First pass removing to_json_string/from_json_string.

lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py

@@ -52,4 +52,4 @@ def main():
     FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
 
 if __name__ == "__main__":
-    main()
+    main()

lib/galaxy/datatypes/converters/fasta_to_len.py

@@ -49,4 +49,4 @@ def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word
     out.close()
 
 if __name__ == "__main__" :
-    compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True )
+    compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True )

lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py

@@ -40,4 +40,4 @@ def __main__():
         print >> out, "%s\t%s" %( fasta_title, sequence )
     out.close()
 
-if __name__ == "__main__" : __main__()
+if __name__ == "__main__" : __main__()

lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py

@@ -52,4 +52,4 @@ def __main__():
 
     outfile.close()
 
-if __name__ == "__main__": __main__()
+if __name__ == "__main__": __main__()

lib/galaxy/datatypes/converters/interval_to_coverage.py

@@ -149,4 +149,4 @@ if __name__ == "__main__":
                                      fix_strand=True )
     main( interval, coverage )
     temp_file.close()
-    coverage.close()
+    coverage.close()

lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py

@@ -26,4 +26,4 @@ def main():
     FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
 
 if __name__ == "__main__":
-    main()
+    main()

lib/galaxy/datatypes/tabular.py

@@ -14,7 +14,7 @@ from galaxy.datatypes import metadata
 from galaxy.datatypes.checkers import is_gzip
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import get_headers, get_test_fname
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 import dataproviders
 
 log = logging.getLogger(__name__)
@@ -272,7 +272,7 @@ class Tabular( data.Text ):
         while cursor and ck_data[-1] != '\n':
             ck_data += cursor
             cursor = f.read(1)
-        return to_json_string( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } )
+        return dumps( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } )
 
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
         preview = util.string_as_bool( preview )

lib/galaxy/datatypes/util/__init__.py

@@ -1,3 +1,3 @@
 """
 Utilities for Galaxy datatypes.
-"""
+"""

lib/galaxy/external_services/result_handlers/basic.py

@@ -1,4 +1,4 @@
-from galaxy.util.json import to_json_string, from_json_string
+from galaxy.util.json import dumps, loads
 from galaxy.util.template import fill_template
 import logging
 
@@ -44,7 +44,7 @@ class ExternalServiceActionJSONResultHandler( ExternalServiceActionResultHandler
     type = 'json_display'
 
     def handle_result( self, result, param_dict, trans ):
-        rval = from_json_string( result.content )
+        rval = loads( result.content )
         return trans.fill_template( '/external_services/generic_json.mako', result = rval, param_dict = param_dict, action=self.parent )
 
 class ExternalServiceActionJQueryGridResultHandler( ExternalServiceActionResultHandler ):
@@ -53,7 +53,7 @@ class ExternalServiceActionJQueryGridResultHandler( ExternalServiceActionResultH
     type = 'jquery_grid'
 
     def handle_result( self, result, param_dict, trans ):
-        rval = from_json_string( result.content )
+        rval = loads( result.content )
         return trans.fill_template( '/external_services/generic_jquery_grid.mako', result = rval, param_dict = param_dict, action=self.parent )
 
 result_type_to_class = {}

lib/galaxy/jobs/__init__.py

@@ -25,7 +25,7 @@ from galaxy.jobs.mapper import JobRunnerMapper
 from galaxy.jobs.runners import BaseJobRunner, JobState
 from galaxy.util.bunch import Bunch
 from galaxy.util.expressions import ExpressionContext
-from galaxy.util.json import from_json_string
+from galaxy.util.json import loads
 from galaxy.util import unicodify
 
 from .output_checker import check_output
@@ -723,7 +723,7 @@ class JobWrapper( object ):
         self.job_runner_mapper = JobRunnerMapper( self, queue.dispatcher.url_to_destination, self.app.job_config )
         self.params = None
         if job.params:
-            self.params = from_json_string( job.params )
+            self.params = loads( job.params )
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination( from_job=job )
 
@@ -1390,7 +1390,7 @@ class JobWrapper( object ):
         if os.path.exists( meta_file ):
             for line in open( meta_file, 'r' ):
                 try:
-                    line = from_json_string( line )
+                    line = loads( line )
                     assert 'type' in line
                 except:
                     log.exception( '(%s) Got JSON data from tool, but data is improperly formatted or no "type" key in data' % self.job_id )

lib/galaxy/jobs/actions/__init__.py

@@ -1,4 +1,4 @@
 """
 This package contains job action classes.
 
-"""
+"""

lib/galaxy/jobs/actions/post.py

@@ -5,7 +5,7 @@ Actions to be run at job completion.  Currently only used in workflows.
 import datetime
 import logging
 from galaxy.util import send_mail
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 
 log = logging.getLogger( __name__ )
 
@@ -461,7 +461,7 @@ class ActionBox(object):
             else:
                 # Not pja stuff.
                 pass
-        return to_json_string(npd)
+        return dumps(npd)
 
     @classmethod
     def get_add_list(cls):

lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py

@@ -83,7 +83,7 @@ class SMRTPortalPlugin( DataTransfer ):
                 return self.job_states.INVALID
             url = 'http://' + job.params[ 'smrt_host' ] + self.api_path + '/Jobs/' + job.params[ 'smrt_job_id' ] + '/Status'
             r = urllib2.urlopen( url )
-            status = json.from_json_string( r.read() )
+            status = json.loads( r.read() )
             # TODO: error handling: unexpected json or bad response, bad url, etc.
             if status[ 'Code' ] == 'Completed':
                 log.debug( "SMRT Portal job '%s' is Completed.  Initiating transfer." % job.params[ 'smrt_job_id' ] )

lib/galaxy/jobs/transfer_manager.py

@@ -82,7 +82,7 @@ class TransferManager( object ):
                     sock = socket.socket( socket.AF_INET, socket.SOCK_STREAM )
                     sock.settimeout( 5 )
                     sock.connect( ( 'localhost', tj.socket ) )
-                    sock.send( json.to_json_string( request ) )
+                    sock.send( json.dumps( request ) )
                     response = sock.recv( 8192 )
                     valid, response = json.validate_jsonrpc_response( response, id=request['id'] )
                     if not valid:

lib/galaxy/managers/context.py

@@ -4,7 +4,7 @@ Mixins for transaction-like objects.
 
 import os
 
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from galaxy.util import bunch
 
 class ProvidesAppContext( object ):
@@ -19,7 +19,7 @@ class ProvidesAppContext( object ):
         Application-level logging of user actions.
         """
         if self.app.config.log_actions:
-            action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) )
+            action = self.app.model.UserAction(action=action, context=context, params=unicode( dumps( params ) ) )
             try:
                 if user:
                     action.user = user

lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py

@@ -10,7 +10,7 @@ from migrate.changeset import *
 from sqlalchemy.exc import *
 
 from galaxy.model.custom_types import *
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow
@@ -62,7 +62,7 @@ def upgrade(migrate_engine):
     for r in result:
         sample_id = r[0]
         if r[1]:
-            dataset_files = from_json_string(r[1])
+            dataset_files = loads(r[1])
             for df in dataset_files:
                 if type(df) == type(dict()):
                     cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')"

lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py

@@ -6,7 +6,7 @@ from sqlalchemy import *
 from sqlalchemy.orm import *
 from migrate import *
 from migrate.changeset import *
-from galaxy.util.json import from_json_string
+from galaxy.util.json import loads
 
 import logging
 log = logging.getLogger( __name__ )
@@ -41,7 +41,7 @@ def upgrade(migrate_engine):
         viz_id = viz['viz_id']
         viz_rev_id = viz['viz_rev_id']
         if viz[Visualization_revision_table.c.config]:
-            dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'")
+            dbkey = loads(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'")
             migrate_engine.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id))
             migrate_engine.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id))
 

lib/galaxy/model/migrate/versions/0057_request_notify.py

@@ -10,7 +10,7 @@ from migrate.changeset import *
 from sqlalchemy.exc import *
 
 from galaxy.model.custom_types import *
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow
@@ -46,13 +46,13 @@ def upgrade(migrate_engine):
             id = int(r[0])
             notify_old = r[1]
             notify_new = dict(email=[], sample_states=[], body='', subject='')
-            cmd = "update request set notification='%s' where id=%i" % (to_json_string(notify_new), id)
+            cmd = "update request set notification='%s' where id=%i" % (dumps(notify_new), id)
             migrate_engine.execute( cmd )
 
         cmd = "SELECT id, notification FROM request"
         result = migrate_engine.execute( cmd )
         for r in result:
-            rr = from_json_string(str(r[1]))
+            rr = loads(str(r[1]))
 
         # remove the 'notify' column for non-sqlite databases.
         if migrate_engine.name != 'sqlite':

lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py

@@ -10,7 +10,7 @@ from migrate.changeset import *
 from sqlalchemy.exc import *
 
 from galaxy.model.custom_types import *
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow

lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py

@@ -9,7 +9,7 @@ from sqlalchemy.orm import *
 from migrate import *
 from migrate.changeset import *
 from sqlalchemy.exc import *
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 from galaxy.model.custom_types import _sniffnfix_pg9_hex
 
 import datetime
@@ -53,13 +53,13 @@ def upgrade(migrate_engine):
         fields = str( row[1] )
         if not fields.strip():
             continue
-        fields_list = from_json_string( _sniffnfix_pg9_hex( fields ) )
+        fields_list = loads( _sniffnfix_pg9_hex( fields ) )
         if len( fields_list ):
             for index, field in enumerate( fields_list ):
                 field[ 'name' ] = 'field_%i' % index
                 field[ 'helptext' ] = field[ 'helptext' ].replace("'", "''").replace('"', "")
                 field[ 'label' ] = field[ 'label' ].replace("'", "''")
-            fields_json = to_json_string( fields_list )
+            fields_json = dumps( fields_list )
             if migrate_engine.name == 'mysql':
                 cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( fields_json, form_definition_id )
             else:
@@ -76,16 +76,16 @@ def upgrade(migrate_engine):
         if not str( row[1] ).strip():
             continue
         row1 = str(row[1]).replace('\n', '').replace('\r', '')
-        values_list = from_json_string( str( row1 ).strip() )
+        values_list = loads( str( row1 ).strip() )
         if not str( row[2] ).strip():
             continue
-        fields_list = from_json_string( str( row[2] ).strip() )
+        fields_list = loads( str( row[2] ).strip() )
         if fields_list and type(values_list) == type(list()):
             values_dict = {}
             for field_index, field in enumerate( fields_list ):
                 field_name = field[ 'name' ]
                 values_dict[ field_name ] = get_value(values_list, field_index )
-            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( to_json_string( values_dict ), form_values_id )
+            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( dumps( values_dict ), form_values_id )
             migrate_engine.execute( cmd )
 
 def downgrade(migrate_engine):
@@ -110,17 +110,17 @@ def downgrade(migrate_engine):
         form_values_id = int( row[0] )
         if not str( row[1] ).strip():
             continue
-        values_dict = from_json_string( str( row[1] ) )
+        values_dict = loads( str( row[1] ) )
         if not str( row[2] ).strip():
             continue
-        fields_list = from_json_string( str( row[2] ) )
+        fields_list = loads( str( row[2] ) )
         if fields_list:
             values_list = []
             for field_index, field in enumerate( fields_list ):
                 field_name = field[ 'name' ]
                 field_value = values_dict[ field_name ]
                 values_list.append( field_value )
-            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( to_json_string( values_list ), form_values_id )
+            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( dumps( values_list ), form_values_id )
             migrate_engine.execute( cmd )
     # remove name attribute from the field column of the form_definition table
     cmd = "SELECT f.id, f.fields FROM form_definition AS f"
@@ -130,13 +130,13 @@ def downgrade(migrate_engine):
         fields = str( row[1] )
         if not fields.strip():
             continue
-        fields_list = from_json_string( _sniffnfix_pg9_hex( fields ) )
+        fields_list = loads( _sniffnfix_pg9_hex( fields ) )
         if len( fields_list ):
             for index, field in enumerate( fields_list ):
                 if field.has_key( 'name' ):
                     del field[ 'name' ]
             if migrate_engine.name == 'mysql':
-                cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( to_json_string( fields_list ), form_definition_id )
+                cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( dumps( fields_list ), form_definition_id )
             else:
-                cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" %( to_json_string( fields_list ), form_definition_id )
+                cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" %( dumps( fields_list ), form_definition_id )
         migrate_engine.execute( cmd )

lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py

@@ -13,7 +13,7 @@ from sqlalchemy.exc import *
 
 from galaxy.model.custom_types import *
 
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow
@@ -104,7 +104,7 @@ def create_sequencer_form_definition():
                                      'layout': 'none',
                                      'default': '' } )
     form_definition_type = 'Sequencer Information Form'
-    form_definition_layout = to_json_string('[]')
+    form_definition_layout = dumps('[]')
     cmd = "INSERT INTO form_definition VALUES ( %s, %s, %s, '%s', '%s', %s, '%s', '%s', '%s' )"
     cmd = cmd % ( nextval( 'form_definition' ),
                   localtimestamp(),
@@ -112,7 +112,7 @@ def create_sequencer_form_definition():
                   form_definition_name,
                   form_definition_desc,
                   form_definition_current_id,
-                  to_json_string( form_definition_fields ),
+                  dumps( form_definition_fields ),
                   form_definition_type,
                   form_definition_layout )
     migrate_engine.execute( cmd )
@@ -134,7 +134,7 @@ def get_sequencer_id( sequencer_info ):
         values = str( row[1] )
         if not values.strip():
             continue
-        values = from_json_string( values )
+        values = loads( values )
         # proceed only if sequencer_info is a valid list
         if values and type( values ) == type( dict() ):
             if sequencer_info.get( 'host', '' ) == values.get( 'field_0', '' ) \
@@ -148,7 +148,7 @@ def get_sequencer_id( sequencer_info ):
 def add_sequencer( sequencer_index, sequencer_form_definition_id, sequencer_info ):
     '''Adds a new sequencer to the sequencer table along with its form values.'''
     # Create a new form values record with the supplied sequencer information
-    values = to_json_string( { 'field_0': sequencer_info.get( 'host', '' ),
+    values = dumps( { 'field_0': sequencer_info.get( 'host', '' ),
                                'field_1': sequencer_info.get( 'username', '' ),
                                'field_2': sequencer_info.get( 'password', '' ),
                                'field_3': sequencer_info.get( 'data_dir', '' ),
@@ -233,7 +233,7 @@ def upgrade(migrate_engine):
             # skip if sequencer_info is empty
             if not sequencer_info.strip() or sequencer_info in ['None', 'null']:
                 continue
-            sequencer_info = from_json_string( sequencer_info.strip() )
+            sequencer_info = loads( sequencer_info.strip() )
             # proceed only if sequencer_info is a valid dict
             if sequencer_info and type( sequencer_info ) == type( dict() ):
                 # check if this sequencer has already been added to the sequencer table
@@ -277,9 +277,9 @@ def downgrade(migrate_engine):
         result = migrate_engine.execute( cmd )
         for row in result:
             request_type_id = row[0]
-            seq_values = from_json_string( str( row[1] ) )
+            seq_values = loads( str( row[1] ) )
             # create the datatx_info json dict
-            datatx_info = to_json_string( dict( host = seq_values.get( 'field_0', '' ),
+            datatx_info = dumps( dict( host = seq_values.get( 'field_0', '' ),
                                                 username = seq_values.get( 'field_1', '' ),
                                                 password = seq_values.get( 'field_2', '' ),
                                                 data_dir = seq_values.get( 'field_3', '' ),

lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py

@@ -15,7 +15,7 @@ from sqlalchemy.exc import *
 
 from galaxy.model.custom_types import *
 
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow

lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py

@@ -9,7 +9,7 @@ from migrate.changeset import *
 from sqlalchemy.exc import *
 import binascii
 
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import logging
 log = logging.getLogger( __name__ )
@@ -42,11 +42,11 @@ def upgrade(migrate_engine):
         # first check if loading the dict from the json succeeds
         # if that fails, it means that the content field is corrupted.
         try:
-            field_values_dict = from_json_string( _sniffnfix_pg9_hex( str( row['field_values'] ) ) )
+            field_values_dict = loads( _sniffnfix_pg9_hex( str( row['field_values'] ) ) )
         except Exception, e:
             corrupted_rows = corrupted_rows + 1
             # content field is corrupted
-            fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fdfields'] ) ) )
+            fields_list = loads( _sniffnfix_pg9_hex( str( row['fdfields'] ) ) )
             field_values_str = _sniffnfix_pg9_hex( str( row['field_values'] ) )
             try:
                 #Encoding errors?  Just to be safe.
@@ -85,7 +85,7 @@ def upgrade(migrate_engine):
                     # add to the new values dict
                     field_values_dict[ field['name'] ] = value
             # update the db
-            json_values = to_json_string(field_values_dict)
+            json_values = dumps(field_values_dict)
             cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( json_values, int( row['id'] ) )
             migrate_engine.execute( cmd )
             try:

lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py

@@ -12,7 +12,7 @@ now = datetime.datetime.utcnow
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import *
 from galaxy.model.custom_types import _sniffnfix_pg9_hex
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import sys, logging
 log = logging.getLogger( __name__ )
@@ -77,7 +77,7 @@ def upgrade(migrate_engine):
     for row in result:
         if row[1]:
             tool_shed_repository_id = row[0]
-            repository_metadata = from_json_string( _sniffnfix_pg9_hex( str( row[1] ) ) )
+            repository_metadata = loads( _sniffnfix_pg9_hex( str( row[1] ) ) )
             # Create a new row in the tool table for each tool included in repository.  We will NOT
             # handle tool_version_associaions because we do not have the information we need to do so.
             tools = repository_metadata.get( 'tools', [] )

lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py

@@ -22,4 +22,4 @@ def downgrade(migrate_engine):
     try:
         user.c.password.alter(type=String(40))
     except:
-        log.exception( "Altering password column failed" )
+        log.exception( "Altering password column failed" )

lib/galaxy/model/migrate/versions/0117_add_user_activation.py

@@ -54,4 +54,4 @@ def downgrade(migrate_engine):
         user_active.drop()
         user_activation_token.drop()
     except Exception, e:
-        log.debug( "Dropping 'active' and 'activation_token' columns from galaxy_user table failed: %s" % ( str( e ) ) )
+        log.debug( "Dropping 'active' and 'activation_token' columns from galaxy_user table failed: %s" % ( str( e ) ) )

lib/galaxy/model/orm/logging_connection_proxy.py

@@ -45,4 +45,4 @@ class TraceLoggerProxy(ConnectionProxy):
         self.trace_logger.log( "sqlalchemy_query",
             message="Query executed", statement=statement, parameters=parameters,
             executemany=executemany, duration=duration )
-        return rval
+        return rval

lib/galaxy/model/search.py

@@ -39,7 +39,7 @@ JobToInputLibraryDatasetAssociation, JobToInputDatasetAssociation, JobToOutputDa
 Page, PageRevision)
 from galaxy.model.tool_shed_install import ToolVersion
 
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from sqlalchemy import and_
 from sqlalchemy.orm import aliased
 
@@ -429,7 +429,7 @@ def job_param_filter(view, left, operator, right):
         and_(
             Job.id == alias.job_id,
             alias.name == param_name,
-            alias.value == to_json_string(right)
+            alias.value == dumps(right)
         )
     )
 

lib/galaxy/model/tool_shed_install/migrate/versions/0001_add_tool_shed_repository_table.py

@@ -1 +0,0 @@
-../../../migrate/versions/0082_add_tool_shed_repository_table.py

lib/galaxy/model/tool_shed_install/migrate/versions/0001_add_tool_shed_repository_table.py

@@ -0,0 +1,51 @@
+"""
+Migration script to add the tool_shed_repository table.
+"""
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+import sys, logging
+from galaxy.model.custom_types import *
+from sqlalchemy.exc import *
+import datetime
+now = datetime.datetime.utcnow
+
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+# New table to store information about cloned tool shed repositories.
+ToolShedRepository_table = Table( "tool_shed_repository", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "tool_shed", TrimmedString( 255 ), index=True ),
+    Column( "name", TrimmedString( 255 ), index=True ),
+    Column( "description" , TEXT ),
+    Column( "owner", TrimmedString( 255 ), index=True ),
+    Column( "changeset_revision", TrimmedString( 255 ), index=True ),
+    Column( "deleted", Boolean, index=True, default=False ) )
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    try:
+        ToolShedRepository_table.create()
+    except Exception, e:
+        log.debug( "Creating tool_shed_repository table failed: %s" % str( e ) )
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    try:
+        ToolShedRepository_table.drop()
+    except Exception, e:
+        log.debug( "Dropping tool_shed_repository table failed: %s" % str( e ) )

lib/galaxy/model/tool_shed_install/migrate/versions/0002_add_tool_shed_repository_table_columns.py

@@ -1 +0,0 @@
-../../../migrate/versions/0086_add_tool_shed_repository_table_columns.py

lib/galaxy/model/tool_shed_install/migrate/versions/0002_add_tool_shed_repository_table_columns.py

@@ -0,0 +1,79 @@
+"""
+Migration script to add the metadata, update_available and includes_datatypes columns to the tool_shed_repository table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+def get_default_false(migrate_engine):
+    if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        return "0"
+    elif migrate_engine.name in ['postgresql', 'postgres']:
+        return "false"
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    c = Column( "metadata", JSONType(), nullable=True )
+    try:
+        c.create( ToolShedRepository_table )
+        assert c is ToolShedRepository_table.c.metadata
+    except Exception, e:
+        print "Adding metadata column to the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Adding metadata column to the tool_shed_repository table failed: %s" % str( e ) )
+    c = Column( "includes_datatypes", Boolean, index=True, default=False )
+    try:
+        c.create( ToolShedRepository_table, index_name="ix_tool_shed_repository_includes_datatypes")
+        assert c is ToolShedRepository_table.c.includes_datatypes
+        migrate_engine.execute( "UPDATE tool_shed_repository SET includes_datatypes=%s" % get_default_false(migrate_engine))
+    except Exception, e:
+        print "Adding includes_datatypes column to the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Adding includes_datatypes column to the tool_shed_repository table failed: %s" % str( e ) )
+    c = Column( "update_available", Boolean, default=False )
+    try:
+        c.create( ToolShedRepository_table )
+        assert c is ToolShedRepository_table.c.update_available
+        migrate_engine.execute( "UPDATE tool_shed_repository SET update_available=%s" % get_default_false(migrate_engine))
+    except Exception, e:
+        print "Adding update_available column to the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Adding update_available column to the tool_shed_repository table failed: %s" % str( e ) )
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    try:
+        ToolShedRepository_table.c.metadata.drop()
+    except Exception, e:
+        print "Dropping column metadata from the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Dropping column metadata from the tool_shed_repository table failed: %s" % str( e ) )
+    try:
+        ToolShedRepository_table.c.includes_datatypes.drop()
+    except Exception, e:
+        print "Dropping column includes_datatypes from the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Dropping column includes_datatypes from the tool_shed_repository table failed: %s" % str( e ) )
+    try:
+        ToolShedRepository_table.c.update_available.drop()
+    except Exception, e:
+        print "Dropping column update_available from the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Dropping column update_available from the tool_shed_repository table failed: %s" % str( e ) )

lib/galaxy/model/tool_shed_install/migrate/versions/0003_tool_id_guid_map_table.py

@@ -1 +0,0 @@
-../../../migrate/versions/0087_tool_id_guid_map_table.py

lib/galaxy/model/tool_shed_install/migrate/versions/0003_tool_id_guid_map_table.py

@@ -0,0 +1,52 @@
+"""
+Migration script to create the tool_id_guid_map table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+ToolIdGuidMap_table = Table( "tool_id_guid_map", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "tool_id", String( 255 ) ),
+    Column( "tool_version", TEXT ),
+    Column( "tool_shed", TrimmedString( 255 ) ),
+    Column( "repository_owner", TrimmedString( 255 ) ),
+    Column( "repository_name", TrimmedString( 255 ) ),
+    Column( "guid", TEXT, index=True, unique=True ) )
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    try:
+        ToolIdGuidMap_table.create()
+    except Exception, e:
+        log.debug( "Creating tool_id_guid_map table failed: %s" % str( e ) )
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    try:
+        ToolIdGuidMap_table.drop()
+    except Exception, e:
+        log.debug( "Dropping tool_id_guid_map table failed: %s" % str( e ) )

lib/galaxy/model/tool_shed_install/migrate/versions/0004_add_installed_changeset_revison_column.py

@@ -1 +0,0 @@
-../../../migrate/versions/0088_add_installed_changeset_revison_column.py

lib/galaxy/model/tool_shed_install/migrate/versions/0004_add_installed_changeset_revison_column.py

@@ -0,0 +1,64 @@
+"""
+Migration script to add the installed_changeset_revision column to the tool_shed_repository table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    col = Column( "installed_changeset_revision", TrimmedString( 255 ) )
+    try:
+        col.create( ToolShedRepository_table )
+        assert col is ToolShedRepository_table.c.installed_changeset_revision
+    except Exception, e:
+        print "Adding installed_changeset_revision column to the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Adding installed_changeset_revision column to the tool_shed_repository table failed: %s" % str( e ) )
+    # Update each row by setting the value of installed_changeset_revison to be the value of changeset_revision.
+    # This will be problematic if the value of changeset_revision was updated to something other than the value
+    # that it was when the repository was installed (because the install path determined in real time will attempt to
+    # find the repository using the updated changeset_revison instead of the required installed_changeset_revision),
+    # but at the time this script was written, this scenario is extremely unlikely.
+    cmd = "SELECT id AS id, " \
+        + "installed_changeset_revision AS installed_changeset_revision, " \
+        + "changeset_revision AS changeset_revision " \
+        + "FROM tool_shed_repository;"
+    tool_shed_repositories = migrate_engine.execute( cmd ).fetchall()
+    update_count = 0
+    for row in tool_shed_repositories:
+        cmd = "UPDATE tool_shed_repository " \
+            + "SET installed_changeset_revision = '%s' "  % row.changeset_revision \
+            + "WHERE changeset_revision = '%s';" % row.changeset_revision
+        migrate_engine.execute( cmd )
+        update_count += 1
+    print "Updated the installed_changeset_revision column for ", update_count, " rows in the tool_shed_repository table.  "
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    try:
+        ToolShedRepository_table.c.installed_changeset_revision.drop()
+    except Exception, e:
+        print "Dropping column installed_changeset_revision from the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Dropping column installed_changeset_revision from the tool_shed_repository table failed: %s" % str( e ) )

lib/galaxy/model/tool_shed_install/migrate/versions/0005_add_tool_shed_repository_table_columns.py

@@ -1 +0,0 @@
-../../../migrate/versions/0090_add_tool_shed_repository_table_columns.py

lib/galaxy/model/tool_shed_install/migrate/versions/0005_add_tool_shed_repository_table_columns.py

@@ -0,0 +1,63 @@
+"""
+Migration script to add the uninstalled and dist_to_shed columns to the tool_shed_repository table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+def default_false(migrate_engine):
+    if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        return "0"
+    elif migrate_engine.name in ['postgresql', 'postgres']:
+        return "false"
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    c = Column( "uninstalled", Boolean, default=False )
+    try:
+        c.create( ToolShedRepository_table )
+        assert c is ToolShedRepository_table.c.uninstalled
+        migrate_engine.execute( "UPDATE tool_shed_repository SET uninstalled=%s" % default_false(migrate_engine) )
+    except Exception, e:
+        print "Adding uninstalled column to the tool_shed_repository table failed: %s" % str( e )
+    c = Column( "dist_to_shed", Boolean, default=False )
+    try:
+        c.create( ToolShedRepository_table )
+        assert c is ToolShedRepository_table.c.dist_to_shed
+        migrate_engine.execute( "UPDATE tool_shed_repository SET dist_to_shed=%s" % default_false(migrate_engine) )
+    except Exception, e:
+        print "Adding dist_to_shed column to the tool_shed_repository table failed: %s" % str( e )
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    try:
+        ToolShedRepository_table.c.uninstalled.drop()
+    except Exception, e:
+        print "Dropping column uninstalled from the tool_shed_repository table failed: %s" % str( e )
+    try:
+        ToolShedRepository_table.c.dist_to_shed.drop()
+    except Exception, e:
+        print "Dropping column dist_to_shed from the tool_shed_repository table failed: %s" % str( e )

lib/galaxy/model/tool_shed_install/migrate/versions/0006_add_tool_version_tables.py

@@ -1 +0,0 @@
-../../../migrate/versions/0091_add_tool_version_tables.py

lib/galaxy/model/tool_shed_install/migrate/versions/0006_add_tool_version_tables.py

@@ -0,0 +1,122 @@
+"""
+Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+from galaxy.model.custom_types import _sniffnfix_pg9_hex
+from galaxy.util.json import loads, dumps
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+#migrate_engine = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def nextval( table, col='id' ):
+    if migrate_engine.name == 'postgres':
+        return "nextval('%s_%s_seq')" % ( table, col )
+    elif migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        return "null"
+    else:
+        raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name )
+
+def localtimestamp():
+   if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql':
+       return "LOCALTIMESTAMP"
+   elif migrate_engine.name == 'sqlite':
+       return "current_date || ' ' || current_time"
+   else:
+       raise Exception( 'Unable to convert data for unknown database type: %s' % db )
+
+ToolVersion_table = Table( "tool_version", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "tool_id", String( 255 ) ),
+    Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=True ) )
+
+ToolVersionAssociation_table = Table( "tool_version_association", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "tool_id", Integer, ForeignKey( "tool_version.id" ), index=True, nullable=False ),
+    Column( "parent_id", Integer, ForeignKey( "tool_version.id" ), index=True, nullable=False ) )
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+
+    ToolIdGuidMap_table = Table( "tool_id_guid_map", metadata, autoload=True )
+
+    metadata.reflect()
+    # Create the tables.
+    try:
+        ToolVersion_table.create()
+    except Exception, e:
+        log.debug( "Creating tool_version table failed: %s" % str( e ) )
+    try:
+        ToolVersionAssociation_table.create()
+    except Exception, e:
+        log.debug( "Creating tool_version_association table failed: %s" % str( e ) )
+    # Populate the tool table with tools included in installed tool shed repositories.
+    cmd = "SELECT id, metadata FROM tool_shed_repository"
+    result = migrate_engine.execute( cmd )
+    count = 0
+    for row in result:
+        if row[1]:
+            tool_shed_repository_id = row[0]
+            repository_metadata = loads( _sniffnfix_pg9_hex( str( row[1] ) ) )
+            # Create a new row in the tool table for each tool included in repository.  We will NOT
+            # handle tool_version_associaions because we do not have the information we need to do so.
+            tools = repository_metadata.get( 'tools', [] )
+            for tool_dict in tools:
+                cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" % \
+                    ( nextval( 'tool_version' ), localtimestamp(), localtimestamp(), tool_dict[ 'guid' ], tool_shed_repository_id )
+                migrate_engine.execute( cmd )
+                count += 1
+    print "Added %d rows to the new tool_version table." % count
+    # Drop the tool_id_guid_map table since the 2 new tables render it unnecessary.
+    try:
+        ToolIdGuidMap_table.drop()
+    except Exception, e:
+        log.debug( "Dropping tool_id_guid_map table failed: %s" % str( e ) )
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+
+    ToolIdGuidMap_table = Table( "tool_id_guid_map", metadata,
+        Column( "id", Integer, primary_key=True ),
+        Column( "create_time", DateTime, default=now ),
+        Column( "update_time", DateTime, default=now, onupdate=now ),
+        Column( "tool_id", String( 255 ) ),
+        Column( "tool_version", TEXT ),
+        Column( "tool_shed", TrimmedString( 255 ) ),
+        Column( "repository_owner", TrimmedString( 255 ) ),
+        Column( "repository_name", TrimmedString( 255 ) ),
+        Column( "guid", TEXT, index=True, unique=True ) )
+
+    metadata.reflect()
+    try:
+        ToolVersionAssociation_table.drop()
+    except Exception, e:
+        log.debug( "Dropping tool_version_association table failed: %s" % str( e ) )
+    try:
+        ToolVersion_table.drop()
+    except Exception, e:
+        log.debug( "Dropping tool_version table failed: %s" % str( e ) )
+    try:
+        ToolIdGuidMap_table.create()
+    except Exception, e:
+        log.debug( "Creating tool_id_guid_map table failed: %s" % str( e ) )

lib/galaxy/model/tool_shed_install/migrate/versions/0007_add_migrate_tools_table.py

@@ -1 +0,0 @@
-../../../migrate/versions/0092_add_migrate_tools_table.py

lib/galaxy/model/tool_shed_install/migrate/versions/0007_add_migrate_tools_table.py

@@ -0,0 +1,50 @@
+"""
+Migration script to create the migrate_tools table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+MigrateTools_table = Table( "migrate_tools", metadata,
+    Column( "repository_id", TrimmedString( 255 ) ),
+    Column( "repository_path", TEXT ),
+    Column( "version", Integer ) )
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+
+    metadata.reflect()
+    # Create the table.
+    try:
+        MigrateTools_table.create()
+        cmd = "INSERT INTO migrate_tools VALUES ('GalaxyTools', 'lib/galaxy/tool_shed/migrate', %d)" % 1
+        migrate_engine.execute( cmd )
+    except Exception, e:
+        log.debug( "Creating migrate_tools table failed: %s" % str( e ) )
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    try:
+        MigrateTools_table.drop()
+    except Exception, e:
+        log.debug( "Dropping migrate_tools table failed: %s" % str( e ) )

lib/galaxy/model/tool_shed_install/migrate/versions/0008_add_ctx_rev_column.py

@@ -1 +0,0 @@
-../../../migrate/versions/0097_add_ctx_rev_column.py

lib/galaxy/model/tool_shed_install/migrate/versions/0008_add_ctx_rev_column.py

@@ -0,0 +1,44 @@
+"""
+Migration script to add the ctx_rev column to the tool_shed_repository table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    col = Column( "ctx_rev", TrimmedString( 10 ) )
+    try:
+        col.create( ToolShedRepository_table )
+        assert col is ToolShedRepository_table.c.ctx_rev
+    except Exception, e:
+        print "Adding ctx_rev column to the tool_shed_repository table failed: %s" % str( e )
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    try:
+        ToolShedRepository_table.c.ctx_rev.drop()
+    except Exception, e:
+        print "Dropping column ctx_rev from the tool_shed_repository table failed: %s" % str( e )

lib/galaxy/model/tool_shed_install/migrate/versions/0009_add_tool_dependency_table.py

@@ -1 +0,0 @@
-../../../migrate/versions/0099_add_tool_dependency_table.py

lib/galaxy/model/tool_shed_install/migrate/versions/0009_add_tool_dependency_table.py

@@ -0,0 +1,51 @@
+"""
+Migration script to add the tool_dependency table.
+"""
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+import sys, logging
+from galaxy.model.custom_types import *
+from sqlalchemy.exc import *
+import datetime
+now = datetime.datetime.utcnow
+
+log = logging.getLogger( __name__ )
+log.setLevel( logging.DEBUG )
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+# New table to store information about cloned tool shed repositories.
+ToolDependency_table = Table( "tool_dependency", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=False ),
+    Column( "installed_changeset_revision", TrimmedString( 255 ) ),
+    Column( "name", TrimmedString( 255 ) ),
+    Column( "version", TrimmedString( 40 ) ),
+    Column( "type", TrimmedString( 40 ) ),
+    Column( "uninstalled", Boolean, default=False ) )
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    try:
+        ToolDependency_table.create()
+    except Exception, e:
+        log.debug( "Creating tool_dependency table failed: %s" % str( e ) )
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    try:
+        ToolDependency_table.drop()
+    except Exception, e:
+        log.debug( "Dropping tool_dependency table failed: %s" % str( e ) )

lib/galaxy/model/tool_shed_install/migrate/versions/0010_alter_tool_dependency_table_version_column.py

@@ -1 +0,0 @@
-../../../migrate/versions/0100_alter_tool_dependency_table_version_column.py

lib/galaxy/model/tool_shed_install/migrate/versions/0010_alter_tool_dependency_table_version_column.py

@@ -0,0 +1,54 @@
+"""
+Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
+    # Change the tool_dependency table's version column from TrimmedString to Text.
+    if migrate_engine.name in ['postgresql', 'postgres']:
+        cmd = "ALTER TABLE tool_dependency ALTER COLUMN version TYPE Text;"
+    elif migrate_engine.name == 'mysql':
+        cmd = "ALTER TABLE tool_dependency MODIFY COLUMN version Text;"
+    else:
+        # We don't have to do anything for sqlite tables.  From the sqlite documentation at http://sqlite.org/datatype3.html:
+        # 1.0 Storage Classes and Datatypes
+        # Each value stored in an SQLite database (or manipulated by the database engine) has one of the following storage classes:
+        # NULL. The value is a NULL value.
+        # INTEGER. The value is a signed integer, stored in 1, 2, 3, 4, 6, or 8 bytes depending on the magnitude of the value.
+        # REAL. The value is a floating point value, stored as an 8-byte IEEE floating point number.
+        # TEXT. The value is a text string, stored using the database encoding (UTF-8, UTF-16BE or UTF-16LE).
+        # BLOB. The value is a blob of data, stored exactly as it was input.
+        cmd = None
+    if cmd:
+        try:
+            migrate_engine.execute( cmd )
+        except Exception, e:
+            log.debug( "Altering tool_dependency.version column from TrimmedString(40) to Text failed: %s" % str( e ) )
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    # Not necessary to change column type Text to TrimmedString(40).
+    pass

lib/galaxy/model/tool_shed_install/migrate/versions/0011_drop_installed_changeset_revision_column.py

@@ -1 +0,0 @@
-../../../migrate/versions/0101_drop_installed_changeset_revision_column.py

lib/galaxy/model/tool_shed_install/migrate/versions/0011_drop_installed_changeset_revision_column.py

@@ -0,0 +1,41 @@
+"""
+Migration script to drop the installed_changeset_revision column from the tool_dependency table.
+"""
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+import sys, logging
+from galaxy.model.custom_types import *
+from sqlalchemy.exc import *
+import datetime
+now = datetime.datetime.utcnow
+
+log = logging.getLogger( __name__ )
+log.setLevel( logging.DEBUG )
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    try:
+        ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
+    except NoSuchTableError:
+        ToolDependency_table = None
+        log.debug( "Failed loading table tool_dependency" )
+    if ToolDependency_table is not None:
+        try:
+            col = ToolDependency_table.c.installed_changeset_revision
+            col.drop()
+        except Exception, e:
+            log.debug( "Dropping column 'installed_changeset_revision' from tool_dependency table failed: %s" % ( str( e ) ) )
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    pass

lib/galaxy/model/tool_shed_install/migrate/versions/0012_add_tool_dependency_status_columns.py

@@ -1 +0,0 @@
-../../../migrate/versions/0102_add_tool_dependency_status_columns.py

lib/galaxy/model/tool_shed_install/migrate/versions/0012_add_tool_dependency_status_columns.py

@@ -0,0 +1,71 @@
+"""
+Migration script to add status and error_message columns to the tool_dependency table and drop the uninstalled column from the tool_dependency table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
+    if migrate_engine.name == 'sqlite':
+        col = Column( "status", TrimmedString( 255 ))
+    else:
+        col = Column( "status", TrimmedString( 255 ), nullable=False)
+    try:
+        col.create( ToolDependency_table )
+        assert col is ToolDependency_table.c.status
+    except Exception, e:
+        print "Adding status column to the tool_dependency table failed: %s" % str( e )
+    col = Column( "error_message", TEXT )
+    try:
+        col.create( ToolDependency_table )
+        assert col is ToolDependency_table.c.error_message
+    except Exception, e:
+        print "Adding error_message column to the tool_dependency table failed: %s" % str( e )
+
+    if migrate_engine.name != 'sqlite':
+        #This breaks in sqlite due to failure to drop check constraint.
+        # TODO move to alembic.
+        try:
+            ToolDependency_table.c.uninstalled.drop()
+        except Exception, e:
+            print "Dropping uninstalled column from the tool_dependency table failed: %s" % str( e )
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
+    try:
+        ToolDependency_table.c.status.drop()
+    except Exception, e:
+        print "Dropping column status from the tool_dependency table failed: %s" % str( e )
+    try:
+        ToolDependency_table.c.error_message.drop()
+    except Exception, e:
+        print "Dropping column error_message from the tool_dependency table failed: %s" % str( e )
+    col = Column( "uninstalled", Boolean, default=False )
+    try:
+        col.create( ToolDependency_table )
+        assert col is ToolDependency_table.c.uninstalled
+    except Exception, e:
+        print "Adding uninstalled column to the tool_dependency table failed: %s" % str( e )

lib/galaxy/model/tool_shed_install/migrate/versions/0013_add_tool_shed_repository_status_columns.py

@@ -1 +0,0 @@
-../../../migrate/versions/0103_add_tool_shed_repository_status_columns.py

lib/galaxy/model/tool_shed_install/migrate/versions/0013_add_tool_shed_repository_status_columns.py

@@ -0,0 +1,69 @@
+"""Migration script to add status and error_message columns to the tool_shed_repository table."""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+metadata = MetaData()
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    # Add the status column to the tool_shed_repository table.
+    col = Column( "status", TrimmedString( 255 ) )
+    try:
+        col.create( ToolShedRepository_table )
+        assert col is ToolShedRepository_table.c.status
+    except Exception, e:
+        print "Adding status column to the tool_shed_repository table failed: %s" % str( e )
+    # Add the error_message column to the tool_shed_repository table.
+    col = Column( "error_message", TEXT )
+    try:
+        col.create( ToolShedRepository_table )
+        assert col is ToolShedRepository_table.c.error_message
+    except Exception, e:
+        print "Adding error_message column to the tool_shed_repository table failed: %s" % str( e )
+    # Update the status column value for tool_shed_repositories to the default value 'Installed'.
+    cmd = "UPDATE tool_shed_repository SET status = 'Installed';"
+    try:
+        migrate_engine.execute( cmd )
+    except Exception, e:
+        print "Exception executing sql command: "
+        print cmd
+        print str( e )
+    # Update the status column for tool_shed_repositories that have been uninstalled.
+    cmd = "UPDATE tool_shed_repository SET status = 'Uninstalled' WHERE uninstalled;"
+    try:
+        migrate_engine.execute( cmd )
+    except Exception, e:
+        print "Exception executing sql command: "
+        print cmd
+        print str( e )
+    # Update the status column for tool_shed_repositories that have been deactivated.
+    cmd = "UPDATE tool_shed_repository SET status = 'Deactivated' where deleted and not uninstalled;"
+    try:
+        migrate_engine.execute( cmd )
+    except Exception, e:
+        print "Exception executing sql command: "
+        print cmd
+        print str( e )
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    try:
+        ToolShedRepository_table.c.status.drop()
+    except Exception, e:
+        print "Dropping column status from the tool_shed_repository table failed: %s" % str( e )
+    try:
+        ToolShedRepository_table.c.error_message.drop()
+    except Exception, e:
+        print "Dropping column error_message from the tool_shed_repository table failed: %s" % str( e )

lib/galaxy/model/tool_shed_install/migrate/versions/0014_add_repository_dependency_tables.py

@@ -1 +0,0 @@
-../../../migrate/versions/0109_add_repository_dependency_tables.py

lib/galaxy/model/tool_shed_install/migrate/versions/0014_add_repository_dependency_tables.py

@@ -0,0 +1,60 @@
+"""
+Migration script to add the repository_dependency and repository_repository_dependency_association tables.
+"""
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+import sys, logging
+from galaxy.model.custom_types import *
+from sqlalchemy.exc import *
+import datetime
+now = datetime.datetime.utcnow
+
+log = logging.getLogger( __name__ )
+log.setLevel( logging.DEBUG )
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+RepositoryDependency_table = Table( "repository_dependency", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=False ) )
+
+RepositoryRepositoryDependencyAssociation_table = Table( "repository_repository_dependency_association", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True ),
+    Column( "repository_dependency_id", Integer, ForeignKey( "repository_dependency.id" ), index=True ) )
+
+def upgrade(migrate_engine):
+    print __doc__
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    try:
+        RepositoryDependency_table.create()
+    except Exception, e:
+        log.debug( "Creating repository_dependency table failed: %s" % str( e ) )
+    try:
+        RepositoryRepositoryDependencyAssociation_table.create()
+    except Exception, e:
+        log.debug( "Creating repository_repository_dependency_association table failed: %s" % str( e ) )
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    try:
+        RepositoryRepositoryDependencyAssociation_table.drop()
+    except Exception, e:
+        log.debug( "Dropping repository_repository_dependency_association table failed: %s" % str( e ) )
+    try:
+        RepositoryDependency_table.drop()
+    except Exception, e:
+        log.debug( "Dropping repository_dependency table failed: %s" % str( e ) )

lib/galaxy/model/tool_shed_install/migrate/versions/0015_update_migrate_tools_table.py

@@ -1 +0,0 @@
-../../../migrate/versions/0113_update_migrate_tools_table.py

lib/galaxy/model/tool_shed_install/migrate/versions/0015_update_migrate_tools_table.py

@@ -0,0 +1,38 @@
+"""
+Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+def upgrade(migrate_engine):
+    print __doc__
+    # Create the table.
+    try:
+        cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';"
+        migrate_engine.execute( cmd )
+    except Exception, e:
+        log.debug( "Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed: %s" % str( e ) )
+
+def downgrade(migrate_engine):
+    try:
+        cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';"
+        migrate_engine.execute( cmd )
+    except Exception, e:
+        log.debug( "Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed: %s" % str( e ) )

lib/galaxy/model/tool_shed_install/migrate/versions/0016_update_migrate_tools_table_again.py

@@ -1 +0,0 @@
-../../../migrate/versions/0114_update_migrate_tools_table_again.py

lib/galaxy/model/tool_shed_install/migrate/versions/0016_update_migrate_tools_table_again.py

@@ -0,0 +1,40 @@
+"""
+Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+
+def upgrade(migrate_engine):
+    print __doc__
+    # Create the table.
+    try:
+        cmd = "UPDATE migrate_tools set repository_path='lib/tool_shed/galaxy_install/migrate';"
+        migrate_engine.execute( cmd )
+    except Exception, e:
+        log.debug( "Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed: %s" % str( e ) )
+
+def downgrade(migrate_engine):
+    try:
+        cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';"
+        migrate_engine.execute( cmd )
+    except Exception, e:
+        log.debug( "Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed: %s" % str( e ) )
+

lib/galaxy/model/tool_shed_install/migrate/versions/0017_drop_update_available_col_add_tool_shed_status_col.py

@@ -1 +0,0 @@
-../../../migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py

lib/galaxy/model/tool_shed_install/migrate/versions/0017_drop_update_available_col_add_tool_shed_status_col.py

@@ -0,0 +1,77 @@
+"""
+Migration script to drop the update_available Boolean column and replace it with the tool_shed_status JSONType column in the tool_shed_repository table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+import sys, logging
+from galaxy.model.custom_types import *
+from sqlalchemy.exc import *
+import datetime
+now = datetime.datetime.utcnow
+
+log = logging.getLogger( __name__ )
+log.setLevel( logging.DEBUG )
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData()
+
+def default_false( migrate_engine ):
+    if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        return "0"
+    elif migrate_engine.name in [ 'postgresql', 'postgres' ]:
+        return "false"
+
+def upgrade( migrate_engine ):
+    metadata.bind = migrate_engine
+    print __doc__
+    metadata.reflect()
+    try:
+        ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    except NoSuchTableError:
+        ToolShedRepository_table = None
+        log.debug( "Failed loading table tool_shed_repository" )
+    if ToolShedRepository_table is not None:
+        # For some unknown reason it is no longer possible to drop a column in a migration script if using the sqlite database.
+        if migrate_engine.name != 'sqlite':
+            try:
+                col = ToolShedRepository_table.c.update_available
+                col.drop()
+            except Exception, e:
+                print "Dropping column update_available from the tool_shed_repository table failed: %s" % str( e )
+        c = Column( "tool_shed_status", JSONType, nullable=True )
+        try:
+            c.create( ToolShedRepository_table )
+            assert c is ToolShedRepository_table.c.tool_shed_status
+        except Exception, e:
+            print "Adding tool_shed_status column to the tool_shed_repository table failed: %s" % str( e )
+
+def downgrade( migrate_engine ):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    try:
+        ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    except NoSuchTableError:
+        ToolShedRepository_table = None
+        log.debug( "Failed loading table tool_shed_repository" )
+    if ToolShedRepository_table is not None:
+        # For some unknown reason it is no longer possible to drop a column in a migration script if using the sqlite database.
+        if migrate_engine.name != 'sqlite':
+            try:
+                col = ToolShedRepository_table.c.tool_shed_status
+                col.drop()
+            except Exception, e:
+                print "Dropping column tool_shed_status from the tool_shed_repository table failed: %s" % str( e )
+            c = Column( "update_available", Boolean, default=False )
+            try:
+                c.create( ToolShedRepository_table )
+                assert c is ToolShedRepository_table.c.update_available
+                migrate_engine.execute( "UPDATE tool_shed_repository SET update_available=%s" % default_false( migrate_engine ) )
+            except Exception, e:
+                print "Adding column update_available to the tool_shed_repository table failed: %s" % str( e )

lib/galaxy/openid/__init__.py

@@ -1,3 +1,3 @@
 """
 OpenID functionality
-"""
+"""

lib/galaxy/tools/actions/__init__.py

@@ -4,7 +4,7 @@ from galaxy import model
 from galaxy.tools.parameters import DataToolParameter
 from galaxy.tools.parameters import DataCollectionToolParameter
 from galaxy.tools.parameters.wrapped import WrappedParameters
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from galaxy.util.none_like import NoneDataset
 from galaxy.util.odict import odict
 from galaxy.util.template import fill_template
@@ -324,7 +324,7 @@ class DefaultToolAction( object ):
             job.add_output_dataset( name, dataset )
         job.object_store_id = object_store_populator.object_store_id
         if job_params:
-            job.params = to_json_string( job_params )
+            job.params = dumps( job_params )
         job.set_handler(tool.get_job_handler(job_params))
         trans.sa_session.add( job )
         # Now that we have a job id, we can remap any outputs if this is a rerun and the user chose to continue dependent jobs

lib/galaxy/tools/actions/metadata.py

@@ -1,7 +1,7 @@
 from __init__ import ToolAction
 from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
 from galaxy.util.odict import odict
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 
 import logging
 log = logging.getLogger( __name__ )
@@ -50,7 +50,7 @@ class SetMetadataToolAction( ToolAction ):
         if user:
             job.user_id = user.id
         if job_params:
-            job.params = to_json_string( job_params )
+            job.params = dumps( job_params )
         start_job_state = job.state #should be job.states.NEW
         try:
             # For backward compatibility, some tools may not have versions yet.

lib/galaxy/tools/actions/upload_common.py

@@ -7,7 +7,7 @@ from cgi import FieldStorage
 from galaxy import datatypes, util
 from galaxy.util.odict import odict
 from galaxy.datatypes import sniff
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from galaxy.model.orm import eagerload_all
 from galaxy.exceptions import ObjectInvalid
 
@@ -342,7 +342,7 @@ def create_paramfile( trans, uploaded_datasets ):
             # user cannot remove it unless the parent directory is writable.
             if link_data_only == 'copy_files' and trans.app.config.external_chown_script:
                 _chown( uploaded_dataset.path )
-        json_file.write( to_json_string( json ) + '\n' )
+        json_file.write( dumps( json ) + '\n' )
     json_file.close()
     if trans.app.config.external_chown_script:
         _chown( json_file_path )
@@ -375,7 +375,7 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None, his
 
     for name, value in tool.params_to_strings( params, trans.app ).iteritems():
         job.add_parameter( name, value )
-    job.add_parameter( 'paramfile', to_json_string( json_file_path ) )
+    job.add_parameter( 'paramfile', dumps( json_file_path ) )
     object_store_id = None
     for i, dataset in enumerate( data_list ):
         if folder:

lib/galaxy/tools/imp_exp/__init__.py

@@ -8,7 +8,7 @@ from galaxy import model
 from galaxy.tools.parameters.basic import UnvalidatedValue
 from galaxy.web.framework.helpers import to_unicode
 from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 from galaxy.web.base.controller import UsesHistoryMixin
 
 log = logging.getLogger(__name__)
@@ -108,7 +108,7 @@ class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
                 #
                 history_attr_file_name = os.path.join( archive_dir, 'history_attrs.txt')
                 history_attr_str = read_file_contents( history_attr_file_name )
-                history_attrs = from_json_string( history_attr_str )
+                history_attrs = loads( history_attr_str )
 
                 # Create history.
                 new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), \
@@ -134,12 +134,12 @@ class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
                 #
                 datasets_attrs_file_name = os.path.join( archive_dir, 'datasets_attrs.txt')
                 datasets_attr_str = read_file_contents( datasets_attrs_file_name )
-                datasets_attrs = from_json_string( datasets_attr_str )
-                
+                datasets_attrs = loads( datasets_attr_str )
+
                 if os.path.exists( datasets_attrs_file_name + ".provenance" ):
                     provenance_attr_str = read_file_contents( datasets_attrs_file_name + ".provenance" )
-                    provenance_attrs = from_json_string( provenance_attr_str )
-                    datasets_attrs += provenance_attrs                    
+                    provenance_attrs = loads( provenance_attr_str )
+                    datasets_attrs += provenance_attrs
 
                 # Get counts of how often each dataset file is used; a file can
                 # be linked to multiple dataset objects (HDAs).
@@ -230,7 +230,7 @@ class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
                             return self.sa_session.query( model.HistoryDatasetAssociation ) \
                                             .filter_by( history=new_history, hid=obj_dct['hid'] ).first()
                     return obj_dct
-                jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda )
+                jobs_attrs = loads( jobs_attr_str, object_hook=as_hda )
 
                 # Create each job.
                 for job_attrs in jobs_attrs:
@@ -279,7 +279,7 @@ class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
                                             .filter_by( history=new_history, hid=value.hid ).first()
                             value = input_hda.id
                         #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id )
-                        imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) )
+                        imported_job.add_parameter( name, dumps( value, cls=HistoryDatasetAssociationIDEncoder ) )
 
                     # TODO: Connect jobs to input datasets.
 
@@ -292,14 +292,14 @@ class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
                             imported_job.add_output_dataset( output_hda.name, output_hda )
 
                     # Connect jobs to input datasets.
-                    if 'input_mapping' in job_attrs: 
+                    if 'input_mapping' in job_attrs:
                         for input_name, input_hid in job_attrs[ 'input_mapping' ].items():
                             #print "%s job has input dataset %i" % (imported_job.id, input_hid)
                             input_hda = self.sa_session.query( model.HistoryDatasetAssociation ) \
                                             .filter_by( history=new_history, hid=input_hid ).first()
                             if input_hda:
                                 imported_job.add_input_dataset( input_name, input_hda )
-                            
+
 
                     self.sa_session.flush()
 
@@ -409,7 +409,7 @@ class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
         }
         history_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name
         history_attrs_out = open( history_attrs_filename, 'w' )
-        history_attrs_out.write( to_json_string( history_attrs ) )
+        history_attrs_out.write( dumps( history_attrs ) )
         history_attrs_out.close()
         jeha.history_attrs_filename = history_attrs_filename
 
@@ -427,12 +427,12 @@ class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
                 included_datasets.append( dataset )
         datasets_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name
         datasets_attrs_out = open( datasets_attrs_filename, 'w' )
-        datasets_attrs_out.write( to_json_string( datasets_attrs, cls=HistoryDatasetAssociationEncoder ) )
+        datasets_attrs_out.write( dumps( datasets_attrs, cls=HistoryDatasetAssociationEncoder ) )
         datasets_attrs_out.close()
         jeha.datasets_attrs_filename = datasets_attrs_filename
-        
+
         provenance_attrs_out = open( datasets_attrs_filename + ".provenance", 'w' )
-        provenance_attrs_out.write( to_json_string( provenance_attrs, cls=HistoryDatasetAssociationEncoder ) )
+        provenance_attrs_out.write( dumps( provenance_attrs, cls=HistoryDatasetAssociationEncoder ) )
         provenance_attrs_out.close()
 
         #
@@ -477,7 +477,7 @@ class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
             job_attrs[ 'exit_code' ] = job.exit_code
             job_attrs[ 'create_time' ] = job.create_time.isoformat()
             job_attrs[ 'update_time' ] = job.update_time.isoformat()
-            
+
 
             # Get the job's parameters
             try:
@@ -509,7 +509,7 @@ class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
 
         jobs_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name
         jobs_attrs_out = open( jobs_attrs_filename, 'w' )
-        jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) )
+        jobs_attrs_out.write( dumps( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) )
         jobs_attrs_out.close()
         jeha.jobs_attrs_filename = jobs_attrs_filename
 

lib/galaxy/tools/imp_exp/export_history.py

@@ -39,7 +39,7 @@ def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, ou
         except OverflowError:
             pass
         datasets_attr_in.close()
-        datasets_attrs = from_json_string( datasets_attr_str )
+        datasets_attrs = loads( datasets_attr_str )
 
         # Add datasets to archive and update dataset attributes.
         # TODO: security check to ensure that files added are in Galaxy dataset directory?
@@ -54,7 +54,7 @@ def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, ou
 
         # Rewrite dataset attributes file.
         datasets_attrs_out = open( datasets_attrs_file, 'w' )
-        datasets_attrs_out.write( to_json_string( datasets_attrs ) )
+        datasets_attrs_out.write( dumps( datasets_attrs ) )
         datasets_attrs_out.close()
 
         # Finish archive.
@@ -80,4 +80,4 @@ if __name__ == "__main__":
 
     # Create archive.
     status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip )
-    print status
+    print status

lib/galaxy/tools/parameters/__init__.py

@@ -85,7 +85,7 @@ def params_to_strings( params, param_values, app ):
     for key, value in param_values.iteritems():
         if key in params:
             value = params[ key ].value_to_basic( value, app )
-        rval[ key ] = str( to_json_string( value ) )
+        rval[ key ] = str( dumps( value ) )
     return rval
 
 
@@ -98,7 +98,7 @@ def params_from_strings( params, param_values, app, ignore_errors=False ):
     """
     rval = dict()
     for key, value in param_values.iteritems():
-        value = json_fix( from_json_string( value ) )
+        value = json_fix( loads( value ) )
         if key in params:
             value = params[key].value_from_basic( value, app, ignore_errors )
         rval[ key ] = value

lib/galaxy/tools/util/__init__.py

@@ -3,4 +3,4 @@ Utilities used by various Galaxy tools
 
 FIXME: These are used by tool scripts, not the framework, and should not live
        in this package.
-"""
+"""

lib/galaxy/util/__init__.py

@@ -338,8 +338,8 @@ def shrink_string_by_size( value, size, join_by="..", left_larger=True, beginnin
 
 def pretty_print_json(json_data, is_json_string=False):
     if is_json_string:
-        json_data = json.from_json_string(json_data)
-    return json.to_json_string(json_data, sort_keys=True, indent=4)
+        json_data = json.loads(json_data)
+    return json.dumps(json_data, sort_keys=True, indent=4)
 
 # characters that are valid
 valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!")

lib/galaxy/util/backports/__init__.py

@@ -1,3 +1,3 @@
 """
 Modules for providing backward compatibility with future versions of Python
-"""
+"""

lib/galaxy/util/backports/importlib/__init__.py

@@ -39,4 +39,4 @@ def import_module(name, package=None):
 
     ## Note: this was copied from
     ## http://svn.python.org/projects/python/trunk/Lib/importlib/__init__.py
-    ## on 24 September 2012
+    ## on 24 September 2012

lib/galaxy/util/dbkeys.py

@@ -3,7 +3,7 @@ Functionality for dealing with dbkeys.
 """
 #dbkeys read from disk using builds.txt
 from galaxy.util import read_dbnames
-from galaxy.util.json import from_json_string
+from galaxy.util.json import loads
 import os.path
 
 
@@ -38,7 +38,7 @@ class GenomeBuilds( object ):
                     rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) )
             user = trans.user
             if user and 'dbkeys' in user.preferences:
-                user_keys = from_json_string( user.preferences['dbkeys'] )
+                user_keys = loads( user.preferences['dbkeys'] )
                 for key, chrom_dict in user_keys.iteritems():
                     rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) )
         # Load old builds.txt static keys
@@ -61,8 +61,8 @@ class GenomeBuilds( object ):
                 chrom_info = db_dataset.file_name
             else:
                 # Do Custom Build handling
-                if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
-                    custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ dbkey ]
+                if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in loads( trans.user.preferences[ 'dbkeys' ] ) ):
+                    custom_build_dict = loads( trans.user.preferences[ 'dbkeys' ] )[ dbkey ]
                     # HACK: the attempt to get chrom_info below will trigger the
                     # fasta-to-len converter if the dataset is not available or,
                     # which will in turn create a recursive loop when

lib/galaxy/util/json.py

@@ -1,6 +1,6 @@
 from __future__ import absolute_import
 
-__all__ = [ "to_json_string", "from_json_string", "json_fix", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response" ]
+__all__ = [ "dumps", "loads", "json_fix", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response" ]
 
 import json
 import logging
@@ -9,6 +9,8 @@ import string
 
 to_json_string = json.dumps
 from_json_string = json.loads
+dumps = json.dumps
+loads = json.loads
 
 log = logging.getLogger( __name__ )
 
@@ -28,7 +30,7 @@ def json_fix( val ):
 
 def validate_jsonrpc_request( request, regular_methods, notification_methods ):
     try:
-        request = from_json_string( request )
+        request = loads( request )
     except Exception, e:
         return False, request, jsonrpc_response( id=None,
                                                  error=dict( code=-32700,
@@ -65,7 +67,7 @@ def validate_jsonrpc_request( request, regular_methods, notification_methods ):
 
 def validate_jsonrpc_response( response, id=None ):
     try:
-        response = from_json_string( response )
+        response = loads( response )
     except Exception, e:
         log.error( 'Response was not valid JSON: %s' % str( e ) )
         log.debug( 'Response was: %s' % response )

lib/galaxy/util/log/__init__.py

@@ -2,4 +2,4 @@ class TraceLogger( object ):
 	def __init__( self, name ):
 		self.name = name
 	def log( **kwargs ):
-		raise TypeError( "Abstract Method" )
+		raise TypeError( "Abstract Method" )

lib/galaxy/util/pastescript/serve.py

@@ -1056,4 +1056,4 @@ def invoke(command, command_name, options, args):
     except BadCommand, e:
         print e.message
         exit_code = e.exit_code
-    sys.exit(exit_code)
+    sys.exit(exit_code)

lib/galaxy/visualization/data_providers/__init__.py

@@ -1,3 +1,3 @@
 """
 Galaxy visualization/visual analysis data providers.
-"""
+"""

lib/galaxy/visualization/data_providers/basic.py

@@ -1,6 +1,6 @@
 import sys
 from galaxy.datatypes.tabular import Tabular
-from galaxy.util.json import from_json_string
+from galaxy.util.json import loads
 
 class BaseDataProvider( object ):
     """
@@ -96,7 +96,7 @@ class ColumnDataProvider( BaseDataProvider ):
             start_val = int( self.original_dataset.metadata.comment_lines )
 
         # columns is an array of ints for now (should handle column names later)
-        columns = from_json_string( columns )
+        columns = loads( columns )
         for column in columns:
             assert( ( column < self.original_dataset.metadata.columns )
             and     ( column >= 0 ) ),(

lib/galaxy/visualization/data_providers/genome.py

@@ -17,7 +17,7 @@ from bx.bbi.bigbed_file import BigBedFile
 from pysam import csamtools, ctabix
 
 from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFFeature, GFFInterval, GFFReaderWrapper, parse_gff_attributes
-from galaxy.util.json import from_json_string
+from galaxy.util.json import loads
 from galaxy.visualization.data_providers.basic import BaseDataProvider
 from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar
 from galaxy.datatypes.interval import Bed, Gff, Gtf
@@ -409,7 +409,7 @@ class IntervalDataProvider( GenomeDataProvider ):
         #
         # First three entries are mandatory, others are optional.
         #
-        filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) )
+        filter_cols = loads( kwargs.get( "filter_cols", "[]" ) )
         no_detail = ( "no_detail" in kwargs )
         rval = []
         message = None
@@ -490,7 +490,7 @@ class BedDataProvider( GenomeDataProvider ):
         #
         # First three entries are mandatory, others are optional.
         #
-        filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) )
+        filter_cols = loads( kwargs.get( "filter_cols", "[]" ) )
         no_detail = ( "no_detail" in kwargs )
         rval = []
         message = None
@@ -1336,7 +1336,7 @@ class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ):
         #
         # First three entries are mandatory, others are optional.
         #
-        filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) )
+        filter_cols = loads( kwargs.get( "filter_cols", "[]" ) )
         no_detail = ( "no_detail" in kwargs )
         for count, val in enumerate( iterator ):
             start, end, offset = val[0], val[1], val[2]
@@ -1404,7 +1404,7 @@ class RawGFFDataProvider( GenomeDataProvider ):
         """
         Process data from an iterator to a format that can be provided to client.
         """
-        filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) )
+        filter_cols = loads( kwargs.get( "filter_cols", "[]" ) )
         no_detail = ( "no_detail" in kwargs )
         results = []
         message = None
@@ -1446,7 +1446,7 @@ class GtfTabixDataProvider( TabixDataProvider ):
             feature.append( GFFInterval( None, line.split( '\t') ) )
 
         # Process data.
-        filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) )
+        filter_cols = loads( kwargs.get( "filter_cols", "[]" ) )
         no_detail = ( "no_detail" in kwargs )
         results = []
         message = None

lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py

@@ -105,4 +105,4 @@ class Nexus_Parser(Newick_Parser):
                 else:
                     self.inCommentBlock = False
                     return "Nextline"   # need to move on to the nextline after getting out of comment
-        return ""
+        return ""

lib/galaxy/visualization/genome/__init__.py

@@ -1,3 +1,3 @@
 """
 Code for Galaxy genome visualizations.
-"""
+"""

lib/galaxy/visualization/genomes.py

@@ -1,6 +1,6 @@
 import os, re, sys, glob, logging
 from bx.seq.twobit import TwoBitFile
-from galaxy.util.json import from_json_string
+from galaxy.util.json import loads
 from galaxy import model, util
 from galaxy.util.bunch import Bunch
 
@@ -221,7 +221,7 @@ class Genomes( object ):
         user = trans.get_user()
         if user:
             if 'dbkeys' in user.preferences:
-                user_keys_dict = from_json_string( user.preferences[ 'dbkeys' ] )
+                user_keys_dict = loads( user.preferences[ 'dbkeys' ] )
             dbkeys.extend( [ (attributes[ 'name' ], key ) for key, attributes in user_keys_dict.items() ] )
 
         # Add app keys to dbkeys.
@@ -257,7 +257,7 @@ class Genomes( object ):
 
         # Look first in user's custom builds.
         if dbkey_user and 'dbkeys' in dbkey_user.preferences:
-            user_keys = from_json_string( dbkey_user.preferences['dbkeys'] )
+            user_keys = loads( dbkey_user.preferences['dbkeys'] )
             if dbkey in user_keys:
                 dbkey_attributes = user_keys[ dbkey ]
                 dbkey_name = dbkey_attributes[ 'name' ]
@@ -310,7 +310,7 @@ class Genomes( object ):
 
         # Look for key in owner's custom builds.
         if dbkey_owner and 'dbkeys' in dbkey_owner.preferences:
-            user_keys = from_json_string( dbkey_owner.preferences[ 'dbkeys' ] )
+            user_keys = loads( dbkey_owner.preferences[ 'dbkeys' ] )
             if dbkey in user_keys:
                 dbkey_attributes = user_keys[ dbkey ]
                 if 'fasta' in dbkey_attributes:
@@ -342,7 +342,7 @@ class Genomes( object ):
             # Built-in twobit.
             twobit_file_name = self.genomes[dbkey].twobit_file
         else:
-            user_keys = from_json_string( dbkey_user.preferences['dbkeys'] )
+            user_keys = loads( dbkey_user.preferences['dbkeys'] )
             dbkey_attributes = user_keys[ dbkey ]
             fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] )
             msg = fasta_dataset.convert_dataset( trans, 'twobit' )

lib/galaxy/visualization/registry.py

@@ -791,7 +791,7 @@ class ResourceParser( object ):
         'int'   : lambda param: int( param ),
         'float' : lambda param: float( param ),
         #'date'  : lambda param: ,
-        'json'  : ( lambda param: galaxy.util.json.from_json_string(
+        'json'  : ( lambda param: galaxy.util.json.loads(
                         galaxy.util.sanitize_html.sanitize_html( param ) ) ),
     }
 

lib/galaxy/visualization/tracks/__init__.py

@@ -1 +1 @@
-""" Summary.py required to be in this module due to pickling. """
+""" Summary.py required to be in this module due to pickling. """

lib/galaxy/web/base/controller.py

@@ -42,7 +42,7 @@ from galaxy.datatypes.metadata import FileParameter
 from galaxy.tools.parameters import RuntimeValue, visit_input_values
 from galaxy.tools.parameters.basic import DataToolParameter
 from galaxy.tools.parameters.basic import DataCollectionToolParameter
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from galaxy.workflow.modules import ToolModule
 from galaxy.workflow.steps import attach_ordered_steps
 from galaxy.util import validation
@@ -1706,7 +1706,7 @@ class UsesStoredWorkflowMixin( SharableItemSecurityMixin, UsesAnnotations ):
                     missing_tool_tups.append( missing_tool_tup )
                 # Save the entire step_dict in the unused config field, be parsed later
                 # when we do have the tool
-                step.config = to_json_string(step_dict)
+                step.config = dumps(step_dict)
             if step.tool_errors:
                 workflow.has_errors = True
             # Stick this in the step temporarily

lib/galaxy/web/form_builder.py

@@ -7,7 +7,7 @@ import logging, sys, os, time
 from operator import itemgetter
 from cgi import escape
 from galaxy.util import restore_text, relpath, nice_size, unicodify
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from galaxy.web import url_for
 from binascii import hexlify
 
@@ -563,7 +563,7 @@ class SwitchingSelectField(BaseField):
         html += '<input name="__switch_default__" type="hidden" value="%s" />' % self.default_field
         options = []
         for name, delegate_field in self.delegate_fields.items():
-            field = to_json_string( delegate_field.to_dict() )
+            field = dumps( delegate_field.to_dict() )
             option = " '%s': %s" % ( name, field )
             options.append( option )
         html += '<script>$(document).ready( function() {\nvar switchOptions = {\n'

lib/galaxy/web/framework/decorators.py

@@ -10,7 +10,7 @@ from galaxy.web.framework import url_for
 from galaxy import util
 from galaxy.exceptions import error_codes
 from galaxy.exceptions import MessageException
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import logging
 log = logging.getLogger( __name__ )
@@ -44,7 +44,7 @@ def json( func, **json_kwargs ):
     @wraps(func)
     def call_and_format( self, trans, *args, **kwargs ):
         trans.response.set_content_type( JSON_CONTENT_TYPE )
-        return to_json_string( func( self, trans, *args, **kwargs ), **json_kwargs )
+        return dumps( func( self, trans, *args, **kwargs ), **json_kwargs )
     if not hasattr( func, '_orig' ):
         call_and_format._orig = func
     return expose( _save_orig_fn( call_and_format, func ) )
@@ -133,9 +133,9 @@ def expose_api( func, to_json=True, user_required=True ):
         try:
             rval = func( self, trans, *args, **kwargs)
             if to_json and trans.debug:
-                rval = to_json_string( rval, indent=4, sort_keys=True )
+                rval = dumps( rval, indent=4, sort_keys=True )
             elif to_json:
-                rval = to_json_string( rval )
+                rval = dumps( rval )
             return rval
         except paste.httpexceptions.HTTPException:
             raise  # handled
@@ -160,7 +160,7 @@ def __extract_payload_from_request(trans, func, kwargs):
         for k, v in payload.iteritems():
             if isinstance(v, (str, unicode)):
                 try:
-                    payload[k] = from_json_string(v)
+                    payload[k] = loads(v)
                 except:
                     # may not actually be json, just continue
                     pass
@@ -169,7 +169,7 @@ def __extract_payload_from_request(trans, func, kwargs):
         # Assume application/json content type and parse request body manually, since wsgi won't do it. However, the order of this check
         # should ideally be in reverse, with the if clause being a check for application/json and the else clause assuming a standard encoding
         # such as multipart/form-data. Leaving it as is for backward compatibility, just in case.
-        payload = util.recursively_stringify_dictionary_keys( from_json_string( trans.request.body ) )
+        payload = util.recursively_stringify_dictionary_keys( loads( trans.request.body ) )
     return payload
 
 def expose_api_raw( func ):
@@ -242,9 +242,9 @@ def _future_expose_api( func, to_json=True, user_required=True ):
         try:
             rval = func( self, trans, *args, **kwargs)
             if to_json and trans.debug:
-                rval = to_json_string( rval, indent=4, sort_keys=True )
+                rval = dumps( rval, indent=4, sort_keys=True )
             elif to_json:
-                rval = to_json_string( rval )
+                rval = dumps( rval )
             return rval
         except MessageException as e:
             traceback_string = format_exc()
@@ -316,7 +316,7 @@ def __api_error_response( trans, **kwds ):
         # non-success (i.e. not 200 or 201) has been set, do not override
         # underlying controller.
         response.status = status_code
-    return to_json_string( error_dict )
+    return dumps( error_dict )
 
 
 # TODO: rename as expose_api and make default.

lib/galaxy/web/framework/helpers/__init__.py

@@ -7,7 +7,7 @@ from cgi import escape
 from datetime import datetime, timedelta
 from galaxy import eggs
 from galaxy.util import hash_util
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 eggs.require( "MarkupSafe" ) #required by WebHelpers
 eggs.require( "WebHelpers" )
 from webhelpers import date

lib/galaxy/web/framework/helpers/grids.py

@@ -3,7 +3,7 @@ import math
 
 from galaxy.model.item_attrs import RuntimeException, UsesAnnotations, UsesItemRatings
 from galaxy.util import sanitize_text
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 from galaxy.util.odict import odict
 from galaxy.web.framework import decorators
 from galaxy.web.framework import url_for
@@ -72,11 +72,11 @@ class Grid( object ):
         if self.preserve_state:
             pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name )
             if pref_name in trans.get_user().preferences:
-                saved_filter = from_json_string( trans.get_user().preferences[pref_name] )
+                saved_filter = loads( trans.get_user().preferences[pref_name] )
                 base_filter.update( saved_filter )
             pref_name = unicode( self.__class__.__name__ + self.cur_sort_key_pref_name )
             if pref_name in trans.get_user().preferences:
-                base_sort_key = from_json_string( trans.get_user().preferences[pref_name] )
+                base_sort_key = loads( trans.get_user().preferences[pref_name] )
         # Build initial query
         query = self.build_initial_query( trans, **kwargs )
         query = self.apply_query_filter( trans, query, **kwargs )
@@ -108,28 +108,28 @@ class Grid( object ):
                     column_filter = base_filter.get( column.key )
                 
                 # Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings.
-                def from_json_string_recurse(item):
+                def loads_recurse(item):
                     decoded_list = []
                     if isinstance( item, basestring):
                         try:
                             # Not clear what we're decoding, so recurse to ensure that we catch everything.
-                             decoded_item = from_json_string( item )
+                             decoded_item = loads( item )
                              if isinstance( decoded_item, list):
-                                 decoded_list = from_json_string_recurse( decoded_item )
+                                 decoded_list = loads_recurse( decoded_item )
                              else:
                                  decoded_list = [ unicode( decoded_item ) ]
                         except ValueError:
                             decoded_list = [ unicode ( item ) ]
                     elif isinstance( item, list):
                         for element in item:
-                            a_list = from_json_string_recurse( element )
+                            a_list = loads_recurse( element )
                             decoded_list = decoded_list + a_list
                     return decoded_list
                 # If column filter found, apply it.
                 if column_filter is not None:
                     # TextColumns may have a mix of json and strings.
                     if isinstance( column, TextColumn ):
-                        column_filter = from_json_string_recurse( column_filter )
+                        column_filter = loads_recurse( column_filter )
                         if len( column_filter ) == 1:
                             column_filter = column_filter[0]
                     # Interpret ',' as a separator for multiple terms.
@@ -159,7 +159,7 @@ class Grid( object ):
                         for filter in column_filter:
                             if not isinstance( filter, basestring ):
                                 filter = unicode( filter ).encode("utf-8")
-                        extra_url_args[ "f-" + column.key ] = to_json_string( column_filter )
+                        extra_url_args[ "f-" + column.key ] = dumps( column_filter )
                     else:
                         # Process singleton filter.
                         if not isinstance( column_filter, basestring ):
@@ -229,10 +229,10 @@ class Grid( object ):
         # Preserve grid state: save current filter and sort key.
         if self.preserve_state:
             pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name )
-            trans.get_user().preferences[pref_name] = unicode( to_json_string( cur_filter_dict ) )
+            trans.get_user().preferences[pref_name] = unicode( dumps( cur_filter_dict ) )
             if sort_key:
                 pref_name = unicode( self.__class__.__name__ + self.cur_sort_key_pref_name )
-                trans.get_user().preferences[pref_name] = unicode( to_json_string( sort_key ) )
+                trans.get_user().preferences[pref_name] = unicode( dumps( sort_key ) )
             trans.sa_session.flush()
         # Log grid view.
         context = unicode( self.__class__.__name__ )

lib/galaxy/web/framework/middleware/__init__.py

@@ -1,3 +1,3 @@
 """
 WSGI Middleware.
-"""
+"""

lib/galaxy/web/framework/middleware/error.py

@@ -483,4 +483,4 @@ for i in range(len(doc_lines)):
     if doc_lines[i].strip().startswith('Settings'):
         make_error_middleware.__doc__ = ''.join(doc_lines[i:])
         break
-del i, doc_lines
+del i, doc_lines

lib/galaxy/web/framework/middleware/profile.py

@@ -180,4 +180,4 @@ def func_std_string( func_name ):
         else:
             return name
     else:
-        return "%s:%d(%s)" % func_name
+        return "%s:%d(%s)" % func_name

lib/galaxy/web/framework/middleware/sentry.py

@@ -64,4 +64,4 @@ class Sentry(object):
         # Galaxy: store event_id in environment so we can show it to the user
         environ['sentry_event_id'] = event_id[0]
 
-        return event_id
+        return event_id

lib/galaxy/webapps/__init__.py

@@ -1,3 +1,3 @@
 """Galaxy webapps root package -- this is a namespace package."""
 
-__import__( "pkg_resources" ).declare_namespace( __name__ )
+__import__( "pkg_resources" ).declare_namespace( __name__ )

lib/galaxy/webapps/demo_sequencer/controllers/__init__.py

@@ -1 +1 @@
-"""Galaxy demo sequencer emulator controllers."""
+"""Galaxy demo sequencer emulator controllers."""

lib/galaxy/webapps/demo_sequencer/controllers/common.py

@@ -29,7 +29,7 @@ class CommonController( BaseUIController ):
                 response = self.handle_request( trans, url, http_method, **request_params )
                 # Handle response, currently only handles json
                 if response_type == 'json':
-                    response = from_json_string( response )
+                    response = loads( response )
                     # Handle response that is an error, for example:
                     # { "Success":false, "Message":"some error string" }
                     if 'Success' in response and response[ 'Success' ] == 'false':
@@ -121,7 +121,7 @@ class CommonController( BaseUIController ):
             response = self.handle_request( trans, url, http_method, **request_params )
             # Handle response, currently only handles json
             if response_type == 'json':
-                response = from_json_string( response )
+                response = loads( response )
                 # Handle response that is an error, for example:
                 # { "Success":false, "Message":"some error string" }
                 if 'Success' in response and response[ 'Success' ] == 'false':
@@ -211,12 +211,12 @@ class CommonController( BaseUIController ):
                                                           **params ) )
     def put( self, url, **kwd ):
         opener = urllib2.build_opener( urllib2.HTTPHandler )
-        request = urllib2.Request( url, data=to_json_string( kwd ) )
+        request = urllib2.Request( url, data=dumps( kwd ) )
         request.add_header( 'Content-Type', 'application/json' )
         request.get_method = lambda: 'PUT'
         url = opener.open( request )
         output = url.read()
-        return from_json_string( output )
+        return loads( output )
     @web.expose
     def login( self, trans, **kwd ):
         trans.app.sequencer_actions_registry.authenticated = True

lib/galaxy/webapps/demo_sequencer/framework/__init__.py

@@ -17,8 +17,8 @@ from Cheetah.Template import Template
 from galaxy.web.framework import helpers
 
 from galaxy import util
-from galaxy.util.json import to_json_string
-from galaxy.util.json import from_json_string
+from galaxy.util.json import dumps
+from galaxy.util.json import loads
 from galaxy.web.framework import url_for
 from galaxy.web.framework.decorators import expose
 from galaxy.web.framework.decorators import json

lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py

@@ -113,7 +113,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
         if raw_text:
             # If successful, the response from get_ordered_installable_revisions will be a list of
             # changeset_revision hash strings.
-            changeset_revisions = json.from_json_string( raw_text )
+            changeset_revisions = json.loads( raw_text )
             if len( changeset_revisions ) >= 1:
                 return changeset_revisions[ -1 ]
         return hg_util.INITIAL_CHANGELOG_HASH
@@ -146,7 +146,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
         if index is None:
             raise HTTPBadRequest( detail="Missing required parameter 'index'." )
         repository = suc.get_tool_shed_repository_by_id( trans.app, tool_shed_repository_id )
-        exported_workflows = json.from_json_string( self.exported_workflows( trans, tool_shed_repository_id ) )
+        exported_workflows = json.loads( self.exported_workflows( trans, tool_shed_repository_id ) )
         # Since we don't have an in-memory object with an id, we'll identify the exported workflow via its location (i.e., index) in the list.
         exported_workflow = exported_workflows[ int( index ) ]
         workflow_name = exported_workflow[ 'workflow_name' ]
@@ -173,7 +173,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
         if not tool_shed_repository_id:
             raise HTTPBadRequest( detail="Missing required parameter 'id'." )
         repository = suc.get_tool_shed_repository_by_id( trans.app, tool_shed_repository_id )
-        exported_workflows = json.from_json_string( self.exported_workflows( trans, tool_shed_repository_id ) )
+        exported_workflows = json.loads( self.exported_workflows( trans, tool_shed_repository_id ) )
         imported_workflow_dicts = []
         for exported_workflow_dict in exported_workflows:
             workflow_name = exported_workflow_dict[ 'workflow_name' ]
@@ -438,7 +438,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
             results[ 'repository_status' ].append( message )
         stop_time = strftime( "%Y-%m-%d %H:%M:%S" )
         results[ 'stop_time' ] = stop_time
-        return json.to_json_string( results, sort_keys=True, indent=4 )
+        return json.dumps( results, sort_keys=True, indent=4 )
 
     @expose_api
     def show( self, trans, id, **kwd ):

lib/galaxy/webapps/galaxy/api/tools.py

@@ -7,7 +7,7 @@ from galaxy.web.base.controller import BaseAPIController
 from galaxy.web.base.controller import UsesVisualizationMixin
 from galaxy.web.base.controller import UsesHistoryMixin
 from galaxy.visualization.genomes import GenomeRegion
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from galaxy.visualization.data_providers.genome import *
 
 from galaxy.managers.collections_util import dictify_dataset_collection_instance
@@ -248,7 +248,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix
         # TODO: need to handle updates to conditional parameters; conditional
         # params are stored in dicts (and dicts within dicts).
         new_inputs = payload[ 'inputs' ]
-        tool_params.update( dict( [ ( key, to_json_string( value ) ) for key, value in new_inputs.items() if key in tool.inputs and new_inputs[ key ] is not None ] ) )
+        tool_params.update( dict( [ ( key, dumps( value ) ) for key, value in new_inputs.items() if key in tool.inputs and new_inputs[ key ] is not None ] ) )
         tool_params = tool.params_from_strings( tool_params, self.app )
 
         #