org.helm.notation2.wsadapter.NucleotideWSLoader.java Source code

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Here is the source code for org.helm.notation2.wsadapter.NucleotideWSLoader.java

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/**
 * ***************************************************************************** Copyright C 2015, The Pistoia Alliance
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
 * documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
 * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
 * permit persons to whom the Software is furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
 * Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
 * WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 * COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 *****************************************************************************
 */
package org.helm.notation2.wsadapter;

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.URISyntaxException;
import java.util.HashMap;
import java.util.Map;

import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.methods.CloseableHttpResponse;
// import org.apache.http.impl.client.WinHttpClients;
import org.apache.http.util.EntityUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.fasterxml.jackson.core.JsonFactory;
import com.fasterxml.jackson.core.JsonParseException;
import com.fasterxml.jackson.core.JsonParser;

/**
 * 
 * {@code NucleotideWSLoader} loads nucleotides from the webservice configured in {@code MonomerStoreConfiguration}.
 * 
 * @author <a href="mailto:lanig@quattro-research.com">Marco Lanig</a>
 * @version $Id$
 */
public class NucleotideWSLoader {

    /** The Logger for this class */
    private static final Logger LOG = LoggerFactory.getLogger(NucleotideWSLoader.class);

    /**
     * Default constructor.
     * 
     * @throws IOException
     */
    public NucleotideWSLoader() throws IOException {
    }

    /**
     * Loads the nucleotide store using the URL configured in {@code MonomerStoreConfiguration}.
     * 
     * @return Map containing nucleotides
     * 
     * @throws IOException
     * @throws URISyntaxException
     */
    public Map<String, String> loadNucleotideStore() throws IOException, URISyntaxException {

        Map<String, String> nucleotides = new HashMap<String, String>();
        LOG.debug("Loading nucleotide store by Webservice Loader");
        LOG.debug(MonomerStoreConfiguration.getInstance().toString());
        CloseableHttpResponse response = null;
        try {
            response = WSAdapterUtils
                    .getResource(MonomerStoreConfiguration.getInstance().getWebserviceNucleotidesFullURL());
            LOG.debug(response.getStatusLine().toString());

            JsonFactory jsonf = new JsonFactory();
            InputStream instream = response.getEntity().getContent();

            JsonParser jsonParser = jsonf.createJsonParser(instream);
            nucleotides = deserializeNucleotideStore(jsonParser);
            LOG.debug(nucleotides.size() + " nucleotides loaded");

            EntityUtils.consume(response.getEntity());

        } catch (ClientProtocolException e) {

            /* read file */
            JsonFactory jsonf = new JsonFactory();
            InputStream instream = new FileInputStream(
                    new File(MonomerStoreConfiguration.getInstance().getWebserviceNucleotidesFullURL()));

            JsonParser jsonParser = jsonf.createJsonParser(instream);
            nucleotides = deserializeNucleotideStore(jsonParser);
            LOG.debug(nucleotides.size() + " nucleotides loaded");

        } finally {

            if (response != null) {
                response.close();
            }
        }

        return nucleotides;
    }

    /**
     * Private routine to deserialize nucleotide Store JSON. This is done manually to give more freedom regarding data
     * returned by the webservice.
     * 
     * @param parser the JSONParser containing JSONData.
     * @return Map containing nucleotides
     * 
     * @throws JsonParseException
     * @throws IOException
     */
    private Map<String, String> deserializeNucleotideStore(JsonParser parser)
            throws JsonParseException, IOException {
        Map<String, String> nucleotides = new HashMap<String, String>();
        String currentNucleotideSymbol = "";
        String currentNucleotideNotation = "";
        boolean foundSymbol = false;
        boolean foundNotation = false;

        parser.nextToken();
        while (parser.hasCurrentToken()) {
            String fieldName = parser.getCurrentName();

            if (fieldName != null) {
                switch (fieldName) {
                case "symbol":
                    parser.nextToken();
                    currentNucleotideSymbol = parser.getText();
                    foundSymbol = true;
                    break;
                case "notation":
                    parser.nextToken();
                    currentNucleotideNotation = parser.getText();
                    foundNotation = true;
                    break;
                default:
                    break;
                }

                if (foundSymbol && foundNotation) {
                    nucleotides.put(currentNucleotideSymbol, currentNucleotideNotation);
                    foundNotation = false;
                    foundSymbol = false;
                }
            }
            parser.nextToken();
        }

        return nucleotides;
    }

}