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;
}
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_update(sra_meta_stats_node_group* g,
const int64_t spot_id, const uint32_t spot_len,
const uint32_t bio_spot_len, const uint32_t cmp_spot_len)
{
rc_t rc = 0;
uint64_t u64;
int64_t i64;
if( (rc = sra_meta_stats_node_read(g->node_spot_count, &u64)) == 0 ) {
if( u64 + 1 < u64 ) {
rc = RC(rcVDB, rcFunction, rcUpdating, rcMetadata, rcOutofrange);
} else {
if( spot_id != 0 ) {
++u64;
}
rc = KMDataNodeWriteB64(g->node_spot_count, &u64);
}
}
if( (rc = sra_meta_stats_node_read(g->node_base_count, &u64)) == 0 ) {
if( u64 + 1 < u64 ) {
rc = RC(rcVDB, rcFunction, rcUpdating, rcMetadata, rcOutofrange);
} else {
u64 += spot_len;
rc = KMDataNodeWriteB64(g->node_base_count, &u64);
}
}
if( (rc = sra_meta_stats_node_read(g->node_bio_base_count, &u64)) == 0 ) {
if( u64 + bio_spot_len < u64 ) {
rc = RC(rcVDB, rcFunction, rcUpdating, rcMetadata, rcOutofrange);
} else {
u64 += bio_spot_len;
rc = KMDataNodeWriteB64(g->node_bio_base_count, &u64);
}
}
if( g->node_cmp_base_count != NULL ) {
if( (rc = sra_meta_stats_node_read(g->node_cmp_base_count, &u64)) == 0 ) {
if( u64 + cmp_spot_len < u64 ) {
rc = RC(rcVDB, rcFunction, rcUpdating, rcMetadata, rcOutofrange);
} else {
u64 += cmp_spot_len;
rc = KMDataNodeWriteB64(g->node_cmp_base_count, &u64);
}
}
}
if( (rc = sra_meta_stats_node_read(g->node_spot_max, &i64)) == 0 ) {
if( i64 == 0 || i64 < spot_id ) {
i64 = spot_id;
rc = KMDataNodeWriteB64(g->node_spot_max, &i64);
}
}
if( (rc = sra_meta_stats_node_read(g->node_spot_min, &i64)) == 0 ) {
if( i64 == 0 || i64 > spot_id ) {
i64 = spot_id;
rc = KMDataNodeWriteB64(g->node_spot_min, &i64);
}
}
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;
}
inline rc_t WriteB64 ( const void *b64 ) throw()
{ return KMDataNodeWriteB64 ( this, b64 ); }
