c7da6212382f6efa86b8c2f4ca9f267d8273bfdc
max
  Mon Mar 9 03:08:07 2015 -0700
fixing the help message and the tester in hgBeacon.

diff --git src/hg/hgBeacon/testBeacon src/hg/hgBeacon/testBeacon
index 429254c..a0cbdcf 100755
--- src/hg/hgBeacon/testBeacon
+++ src/hg/hgBeacon/testBeacon
@@ -1,68 +1,68 @@
 #!/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):
+def queryServer(chrom, pos, allele, referenceBases, 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)
+        ret = hgBeacon.lookupAlleleJson(chrom, pos, allele, None, reference, dataset)
     else:
-        url = baseUrl+"?chromosome=%s&position=%s&allele=%s" % (chrom, str(pos), allele)
+        url = baseUrl+"?chromosome=%s&position=%s&alternateBases=%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")
+        rep = queryServer("1", str(maxInt), "T", None, "", "")
         self.assertTrue(rep["query"]["position"]==maxInt)
         self.assertTrue(rep["query"]["reference"]=="GRCh37")
-        self.assertTrue(rep["query"]["allele"]=="T")
+        self.assertTrue(rep["query"]["alternateBases"]=="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", "", "")
+        rep = queryServer("test", str(pos), "A", None, "", "")
         self.assertTrue(rep["response"]["exists"]=="true")
 
     def test_allele_false(self):
         " test false reply "
         pos = 10000
-        rep = queryServer("test", str(pos), "A", "", "test")
+        rep = queryServer("test", str(pos), "A", None, "", "")
         self.assertTrue(rep["response"]["exists"]=="false")
 
 #if __name__ == '__main__':
     #unittest.main()
 suite = unittest.TestLoader().loadTestsFromTestCase(TestBeacon)
 unittest.TextTestRunner(verbosity=2).run(suite)