Looking For A Reason Why My Java Code Could Not Create Pathway Image Using Reactome Restful Api

Question

[samsara]

I have been struggling with Reactome RESTful API to generate pathway diagram for a while. When performed HTTP GET requesto to http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/RESTfulWS/pathwayDiagram/109581/png, API returns base64 encoded image. Here, 109581 is Pathway database identifier. For some reason I am unable to write it to PNG image in java.

I am using Apache Commons Codec for base64 decoding and jersey for REST client.

Could you please find out the reason why i am unable to write to image after decoding base64 string ?

import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.ClientResponse;
import com.sun.jersey.api.client.WebResource;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import org.apache.commons.codec.binary.Base64;

/**
 *
 * @author bishwa
 */
public class ReactomeRESTJava {

    public static void writeImage(String encodedString) throws IOException
    {
        // Decode InputcodedString
        byte[] decodedByteArray = Base64.decodeBase64(encodedString);
        // convert byte into string
        String decodedString = new String(decodedByteArray);
        //System.out.println(decodedString);

        BufferedWriter out = new BufferedWriter(new FileWriter("test.png"));
        out.write(decodedString);
        out.close();

    }

    public static void main(String[] args) {
        // TODO code application logic here
        try
        {
            // Parameters ------------------------------------------------------
            String baseURL="http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI"
                    + "/RESTfulWS/";
            //String method="POST";
            String method="GET";
            String url = "pathwayDiagram/109581/png";
            String input= "ID=170075,176374,68557";

            Client client1 = Client.create();
            WebResource webRS = client1.resource(baseURL+url);

            ClientResponse response = null ;

            // perform GET of POST request
            System.out.println("Fetching ..");
            switch (method) 
            {
                case "POST":
                    response = webRS.accept("application/json")
                            .post(ClientResponse.class, input);
                    break;
                case "GET":
                    response = webRS.accept("text/plain")
                            .get(ClientResponse.class);
                    break;
            }

            // throw response error codes
            if(response.getStatus() != 200)
            {
                throw new RuntimeException("Failed: HTTP error code: "
                        + response.getStatus());
            }

            String output = response.getEntity(String.class);
            //System.out.println("Output from Server ..\n");
            //System.out.println(output);

            // write base64 coded string to png image
            System.out.println("Writing image to a file...");
            writeImage(output);

        } catch (RuntimeException | IOException e){}
    }
}

[Pierre Lindenbaum]

what do you mean "I'm unable to write..." ? What is the exact error ?

[samsara]

The image written is blank.

Answer 1

[Pierre Lindenbaum]

you should never write an array of bytes using a *Writer : UTF-8 or any 'Locale' characters will be interpreted. seehttp://stackoverflow.com/questions/5223760/writer-or-outputstream Use a *OutputStream instead.

You'd better use:

FileOutputStream out=new FileOutputStream(new File("image.png"));
out.write(decodedByteArray);
out.close();