static void get_meta_info( vdb_info_data * data, const KMetadata * meta )
{
const KMDataNode * node;
rc_t rc = KMetadataOpenNodeRead ( meta, &node, "schema" );
if ( rc == 0 )
{
size_t size;
rc = KMDataNodeReadAttr ( node, "name", data->schema_name, sizeof data->schema_name, &size );
if ( rc == 0 )
data->schema_name[ size ] = 0;
KMDataNodeRelease ( node );
}
rc = KMetadataOpenNodeRead ( meta, &node, "LOAD/timestamp" );
if ( rc == 0 )
{
rc = KMDataNodeReadAsU64 ( node, &data->ts.timestamp );
if ( rc == 0 )
{
KTime time_rec;
KTimeLocal ( &time_rec, data->ts.timestamp );
data->ts.year = time_rec.year;
data->ts.month = time_rec.month + 1;
data->ts.day = time_rec.day + 1;
data->ts.hour = time_rec.hour;
data->ts.minute= time_rec.minute;
}
KMDataNodeRelease ( node );
}
get_meta_event( meta, "SOFTWARE/formatter", &data->formatter );
get_meta_event( meta, "SOFTWARE/loader", &data->loader );
get_meta_event( meta, "SOFTWARE/update", &data->update );
}
/* FillOutTableRead
* creates an empty cursor
* accesses metadata
*/
static rc_t ReadSpotSequence_v1(SRATable *self)
{
const KMDataNode *n;
rc_t rc = KMetadataOpenNodeRead(self->meta, &n, ".seq");
if (rc == 0)
{
rc = KMDataNodeReadAsU64(n, &self->spot_count);
KMDataNodeRelease(n);
}
return rc;
}
static
rc_t sra_meta_stats_node_read(KMDataNode* node, void* value)
{
rc_t rc = KMDataNodeReadAsU64(node, value);
if ( rc != 0 )
{
if ( GetRCState ( rc ) == rcIncomplete && GetRCObject ( rc ) == rcTransfer )
{
* ( uint64_t* ) value = 0;
rc = 0;
}
}
return rc;
}
static rc_t qual_stats(const Params* prm, const VDatabase* db) {
rc_t rc = 0;
const char tblName[] = "SEQUENCE";
const VTable* tbl = NULL;
const KMetadata* meta = NULL;
const KMDataNode* node = NULL;
assert(prm && db);
if (rc == 0) {
rc = VDatabaseOpenTableRead(db, &tbl, tblName);
DISP_RC2(rc, tblName, "while calling VDatabaseOpenTableRead");
}
if (rc == 0) {
rc = VTableOpenMetadataRead(tbl, &meta);
DISP_RC2(rc, tblName, "while calling VTableOpenMetadataRead");
}
if (rc == 0) {
bool found = false;
const char path[] = "STATS/QUALITY";
rc = KMetadataOpenNodeRead(meta, &node, path);
if (rc == 0)
{ found = true; }
else if (GetRCState(rc) == rcNotFound)
{ rc = 0; }
DISP_RC2(rc, path, "while calling KMetadataOpenNodeRead");
if (found) {
uint32_t i = 0;
int nbr = 0;
uint32_t count = 0;
KNamelist* names = NULL;
int* quals = NULL;
if (rc == 0) {
rc = KMDataNodeListChild(node, &names);
DISP_RC2(rc, path, "while calling KMDataNodeListChild");
}
if (rc == 0) {
rc = KNamelistCount(names, &count);
DISP_RC2(rc, path, "while calling KNamelistCount");
if (rc == 0 && count > 0) {
quals = calloc(count, sizeof *quals);
if (quals == NULL) {
rc = RC(rcExe,
rcStorage, rcAllocating, rcMemory, rcExhausted);
}
}
}
for (i = 0; i < count && rc == 0; ++i) {
/* uint64_t u = 0;
const KMDataNode* n = NULL; */
const char* nodeName = NULL;
const char* name = NULL;
rc = KNamelistGet(names, i, &nodeName);
DISP_RC2(rc, path, "while calling KNamelistGet");
if (rc)
{ break; }
name = nodeName;
/* rc = KMDataNodeOpenNodeRead(node, &n, name);
DISP_RC(rc, name);
if (rc == 0) {
rc = KMDataNodeReadAsU64(n, &u);
DISP_RC(rc, name);
} */
if (rc == 0) {
char* c = strchr(name, '_');
if (c != NULL && *(c + 1) != '\0') {
name = c + 1;
if (sscanf(name, "%d", &quals[i]) != 1) {
rc = RC(rcExe,
rcNode, rcParsing, rcName, rcUnexpected);
PLOGERR(klogInt,
(klogInt, rc, "$(name)", "name=%s", nodeName));
}
}
/* OUTMSG(("QUALITY %s %lu\n", name, u)); */
}
/* DESTRUCT(KMDataNode, n); */
}
if (rc == 0 && count > 0)
{ ksort(quals, count, sizeof *quals, sort_callback, NULL); }
if (rc == 0) {
OUTMSG(("%s", prm->dbPath));
}
for (i = 0, nbr = 0; i < count && rc == 0; ++i, ++nbr) {
uint64_t u = 0;
char name[64];
const KMDataNode* n = NULL;
sprintf(name, "PHRED_%d", quals[i]);
rc = KMDataNodeOpenNodeRead(node, &n, name);
DISP_RC(rc, name);
if (rc == 0) {
rc = KMDataNodeReadAsU64(n, &u);
DISP_RC(rc, name);
if (rc == 0) {
while (nbr < quals[i]) {
OUTMSG(("\t0"));
++nbr;
}
OUTMSG(("\t%lu", u));
/* OUTMSG(("QUALITY %d %lu\n", quals[i], u)); */
}
}
DESTRUCT(KMDataNode, n);
}
while (rc == 0 && nbr <= 40) {
OUTMSG(("\t0"));
nbr++;
}
if (rc == 0) {
OUTMSG(("\n"));
}
DESTRUCT(KNamelist, names);
}
}
DESTRUCT(KMDataNode, node);
DESTRUCT(KMetadata, meta);
DESTRUCT(VTable, tbl);
return rc;
}
inline rc_t Read ( uint64_t *value ) const throw()
{ return KMDataNodeReadAsU64 ( this, value ); }