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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.
*
* ===========================================================================
*
*/
typedef struct MappingRowSet MappingRowSet;
#define ROWSET_IMPL MappingRowSet
typedef struct MappingRowSetIterator MappingRowSetIterator;
#define ROWSET_ITER_IMPL MappingRowSetIterator
#include "row-set-priv.h"
#include "tbl-pair.h"
#include "idx-mapping.h"
#include "map-file.h"
#include "ctx.h"
#include "caps.h"
#include "except.h"
#include "status.h"
#include "mem.h"
#include "sra-sort.h"
#include <klib/rc.h>
FILE_ENTRY ( mapping-row-set );
/*--------------------------------------------------------------------------
* MappingRowSetIterator
* interface to iterate RowSets
*/
struct MappingRowSetIterator
{
RowSetIterator dad;
/* base row-id */
int64_t row_id;
/* last row-id + 1 */
int64_t last_excl;
/* takes its input from new=>old index */
const MapFile *idx;
/* working data within map */
IdxMapping *map;
size_t max_elems;
size_t num_elems;
bool large;
};
/*--------------------------------------------------------------------------
* MappingRowSet
* implementation of RowSet based upon auto-generated id pairs
*/
struct MappingRowSet
{
RowSet dad;
/* keep-alive reference */
MappingRowSetIterator *iter;
/* working data within map */
IdxMapping *map;
size_t num_elems;
size_t cur_elem;
};
static
void MappingRowSetWhack ( MappingRowSet *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
RowSetIteratorRelease ( & self -> iter -> dad, ctx );
MemFree ( ctx, self, sizeof *self );
}
static
size_t MappingRowSetNextStat ( MappingRowSet *self, const ctx_t *ctx,
int64_t *ids, size_t max_ids )
{
FUNC_ENTRY ( ctx );
/* the starting row-id is taken from row-set-iterator
and offset by our current element counter */
int64_t row_id = self -> iter -> row_id + self -> cur_elem;
/* limit id generation to request */
size_t i, to_set = self -> num_elems - self -> cur_elem;
if ( to_set > max_ids )
to_set = max_ids;
/* fill request with serial numbers
could just as easily be the same number
the important thing is to limit the count
and produce the correct range */
for ( i = 0; i < to_set; ++ i )
ids [ i ] = row_id + i;
/* advance counter */
self -> cur_elem += to_set;
return to_set;
}
static
size_t MappingRowSetNextPhys ( MappingRowSet *self, const ctx_t *ctx,
int64_t *ids, size_t max_ids )
{
FUNC_ENTRY ( ctx );
/* limit copy to request */
size_t i, to_copy = self -> num_elems - self -> cur_elem;
if ( to_copy > max_ids )
to_copy = max_ids;
/* copy out old-ids */
for ( i = 0; i < to_copy; ++ i )
ids [ i ] = self -> map [ self -> cur_elem + i ] . old_id;
/* advance counter */
self -> cur_elem += to_copy;
return to_copy;
}
static
void MappingRowSetReset ( MappingRowSet *self, const ctx_t *ctx, bool for_static );
static RowSet_vt MappingRowSetPhys_vt =
{
MappingRowSetWhack,
MappingRowSetNextPhys,
MappingRowSetReset
};
static RowSet_vt MappingRowSetStat_vt =
{
MappingRowSetWhack,
MappingRowSetNextStat,
MappingRowSetReset
};
static
void MappingRowSetReset ( MappingRowSet *self, const ctx_t *ctx, bool for_static )
{
FUNC_ENTRY ( ctx );
if ( for_static )
{
/* go static */
self -> dad . vt = & MappingRowSetStat_vt;
}
else
{
size_t i, max_elems;
MappingRowSetIterator *iter = self -> iter;
/* go physical */
self -> dad . vt = & MappingRowSetPhys_vt;
/* limit id generation */
max_elems = iter -> max_elems;
if ( iter -> row_id + max_elems >= iter -> last_excl )
max_elems = ( size_t ) ( iter -> last_excl - iter -> row_id );
STATUS ( 4, "auto-generating %,zu ( old_id, new_id ) pairs where new_id >= %ld",
max_elems, iter -> row_id );
for ( i = 0; i < max_elems; ++ i )
iter -> map [ i ] . old_id = iter -> map [ i ] . new_id = iter -> row_id + i;
self -> num_elems = iter -> num_elems = max_elems;
}
/* ready */
self -> cur_elem = 0;
}
static
void MapFileMappingRowSetReset ( MappingRowSet *self, const ctx_t *ctx, bool for_static );
static RowSet_vt MapFileMappingRowSetPhys_vt =
{
MappingRowSetWhack,
MappingRowSetNextPhys,
MapFileMappingRowSetReset
};
static RowSet_vt MapFileMappingRowSetStat_vt =
{
MappingRowSetWhack,
MappingRowSetNextStat,
MapFileMappingRowSetReset
};
static
void MapFileMappingRowSetReset ( MappingRowSet *self, const ctx_t *ctx, bool for_static )
{
FUNC_ENTRY ( ctx );
if ( for_static )
{
/* go static */
self -> dad . vt = & MapFileMappingRowSetStat_vt;
}
else
{
MappingRowSetIterator *iter = self -> iter;
/* go physical */
self -> dad . vt = & MapFileMappingRowSetPhys_vt;
/* read new-ids from file, selecting only those within range */
STATUS ( 3, "selecting first %,zu ( old_id, new_id ) pairs from old=>new where new_id >= %,ld",
iter -> max_elems, iter -> row_id );
ON_FAIL ( iter -> num_elems = MapFileSelectOldToNewPairs ( iter -> idx, ctx,
iter -> row_id, iter -> map, iter -> max_elems ) )
return;
self -> num_elems = iter -> num_elems;
STATUS ( 3, "selected %,zu ( old_id, new_id ) pairs", self -> num_elems );
}
/* ready */
self -> cur_elem = 0;
}
/*--------------------------------------------------------------------------
* MappingRowSetIterator
* interface to iterate RowSets
*/
static
void MappingRowSetIteratorWhack ( MappingRowSetIterator *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
if ( self -> map != NULL )
MemFree ( ctx, self -> map, sizeof self -> map [ 0 ] * self -> max_elems );
RowSetIteratorDestroy ( & self -> dad, ctx );
MemFree ( ctx, self, sizeof * self );
}
static
void MapFileMappingRowSetIteratorWhack ( MappingRowSetIterator *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
if ( self -> map != NULL )
MemFree ( ctx, self -> map, sizeof self -> map [ 0 ] * self -> max_elems );
MapFileRelease ( self -> idx, ctx );
RowSetIteratorDestroy ( & self -> dad, ctx );
MemFree ( ctx, self, sizeof * self );
}
static
RowSet *MappingRowSetIteratorMakeTheRowSet ( MappingRowSetIterator *self, const ctx_t *ctx, const RowSet_vt *vt )
{
FUNC_ENTRY ( ctx );
MappingRowSet *rs;
TRY ( rs = MemAlloc ( ctx, sizeof * rs, false ) )
{
TRY ( RowSetInit ( & rs -> dad, ctx, vt ) )
{
/* initialize the row-set with map and self reference */
rs -> map = self -> map;
rs -> iter = ( MappingRowSetIterator* ) RowSetIteratorDuplicate ( & self -> dad, ctx );
rs -> num_elems = self -> num_elems;
rs -> cur_elem = 0;
return & rs -> dad;
}
MemFree ( ctx, rs, sizeof * rs );
}
return NULL;
}
static
struct IdxMapping *MappingRowSetIteratorGetIdxMapping ( MappingRowSetIterator *self, const ctx_t *ctx, size_t *num_items )
{
FUNC_ENTRY ( ctx );
if ( self -> map == NULL )
{
rc_t rc = RC ( rcExe, rcCursor, rcAccessing, rcSelf, rcInconsistent );
ERROR ( rc, "IdxMapping array is NULL" );
if ( num_items != NULL )
* num_items = 0;
return NULL;
}
if ( num_items != NULL )
* num_items = self -> num_elems;
return self -> map;
}
static
int64_t *MappingRowSetIteratorGetSourceIds ( MappingRowSetIterator *self, const ctx_t *ctx, uint32_t **opt_ord, size_t *num_items )
{
FUNC_ENTRY ( ctx );
ANNOTATE ( "CALLING GetSourceIds ON MAPPING ROWSET ITERATOR" );
if ( opt_ord != NULL )
* opt_ord = NULL;
if ( num_items != NULL )
* num_items = 0;
return NULL;
}
static
void MappingRowSetIteratorAllocMap ( MappingRowSetIterator *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
/* determine the maximum number of elements */
const Tool *tp = ctx -> caps -> tool;
uint64_t count = self -> last_excl - self -> row_id;
self -> max_elems = self -> large ? tp -> max_large_idx_ids : tp -> max_idx_ids;
if ( ( uint64_t ) self -> max_elems > count )
self -> max_elems = ( size_t ) count;
/* try to allocate the memory
this may be limited by the MemBank */
do
{
CLEAR ();
TRY ( self -> map = MemAlloc ( ctx, sizeof self -> map [ 0 ] * self -> max_elems, false ) )
{
STATUS ( 4, "allocated mapping array of %,u elements", self -> max_elems );
return;
}
self -> max_elems >>= 1;
}
while ( self -> max_elems >= ctx -> caps -> tool -> min_idx_ids );
ANNOTATE ( "failed to allocate map for row-set" );
}
static
RowSet *MappingRowSetIteratorNextInt ( MappingRowSetIterator *self, const ctx_t *ctx, const RowSet_vt *vt )
{
/* no FUNC_ENTRY */
RowSet *rs = NULL;
/* on first invocation, allocate the map */
if ( self -> map == NULL )
{
ON_FAIL ( MappingRowSetIteratorAllocMap ( self, ctx ) )
return NULL;
}
/* advance row_id */
self -> row_id += self -> num_elems;
self -> num_elems = 0;
/* create the empty row-set */
if ( self -> row_id < self -> last_excl )
rs = MappingRowSetIteratorMakeTheRowSet ( self, ctx, vt );
return rs;
}
static
RowSet *MappingRowSetIteratorNext ( MappingRowSetIterator *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
return MappingRowSetIteratorNextInt ( self, ctx, & MappingRowSetPhys_vt );
}
static
RowSet *MapFileMappingRowSetIteratorNext ( MappingRowSetIterator *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
return MappingRowSetIteratorNextInt ( self, ctx, & MapFileMappingRowSetPhys_vt );
}
/*--------------------------------------------------------------------------
* TablePair
*/
static RowSetIterator_vt MappingRowSetIterator_vt =
{
MappingRowSetIteratorWhack,
MappingRowSetIteratorGetIdxMapping,
MappingRowSetIteratorGetSourceIds,
MappingRowSetIteratorNext
};
/* MakeMappingRowSetIterator
* runs from first to last id in cursor
*/
RowSetIterator *TablePairMakeMappingRowSetIterator ( TablePair *self, const ctx_t *ctx, bool large )
{
FUNC_ENTRY ( ctx );
if ( self -> first_id > self -> last_excl )
{
rc_t rc = RC ( rcExe, rcCursor, rcConstructing, rcRange, rcInvalid );
INTERNAL_ERROR ( rc, "union of all column ranges improperly set" );
}
else
{
MappingRowSetIterator *rsi;
TRY ( rsi = MemAlloc ( ctx, sizeof * rsi, true ) )
{
TRY ( RowSetIteratorInit ( & rsi -> dad, ctx, & MappingRowSetIterator_vt ) )
{
rsi -> row_id = self -> first_id;
rsi -> last_excl = self -> last_excl;
rsi -> large = large;
return & rsi -> dad;
}
MemFree ( ctx, rsi, sizeof * rsi );
}
}
return NULL;
}
/*--------------------------------------------------------------------------
* MapFile
*/
static RowSetIterator_vt MapFileMappingRowSetIterator_vt =
{
MapFileMappingRowSetIteratorWhack,
MappingRowSetIteratorGetIdxMapping,
MappingRowSetIteratorGetSourceIds,
MapFileMappingRowSetIteratorNext
};
RowSetIterator * MapFileMakeMappingRowSetIterator ( const MapFile *self, const ctx_t *ctx, bool large )
{
FUNC_ENTRY ( ctx );
MappingRowSetIterator *rsi;
/* create the iterator */
TRY ( rsi = MemAlloc ( ctx, sizeof * rsi, true ) )
{
TRY ( RowSetIteratorInit ( & rsi -> dad, ctx, & MapFileMappingRowSetIterator_vt ) )
{
/* initialize the row-set with map and self reference */
TRY ( rsi -> row_id = MapFileFirst ( self, ctx ) )
{
TRY ( rsi -> last_excl = rsi -> row_id + MapFileCount ( self, ctx ) )
{
TRY ( rsi -> idx = MapFileDuplicate ( self, ctx ) )
{
rsi -> large = large;
return & rsi -> dad;
}
}
}
}
MemFree ( ctx, rsi, sizeof * rsi );
}
return NULL;
}
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