Example.java

// -*- java -*-
 
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Map;
import java.util.HashMap;
import java.util.Date;
 
import org.springframework.web.client.RestTemplate;
import org.springframework.web.client.HttpClientErrorException;
import org.springframework.web.client.DefaultResponseErrorHandler;
import org.springframework.http.client.ClientHttpResponse;
import org.springframework.util.MultiValueMap;
import org.springframework.util.LinkedMultiValueMap;
 
import net.arnx.jsonic.JSON;
 
public class Example {
    static class BlastCondition {
        MultiValueMap<String, String> params;
        BlastCondition() {
            params = new LinkedMultiValueMap<String, String>();
            params.set("querySequence", null);
            params.set("datasets",      null);
            params.set("database",      null);
            params.set("program",       null);
            params.set("parameters",    null);
            params.set("format",        null);
            params.set("result",        null);
            params.set("address",       null);
        }
    }
 
    static final String WABI_URL_ROOT = "http://ddbj.nig.ac.jp/wabi";
    static final long GET_INTERVAL = 1000; // Note: 1000 (milli sec)
 
    static BlastCondition readBlastCondition() throws IOException {
        BlastCondition cond = new BlastCondition();
        BufferedReader reader1 = new BufferedReader(new FileReader("blast_condition.fasta"));
        StringBuilder buffer1 = new StringBuilder();
        for (int ch = reader1.read(); reader1.ready(); ch = reader1.read()) {
            buffer1.append((char)ch);
        }
        cond.params.set("querySequence", buffer1.toString());
        BufferedReader reader2 = new BufferedReader(new FileReader("blast_condition.txt"));
        StringBuilder buffer2 = new StringBuilder();
        for (String line = reader2.readLine(); null!=(line = reader2.readLine());) {
            String[] tokens = line.split("\t");
            if (!cond.params.containsKey(tokens[0])) continue;
            cond.params.set(tokens[0], tokens[1]);
        }
        return cond;
    }
 
    static String postToWabi(BlastCondition blastCondition) {
        RestTemplate rest = new RestTemplate();
        rest.setErrorHandler(new DefaultResponseErrorHandler() {
                public void handleError(ClientHttpResponse response) throws IOException {
                    HashMap<String, Object> result = JSON.decode(response.getBody(), HashMap.class);
                    System.err.println("BLAST condition errors: " + result.get("error-messages"));
                    super.handleError(response);
                }
            });
        String response = rest.postForObject(WABI_URL_ROOT + "/blast", blastCondition.params, String.class);
        Map<String, Object> result = JSON.decode(response, HashMap.class);
        return (String)result.get("requestId");
    }
 
    static void getStatus(String requestId) throws InterruptedException {
        try {
            RestTemplate rest = new RestTemplate();
            String url = WABI_URL_ROOT + "/blast/" + requestId + "?info=status&format=json";
            while (true) {
                Thread.sleep(GET_INTERVAL);
                String response = rest.getForObject(url, String.class);
                Map<String, Object> result = JSON.decode(response, HashMap.class);
                String status = (String)result.get("status");
                if ("waiting".equals(status)) {
                    System.out.println(new Date() + ": waiting");
                    continue;
                } else if ("running".equals(status)) {
                    System.out.println(new Date() + ": running");
                    continue;
                } else if ("finished".equals(status)) {
                    System.out.println(new Date() + ": finished");
                    return;
                } else {
                    throw new RuntimeException("No such Request-id. time-out");
                }
            }
        } catch (HttpClientErrorException e) {
            throw new RuntimeException("No such Request-id. Cause: time-out or wrong Request-ID");
        }
    }
 
    static String getResult(String requestId) {
        try {
            RestTemplate rest = new RestTemplate();
            String response = rest.getForObject(WABI_URL_ROOT + "/blast/" + requestId + "?info=result&format=bigfile", String.class);
            return response;
        } catch (HttpClientErrorException e) {
            throw new RuntimeException("BLAST result not found. Cause: time-out, not-finished, or wrong Request-ID");
        }
    }
 
    public static void main(String[] args) {
        try {
            BlastCondition blastCondition = readBlastCondition();
            System.out.println("Load BLAST condition");
 
            String requestId = postToWabi(blastCondition);
            System.out.println("POST : success (Request-ID=" + requestId + ")");
 
            getStatus(requestId);
            System.out.println("Request : finished");
 
            String result = getResult(requestId);
            System.out.println("GET BLAST result : success");
            FileWriter writer = new FileWriter(requestId + ".txt");
            writer.write(result);
            writer.flush();
            writer.close();
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
}
 
// Example.java ends here