Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

scripts/api/common.py

@@ -1,3 +1,4 @@
+import json
 import logging
 import os
 import sys
@@ -10,9 +11,6 @@ sys.path = new_path
 from galaxy import eggs
 import pkg_resources
 
-pkg_resources.require( "simplejson" )
-import simplejson
-
 pkg_resources.require( "pycrypto" )
 from Crypto.Cipher import Blowfish
 from Crypto.Util.randpool import RandomPool
@@ -35,30 +33,30 @@ def get( api_key, url ):
     # Do the actual GET.
     url = make_url( api_key, url )
     try:
-        return simplejson.loads( urllib2.urlopen( url ).read() )
-    except simplejson.decoder.JSONDecodeError, e:
+        return json.loads( urllib2.urlopen( url ).read() )
+    except json.decoder.JSONDecodeError, e:
         print "URL did not return JSON data"
         sys.exit(1)
 
 def post( api_key, url, data ):
     # Do the actual POST.
     url = make_url( api_key, url )
-    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ) )
-    return simplejson.loads( urllib2.urlopen( req ).read() )
+    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ) )
+    return json.loads( urllib2.urlopen( req ).read() )
 
 def put( api_key, url, data ):
     # Do the actual PUT
     url = make_url( api_key, url )
-    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
+    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
     req.get_method = lambda: 'PUT'
-    return simplejson.loads( urllib2.urlopen( req ).read() )
+    return json.loads( urllib2.urlopen( req ).read() )
 
 def __del( api_key, url, data ):
     # Do the actual DELETE
     url = make_url( api_key, url )
-    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
+    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
     req.get_method = lambda: 'DELETE'
-    return simplejson.loads( urllib2.urlopen( req ).read() )
+    return json.loads( urllib2.urlopen( req ).read() )
 
 
 def display( api_key, url, return_formatted=True ):

scripts/api/workflow_import_from_file_rpark.py

@@ -11,11 +11,11 @@ sys.path.insert( 0, os.path.dirname( __file__ ) )
 from common import submit
 
 ### Rpark edit ###
-import simplejson
+import json
 
 def openWorkflow(in_file):        
     with open(in_file) as f:
-        temp_data = simplejson.load(f)
+        temp_data = json.load(f)
     return temp_data;
 
 

scripts/drmaa_external_killer.py

@@ -4,10 +4,11 @@
 Terminates a DRMAA job if given a job id and (appropriate) user id.
 """
 
-import os
-import sys
 import errno
+import json
+import os
 import pwd
+import sys
 #import drmaa
 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
@@ -15,8 +16,6 @@ sys.path = new_path
 
 from galaxy import eggs
 import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson as json
 pkg_resources.require("drmaa")
 import drmaa
 

scripts/drmaa_external_runner.py

@@ -10,8 +10,8 @@ import os
 import sys
 import errno
 import pwd
+import json
 
-#import simplejson as json
 #import drmaa
 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] )  # remove scripts/ from the path
@@ -19,8 +19,6 @@ sys.path = new_path
 
 from galaxy import eggs
 import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson as json
 pkg_resources.require("drmaa")
 import drmaa
 

scripts/external_chown_script.py

@@ -1,17 +1,17 @@
 #!/usr/bin/env python
-import os
-import sys
 import errno
+import json
+import os
 import pwd
+import sys
 #import drmaa
+
 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
 from galaxy import eggs
 import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson as json
 pkg_resources.require("drmaa")
 import drmaa
 

scripts/extract_dataset_part.py

@@ -6,9 +6,10 @@ Used by jobs that split large files into pieces to be processed concurrently
 on a gid in a scatter-gather mode. This does part of the scatter.
 
 """
+import json
+import logging
 import os
 import sys
-import logging
 logging.basicConfig()
 log = logging.getLogger( __name__ )
 
@@ -16,11 +17,6 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson
-
 # This junk is here to prevent loading errors
 import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers
 galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
@@ -33,7 +29,7 @@ def __main__():
     if not os.path.isfile(file_path):
         #Nothing to do - some splitters don't write a JSON file
         sys.exit(0)
-    data = simplejson.load(open(file_path, 'r'))
+    data = json.load(open(file_path, 'r'))
     try:
         class_name_parts = data['class_name'].split('.')
         module_name = '.'.join(class_name_parts[:-1])

scripts/galaxy_messaging/server/data_transfer.py

@@ -13,12 +13,21 @@ python data_transfer.py <config_file>
 
 """
 import ConfigParser
-import sys, os, time, traceback
+import cookielib
+import datetime
+import logging
 import optparse
-import urllib,urllib2, cookielib, shutil
-import logging, time, datetime
+import os
+import shutil
+import sys
+import time
+import time
+import traceback
+import urllib
+import urllib2
 import xml.dom.minidom
 
+
 from xml_helper import get_value, get_value_index
 
 log = logging.getLogger( "datatx_" + str( os.getpid() ) )
@@ -39,14 +48,11 @@ new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
 from galaxy import eggs
-from galaxy.util.json import from_json_string, to_json_string
 from galaxy.model import SampleDataset
 from galaxy.web.api.samples import SamplesAPIController
 import pkg_resources
 pkg_resources.require( "pexpect" )
 import pexpect
-pkg_resources.require( "simplejson" )
-import simplejson
 
 log.debug(str(dir(api)))
 

scripts/set_metadata.py

@@ -10,9 +10,11 @@ import logging
 logging.basicConfig()
 log = logging.getLogger( __name__ )
 
+import cPickle
+import json
 import os
 import sys
-import cPickle
+
 # ensure supported version
 from check_python import check_python
 try:
@@ -26,8 +28,6 @@ sys.path = new_path
 
 from galaxy import eggs
 import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson
 import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
 galaxy.model.Job()  # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
 from galaxy.util import stringify_dictionary_keys
@@ -107,17 +107,17 @@ def __main__():
                 dataset.extension = ext_override[ dataset.dataset.id ]
             # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
             if override_metadata:
-                override_metadata = simplejson.load( open( override_metadata ) )
+                override_metadata = json.load( open( override_metadata ) )
                 for metadata_name, metadata_file_override in override_metadata:
                     if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ):
                         metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override )
                     setattr( dataset.metadata, metadata_name, metadata_file_override )
-            kwds = stringify_dictionary_keys( simplejson.load( open( filename_kwds ) ) )  # load kwds; need to ensure our keywords are not unicode
+            kwds = stringify_dictionary_keys( json.load( open( filename_kwds ) ) )  # load kwds; need to ensure our keywords are not unicode
             dataset.datatype.set_meta( dataset, **kwds )
             dataset.metadata.to_JSON_dict( filename_out )  # write out results of set_meta
-            simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) )  # setting metadata has succeeded
+            json.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) )  # setting metadata has succeeded
         except Exception, e:
-            simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) )  # setting metadata has failed somehow
+            json.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) )  # setting metadata has failed somehow
     clear_mappers()
     # Shut down any additional threads that might have been created via the ObjectStore
     object_store.shutdown()