org.shangridocs.services.pubmed.PubmedResource.java Source code

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Here is the source code for org.shangridocs.services.pubmed.PubmedResource.java

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/**
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You 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 org.shangridocs.services.pubmed;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.logging.Logger;

import javax.servlet.ServletContext;
import javax.ws.rs.Consumes;
import javax.ws.rs.GET;
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;

import org.apache.commons.io.IOUtils;
import org.apache.cxf.jaxrs.client.WebClient;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.JSONValue;

@Path("/pubmed")
public class PubmedResource {

    private static final String PUBMED_BASE_URL = "org.shangridocs.pubmed.baseUrl";

    private static final String PUBMED_ID_BASE_URL = "org.shangridocs.pubmed.ids.baseUrl";

    private static final String PUBMED_BASE = "http://www.ncbi.nlm.nih.gov/pubmed/";

    private String pubMedBaseUrlStr;

    private String pubMedIdBaseUrlStr;

    private static final Logger LOG = Logger.getLogger(PubmedResource.class.getName());

    public PubmedResource(@Context ServletContext sc) {
        pubMedBaseUrlStr = sc.getInitParameter(PUBMED_BASE_URL);
        pubMedIdBaseUrlStr = sc.getInitParameter(PUBMED_ID_BASE_URL);
    }

    @PUT
    @Path("/text")
    @Consumes("text/plain")
    @Produces("text/plain")
    public Response getPubIds(InputStream is) throws IOException {
        String searchText = IOUtils.toString(is, "UTF-8");
        String pubMedSearchUrlStr = pubMedBaseUrlStr;
        LOG.info("searching " + pubMedSearchUrlStr + " for terms " + searchText);
        WebClient client = WebClient.create(pubMedSearchUrlStr).query("db", "pubmed").query("retmode", "json")
                .query("term", searchText).accept("application/json");
        Response r = client.get();
        String responseJson = r.readEntity(String.class);
        LOG.info("Call to " + pubMedSearchUrlStr + " returned: " + responseJson);
        Object jsonObj = JSONValue.parse(responseJson);
        JSONObject jObj = (JSONObject) jsonObj;
        JSONObject eSearchObj = (JSONObject) jObj.get("esearchresult");
        JSONArray idArr = (JSONArray) eSearchObj.get("idlist");
        StringBuilder responseBldr = new StringBuilder();
        for (int i = 0; i < idArr.size(); i++) {
            responseBldr.append(idArr.get(i));
            if (i + 1 < idArr.size()) {
                responseBldr.append(",");
            }
        }

        return Response.ok(responseBldr.toString(), MediaType.TEXT_PLAIN).build();

    }

    @PUT
    @Path("/ids")
    @Consumes("text/plain")
    @Produces("application/json")
    public Response getPubMedURLs(InputStream is) throws IOException {
        String ids = IOUtils.toString(is, "UTF-8");
        String pubMedSearchUrlStr = pubMedIdBaseUrlStr;
        LOG.info("searching " + pubMedSearchUrlStr + " for ids " + ids);
        WebClient client = WebClient.create(pubMedSearchUrlStr).query("db", "pubmed").query("retmode", "json")
                .query("rettype", "abstract").query("id", ids).accept("application/json");
        Response r = client.get();
        String responseJson = r.readEntity(String.class);
        LOG.info("Call to " + pubMedSearchUrlStr + " returned: " + responseJson);
        Object jsonObj = JSONValue.parse(responseJson);
        JSONObject jObj = (JSONObject) jsonObj;
        JSONObject resultObj = (JSONObject) jObj.get("result");
        JSONArray idArr = (JSONArray) resultObj.get("uids");
        StringBuilder responseBldr = new StringBuilder();
        responseBldr.append("[");
        for (int i = 0; i < idArr.size(); i++) {
            String id = (String) idArr.get(i);
            JSONObject idObj = (JSONObject) resultObj.get(id);
            String title = (String) idObj.get("title");
            responseBldr.append("{\"id\" : \"");
            responseBldr.append(id);
            responseBldr.append("\",");
            responseBldr.append("\"url\" : \"");
            responseBldr.append(PUBMED_BASE);
            responseBldr.append(idArr.get(i));
            responseBldr.append("\", \"title\" : \"");
            responseBldr.append(title);
            responseBldr.append("\"");
            responseBldr.append("}");
            if (i + 1 < idArr.size()) {
                responseBldr.append(",");
            }
        }

        responseBldr.append("]");

        return Response.ok(responseBldr.toString(), MediaType.APPLICATION_JSON).build();

    }

    @PUT
    @Path("/query")
    @Consumes("text/plain")
    @Produces("application/json")
    public Response query(InputStream is) throws IOException {
        Response r = getPubIds(is);
        String resp = r.readEntity(String.class);
        ByteArrayInputStream idStream = new ByteArrayInputStream(resp.getBytes());
        return getPubMedURLs(idStream);
    }

    @GET
    @Path("/status")
    @Produces("text/html")
    public Response status() {
        return Response
                .ok("<h1>This is Tika PubMed Proxy: running correctly</h1><h2>PubMed Search Proxy: /text</h2><p>"
                        + pubMedBaseUrlStr + "</p><h2>PubMed ID URL Proxy: /ids</h2><p>" + pubMedIdBaseUrlStr
                        + "</p>")
                .build();
    }

}