--- a/data_manager/data_manager_rsync.py	Tue Apr 04 18:13:26 2017 -0400
+++ b/data_manager/data_manager_rsync.py	Thu Nov 28 15:47:47 2019 -0500
@@ -2,6 +2,7 @@
 # Dan Blankenberg
 from __future__ import print_function
 
+import base64
 import datetime
 import logging
 import optparse
@@ -25,7 +26,7 @@
 _log_name = __name__
 if _log_name == '__builtin__':
     _log_name = 'toolshed.installed.g2.rsync.data.manager'
-log = logging.getLogger( _log_name )
+log = logging.getLogger(_log_name)
 
 # Get the Data from the Galaxy Project rsync server
 RSYNC_CMD = 'rsync'
@@ -35,16 +36,16 @@
 
 # Pull the Tool Data Table files from github
 # FIXME: These files should be accessible from the rsync server directly.
-TOOL_DATA_TABLE_CONF_XML_URLS = {'main': "https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/master/files/galaxy/usegalaxy.org/config/tool_data_table_conf.xml",
-                                 'test': "https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/master/files/galaxy/test.galaxyproject.org/config/tool_data_table_conf.xml" }
+TOOL_DATA_TABLE_CONF_XML_URLS = {'main': "https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/master/env/main/files/galaxy/config/tool_data_table_conf.xml",
+                                 'test': "https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/master/env/test/files/galaxy/config/tool_data_table_conf.xml"}
 
 # Replace data table source entries with local temporary location
 GALAXY_DATA_CANONICAL_PATH = "/galaxy/data/"
-TOOL_DATA_TABLE_CONF_XML_REPLACE_SOURCE = '<file path="%slocation/' % ( GALAXY_DATA_CANONICAL_PATH )
+TOOL_DATA_TABLE_CONF_XML_REPLACE_SOURCE = '<file path="%slocation/' % (GALAXY_DATA_CANONICAL_PATH)
 TOOL_DATA_TABLE_CONF_XML_REPLACE_TARGET = '<file path="%s/'
 
 # Some basic Caching, so we don't have to reload and download everything every time
-CACHE_TIME = datetime.timedelta( minutes=10 )
+CACHE_TIME = datetime.timedelta(minutes=10)
 TOOL_DATA_TABLES_LOADED_BY_URL = {}
 
 # Entries will not be selected by default
@@ -60,179 +61,179 @@
 
 
 # --- These methods are called by/within the Galaxy Application
-def exec_before_job( app, inp_data, out_data, param_dict, tool=None, **kwd ):
+def exec_before_job(app, inp_data, out_data, param_dict, tool=None, **kwd):
     # Look for any data tables that haven't been defined for this data manager before and dynamically add them to Galaxy
-    param_dict = dict( **param_dict )
-    param_dict['data_table_entries'] = param_dict.get( 'data_table_entries', [] )
-    if not isinstance( param_dict['data_table_entries'], list ):
+    param_dict = dict(**param_dict)
+    param_dict['data_table_entries'] = param_dict.get('data_table_entries', [])
+    if not isinstance(param_dict['data_table_entries'], list):
         param_dict['data_table_entries'] = [param_dict['data_table_entries']]
-    param_dict['data_table_entries'] = ",".join( param_dict['data_table_entries'] )
+    param_dict['data_table_entries'] = ",".join(param_dict['data_table_entries'])
     if tool:
         tool_shed_repository = tool.tool_shed_repository
     else:
         tool_shed_repository = None
     tdtm = None
-    data_manager = app.data_managers.get_manager( tool.data_manager_id, None )
-    data_table_entries = get_data_table_entries( param_dict )
-    data_tables = load_data_tables_from_url( data_table_class=app.tool_data_tables.__class__ ).get( 'data_tables' )
+    data_manager = app.data_managers.get_manager(tool.data_manager_id, None)
+    data_table_entries = get_data_table_entries(param_dict)
+    data_tables = load_data_tables_from_url(data_table_class=app.tool_data_tables.__class__).get('data_tables')
     for data_table_name, entries in data_table_entries.items():
         # get data table managed by this data Manager
-        has_data_table = app.tool_data_tables.get_tables().get( data_table_name )
+        has_data_table = app.tool_data_tables.get_tables().get(str(data_table_name))
         if has_data_table:
-            has_data_table = bool( has_data_table.get_filename_for_source( data_manager, None ) )
+            has_data_table = bool(has_data_table.get_filename_for_source(data_manager, None))
         if not has_data_table:
             if tdtm is None:
                 from tool_shed.tools import data_table_manager
-                tdtm = data_table_manager.ToolDataTableManager( app )
-                target_dir, tool_path, relative_target_dir = tdtm.get_target_install_dir( tool_shed_repository )
+                tdtm = data_table_manager.ToolDataTableManager(app)
+                target_dir, tool_path, relative_target_dir = tdtm.get_target_install_dir(tool_shed_repository)
             # Dynamically add this data table
-            log.debug( "Attempting to dynamically create a missing Tool Data Table named %s." % data_table_name )
+            log.debug("Attempting to dynamically create a missing Tool Data Table named %s." % data_table_name)
             data_table = data_tables[data_table_name]
-            repo_info = tdtm.generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=None )
+            repo_info = tdtm.generate_repository_info_elem_from_repository(tool_shed_repository, parent_elem=None)
             if repo_info is not None:
-                repo_info = tostring( repo_info )
-            tmp_file = tempfile.NamedTemporaryFile()
-            tmp_file.write( get_new_xml_definition( app, data_table, data_manager, repo_info, target_dir ) )
+                repo_info = tostring(repo_info)
+            tmp_file = tempfile.NamedTemporaryFile(mode="w")
+            tmp_file.write(get_new_xml_definition(app, data_table, data_manager, repo_info, target_dir))
             tmp_file.flush()
-            app.tool_data_tables.add_new_entries_from_config_file( tmp_file.name, None, app.config.shed_tool_data_table_config, persist=True )
+            app.tool_data_tables.add_new_entries_from_config_file(tmp_file.name, None, app.config.shed_tool_data_table_config, persist=True)
             tmp_file.close()
 
 
-def galaxy_code_get_available_data_tables( trans ):
+def galaxy_code_get_available_data_tables(trans):
     # list of data tables
-    found_tables = get_available_tables( trans )
-    rval = [ ( x, x, DEFAULT_SELECTED ) for x in found_tables]
+    found_tables = get_available_tables(trans)
+    rval = [(x, x, DEFAULT_SELECTED) for x in found_tables]
     return rval
 
 
-def galaxy_code_get_available_data_tables_entries( trans, dbkey, data_table_names ):
+def galaxy_code_get_available_data_tables_entries(trans, dbkey, data_table_names):
     # available entries, optionally filtered by dbkey and table names
-    if dbkey in [ None, '', '?' ]:
+    if dbkey in [None, '', '?']:
         dbkey = None
-    if data_table_names in [ None, '', '?' ]:
+    if data_table_names in [None, '', '?']:
         data_table_names = None
-    found_tables = get_available_tables_for_dbkey( trans, dbkey, data_table_names )
-    dbkey_text = '(%s) ' % ( dbkey ) if dbkey else ''
-    rval = [( "%s%s" % ( dbkey_text, x[0] ), dumps( dict( name=x[0].split( ': ' )[0], entry=x[1] ) ).encode( 'base64' ).rstrip(), DEFAULT_SELECTED ) for x in found_tables.items()]
+    found_tables = get_available_tables_for_dbkey(trans, dbkey, data_table_names)
+    dbkey_text = '(%s) ' % (dbkey) if dbkey else ''
+    rval = [("%s%s" % (dbkey_text, x[0]), base64.b64encode(dumps(dict(name=x[0].split(': ')[0], entry=x[1]), sort_keys=True).rstrip().encode('utf-8')).decode('utf-8'), DEFAULT_SELECTED) for x in found_tables.items()]
     return rval
 
 # --- End Galaxy called Methods ---
 
 
-def rsync_urljoin( base, url ):
+def rsync_urljoin(base, url):
     # urlparse.urljoin doesn't work correctly for our use-case
-    # probably because it doesn't recognize the rsync scheme
-    base = base.rstrip( '/' )
-    url = url.lstrip( '/' )
-    return "%s/%s" % ( base, url )
+    # probably because it doesn't recognize rhe rsync scheme
+    base = base.rstrip('/')
+    url = url.lstrip('/')
+    return "%s/%s" % (base, url)
 
 
-def rsync_list_dir( server, dir=None, skip_names=[] ):
+def rsync_list_dir(server, dir=None, skip_names=[]):
     # drwxr-xr-x          50 2014/05/16 20:58:11 .
     if dir:
-        dir = rsync_urljoin( server, dir )
+        dir = rsync_urljoin(server, dir)
     else:
         dir = server
     rsync_response = tempfile.NamedTemporaryFile()
     rsync_stderr = tempfile.NamedTemporaryFile()
-    rsync_cmd = [ RSYNC_CMD, '--list-only', dir ]
-    return_code = subprocess.call( rsync_cmd, stdout=rsync_response, stderr=rsync_stderr )
+    rsync_cmd = [RSYNC_CMD, '--list-only', dir]
+    return_code = subprocess.call(rsync_cmd, stdout=rsync_response, stderr=rsync_stderr)
     rsync_response.flush()
     rsync_response.seek(0)
     rsync_stderr.flush()
     rsync_stderr.seek(0)
     if return_code:
-        msg = "stdout:\n%s\nstderr:\n%s" % ( rsync_response.read(), rsync_stderr.read() )
+        msg = "stdout:\n%s\nstderr:\n%s" % (rsync_response.read(), rsync_stderr.read())
         rsync_response.close()
         rsync_stderr.close()
-        raise Exception( 'Failed to execute rsync command (%s), returncode=%s. Rsync_output:\n%s' % (  rsync_cmd, return_code, msg ) )
+        raise Exception('Failed to execute rsync command (%s), returncode=%s. Rsync_output:\n%s' % (rsync_cmd, return_code, msg))
     rsync_stderr.close()
     rval = {}
     for line in rsync_response:
-        perms, line = line.split( None, 1 )
+        perms, line = line.split(None, 1)
         line = line.strip()
-        size, line = line.split( None, 1 )
+        size, line = line.split(None, 1)
         line = line.strip()
-        date, line = line.split( None, 1 )
+        date, line = line.split(None, 1)
         line = line.strip()
-        time, line = line.split( None, 1 )
+        time, line = line.split(None, 1)
         name = line.strip()
         if name in skip_names:
             continue
         size = line.strip()
-        rval[ name ] = dict( name=name, permissions=perms, bytes=size, date=date, time=time )
+        rval[name] = dict(name=name, permissions=perms, bytes=size, date=date, time=time)
     rsync_response.close()
     return rval
 
 
-def rsync_sync_to_dir( source, target ):
+def rsync_sync_to_dir(source, target):
     rsync_response = tempfile.NamedTemporaryFile()
     rsync_stderr = tempfile.NamedTemporaryFile()
-    rsync_cmd = [ RSYNC_CMD, '-avzP', source, target ]
-    return_code = subprocess.call( rsync_cmd, stdout=rsync_response, stderr=rsync_stderr )
+    rsync_cmd = [RSYNC_CMD, '-avzP', source, target]
+    return_code = subprocess.call(rsync_cmd, stdout=rsync_response, stderr=rsync_stderr)
     rsync_response.flush()
     rsync_response.seek(0)
     rsync_stderr.flush()
     rsync_stderr.seek(0)
     if return_code:
-        msg = "stdout:\n%s\nstderr:\n%s" % ( rsync_response.read(), rsync_stderr.read() )
+        msg = "stdout:\n%s\nstderr:\n%s" % (rsync_response.read(), rsync_stderr.read())
         rsync_response.close()
         rsync_stderr.close()
-        raise Exception( 'Failed to execute rsync command (%s), returncode=%s. Rsync_output:\n%s' % (  rsync_cmd, return_code, msg ) )
+        raise Exception('Failed to execute rsync command (%s), returncode=%s. Rsync_output:\n%s' % (rsync_cmd, return_code, msg))
     rsync_response.close()
     rsync_stderr.close()
     return return_code
 
 
-def data_table_needs_refresh( cached_data_table, url ):
+def data_table_needs_refresh(cached_data_table, url):
     if cached_data_table is None:
         return True, {}
-    if datetime.datetime.now() - cached_data_table.get( 'time_loaded' ) > CACHE_TIME:
-        data_table_text = urlopen( url ).read()
-        if cached_data_table.get( 'data_table_text', None ) != data_table_text:
+    if datetime.datetime.now() - cached_data_table.get('time_loaded') > CACHE_TIME:
+        data_table_text = urlopen(url).read().decode('utf-8')
+        if cached_data_table.get('data_table_text', None) != data_table_text:
             return True, {'data_table_text': data_table_text}
-        loc_file_attrs = rsync_list_dir( RSYNC_SERVER, LOCATION_DIR )
-        if cached_data_table.get( 'loc_file_attrs', None ) != loc_file_attrs:
+        loc_file_attrs = rsync_list_dir(RSYNC_SERVER, LOCATION_DIR)
+        if cached_data_table.get('loc_file_attrs', None) != loc_file_attrs:
             return True, {'loc_file_attrs': loc_file_attrs}
     return False, {}
 
 
-def load_data_tables_from_url( url=None, site='main', data_table_class=None  ):
+def load_data_tables_from_url(url=None, site='main', data_table_class=None):
     if not url:
-        url = TOOL_DATA_TABLE_CONF_XML_URLS.get( site, None )
-    assert url, ValueError( 'You must provide either a URL or a site=name.' )
+        url = TOOL_DATA_TABLE_CONF_XML_URLS.get(site, None)
+    assert url, ValueError('You must provide either a URL or a site=name.')
 
-    cached_data_table = TOOL_DATA_TABLES_LOADED_BY_URL.get( url, None )
-    refresh, attribs = data_table_needs_refresh( cached_data_table, url )
+    cached_data_table = TOOL_DATA_TABLES_LOADED_BY_URL.get(url, None)
+    refresh, attribs = data_table_needs_refresh(cached_data_table, url)
     if refresh:
-        data_table_text = attribs.get( 'data_table_text' )or urlopen( url ).read()
-        loc_file_attrs = attribs.get( 'loc_file_attrs' ) or rsync_list_dir( RSYNC_SERVER, LOCATION_DIR )
+        data_table_text = attribs.get('data_table_text') or urlopen(url).read().decode('utf-8')
+        loc_file_attrs = attribs.get('loc_file_attrs') or rsync_list_dir(RSYNC_SERVER, LOCATION_DIR)
 
-        tmp_dir = tempfile.mkdtemp( prefix='rsync_g2_' )
-        tmp_loc_dir = os.path.join( tmp_dir, 'location' )
-        os.mkdir( tmp_loc_dir )
-        rsync_sync_to_dir( rsync_urljoin( RSYNC_SERVER, LOCATION_DIR ), os.path.abspath( tmp_loc_dir ) )
+        tmp_dir = tempfile.mkdtemp(prefix='rsync_g2_')
+        tmp_loc_dir = os.path.join(tmp_dir, 'location')
+        os.mkdir(tmp_loc_dir)
+        rsync_sync_to_dir(rsync_urljoin(RSYNC_SERVER, LOCATION_DIR), os.path.abspath(tmp_loc_dir))
 
-        new_data_table_text = data_table_text.replace( TOOL_DATA_TABLE_CONF_XML_REPLACE_SOURCE, TOOL_DATA_TABLE_CONF_XML_REPLACE_TARGET % ( tmp_loc_dir ) )
-        data_table_fh = tempfile.NamedTemporaryFile( dir=tmp_dir, prefix='rysnc_data_manager_data_table_conf_' )
-        data_table_fh.write( new_data_table_text )
+        new_data_table_text = data_table_text.replace(TOOL_DATA_TABLE_CONF_XML_REPLACE_SOURCE, TOOL_DATA_TABLE_CONF_XML_REPLACE_TARGET % (tmp_loc_dir))
+        data_table_fh = tempfile.NamedTemporaryFile(dir=tmp_dir, prefix='rysnc_data_manager_data_table_conf_', mode="w")
+        data_table_fh.write(new_data_table_text)
         data_table_fh.flush()
-        tmp_data_dir = os.path.join( tmp_dir, 'tool-data' )
-        os.mkdir( tmp_data_dir )
-        data_tables = data_table_class( tmp_data_dir, config_filename=data_table_fh.name )
+        tmp_data_dir = os.path.join(tmp_dir, 'tool-data')
+        os.mkdir(tmp_data_dir)
+        data_tables = data_table_class(tmp_data_dir, config_filename=data_table_fh.name)
         for name, data_table in list(data_tables.data_tables.items()):
-            if name in EXCLUDE_DATA_TABLES or not data_table_has_path_column( data_table ):
-                log.debug( 'Removing data table "%s" because it is excluded by name or does not have a defined "path" column.', name )
+            if name in EXCLUDE_DATA_TABLES or not data_table_has_path_column(data_table):
+                log.debug('Removing data table "%s" because it is excluded by name or does not have a defined "path" column.', name)
                 del data_tables.data_tables[name]
-        cached_data_table = { 'data_tables': data_tables, 'tmp_dir': tmp_dir, 'data_table_text': data_table_text, 'tmp_loc_dir': tmp_loc_dir, 'loc_file_attrs': loc_file_attrs, 'time_loaded': datetime.datetime.now() }
-        TOOL_DATA_TABLES_LOADED_BY_URL[ url ] = cached_data_table
+        cached_data_table = {'data_tables': data_tables, 'tmp_dir': tmp_dir, 'data_table_text': data_table_text, 'tmp_loc_dir': tmp_loc_dir, 'loc_file_attrs': loc_file_attrs, 'time_loaded': datetime.datetime.now()}
+        TOOL_DATA_TABLES_LOADED_BY_URL[url] = cached_data_table
         # delete the files
         data_table_fh.close()
-        cleanup_before_exit( tmp_dir )
+        cleanup_before_exit(tmp_dir)
     return cached_data_table
 
 
-def data_table_has_path_column( data_table ):
+def data_table_has_path_column(data_table):
     col_names = data_table.get_column_name_list()
     for name in PATH_COLUMN_NAMES:
         if name in col_names:
@@ -240,29 +241,29 @@
     return False
 
 
-def get_available_tables( trans ):
+def get_available_tables(trans):
     # list of data tables
-    data_tables = load_data_tables_from_url( data_table_class=trans.app.tool_data_tables.__class__ )
-    return list(data_tables.get( 'data_tables' ).get_tables().keys())
+    data_tables = load_data_tables_from_url(data_table_class=trans.app.tool_data_tables.__class__)
+    return data_tables.get('data_tables').get_tables().keys()
 
 
-def get_new_xml_definition( app, data_table, data_manager, repo_info=None, location_file_dir=None ):
-    sub_dict = { 'table_name': data_table.name, 'comment_char': '', 'columns': '', 'file_path': '' }
-    sub_dict.update( data_manager.get_tool_shed_repository_info_dict() )
+def get_new_xml_definition(app, data_table, data_manager, repo_info=None, location_file_dir=None):
+    sub_dict = {'table_name': data_table.name, 'comment_char': '', 'columns': '', 'file_path': ''}
+    sub_dict.update(data_manager.get_tool_shed_repository_info_dict())
     if data_table.comment_char:
-        sub_dict['comment_char'] = 'comment_char="%s"' % ( data_table.comment_char )
-    for i, name in enumerate( data_table.get_column_name_list() ):
+        sub_dict['comment_char'] = 'comment_char="%s"' % (data_table.comment_char)
+    for i, name in enumerate(data_table.get_column_name_list()):
         if name is not None:
-            sub_dict['columns'] = "%s\n%s" % ( sub_dict['columns'], '<column name="%s" index="%s" />' % ( name, i ) )
+            sub_dict['columns'] = "%s\n%s" % (sub_dict['columns'], '<column name="%s" index="%s" />' % (name, i))
     location_file_dir = location_file_dir or app.config.galaxy_data_manager_data_path
     for filename in data_table.filenames.keys():
-        sub_dict['file_path'] = basename( filename )
-        sub_dict['file_path'] = os.path.join( location_file_dir, sub_dict['file_path'] )  # os.path.abspath?
-        if not os.path.exists( sub_dict['file_path'] ):
+        sub_dict['file_path'] = basename(filename)
+        sub_dict['file_path'] = os.path.join(location_file_dir, sub_dict['file_path'])  # os.path.abspath?
+        if not os.path.exists(sub_dict['file_path']):
             # Create empty file
-            open( sub_dict['file_path'], 'wb+' ).close()
+            open(sub_dict['file_path'], 'wb+').close()
         break
-    sub_dict[ 'repo_info' ] = repo_info or ''
+    sub_dict['repo_info'] = repo_info or ''
     return """
             <tables><table name="%(table_name)s" %(comment_char)s>
                 %(columns)s
@@ -272,32 +273,32 @@
            """ % sub_dict
 
 
-def get_available_tables_for_dbkey( trans, dbkey, data_table_names ):
-    data_tables = load_data_tables_from_url( data_table_class=trans.app.tool_data_tables.__class__ )
+def get_available_tables_for_dbkey(trans, dbkey, data_table_names):
+    data_tables = load_data_tables_from_url(data_table_class=trans.app.tool_data_tables.__class__)
     rval = {}
-    for name, data_table in data_tables.get( 'data_tables' ).get_tables().items():
-        if ( not data_table_names or name in data_table_names ):
+    for name, data_table in data_tables.get('data_tables').get_tables().items():
+        if (not data_table_names or name in data_table_names):
             # TODO: check that columns are similiar
             if not dbkey:
                 entry_getter = data_table.get_named_fields_list()
             else:
-                entry_getter = data_table.get_entries( 'dbkey', dbkey, None, default=[] )
+                entry_getter = data_table.get_entries('dbkey', dbkey, None, default=[])
             for entry in entry_getter:
-                name = "%s: %s" % ( data_table.name, dumps( entry ) )
+                name = "%s: %s" % (data_table.name, dumps(entry))
                 rval[name] = entry
     return rval
 
 
-def split_path_all( path ):
+def split_path_all(path):
     rval = []
-    path = path.rstrip( '/' )
+    path = path.rstrip('/')
     while True:
-        head, tail = os.path.split( path )
+        head, tail = os.path.split(path)
         if tail:
-            rval.append( tail )
+            rval.append(tail)
             path = head
         elif head:
-            rval.append( head )
+            rval.append(head)
             break
         else:
             break
@@ -305,85 +306,85 @@
     return rval
 
 
-def get_data_for_path( path, data_root_dir ):
+def get_data_for_path(path, data_root_dir):
     # We list dir with a /, but copy data without
     # listing with / gives a . entry when its a dir
     # cloning without the / will copy that whole directory into the target,
     # instead of just that target's contents
-    if path.startswith( GALAXY_DATA_CANONICAL_PATH ):
-        path = path[ len( GALAXY_DATA_CANONICAL_PATH ):]
+    if path.startswith(GALAXY_DATA_CANONICAL_PATH):
+        path = path[len(GALAXY_DATA_CANONICAL_PATH):]
     make_path = path
-    rsync_source = rsync_urljoin( rsync_urljoin( RSYNC_SERVER, INDEX_DIR ), path )
-    if rsync_source.endswith( '/' ):
+    rsync_source = rsync_urljoin(rsync_urljoin(RSYNC_SERVER, INDEX_DIR), path)
+    if rsync_source.endswith('/'):
         rsync_source = rsync_source[:-1]
     try:
-        dir_list = rsync_list_dir( rsync_source + "/" )
+        dir_list = rsync_list_dir(rsync_source + "/")
     except Exception:
         dir_list = None
     while not dir_list or '.' not in dir_list:
-        head, tail = os.path.split( make_path )
+        head, tail = os.path.split(make_path)
         if not head:
             head = tail
         make_path = head
-        rsync_source = rsync_urljoin( rsync_urljoin( RSYNC_SERVER, INDEX_DIR ), head )  # if we error here, likely due to a connection issue
-        if rsync_source.endswith( '/' ):
+        rsync_source = rsync_urljoin(rsync_urljoin(RSYNC_SERVER, INDEX_DIR), head)  # if we error here, likely due to a connection issue
+        if rsync_source.endswith('/'):
             rsync_source = rsync_source[:-1]
-        dir_list = rsync_list_dir( rsync_source + "/" )
-    split_path = split_path_all( make_path )
+        dir_list = rsync_list_dir(rsync_source + "/")
+    split_path = split_path_all(make_path)
     target_path = data_root_dir
     for p in split_path[:-1]:
-        target_path = os.path.join( target_path, p )
-        if not os.path.exists( target_path ):
-            os.mkdir( target_path )
-    rsync_sync_to_dir( rsync_source, target_path )
+        target_path = os.path.join(target_path, p)
+        if not os.path.exists(target_path):
+            os.mkdir(target_path)
+    rsync_sync_to_dir(rsync_source, target_path)
     return path
 
 
-def get_data_and_munge_path( data_table_name, data_table_entry, data_root_dir ):
+def get_data_and_munge_path(data_table_name, data_table_entry, data_root_dir):
     path_cols = []
     for key, value in data_table_entry.items():
         if key in PATH_COLUMN_NAMES:
-            path_cols.append( ( key, value ) )
+            path_cols.append((key, value))
     if path_cols:
         for col_name, value in path_cols:
-            if value.startswith( GALAXY_DATA_CANONICAL_PATH ):
-                data_table_entry[col_name] = get_data_for_path( value, data_root_dir )
+            if value.startswith(GALAXY_DATA_CANONICAL_PATH):
+                data_table_entry[col_name] = get_data_for_path(value, data_root_dir)
             else:
                 print('unable to determine location of rsync data for', data_table_name, data_table_entry)
     return data_table_entry
 
 
-def fulfill_data_table_entries( data_table_entries, data_manager_dict, data_root_dir ):
+def fulfill_data_table_entries(data_table_entries, data_manager_dict, data_root_dir):
     for data_table_name, entries in data_table_entries.items():
         for entry in entries:
-            entry = get_data_and_munge_path( data_table_name, entry, data_root_dir )
-            _add_data_table_entry( data_manager_dict, data_table_name, entry )
+            entry = get_data_and_munge_path(data_table_name, entry, data_root_dir)
+            _add_data_table_entry(data_manager_dict, data_table_name, entry)
     return data_manager_dict
 
 
-def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
-    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
-    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] )
-    data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
+def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
+    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
     return data_manager_dict
 
 
-def cleanup_before_exit( tmp_dir ):
-    if tmp_dir and os.path.exists( tmp_dir ):
-        shutil.rmtree( tmp_dir )
+def cleanup_before_exit(tmp_dir):
+    if tmp_dir and os.path.exists(tmp_dir):
+        shutil.rmtree(tmp_dir)
 
 
-def get_data_table_entries( params ):
+def get_data_table_entries(params):
     rval = {}
-    data_table_entries = params.get( 'data_table_entries', None )
+    data_table_entries = params.get('data_table_entries', None)
     if data_table_entries:
-        for entry_text in data_table_entries.split( ',' ):
-            entry_text = entry_text.strip().decode( 'base64' )
-            entry_dict = loads( entry_text )
+        for entry_text in data_table_entries.split(','):
+            entry_text = base64.b64decode(entry_text.strip().encode('utf-8'))
+            entry_dict = loads(entry_text)
             data_table_name = entry_dict['name']
             data_table_entry = entry_dict['entry']
-            rval[ data_table_name ] = rval.get( data_table_name, [] )
-            rval[ data_table_name ].append( data_table_entry )
+            rval[data_table_name] = rval.get(data_table_name, [])
+            rval[data_table_name].append(data_table_entry)
     return rval
 
 
@@ -393,18 +394,18 @@
 
     filename = args[0]
 
-    params = loads( open( filename ).read() )
-    target_directory = params[ 'output_data' ][0]['extra_files_path']
-    os.mkdir( target_directory )
+    params = loads(open(filename).read())
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
     data_manager_dict = {}
 
-    data_table_entries = get_data_table_entries( params['param_dict'] )
+    data_table_entries = get_data_table_entries(params['param_dict'])
 
     # Populate the data Tables
-    data_manager_dict = fulfill_data_table_entries( data_table_entries, data_manager_dict, target_directory )
+    data_manager_dict = fulfill_data_table_entries(data_table_entries, data_manager_dict, target_directory)
 
     # save info to json file
-    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+    open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True))
 
 
 if __name__ == "__main__":