net.bioclipse.cir.business.CirManager.java Source code

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Here is the source code for net.bioclipse.cir.business.CirManager.java

Source

/*******************************************************************************
 * Copyright (c) 2012  Egon Willighagen <egonw@users.sf.net>
 *
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 *
 * Contact: http://www.bioclipse.net/
 ******************************************************************************/
package net.bioclipse.cir.business;

import java.io.IOException;
import java.io.InputStream;
import java.util.HashMap;
import java.util.Map;

import net.bioclipse.cdk.business.CDKManager;
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.managers.business.IBioclipseManager;

import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.httpclient.HttpException;
import org.apache.commons.httpclient.HttpMethodBase;
import org.apache.commons.httpclient.methods.GetMethod;
import org.openscience.cdk.io.formats.IChemFormat;
import org.openscience.cdk.io.formats.MDLV2000Format;

public class CirManager implements IBioclipseManager {

    private static final String SERVICE = "http://cactus.nci.nih.gov/chemical/structure/";
    private final CDKManager cdk = new CDKManager();

    /**
     * Gives a short one word name of the manager used as variable name when
     * scripting.
     */
    public String getManagerName() {
        return "cir";
    }

    public ICDKMolecule getByName(String name) throws BioclipseException {
        HttpClient client = new HttpClient();
        String fullURL = SERVICE + name + "/sdf";
        System.out.println(("URL: " + fullURL));
        GetMethod method = new GetMethod(fullURL);
        addMethodHeaders(method, new HashMap<String, String>() {
            {
                put("Accept", "text/plain");
            }
        });
        try {
            client.executeMethod(method);
            String content = method.getResponseBodyAsString();
            if (content.contains("http://www.w3.org/1999/xhtml")) {
                throw new BioclipseException("HTML page returned: probably multiple search hits");
            }
            InputStream reader = method.getResponseBodyAsStream();
            return cdk.loadMolecule(reader, (IChemFormat) MDLV2000Format.getInstance(), null, null);
        } catch (HttpException exception) {
            throw new BioclipseException("Error while accessing CIR: " + exception.getMessage(), exception);
        } catch (IOException exception) {
            throw new BioclipseException("Error while reading the CIR response: " + exception.getMessage(),
                    exception);
        }
    }

    private static HttpMethodBase addMethodHeaders(HttpMethodBase method, Map<String, String> extraHeaders) {
        // add other headers
        if (extraHeaders != null) {
            for (String header : extraHeaders.keySet()) {
                method.setRequestHeader(header, extraHeaders.get(header));
            }
        }
        return method;
    }
}