org.opencb.cellbase.client.rest.ClinicalVariantClient Maven / Gradle / Ivy

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/*
 * Copyright 2015-2020 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.cellbase.client.rest;

import org.opencb.biodata.models.variant.Variant;
import org.opencb.cellbase.client.config.ClientConfiguration;
import org.opencb.cellbase.core.result.CellBaseDataResponse;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;


import java.io.IOException;

/**
 * Created by fjlopez on 07/07/17.
 */
public class ClinicalVariantClient extends ParentRestClient {

    ClinicalVariantClient(String species, String assembly, String dataRelease, String apiKey, ClientConfiguration configuration) {
        super(species, assembly, dataRelease, apiKey, configuration);

        this.clazz = Variant.class;

        this.category = "clinical";
        this.subcategory = "variant";

    }

    public CellBaseDataResponse search(Query query, QueryOptions queryOptions) throws IOException {
        return execute("search", query, queryOptions, clazz);
    }

    public CellBaseDataResponse alleleOriginLabels() throws IOException {
        return execute("alleleOriginLabels", new Query(), new QueryOptions(), String.class);
    }

    public CellBaseDataResponse clinsigLabels() throws IOException {
        return execute("clinsigLabels", new Query(), new QueryOptions(), String.class);
    }

    public CellBaseDataResponse consistencyLabels() throws IOException {
        return execute("consistencyLabels", new Query(), new QueryOptions(), String.class);
    }

    public CellBaseDataResponse modeInheritanceLabels() throws IOException {
        return execute("modeInheritanceLabels", new Query(), new QueryOptions(), String.class);
    }

    public CellBaseDataResponse variantTypes() throws IOException {
        return execute("type", new Query(), new QueryOptions(), String.class);
    }
}