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;
}
rc_t copy_database_meta ( const VDatabase *src_db, VDatabase *dst_db,
const char * excluded_nodes,
const bool show_meta )
{
const KMetadata *src_meta;
rc_t rc;
if ( src_db == NULL || dst_db == NULL )
return RC( rcExe, rcNoTarg, rcCopying, rcParam, rcNull );
/* it is OK if excluded_nodes is NULL */
rc = VDatabaseOpenMetadataRead ( src_db, & src_meta );
DISP_RC( rc, "copy_database_meta:VDatabaseOpenMetadataRead() failed" );
if ( rc == 0 )
{
KMetadata *dst_meta;
rc = VDatabaseOpenMetadataUpdate ( dst_db, & dst_meta );
DISP_RC( rc, "copy_database_meta:VDatabaseOpenMetadataUpdate() failed" );
if ( rc == 0 )
{
if ( show_meta )
KOutMsg( "+++copy current db-metadata\n" );
rc = copy_stray_metadata ( src_meta, dst_meta, excluded_nodes,
show_meta );
if ( show_meta )
KOutMsg( "+++end of copy db-current metadata\n" );
KMetadataRelease ( dst_meta );
}
KMetadataRelease ( src_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;
}
inline rc_t OpenMetadata ( KMetadata **meta ) throw ()
{ return VDatabaseOpenMetadataUpdate ( this, meta ); }
