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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 "sra-sort.h"
#include "db-pair.h"
#include "ctx.h"
#include "caps.h"
#include "mem.h"
#include "except.h"
#include "status.h"
#include <sra/sraschema.h>
#include <vdb/manager.h>
#include <vdb/schema.h>
#include <vdb/database.h>
#include <vdb/table.h>
#include <kfg/config.h>
#include <klib/text.h>
#include <klib/rc.h>
#include <string.h>
FILE_ENTRY ( run );
static
void typename_to_config_path ( const char *in, char *out )
{
bool end;
uint32_t i;
for ( end = false, i = 0; ! end; ++ i )
{
switch ( out [ i ] = in [ i ] )
{
case ':':
out [ i ] = '/';
break;
case ' ':
case '#':
out [ i ] = 0;
case 0:
end = true;
return;
}
}
}
static
bool map_typename_builtin ( const ctx_t *ctx, const char *sub_node, const char *in, char *out, char *schema_src, size_t size )
{
FUNC_ENTRY ( ctx );
size_t copied;
#define ALIGN_EVIDENCE_MAP "NCBI:align:db:alignment_evidence_sorted"
#define ALIGN_UNSORTED_MAP "NCBI:align:db:alignment_sorted"
#define ALIGN_SRC "/usr/lib/ncbi-vdb/align/align.vschema"
if ( strcmp ( out, "NCBI/align/db/alignment_evidence" ) == 0 )
copied = string_copy ( out, size, ALIGN_EVIDENCE_MAP, sizeof ALIGN_EVIDENCE_MAP - 1 );
else if ( strcmp ( out, "NCBI/align/db/alignment_unsorted" ) == 0 )
copied = string_copy ( out, size, ALIGN_UNSORTED_MAP, sizeof ALIGN_UNSORTED_MAP - 1 );
else
{
strcpy ( out, in );
schema_src [ 0 ] = 0;
return false;
}
if ( copied != size )
{
out [ copied ] = 0;
copied = string_copy ( schema_src, size, ALIGN_SRC, sizeof ALIGN_SRC - 1 );
}
if ( copied == size )
{
rc_t rc = RC ( rcExe, rcType, rcCopying, rcBuffer, rcInsufficient );
INTERNAL_ERROR ( rc, "failed to copy a built-in constant" );
strcpy ( out, in );
schema_src [ 0 ] = 0;
return false;
}
#undef ALIGN_EVIDENCE_MAP
#undef ALIGN_UNSORTED_MAP
#undef ALIGN_SRC
schema_src [ copied ] = 0;
return true;
}
static
bool map_typename ( const ctx_t *ctx, const char *sub_node, const char *in, char *out, char *schema_src, size_t size )
{
FUNC_ENTRY ( ctx );
rc_t rc;
const KConfigNode *n;
size_t num_read, remaining;
typename_to_config_path ( in, out );
rc = KConfigOpenNodeRead ( ctx -> caps -> cfg, & n, "sra-sort/%s/%s", sub_node, out );
if ( rc != 0 )
return map_typename_builtin ( ctx, sub_node, in, out, schema_src, size );
rc = KConfigNodeRead ( n, 0, out, size - 1, & num_read, & remaining );
if ( rc != 0 )
ERROR ( rc, "KConfigNodeRead failed" );
else if ( remaining != 0 )
{
rc = RC ( rcExe, rcNode, rcReading, rcBuffer, rcInsufficient );
ERROR ( rc, "type map of '%s' is too long", in );
}
else
{
out [ num_read ] = 0;
typename_to_config_path ( out, schema_src );
KConfigNodeRelease ( n );
rc = KConfigOpenNodeRead ( ctx -> caps -> cfg, & n, "sra-sort/schema-src/%s", schema_src );
if ( rc != 0 )
ERROR ( rc, "KConfigOpenNodeRead - failed to find entry 'sra-sort/schema-src/%s'", schema_src );
else
{
rc = KConfigNodeRead ( n, 0, schema_src, size - 1, & num_read, & remaining );
if ( rc != 0 )
ERROR ( rc, "KConfigNodeRead failed" );
else if ( remaining != 0 )
{
rc = RC ( rcExe, rcNode, rcReading, rcBuffer, rcInsufficient );
ERROR ( rc, "type map of '%s' is too long", in );
}
else
{
schema_src [ num_read ] = 0;
}
}
}
KConfigNodeRelease ( n );
return true;
}
static
VSchema *map_schema_types ( TypeParams *type, const ctx_t *ctx, const VSchema *src_schema )
{
FUNC_ENTRY ( ctx );
bool mapped;
char schema_src [ 256 ];
assert ( sizeof schema_src == sizeof type -> dst_type );
TRY ( mapped = map_typename ( ctx, "out-map", type -> src_type, type -> dst_type, schema_src, sizeof schema_src ) )
{
rc_t rc;
VSchema *dst_schema;
if ( ! mapped )
{
type -> view_type [ 0 ] = 0;
rc = VSchemaAddRef ( src_schema );
if ( rc != 0 )
ERROR ( rc, "VSchemaAddRef failed" );
return ( VSchema* ) src_schema;
}
rc = VDBManagerMakeSchema ( ctx -> caps -> vdb, & dst_schema );
if ( rc != 0 )
ERROR ( rc, "VDBManagerMakeSchema failed" );
else
{
rc = VSchemaParseFile ( dst_schema, "%s", schema_src );
if ( rc != 0 )
ERROR ( rc, "VSchemaParseFile failed adding file '%s' for destination", src_schema );
else
{
TRY ( mapped = map_typename ( ctx, "view-map", type -> src_type, type -> view_type, schema_src, sizeof schema_src ) )
{
if ( ! mapped )
{
type -> view_type [ 0 ] = 0;
return dst_schema;
}
rc = VSchemaParseFile ( dst_schema, "%s", schema_src );
if ( rc == 0 )
return dst_schema;
ERROR ( rc, "VSchemaParseFile failed adding file '%s' for view", src_schema );
}
}
VSchemaRelease ( dst_schema );
}
}
return NULL;
}
/* open_db
* called from run
* determines the type of schema
* opens output object
* dispatches to the appropriate handler
*/
static
void open_db ( const ctx_t *ctx, const VDatabase **srcp )
{
FUNC_ENTRY ( ctx );
const VDatabase *src = *srcp;
const VSchema *src_schema;
rc_t rc = VDatabaseOpenSchema ( src, & src_schema );
if ( rc != 0 )
ERROR ( rc, "VDatabaseOpenSchema failed" );
else
{
TypeParams type;
rc = VDatabaseTypespec ( src, type . src_type, sizeof type . src_type );
if ( rc != 0 )
ERROR ( rc, "failed to obtain database typespec" );
else
{
VSchema *dst_schema;
/* map input type to output type */
TRY ( dst_schema = map_schema_types ( & type, ctx, src_schema ) )
{
const Tool *tp = ctx -> caps -> tool;
/* if view was remapped, reopen the database */
if ( type . view_type [ 0 ] != 0 )
{
VSchemaRelease ( src_schema );
rc = VSchemaAddRef ( dst_schema );
if ( rc != 0 )
{
ERROR ( rc, "VSchemaAddRef failed" );
src_schema = NULL;
}
else
{
src_schema = dst_schema;
VDatabaseRelease ( src );
rc = VDBManagerOpenDBRead ( ctx -> caps -> vdb, srcp, src_schema, "%s", tp -> src_path );
if ( rc != 0 )
ERROR ( rc, "VDBManagerOpenDBRead failed reopening db '%s'", tp -> src_path );
src = *srcp;
}
}
if ( ! FAILED () )
{
VDatabase *dst;
rc = VDBManagerCreateDB ( ctx -> caps -> vdb, & dst, dst_schema,
type . dst_type, tp -> db . cmode, "%s", tp -> dst_path );
if ( rc != 0 )
ERROR ( rc, "VDBManagerCreateDB failed to create '%s' with type '%s'", tp -> dst_path, type . dst_type );
else
{
rc = VDatabaseColumnCreateParams ( dst, tp -> col . cmode, tp -> col . checksum, tp -> col . pgsize );
if ( rc != 0 )
ERROR ( rc, "VDatabaseColumnCreateParams: failed to set column create params on db '%s'", tp -> dst_path );
else
{
DbPair *pb;
/* TBD - this has to be fixed to use proper stuff */
const char *name = strrchr ( tp -> src_path, '/' );
if ( name ++ == NULL )
name = tp -> src_path;
TRY ( pb = DbPairMake ( ctx, src, dst, name ) )
{
DbPairRun ( pb, ctx );
DbPairRelease ( pb, ctx );
}
}
rc = VDatabaseRelease ( dst );
if ( rc != 0 )
ERROR ( rc, "VDatabaseRelease failed on '%s'", tp -> dst_path );
}
}
VSchemaRelease ( dst_schema );
}
}
VSchemaRelease ( src_schema );
}
}
/* open_tbl
* called from run
* determines the type of schema
* opens output object
* dispatches to the appropriate handler
*/
static
void open_tbl ( const ctx_t *ctx, const VTable **tblp )
{
FUNC_ENTRY ( ctx );
rc_t rc = RC ( rcExe, rcFunction, rcExecuting, rcFunction, rcUnsupported );
ERROR ( rc, "unimplemented function" );
}
/* run
* called from KMain
* determines the type of object being copied/sorted
* opens input object
* dispatches to the appropriate handler
*/
void run ( const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
VDBManager *mgr = ctx -> caps -> vdb;
const Tool *tp = ctx -> caps -> tool;
const VDatabase *db;
rc_t rc = VDBManagerOpenDBRead ( mgr, & db, NULL, "%s", tp -> src_path );
if ( rc == 0 )
{
open_db ( ctx, & db );
VDatabaseRelease ( db );
}
else
{
const VTable *tbl;
rc_t rc2 = VDBManagerOpenTableRead ( mgr, & tbl, NULL, "%s", tp -> src_path );
if ( rc2 == 0 )
{
rc = 0;
open_tbl ( ctx, & tbl );
VTableRelease ( tbl );
}
else
{
VSchema *sra_dflt;
rc2 = VDBManagerMakeSRASchema ( mgr, & sra_dflt );
if ( rc2 == 0 )
{
rc2 = VDBManagerOpenTableRead ( mgr, & tbl, sra_dflt, "%s", tp -> src_path );
if ( rc2 == 0 )
{
rc = 0;
open_tbl ( ctx, & tbl );
VTableRelease ( tbl );
}
VSchemaRelease ( sra_dflt );
}
}
}
if ( rc != 0 )
ERROR ( rc, "failed to open object '%s'", tp -> src_path );
}
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