static
rc_t RestoreReadMake ( RestoreRead **objp, const VTable *tbl, const VCursor* native_curs )
{
rc_t rc;
char name[]="PRIMARY_ALIGNMENT";
/* create the object */
RestoreRead *obj = malloc ( sizeof * obj );
memset(obj,0,sizeof * obj);
if ( obj == NULL )
{
*objp=0;
rc = RC ( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
}
else
{
rc = VCursorLinkedCursorGet(native_curs,name,&obj->curs);
if(rc == 0){
VCursorAddRef(obj->curs);
} else {
/* get at the parent database */
const VDatabase *db;
rc = VTableOpenParentRead ( tbl, & db );
if ( rc == 0 )
{
const VTable *patbl;
/* open the primary alignment table */
rc = VDatabaseOpenTableRead ( db, & patbl, name );
VDatabaseRelease ( db );
if ( rc == 0 )
{
/* create a cursor */
rc = VTableCreateCachedCursorRead( patbl, &obj->curs, 32*1024*1024UL );
VTableRelease ( patbl );
if ( rc == 0 )
{
/* add columns to cursor */
rc = VCursorAddColumn ( obj -> curs, & obj -> read_idx, "( INSDC:4na:bin ) READ" );
if ( rc == 0 )
{
rc = VCursorOpen ( obj -> curs );
if ( rc == 0 )
{
VCursorLinkedCursorSet( native_curs, name, obj->curs );
SUB_DEBUG( ( "SUB.Make in 'seq-restore-read.c'\n" ) );
* objp = obj;
return 0;
}
}
VCursorRelease ( obj -> curs );
}
}
}
free ( obj );
}
}
return rc;
}
rc_t AlignRefTableCursor(const VTable* table, const VCursor *native_curs, const VCursor** ref_cursor,const VTable **reftbl)
{
rc_t rc = 0;
char ref_tbl_name[512] = "REFERENCE";
const KMetadata* meta;
const VCursor *curs;
if( (rc = VTableOpenMetadataRead(table, &meta)) == 0 ) {
const KMDataNode* node;
if( (rc = KMetadataOpenNodeRead(meta, &node, "CONFIG/REF_TABLE")) == 0 ) {
size_t sz;
rc = KMDataNodeReadCString(node, ref_tbl_name, sizeof(ref_tbl_name), &sz);
ref_tbl_name[sz] = '\0';
KMDataNodeRelease(node);
}
KMetadataRelease(meta);
}
rc = VCursorLinkedCursorGet(native_curs,ref_tbl_name,&curs);
if(rc != 0){
const VDatabase *db;
const VTable *tbl;
/* get at the parent database */
rc = VTableOpenParentRead ( table, & db );
if(rc != 0) return rc;
/* open the table */
rc = VDatabaseOpenTableRead ( db, &tbl, ref_tbl_name);
VDatabaseRelease ( db );
if(rc != 0) return rc;
/* create a cursor */
rc = VTableCreateCachedCursorRead(tbl, &curs,256*1024*1024);
if(reftbl){
*reftbl = tbl;
} else {
VTableRelease(tbl);
}
if(rc != 0) return rc;
rc = VCursorPermitPostOpenAdd( curs );
if(rc != 0) return rc;
rc = VCursorOpen( curs );
if(rc != 0) return rc;
if(native_curs){
rc = VCursorLinkedCursorSet(native_curs,ref_tbl_name,curs);
}
if(rc != 0) return rc;
} else {
VCursorAddRef(curs);
}
*ref_cursor = curs;
return 0;
}
static
rc_t open_RR_cursor( Read_Restorer * obj, const VTable *tbl, const VCursor* native_curs, const char * tablename )
{
rc_t rc = VCursorLinkedCursorGet( native_curs, tablename, &obj->curs );
if ( rc != 0 )
{
/* get at the parent database */
const VDatabase *db;
rc = VTableOpenParentRead ( tbl, & db );
if ( rc == 0 )
{
const VTable *patbl;
/* open the primary alignment table */
rc = VDatabaseOpenTableRead ( db, & patbl, tablename );
VDatabaseRelease ( db );
if ( rc == 0 )
{
/* create a cursor */
rc = VTableCreateCachedCursorRead( patbl, &obj->curs, 32*1024*1024UL );
/* rc = VTableCreateCursorRead( patbl, &obj->curs ); */
VTableRelease ( patbl );
if ( rc == 0 )
rc = VCursorLinkedCursorSet( native_curs, tablename, obj->curs );
}
}
}
if ( rc == 0 )
{
/* add columns to cursor */
rc = VCursorAddColumn ( obj -> curs, & obj -> read_idx, "( INSDC:4na:bin ) READ" );
if ( GetRCState(rc) == rcExists )
rc = 0;
if ( rc == 0 )
{
rc = VCursorOpen ( obj -> curs );
}
}
return rc;
}
