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

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Here is the source code for org.helm.notation2.wsadapter.MonomerWSSaver.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.IOException;
import java.io.InputStream;

import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.util.EntityUtils;
import org.helm.notation2.Monomer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

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

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

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

    /**
     * Adds or updates a single monomer to the monomer store using the URL configured in {@code MonomerStoreConfiguration}
     * .
     * 
     * @param monomer to save
     */
    public String saveMonomerToStore(Monomer monomer) {
        String res = "";
        CloseableHttpResponse response = null;

        try {
            response = WSAdapterUtils.putResource(monomer.toJSON(),
                    MonomerStoreConfiguration.getInstance().getWebserviceNucleotidesPutFullURL());
            LOG.debug(response.getStatusLine().toString());

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

            JsonParser jsonParser = jsonf.createParser(instream);

            while (!jsonParser.isClosed()) {
                JsonToken jsonToken = jsonParser.nextToken();
                if (JsonToken.FIELD_NAME.equals(jsonToken)) {
                    String fieldName = jsonParser.getCurrentName();
                    LOG.debug("Field name: " + fieldName);
                    jsonParser.nextToken();
                    if (fieldName.equals("monomerShortName")) {
                        res = jsonParser.getValueAsString();
                        break;
                    }
                }
            }

            EntityUtils.consume(response.getEntity());

        } catch (Exception e) {
            LOG.error("Saving monomer failed!", e);
            return "";
        } finally {
            try {
                if (response != null) {
                    response.close();
                }
            } catch (IOException e) {
                LOG.debug("Closing resources failed.", e);
                return res;
            }
        }

        return res;
    }
}