public static Set<VariantQueryParam> validParams(Query query) { Set<VariantQueryParam> params = new HashSet<>(query == null ? 0 : query.size()); for (VariantQueryParam queryParam : values()) { if (isValidParam(query, queryParam)) { params.add(queryParam); } } return params; }
public static void getQueryFromConfig(Query query, Configuration conf) { for (VariantQueryParam param : VariantQueryParam.values()) { String value = conf.get(param.key(), conf.get("--" + param.key())); if (value != null && !value.isEmpty()) { query.put(param.key(), value); } } }
public static Query getVariantQuery(Map<String, ?> queryOptions) { Query query = new Query(); for (VariantQueryParam queryParams : VariantQueryParam.values()) { if (queryOptions.containsKey(queryParams.key())) { query.put(queryParams.key(), queryOptions.get(queryParams.key())); } } if (queryOptions.containsKey(VariantCatalogQueryUtils.SAMPLE_ANNOTATION.key())) { query.put(VariantCatalogQueryUtils.SAMPLE_ANNOTATION.key(), queryOptions.get(VariantCatalogQueryUtils.SAMPLE_ANNOTATION.key())); } if (queryOptions.containsKey(VariantCatalogQueryUtils.PROJECT.key())) { query.put(VariantCatalogQueryUtils.PROJECT.key(), queryOptions.get(VariantCatalogQueryUtils.PROJECT.key())); } if (queryOptions.containsKey(VariantCatalogQueryUtils.FAMILY.key())) { query.put(VariantCatalogQueryUtils.FAMILY.key(), queryOptions.get(VariantCatalogQueryUtils.FAMILY.key())); } if (queryOptions.containsKey(VariantCatalogQueryUtils.FAMILY_PHENOTYPE.key())) { query.put(VariantCatalogQueryUtils.FAMILY_PHENOTYPE.key(), queryOptions.get(VariantCatalogQueryUtils.FAMILY_PHENOTYPE.key())); } if (queryOptions.containsKey(VariantCatalogQueryUtils.MODE_OF_INHERITANCE.key())) { query.put(VariantCatalogQueryUtils.MODE_OF_INHERITANCE.key(), queryOptions.get(VariantCatalogQueryUtils.MODE_OF_INHERITANCE.key())); } if (queryOptions.containsKey(VariantCatalogQueryUtils.PANEL.key())) { query.put(VariantCatalogQueryUtils.PANEL.key(), queryOptions.get(VariantCatalogQueryUtils.PANEL.key())); } return query; }
for (VariantQueryParam acceptedValue : VariantQueryParam.values()) { if (options.get(acceptedValue.key()) != null) { query.put(acceptedValue.key(), options.get(acceptedValue.key()));