servicetest.py

import requests
import json

# a helper function that returns the error message in case there is one and
# None otherwise
def get_err_msg(x):
    if 'errorMessage' in x:
        return x['errorMessage']
    else:
        return None

# simple function to stringify a list
def iterable_to_str(xs, sep=' '):
    return sep.join([str(x) for x in xs])

# do a conversion using the JSON rest service and print out the results
def convert(req_dict):
    # prepare and POST the JSON request
    print '======= PERFORMING CONVERSION ======='
    print \
        'converting from "%s" to "%s":' \
        % ((req_dict['fromUnits'] if 'fromUnits' in req_dict else 'feature name'), req_dict['toUnits'])
    resp = requests.post(
        #'http://localhost:8888/resources/conversion/convert.json',
        'http://cgd.jax.org/mousemapconverter/resources/conversion/convert.json',
        data=json.dumps(req_dict),
        headers={'Content-type': 'application/json', 'Accept': 'application/json'})

    # parse the response and print the results checking for error messages
    print 'status code:', resp.status_code
    if resp.status_code == 200:
        print 'JSON response:', resp.text
        
        resp_coords = json.loads(resp.text)
        err_msg = get_err_msg(resp_coords)
        if err_msg is not None:
            print 'conversion failed:', err_msg
        else:
            # iterate through all of the returned cordinates and print them out
            for in_coord, out_coord in zip(req_dict['dataToConvert'], resp_coords):
                err_msg = get_err_msg(out_coord)
                if err_msg is not None:
                    print 'conversion failed:', err_msg
                elif isinstance(in_coord, list) or isinstance(in_coord, tuple):
                    print 'input:', iterable_to_str(in_coord), 'output:', iterable_to_str(out_coord)
                else:
                    print 'input:', in_coord, 'output:', iterable_to_str(out_coord)
    else:
        print 'conversion failed'

def main():
    # start by converting from genome feature IDs (so no fromUnits needed). Note
    # that some of these IDs will be represented
    req_dict = {
        'toUnits' : 'mm10',
        'dataToConvert' : [
            'rs3675244',
            'rs3711314',
            # note that the RS# will just return a chromosome and position
            # while genes like 'Brca1' will return two positions to represent
            # the start and end of the gene.
            'Brca1',
            'rs3023460',
            'rs3707114',
            'rs3706767'],
    }
    convert(req_dict)
    
    # change the toUnits to the male shifman map and start again
    req_dict['toUnits'] = 'maleShifmanMap'
    convert(req_dict)
    
    # now lets convert from coordinates and also allow per data-point errors
    req_dict = {
        'allowPerDataPointErrors' : True,
        'fromUnits' : 'mm9',
        'toUnits' : 'averageShifmanMap',
        'dataToConvert' : [
            ['1', 92887845],
            # note that we can have an arbitrary number of coordinates
            # following the chromosome identifier
            ['2', 7821365, 8821365, 9821365],
            ['1', 172956646],
            ['5', 92572826],
            ['6', 47433029],
            # because we set allowPerDataPointErrors to True we should
            # get an error message for this element and successfully
            # process the others
            ['bogus_chromosome', 47433029],
            ['4', 41364422],
            ['1', 131246731],
            ['Chr7', 61246731],
            ['X', 8574635, 9253654],
        ]
    }
    convert(req_dict)

if __name__ == '__main__':
    main()