Using ChEMBL web services via proxy.

It is common practice for organizations and companies to make use of proxy servers to connect to services outside their network. This can cause problems for users of the ChEMBL web services who sit behind a proxy server. So to help those users who have asked, we provide the following quick guide, which demonstrates how to access ChEMBL web services via a proxy.

Most software libraries respect proxy settings from environmental variables. You can set the proxy variable once, normally HTTP_PROXY and then use that variable to set other related proxy environment variables:

	export HTTP_PROXY="http://10.10.1.10:3128"
	export HTTPS_PROXY=$HTTP_PROXY

view raw proxies.sh hosted with ❤ by GitHub

Or if you have different proxies responsible for different protocols:

	export HTTP_PROXY=10.10.1.10:3128
	export HTTPS_PROXY=10.10.1.11:1080
	export FTP_PROXY=10.10.1.10:3128

view raw proxies.sh hosted with ❤ by GitHub

On Windows, this would be:

	set http_proxy=10.10.1.10:3128
	set https_proxy=10.10.1.11:1080
	set ftp_proxy=10.10.1.10:3128

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If you are accessing the ChEMBL web services programmatically and you prefer not to clutter your environment, you can consider adding the proxy settings to your scripts. Here are some python based recipes:

1. Official ChEMBL client library

If you are working in a python based environment, we recommend you to use our client library (chembl_webresource_client), for accessing ChEMBL web services. It already offers many advantages over accessing the ChEMBL web services directly and handling proxies is yet another. All you need to do is configure proxies once and you are done:

	# Python modules used for API access...
	from chembl_webresource_client import *
	from chembl_webresource_client.settings import Settings
	# Set proxies:
	Settings.Instance().PROXIES = {
	"http" : "http://10.10.1.10:3128",
	"https" : "https://10.10.1.11:1080",
	"ftp" : "ftp://10.10.1.10:3128"
	}
	# Then use the client normally:
	compounds = CompoundResource()
	record = compounds.get('CHEMBL554')

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2. Python requests library

If you decide to use requests, you have to add 'proxies' parameter to every 'get' and 'post' function call:

	import requests
	import json
	chembl_url = "https://www.ebi.ac.uk/chemblws/compounds/{}"
	proxyDict = {
	"http" : "http://10.10.1.10:3128",
	"https" : "https://10.10.1.11:1080,
	"ftp" : "ftp://10.10.1.10:3128"
	}
	r = json.load(requests.get(chembl_url.format('CHEMBL554'), proxies=proxyDict))[u'compounds']

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3. Python urllib2 library

Finally, in the lowest level library, 'urllib2' you can set a ProxyHandler and register it to URL opener:

	import urllib2
	import json
	import proxy_opener
	chembl_url = "https://www.ebi.ac.uk/chemblws/compounds/{}"
	proxy = urllib2.ProxyHandler({'http': 'http://myuserid:mypassword@myproxyserver:port','https':'http://myuserid:mypassword@myproxyserver:port'})
	opener = urllib2.build_opener(proxy)
	urllib2.install_opener(opener)
	tmp = json.load(urllib2.urlopen(chembl_url.format('CHEMBL554')))[u'compounds']

view raw proxies_urllib2.py hosted with ❤ by GitHub

We would like to thank Dr. Christine Rudolph for the idea and providing code snippets.