NistController

gistfile1.txt

"""
Controller for integration with NIST data.

Place this in: <galaxy_home>/lib/galaxy/webapps/galaxy/controllers
and then it can be accessed via URL:

    http://<galaxy_url>/nist_controller/get_nistdata
    e.g.
    http://dev1.ab.wurnet.nl:8088/nist_controller/get_nistdata

"""

import urllib2
from galaxy.web.base.controller import BaseUIController, url_for, error, web


class NistController( BaseUIController ):
    """
    Provides some services for the NIST html report
    """

    @web.expose
    def get_nistdata( self, trans, casnr=None ):
        """
        Generate a redirect to NIST webbook web app
        casNr example: "C537268"
        
        """
        
        nist_response = _fire_query_and_return_content("http://webbook.nist.gov/cgi/cbook.cgi?JCAMP="+ casnr + "&Index=0&Type=Mass")
        peak_table = nist_response.split("##PEAK TABLE=(XY..XY)")[1].split("##END=")[0]
        peak_table = peak_table.replace("\n", " ").strip()
        return peak_table
    
    
    
    
    
def _fire_query_and_return_content(url):
    '''
    This method will fire the HTTP call and 
    return the results 
    '''
    
    try:
        data = urllib2.urlopen(url).read()
        
        return data
        
    except urllib2.HTTPError, e:
        raise Exception( "HTTP error for URL: " + url + " : %s - " % e.code + e.reason)
    except urllib2.URLError, e:
        raise Exception( "Network error: %s" % e.reason.args[1] + ". Error accessing remote service [" + url + "]  ")