API Clients

API clients handle the underlying details of how network requests are made and how responses are decoded. We are using Core API which is a format-independent Document Object Model for representing Web APIs. It is recommended to use the Core API clients described below for a more robust and intuitive way to interact with the JASPAR API rather than constructing HTTP requests and decoding responses.

Currently, Core API provides three clients:

As a way of getting started, you can interact with the JASPAR API using the sample calls provided below.

Command line client

# Install the command line client
$ pip install coreapi-cli
To interact with the API: 
  1. # Load the schema document
  2. $ coreapi get https://jaspar2020.genereg.net/api/v1/docs
  3.  
  4. # Interact with the API endpoint
  5. $ coreapi action matrix list -p page=... -p page_size=... -p search=... -p order=... -p collection=... -p name=... -p tax_group=... -p tax_id=... -p tf_class=... -p tf_family=... -p data_type=... -p version=... -p release=...
  6.  
  7. # For example
  8. coreapi action matrix list -p collection=CORE -p tax_group=vertebrates -p version=latest -p name=SMAD3

Python client

# Install the Python client library
$ pip install coreapi
To interact with the API: 
  1. import coreapi
  2.  
  3. # Initialize a client & load the schema document
  4. client = coreapi.Client()
  5. schema = client.get("https://jaspar2020.genereg.net/api/v1/docs")
  6.  
  7. # Interact with the API endpoint
  8. action = ["matrix", "list"]
  9. params = {
  10.     "page": ...,
  11.     "page_size": ...,
  12.     "search": ...,
  13.     "order": ...,
  14.     "collection": ...,
  15.     "name": ...,
  16.     "tax_group": ...,
  17.     "tax_id": ...,
  18.     "tf_class": ...,
  19.     "tf_family": ...,
  20.     "data_type": ...,
  21.     "version": ...,
  22.     "release": ...,
  23. }
  24. result = client.action(schema, action, params=params)
  25.  
  26. # For example
  27. params = {
  28.     "collection": 'CORE',
  29.     "name": 'SMAD3',
  30.     "tax_group": 'vertebrates',
  31.     "version": 'latest',
  32.     "release": '2018',
  33. }
  34. result = client.action(schema, action, params=params)

JavaScript client

  1. <!-- Load the JavaScript client library -->
  2. <script src="https://jaspar2020.genereg.net/static/rest_framework/js/coreapi-0.1.0.js"></script>
  3. <script src="https://jaspar2020.genereg.net/api/v1/docs/schema.js"></script>
To interact with the API: 
  1. var coreapi = window.coreapi  // Loaded by `coreapi.js`
  2. var schema = window.schema    // Loaded by `schema.js`
  3.  
  4. // Initialize a client
  5. var client = new coreapi.Client()
  6.  
  7. // Interact with the API endpoint
  8. var action = ["matrix", "list"]
  9. var params = {
  10.     page: ...,
  11.     page_size: ...,
  12.     search: ...,
  13.     order: ...,
  14.     collection: ...,
  15.     name: ...,
  16.     tax_group: ...,
  17.     tax_id: ...,
  18.     tf_class: ...,
  19.     tf_family: ...,
  20.     data_type: ...,
  21.     version: ...,
  22.     release: ...,
  23. }
  24. client.action(schema, action, params).then(function(result) {
  25.     // Return value is in 'result'
  26. })

Sample calls

These are sample calls to API from different languages. You can create the query url by using our Live API

  1. $.ajax({
  2.     url: 'https://jaspar2020.genereg.net/api/v1/matrix?format=jsonp',
  3.     dataType: 'jsonp',
  4.     jsonp: false,
  5.     jsonpCallback: 'callback',
  6.     success: function(data){
  7.         //Use data and do something
  8.     },
  9. });
  1. import requests, sys
  2.  
  3. query_url = "https://jaspar2020.genereg.net/api/v1/matrix?format=json"
  4.  
  5. result = requests.get(query_url)
  6.  
  7. if not result.ok:
  8.   r.raise_for_status()
  9.   sys.exit()
  10.  
  11. decoded = result.json()
  12. print(repr(decoded))
  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://jaspar2020.genereg.net/api/v1/';
  9. my $ext = 'matrix?format=json';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'application/json' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. use JSON;
  18. use Data::Dumper;
  19. if(length $response->{content}) {
  20.   my $hash = decode_json($response->{content});
  21.   local $Data::Dumper::Terse = 1;
  22.   local $Data::Dumper::Indent = 1;
  23.   print Dumper $hash;
  24.   print "\n";
  25. }
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://jaspar2020.genereg.net/api/v1/'
  5. path = 'matrix?format=json'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15.   puts "Invalid response: #{response.code}"
  16.   puts response.body
  17.   exit
  18. end
  19.  
  20. require 'rubygems'
  21. require 'json'
  22. require 'yaml'
  23.  
  24. result = JSON.parse(response.body)
  25. puts YAML::dump(result)
  1. library(jsonlite)
  2. url <- "https://jaspar2020.genereg.net/api/v1/matrix?format=json"
  3.  
  4. result <- fromJSON(url)
  5. #create a dataframe
  6. df <- result$results
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10. public class JASPARRest {
  11.  
  12.   public static void main(String[] args) throws Exception {
  13.     String server = "https://jaspar2020.genereg.net/api/v1/";
  14.     String ext = "matrix?format=json";
  15.     URL url = new URL(server + ext);
  16.  
  17.     URLConnection connection = url.openConnection();
  18.     HttpURLConnection httpConnection = (HttpURLConnection)connection;
  19.     
  20.     httpConnection.setRequestProperty("Content-Type", "application/json");
  21.     
  22.     InputStream response = connection.getInputStream();
  23.     int responseCode = httpConnection.getResponseCode();
  24.  
  25.     if(responseCode != 200) {
  26.       throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  27.     }
  28.  
  29.     String output;
  30.     Reader reader = null;
  31.     try {
  32.       reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  33.       StringBuilder builder = new StringBuilder();
  34.       char[] buffer = new char[8192];
  35.       int read;
  36.       while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  37.         builder.append(buffer, 0, read);
  38.       }
  39.       output = builder.toString();
  40.     } 
  41.     finally {
  42.         if (reader != null) try {
  43.           reader.close(); 
  44.         } catch (IOException logOrIgnore) {
  45.           logOrIgnore.printStackTrace();
  46.         }
  47.     }
  48.     System.out.println(output);
  49.   }
  50. }
  1. curl 'https://jaspar2020.genereg.net/api/v1/matrix?format=json' -H 'Content-type:application/json'