Python makes the REST look easy

Web services are becoming an increasingly common phenomenon in the field of chemoinformatics, where data and services are now being published more openly on the internet. For those unfamiliar with the concept of web services, Wikipedia spells it out to be "application programming interfaces (API) or web APIs that are accessed via Hypertext Transfer Protocol (HTTP) and executed on a remote system hosting the requested services."

Traditionally people used SOAP web services, however they have waned in popularity relative to a new paradigm of web service called REST, which stands for Representational State Transfer. More information on RESTful web services can be found at the above link.

I would just like to illustrate with the use of some code, the simplicity of accessing some RESTful web services using Python. The web services we will be accessing are chemoinformatics web services running on a server at the University of Indiana under the CHEMBIOGrid projects.

The two services we will be accessing are:
1. 3D structure for a PubChem compound, retrieved from the Pub3D database
2. Generation of a 3D structure from a SMILES string, using the smi23d program

The code to access these services is shown below.

'''
Created on Jul 22, 2010
Program to access a REST web service hosted at Indiana University
@author: ed
'''
import urllib2, os, sys

class ChemoinformaticsRESTWebServices():
def __init__(self,url):
self.url = url

def callWS(self,parameter):
try:
url = self.url+parameter
data = urllib2.urlopen(url).read()
print data
except urllib2.HTTPError, e:
print "HTTP error: %d" % e.code
except urllib2.URLError, e:
print "Network error: %s" % e.reason.args[1]

if __name__ == '__main__':
#3D structure for a PubChem compound, retrieved from the Pub3D database
ws = ChemoinformaticsRESTWebServices("http://cheminfov.informatics.indiana.edu/rest/db/pub3d/")
ws.callWS(sys.argv[1])
ws.callWS(sys.argv[2])
#Generation of a 3D structure from a SMILES string, using the smi23d program
ws2 = ChemoinformaticsRESTWebServices("http://cheminfov.informatics.indiana.edu/rest/thread/d3.py/SMILES/")
ws2.callWS(sys.argv[3])