edu.vt.vbi.patric.mashup.PSICQUICInterface.java Source code

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Here is the source code for edu.vt.vbi.patric.mashup.PSICQUICInterface.java

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/*******************************************************************************
 * Copyright 2014 Virginia Polytechnic Institute and State University
 *
 * 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 edu.vt.vbi.patric.mashup;

import edu.vt.vbi.patric.mashup.xmlHandler.IntActHandler;
import org.apache.commons.io.IOUtils;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.StringWriter;
import java.net.URL;

public class PSICQUICInterface {

    private static final Logger LOGGER = LoggerFactory.getLogger(PSICQUICInterface.class);

    protected String baseURL = "http://www.ebi.ac.uk/Tools/webservices/psicquic/";

    // http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/species:356?format=count
    // http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/species:356?format=xml25

    protected String baseURLQuery = "/webservices/current/search/query/";

    public PSICQUICInterface() {
    }

    public String getCounts(String db, String term) throws java.rmi.RemoteException {
        String result = "-1";
        try {
            String url = baseURL + db + baseURLQuery + term + "?format=count";
            LOGGER.trace(url);

            StringWriter writer = new StringWriter();
            IOUtils.copy((new URL(url)).openStream(), writer);
            result = writer.toString();
        } catch (Exception e) {
            LOGGER.error(e.getMessage(), e);
        }
        return result;
    }

    @SuppressWarnings("unchecked")
    public JSONObject getResults(String db, String term, int startAt, int count) throws java.rmi.RemoteException {
        JSONObject result = new JSONObject();
        try {
            String search_count = getCounts(db, term);
            String url = baseURL + db + baseURLQuery + term + "?format=xml25&firstResult=" + startAt
                    + "&maxResults=" + count;

            LOGGER.trace(url);

            JSONArray subList = null;

            if (db.equals("intact")) {
                IntActHandler psicquicHandler = new IntActHandler(url);
                subList = psicquicHandler.getParsedJSON();
            }

            result.put("results", subList);
            result.put("total", search_count);
        } catch (Exception e) {
            LOGGER.error(e.getMessage(), e);
        }

        return result;
    }
}