rc_t WriteFileMeta(SIndexObj* obj)
{
rc_t rc = 0;
KMDataNode* nd = NULL;
PLOGMSG(klogInfo, (klogInfo, "Meta $(f) on index $(i): file size $(s), buffer $(b)",
PLOG_4(PLOG_S(f),PLOG_S(i),PLOG_U64(s),PLOG_U32(b)), obj->file, obj->index, obj->file_size, obj->buffer_sz));
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(obj->meta, &nd, "Format")) == 0 ) {
KMDataNode* opt = NULL;
rc = KMDataNodeWriteCString(nd, obj->format);
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(nd, &opt, "Options")) == 0 ) {
KMDataNode* ond = NULL;
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &ond, "accession")) == 0 ) {
rc = KMDataNodeWriteCString(ond, g_accession);
KMDataNodeRelease(ond);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &ond, "minSpotId")) == 0 ) {
rc = KMDataNodeWriteB64(ond, &obj->minSpotId);
KMDataNodeRelease(ond);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &ond, "maxSpotId")) == 0 ) {
rc = KMDataNodeWriteB64(ond, &obj->maxSpotId);
KMDataNodeRelease(ond);
}
KMDataNodeRelease(opt);
}
KMDataNodeRelease(nd);
}
if( rc == 0 && obj->file_size > 0 && (rc = KMDataNodeOpenNodeUpdate(obj->meta, &nd, "Size")) == 0 ) {
rc = KMDataNodeWriteB64(nd, &obj->file_size);
KMDataNodeRelease(nd);
}
if( rc == 0 && obj->buffer_sz > 0 && (rc = KMDataNodeOpenNodeUpdate(obj->meta, &nd, "Buffer")) == 0 ) {
rc = KMDataNodeWriteB32(nd, &obj->buffer_sz);
KMDataNodeRelease(nd);
}
if( rc == 0 && strlen(obj->index) > 0 && (rc = KMDataNodeOpenNodeUpdate(obj->meta, &nd, "Index")) == 0 ) {
rc = KMDataNodeWriteCString(nd, obj->index);
KMDataNodeRelease(nd);
}
if( rc == 0 && obj->file_size > 0 && (rc = KMDataNodeOpenNodeUpdate(obj->meta, &nd, "md5")) == 0 ) {
char x[5];
int i;
for( i = 0; rc == 0 && i < sizeof(obj->md5_digest); i++ ) {
int l = snprintf(x, 4, "%02x", obj->md5_digest[i]);
rc = KMDataNodeAppend(nd, x, l);
}
KMDataNodeRelease(nd);
}
return rc;
}
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 enter_vdbcopy_node( KMetadata *dst_meta, const bool show_meta )
{
rc_t rc;
KMDataNode *hist_node;
if ( show_meta )
KOutMsg( "--- entering Copy entry...\n" );
rc = KMetadataOpenNodeUpdate ( dst_meta, &hist_node, "HISTORY" );
DISP_RC( rc, "enter_vdbcopy_node:KMetadataOpenNodeUpdate('HISTORY') failed" );
if ( rc == 0 )
{
char event_name[ 32 ];
uint32_t index = get_child_count( hist_node ) + 1;
rc = string_printf ( event_name, sizeof( event_name ), NULL, "EVENT_%u", index );
DISP_RC( rc, "enter_vdbcopy_node:string_printf(EVENT_NR) failed" );
if ( rc == 0 )
{
KMDataNode *event_node;
rc = KMDataNodeOpenNodeUpdate ( hist_node, &event_node, event_name );
DISP_RC( rc, "enter_vdbcopy_node:KMDataNodeOpenNodeUpdate('EVENT_NR') failed" );
if ( rc == 0 )
{
rc = enter_date_name_vers( event_node );
KMDataNodeRelease ( event_node );
}
}
KMDataNodeRelease ( hist_node );
}
return rc;
}
LIB_EXPORT rc_t CC TableWriterSeq_Whack(const TableWriterSeq* cself, bool commit, uint64_t* rows)
{
rc_t rc = 0;
if( cself != NULL ) {
TableWriterSeq* self = (TableWriterSeq*)cself;
VTable *vtbl;
TableReader_Whack(cself->tmpkey_reader);
if (commit && (rc = TableWriter_GetVTable(cself->base, &vtbl)) == 0 ) {
KMetadata* meta;
if ((rc = VTableOpenMetadataUpdate(vtbl, &meta)) == 0) {
KMDataNode* node = NULL;
if (cself->stats) {
if ((rc = KMetadataOpenNodeUpdate(meta, &node, "MATE_STATISTICS")) == 0) {
rc = TableWriterSeq_WriteStatistics(cself, node);
KMDataNodeRelease(node);
}
}
if ((rc = KMetadataOpenNodeUpdate(meta, &node, "unaligned")) == 0) {
KMDataNode *sub = NULL;
KMDataNodeOpenNodeUpdate(node, &sub, "first-unaligned");
KMDataNodeWriteB64(sub, &self->firstUnaligned);
KMDataNodeRelease(sub);
KMDataNodeOpenNodeUpdate(node, &sub, "first-half-aligned");
KMDataNodeWriteB64(sub, &self->firstHalfAligned);
KMDataNodeRelease(sub);
KMDataNodeRelease(node);
}
KMetadataRelease(meta);
}
}
rc = TableWriter_Whack(cself->base, commit && (rc == 0), rows);
KVectorRelease(cself->stats);
free(self->qual_buf);
free(self);
}
return rc;
}
static rc_t group_stats_write_node(KMDataNode *const node,
char const name[],
void const *const value)
{
KMDataNode *subnode;
rc_t rc = KMDataNodeOpenNodeUpdate(node, &subnode, "%s", name);
if (rc == 0) {
rc = KMDataNodeWriteB64(subnode, value);
KMDataNodeRelease(subnode);
}
return rc;
}
static
rc_t sra_meta_stats_node_group_open(KMDataNode* parent, sra_meta_stats_node_group* g, bool compressed)
{
rc_t rc = 0;
assert(parent && g);
if( (rc = KMDataNodeOpenNodeUpdate(parent, &g->node_spot_count, "SPOT_COUNT")) == 0 &&
(rc = KMDataNodeOpenNodeUpdate(parent, &g->node_base_count, "BASE_COUNT")) == 0 &&
(rc = KMDataNodeOpenNodeUpdate(parent, &g->node_bio_base_count, "BIO_BASE_COUNT")) == 0 &&
(rc = KMDataNodeOpenNodeUpdate(parent, &g->node_spot_min, "SPOT_MIN")) == 0 &&
(rc = KMDataNodeOpenNodeUpdate(parent, &g->node_spot_max, "SPOT_MAX")) == 0 ) {
if( compressed ) {
rc = KMDataNodeOpenNodeUpdate(parent, &g->node_cmp_base_count, "CMP_BASE_COUNT");
}
}
return rc;
}
static rc_t enter_schema_update( KMetadata *dst_meta, const bool show_meta )
{
rc_t rc;
KMDataNode *sw_node;
if ( show_meta )
KOutMsg( "--- entering schema-update\n" );
rc = KMetadataOpenNodeUpdate ( dst_meta, &sw_node, "SOFTWARE" );
DISP_RC( rc, "enter_schema_update:KMetadataOpenNodeUpdate('SOFTWARE') failed" );
if ( rc == 0 )
{
KMDataNode *update_node;
rc = KMDataNodeOpenNodeUpdate ( sw_node, &update_node, "update" );
DISP_RC( rc, "enter_schema_update:KMDataNodeOpenNodeUpdate('update') failed" );
if ( rc == 0 )
{
rc = enter_date_name_vers( update_node );
KMDataNodeRelease ( update_node );
}
KMDataNodeRelease ( sw_node );
}
return rc;
}
static
rc_t MakeIndexes(const SRATable* stbl, KTable* ktbl, KMetadata* meta)
{
rc_t rc = 0;
int i;
char* buffer = NULL;
size_t buffer_sz = g_file_block_sz * 100;
SIndexObj idx[] = {
/* meta, file, format, index, func, file_size, buffer_sz, minSpotId, maxSpotId */
{NULL, "fastq", "fastq", "fuse-fastq", Fastq_Idx, 0, 0, 0, 0},
{NULL, "sff", "SFF", "fuse-sff", SFF_Idx, 0, 0, 0, 0},
{NULL, "fastq.gz", "fastq-gzip", "fuse-fastq-gz", FastqGzip_Idx, 0, 0, 0, 0},
{NULL, "sff.gz", "SFF-gzip", "fuse-sff-gz", SFFGzip_Idx, 0, 0, 0, 0}
};
for(i = 0; rc == 0 && i < sizeof(idx) / sizeof(idx[0]); i++) {
KMDataNode* parent = NULL;
if( (rc = KMetadataOpenNodeUpdate(meta, &parent, "/FUSE")) == 0 ) {
KMDataNodeDropChild(parent, "root"); /* drop old stuff */
if( g_ungzip || strcmp(&idx[i].file[strlen(idx[i].file) - 3], ".gz") == 0 ) {
STSMSG(0, ("Preparing index %s", idx[i].index));
MD5StateInit(&idx[i].md5);
SLListInit(&idx[i].li);
KMDataNodeDropChild(parent, "%s.tmp", idx[i].file);
if( (rc = KMDataNodeOpenNodeUpdate(parent, &idx[i].meta, "%s.tmp", idx[i].file)) == 0 ) {
if( idx[i].func != NULL ) {
if( buffer == NULL ) {
if( (buffer = malloc(buffer_sz)) == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
}
rc = idx[i].func(stbl, &idx[i], buffer, buffer_sz);
if( rc == 0 ) {
MD5StateFinish(&idx[i].md5, idx[i].md5_digest);
rc = CommitIndex(ktbl, idx[i].index, &idx[i].li);
}
}
if( rc == 0 ) {
rc = WriteFileMeta(&idx[i]);
}
KMDataNodeRelease(idx[i].meta);
}
if( GetRCState(rc) == rcUnsupported ) {
KMDataNodeDropChild(parent, "%s", idx[i].file);
PLOGERR(klogWarn, (klogWarn, rc, "Index $(i) is not supported for this table", PLOG_S(i), idx[i].index));
rc = 0;
} else if( rc == 0 ) {
char f[4096];
strcpy(f, idx[i].file);
strcat(f, ".tmp");
KMDataNodeDropChild(parent, "%s", idx[i].file);
rc = KMDataNodeRenameChild(parent, f, idx[i].file);
}
} else if( !g_ungzip ) {
KTableDropIndex(ktbl, idx[i].index);
KMDataNodeDropChild(parent, "%s", idx[i].file);
}
KMDataNodeDropChild(parent, "%s.tmp", idx[i].file);
KMDataNodeRelease(parent);
}
SLListWhack(&idx[i].li, WhackIndexData, NULL);
}
free(buffer);
return rc;
}
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 copy_metadata_child ( const KMDataNode *src_root, KMDataNode *dst_root,
const char *node_path, const bool show_meta )
{
const KMDataNode *snode;
KMDataNode *dnode;
KNamelist *names;
rc_t rc = KMDataNodeOpenNodeRead ( src_root, & snode, node_path );
DISP_RC( rc, "copy_metadata_child:KMDataNodeOpenNodeRead(src) failed" );
if ( rc != 0 ) return rc;
if ( show_meta )
KOutMsg( "copy child-node: %s\n", node_path );
rc = KMDataNodeOpenNodeUpdate ( dst_root, & dnode, node_path );
DISP_RC( rc, "copy_metadata_child:KMDataNodeOpenNodeUpdate(dst) failed" );
if ( rc == 0 )
{
rc = copy_metadata_data ( snode, dnode );
if ( rc == 0 )
rc = copy_metadata_attribs ( snode, dnode, node_path, show_meta );
KMDataNodeRelease ( dnode );
}
else
{
PLOGMSG( klogInfo, ( klogInfo,
"cannot open child-node(dst): $(node)", "node=%s", node_path ));
}
if ( rc == 0 || ( GetRCState( rc ) == rcBusy ) )
{
rc = KMDataNodeListChild ( snode, & names );
DISP_RC( rc, "copy_metadata_child:KMDataNodeListChild(src) failed" );
if ( rc == 0 )
{
uint32_t i, count;
char temp_path[ 1024 ];
size_t temp_len;
string_copy ( temp_path, ( sizeof temp_path ) - 1, node_path, string_size( node_path ) );
temp_len = string_size( temp_path );
temp_path[ temp_len++ ] = '/';
temp_path[ temp_len ] = 0;
rc = KNamelistCount ( names, & count );
for ( i = 0; rc == 0 && i < count; ++ i )
{
const char *child_name;
rc = KNamelistGet ( names, i, & child_name );
if ( rc == 0 )
{
string_copy( temp_path + temp_len, ( sizeof temp_path ) - temp_len, child_name, string_size( child_name ) );
rc = copy_metadata_child ( src_root, dst_root, temp_path, show_meta );
temp_path[ temp_len ] = 0;
}
}
KNamelistRelease ( names );
}
}
KMDataNodeRelease ( snode );
return rc;
}
