biomine.bmvis2.crawling.CrawlerFetch.java Source code

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Here is the source code for biomine.bmvis2.crawling.CrawlerFetch.java

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/*
 * Copyright 2012 University of Helsinki.
 *
 * This file is part of BMVis.
 *
 * BMVis is free software: you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * BMVis is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BMVis.  If not, see
 * <http://www.gnu.org/licenses/>.
 */

package biomine.bmvis2.crawling;

import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;

import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.JSONValue;

import biomine.bmgraph.BMGraph;
import biomine.bmgraph.BMGraphUtils;

/**
 * Pulls graph data from crawlers web api.
 * @author alhartik
 *
 */
public class CrawlerFetch {

    private URL statusUrl;

    public CrawlerFetch(Collection<String> queryNodes, boolean onlyNeighborHood, String database)
            throws IOException {

        URL queryUrl = null;

        queryUrl = new URL(WebConstants.DEFAULT_BASEURL + "/query.cgi");
        StringBuffer startNodesBuf = new StringBuffer();

        for (String nod : queryNodes)
            startNodesBuf.append(nod.replace(" ", "\\ ") + " ");

        if (queryNodes.isEmpty() == false)
            startNodesBuf.deleteCharAt(startNodesBuf.length() - 1);

        String key = onlyNeighborHood ? "end_nodes" : "start_nodes";

        HashMap<String, String> parameters = new HashMap<String, String>();
        parameters.put(key, startNodesBuf.toString());
        if (database != null)
            parameters.put("database", database);
        String qc = URLUtils.getURLContents(queryUrl, parameters);

        queryId = qc.split("\"")[3];

        //      System.out.println("q = " + queryId);

        statusUrl = new URL(WebConstants.DEFAULT_BASEURL + "/status.cgi?query=" + queryId);
    }

    private void d(Object o) {
        //System.err.println("QUERY:"+o.toString());
    }

    private String queryId;
    String status;
    JSONObject statusObject;
    ArrayList<String> messages = new ArrayList<String>();

    int lastage = -1;

    public void update() throws IOException {

        status = URLUtils.getURLContents(statusUrl);
        statusObject = (JSONObject) JSONValue.parse(status);
        JSONObject obj = (JSONObject) JSONValue.parse(status);
        JSONArray errors = ((JSONArray) obj.get("errors"));

        d("obj = " + obj);
        int age = ((Long) obj.get("age")).intValue();
        d("age = " + age);

        lastage = age;
        messages.clear();
        for (Object o : errors) {
            JSONObject error = (JSONObject) o;
            JSONArray mesarr = (JSONArray) error.get("messages");

            for (int i = 0; i < mesarr.size(); i++) {
                String err = mesarr.get(i).toString();
                messages.add(err);
                d("err = " + err);
            }
        }

        JSONArray mesarr = (JSONArray) obj.get("messages");

        for (int i = 0; i < mesarr.size(); i++) {
            String err = mesarr.get(i).toString();
            messages.add(err);
            d("err = " + err);
        }
    }

    public String getMessages() {
        StringBuffer ret = new StringBuffer();
        for (String str : messages) {
            ret.append(str);
            ret.append("\n");
        }
        return ret.toString();
    }

    public boolean isReady() {
        if (statusObject == null)
            return false;
        String state = statusObject.get("status").toString();

        return state.equals("completed");
    }

    public boolean isError() {
        if (statusObject == null)
            return false;
        String state = statusObject.get("status").toString();
        return state.matches("errors?");
    }

    public boolean isDone() {
        return isReady() || isError();
    }

    public BMGraph getBMGraph() throws IOException {
        if (!isReady())
            return null;
        URL graphUrl = new URL(WebConstants.DEFAULT_BASEURL + "download.cgi?file=" + queryId + "/graph.bmg");
        InputStream is = graphUrl.openConnection().getInputStream();
        return BMGraphUtils.readBMGraph(is);

    }

    public String getState() {
        if (statusObject == null)
            return "";
        return statusObject.get("status").toString();
    }

    //   public static void main(String[] args) throws IOException,
    //         InterruptedException {
    //
    //      CrawlerQuery c = new CrawlerQuery(Collections.singleton("APP"));
    //      while(!c.isReady()&&!c.isError()){
    //         c.update();
    //
    //         String messages = c.getMessages();
    //            System.out.println(messages);
    //      
    //         Thread.sleep(1000);
    //      }
    //      if(c.isReady()){
    //         BMGraph graph = c.getBMGraph();
    //         System.out.println(graph.getNodes());
    //      }
    //   }
}