D²P² Online Data API

#/usr/bin/env python
import json
import urllib2

#This example uses the POST method, for GET you can
#put the ["P04637"] as part of the URL as /api/seqid/["P04637"]
#this is interpreted as a GET request of the form ?seqids=["P04637"]

data = 'seqids=["P04637"]'
request = urllib2.Request('http://d2p2.pro/api/seqid', data)
response = json.loads(urllib2.urlopen(request).read())

for record in response['P04637'][0][2]['disorder']['disranges']:
    print "\t".join(record)
            

In older versions of Ruby (1.8) you will need to install the json gem with rubygems. For newer versions the json package should already be available.

#/usr/bin/env ruby
require "net/http"
require "uri"
require "rubygems"
require "json"

uri = URI('http://d2p2.pro/api/seqid')
request = Net::HTTP.post_form(uri, 'seqids' => '["P04637"]')
response = JSON.parse(request.body)

response['P04637'][0][2]['disorder']['disranges'].each do | record |
    puts record.join("\t")
end
            

#!/usr/bin/env R

library('rjson');

response = fromJSON(readLines('http://d2p2.pro/api/seqid/["P04637"]', warn=FALSE));

for (record in response$P04637[[1]][[3]]$disorder$disranges) { 
    print(paste(record,sep="\t"));
}
            

#/usr/bin/env php
<?php

$response = json_decode(file_get_contents('http://d2p2.pro/api/seqid/["P04637"]'),true);

foreach ($response['P04637'][0][2]['disorder']['disranges'] as $record) {
    echo implode("\t",$record);
    echo "\n";
}

?>
            

This Java example creates a class for requesting D²P² data. I make use of Codehaus' Jackson high performance JSON parser. There is no trivial Java library for dealing with JSON, usually you have to define a full object oriented schema of the JSON to be vivified into full Java objects. However, you can ask Jackson to use a default schema which does something relatively sensible.

import org.codehaus.jackson.map.ObjectMapper;

import java.net.URL;
import java.net.MalformedURLException;
import java.net.URLConnection;
import java.io.*;
import java.util.*;

public class D2P2Request {
        
    private URL url = null;
    private URLConnection con = null;
    private Map results = null;
    
    public Map getResults() {
        return results;
    }

    public D2P2Request(ArrayList ids) {
        buildURL(ids);
        connect();
        parse();
    }

    public void buildURL(ArrayList ids) {
        StringBuilder built_url = new StringBuilder("http://d2p2.pro/api/seqid/[");
        for (String id: ids) {
            built_url.append("\"");
            built_url.append(id);
            built_url.append("\",");
        }
        built_url.replace(built_url.lastIndexOf(","), built_url.lastIndexOf(",") + 1, "]");

        try {
            this.url = new URL(built_url.toString());
        } catch (MalformedURLException e) {
            System.err.println("D2P2 request URL was malformed.");
            System.exit(1);
        }

    }

    public void connect () {
        try {
            this.con = this.url.openConnection();
            this.con.setDoInput(true);  
        } catch (IOException e) {
            System.err.println("Couldn't connect to the D2P2 service.");
            System.exit(1);
        }
    }

    public void parse () {
        ObjectMapper mapper = new ObjectMapper();
        try {
            this.results = mapper.readValue(this.con.getInputStream(), Map.class);
        } catch (IOException e) {
            System.err.println("The response from D2P2 couldn't be parsed by Jackson.");
            System.exit(1);
        }

        if (this.results.get("error") != null) {
            String error = (String) results.get("error");
            System.out.println("D2P2 reports error: "+error);
            System.exit(1);
        }
    }

    public static void main(String args[]) {

        //Specify the list of sequence IDs you wish to retreive assignments for
        ArrayList seqids = new ArrayList();
        seqids.add("P04637");

        //Construct a D2P2Request and get the results
        D2P2Request request = new D2P2Request(seqids);
        Map results = request.getResults();
        

        ArrayList matched_assignments = (ArrayList) results.get("P04637");
        ArrayList assignments = (ArrayList) matched_assignments.get(0);
        String id  = (String) assignments.get(0);
        String genome  = (String) assignments.get(1);
        Map assignment_types = (Map) assignments.get(2);
        Map disorder_assignments = (Map) assignment_types.get("disorder");
        ArrayList disorder_ranges = (ArrayList) disorder_assignments.get("disranges");
        System.out.println(disorder_ranges.get(0));

    }
}
            

If you wish to embed D²P² data directly into your own web resource this can be acheived client side with something like the following JavaScript. I make extensive use of jQuery in this example, if you are using another JS framework please submit an equivalent example.

<!DOCTYPE html>
<html>
    <head>
        <!-- Use jQuery to make it easy to do a CORS AJAX request for the data from d2p2.pro-->
        <script src="//ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
        <script>
        //Make a CORS cross domain AJAX request
        $.getJSON('http://d2p2.pro/api/seqid/["P04637"]', function(data) {
          var records = [];
          //Build a set of table rows with the disordered region predictions
          $.each(data['P04637'][0][2]['disorder']['disranges'], function(key,val) {
            records.push('<tr id="' + key + '"><td>' + val[0] + '</td><td>' + val[1] + '&rarr;' + val[2] + '</td></tr>');
          });

          //Inject the records into the <body> tag inside a table with all the results
          //Change the appendTo('body') to any jQuery identifier for where you wish 
          //to inject the results in your website
          $('<table/>', {
            'class': 'disorder-ranges',
            html: records.join('')
          }).appendTo('body');
        }); 
        </script>
    </head>
    <body>
    </body>
</html>
            

The following are hints at how you might start using the D²P² API with closed languages we can't fully support.

Mathematica

response = Import["http://d2p2.pro/api/seqid/['P04637']", "JSON"];