diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index c397d7a9206..c8c757807a9 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -16,6 +16,8 @@ import sys
import tempfile
import threading
from datetime import timedelta
+from six import string_types
+
from galaxy.exceptions import ConfigurationError
from galaxy.util import listify
from galaxy.util import string_as_bool
@@ -125,7 +127,7 @@ class Configuration( object ):
self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) )
self.hours_between_check = kwargs.get( 'hours_between_check', 12 )
self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) )
- if isinstance( self.hours_between_check, basestring ):
+ if isinstance( self.hours_between_check, string_types ):
self.hours_between_check = float( self.hours_between_check )
try:
if isinstance( self.hours_between_check, int ):
diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index af276616b32..f8a8b60f736 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -7,11 +7,13 @@ import tempfile
import zipfile
from cgi import escape
from inspect import isclass
+from six import string_types
from . import metadata
from galaxy import util
from galaxy.datatypes.metadata import MetadataElement # import directly to maintain ease of use in Datatype class definitions
from galaxy.util import inflector
+from galaxy.util import unicodify
from galaxy.util.bunch import Bunch
from galaxy.util.odict import odict
from galaxy.util.sanitize_html import sanitize_html
@@ -201,10 +203,7 @@ class Data( object ):
line = line.strip()
if not line:
continue
- if isinstance(line, unicode):
- out.append( '| %s |
' % escape( line ) )
- else:
- out.append( '| %s |
' % escape( unicode( line, 'utf-8' ) ) )
+ out.append( '| %s |
' % escape( unicodify( line, 'utf-8' ) ) )
out.append( '' )
out = "".join( out )
except Exception as exc:
@@ -327,7 +326,7 @@ class Data( object ):
# Prevent IE8 from sniffing content type since we're explicit about it. This prevents intentionally text/plain
# content from being rendered in the browser
trans.response.headers['X-Content-Type-Options'] = 'nosniff'
- if isinstance( data, basestring ):
+ if isinstance( data, string_types ):
return data
if filename and filename != "index":
# For files in extra_files_path
@@ -385,11 +384,8 @@ class Data( object ):
def display_name(self, dataset):
"""Returns formatted html of dataset name"""
try:
- if isinstance(dataset.name, unicode):
- return escape( dataset.name )
- else:
- return escape( unicode( dataset.name, 'utf-8 ') )
- except:
+ return escape( unicodify( dataset.name, 'utf-8' ) )
+ except Exception:
return "name unavailable"
def display_info(self, dataset):
@@ -404,9 +400,7 @@ class Data( object ):
if info.find( '\n' ) >= 0:
info = info.replace( '\n', '
' )
- # Convert to unicode to display non-ascii characters.
- if not isinstance(info, unicode):
- info = unicode( info, 'utf-8')
+ info = unicodify( info, 'utf-8' )
return info
except:
diff --git a/lib/galaxy/datatypes/display_applications/application.py b/lib/galaxy/datatypes/display_applications/application.py
index 94b4e0a1089..65308d59a88 100644
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -1,14 +1,16 @@
# Contains objects for using external display applications
import logging
import urllib
+from six import string_types
+from urllib import quote_plus
+from copy import deepcopy
+
from galaxy.util import parse_xml, string_as_bool
from galaxy.util.odict import odict
from galaxy.util.template import fill_template
from galaxy.web import url_for
from parameters import DisplayApplicationParameter, DisplayApplicationDataParameter, DEFAULT_DATASET_NAME
-from urllib import quote_plus
from util import encode_dataset_user
-from copy import deepcopy
log = logging.getLogger( __name__ )
@@ -157,7 +159,7 @@ class DynamicDisplayApplicationBuilder( object ):
display_application.add_data_table_watch( data_table.name, version )
links = []
for line in data_iter:
- if isinstance( line, basestring ):
+ if isinstance( line, string_types ):
if not skip_startswith or not line.startswith( skip_startswith ):
line = line.rstrip( '\n\r' )
if not line:
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 2dbebd9ff18..d85807d1309 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -13,9 +13,11 @@ import tempfile
import zipfile
from encodings import search_function as encodings_search_function
+from six import text_type
from galaxy import util
from galaxy.util import multi_byte
+from galaxy.util import unicodify
from galaxy.util.checkers import check_binary, check_html, is_gzip
from galaxy.datatypes.binary import Binary
@@ -51,7 +53,7 @@ def stream_to_open_named_file( stream, fd, filename, source_encoding=None, sourc
is_compressed = True
else:
try:
- if unicode( chunk[:2] ) == unicode( util.gzip_magic ):
+ if text_type( chunk[:2] ) == text_type( util.gzip_magic ):
is_compressed = True
except:
pass
@@ -63,7 +65,7 @@ def stream_to_open_named_file( stream, fd, filename, source_encoding=None, sourc
is_binary = util.is_binary( chunk )
data_checked = True
if not is_compressed and not is_binary:
- if not isinstance( chunk, unicode ):
+ if not isinstance( chunk, text_type ):
chunk = chunk.decode( source_encoding, source_error )
os.write( fd, chunk.encode( target_encoding, target_error ) )
else:
@@ -200,7 +202,7 @@ def get_headers( fname, sep, count=60, is_multi_byte=False ):
line = line.rstrip('\n\r')
if is_multi_byte:
# TODO: fix this - sep is never found in line
- line = unicode( line, 'utf-8' )
+ line = unicodify( line, 'utf-8' )
sep = sep.encode( 'utf-8' )
headers.append( line.split(sep) )
if idx == count:
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index 39f46ea8ad9..07c1750a9ea 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -1,6 +1,8 @@
"""
Manager and Serializer for Datasets.
"""
+from six import string_types
+
from galaxy import model
from galaxy import exceptions
import galaxy.datatypes.metadata
@@ -379,7 +381,7 @@ class _UnflattenedMetadataDatasetAssociationSerializer( base.ModelSerializer,
# common to lddas and hdas - from mapping.py
'copied_from_history_dataset_association_id' : self.serialize_id,
'copied_from_library_dataset_dataset_association_id': self.serialize_id,
- 'info' : lambda i, k, **c: i.info.strip() if isinstance( i.info, basestring ) else i.info,
+ 'info' : lambda i, k, **c: i.info.strip() if isinstance( i.info, string_types ) else i.info,
'blurb' : lambda i, k, **c: i.blurb,
'peek' : lambda i, k, **c: i.display_peek() if i.peek and i.peek != 'no peek' else None,
diff --git a/lib/galaxy/managers/taggable.py b/lib/galaxy/managers/taggable.py
index 6ae9fd741d4..4be6f2b6c2c 100644
--- a/lib/galaxy/managers/taggable.py
+++ b/lib/galaxy/managers/taggable.py
@@ -5,6 +5,9 @@ Mixins for Taggable model managers and serializers.
# from galaxy import exceptions as galaxy_exceptions
import logging
+
+from galaxy.util import unicodify
+
log = logging.getLogger( __name__ )
@@ -34,7 +37,7 @@ def _tags_from_strings( item, tag_handler, new_tags_list, user=None ):
# TODO: duped from tags manager - de-dupe when moved to taggable mixin
tag_handler.delete_item_tags( user, item )
new_tags_str = ','.join( new_tags_list )
- tag_handler.apply_item_tags( user, item, unicode( new_tags_str.encode( 'utf-8' ), 'utf-8' ) )
+ tag_handler.apply_item_tags( user, item, unicodify( new_tags_str, 'utf-8' ) )
# TODO:!! does the creation of new_tags_list mean there are now more and more unused tag rows in the db?
diff --git a/lib/galaxy/managers/tags.py b/lib/galaxy/managers/tags.py
index 304e198552e..dcc7fa286b9 100644
--- a/lib/galaxy/managers/tags.py
+++ b/lib/galaxy/managers/tags.py
@@ -1,6 +1,8 @@
import logging
import re
+from galaxy.util import unicodify
+from six import string_types
from sqlalchemy.sql import select
from sqlalchemy.sql.expression import func
@@ -41,7 +43,7 @@ class TagManager( object ):
self.delete_item_tags( user, item )
new_tags_str = ','.join( new_tags_list )
- self.apply_item_tags( user, item, unicode( new_tags_str.encode( 'utf-8' ), 'utf-8' ) )
+ self.apply_item_tags( user, item, unicodify( new_tags_str, 'utf-8' ) )
self.app.model.context.flush()
return item.tags
@@ -114,7 +116,7 @@ class TagManager( object ):
def item_has_tag( self, user, item, tag ):
"""Returns true if item is has a given tag."""
# Get tag name.
- if isinstance( tag, basestring ):
+ if isinstance( tag, string_types ):
tag_name = tag
elif isinstance( tag, self.app.model.Tag ):
tag_name = tag.name
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index a101e7a9a38..d3cc43cbb7c 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -17,6 +17,7 @@ from datetime import datetime, timedelta
from itertools import ifilter, imap
from string import Template
from uuid import UUID, uuid4
+from six import string_types
from sqlalchemy import and_, func, not_, or_, true, join, select
from sqlalchemy.orm import joinedload, object_session, aliased
@@ -37,10 +38,11 @@ from galaxy.model.item_attrs import UsesAnnotations
from galaxy.util.dictifiable import Dictifiable
from galaxy.security import get_permitted_actions
from galaxy.util import Params, restore_text, send_mail
-from galaxy.util.multi_byte import is_multi_byte
from galaxy.util import ready_name_for_url, unique_id
-from galaxy.util.bunch import Bunch
+from galaxy.util import unicodify
+from galaxy.util.multi_byte import is_multi_byte
from galaxy.util.hash_util import new_secure_hash
+from galaxy.util.bunch import Bunch
from galaxy.util.directory_hash import directory_hash_id
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web.framework.helpers import to_unicode
@@ -100,8 +102,7 @@ class HasName:
object. If string, convert to unicode object assuming 'utf-8' format.
"""
name = self.name
- if isinstance(name, str):
- name = unicode(name, 'utf-8')
+ name = unicodify( name, 'utf-8' )
return name
@@ -112,18 +113,13 @@ class JobLike:
self.numeric_metrics = []
def add_metric( self, plugin, metric_name, metric_value ):
- if isinstance( plugin, str ):
- plugin = unicode( plugin, 'utf-8' )
-
- if isinstance( metric_name, str ):
- metric_name = unicode( metric_name, 'utf-8' )
-
+ plugin = unicodify( plugin, 'utf-8' )
+ metric_name = unicodify( metric_name, 'utf-8' )
if isinstance( metric_value, numbers.Number ):
metric = self._numeric_metric( plugin, metric_name, metric_value )
self.numeric_metrics.append( metric )
else:
- if isinstance( metric_value, str ):
- metric_value = unicode( metric_value, 'utf-8' )
+ metric_value = unicodify( metric_value, 'utf-8' )
if len( metric_value ) > 1022:
# Truncate these values - not needed with sqlite
# but other backends must need it.
@@ -2178,7 +2174,7 @@ class DatasetInstance( object ):
data_source = source_list
else:
# Convert.
- if isinstance( source_list, str ):
+ if isinstance( source_list, string_types ):
source_list = [ source_list ]
# Loop through sources until viable one is found.
@@ -2413,7 +2409,7 @@ class HistoryDatasetAssociation( DatasetInstance, Dictifiable, UsesAnnotations,
update_time=hda.update_time.isoformat(),
data_type=hda.datatype.__class__.__module__ + '.' + hda.datatype.__class__.__name__,
genome_build=hda.dbkey,
- misc_info=hda.info.strip() if isinstance( hda.info, basestring ) else hda.info,
+ misc_info=hda.info.strip() if isinstance( hda.info, string_types ) else hda.info,
misc_blurb=hda.blurb )
# add tags string list
diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py
index 49f8f79b457..b081a08bd76 100644
--- a/lib/galaxy/model/metadata.py
+++ b/lib/galaxy/model/metadata.py
@@ -14,6 +14,7 @@ import weakref
from os.path import abspath
+from six import string_types
from sqlalchemy.orm import object_session
import galaxy.model
@@ -151,7 +152,7 @@ class MetadataCollection( object ):
JSONified_dict = json.load( open( filename ) )
elif json_dict is not None:
log.debug( 'loading metadata from dict for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
- if isinstance( json_dict, basestring ):
+ if isinstance( json_dict, string_types ):
JSONified_dict = json.loads( json_dict )
elif isinstance( json_dict, dict ):
JSONified_dict = json_dict
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index f636bd24d5a..b84a62364c2 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -18,6 +18,7 @@ from cgi import FieldStorage
from xml.etree import ElementTree
from mako.template import Template
from paste import httpexceptions
+from six import string_types
from galaxy import model
from galaxy.managers import histories
@@ -43,10 +44,12 @@ from galaxy.tools.toolbox import BaseGalaxyToolBox
from galaxy.util import rst_to_html, string_as_bool
from galaxy.util import ExecutionTimer
from galaxy.util import listify
+from galaxy.util import unicodify
from galaxy.tools.parameters.meta import expand_meta_parameters
from galaxy.util.bunch import Bunch
from galaxy.util.expressions import ExpressionContext
from galaxy.util.hash_util import hmac_new
+from galaxy.util.json import json_fix
from galaxy.util.odict import odict
from galaxy.util.template import fill_template
from galaxy.web import url_for
@@ -1191,7 +1194,7 @@ class Tool( object, Dictifiable ):
if isinstance( out_data, odict ):
return job, out_data.items()
else:
- if isinstance( out_data, str ):
+ if isinstance( out_data, string_types ):
message = out_data
else:
message = 'Failure executing tool (invalid data returned from tool execution)'
@@ -1742,7 +1745,7 @@ class Tool( object, Dictifiable ):
return 'true'
else:
return 'false'
- elif isinstance(v, basestring) or isnumber:
+ elif isinstance(v, string_types) or isnumber:
return v
elif isinstance(v, dict) and hasattr(v, '__class__'):
return v
@@ -1850,8 +1853,7 @@ class Tool( object, Dictifiable ):
tool_help = ''
if self.help:
tool_help = self.help.render( static_path=url_for( '/static' ), host_url=url_for( '/', qualified=True ) )
- if type( tool_help ) is not unicode:
- tool_help = unicode( tool_help, 'utf-8' )
+ tool_help = unicodify( tool_help, 'utf-8' )
# create tool versions
tool_versions = []
@@ -2362,16 +2364,5 @@ class BadValue( object ):
self.value = value
-def json_fix( val ):
- if isinstance( val, list ):
- return [ json_fix( v ) for v in val ]
- elif isinstance( val, dict ):
- return dict( [ ( json_fix( k ), json_fix( v ) ) for ( k, v ) in val.iteritems() ] )
- elif isinstance( val, unicode ):
- return val.encode( "utf8" )
- else:
- return val
-
-
class InterruptedUpload( Exception ):
pass
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index a28543404c6..4f695d5062f 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -1,5 +1,6 @@
import json
import re
+from six import string_types
from galaxy.exceptions import ObjectInvalid
from galaxy.model import LibraryDatasetDatasetAssociation
@@ -316,7 +317,7 @@ class DefaultToolAction( object ):
# or an actual object to copy.
metadata_source = output.metadata_source
if metadata_source:
- if isinstance( metadata_source, basestring ):
+ if isinstance( metadata_source, string_types ):
metadata_source = inp_data[metadata_source]
if metadata_source is not None:
diff --git a/lib/galaxy/tools/data_manager/manager.py b/lib/galaxy/tools/data_manager/manager.py
index a2df7de272b..9b4570e1473 100644
--- a/lib/galaxy/tools/data_manager/manager.py
+++ b/lib/galaxy/tools/data_manager/manager.py
@@ -1,6 +1,7 @@
import errno
import json
import os
+from six import string_types
from galaxy import util
from galaxy.util.odict import odict
@@ -369,7 +370,7 @@ class DataManager( object ):
value = kwd.get( column_name )
if data_table_name in self.value_translation_by_data_table_column and column_name in self.value_translation_by_data_table_column[ data_table_name ]:
for value_translation in self.value_translation_by_data_table_column[ data_table_name ][ column_name ]:
- if isinstance( value_translation, basestring ):
+ if isinstance( value_translation, string_types ):
value = fill_template( value_translation, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd )
else:
value = value_translation( value )
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index ba638ab9ae7..e6a2314601e 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -1,6 +1,7 @@
import json
import os
import tempfile
+from six import string_types
from galaxy import model
from galaxy.util.object_wrapper import wrap_with_safe_string
@@ -542,7 +543,7 @@ class ToolEvaluator( object ):
return None
def __build_config_file_text( self, content ):
- if isinstance( content, basestring ):
+ if isinstance( content, string_types ):
return content, True
content_format = content["format"]
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 10f4ecbbe76..05a20963a94 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -6,7 +6,9 @@ import logging
import re
import os
import os.path
+from six import string_types
from xml.etree.ElementTree import XML
+
from galaxy import util
from galaxy.web import form_builder
from galaxy.util import string_as_bool, sanitize_param, unicodify
@@ -30,7 +32,7 @@ WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' )
def contains_workflow_parameter(value, search=False):
- if not isinstance( value, basestring ):
+ if not isinstance( value, string_types ):
return False
if search and WORKFLOW_PARAMETER_REGULAR_EXPRESSION.search(value):
return True
@@ -141,8 +143,6 @@ class ToolParameter( object, Dictifiable ):
def to_string( self, value, app ):
"""Convert a value to a string representation suitable for persisting"""
- if not isinstance( value, basestring ):
- value = str( value )
return unicodify( value )
def to_python( self, value, app ):
@@ -158,9 +158,6 @@ class ToolParameter( object, Dictifiable ):
return self.to_string( value, app )
def value_from_basic( self, value, app, ignore_errors=False ):
- # HACK: Some things don't deal with unicode well, psycopg problem?
- if type( value ) == unicode:
- value = str( value )
# Handle Runtime values (valid for any parameter?)
if isinstance( value, dict ) and '__class__' in value and value['__class__'] == "RuntimeValue":
return RuntimeValue()
@@ -184,7 +181,7 @@ class ToolParameter( object, Dictifiable ):
"""Called via __str__ when used in the Cheetah template"""
if value is None:
value = ""
- elif not isinstance( value, basestring ):
+ elif not isinstance( value, string_types ):
value = str( value )
if self.tool is None or self.tool.options.sanitize:
if self.sanitizer:
@@ -555,7 +552,7 @@ class FileToolParameter( ToolParameter ):
def to_string( self, value, app ):
if value in [ None, '' ]:
return None
- elif isinstance( value, unicode ) or isinstance( value, str ):
+ elif isinstance( value, string_types ):
return value
elif isinstance( value, dict ):
# or should we jsonify?
@@ -568,7 +565,7 @@ class FileToolParameter( ToolParameter ):
def to_python( self, value, app ):
if value is None:
return None
- elif isinstance( value, unicode ) or isinstance( value, str ):
+ elif isinstance( value, string_types ):
return value
else:
raise Exception( "FileToolParameter cannot be persisted" )
@@ -907,7 +904,7 @@ class SelectToolParameter( ToolParameter ):
if value == '':
value = None
else:
- if isinstance( value, basestring ):
+ if isinstance( value, string_types ):
# Split on all whitespace. This not only provides flexibility
# in interpreting values but also is needed because many browsers
# use \r\n to separate lines.
@@ -1172,7 +1169,7 @@ class ColumnListParameter( SelectToolParameter ):
"""
if self.multiple:
# split on newline and ,
- if isinstance( value, list ) or isinstance( value, basestring ):
+ if isinstance( value, list ) or isinstance( value, string_types ):
column_list = []
if not isinstance( value, list ):
value = value.split( '\n' )
@@ -1196,7 +1193,7 @@ class ColumnListParameter( SelectToolParameter ):
@staticmethod
def _strip_c(column):
- if isinstance(column, basestring):
+ if isinstance(column, string_types):
if column.startswith( 'c' ):
column = column.strip().lower()[1:]
return column
@@ -1837,7 +1834,7 @@ class DataToolParameter( BaseDataToolParameter ):
raise ValueError( "History does not include a dataset of the required format / build" )
if value in [ None, "None", '' ]:
return None
- if isinstance( value, str ) and value.find( "," ) > 0:
+ if isinstance( value, string_types ) and value.find( "," ) > 0:
value = [ int( value_part ) for value_part in value.split( "," ) ]
if isinstance( value, list ):
rval = []
@@ -1900,7 +1897,7 @@ class DataToolParameter( BaseDataToolParameter ):
return rval
def to_string( self, value, app ):
- if value is None or isinstance( value, basestring ):
+ if value is None or isinstance( value, string_types ):
return value
elif isinstance( value, int ):
return str( value )
@@ -1934,7 +1931,7 @@ class DataToolParameter( BaseDataToolParameter ):
else:
return app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( value ) )
- if isinstance(value, str) and value.find(",") > -1:
+ if isinstance(value, string_types) and value.find(",") > -1:
values = value.split(",")
return [v for v in map( single_to_python, values ) if v not in none_values]
else:
@@ -2150,7 +2147,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" )
if value in [None, "None"]:
return None
- if isinstance( value, str ) and value.find( "," ) > 0:
+ if isinstance( value, string_types ) and value.find( "," ) > 0:
value = [ int( value_part ) for value_part in value.split( "," ) ]
elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ):
rval = value
@@ -2168,7 +2165,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
if isinstance( value, dict ) and 'src' in value and 'id' in value:
if value['src'] == 'hdca':
rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.security.decode_id(value['id']) )
- elif isinstance( value, basestring ):
+ elif isinstance( value, string_types ):
if value.startswith( "dce:" ):
rval = trans.sa_session.query( trans.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] )
elif value.startswith( "hdca:" ):
@@ -2182,7 +2179,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
return rval
def to_string( self, value, app ):
- if value is None or isinstance( value, basestring ):
+ if value is None or isinstance( value, string_types ):
return value
elif isinstance( value, RuntimeValue ):
return None
@@ -2201,7 +2198,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
if value is None or value == '' or value == 'None':
return value
- if not isinstance( value, basestring ):
+ if not isinstance( value, string_types ):
raise ValueError( "Can not convert data collection parameter value to python object - %s" % value )
if value.startswith( "dce:" ):
@@ -2358,7 +2355,7 @@ class LibraryDatasetToolParameter( ToolParameter ):
encoded_id = None
if isinstance(item, dict):
encoded_id = item.get('id')
- elif isinstance(item, basestring):
+ elif isinstance(item, string_types):
encoded_id = item
else:
lst = []
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index e82685e4dfd..da07012a932 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -8,6 +8,8 @@ log = logging.getLogger( __name__ )
import os
import StringIO
import unicodedata
+from six import text_type
+
from basic import ToolParameter
from galaxy.datatypes import sniff
from galaxy.util import inflector
@@ -32,7 +34,7 @@ class Group( object, Dictifiable ):
def value_to_basic( self, value, app ):
"""
Convert value to a (possibly nested) representation using only basic
- types (dict, list, tuple, str, unicode, int, long, float, bool, None)
+ types (dict, list, tuple, string_types, int, long, float, bool, None)
"""
return value
@@ -431,7 +433,7 @@ class UploadDataset( Group ):
if ftp_files is not None:
# Normalize input paths to ensure utf-8 encoding is normal form c.
# This allows for comparison when the filesystem uses a different encoding than the browser.
- ftp_files = [unicodedata.normalize('NFC', f) for f in ftp_files if isinstance(f, unicode)]
+ ftp_files = [unicodedata.normalize('NFC', f) for f in ftp_files if isinstance(f, text_type)]
if trans.user is None:
log.warning( 'Anonymous user passed values in ftp_files: %s' % ftp_files )
ftp_files = []
@@ -443,7 +445,7 @@ class UploadDataset( Group ):
path = relpath( os.path.join( dirpath, filename ), user_ftp_dir )
if not os.path.islink( os.path.join( dirpath, filename ) ):
# Normalize filesystem paths
- if isinstance(path, unicode):
+ if isinstance(path, text_type):
valid_files.append(unicodedata.normalize('NFC', path ))
else:
valid_files.append(path)
diff --git a/lib/galaxy/tools/parameters/sanitize.py b/lib/galaxy/tools/parameters/sanitize.py
index 5b70f5742d6..ac22df8ac9d 100644
--- a/lib/galaxy/tools/parameters/sanitize.py
+++ b/lib/galaxy/tools/parameters/sanitize.py
@@ -4,6 +4,8 @@ Tool Parameter specific sanitizing.
import logging
import string
+from six import string_types
+
import galaxy.util
log = logging.getLogger( __name__ )
@@ -134,7 +136,7 @@ class ToolParameterSanitizer( object ):
def restore_param( self, value ):
if self.sanitize:
- if isinstance( value, basestring ):
+ if isinstance( value, string_types ):
return self.restore_text( value )
elif isinstance( value, list ):
return map( self.restore_text, value )
@@ -160,7 +162,7 @@ class ToolParameterSanitizer( object ):
"""Clean incoming parameters (strings or lists)"""
if not self.sanitize:
return value
- if isinstance( value, basestring ):
+ if isinstance( value, string_types ):
return self.sanitize_text( value )
elif isinstance( value, list ):
return map( self.sanitize_text, value )
diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index d802fd8429e..6451d3d44ba 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -4,6 +4,8 @@ Classes related to parameter validation.
import logging
import re
+from six import string_types
+
from galaxy import model
from galaxy import util
@@ -383,7 +385,7 @@ class MetadataInDataTableColumnValidator( Validator ):
self.valid_values = []
self._data_table_content_version = None
self._tool_data_table = tool_data_table
- if isinstance( metadata_column, basestring ):
+ if isinstance( metadata_column, string_types ):
metadata_column = tool_data_table.columns[ metadata_column ]
self._metadata_column = metadata_column
self._load_values()
diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
index 83b7b50e41a..916cab780b0 100644
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -1,6 +1,8 @@
import logging
import os
import os.path
+from six import string_types
+
import galaxy.tools.parameters.basic
import galaxy.tools.parameters.grouping
from galaxy.util import string_as_bool
@@ -117,7 +119,7 @@ class ToolTestBuilder( object ):
log.info( msg )
def __split_if_str( self, value ):
- split = isinstance(value, str)
+ split = isinstance(value, string_types)
if split:
value = value.split(",")
return value
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 6be669b0936..6278e64e95c 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -22,21 +22,23 @@ import sys
import time
import tempfile
import threading
-from six.moves.urllib import parse as urlparse
-from six import iteritems
-
-from galaxy.util import json
-from datetime import datetime
-
-from six import PY3
-from six import string_types, text_type
-from six.moves import xrange
-from six.moves import email_mime_text
-from six.moves import zip
from os.path import relpath
from hashlib import md5
+from six import binary_type
+from six import iteritems
+from six import PY3
+from six import string_types, text_type
+from six.moves import email_mime_text
+from six.moves.urllib import parse as urlparse
+from six.moves import xrange
+from six.moves import zip
+from xml.etree import ElementTree, ElementInclude
+
+from galaxy.util import json
+from datetime import datetime
+
try:
import docutils.core as docutils_core
import docutils.writers.html4css1 as docutils_html4css1
@@ -44,8 +46,6 @@ except ImportError:
docutils_core = None
docutils_html4css1 = None
-from xml.etree import ElementTree, ElementInclude
-
from .inflection import Inflector, English
inflector = Inflector(English)
@@ -848,17 +848,25 @@ def roundify(amount, sfs=2):
return amount[0:sfs] + '0' * (len(amount) - sfs)
-def unicodify( value, encoding=DEFAULT_ENCODING, error='replace', default=None ):
+def unicodify(value, encoding=DEFAULT_ENCODING, error='replace', default=None):
"""
- Returns a unicode string or None
+ Returns a unicode string or None.
"""
-
- if isinstance( value, text_type ):
- return value
+ if value is None:
+ return None
try:
- return text_type( str( value ), encoding, error )
- except:
+ if not isinstance(value, string_types) and not isinstance(value, binary_type):
+ # In Python 2, value is not an instance of basestring
+ # In Python 3, value is not an instance of bytes or str
+ value = str(value)
+ # Now in Python 2, value is an instance of basestring, but may be not unicode
+ # Now in Python 3, value is an instance of bytes or str
+ if not isinstance(value, text_type):
+ value = text_type(value, encoding, error)
+ except Exception:
+ log.exception("value %s could not be coerced to unicode" % value)
return default
+ return value
def smart_str(s, encoding='utf-8', strings_only=False, errors='strict'):
diff --git a/lib/galaxy/util/sanitize_html.py b/lib/galaxy/util/sanitize_html.py
index 5f34e9fdda1..2aabbe2dccd 100644
--- a/lib/galaxy/util/sanitize_html.py
+++ b/lib/galaxy/util/sanitize_html.py
@@ -5,8 +5,8 @@ HTML Sanitizer (ripped from feedparser)
import re
import sgmllib
+from galaxy.util import unicodify
from six import unichr
-from six import text_type as unicode
# reversable htmlentitydefs mappings for Python 2.2
@@ -22,6 +22,7 @@ except:
name2codepoint[name] = ord(codepoint)
codepoint2name[ord(codepoint)] = name
+
_cp1252 = {
unichr(128): unichr(8364), # euro sign
unichr(130): unichr(8218), # single low-9 quotation mark
@@ -87,8 +88,6 @@ class _BaseHTMLProcessor(sgmllib.SGMLParser):
data = re.sub(r'<([^<>\s]+?)\s*/>', self._shorttag_replace, data)
data = data.replace(''', "'")
data = data.replace('"', '"')
- if self.encoding and isinstance(data, unicode):
- data = data.encode(self.encoding)
sgmllib.SGMLParser.feed(self, data)
sgmllib.SGMLParser.close(self)
@@ -111,23 +110,12 @@ class _BaseHTMLProcessor(sgmllib.SGMLParser):
for key, value in attrs:
value = value.replace('>', '>').replace('<', '<').replace('"', '"')
value = self.bare_ampersand.sub("&", value)
- # thanks to Kevin Marks for this breathtaking hack to deal with (valid) high-bit attribute values in UTF-8 feeds
- if isinstance(value, unicode):
- try:
- value = unicode(value, self.encoding)
- except:
- value = unicode(value, 'iso-8859-1')
- uattrs.append((unicode(key, self.encoding), value))
- strattrs = u''.join([u' %s="%s"' % (key, val) for key, val in uattrs])
- if self.encoding:
- try:
- strattrs = strattrs.encode(self.encoding)
- except:
- pass
+ uattrs.append((key, value))
+ strattrs = ''.join([' %s="%s"' % (k, v) for k, v in uattrs])
if tag in self.elements_no_end_tag:
- self.pieces.append('<%(tag)s%(strattrs)s />' % locals())
+ self.pieces.append('<%s%s />' % (tag, strattrs))
else:
- self.pieces.append('<%(tag)s%(strattrs)s>' % locals())
+ self.pieces.append('<%s%s>' % (tag, strattrs))
def unknown_endtag(self, tag):
# called for each end tag, e.g. for , tag will be 'pre'
@@ -446,7 +434,7 @@ class _HTMLSanitizer(_BaseHTMLProcessor):
def sanitize_html(htmlSource, encoding="utf-8", type="text/html"):
p = _HTMLSanitizer(encoding, type)
- p.feed(htmlSource)
+ p.feed(unicodify(htmlSource, encoding))
data = p.output()
data = data.strip().replace('\r\n', '\n')
return data
diff --git a/lib/galaxy/visualization/data_providers/registry.py b/lib/galaxy/visualization/data_providers/registry.py
index 9ab9a980356..4fd655fb6f2 100644
--- a/lib/galaxy/visualization/data_providers/registry.py
+++ b/lib/galaxy/visualization/data_providers/registry.py
@@ -1,3 +1,5 @@
+from six import string_types
+
from galaxy.visualization.data_providers.basic import ColumnDataProvider
from galaxy.visualization.data_providers import genome
from galaxy.model import NoConverterException
@@ -97,7 +99,7 @@ class DataProviderRegistry( object ):
original_dataset=original_dataset )
else:
source_list = data_provider_mapping[ source ]
- if isinstance( source_list, str ):
+ if isinstance( source_list, string_types ):
source_list = [ source_list ]
# Find a valid data provider in the source list.
diff --git a/lib/galaxy/visualization/plugins/config_parser.py b/lib/galaxy/visualization/plugins/config_parser.py
index eb79095d362..a0e8d39aca1 100644
--- a/lib/galaxy/visualization/plugins/config_parser.py
+++ b/lib/galaxy/visualization/plugins/config_parser.py
@@ -1,3 +1,5 @@
+from six import string_types
+
import galaxy.model
from galaxy import util
@@ -290,7 +292,7 @@ class DataSourceParser( object ):
# TODO: too dangerous - constrain these to some allowed list
# TODO: does this err if no test_attr - it should...
test_attr = test_elem.get( 'test_attr' )
- test_attr = test_attr.split( self.ATTRIBUTE_SPLIT_CHAR ) if isinstance( test_attr, str ) else []
+ test_attr = test_attr.split( self.ATTRIBUTE_SPLIT_CHAR ) if isinstance( test_attr, string_types ) else []
# log.debug( 'test_type: %s, test_attr: %s, test_result: %s', test_type, test_attr, test_result )
# build a lambda function that gets the desired attribute to test
diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index 8340b227d0b..68d4753e546 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -5,6 +5,7 @@ import logging
import operator
import re
+from six import string_types, text_type
from sqlalchemy import true
from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
@@ -221,7 +222,7 @@ class BaseAPIController( BaseController ):
def _parse_serialization_params( self, kwd, default_view ):
view = kwd.get( 'view', None )
keys = kwd.get( 'keys' )
- if isinstance( keys, basestring ):
+ if isinstance( keys, string_types ):
keys = keys.split( ',' )
return dict( view=view, keys=keys, default_view=default_view )
@@ -373,11 +374,11 @@ class ExportsHistoryMixin:
def queue_history_export( self, trans, history, gzip=True, include_hidden=False, include_deleted=False ):
# Convert options to booleans.
- if isinstance( gzip, basestring ):
+ if isinstance( gzip, string_types ):
gzip = ( gzip in [ 'True', 'true', 'T', 't' ] )
- if isinstance( include_hidden, basestring ):
+ if isinstance( include_hidden, string_types ):
include_hidden = ( include_hidden in [ 'True', 'true', 'T', 't' ] )
- if isinstance( include_deleted, basestring ):
+ if isinstance( include_deleted, string_types ):
include_deleted = ( include_deleted in [ 'True', 'true', 'T', 't' ] )
# Run job to do export.
@@ -1563,7 +1564,7 @@ class UsesFormDefinitionsMixin:
else:
# Form was submitted via refresh_on_change
widget.value = 'new'
- elif value == unicode( 'none' ):
+ elif value == text_type( 'none' ):
widget.value = ''
else:
widget.value = value
diff --git a/lib/galaxy/web/base/controllers/admin.py b/lib/galaxy/web/base/controllers/admin.py
index 57ffca7b485..4da30f61b79 100644
--- a/lib/galaxy/web/base/controllers/admin.py
+++ b/lib/galaxy/web/base/controllers/admin.py
@@ -1,6 +1,7 @@
import logging
import os
from datetime import datetime, timedelta
+from six import string_types
from string import punctuation as PUNCTUATION
from sqlalchemy import and_, false, func, or_
@@ -1129,7 +1130,7 @@ class Admin( object ):
# write the configured sanitize_whitelist_file with new whitelist
# and update in-memory list.
with open(trans.app.config.sanitize_whitelist_file, 'wt') as f:
- if isinstance(tools_to_whitelist, basestring):
+ if isinstance(tools_to_whitelist, string_types):
tools_to_whitelist = [tools_to_whitelist]
new_whitelist = sorted([tid for tid in tools_to_whitelist if tid in trans.app.toolbox.tools_by_id])
f.write("\n".join(new_whitelist))
diff --git a/lib/galaxy/web/form_builder.py b/lib/galaxy/web/form_builder.py
index 2fecaf3f5d1..7cab4188cdd 100644
--- a/lib/galaxy/web/form_builder.py
+++ b/lib/galaxy/web/form_builder.py
@@ -5,6 +5,7 @@ import os
import time
import logging
+from six import string_types
from operator import itemgetter
from cgi import escape
from galaxy.util import restore_text, relpath, nice_size, unicodify
@@ -42,8 +43,6 @@ class TextField(BaseField):
def get_html( self, prefix="", disabled=False ):
value = self.value
- if not isinstance( value, basestring ):
- value = str( value )
value = unicodify( value )
return unicodify( ''
% ( prefix, self.name, self.size, escape( value, quote=True ), self.get_disabled_str( disabled ) ) )
@@ -114,7 +113,7 @@ class CheckboxField(BaseField):
def __init__( self, name, checked=None, refresh_on_change=False, refresh_on_change_values=None ):
self.name = name
- self.checked = ( checked is True ) or ( isinstance( checked, basestring ) and ( checked.lower() in ( "yes", "true", "on" ) ) )
+ self.checked = ( checked is True ) or ( isinstance( checked, string_types ) and ( checked.lower() in ( "yes", "true", "on" ) ) )
self.refresh_on_change = refresh_on_change
self.refresh_on_change_values = refresh_on_change_values or []
if self.refresh_on_change:
@@ -140,7 +139,7 @@ class CheckboxField(BaseField):
return isinstance( value, list ) and ( '__CHECKED__' in value or len( value ) == 2 )
def set_checked(self, value):
- if isinstance( value, basestring ):
+ if isinstance( value, string_types ):
self.checked = value.lower() in [ "yes", "true", "on" ]
else:
self.checked = value
@@ -328,10 +327,6 @@ class SelectField(BaseField):
rval.append( '' % ( prefix, self.name ) ) # placeholder for the insertion of the Select All/Unselect All buttons
for text, value, selected in self.options:
style = ""
- if not isinstance( value, basestring ):
- value = str( value )
- if not isinstance( text, basestring ):
- text = str( text )
text = unicodify( text )
escaped_value = escape( unicodify( value ), quote=True )
uniq_id = "%s%s|%s" % (prefix, self.name, escaped_value)
@@ -386,14 +381,10 @@ class SelectField(BaseField):
if selected:
selected_text = " selected"
last_selected_value = value
- if not isinstance( last_selected_value, basestring ):
+ if not isinstance( last_selected_value, string_types ):
last_selected_value = str( last_selected_value )
else:
selected_text = ""
- if not isinstance( value, basestring ):
- value = str( value )
- if not isinstance( text, basestring ):
- text = str( text )
rval.append( '' % ( escape( unicodify( value ), quote=True ), selected_text, escape( unicodify( text ), quote=True ) ) )
if last_selected_value:
last_selected_value = ' last_selected_value="%s"' % escape( unicodify( last_selected_value ), quote=True )
diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py
index 85db7e3df42..c560427dcff 100644
--- a/lib/galaxy/web/framework/base.py
+++ b/lib/galaxy/web/framework/base.py
@@ -12,6 +12,7 @@ import types
import routes
import webob
+from six import string_types
from Cookie import SimpleCookie
# We will use some very basic HTTP/wsgi utilities from the paste library
@@ -209,7 +210,7 @@ class WebApplication( object ):
if isinstance( body, ( types.GeneratorType, list, tuple ) ):
# Recursively stream the iterable
return flatten( body )
- elif isinstance( body, basestring ):
+ elif isinstance( body, string_types ):
# Wrap the string so it can be iterated
return [ body ]
elif body is None:
diff --git a/lib/galaxy/web/framework/decorators.py b/lib/galaxy/web/framework/decorators.py
index 9830bfbb21f..65aca60d28d 100644
--- a/lib/galaxy/web/framework/decorators.py
+++ b/lib/galaxy/web/framework/decorators.py
@@ -1,6 +1,7 @@
import inspect
from traceback import format_exc
from functools import wraps
+from six import string_types
import paste.httpexceptions
@@ -163,7 +164,7 @@ def __extract_payload_from_request(trans, func, kwargs):
for arg in named_args:
payload.pop(arg, None)
for k, v in payload.iteritems():
- if isinstance(v, (str, unicode)):
+ if isinstance(v, string_types):
try:
payload[k] = loads(v)
except:
diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py
index f84facaaa39..6ca9b41cdcb 100644
--- a/lib/galaxy/web/framework/helpers/__init__.py
+++ b/lib/galaxy/web/framework/helpers/__init__.py
@@ -4,7 +4,9 @@ Galaxy web framework helpers
import time
from datetime import datetime, timedelta
+
from galaxy.util import hash_util
+from galaxy.util import unicodify
from galaxy.util.json import safe_dumps as dumps # noqa (used by mako templates)
from webhelpers import date
from webhelpers.html.tags import stylesheet_link, javascript_link
@@ -103,11 +105,7 @@ def to_unicode( a_string ):
Convert a string to unicode in utf-8 format; if string is already unicode,
does nothing because string's encoding cannot be determined by introspection.
"""
- a_string_type = type( a_string )
- if a_string_type is str:
- return unicode( a_string, 'utf-8' )
- elif a_string_type is unicode:
- return a_string
+ return unicodify( a_string, 'utf-8' )
def is_true( val ):
diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py
index b0204953a74..489ab60421b 100644
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -1,6 +1,11 @@
import logging
import math
+from markupsafe import escape
+from six import text_type
+from six import string_types
+from sqlalchemy.sql.expression import and_, func, or_, null, false, true
+
from galaxy.model.item_attrs import RuntimeException, UsesAnnotations, UsesItemRatings
from galaxy.util import sanitize_text
from galaxy.util.json import loads, dumps
@@ -8,9 +13,6 @@ from galaxy.util.odict import odict
from galaxy.web.framework import decorators
from galaxy.web.framework import url_for
from galaxy.web.framework.helpers import iff
-from markupsafe import escape
-
-from sqlalchemy.sql.expression import and_, func, or_, null, false, true
log = logging.getLogger( __name__ )
@@ -73,11 +75,11 @@ class Grid( object ):
base_filter = self.default_filter.copy()
base_sort_key = self.default_sort_key
if self.preserve_state:
- pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name )
+ pref_name = text_type( self.__class__.__name__ + self.cur_filter_pref_name )
if pref_name in trans.get_user().preferences:
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 )
+ pref_name = text_type( self.__class__.__name__ + self.cur_sort_key_pref_name )
if pref_name in trans.get_user().preferences:
base_sort_key = loads( trans.get_user().preferences[pref_name] )
# Build initial query
@@ -113,16 +115,16 @@ class Grid( object ):
# Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings.
def loads_recurse(item):
decoded_list = []
- if isinstance( item, basestring):
+ if isinstance( item, string_types):
try:
# Not clear what we're decoding, so recurse to ensure that we catch everything.
decoded_item = loads( item )
if isinstance( decoded_item, list):
decoded_list = loads_recurse( decoded_item )
else:
- decoded_list = [ unicode( decoded_item ) ]
+ decoded_list = [ text_type( decoded_item ) ]
except ValueError:
- decoded_list = [ unicode( item ) ]
+ decoded_list = [ text_type( item ) ]
elif isinstance( item, list):
for element in item:
a_list = loads_recurse( element )
@@ -136,7 +138,7 @@ class Grid( object ):
if len( column_filter ) == 1:
column_filter = column_filter[0]
# Interpret ',' as a separator for multiple terms.
- if isinstance( column_filter, basestring ) and column_filter.find(',') != -1:
+ if isinstance( column_filter, string_types ) and column_filter.find(',') != -1:
column_filter = column_filter.split(',')
# Check if filter is empty
@@ -145,7 +147,7 @@ class Grid( object ):
column_filter = [x for x in column_filter if x != '']
if len(column_filter) == 0:
continue
- elif isinstance(column_filter, basestring):
+ elif isinstance(column_filter, string_types):
# If filter criterion is empty, do nothing.
if column_filter == '':
continue
@@ -159,14 +161,12 @@ class Grid( object ):
# that we can encode to UTF-8 and thus handle user input to filters.
if isinstance( column_filter, list ):
# Filter is a list; process each item.
- for filter in column_filter:
- if not isinstance( filter, basestring ):
- filter = unicode( filter ).encode("utf-8")
+ column_filter = [ text_type(_).encode('utf-8') if not isinstance(_, string_types) else _ for _ in column_filter ]
extra_url_args[ "f-" + column.key ] = dumps( column_filter )
else:
# Process singleton filter.
- if not isinstance( column_filter, basestring ):
- column_filter = unicode(column_filter)
+ if not isinstance( column_filter, string_types ):
+ column_filter = text_type(column_filter)
extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8")
# Process sort arguments.
sort_key = None
@@ -231,14 +231,14 @@ class Grid( object ):
self.cur_filter_dict = cur_filter_dict
# 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( dumps( cur_filter_dict ) )
+ pref_name = text_type( self.__class__.__name__ + self.cur_filter_pref_name )
+ trans.get_user().preferences[pref_name] = text_type( 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( dumps( sort_key ) )
+ pref_name = text_type( self.__class__.__name__ + self.cur_sort_key_pref_name )
+ trans.get_user().preferences[pref_name] = text_type( dumps( sort_key ) )
trans.sa_session.flush()
# Log grid view.
- context = unicode( self.__class__.__name__ )
+ context = text_type( self.__class__.__name__ )
params = cur_filter_dict.copy()
params['sort'] = sort_key
params['async'] = ( 'async' in kwargs )
@@ -248,7 +248,7 @@ class Grid( object ):
# is effectively 'wiped' out. Nate believes it has something to do with our use of session( autocommit=True )
# in mapping.py. If you change that to False, the log_action doesn't affect the query
# Below, I'm rendering the template first (that uses query), then calling log_action, then returning the page
- # trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params )
+ # trans.log_action( trans.get_user(), text_type( "grid.view" ), context, params )
# Render grid.
def url( *args, **kwargs ):
@@ -310,7 +310,7 @@ class Grid( object ):
# Pass back kwargs so that grid template can set and use args without
# grid explicitly having to pass them.
kwargs=kwargs )
- trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params )
+ trans.log_action( trans.get_user(), text_type( "grid.view" ), context, params )
return page
def get_ids( self, **kwargs ):
@@ -429,7 +429,7 @@ class TextColumn( GridColumn ):
def get_filter( self, trans, user, column_filter ):
""" Returns a SQLAlchemy criterion derived from column_filter. """
- if isinstance( column_filter, basestring ):
+ if isinstance( column_filter, string_types ):
return self.get_single_filter( user, column_filter )
elif isinstance( column_filter, list ):
clause_list = []
diff --git a/lib/galaxy/web/framework/middleware/translogger.py b/lib/galaxy/web/framework/middleware/translogger.py
index 0af2ebbf79b..a112685472b 100644
--- a/lib/galaxy/web/framework/middleware/translogger.py
+++ b/lib/galaxy/web/framework/middleware/translogger.py
@@ -7,6 +7,7 @@ Middleware for logging requests, using Apache combined log format
import logging
import time
import urllib
+from six import string_types
class TransLogger(object):
@@ -104,9 +105,9 @@ def make_filter(
setup_console_handler=True,
set_logger_level=logging.DEBUG):
from paste.util.converters import asbool
- if isinstance(logging_level, basestring):
+ if isinstance(logging_level, string_types):
logging_level = logging._levelNames[logging_level]
- if isinstance(set_logger_level, basestring):
+ if isinstance(set_logger_level, string_types):
set_logger_level = logging._levelNames[set_logger_level]
return TransLogger(
app,
diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index ba942a5723c..10424a154b2 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -16,6 +16,7 @@ import mako.runtime
import mako.lookup
from babel.support import Translations
from babel import Locale
+from six import string_types
from sqlalchemy import and_, true
from sqlalchemy.orm.exc import NoResultFound
from sqlalchemy.orm import joinedload
@@ -277,7 +278,7 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
# singular match
def matches_allowed_origin( origin, allowed_origin ):
- if isinstance( allowed_origin, str ):
+ if isinstance( allowed_origin, string_types ):
return origin == allowed_origin
match = allowed_origin.match( origin )
return match and match.group() == origin
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index eae3004ae58..b80c228a804 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -1,6 +1,8 @@
"""
API operations on the contents of a history dataset.
"""
+from six import string_types
+
from galaxy import model
from galaxy import exceptions as galaxy_exceptions
from galaxy import web
@@ -30,7 +32,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
def _parse_serialization_params( self, kwd, default_view ):
view = kwd.get( 'view', None )
keys = kwd.get( 'keys' )
- if isinstance( keys, basestring ):
+ if isinstance( keys, string_types ):
keys = keys.split( ',' )
return dict( view=view, keys=keys, default_view=default_view )
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 64f045f7e96..1a6ac72c7a4 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -7,6 +7,7 @@ API operations on a jobs.
import json
import logging
+from six import string_types
from sqlalchemy import and_, false, or_
from sqlalchemy.orm import aliased
@@ -73,7 +74,7 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ):
def build_and_apply_filters( query, objects, filter_func ):
if objects is not None:
- if isinstance( objects, basestring ):
+ if isinstance( objects, string_types ):
query = query.filter( filter_func( objects ) )
elif isinstance( objects, list ):
t = []
@@ -310,7 +311,7 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ):
)
)
else:
- if isinstance( payload[ 'state' ], basestring ):
+ if isinstance( payload[ 'state' ], string_types ):
query = query.filter( trans.app.model.Job.state == payload[ 'state' ] )
elif isinstance( payload[ 'state' ], list ):
o = []
diff --git a/lib/galaxy/webapps/galaxy/api/lda_datasets.py b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
index 6dff54fdf4c..687459afd38 100644
--- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
@@ -8,6 +8,7 @@ import string
import sys
import tempfile
import zipfile
+
from galaxy import exceptions
from galaxy import util
from galaxy import web
diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py
index 17a3afd3f5c..7f40a214d1f 100644
--- a/lib/galaxy/webapps/galaxy/api/visualizations.py
+++ b/lib/galaxy/webapps/galaxy/api/visualizations.py
@@ -4,6 +4,7 @@ Visualizations resource control over the API.
NOTE!: this is a work in progress and functionality and data structures
may change often.
"""
+from six import string_types
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import UsesVisualizationMixin
@@ -170,7 +171,7 @@ class VisualizationsController( BaseAPIController, UsesVisualizationMixin, Shara
for key, val in payload.items():
# TODO: validate types in VALID_TYPES/registry names at the mixin/model level?
if key == 'type':
- if not ( isinstance( val, str ) or isinstance( val, unicode ) ):
+ if not isinstance( val, string_types ):
raise ValidationError( '%s must be a string or unicode: %s' % ( key, str( type( val ) ) ) )
val = util.sanitize_html.sanitize_html( val, 'utf-8' )
elif key == 'config':
@@ -178,22 +179,22 @@ class VisualizationsController( BaseAPIController, UsesVisualizationMixin, Shara
raise ValidationError( '%s must be a dictionary: %s' % ( key, str( type( val ) ) ) )
elif key == 'annotation':
- if not ( isinstance( val, str ) or isinstance( val, unicode ) ):
+ if not isinstance( val, string_types ):
raise ValidationError( '%s must be a string or unicode: %s' % ( key, str( type( val ) ) ) )
val = util.sanitize_html.sanitize_html( val, 'utf-8' )
# these are keys that actually only be *updated* at the revision level and not here
# (they are still valid for create, tho)
elif key == 'title':
- if not ( isinstance( val, str ) or isinstance( val, unicode ) ):
+ if not isinstance( val, string_types ):
raise ValidationError( '%s must be a string or unicode: %s' % ( key, str( type( val ) ) ) )
val = util.sanitize_html.sanitize_html( val, 'utf-8' )
elif key == 'slug':
- if not ( isinstance( val, str ) or isinstance( val, unicode ) ):
+ if not isinstance( val, string_types ):
raise ValidationError( '%s must be a string: %s' % ( key, str( type( val ) ) ) )
val = util.sanitize_html.sanitize_html( val, 'utf-8' )
elif key == 'dbkey':
- if not ( isinstance( val, str ) or isinstance( val, unicode ) ):
+ if not isinstance( val, string_types ):
raise ValidationError( '%s must be a string or unicode: %s' % ( key, str( type( val ) ) ) )
val = util.sanitize_html.sanitize_html( val, 'utf-8' )
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index 92ffd7d5ff7..dc671b12ca5 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -3,6 +3,7 @@ import os
import shutil
from sqlalchemy import false, or_
+from six import string_types
import tool_shed.repository_types.util as rt_util
from admin import AdminGalaxy
@@ -1334,7 +1335,7 @@ class AdminToolshed( AdminGalaxy ):
repo_info_dicts = []
repo_info_dict = kwd.get( 'repo_info_dict', None )
if repo_info_dict:
- if isinstance( repo_info_dict, basestring ):
+ if isinstance( repo_info_dict, string_types ):
repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict )
else:
# Entering this else block occurs only if the tool_shed_repository does not include any valid tools.
diff --git a/lib/galaxy/webapps/galaxy/controllers/data_manager.py b/lib/galaxy/webapps/galaxy/controllers/data_manager.py
index 9a7337f19bd..6bfbd241ccd 100644
--- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py
+++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py
@@ -1,4 +1,5 @@
from markupsafe import escape
+from six import string_types
import paste.httpexceptions
import galaxy.queue_worker
@@ -87,7 +88,7 @@ class DataManager( BaseUIController ):
@web.expose
@web.require_admin
def reload_tool_data_tables( self, trans, table_name=None, **kwd ):
- if table_name and isinstance( table_name, basestring ):
+ if table_name and isinstance( table_name, string_types ):
table_name = table_name.split( "," )
# Reload the tool data tables
table_names = self.app.tool_data_tables.reload_tables( table_names=table_name )
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index ba531999960..08c1687f847 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -4,6 +4,7 @@ import urllib
from markupsafe import escape
import paste.httpexceptions
+from six import string_types, text_type
from sqlalchemy import false, true
from galaxy import datatypes, model, util, web
@@ -219,7 +220,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
""" Primarily used for the S3ObjectStore - get the status of data transfer
if the file is not in cache """
data = self._check_dataset(trans, dataset_id)
- if isinstance( data, basestring ):
+ if isinstance( data, string_types ):
return data
log.debug( "Checking transfer status for dataset %s..." % data.dataset.id )
@@ -651,7 +652,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
if not dataset:
web.httpexceptions.HTTPNotFound()
annotation = self.get_item_annotation_str( trans.sa_session, trans.user, dataset )
- if annotation and isinstance( annotation, unicode ):
+ if annotation and isinstance( annotation, text_type ):
annotation = annotation.encode( 'ascii', 'replace' ) # paste needs ascii here
return annotation
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index 62974a60b70..e2f54cb5c68 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -2,6 +2,7 @@ import logging
import urllib
from markupsafe import escape
+from six import string_types
from sqlalchemy import and_, false, func, null, true
from sqlalchemy.orm import eagerload_all
@@ -1331,7 +1332,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
new_name = name[i]
# skip if name is empty
- if not isinstance( new_name, basestring ) or not new_name.strip():
+ if not isinstance( new_name, string_types ) or not new_name.strip():
change_msgs.append( "You must specify a valid name for History: " + cur_name )
continue
diff --git a/lib/galaxy/webapps/galaxy/controllers/library_common.py b/lib/galaxy/webapps/galaxy/controllers/library_common.py
index cf3d04ac3dd..f809f6baac3 100644
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -19,6 +19,7 @@ from galaxy import util, web
from galaxy.security import Action
from galaxy.tools.actions import upload_common
from galaxy.util import inflector
+from galaxy.util import unicodify
from galaxy.util.json import dumps, loads
from galaxy.util.streamball import StreamBall
from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems
@@ -86,7 +87,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
job_ldda = job_ldda.copied_from_library_dataset_dataset_association
rval[id] = {
"state": data.state,
- "html": unicode( trans.fill_template( "library/common/library_item_info.mako", ldda=data ), 'utf-8' )
+ "html": unicodify( trans.fill_template( "library/common/library_item_info.mako", ldda=data ), 'utf-8' )
# "force_history_refresh": force_history_refresh
}
return rval
diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index 43050a8b4cf..b3eef7bf8d1 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -3,6 +3,7 @@ from sqlalchemy import and_, desc, false, true
from galaxy import managers, model, util, web
from galaxy.model.item_attrs import UsesItemRatings
+from galaxy.util import unicodify
from galaxy.util.json import loads
from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor
from galaxy.web import error, url_for
@@ -625,7 +626,7 @@ class PageController( BaseUIController, SharableMixin,
ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, page )
# Output is string, so convert to unicode for display.
- page_content = unicode( processor.output(), 'utf-8' )
+ page_content = unicodify( processor.output(), 'utf-8' )
return trans.fill_template_mako( "page/display.mako", item=page,
item_data=page_content,
user_item_rating=user_item_rating,
diff --git a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py
index 6ececf57a49..dd917846dbd 100644
--- a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py
@@ -1,6 +1,7 @@
from __future__ import absolute_import
import logging
import os
+from six import text_type
from galaxy import model, util
from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, web
@@ -465,7 +466,7 @@ class RequestsAdmin( BaseUIController, UsesFormDefinitionsMixin ):
# Eliminate the output created using ssh from the tree
if password_str in output:
output = output.replace( password_str, '' )
- return unicode( output.replace( '\r\n', '
' ) )
+ return text_type( output.replace( '\r\n', '
' ) )
@web.json
def open_folder( self, trans, request_id, external_service_id, key ):
diff --git a/lib/galaxy/webapps/galaxy/controllers/requests_common.py b/lib/galaxy/webapps/galaxy/controllers/requests_common.py
index ae2168a0f95..0ca93fcfd44 100644
--- a/lib/galaxy/webapps/galaxy/controllers/requests_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/requests_common.py
@@ -6,6 +6,7 @@ from sqlalchemy import and_, false, func, select
from markupsafe import escape
from galaxy import model, util, web
+from galaxy.util import unicodify
from galaxy.security.validate_user_input import validate_email
from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin
from galaxy.web.form_builder import build_select_field, CheckboxField, SelectField, TextField
@@ -121,9 +122,9 @@ class RequestsCommon( BaseUIController, UsesFormDefinitionsMixin ):
sample = trans.sa_session.query( self.app.model.Sample ).get( id )
if sample.state.name != state:
rval[ id ] = { "state": sample.state.name,
- "html_state": unicode( trans.fill_template( "requests/common/sample_state.mako",
- sample=sample),
- 'utf-8' ) }
+ "html_state": unicodify( trans.fill_template( "requests/common/sample_state.mako",
+ sample=sample),
+ 'utf-8' ) }
return rval
@web.json
@@ -142,9 +143,9 @@ class RequestsCommon( BaseUIController, UsesFormDefinitionsMixin ):
sample = trans.sa_session.query( self.app.model.Sample ).get( id )
if len( sample.datasets ) != number_of_datasets:
rval[ id ] = { "datasets": len( sample.datasets ),
- "html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako",
- sample=sample),
- 'utf-8' ) }
+ "html_datasets": unicodify( trans.fill_template( "requests/common/sample_datasets.mako",
+ sample=sample),
+ 'utf-8' ) }
return rval
@web.json
@@ -163,9 +164,9 @@ class RequestsCommon( BaseUIController, UsesFormDefinitionsMixin ):
sample_dataset = trans.sa_session.query( self.app.model.SampleDataset ).get( trans.security.decode_id( id ) )
if sample_dataset.status != transfer_status:
rval[ id ] = { "status": sample_dataset.status,
- "html_status": unicode( trans.fill_template( "requests/common/sample_dataset_transfer_status.mako",
- sample_dataset=sample_dataset),
- 'utf-8' ) }
+ "html_status": unicodify( trans.fill_template( "requests/common/sample_dataset_transfer_status.mako",
+ sample_dataset=sample_dataset),
+ 'utf-8' ) }
return rval
@web.expose
diff --git a/lib/galaxy/webapps/galaxy/controllers/tag.py b/lib/galaxy/webapps/galaxy/controllers/tag.py
index 3414c20709b..3e6dd444c90 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tag.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tag.py
@@ -3,12 +3,13 @@ Tags Controller: handles tagging/untagging of entities
and provides autocomplete support.
"""
-from galaxy import web
-from galaxy.web.base.controller import BaseUIController, UsesTagsMixin
-
+from six import text_type
from sqlalchemy.sql import select
from sqlalchemy.sql.expression import and_, func
+from galaxy import web
+from galaxy.web.base.controller import BaseUIController, UsesTagsMixin
+
import logging
log = logging.getLogger( __name__ )
@@ -47,7 +48,7 @@ class TagsController ( BaseUIController, UsesTagsMixin ):
trans.sa_session.flush()
# Log.
params = dict( item_id=item.id, item_class=item_class, tag=new_tag )
- trans.log_action( user, unicode( "tag" ), context, params )
+ trans.log_action( user, text_type( "tag" ), context, params )
@web.expose
@web.require_login( "remove tag from an item" )
@@ -62,7 +63,7 @@ class TagsController ( BaseUIController, UsesTagsMixin ):
trans.sa_session.flush()
# Log.
params = dict( item_id=item.id, item_class=item_class, tag=tag_name )
- trans.log_action( user, unicode( "untag" ), context, params )
+ trans.log_action( user, text_type( "untag" ), context, params )
# Retag an item. All previous tags are deleted and new tags are applied.
@web.expose
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index 70d757d7e36..2262a8e4fa6 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -2,9 +2,10 @@ from __future__ import absolute_import
import logging
-from sqlalchemy import and_, desc, false, or_, true
-from paste.httpexceptions import HTTPNotFound, HTTPBadRequest
from markupsafe import escape
+from paste.httpexceptions import HTTPNotFound, HTTPBadRequest
+from six import string_types
+from sqlalchemy import and_, desc, false, or_, true
from galaxy import managers
from galaxy import model, web
@@ -808,7 +809,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
# post to saved in order to save a visualization
if type is None or config is None:
return HTTPBadRequest( 'A visualization type and config are required to save a visualization' )
- if isinstance( config, basestring ):
+ if isinstance( config, string_types ):
config = loads( config )
title = title or DEFAULT_VISUALIZATION_NAME
@@ -931,7 +932,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
dataset = self.get_hda_or_ldda( trans, dataset_dict[ 'hda_ldda'], dataset_dict[ 'id' ] )
genome_data = self._get_genome_data( trans, dataset, dbkey )
- if not isinstance( genome_data, str ):
+ if not isinstance( genome_data, string_types ):
track[ 'preloaded_data' ] = genome_data
# define app configuration for generic mako template
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index 81a57007dba..63cf2dc511e 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -19,6 +19,7 @@ from galaxy import web
from galaxy.managers import workflows
from galaxy.model.item_attrs import UsesItemRatings
from galaxy.model.mapping import desc
+from galaxy.util import unicodify
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import error, url_for
from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
@@ -752,7 +753,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
workflow_svg=self._workflow_to_svg_canvas( trans, stored ).standalone_xml()
)
# strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters.
- request = unicode( request_raw.strip(), 'utf-8' )
+ request = unicodify( request_raw.strip(), 'utf-8' )
# Do request and get result.
auth_header = base64.b64encode( '%s:%s' % ( myexp_username, myexp_password ))
diff --git a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
index a7117efccbc..ed62395b2d1 100644
--- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
+++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
@@ -9,6 +9,7 @@ import urlparse
from paste.auth.basic import AuthBasicAuthenticator
from paste.httpheaders import AUTH_TYPE
from paste.httpheaders import REMOTE_USER
+from six import string_types
from galaxy.util import asbool
from galaxy.util.hash_util import new_secure_hash
@@ -99,7 +100,7 @@ class Hg( object ):
# If all of these mechanisms fail, Mercurial will fail, printing an error message. In this case, it
# will not let you commit until you set up a username.
result = self.authentication( environ )
- if not isinstance( result, str ) and cmd == 'unbundle' and 'wsgi.input' in environ:
+ if not isinstance( result, string_types ) and cmd == 'unbundle' and 'wsgi.input' in environ:
bundle_data_stream = environ[ 'wsgi.input' ]
# Convert the incoming mercurial bundle into a json object and persit it to a temporary file for inspection.
fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-hg-bundle" )
@@ -139,7 +140,7 @@ class Hg( object ):
if len( entry ) == 2:
# We possibly found an altered file entry.
filename, change_list = entry
- if filename and isinstance( filename, str ):
+ if filename and isinstance( filename, string_types ):
if filename == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
# Make sure the any complex repository dependency definitions contain valid tags.
is_valid, error_msg = self.repository_tags_are_valid( filename, change_list )
@@ -158,7 +159,7 @@ class Hg( object ):
if len( entry ) == 2:
# We possibly found an altered file entry.
filename, change_list = entry
- if filename and isinstance( filename, str ):
+ if filename and isinstance( filename, string_types ):
if filename == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME:
# Make sure the any complex repository dependency definitions contain valid tags.
is_valid, error_msg = self.repository_tags_are_valid( filename, change_list )
@@ -179,7 +180,7 @@ class Hg( object ):
if len( entry ) == 2:
# We possibly found an altered file entry.
filename, change_list = entry
- if filename and isinstance( filename, str ):
+ if filename and isinstance( filename, string_types ):
if filename in [ rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME,
rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME ]:
# We check both files since tool dependency definitions files can contain complex
@@ -188,7 +189,7 @@ class Hg( object ):
if not is_valid:
log.debug( error_msg )
return self.__display_exception_remotely( start_response, error_msg )
- if isinstance( result, str ):
+ if isinstance( result, string_types ):
# Authentication was successful
AUTH_TYPE.update( environ, 'basic' )
REMOTE_USER.update( environ, result )
diff --git a/lib/galaxy_utils/sequence/fasta.py b/lib/galaxy_utils/sequence/fasta.py
index 113061502a2..fd078a3d198 100644
--- a/lib/galaxy_utils/sequence/fasta.py
+++ b/lib/galaxy_utils/sequence/fasta.py
@@ -1,4 +1,5 @@
# Dan Blankenberg
+from six import string_types
class fastaSequence( object ):
@@ -63,7 +64,7 @@ class fastaNamedReader( object ):
return self.file.close()
def get( self, sequence_id ):
- if not isinstance( sequence_id, basestring ):
+ if not isinstance( sequence_id, string_types ):
sequence_id = sequence_id.identifier
rval = None
if sequence_id in self.offset_dict:
diff --git a/lib/galaxy_utils/sequence/fastq.py b/lib/galaxy_utils/sequence/fastq.py
index af4509b9bae..88097206ec9 100644
--- a/lib/galaxy_utils/sequence/fastq.py
+++ b/lib/galaxy_utils/sequence/fastq.py
@@ -2,6 +2,7 @@
import math
import string
import transform
+from six import string_types
from sequence import SequencingRead
from fasta import fastaSequence
@@ -633,7 +634,7 @@ class fastqNamedReader( object ):
def get( self, sequence_identifier ):
# Input is either a sequence ID or a sequence object
- if not isinstance( sequence_identifier, basestring ):
+ if not isinstance( sequence_identifier, string_types ):
# Input was a sequence object (not a sequence ID). Get the sequence ID
sequence_identifier = sequence_identifier.identifier
# Get only the ID part of the sequence header
@@ -764,7 +765,7 @@ class fastqJoiner( object ):
def is_first_mate( self, sequence_id ):
is_first = None
- if not isinstance( sequence_id, basestring ):
+ if not isinstance( sequence_id, string_types ):
sequence_id = sequence_id.identifier
sequence_id, sequence_sep, sequence_desc = sequence_id.partition(' ')
if sequence_id[-2] == '/':
diff --git a/lib/pulsar/client/interface.py b/lib/pulsar/client/interface.py
index 9d625f72c60..c346c573890 100644
--- a/lib/pulsar/client/interface.py
+++ b/lib/pulsar/client/interface.py
@@ -3,10 +3,8 @@ from abc import abstractmethod
from string import Template
from six import BytesIO
-try:
- from six import text_type
-except ImportError:
- from galaxy.util import unicodify as text_type
+from six import text_type
+
try:
from urllib import urlencode
except ImportError:
diff --git a/lib/pulsar/client/manager.py b/lib/pulsar/client/manager.py
index ff4e4e9164a..d03b60a8411 100644
--- a/lib/pulsar/client/manager.py
+++ b/lib/pulsar/client/manager.py
@@ -5,6 +5,7 @@ try:
except ImportError:
from queue import Queue
from os import getenv
+from six import string_types
from .client import JobClient
from .client import InputCachingJobClient
@@ -261,11 +262,7 @@ class ClientCacher(object):
def _parse_destination_params(destination_params):
- try:
- unicode_type = unicode
- except NameError:
- unicode_type = str
- if isinstance(destination_params, str) or isinstance(destination_params, unicode_type):
+ if isinstance(destination_params, string_types):
destination_params = url_to_destination_params(destination_params)
return destination_params
diff --git a/lib/tool_shed/galaxy_install/install_manager.py b/lib/tool_shed/galaxy_install/install_manager.py
index 5574fc84944..8351a935777 100644
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -6,6 +6,7 @@ import tempfile
import traceback
from fabric.api import lcd
+from six import string_types
from sqlalchemy import or_
from galaxy import exceptions, util
@@ -842,7 +843,7 @@ class InstallRepositoryManager( object ):
str( tool_panel_section_key ) )
else:
tool_section = None
- if isinstance( repo_info_dict, basestring ):
+ if isinstance( repo_info_dict, string_types ):
repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict )
# Clone each repository to the configured location.
self.update_tool_shed_repository_status( tool_shed_repository,
diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
index ae91b56feec..ea0552f0107 100644
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
@@ -1,6 +1,7 @@
import logging
import os
import stat
+from six import string_types
log = logging.getLogger( __name__ )
@@ -76,7 +77,7 @@ class EnvFileBuilder( object ):
log.exception( str( e ) )
return 1
# Convert the received text to a list, in order to support adding one or more lines to the file.
- if isinstance( text, basestring ):
+ if isinstance( text, string_types ):
text = [ text ]
for line in text:
line = line.rstrip()
diff --git a/lib/tool_shed/util/basic_util.py b/lib/tool_shed/util/basic_util.py
index 3e13b44a320..3d530dbde3b 100644
--- a/lib/tool_shed/util/basic_util.py
+++ b/lib/tool_shed/util/basic_util.py
@@ -5,6 +5,7 @@ import sys
from string import Template
import markupsafe
+from six import text_type
from galaxy.util import nice_size, unicodify
@@ -144,7 +145,7 @@ def to_html_string( text ):
text = unicodify( text )
except UnicodeDecodeError, e:
return "Error decoding string: %s" % str( e )
- text = unicode( markupsafe.escape( text ) )
+ text = text_type( markupsafe.escape( text ) )
text = text.replace( '\n', '
' )
text = text.replace( ' ', ' ' )
text = text.replace( ' ', ' ' )
diff --git a/lib/tool_shed/util/common_util.py b/lib/tool_shed/util/common_util.py
index 091235c4d71..14c37001c3e 100644
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -3,6 +3,7 @@ import logging
import os
import urllib
import urllib2
+from six import string_types
from galaxy import util
from galaxy.util.odict import odict
@@ -363,7 +364,7 @@ def url_join( base_url, pathspec=None, params=None ):
"""Return a valid URL produced by appending a base URL and a set of request parameters."""
url = base_url.rstrip( '/' )
if pathspec is not None:
- if not isinstance( pathspec, basestring ):
+ if not isinstance( pathspec, string_types ):
pathspec = '/'.join( pathspec )
url = '%s/%s' % ( url, pathspec )
if params is not None:
diff --git a/lib/tool_shed/util/tool_util.py b/lib/tool_shed/util/tool_util.py
index d88d9df14ca..72bc36c331a 100644
--- a/lib/tool_shed/util/tool_util.py
+++ b/lib/tool_shed/util/tool_util.py
@@ -5,6 +5,7 @@ import shutil
import galaxy.tools
from galaxy import util
from galaxy.util import checkers
+from galaxy.util import unicodify
from galaxy.util.expressions import ExpressionContext
from galaxy.web.form_builder import SelectField
@@ -131,7 +132,7 @@ def get_headers( fname, sep, count=60, is_multi_byte=False ):
for idx, line in enumerate( file( fname ) ):
line = line.rstrip( '\n\r' )
if is_multi_byte:
- line = unicode( line, 'utf-8' )
+ line = unicodify( line, 'utf-8' )
sep = sep.encode( 'utf-8' )
headers.append( line.split( sep ) )
if idx == count: