edu.emory.bmi.medicurator.tcia.TciaQuery.java Source code

Introduction

Here is the source code for edu.emory.bmi.medicurator.tcia.TciaQuery.java

Source

/*
 * Title:        Medicurator
 * Description:  Near duplicate detection framework for heterogeneous medical data sources
 * Licence:      Apache License Version 2.0 - http://www.apache.org/licenses/
 *
 * Copyright (c) 2016, Yiru Chen <chen1ru@pku.edu.cn>
 */
package edu.emory.bmi.medicurator.tcia;

import java.lang.StringBuilder;
import java.util.Scanner;

import edu.emory.bmi.medicurator.Constants;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.*;
import org.apache.http.impl.client.*;
import org.apache.http.*;
import org.apache.http.conn.ssl.*;
import org.apache.http.auth.*;
import javax.net.ssl.*;
import java.security.cert.*;
import org.apache.http.client.config.RequestConfig;
import org.apache.http.HttpEntity;
import java.io.InputStream;
import java.net.*;

/**
 * Build query of TCIA RESTful API, send query and get result
 * User needs to fill the TCIA_API_KEY in Constants before usage
 */
public class TciaQuery {
    private static final String BASE_URL = "https://services.cancerimagingarchive.net/services/v3/TCIA/query/";
    private static final String API_KEY = Constants.TCIA_API_KEY;

    StringBuilder query;
    String method;

    /**
     * create a new query with specified method(getPatient, getSeries, getImage...)
     * @param method
      */
    public TciaQuery(String method) {
        query = new StringBuilder();
        this.method = method;
        String format = "format=json&";
        if (method.equals("getImage") || method.equals("getSingleImage"))
            format = "";
        query.append(BASE_URL + method + "?" + format + "api_key=" + API_KEY + "&");
    }

    //add a parameter
    public void param(String key, String value) {
        if (value == null)
            return;
        query.append(key + "=" + URLEncoder.encode(value) + "&");
    }

    //get the query URL
    public String getQuery() {
        System.out.println(query.toString());
        return query.toString();
    }

    //create a insecure ssl client
    private HttpClient getInsecureClient() throws Exception {
        SSLContext sslContext = new SSLContextBuilder().loadTrustMaterial(null, new TrustStrategy() {
            public boolean isTrusted(X509Certificate[] chain, String authType) throws CertificateException {
                return true;
            }
        }).build();
        SSLConnectionSocketFactory sslsf = new SSLConnectionSocketFactory(sslContext);
        HttpClientBuilder builder = HttpClientBuilder.create();
        builder.setSSLSocketFactory(sslsf);
        if (Constants.PROXY_HOST != null && Constants.PROXY_PORT != null) {
            HttpHost proxy = new HttpHost(Constants.PROXY_HOST, Constants.PROXY_PORT, "http");
            builder.setProxy(proxy);
        }
        if (Constants.PROXY_USERNAME != null && Constants.PROXY_PASSWORD != null) {
            Credentials credentials = new UsernamePasswordCredentials(Constants.PROXY_USERNAME,
                    Constants.PROXY_PASSWORD);
            CredentialsProvider credsProvider = new BasicCredentialsProvider();
            credsProvider.setCredentials(AuthScope.ANY, credentials);
            builder.setDefaultCredentialsProvider(credsProvider);
        }
        return builder.build();
    }

    //send query and get text result
    public String getResult() {
        try {
            HttpGet request = new HttpGet(getQuery());
            HttpClient client = getInsecureClient();
            HttpResponse response = client.execute(request);
            HttpEntity entity = response.getEntity();
            Scanner s = new Scanner(entity.getContent());
            String str = s.nextLine();
            System.out.println(str);
            return str;
        } catch (Exception e) {
            System.out.println("[ERROR] when excute TCIA TESTful API " + getQuery() + " -- " + e);
            return "";
        }
    }

    //send query and get raw data result
    public InputStream getRawResult() {
        try {
            HttpGet request = new HttpGet(getQuery());
            HttpClient client = getInsecureClient();
            HttpResponse response = client.execute(request);
            HttpEntity entity = response.getEntity();
            return entity.getContent();
        } catch (Exception e) {
            System.out.println("[ERROR] when excute TCIA TESTful API " + getQuery() + " -- " + e);
            return null;
        }
    }
}