testBeacon

#!/usr/bin/env python
import sys, json, urllib2
import unittest
import imp
import os.path

if os.path.isfile("query"):
    imp.load_source("query", "query") # hgBeacon does not have the .py extension
    import query as hgBeacon
else:
    imp.load_source("hgBeacon", "hgBeacon") # hgBeacon does not have the .py extension
    import hgBeacon

baseUrl = None
if len(sys.argv)!=1:
    baseUrl = sys.argv[1]

def queryServer(chrom, pos, allele, reference, dataset):
    " if baseUrl is set, query via http. Otherwise just call the script directly "
    if baseUrl == None:
        ret = hgBeacon.lookupAlleleJson(chrom, pos, allele, reference, dataset)
    else:
        url = baseUrl+"?chromosome=%s&position=%s&allele=%s" % (chrom, str(pos), allele)
        if reference!="":
            url=url+"&reference=%s" % reference
        if dataset!="":
            url=url+"&dataset=%s" % dataset

        data = urllib2.urlopen(url).read()
        ret = json.loads(data)
    return ret

class TestBeacon(unittest.TestCase):

    def test_outside(self):
        " test query, beacon "
        maxInt = 2147483646
        rep = queryServer("1", str(maxInt), "T", "", "test")
        self.assertTrue(rep["query"]["position"]==maxInt)
        self.assertTrue(rep["query"]["reference"]=="GRCh37")
        self.assertTrue(rep["query"]["allele"]=="T")
        self.assertTrue(rep["query"]["chromosome"]=="1")
        self.assertTrue(rep["response"]["exists"]=="false")

        bi = rep["beacon"]
        self.assertTrue(bi["id"] != "")
        self.assertTrue(bi["name"] != "")
        self.assertTrue(bi["organization"] != "")
        self.assertTrue(bi["description"] != "")
        self.assertTrue(bi["api"] != "")

    def test_allele(self):
        " test true reply with the special testing chromosome"
        pos = 0
        rep = queryServer("test", str(pos), "A", "", "")
        self.assertTrue(rep["response"]["exists"]=="true")

    def test_allele_false(self):
        " test false reply "
        pos = 10000
        rep = queryServer("test", str(pos), "A", "", "test")
        self.assertTrue(rep["response"]["exists"]=="false")

#if __name__ == '__main__':
    #unittest.main()
suite = unittest.TestLoader().loadTestsFromTestCase(TestBeacon)
unittest.TextTestRunner(verbosity=2).run(suite)