edu.scripps.fl.pubchem.web.pug.PowerUserGateway.java Source code

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Here is the source code for edu.scripps.fl.pubchem.web.pug.PowerUserGateway.java

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/*
 * Copyright 2011 The Scripps Research Institute
 *
 * 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.scripps.fl.pubchem.web.pug;

import java.io.IOException;
import java.io.InputStream;
import java.net.URL;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;

import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.DefaultHttpClient;
import org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.DOMReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * @author Mark Southern
 *  
 *    // Code usage sample
 *    PowerUserGateway pug = PowerUserGateway.newInstance();
 *   Document doc = PUGRequest.newMultiAssayResultRequest(
 *         Arrays.asList(new Integer[]{2546,2551}),
 *         Arrays.asList(new Integer[]{24892677,24892644}),
 *         Type.CID, Output.XML);
 *   pug.setRequest( doc );
 *   pug.submitAndWait(5000);
 *   URL url = pug.getResponseURL();
 *  
 * The following references where helpful:
 * 
 * http://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html
 * http://fiehnlab.ucdavis.edu/staff/scholz/dev/power_user_gateway_in_java/power_user_gateway_NCBI_java
 *  
 */
public class PowerUserGateway {

    public enum Output {
        CSV, ASN1, XML;
    }

    public enum Type {
        AID("pcassay", "aid"), SID("pcsubstance", "sid"), CID("pccompound", "cid"), TID(null, "tid");
        private String database;
        private String type;

        private Type(String database, String type) {
            this.database = database;
            this.type = type;
        }

        public String getDatabase() {
            return database;
        }

        public String getType() {
            return type;
        }

        public static Type getType(String query) {
            if ("CID".equalsIgnoreCase(query))
                return Type.CID;
            else if ("SID".equalsIgnoreCase(query))
                return Type.SID;
            if ("TID".equalsIgnoreCase(query))
                return Type.TID;
            if ("AID".equalsIgnoreCase(query))
                return Type.AID;
            else
                throw new RuntimeException("Cannot determine type from query: " + query);
        }
    }

    private static final Logger log = LoggerFactory.getLogger(PowerUserGateway.class);
    private static final String SITE = "pubchem.ncbi.nlm.nih.gov";
    private static final int PORT = 80;

    private static final String PATH = "/pug/pug.cgi";

    public static Document getDocument(InputStream inputStream) throws Exception {
        DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
        DOMReader reader = new DOMReader();
        Document doc = reader.read(builder.parse(inputStream));
        log.debug(String.format("Received XML:%n%n%s%n%n", doc.asXML()));
        return doc;
    }

    public static PowerUserGateway newInstance() {
        return new PowerUserGateway();
    }

    private Document requestDocument;
    private Document responseDocument;
    private HttpClient client;

    private PowerUserGateway() {
        client = new DefaultHttpClient();
    }

    protected Document createStatusDocument(String requestId) throws Exception {
        InputStream is = getClass().getResourceAsStream("/edu/scripps/fl/pubchem/pug/PugStatus.xml");
        Document doc = getDocument(is);
        Node node = doc.selectSingleNode("//PCT-Request_reqid");
        node.setText("" + requestId);
        return doc;
    }

    protected InputStream fetchResponse(Document document) throws Exception {
        //      PostMethod postMethod = new PostMethod(PATH);
        //      postMethod.setRequestEntity(new StringRequestEntity(document.asXML(), "text/xml", "utf-8"));
        //      client.executeMethod(postMethod);
        //      return postMethod.getResponseBodyAsStream();

        HttpPost post = new HttpPost("http://" + SITE + PATH);
        post.setEntity(new StringEntity(document.asXML(), "text/xml", "utf-8"));
        HttpResponse response = client.execute(post);
        return response.getEntity().getContent();
    }

    public URL getResponseURL() throws IOException {
        URL url = null;
        Node node = getResponse().selectSingleNode("//*/PCT-Download-URL_url");
        if (node != null)
            url = new URL(node.getText());
        return url;
    }

    private String makeRequest() throws Exception {
        InputStream is = fetchResponse(getRequest());
        Document doc = getDocument(is);
        setResponse(doc);
        Node node = doc.selectSingleNode("//PCT-Status[@value='server-error']");
        if (node != null) {
            String msg = node.getParent().getParent().getText();
            throw new Exception(String.format("PUG Error: %s", msg));
        }
        node = doc.selectSingleNode("//*/PCT-Waiting_reqid");
        String requestId = null;
        if (node != null) {
            requestId = node.getText();
            log.debug("PCT-Waiting_reqid: " + requestId);
        }
        return requestId;
    }

    public String requestUpdate(String requestId) throws Exception {
        Document doc = createStatusDocument(requestId);
        setRequest(doc);
        return makeRequest();
    }

    public void setRequest(Document document) {
        requestDocument = document;
    }

    protected void setResponse(Document document) {
        responseDocument = document;
    }

    public Document getRequest() {
        return requestDocument;
    }

    public Document getResponse() {
        return responseDocument;
    }

    public void submitAndWait(long sleepMillis) throws Exception {
        setResponse(null); // clear any existing use
        String requestId = makeRequest();
        while (null != requestId) {
            Thread.sleep(sleepMillis);
            requestId = requestUpdate(requestId);
        }
    }
}