static rc_t pacbio_meta_entry( ld_context *lctx, const char * toolname )
{
KMetadata* meta = NULL;
rc_t rc = VDatabaseOpenMetadataUpdate( lctx->database, &meta );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "Cannot open database-metadata" );
}
else
{
KMDataNode *node = NULL;
rc = KMetadataOpenNodeUpdate( meta, &node, "/" );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "Cannot open database-metadata-root" );
}
else
{
rc = KLoaderMeta_Write( node, toolname, __DATE__, "PacBio HDF5", PACBIO_LOAD_VERS );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "Cannot write pacbio metadata node" );
}
KMDataNodeRelease( node );
}
KMetadataRelease( meta );
}
return rc;
}
static
rc_t DB_Fini(const SParam* p, DB_Handle* h, bool drop)
{
rc_t rc = 0, rc2;
/* THIS FUNCTION MAKES NO ATTEMPT TO PRESERVE INITIAL ERROR CODES
EACH SUCCESSIVE ERROR OVERWRITES THE PREVIOUS CODE */
if( h != NULL ) {
PLOGMSG(klogInfo, (klogInfo, "Fini SEQUENCE", "severity=status"));
if( (rc2 = CGWriterSeq_Whack(h->wseq, !drop, NULL)) != 0 && !drop ) {
drop = true;
rc = rc2;
}
h->wseq = NULL;
h->reads = NULL;
PLOGMSG(klogInfo, (klogInfo, "Fini (PRI&SEC)_ALIGNMENT", "severity=status"));
if( (rc2 = CGWriterAlgn_Whack(h->walgn, !drop, NULL, NULL)) != 0 && !drop ) {
drop = true;
rc = rc2;
}
h->walgn = NULL;
h->mappings = NULL;
PLOGMSG(klogInfo, (klogInfo, "Fini EVIDENCE_INTERVAL", "severity=status"));
if( (rc2 = CGWriterEvdInt_Whack(h->wev_int, !drop, NULL)) != 0 && !drop ) {
drop = true;
rc = rc2;
}
h->wev_int = NULL;
h->ev_int = NULL;
PLOGMSG(klogInfo, (klogInfo, "Fini EVIDENCE_ALIGNMENT", "severity=status"));
if( (rc2 = CGWriterEvdDnbs_Whack(h->wev_dnb, !drop, NULL)) != 0 && !drop ) {
drop = true;
rc = rc2;
}
h->wev_dnb = NULL;
h->ev_dnb = NULL;
PLOGMSG(klogInfo, (klogInfo, "Fini calculating reference coverage", "severity=status"));
if( (rc2 = ReferenceMgr_Release(h->rmgr, !drop, NULL, drop ? false : true)) != 0 && !drop ) {
drop = true;
rc = rc2;
LOGERR(klogErr, rc, "Failed calculating reference coverage");
}
h->rmgr = NULL;
if( rc == 0 )
{
KMetadata* meta;
if( (rc = VDatabaseOpenMetadataUpdate(h->db, &meta)) == 0 ) {
KMDataNode *node;
if( (rc = KMetadataOpenNodeUpdate(meta, &node, "/")) == 0 ) {
if( (rc = KLoaderMeta_Write(node, p->argv0, __DATE__, "Complete Genomics", KAppVersion())) != 0 ) {
LOGERR(klogErr, rc, "Cannot update loader meta");
}
KMDataNodeRelease(node);
}
KMetadataRelease(meta);
}
}
PLOGMSG(klogInfo, (klogInfo, "Fini VDatabaseRelease", "severity=status"));
VDatabaseRelease(h->db);
h->db = NULL;
VSchemaRelease(h->schema);
h->schema = NULL;
if( drop || rc != 0 ) {
rc2 = VDBManagerDrop(h->mgr, kptDatabase, p->out);
if( GetRCState(rc2) == rcNotFound ) {
/* WHAT WOULD BE THE POINT OF RESETTING "rc" TO ZERO? */
rc = 0;
} else if( rc2 != 0 ) {
if ( rc == 0 )
rc = rc2;
PLOGERR(klogErr, (klogErr, rc2, "cannot drop db at '$(path)'", PLOG_S(path), p->out));
}
}
VDBManagerRelease(h->mgr);
h->mgr = NULL;
}
return rc;
}
