1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405
|
/*===========================================================================
*
* 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 SortingRowSet SortingRowSet;
#define ROWSET_IMPL SortingRowSet
typedef struct SortingRowSetIterator SortingRowSetIterator;
#define ROWSET_ITER_IMPL SortingRowSetIterator
#include "row-set-priv.h"
#include "tbl-pair.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>
#include <string.h>
FILE_ENTRY ( sorting-row-set );
/*--------------------------------------------------------------------------
* SortingRowSetIterator
* interface to iterate RowSets
*/
struct SortingRowSetIterator
{
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 */
int64_t *src_ids;
uint32_t *new_ord;
size_t max_elems;
size_t num_elems;
/* if true, use setting for large-columns */
bool large;
/* if true, no need to regenerate new_ord */
bool new_ord_valid;
};
/*--------------------------------------------------------------------------
* SortingRowSet
* implementation of RowSet based upon auto-generated id pairs
*/
struct SortingRowSet
{
RowSet dad;
/* keep-alive reference */
SortingRowSetIterator *iter;
/* working data within map */
int64_t *src_ids;
size_t num_elems;
size_t cur_elem;
};
static
void SortingRowSetWhack ( SortingRowSet *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
RowSetIteratorRelease ( & self -> iter -> dad, ctx );
MemFree ( ctx, self, sizeof *self );
}
static
size_t SortingRowSetNextStat ( SortingRowSet *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 SortingRowSetNextPhys ( SortingRowSet *self, const ctx_t *ctx,
int64_t *ids, size_t max_ids )
{
FUNC_ENTRY ( ctx );
/* limit copy to request */
size_t to_copy = self -> num_elems - self -> cur_elem;
if ( to_copy > max_ids )
to_copy = max_ids;
/* copy out old-ids */
memmove ( ids, & self -> src_ids [ self -> cur_elem ], to_copy * sizeof ids [ 0 ] );
/* advance counter */
self -> cur_elem += to_copy;
return to_copy;
}
static
void SortingRowSetReset ( SortingRowSet *self, const ctx_t *ctx, bool for_static );
static RowSet_vt SortingRowSetPhys_vt =
{
SortingRowSetWhack,
SortingRowSetNextPhys,
SortingRowSetReset
};
static RowSet_vt SortingRowSetStat_vt =
{
SortingRowSetWhack,
SortingRowSetNextStat,
SortingRowSetReset
};
static
void SortingRowSetReset ( SortingRowSet *self, const ctx_t *ctx, bool for_static )
{
FUNC_ENTRY ( ctx );
if ( for_static )
{
/* go static */
self -> dad . vt = & SortingRowSetStat_vt;
}
else
{
SortingRowSetIterator *iter = self -> iter;
/* go physical */
self -> dad . vt = & SortingRowSetPhys_vt;
if ( iter -> new_ord_valid )
{
/* read new-ids from file, selecting old-ids within range */
STATUS ( 3, "selecting first %,zu ids from old=>new where new_id >= %,ld",
iter -> max_elems, iter -> row_id );
iter -> num_elems = MapFileSelectOldToNewSingle ( iter -> idx, ctx,
iter -> row_id, iter -> src_ids, NULL, iter -> max_elems );
}
else
{
/* read new-ids from file, init new-ord, selecting old-ids within range */
STATUS ( 3, "selecting first %,zu ids, new_ord from old=>new where new_id >= %,ld",
iter -> max_elems, iter -> row_id );
TRY ( iter -> num_elems = MapFileSelectOldToNewSingle ( iter -> idx, ctx,
iter -> row_id, iter -> src_ids, iter -> new_ord, iter -> max_elems ) )
{
iter -> new_ord_valid = true;
}
}
if ( FAILED () )
return;
self -> num_elems = iter -> num_elems;
STATUS ( 3, "selected %,zu ids", self -> num_elems );
}
/* ready */
self -> cur_elem = 0;
}
/*--------------------------------------------------------------------------
* SortingRowSetIterator
* interface to iterate RowSets
*/
static
void SortingRowSetIteratorWhack ( SortingRowSetIterator *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
if ( self -> src_ids != NULL )
MemFree ( ctx, self -> src_ids, sizeof self -> src_ids [ 0 ] * self -> max_elems );
if ( self -> new_ord != NULL )
MemFree ( ctx, self -> new_ord, sizeof self -> new_ord [ 0 ] * self -> max_elems );
MapFileRelease ( self -> idx, ctx );
RowSetIteratorDestroy ( & self -> dad, ctx );
MemFree ( ctx, self, sizeof * self );
}
static
RowSet *SortingRowSetIteratorMakeTheRowSet ( SortingRowSetIterator *self, const ctx_t *ctx, const RowSet_vt *vt )
{
FUNC_ENTRY ( ctx );
SortingRowSet *rs;
TRY ( rs = MemAlloc ( ctx, sizeof * rs, false ) )
{
TRY ( RowSetInit ( & rs -> dad, ctx, vt ) )
{
/* initialize the row-set with map and self reference */
rs -> src_ids = self -> src_ids;
rs -> iter = ( SortingRowSetIterator* ) 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 *SortingRowSetIteratorGetIdxMapping ( SortingRowSetIterator *self, const ctx_t *ctx, size_t *num_items )
{
FUNC_ENTRY ( ctx );
ANNOTATE ( "CALLING GetIdxMapping ON SORTING ROWSET ITERATOR" );
if ( num_items != NULL )
* num_items = 0;
return NULL;
}
static
int64_t *SortingRowSetIteratorGetSourceIds ( SortingRowSetIterator *self, const ctx_t *ctx, uint32_t **opt_ord, size_t *num_items )
{
FUNC_ENTRY ( ctx );
if ( opt_ord != NULL )
* opt_ord = self -> new_ord;
if ( self -> src_ids == NULL )
{
rc_t rc = RC ( rcExe, rcCursor, rcAccessing, rcSelf, rcInconsistent );
ERROR ( rc, "source id array is NULL" );
if ( num_items != NULL )
* num_items = 0;
return NULL;
}
if ( num_items != NULL )
* num_items = self -> num_elems;
return self -> src_ids;
}
static
void SortingRowSetIteratorAllocMap ( SortingRowSetIterator *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 -> src_ids = MemAlloc ( ctx, sizeof self -> src_ids [ 0 ] * self -> max_elems, false ) )
{
TRY ( self -> new_ord = MemAlloc ( ctx, sizeof self -> new_ord [ 0 ] * self -> max_elems, false ) )
{
STATUS ( 4, "allocated mapping array of %,u elements", self -> max_elems );
return;
}
MemFree ( ctx, self -> src_ids, sizeof self -> src_ids [ 0 ] * self -> max_elems );
self -> src_ids = NULL;
}
self -> max_elems >>= 1;
}
while ( self -> max_elems >= ctx -> caps -> tool -> min_idx_ids );
ANNOTATE ( "failed to allocate map for row-set" );
}
static
RowSet *SortingRowSetIteratorNext ( SortingRowSetIterator *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
RowSet *rs = NULL;
/* on first invocation, allocate the map */
if ( self -> src_ids == NULL )
{
ON_FAIL ( SortingRowSetIteratorAllocMap ( self, ctx ) )
return NULL;
assert ( self -> src_ids != NULL );
assert ( self -> new_ord != NULL );
}
/* advance row_id */
self -> row_id += self -> num_elems;
self -> num_elems = 0;
self -> new_ord_valid = false;
/* create the empty row-set */
if ( self -> row_id < self -> last_excl )
rs = SortingRowSetIteratorMakeTheRowSet ( self, ctx, & SortingRowSetPhys_vt );
return rs;
}
/*--------------------------------------------------------------------------
* MapFile
*/
static RowSetIterator_vt SortingRowSetIterator_vt =
{
SortingRowSetIteratorWhack,
SortingRowSetIteratorGetIdxMapping,
SortingRowSetIteratorGetSourceIds,
SortingRowSetIteratorNext
};
RowSetIterator * MapFileMakeSortingRowSetIterator ( const MapFile *self, const ctx_t *ctx, bool large )
{
FUNC_ENTRY ( ctx );
SortingRowSetIterator *rsi;
/* create the iterator */
TRY ( rsi = MemAlloc ( ctx, sizeof * rsi, true ) )
{
TRY ( RowSetIteratorInit ( & rsi -> dad, ctx, & SortingRowSetIterator_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;
}
|