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Python 3 support for 3 files.
This commit is contained in:
Nicola Soranzo
+51
-51
@@ -1,12 +1,15 @@
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"""
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Common methods used by the API sample scripts.
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"""
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from __future__ import print_function
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import json
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import logging
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import sys
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import urllib2
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from Crypto.Cipher import Blowfish
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from six.moves.urllib.error import HTTPError
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from six.moves.urllib.request import Request, urlopen
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log = logging.getLogger( __name__ )
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@@ -31,9 +34,9 @@ def get( api_key, url ):
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"""
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url = make_url( api_key, url )
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try:
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return json.loads( urllib2.urlopen( url ).read() )
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except ValueError, e:
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print "URL did not return JSON data: %s" % e
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return json.loads( urlopen( url ).read() )
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except ValueError as e:
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print("URL did not return JSON data: %s" % e)
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sys.exit(1)
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@@ -42,8 +45,8 @@ def post( api_key, url, data ):
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Do the actual POST.
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"""
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url = make_url( api_key, url )
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req = urllib2.Request( url, headers={ 'Content-Type': 'application/json' }, data=json.dumps( data ) )
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return json.loads( urllib2.urlopen( req ).read() )
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req = Request( url, headers={ 'Content-Type': 'application/json' }, data=json.dumps( data ) )
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return json.loads( urlopen( req ).read() )
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def put( api_key, url, data ):
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@@ -51,9 +54,9 @@ def put( api_key, url, data ):
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Do the actual PUT
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"""
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url = make_url( api_key, url )
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req = urllib2.Request( url, headers={ 'Content-Type': 'application/json' }, data=json.dumps( data ))
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req = Request( url, headers={ 'Content-Type': 'application/json' }, data=json.dumps( data ))
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req.get_method = lambda: 'PUT'
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return json.loads( urllib2.urlopen( req ).read() )
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return json.loads( urlopen( req ).read() )
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def __del( api_key, url, data ):
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@@ -61,9 +64,9 @@ def __del( api_key, url, data ):
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Do the actual DELETE
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"""
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url = make_url( api_key, url )
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req = urllib2.Request( url, headers={ 'Content-Type': 'application/json' }, data=json.dumps( data ))
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req = Request( url, headers={ 'Content-Type': 'application/json' }, data=json.dumps( data ))
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req.get_method = lambda: 'DELETE'
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return json.loads( urllib2.urlopen( req ).read() )
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return json.loads( urlopen( req ).read() )
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def display( api_key, url, return_formatted=True ):
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@@ -72,40 +75,37 @@ def display( api_key, url, return_formatted=True ):
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"""
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try:
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r = get( api_key, url )
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except urllib2.HTTPError, e:
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print e
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print e.read( 1024 ) # Only return the first 1K of errors.
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except HTTPError as e:
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print(e)
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print(e.read( 1024 )) # Only return the first 1K of errors.
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sys.exit( 1 )
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if type( r ) == unicode:
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print 'error: %s' % r
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return None
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if not return_formatted:
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return r
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elif type( r ) == list:
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# Response is a collection as defined in the REST style.
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print 'Collection Members'
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print '------------------'
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print('Collection Members')
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print('------------------')
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for n, i in enumerate(r):
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# All collection members should have a name in the response.
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# url is optional
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if 'url' in i:
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print '#%d: %s' % (n + 1, i.pop( 'url' ) )
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print('#%d: %s' % (n + 1, i.pop( 'url' ) ))
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if 'name' in i:
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print ' name: %s' % i.pop( 'name' )
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print(' name: %s' % i.pop( 'name' ))
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for k, v in i.items():
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print ' %s: %s' % ( k, v )
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print ''
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print '%d element(s) in collection' % len( r )
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print(' %s: %s' % ( k, v ))
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print('')
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print('%d element(s) in collection' % len( r ))
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elif type( r ) == dict:
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# Response is an element as defined in the REST style.
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print 'Member Information'
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print '------------------'
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print('Member Information')
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print('------------------')
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for k, v in r.items():
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print '%s: %s' % ( k, v )
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print('%s: %s' % ( k, v ))
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elif type( r ) == str:
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print r
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print(r)
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else:
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print 'response is unknown type: %s' % type( r )
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print('response is unknown type: %s' % type( r ))
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def submit( api_key, url, data, return_formatted=True ):
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@@ -115,34 +115,34 @@ def submit( api_key, url, data, return_formatted=True ):
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"""
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try:
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r = post( api_key, url, data )
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except urllib2.HTTPError, e:
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except HTTPError as e:
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if return_formatted:
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print e
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print e.read( 1024 )
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print(e)
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print(e.read( 1024 ))
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sys.exit( 1 )
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else:
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return 'Error. ' + str( e.read( 1024 ) )
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if not return_formatted:
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return r
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print 'Response'
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print '--------'
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print('Response')
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print('--------')
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if type( r ) == list:
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# Currently the only implemented responses are lists of dicts, because
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# submission creates some number of collection elements.
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for i in r:
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if type( i ) == dict:
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if 'url' in i:
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print i.pop( 'url' )
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print(i.pop( 'url' ))
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else:
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print '----'
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print('----')
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if 'name' in i:
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print ' name: %s' % i.pop( 'name' )
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print(' name: %s' % i.pop( 'name' ))
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for k, v in i.items():
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print ' %s: %s' % ( k, v )
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print(' %s: %s' % ( k, v ))
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else:
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print i
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print(i)
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else:
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print r
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print(r)
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def update( api_key, url, data, return_formatted=True ):
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@@ -152,18 +152,18 @@ def update( api_key, url, data, return_formatted=True ):
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"""
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try:
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r = put( api_key, url, data )
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except urllib2.HTTPError, e:
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except HTTPError as e:
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if return_formatted:
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print e
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print e.read( 1024 )
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print(e)
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print(e.read( 1024 ))
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sys.exit( 1 )
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else:
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return 'Error. ' + str( e.read( 1024 ) )
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if not return_formatted:
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return r
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print 'Response'
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print '--------'
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print r
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print('Response')
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print('--------')
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print(r)
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def delete( api_key, url, data, return_formatted=True ):
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@@ -173,18 +173,18 @@ def delete( api_key, url, data, return_formatted=True ):
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"""
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try:
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r = __del( api_key, url, data )
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except urllib2.HTTPError, e:
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except HTTPError as e:
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if return_formatted:
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print e
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print e.read( 1024 )
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print(e)
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print(e.read( 1024 ))
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sys.exit( 1 )
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else:
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return 'Error. ' + str( e.read( 1024 ) )
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if not return_formatted:
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return r
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print 'Response'
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print '--------'
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print r
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print('Response')
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print('--------')
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print(r)
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def encode_id( config_id_secret, obj_id ):
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@@ -1,7 +1,10 @@
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#!/usr/bin/env python
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from __future__ import print_function
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import os
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import sys
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import urllib2
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from six.moves.urllib.error import URLError
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sys.path.insert( 0, os.path.dirname( __file__ ) )
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@@ -9,9 +12,10 @@ from common import display
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try:
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display( *sys.argv[1:3] )
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except TypeError:
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print 'usage: %s key url' % os.path.basename( sys.argv[0] )
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except TypeError as e:
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print('usage: %s key url' % os.path.basename( sys.argv[0] ))
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print(e)
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sys.exit( 1 )
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except urllib2.URLError, e:
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print str(e)
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except URLError as e:
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print(e)
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sys.exit( 1 )
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@@ -9,6 +9,7 @@ Example calls:
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python workflow_execute.py <api_key> <galaxy_url>/api/workflows <workflow_id> 'hist_id=<history_id>' '38=hda=<file_id>' 'param=tool=name=value'
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python workflow_execute_parameters.py <api_key> http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bowtie' 'param=bowtie_wrapper=suppressHeader=True' 'param=peakcalling_spp=window_size=1000'
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"""
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from __future__ import print_function
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import os
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import sys
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@@ -47,7 +48,7 @@ def main():
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print("TOOL ID ERROR:")
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except IndexError:
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print 'usage: %s key url workflow_id history step=src=dataset_id' % os.path.basename(sys.argv[0])
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print('usage: %s key url workflow_id history step=src=dataset_id' % os.path.basename(sys.argv[0]))
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sys.exit(1)
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submit( sys.argv[1], sys.argv[2], data )
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