fa5b9b718f165eb212073c881c605057c129f933
chmalee
  Fri Apr 12 16:56:56 2019 -0700
Forgot to add link to Ensembl python inspiration, no refs

diff --git src/hg/hubApi/tests/pythonClient.py src/hg/hubApi/tests/pythonClient.py
index f52621d..34935a0 100755
--- src/hg/hubApi/tests/pythonClient.py
+++ src/hg/hubApi/tests/pythonClient.py
@@ -1,165 +1,166 @@
 #!/bin/env python
 
 """
 This code is heavily inspired by the Ensembl python client
+https://github.com/Ensembl/ensembl-rest/wiki/Example-Python-Client
 """
 import argparse
 import json
 import sys
 
 # support python2 and 3
 try:
     from urllib.parse import urlparse, urlencode
     from urllib.request import urlopen, Request
     from urllib.error import HTTPError
 except ImportError:
     from urlparse import urlparse
     from urllib import urlencode
     from urllib2 import urlopen, Request, HTTPError
 
 serverName = "https://api-test.gi.ucsc.edu"
 endpoints = ["/list/publicHubs", "/list/ucscGenomes", "/list/hubGenomes",
     "/list/tracks", "/list/chromosomes", "/getData/sequence", "/getData/track"]
 parameterList = ["hubUrl", "genome", "db", "track", "chrom", "start", "end",
     "maxItemsOutput", "trackLeavesOnly"]
 
 def parseCommandLine():
     parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter,
         description="Test accessing UCSC Genome Browser API",
         epilog="Example usage:\npythonClient.py \"/getData/track\" "
         "\"track=gold;db=hg38;chrom=chrM;maxItemsOutput=2\"")
     parser.add_argument("endpoint", nargs='?',
         help="Endpoint string like \"/list/tracks\" or \"/getData/track/\"", type=str)
     parser.add_argument("parameters", nargs='?',
         help="Parameters to endpoints. semi-colon separated key=value formatted string, "
         "like \"db=hg38;chrom=chrM;maxItemsOutput=2\"",type=str)
     parser.add_argument("-test0", action="store_true", default=False,
         help="Run special test")
     parser.add_argument("-p", "--pretty-print", action="store_true", default=False,
         help="Print json response with newlines")
     parser.add_argument("--show-endpoints", action="store_true", default=False,
         help="List the supported endpoints")
     parser.add_argument("--show-arguments", action="store_true", default=False,
         help="List the supported arguments")
     parser.add_argument("--debug", action="store_true", default=False,
         help="Print final URL of the request.")
     return parser
 
 def tryJsonRequest(requestUrl):
     """
     Wrap call to urlopen in try/except and exit on an HTTP error.
     Returns json response if request is good.
     """
     data = None
     try:
         request = Request(requestUrl)
         response = urlopen(request)
         content = response.read()
         if content:
             data = json.loads(content)
     except HTTPError as e:
         if e.code == 400: # does this work for other status codes?
             msg = json.loads(e.read())
             sys.stderr.write("Error: %s\n" % msg["error"])
             sys.exit(1)
         else:
             sys.stderr.write("Request %s failed with HTTP status %s\nreason:%s\n" %
                 (requestUrl, e.code, e.reason))
         sys.exit(1)
     return data
 
 def runTest0(prettyPrint=False):
     """
     Run test of getting public hub data for "Plants" and print UCSC info
     for the hg38 db and exit
     """
     hubRequest =  serverName + "/list/publicHubs"
     hg38Request = serverName + "/list/ucscGenomes"
 
     # do plants hub test first
     data = tryJsonRequest(hubRequest)
     if data:
         plantData = None
         for obj in data['publicHubs']:
             if obj['shortLabel'] == 'Plants':
                 plantData = obj
         if plantData is not None:
             print("Plants public hub data")
             if prettyPrint:
                 print(json.dumps(plantData,indent=4, separators=(",",":")))
             else:
                 print(json.dumps(plantData))
 
     # now do ucsc hg38 test
     data = tryJsonRequest(hg38Request)
     if data:
         hg38Data = None
         if data['ucscGenomes']['hg38']:
             hg38Data = data['ucscGenomes']['hg38']
         if hg38Data is not None:
             print("hg38/Human information")
             if prettyPrint:
                 print(json.dumps(hg38Data,indent=4, separators=(",",":")))
             else:
                 print(json.dumps(hg38Data))
     sys.exit(0)
 
 def main():
     cmd = parseCommandLine()
     args = cmd.parse_args()
     req =  serverName
 
     if len(sys.argv) == 1:
         cmd.print_help()
         sys.exit(0)
 
     # run special test
     if args.test0:
         runTest0(args.pretty_print)
 
     # check for the show arguments first and exit early
     if args.show_endpoints:
         print("Currently supported endpoints:\n\t%s" % ("\n\t".join(endpoints)))
         sys.exit(0)
     if args.show_arguments:
         print("Currently supported parameters to endpoint functions:\n\t%s" %
             ("\n\t".join(parameterList)))
         sys.exit(0)
 
     # check endpoints
     if args.endpoint:
         if args.endpoint not in endpoints:
             sys.stderr.write("Error: Endpoint '%s' not supported.\n"
                 "Currently supported endpoints are:\n\t%s\n\n" %
                 (args.endpoint, "\n\t".join(endpoints)))
             cmd.print_help()
             sys.exit(1)
         req += args.endpoint
 
     # check params formatted correctly
     if args.parameters:
         params = args.parameters.split(";")
         for param in params:
             arg = param.split("=")[0]
             if arg == param or arg not in parameterList:
                 sys.stderr.write("Unsupported parameter '%s'. "
                     "Currently supported parameters to endpoints:\n\t%s\n"
                     "Please format parameters as arg=val.\n\n" %
                     (arg, "\n\t".join(parameterList)))
                 cmd.print_help()
                 sys.exit(1)
         req += "?" + args.parameters
 
     # make http request and print the output
     data = None
     if args.debug:
         print("request URL: %s\n" % req)
     data = tryJsonRequest(req)
     if data:
         if args.pretty_print:
             print(json.dumps(data, indent=4, separators=(",",":")))
         else:
             print(json.dumps(data))
 
 if __name__ == "__main__":
     main()