code: public void loadClinicalAnnotation() {
  
          /**
           * Initialize VEP reader
           */
          logger.info("Initializing VEP reader...");
          VepFormatReader vepFormatReader = new VepFormatReader(clinicalAnnotationFilename.toString());
          vepFormatReader.open();
          vepFormatReader.pre();
  
          /**
           * Prepare clinical adaptor
           */
          logger.info("Initializing adaptor, connecting to the database...");
          logger.error("Implementation of this functionality  is outdated and must be re-written if needed");
  
          // TODO: this shall be done in a different way - old Java API was deprecated and removed
  
  //        System.out.println("cellBaseConfiguration = " + configuration.getDatabase().getUser());
  //        System.out.println("cellBaseConfiguration = " + configuration.getDatabase().getHost());
  //        System.out.println("cellBaseConfiguration = " + configuration.getDatabase().getPassword());
  //        DBAdaptorFactory dbAdaptorFactory = new MongoDBAdaptorFactory(configuration);
  //        ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalLegacyDBAdaptor("hsapiens", assembly);
  //
  //        /**
  //         * Load annotations
  //         */
  //        logger.info("Reading/Loading variant annotations...");
  //        int nVepAnnotatedVariants = 0;
  //        List<VariantAnnotation> variantAnnotationList = vepFormatReader.read(CLINICAL_ANNOTATION_BATCH_SIZE);
  //        while (!variantAnnotationList.isEmpty()) {
  //            nVepAnnotatedVariants += variantAnnotationList.size();
  //            clinicalDBAdaptor.updateAnnotations(variantAnnotationList, new QueryOptions());
  //            logger.info(Integer.valueOf(nVepAnnotatedVariants) + " read variants with vep annotations");
  //            variantAnnotationList = vepFormatReader.read(CLINICAL_ANNOTATION_BATCH_SIZE);
  //        }
  
  //
  //        vepFormatReader.post();
  //        vepFormatReader.close();
  //        logger.info(nVepAnnotatedVariants + " VEP annotated variants were read from " + clinicalAnnotationFilename.toString());
  //        logger.info("Finished");
      }
docs: TODO: change to private - just for debugging purposes