update query options
@@ -27,7 +27,6 @@ import org.opencb.cellbase.lib.SpeciesUtils;
import org.opencb.cellbase.lib.managers.VariantManager;
import org.opencb.cellbase.server.exception.VersionException;
import org.opencb.cellbase.server.rest.GenericRestWSServer;
-import org.opencb.commons.datastore.core.QueryOptions;
import javax.servlet.http.HttpServletRequest;
import javax.ws.rs.*;
@@ -243,8 +242,10 @@ public class VariantWSServer extends GenericRestWSServer {
Integer cnvExtraPadding,
Boolean checkAminoAcidChange) {
try {
- List<CellBaseDataResult<VariantAnnotation>> queryResults = variantManager.getAnnotationByVariant(new QueryOptions(), variants,
- normalize, skipDecompose, ignorePhase, phased, imprecise, svExtraPadding, cnvExtraPadding, checkAminoAcidChange);
+ VariantQuery query = new VariantQuery(uriParams);
+ List<CellBaseDataResult<VariantAnnotation>> queryResults = variantManager.getAnnotationByVariant(query.toQueryOptions(),
+ variants, normalize, skipDecompose, ignorePhase, phased, imprecise, svExtraPadding, cnvExtraPadding,
+ checkAminoAcidChange);
return createOkResponse(queryResults);
} catch (Exception e) {
return createErrorResponse(e);
