Encode query with Java

From WABI

Contents 1 Summary 2 Description 3 Sample program 4 Link

Summary

Result may not be able to be retrieved normally, if query including non alphanumeric character is used with Java.

Description

You have to encode your query. If qPath is a query to be encoded, please do as follows.

qPath = URLEncoder.encode(qPath, "UTF-8");

Sample program

Following is a sample code that search entries with the condition of Feature Key is 'rRNA', Qualifier name is 'product' and Qualifier value is '16S ribosomal RNA' by using ARSA searchByXMLPath method.

Download this program

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintStream;
import java.net.Socket;
import java.net.URLEncoder;

public class Rest {

	public static void main(String[] args) throws IOException {
		// set server
		String host = "xml.nig.ac.jp";
		int port = 80;

		// set API server
		String url = "/rest/Invoke";

		String qPath = "/ENTRY/DDBJ/feature-table/feature/f_key=='rRNA' AND ";
		qPath += "(/ENTRY/DDBJ/feature-table/feature{/f_key=='rRNA' AND ";
		qPath += "/f_quals/qualifier{/q_name=='product' AND /q_value='16S ribosomal RNA'}}) ";
		String rPath = "/ENTRY/DDBJ/primary-accession,/ENTRY/DDBJ/definition";
		qPath = URLEncoder.encode(qPath, "UTF-8");
		rPath = URLEncoder.encode(rPath, "UTF-8");

		String offset = "1";
		String count = "10";

		// set parameter
		String query = "service=ARSA&method=searchByXMLPath&queryPath=" + qPath
				+ "&returnPath=" + rPath + "&offset=" + offset + "&count="
				+ count;

		// open socket
		Socket socket = new Socket(host, port);

		// send query
		BufferedReader br = new BufferedReader(new InputStreamReader(socket
				.getInputStream()));
		PrintStream pw = new PrintStream(socket.getOutputStream());
		pw.print("POST " + url + " HTTP/1.0\n");
		pw.print("User-Agent: java/socket\n");
		pw.print("Content-Type: application/x-www-form-urlencoded\n");
		pw.print("Content-Length:" + query.length() + "\n\n");
		pw.print(query);

		// get result
		String l = null;
		while ((l = br.readLine()) != null) {
			System.out.println(l);
		}
		pw.close();
		br.close();
	}
}

Link

Japanese page