val;
}
static
uint64_t KConfigGetNodeU64 ( const ctx_t *ctx, const char *path, bool *found )
{
rc_t rc;
uint64_t val = 0;
const KConfigNode *n;
bool dummy;
if ( found == NULL )
found = & dummy;
rc = KConfigOpenNodeRead ( ctx -> caps -> cfg, & n, "sra-sort/map_file_bsize" );
if ( rc == 0 )
{
char buff [ 256 ];
size_t num_read, remaining;
rc = KConfigNodeRead ( n, 0, buff, sizeof buff - 1, & num_read, & remaining );
if ( rc != 0 )
ERROR ( rc, "failed to read KConfig node '%s'", path );
else if ( remaining != 0 )
{
rc = RC ( rcExe, rcNode, rcReading, rcBuffer, rcInsufficient );
ERROR ( rc, "failed to read KConfig node '%s'", path );
}
else
{
char *end;
buff [ num_read ] = 0;
val = strtou64 ( buff, & end, 0 );
if ( end [ 0 ] != 0 )
{
rc = RC ( rcExe, rcNode, rcReading, rcNumeral, rcIncorrect );
ERROR ( rc, "bad '%s' config value: '%s'", path, buff );
}
}
KConfigNodeRelease ( n );
}
return val;
}
static
void initialize_params ( const ctx_t *ctx, Caps *caps, Tool *tp, Selection *sel, Args *args )
{
bool found=false;
uint64_t val;
uint32_t count;
const char *str;
int col_md5 = kcmMD5;
memset ( sel, 0, sizeof * sel );
memset ( tp, 0, sizeof * tp );
tp -> sel = sel;
/* default to host tmp */
tp -> tmpdir = "/tmp";
/* default to mmap dir */
tp -> mmapdir = NULL;
/* default buffer size for map cache */
tp -> map_file_bsize = 64 * 1024 * 1024;
tp -> map_file_random_bsize = tp -> map_file_bsize;
/* default max index ids to gather at a time */
tp -> max_ref_idx_ids = tp -> max_large_idx_ids = tp -> max_idx_ids = 256 * 1024 * 1024;
tp -> max_poslen_ids = 64 * 1024 * 1024;
tp -> min_idx_ids = 64 * 1024 * 1024;
tp -> max_missing_ids = tp -> max_idx_ids;
#if 0
/* refpos cache size */
tp -> refpos_cache_capacity = 100 * 1024 * 1024;
#endif
/* for creating mapping files */
tp -> pid = getpid ();
/* db create defaults */
tp -> db . cmode = kcmCreate;
/* tbl create defaults */
tp -> tbl . cmode = kcmCreate;
/* column create mode defaults */
tp -> col . pgsize = 1;
tp -> col . cmode = kcmInit;
tp -> col . checksum = kcsCRC32;
/* normally do not ignore failures */
tp -> ignore = false;
/* normally do not force overwrite */
tp -> force = false;
/* not needed under normal circumstances */
tp -> write_new_to_old = false;
tp->write_new_to_old=true;
/* default is to sort on old */
tp -> sort_before_old2new = true;
/* when debugging, this can be turned off */
tp -> unlink_idx_files = true;
tp -> idx_consistency_check = false;
/* record them as caps */
caps -> tool = tp;
/* look in config */
/* TBD - COMPLETE THIS */
ON_FAIL ( val = KConfigGetNodeU64 ( ctx, "sra-sort/map_file_bsize", & found ) )
return;
if ( found )
tp -> map_file_bsize = tp -> map_file_random_bsize = ( size_t ) val;
ON_FAIL ( val = KConfigGetNodeU64 ( ctx, "sra-sort/map_file_random_bsize", & found ) )
return;
if ( found )
tp -> map_file_random_bsize = ( size_t ) val;
ON_FAIL ( val = KConfigGetNodeU64 ( ctx, "sra-sort/max_idx_ids", & found ) )
return;
if ( found )
tp -> max_idx_ids = ( size_t ) val;
ON_FAIL ( val = KConfigGetNodeU64 ( ctx, "sra-sort/max_ref_idx_ids", & found ) )
return;
if ( found )
tp -> max_ref_idx_ids = ( size_t ) val;
/* finally look in args */
ON_FAIL ( str = ArgsGetOptStr ( args, ctx, OPT_TEMP_DIR, & count ) )
return;
if ( count != 0 && str [ 0 ] != 0 )
tp -> tmpdir = str;
ON_FAIL ( str = ArgsGetOptStr ( args, ctx, OPT_MMAP_DIR, & count ) )
return;
if ( count != 0 && str [ 0 ] != 0 )
tp -> mmapdir = str;
ON_FAIL ( val = ArgsGetOptU64 ( args, ctx, OPT_MAP_FILE_BSIZE, & count ) )
return;
if ( count != 0 )
tp -> map_file_random_bsize = ( size_t ) val;
ON_FAIL ( val = ArgsGetOptU64 ( args, ctx, OPT_MAX_IDX_IDS, & count ) )
return;
if ( count != 0 )
tp -> max_idx_ids = tp -> max_ref_idx_ids = ( size_t ) val;
ON_FAIL ( val = ArgsGetOptU64 ( args, ctx, OPT_MAX_REF_IDX_IDS, & count ) )
return;
if ( count != 0 )
tp -> max_ref_idx_ids = ( size_t ) val;
ON_FAIL ( val = ArgsGetOptU64 ( args, ctx, OPT_MAX_LARGE_IDX_IDS, & count ) )
return;
if ( count != 0 )
tp -> max_large_idx_ids = ( size_t ) val;
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_IGNORE_FAILURE, & count ) )
return;
if ( count != 0 )
tp -> ignore = true;
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_FORCE, & count ) )
return;
if ( count != 0 )
tp -> force = true;
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_UNSORTED_OLD_NEW, & count ) )
return;
if ( count != 0 )
tp -> sort_before_old2new = false;
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_COLUMN_MD5, & count ) )
return;
if ( count != 0 )
col_md5 = kcmMD5;
else
{
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_NO_COLUMN_CHECKSUM, & count ) )
return;
if ( count != 0 )
col_md5 = 0;
}
tp -> db . cmode |= col_md5;
tp -> tbl . cmode |= col_md5;
tp -> col . cmode |= col_md5;
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_BLOB_CRC32, & count ) )
return;
if ( count != 0 )
tp -> col . checksum = kcsCRC32;
else
{
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_BLOB_MD5, & count ) )
return;
if ( count != 0 )
tp -> col . checksum = kcsMD5;
else
{
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_NO_BLOB_CHECKSUM, & count ) )
return;
if ( count != 0 )
tp -> col . checksum = kcsNone;
}
}
#if _DEBUGGING
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_KEEP_IDX_FILES, & count ) )
return;
if ( count != 0 )
tp -> unlink_idx_files = false;
ON_FAIL ( found = ArgsGetOptBool ( args, ctx, OPT_IDX_CONSISTENCY_CHECK, & count ) )
return;
if ( count != 0 )
tp -> idx_consistency_check = tp -> write_new_to_old = true;
#endif
}
static
void initialize_caps ( const ctx_t *ctx, Caps *caps, Args *args )
{
FUNC_ENTRY ( ctx );
/* get specified limit */
uint32_t count;
size_t mem_limit = ( size_t ) ArgsGetOptU64 ( args, ctx, OPT_MEM_LIMIT, & count );
if ( ! FAILED () && count != 0 )
{
MemBank *mem;
TRY ( mem = MemBankMake ( ctx, mem_limit ) )
{
MemBankRelease ( caps -> mem, ctx );
caps -> mem = mem;
}
}
if ( ! FAILED () )
{
/* here's a chance to pick up special config */
/* TBD */
/* open up KConfig */
rc_t rc = KConfigMake ( ( KConfig** ) & caps -> cfg, NULL );
if ( rc != 0 )
ERROR ( rc, "KConfigMake failed" );
}
}
rc_t copy_stats_metadata( const char * src_path, const char * dst_path );
rc_t CC KMain ( int argc, char *argv [] )
{
DECLARE_CTX_INFO ();
/* initialize context */
Caps caps;
char cp_src_path [ 4096 ];
char cp_dst_path [ 4096 ];
ctx_t main_ctx = { & caps, NULL, & ctx_info };
const ctx_t *ctx = & main_ctx;
CapsInit ( & caps, NULL );
cp_src_path[ 0 ] = 0;
cp_dst_path[ 0 ] = 0;
if ( argc <= 1 )
main_ctx . rc = UsageSummary ( "sra-sort" );
else
{
/* create MemBank with unlimited quota */
TRY ( caps . mem = MemBankMake ( ctx, -1 ) )
{
rc_t rc = VDBManagerMakeUpdate ( & caps . vdb, NULL );
if ( rc != 0 )
ERROR ( rc, "failed to create VDBManager" );
else
{
rc = VDBManagerOpenKDBManagerUpdate ( caps . vdb, & caps . kdb );
if ( rc != 0 )
ERROR ( rc, "failed to create KDBManager" );
else
{
Args * args;
rc = ArgsMakeAndHandle ( & args, argc, argv, 1,
options, sizeof options / sizeof options [ 0 ] );
if ( rc != 0 )
ERROR ( rc, "failed to parse command line" );
else
{
TRY ( initialize_caps ( ctx, & caps, args ) )
{
Tool tp;
Selection sel;
TRY ( initialize_params ( ctx, & caps, & tp, & sel, args ) )
{
uint32_t count;
rc = ArgsParamCount ( args, & count );
if ( rc != 0 )
ERROR ( rc, "ArgsParamCount failed" );
else if ( count < 2 )
{
rc = RC ( rcExe, rcArgv, rcParsing, rcParam, rcInsufficient );
ERROR ( rc, "expected source and destination parameters" );
}
else
{
/* check type of last parameter */
const char *dst;
rc = ArgsParamValue ( args, count - 1, (const void **)& dst );
if ( rc != 0 )
ERROR ( rc, "ArgsParamValue [ %u ] failed", count - 1 );
else
{
enum RCTarget targ = rcNoTarg;
bool dst_is_dir = false;
int dst_type = KDBManagerPathType ( caps . kdb, "%s", dst ) & ~ kptAlias;
if ( dst_type == kptDir )
dst_is_dir = true;
else if ( count != 2 )
{
rc = RC ( rcExe, rcArgv, rcParsing, rcArgv, rcIncorrect );
ERROR ( rc, "multiple source objects require last parameter to be a directory" );
}
else switch ( dst_type )
{
case kptNotFound:
tp . db . cmode |= kcmParents;
tp . tbl . cmode |= kcmParents;
break;
case kptFile:
case kptFile | kptAlias:
rc = RC ( rcExe, rcArgv, rcParsing, rcArgv, rcIncorrect );
ERROR ( rc, "destination object is a file - remove first or rename before trying again" );
break;
case kptDatabase:
targ = rcDatabase;
break;
case kptTable:
targ = rcTable;
break;
case kptPrereleaseTbl:
dst_type = kptTable;
break;
default:
rc = RC ( rcExe, rcArgv, rcParsing, rcArgv, rcIncorrect );
ERROR ( rc, "destination object type cannot be overwritten" );
break;
}
if ( ! FAILED () )
{
if ( dst_is_dir )
{
uint32_t i;
rc_t first_rc = 0;
bool issue_divider_line;
if ( tp . force )
{
tp . db . cmode = kcmInit | ( tp . db . cmode & ~ kcmValueMask );
tp . tbl . cmode = kcmInit | ( tp . tbl . cmode & ~ kcmValueMask );
}
for ( issue_divider_line = false, i = 0; i < count - 1; issue_divider_line = true, ++ i )
{
rc = ArgsParamValue ( args, i, (const void **)& tp . src_path );
if ( rc != 0 )
ERROR ( rc, "ArgParamValue [ %u ] failed", i );
else
{
char dst_path [ 4096 ];
const char *leaf = strrchr ( tp . src_path, '/' );
if ( leaf ++ == NULL )
leaf = tp . src_path;
rc = string_printf ( dst_path, sizeof dst_path, NULL, "%s/%s", dst, leaf );
if ( rc != 0 )
ERROR ( rc, "string_printf on param [ %u ] failed", i );
else
{
size_t size = string_size ( dst_path );
char *ext = string_rchr ( dst_path, size, '.' );
if ( ext != NULL )
{
size -= ext - dst_path;
switch ( size )
{
case 4:
if ( strcase_cmp ( ext, 4, ".sra", 4, 4 ) == 0 )
* ext = 0;
break;
case 5:
if ( strcase_cmp ( ext, 5, ".csra", 5, 5 ) == 0 )
* ext = 0;
break;
}
}
if ( issue_divider_line )
STATUS ( 1, "################################################################" );
tp . dst_path = dst_path;
ON_FAIL ( run ( ctx ) )
{
if ( ! tp . ignore )
break;
if ( first_rc == 0 )
first_rc = ctx -> rc;
CLEAR ();
}
}
}
}
if ( first_rc != 0 )
main_ctx . rc = first_rc;
}
else
{
tp . dst_path = dst;
rc = ArgsParamValue ( args, 0, (const void **)& tp . src_path );
if ( rc != 0 )
ERROR ( rc, "ArgParamValue [ 0 ] failed" );
else
{
int src_type;
switch ( dst_type )
{
case kptDatabase:
case kptTable:
src_type = KDBManagerPathType ( caps . kdb, "%s", tp . src_path ) & ~ kptAlias;
if ( src_type == kptPrereleaseTbl )
src_type = kptTable;
if ( src_type != dst_type )
{
rc = RC ( rcExe, rcArgv, rcParsing, rcArgv, rcIncorrect );
ERROR ( rc, "source and destination object types are not compatible" );
}
else if ( ! tp . force )
{
rc = RC ( rcExe, targ, rcCopying, targ, rcExists );
ERROR ( rc, "destination object cannot be overwritten - try again with '-f'" );
}
else
{
tp . db . cmode = kcmInit | ( tp . db . cmode & ~ kcmValueMask );
tp . tbl . cmode = kcmInit | ( tp . tbl . cmode & ~ kcmValueMask );
}
}
if ( ! FAILED () ) {
string_copy( cp_src_path, sizeof cp_src_path,
tp . src_path, string_size( tp . src_path ) );
string_copy( cp_dst_path, sizeof cp_dst_path,
tp . dst_path, string_size( tp . dst_path ) );
run ( ctx );
}
}
}
}
}
}
}
}
ArgsWhack ( args );
}
}
}
CapsWhack ( & caps, ctx );
}
}
if ( 0 == main_ctx . rc && 0 != cp_src_path[ 0 ] && 0 != cp_dst_path[ 0 ] ) {
main_ctx . rc = copy_stats_metadata( cp_src_path, cp_dst_path );
}
return main_ctx . rc;
}
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