static
void CalcMD5 (void * buffer, size_t size, char hexstr [32])
{
static const char to_hex[16] = "0123456789abcdef";
MD5State state;
uint8_t digest [16];
uint8_t * bin;
char * hex;
int ix;
MD5StateInit (&state);
MD5StateAppend (&state, buffer, size);
MD5StateFinish (&state, digest);
bin = digest;
hex = hexstr;
for (ix = 0; ix < sizeof digest; ++ix)
{
uint8_t upper;
uint8_t lower;
upper = *bin++;
lower = upper & 0xF;
upper >>= 4;
*hex++ = to_hex [upper];
*hex++ = to_hex[lower];
}
}
static
rc_t CC refseq_meta_stats( void *self, const VXformInfo *info, int64_t row_id,
VRowResult *rslt, uint32_t argc, const VRowData argv [] )
{
rc_t rc = 0;
KMDataNode* node;
refseq_meta_stats_data* data = self;
uint64_t i, seq_len = argv[0].u.data.elem_count;
const INSDC_4na_bin * seq = argv[0].u.data.base;
seq += argv[0].u.data.first_elem;
assert(data != NULL);
if( data->buf_sz < seq_len ) {
char* x = realloc(data->buf, seq_len);
if( x == NULL ) {
rc = RC(rcVDB, rcFunction, rcUpdating, rcMemory, rcExhausted);
} else {
data->buf = x;
data->buf_sz = seq_len;
}
}
for(i = 0; rc == 0 && i < seq_len; i++) {
data->buf[i] = INSDC_4na_map_CHARSET[seq[i]];
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(data->stats, &node, "TOTAL_SEQ_LEN")) == 0 ) {
if( data->total_seq_len + seq_len < data->total_seq_len ) {
rc = RC(rcVDB, rcFunction, rcUpdating, rcMetadata, rcOutofrange);
} else {
data->total_seq_len += seq_len;
rc = KMDataNodeWriteB64(node, &data->total_seq_len);
}
KMDataNodeRelease(node);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(data->stats, &node, "CRC32")) == 0 ) {
data->crc32 = CRC32(data->crc32, data->buf, seq_len);
rc = KMDataNodeWriteB32(node, &data->crc32);
KMDataNodeRelease(node);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(data->stats, &node, "MD5")) == 0 ) {
uint8_t digest[16];
MD5State md5;
MD5StateAppend(&data->md5, data->buf, seq_len);
memcpy(&md5, &data->md5, sizeof(md5));
MD5StateFinish(&md5, digest);
rc = KMDataNodeWrite(node, digest, sizeof(digest));
KMDataNodeRelease(node);
}
return rc;
}
static
rc_t KColumnBlobValidateMD5 ( const KColumnBlob *self )
{
rc_t rc;
const KColumn *col = self -> col;
uint8_t buffer [ 8 * 1024 ];
size_t to_read, num_read, total, size;
MD5State md5;
uint8_t digest [ 16 ];
MD5StateInit ( & md5 );
/* calculate checksum */
for ( size = self -> loc . u . blob . size, total = 0; total < size; total += num_read )
{
to_read = size - total;
if ( to_read > sizeof buffer )
to_read = sizeof buffer;
rc = KColumnDataRead ( & col -> df,
& self -> pmorig, total, buffer, to_read, & num_read );
if ( rc != 0 )
return rc;
if ( num_read == 0 )
return RC ( rcDB, rcBlob, rcValidating, rcTransfer, rcIncomplete );
MD5StateAppend ( & md5, buffer, num_read );
}
/* read stored checksum */
rc = KColumnDataRead ( & col -> df,
& self -> pmorig, size, buffer, sizeof digest, & num_read );
if ( rc != 0 )
return rc;
if ( num_read != sizeof digest )
return RC ( rcDB, rcBlob, rcValidating, rcTransfer, rcIncomplete );
/* finish MD5 digest */
MD5StateFinish ( & md5, digest );
if ( memcmp ( buffer, digest, sizeof digest ) != 0 )
return RC ( rcDB, rcBlob, rcValidating, rcBlob, rcCorrupt );
return 0;
}
static rc_t read_loop( const KFile * f, const uint64_t a_pos, const uint64_t count,
const size_t chunk_size, uint8_t digest [ 16 ] )
{
rc_t rc = 0;
uint64_t pos = a_pos;
uint64_t n_bytes = 0;
size_t num_read = 1;
MD5State md5;
char * buffer = malloc( chunk_size );
if ( buffer == NULL )
return RC( rcExe, rcFile, rcPacking, rcMemory, rcExhausted );
MD5StateInit ( &md5 );
while ( rc == 0 && num_read > 0 )
{
size_t chunk = chunk_size;
if ( ( count > 0 ) && ( ( n_bytes + chunk ) > count ) )
{
chunk = ( count - n_bytes );
}
OUTMSG(( "about to read from pos %lu\n", pos ));
rc = KFileRead ( f, pos, buffer, chunk, &num_read );
OUTMSG(( "returned from KFileRead rc = %R, num_read = %zu\n\n", rc, num_read ));
if ( rc == 0 && num_read > 0 )
{
MD5StateAppend ( &md5, buffer, num_read );
pos += num_read;
n_bytes += num_read;
if ( ( count > 0 ) && ( n_bytes >= count ) )
{
num_read = 0;
}
}
}
OUTMSG(( "%lu bytes read total\n", n_bytes ));
free( buffer );
MD5StateFinish ( &md5, digest );
return rc;
}
static
rc_t KColumnBlobValidateBufferMD5 ( const void * buffer, size_t size, const uint8_t cs [ 16 ] )
{
MD5State md5;
uint8_t digest [ 16 ];
MD5StateInit ( & md5 );
/* calculate checksum */
MD5StateAppend ( & md5, buffer, size );
/* finish MD5 digest */
MD5StateFinish ( & md5, digest );
if ( memcmp ( cs, digest, sizeof digest ) != 0 )
return RC ( rcDB, rcBlob, rcValidating, rcBlob, rcCorrupt );
return 0;
}
rc_t KRngSysEntropy (KRng * self, uint8_t * buffer, size_t buff_size)
{
MD5State state;
KDirectory * dir;
const KFile * file;
uint64_t file_pos;
rc_t rc;
if (self == NULL)
return RC (rcKrypto, rcRng, rcWriting, rcSelf, rcNull);
if (buffer == NULL)
return RC (rcKrypto, rcRng, rcWriting, rcParam, rcNull);
rc = KDirectoryNativeDir (&dir);
if (rc == 0)
{
rc = KDirectoryOpenFileRead (dir, &file, "/dev/random");
if (rc)
file = NULL;
}
file_pos = 0;
MD5StateInit (&state);
while (buff_size > 0)
{
if (file)
{
size_t to_read;
size_t num_read;
to_read = (buff_size > 16) ? 16 : buff_size;
rc = KFileRead (file, file_pos, buffer, to_read, &num_read);
if (rc == 0)
{
buffer += num_read;
buff_size -= num_read;
file_pos += num_read; /* superfluous? */
}
}
if (buff_size > 0)
{
uint8_t digest [16];
char buff [1024];
size_t ii;
string_printf (buff, sizeof (buff), &ii,
"%p%zu%lu%lu%lu%lu%s%s%lu",
buffer, buff_size, (uint64_t)clock(),
(uint64_t)time(NULL), (uint64_t)getpid(),
(uint64_t)getuid(), getlogin(), ttyname(0),
(uint64_t)getgid());
MD5StateAppend (&state, buff, sizeof buff);
MD5StateFinish (&state, digest);
ii = (buff_size < sizeof (digest)) ? buff_size : sizeof (digest);
memcpy (buffer, digest, ii);
buff_size -= ii;
buffer += ii;
}
}
KFileRelease (file);
KDirectoryRelease (dir);
return 0;
}
static
rc_t FastqGzip_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
const FastqReader* reader = NULL;
uint16_t zlib_ver = ZLIB_VERNUM;
uint8_t colorSpace = false;
char* colorSpaceKey = "\0";
uint8_t origFormat = false;
uint8_t printLabel = true;
uint8_t printReadId = true;
uint8_t clipQuality = true;
uint32_t minReadLen = 0;
uint16_t qualityOffset = 0;
{{
const SRAColumn* c = NULL;
const uint8_t *platform = SRA_PLATFORM_UNDEFINED;
bitsz_t o, z;
if( (rc = SRATableOpenColumnRead(sratbl, &c, "PLATFORM", sra_platform_id_t)) != 0 ) {
return rc;
}
if( (rc = SRAColumnRead(c, 1, (const void **)&platform, &o, &z)) != 0 ) {
return rc;
}
if( *platform == SRA_PLATFORM_ABSOLID ) {
colorSpace = true;
}
SRAColumnRelease(c);
}}
if( (rc = FastqReaderMake(&reader, sratbl, g_accession,
colorSpace, origFormat, false, printLabel, printReadId,
!clipQuality, minReadLen, qualityOffset, colorSpaceKey[0],
obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
size_t written = 0;
uint32_t blk = 0, spots_per_block = 0, proj_id_qty = 0;
SIndexNode* inode = NULL;
size_t z_blk = 0;
size_t spots_buf_sz = g_file_block_sz * 100;
size_t zbuf_sz = spots_buf_sz + 100;
char* zbuf = malloc(zbuf_sz);
char* spots_buf = malloc(spots_buf_sz);
bool eof = false;
if( zbuf == NULL || spots_buf == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
}
while( rc == 0 ) {
if( (rc = FastqReader_GetNextSpotSplitData(reader, buffer, buffer_sz, &written)) == 0 ) {
if( inode == NULL ) {
spotid_t spotid = 0;
if( (rc = FastqReaderCurrentSpot(reader, &spotid)) != 0 ) {
break;
}
inode = malloc(sizeof(SIndexNode));
if( inode == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
inode->key = obj->file_size;
inode->key_size = 0;
inode->id = spotid;
inode->id_qty = 0;
DEBUG_MSG(5, ("%s open key: spot %ld, offset %lu\n", obj->index, inode->id, inode->key));
}
if( blk + written > spots_buf_sz ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcInsufficient);
break;
}
inode->id_qty++;
memmove(&spots_buf[blk], buffer, written);
blk += written;
if( g_dump ) {
fwrite(buffer, written, 1, stderr);
}
}
if( (eof = (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted)) ) {
rc = 0;
if( inode == NULL ) {
break;
}
}
if( rc == 0 && (eof ||
(proj_id_qty == 0 && inode->id_qty > (spots_per_block * 0.95)) ||
(proj_id_qty > 0 && inode->id_qty >= proj_id_qty) ) ) {
rc = ZLib_DeflateBlock(spots_buf, blk, zbuf, zbuf_sz, &z_blk);
if( z_blk < g_file_block_sz ) {
/* project needed id_qty */
proj_id_qty = g_file_block_sz * inode->id_qty / z_blk * 1.05;
DEBUG_MSG(5, ("%s: project id qty %u\n", obj->index, proj_id_qty));
} else {
DEBUG_MSG(10, ("%s: no projection %u > %u\n", obj->index, z_blk, g_file_block_sz));
}
}
if( rc == 0 && (eof || z_blk >= g_file_block_sz) ) {
obj->file_size += z_blk;
MD5StateAppend(&obj->md5, zbuf, z_blk);
inode->key_size = z_blk;
SLListPushTail(&obj->li, &inode->n);
DEBUG_MSG(5, ("%s close key: spots %lu, size %lu, ratio %hu%%, raw %u\n",
obj->index, inode->id_qty, inode->key_size, (uint16_t)(((float)(blk - z_blk)/blk)*100), blk ));
spots_per_block = inode->id_qty;
inode = NULL;
if( blk > obj->buffer_sz ) {
obj->buffer_sz = blk;
}
blk = 0;
z_blk = 0;
proj_id_qty = 0;
}
if( eof ) {
break;
}
}
rc = rc ? rc : Quitting();
if( rc != 0 ) {
spotid_t spot = 0;
FastqReaderCurrentSpot(reader, &spot);
PLOGERR(klogErr, (klogErr, rc, "spot $(s)", PLOG_U32(s), spot));
}
free(zbuf);
free(spots_buf);
}
if( rc == 0 ) {
KMDataNode* opt = NULL, *nd = NULL;
if( (rc = KMDataNodeOpenNodeUpdate(obj->meta, &opt, "Format/Options")) != 0 ) {
return rc;
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "ZlibVersion")) == 0 ) {
rc = KMDataNodeWriteB16(nd, &zlib_ver);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "colorSpace")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &colorSpace);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "colorSpaceKey")) == 0 ) {
rc = KMDataNodeWrite(nd, colorSpaceKey, 1);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "origFormat")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &origFormat);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "printLabel")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &printLabel);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "printReadId")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &printReadId);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "clipQuality")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &clipQuality);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "minReadLen")) == 0 ) {
rc = KMDataNodeWriteB32(nd, &minReadLen);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "qualityOffset")) == 0 ) {
rc = KMDataNodeWriteB16(nd, &qualityOffset);
KMDataNodeRelease(nd);
}
KMDataNodeRelease(opt);
}
FastqReaderWhack(reader);
return rc;
}
static
rc_t Fastq_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
const FastqReader* reader = NULL;
uint8_t colorSpace = false;
char* colorSpaceKey = "\0";
uint8_t origFormat = false;
uint8_t printLabel = true;
uint8_t printReadId = true;
uint8_t clipQuality = true;
uint32_t minReadLen = 0;
uint16_t qualityOffset = 0;
{{
const SRAColumn* c = NULL;
const uint8_t *platform = SRA_PLATFORM_UNDEFINED;
bitsz_t o, z;
if( (rc = SRATableOpenColumnRead(sratbl, &c, "PLATFORM", sra_platform_id_t)) != 0 ) {
return rc;
}
if( (rc = SRAColumnRead(c, 1, (const void **)&platform, &o, &z)) != 0 ) {
return rc;
}
if( *platform == SRA_PLATFORM_ABSOLID ) {
colorSpace = true;
}
SRAColumnRelease(c);
}}
if( (rc = FastqReaderMake(&reader, sratbl, g_accession,
colorSpace, origFormat, false, printLabel, printReadId,
!clipQuality, minReadLen, qualityOffset, colorSpaceKey[0],
obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
KMDataNode* opt = NULL, *nd = NULL;
if( (rc = KMDataNodeOpenNodeUpdate(obj->meta, &opt, "Format/Options")) != 0 ) {
return rc;
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "colorSpace")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &colorSpace);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "colorSpaceKey")) == 0 ) {
rc = KMDataNodeWrite(nd, colorSpaceKey, 1);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "origFormat")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &origFormat);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "printLabel")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &printLabel);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "printReadId")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &printReadId);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "clipQuality")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &clipQuality);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "minReadLen")) == 0 ) {
rc = KMDataNodeWriteB32(nd, &minReadLen);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "qualityOffset")) == 0 ) {
rc = KMDataNodeWriteB16(nd, &qualityOffset);
KMDataNodeRelease(nd);
}
KMDataNodeRelease(opt);
}
if( rc == 0 ) {
size_t written = 0;
uint32_t blk = 0;
SIndexNode* inode = NULL;
while( rc == 0 ) {
rc = FastqReader_GetNextSpotSplitData(reader, buffer, buffer_sz, &written);
if( blk >= g_file_block_sz || (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted) ) {
inode->key_size = blk;
SLListPushTail(&obj->li, &inode->n);
DEBUG_MSG(5, ("Fastq index closed spots %lu, offset %lu, block size %lu\n",
inode->id_qty, inode->key, inode->key_size));
inode = NULL;
if( blk > obj->buffer_sz ) {
obj->buffer_sz = blk;
}
blk = 0;
}
if( GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted ) {
rc = 0;
break;
}
if( inode == NULL ) {
spotid_t spotid = 0;
if( (rc = FastqReaderCurrentSpot(reader, &spotid)) != 0 ) {
break;
}
inode = malloc(sizeof(SIndexNode));
if( inode == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
inode->key = obj->file_size;
inode->key_size = 0;
inode->id = spotid;
inode->id_qty = 0;
DEBUG_MSG(5, ("Fastq index opened spot %ld, offset %lu\n", inode->id, inode->key));
}
inode->id_qty++;
obj->file_size += written;
blk += written;
MD5StateAppend(&obj->md5, buffer, written);
if( g_dump ) {
fwrite(buffer, written, 1, stderr);
}
}
rc = rc ? rc : Quitting();
if( rc != 0 ) {
spotid_t spot = 0;
FastqReaderCurrentSpot(reader, &spot);
PLOGERR(klogErr, (klogErr, rc, "spot $(s)", PLOG_U32(s), spot));
}
}
FastqReaderWhack(reader);
return rc;
}
static
rc_t SFFGzip_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
uint16_t zlib_ver = ZLIB_VERNUM;
const SFFReader* reader = NULL;
if( (rc = SFFReaderMake(&reader, sratbl, g_accession, obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
size_t written = 0;
uint32_t blk = 0, spots_per_block = 0, proj_id_qty = 0;
SIndexNode* inode = NULL;
size_t z_blk = 0;
size_t spots_buf_sz = g_file_block_sz * 100;
size_t zbuf_sz = spots_buf_sz + 100;
char* zbuf = malloc(zbuf_sz);
char* spots_buf = malloc(spots_buf_sz);
bool eof = false;
if( zbuf == NULL || spots_buf == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
}
while( rc == 0 ) {
if( (rc = SFFReader_GetNextSpotData(reader, buffer, buffer_sz, &written)) == 0 ) {
if( inode == NULL ) {
spotid_t spotid = 0;
if( (rc = SFFReaderCurrentSpot(reader, &spotid)) != 0 ) {
break;
}
inode = malloc(sizeof(SIndexNode));
if( inode == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
inode->key = obj->file_size;
inode->key_size = 0;
inode->id = spotid;
inode->id_qty = 0;
DEBUG_MSG(5, ("%s open key: spot %ld, offset %lu\n", obj->index, inode->id, inode->key));
if( spotid == 1 ) {
char hd[10240];
size_t hd_sz = 0;
if( (rc = SFFReaderHeader(reader, 0, hd, sizeof(hd), &hd_sz)) == 0 ) {
if( hd_sz + written > spots_buf_sz ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcInsufficient);
break;
}
memmove(&spots_buf[blk], hd, hd_sz);
blk += hd_sz;
if( g_dump ) {
fwrite(hd, hd_sz, 1, stderr);
}
}
}
}
if( blk + written > spots_buf_sz ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcInsufficient);
break;
}
inode->id_qty++;
memmove(&spots_buf[blk], buffer, written);
blk += written;
if( g_dump ) {
fwrite(buffer, written, 1, stderr);
}
}
if( (eof = (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted)) ) {
rc = 0;
if( inode == NULL ) {
break;
}
}
if( rc == 0 && (eof ||
(proj_id_qty == 0 && inode->id_qty > (spots_per_block * 0.95)) ||
(proj_id_qty > 0 && inode->id_qty >= proj_id_qty) ) ) {
rc = ZLib_DeflateBlock(spots_buf, blk, zbuf, zbuf_sz, &z_blk);
if( z_blk < g_file_block_sz ) {
/* project needed id_qty */
proj_id_qty = g_file_block_sz * inode->id_qty / z_blk * 1.05;
DEBUG_MSG(5, ("%s: project id qty %lu\n", obj->index, proj_id_qty));
} else {
DEBUG_MSG(10, ("%s: no projection %lu > %lu\n", obj->index, z_blk, g_file_block_sz));
}
}
if( rc == 0 && (eof || z_blk >= g_file_block_sz) ) {
obj->file_size += z_blk;
MD5StateAppend(&obj->md5, zbuf, z_blk);
inode->key_size = z_blk;
SLListPushTail(&obj->li, &inode->n);
DEBUG_MSG(5, ("%s close key: spots %lu, size %lu, ratio %hu%%, raw %lu\n",
obj->index, inode->id_qty, inode->key_size, (uint16_t)(((float)(blk - z_blk)/blk)*100), blk));
spots_per_block = inode->id_qty;
inode = NULL;
if( blk > obj->buffer_sz ) {
obj->buffer_sz = blk;
}
blk = 0;
z_blk = 0;
proj_id_qty = 0;
}
if( eof ) {
break;
}
}
rc = rc ? rc : Quitting();
if( rc != 0 ) {
spotid_t spot = 0;
SFFReaderCurrentSpot(reader, &spot);
PLOGERR(klogErr, (klogErr, rc, "spot $(s)", PLOG_U32(s), spot));
}
free(zbuf);
free(spots_buf);
}
if( rc == 0 ) {
KMDataNode* opt = NULL, *nd = NULL;
if( (rc = KMDataNodeOpenNodeUpdate(obj->meta, &opt, "Format/Options")) != 0 ) {
return rc;
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "ZlibVersion")) == 0 ) {
rc = KMDataNodeWriteB16(nd, &zlib_ver);
KMDataNodeRelease(nd);
}
KMDataNodeRelease(opt);
}
SFFReaderWhack(reader);
return rc;
}
static
rc_t SFF_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
const SFFReader* reader = NULL;
if( (rc = SFFReaderMake(&reader, sratbl, g_accession, obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
size_t written = 0;
uint32_t blk = 0;
SIndexNode* inode = NULL;
while( rc == 0 ) {
rc = SFFReader_GetNextSpotData(reader, buffer, buffer_sz, &written);
if( blk >= g_file_block_sz || (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted) ) {
inode->key_size = blk;
SLListPushTail(&obj->li, &inode->n);
DEBUG_MSG(5, ("SFF index closed spots %lu, offset %lu, block size %lu\n", inode->id_qty, inode->key, inode->key_size));
inode = NULL;
if( blk > obj->buffer_sz ) {
obj->buffer_sz = blk;
}
blk = 0;
}
if( GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted ) {
rc = 0;
break;
}
if( inode == NULL ) {
spotid_t spotid = 0;
if( (rc = SFFReaderCurrentSpot(reader, &spotid)) != 0 ) {
break;
}
inode = malloc(sizeof(SIndexNode));
if( inode == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
inode->key = obj->file_size;
inode->key_size = 0;
inode->id = spotid;
inode->id_qty = 0;
DEBUG_MSG(5, ("SFF index opened spot %ld, offset %lu\n", inode->id, inode->key));
if( spotid == 1 ) {
char hd[10240];
size_t hd_sz = 0;
if( (rc = SFFReaderHeader(reader, 0, hd, sizeof(hd), &hd_sz)) == 0 ) {
obj->file_size += hd_sz;
blk += hd_sz;
MD5StateAppend(&obj->md5, hd, hd_sz);
if( g_dump ) {
fwrite(hd, hd_sz, 1, stderr);
}
}
}
}
obj->file_size += written;
blk += written;
inode->id_qty++;
MD5StateAppend(&obj->md5, buffer, written);
if( g_dump ) {
fwrite(buffer, written, 1, stderr);
}
}
rc = rc ? rc : Quitting();
if( rc != 0 ) {
spotid_t spot = 0;
SFFReaderCurrentSpot(reader, &spot);
PLOGERR(klogErr, (klogErr, rc, "spot $(s)", PLOG_U32(s), spot));
}
}
SFFReaderWhack(reader);
return rc;
}
