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Lint with Python 3 serveral modules.

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Namely the modules I'd like to be shared with planemo, pulsar, etc....
This commit is contained in:
John Chilton
2015-12-17 09:21:25 +00:00
parent 1ec67c864b
commit 66944ba7de
20 changed files with 163 additions and 103 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.ci/flake8_py3_wrapper.sh
Executable
+5
View File
@@ -0,0 +1,5 @@
#!/bin/bash
set -e
flake8 --exclude `paste -sd, .ci/flake8_blacklist.txt` `paste -s .ci/py3_sources.txt`
.ci/py3_sources.txt
+14
View File
@@ -0,0 +1,14 @@
lib/galaxy/util/
lib/galaxy/jobs/runners/util/
lib/pulsar/
lib/galaxy/tools/parser/
lib/galaxy/tools/lint.py
lib/galaxy/tools/lint_util.py
lib/galaxy/tools/loader.py
lib/galaxy/tools/loader_directory.py
lib/galaxy/tools/linters/
lib/galaxy/tools/deps/
lib/galaxy/tools/toolbox/
lib/galaxy/tools/parser/
lib/galaxy/jobs/metrics/
lib/galaxy/objectstore/
lib/galaxy/jobs/metrics/collectl/processes.py
+4
View File
@@ -3,12 +3,16 @@ statistics for a given pid's process and process ancestors.
"""
import collections
import csv
import sys
import tempfile
from galaxy import util
from ..collectl import stats
if sys.version_info > (3,):
long = int
import logging
log = logging.getLogger( __name__ )
lib/galaxy/jobs/metrics/instrumenters/meminfo.py
+5 -1
View File
@@ -1,10 +1,14 @@
import re
import sys
from galaxy import util
from ..instrumenters import InstrumentPlugin
from ...metrics import formatting
if sys.version_info > (3,):
long = int
MEMINFO_LINE = re.compile(r"(\w+)\s*\:\s*(\d+) kB")
# Important (non-verbose) meminfo property titles.
lib/galaxy/objectstore/s3_multipart_upload.py
+1 -1
View File
@@ -24,7 +24,7 @@ except ImportError:
def map_wrap(f):
@functools.wraps(f)
def wrapper(*args, **kwargs):
return apply(f, *args, **kwargs)
return f(*args, **kwargs)
return wrapper
lib/galaxy/tools/toolbox/base.py
+3 -3
View File
@@ -798,7 +798,7 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
tool = self._tools_by_id[ tool_id ]
tarball_files = []
temp_files = []
tool_xml = file( os.path.abspath( tool.config_file ), 'r' ).read()
tool_xml = open( os.path.abspath( tool.config_file ), 'r' ).read()
# Retrieve tool help images and rewrite the tool's xml into a temporary file with the path
# modified to be relative to the repository root.
image_found = False
@@ -820,7 +820,7 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
if image_found:
fd, new_tool_config = tempfile.mkstemp( suffix='.xml' )
os.close( fd )
file( new_tool_config, 'w' ).write( tool_xml )
open( new_tool_config, 'w' ).write( tool_xml )
tool_tup = ( os.path.abspath( new_tool_config ), os.path.split( tool.config_file )[-1] )
temp_files.append( os.path.abspath( new_tool_config ) )
else:
@@ -880,7 +880,7 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
table_definition = table_definition % '\n'.join( data_table_definitions )
fd, table_conf = tempfile.mkstemp()
os.close( fd )
file( table_conf, 'w' ).write( table_definition )
open( table_conf, 'w' ).write( table_definition )
tarball_files.append( ( table_conf, os.path.join( 'tool-data', 'tool_data_table_conf.xml.sample' ) ) )
temp_files.append( table_conf )
# Create the tarball.
lib/galaxy/tools/toolbox/integrated_panel.py
+1 -1
View File
@@ -101,4 +101,4 @@ class ManagesIntegratedToolPanelMixin:
shutil.copy( filename, filename + ".copy" )
filename = filename + ".copy"
shutil.move( filename, destination )
os.chmod( self._integrated_tool_panel_config, 0644 )
os.chmod( self._integrated_tool_panel_config, 0o644 )
lib/galaxy/util/__init__.py
+27 -24
View File
@@ -27,6 +27,9 @@ import urlparse
from galaxy.util import json
from datetime import datetime
from six import string_types, text_type
from six.moves import xrange
from email.MIMEText import MIMEText
from os.path import relpath
@@ -120,7 +123,7 @@ def file_iter(fname, sep=None):
>>> len(lines) != 0
True
"""
for line in file(fname):
for line in open(fname):
if line and line[0] != '#':
yield line.split(sep)
@@ -169,7 +172,7 @@ def xml_to_string( elem, pretty=False ):
elem = pretty_print_xml( elem )
try:
return ElementTree.tostring( elem )
except TypeError, e:
except TypeError as e:
# we assume this is a comment
if hasattr( elem, 'text' ):
return "<!-- %s -->\n" % ( elem.text )
@@ -329,7 +332,7 @@ def pretty_print_time_interval( time=False, precise=False ):
diff = now - datetime.fromtimestamp( time )
elif isinstance( time, datetime ):
diff = now - time
elif isinstance( time, basestring ):
elif isinstance( time, string_types ):
time = datetime.strptime( time, "%Y-%m-%dT%H:%M:%S.%f" )
diff = now - time
else:
@@ -417,7 +420,7 @@ def sanitize_text( text, valid_characters=valid_chars, character_map=mapped_char
"""
if isinstance( text, list ):
return map( lambda x: sanitize_text( x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character ), text )
if not isinstance( text, basestring ):
if not isinstance( text, string_types ):
text = smart_str( text )
return _sanitize_text_helper( text, valid_characters=valid_characters, character_map=character_map )
@@ -452,7 +455,7 @@ def sanitize_lists_to_string( values, valid_characters=valid_chars, character_ma
def sanitize_param( value, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X' ):
"""Clean incoming parameters (strings or lists)"""
if isinstance( value, basestring ):
if isinstance( value, string_types ):
return sanitize_text( value, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character )
elif isinstance( value, list ):
return map( lambda x: sanitize_text( x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character ), value )
@@ -712,7 +715,7 @@ falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
def asbool(obj):
if isinstance(obj, basestring):
if isinstance(obj, string_types):
obj = obj.strip().lower()
if obj in truthy:
return True
@@ -758,7 +761,7 @@ def listify( item, do_strip=False ):
return []
elif isinstance( item, list ):
return item
elif isinstance( item, basestring ) and item.count( ',' ):
elif isinstance( item, string_types ) and item.count( ',' ):
if do_strip:
return [token.strip() for token in item.split( ',' )]
else:
@@ -791,10 +794,10 @@ def unicodify( value, encoding=DEFAULT_ENCODING, error='replace', default=None )
Returns a unicode string or None
"""
if isinstance( value, unicode ):
if isinstance( value, text_type ):
return value
try:
return unicode( str( value ), encoding, error )
return text_type( str( value ), encoding, error )
except:
return default
@@ -809,12 +812,12 @@ def smart_str(s, encoding='utf-8', strings_only=False, errors='strict'):
"""
if strings_only and isinstance(s, (type(None), int)):
return s
if not isinstance(s, basestring):
if not isinstance(s, string_types):
try:
return str(s)
except UnicodeEncodeError:
return unicode(s).encode(encoding, errors)
elif isinstance(s, unicode):
return text_type(s).encode(encoding, errors)
elif isinstance(s, text_type):
return s.encode(encoding, errors)
elif s and encoding != 'utf-8':
return s.decode('utf-8', errors).encode(encoding, errors)
@@ -931,7 +934,7 @@ def read_dbnames(filename):
man_builds.sort()
man_builds = [(build, name) for name, build in man_builds]
db_names = DBNames( db_names + man_builds )
except Exception, e:
except Exception as e:
log.error( "ERROR: Unable to read builds file: %s", e )
if len(db_names) < 1:
db_names = DBNames( [( db_names.default_value, db_names.default_name )] )
@@ -1012,7 +1015,7 @@ def mkstemp_ln( src, prefix='mkstemp_ln_' ):
try:
os.link( src, file )
return (os.path.abspath(file))
except OSError, e:
except OSError as e:
if e.errno == errno.EEXIST:
continue # try again
raise
@@ -1026,14 +1029,14 @@ def umask_fix_perms( path, umask, unmasked_perms, gid=None ):
perms = unmasked_perms & ~umask
try:
st = os.stat( path )
except OSError, e:
except OSError as e:
log.exception( 'Unable to set permissions or group on %s' % path )
return
# fix modes
if stat.S_IMODE( st.st_mode ) != perms:
try:
os.chmod( path, perms )
except Exception, e:
except Exception as e:
log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ),
path,
oct( perms ),
@@ -1043,7 +1046,7 @@ def umask_fix_perms( path, umask, unmasked_perms, gid=None ):
if gid is not None and st.st_gid != gid:
try:
os.chown( path, -1, gid )
except Exception, e:
except Exception as e:
try:
desired_group = grp.getgrgid( gid )
current_group = grp.getgrgid( st.st_gid )
@@ -1165,26 +1168,26 @@ def send_mail( frm, to, subject, body, config ):
try:
s.starttls()
log.debug( 'Initiated SSL/TLS connection to SMTP server: %s' % config.smtp_server )
except RuntimeError, e:
except RuntimeError as e:
log.warning( 'SSL/TLS support is not available to your Python interpreter: %s' % e )
except smtplib.SMTPHeloError, e:
except smtplib.SMTPHeloError as e:
log.error( "The server didn't reply properly to the HELO greeting: %s" % e )
s.close()
raise
except smtplib.SMTPException, e:
except smtplib.SMTPException as e:
log.warning( 'The server does not support the STARTTLS extension: %s' % e )
if config.smtp_username and config.smtp_password:
try:
s.login( config.smtp_username, config.smtp_password )
except smtplib.SMTPHeloError, e:
except smtplib.SMTPHeloError as e:
log.error( "The server didn't reply properly to the HELO greeting: %s" % e )
s.close()
raise
except smtplib.SMTPAuthenticationError, e:
except smtplib.SMTPAuthenticationError as e:
log.error( "The server didn't accept the username/password combination: %s" % e )
s.close()
raise
except smtplib.SMTPException, e:
except smtplib.SMTPException as e:
log.error( "No suitable authentication method was found: %s" % e )
s.close()
raise
@@ -1195,7 +1198,7 @@ def send_mail( frm, to, subject, body, config ):
def force_symlink( source, link_name ):
try:
os.symlink( source, link_name )
except OSError, e:
except OSError as e:
if e.errno == errno.EEXIST:
os.remove( link_name )
os.symlink( source, link_name )
lib/galaxy/util/backports/importlib/__init__.py
+2
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@@ -3,6 +3,8 @@
# code compatible with Python 2.3.
import sys
from six.moves import xrange
def _resolve_name(name, package, level):
"""Return the absolute name of the module to be imported."""
lib/galaxy/util/biostar.py
+4 -3
View File
@@ -9,6 +9,7 @@ import re
from unicodedata import normalize
from galaxy.web.base.controller import url_for
from galaxy.tools.errors import ErrorReporter
from six import text_type
from . import smart_str
log = logging.getLogger( __name__ )
@@ -41,14 +42,14 @@ def biostar_enabled( app ):
# Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/)
def slugify(text, delim=u'-'):
"""Generates an slightly worse ASCII-only slug."""
if not isinstance( text, unicode ):
text = unicode( text )
if not isinstance( text, text_type ):
text = text_type( text )
result = []
for word in _punct_re.split(text.lower()):
word = normalize('NFKD', word).encode('ascii', 'ignore')
if word:
result.append(word)
return unicode(delim.join(result))
return text_type(delim.join(result))
def get_biostar_url( app, payload=None, biostar_action=None ):
lib/galaxy/util/dictobj.py
+5
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@@ -1,6 +1,11 @@
import pickle
def cmp(x, y):
# Builtin in Python 2, but not Python 3.
return (x > y) - (x < y)
class DictionaryObject(object):
"""
Copyright 2012 "Grim Apps"
lib/galaxy/util/inflection.py
+1 -1
View File
@@ -269,7 +269,7 @@ class Inflector:
def __init__( self, Inflector=English ):
assert callable(Inflector), "Inflector should be a callable obj"
self.Inflector = apply(Inflector)
self.Inflector = Inflector()
def pluralize(self, word) :
'''Pluralizes nouns.'''
lib/galaxy/util/json.py
+11 -9
View File
@@ -10,6 +10,8 @@ import math
import random
import string
from six import text_type, string_types
dumps = json.dumps
loads = json.loads
@@ -24,7 +26,7 @@ def json_fix( val ):
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 ):
elif isinstance( val, text_type ):
return val.encode( "utf8" )
else:
return val
@@ -34,7 +36,7 @@ def swap_inf_nan( val ):
"""
This takes an arbitrary object and preps it for jsonifying safely, templating Inf/NaN.
"""
if isinstance(val, basestring):
if isinstance(val, string_types):
# basestring first, because it's a sequence and would otherwise get caught below.
return val
elif isinstance( val, collections.Sequence ):
@@ -76,7 +78,7 @@ def safe_dumps( *args, **kwargs ):
def validate_jsonrpc_request( request, regular_methods, notification_methods ):
try:
request = loads( request )
except Exception, e:
except Exception as e:
return False, request, jsonrpc_response( id=None,
error=dict( code=-32700,
message='Parse error',
@@ -87,14 +89,14 @@ def validate_jsonrpc_request( request, regular_methods, notification_methods ):
assert request['jsonrpc'] == '2.0', \
'Requested JSON-RPC version "%s" != required version "2.0".' % request['jsonrpc']
assert 'method' in request, 'No "method" member was sent with the Request object'
except AssertionError, e:
except AssertionError as e:
return False, request, jsonrpc_response( request=request,
error=dict( code=-32600,
message='Invalid Request',
data=str( e ) ) )
try:
assert request['method'] in ( regular_methods + notification_methods )
except AssertionError, e:
except AssertionError as e:
return False, request, jsonrpc_response( request=request,
error=dict( code=-32601,
message='Method not found',
@@ -102,7 +104,7 @@ def validate_jsonrpc_request( request, regular_methods, notification_methods ):
try:
if request['method'] in regular_methods:
assert 'id' in request, 'No "id" member was sent with the Request object and the requested method "%s" is not a notification method' % request['method']
except AssertionError, e:
except AssertionError as e:
return False, request, jsonrpc_response( request=request,
error=dict( code=-32600,
message='Invalid Request',
@@ -113,7 +115,7 @@ def validate_jsonrpc_request( request, regular_methods, notification_methods ):
def validate_jsonrpc_response( response, id=None ):
try:
response = loads( response )
except Exception, e:
except Exception as e:
log.error( 'Response was not valid JSON: %s' % str( e ) )
log.debug( 'Response was: %s' % response )
return False, response
@@ -127,14 +129,14 @@ def validate_jsonrpc_response( response, id=None ):
'The "code" member of the "error" object in the Response is missing or not an integer.'
assert 'message' in response, \
'The "message" member of the "error" object in the Response is missing.'
except Exception, e:
except Exception as e:
log.error( 'Response was not valid JSON-RPC: %s' % str( e ) )
log.debug( 'Response was: %s' % response )
return False, response
if id is not None:
try:
assert 'id' in response and response['id'] == id
except Exception, e:
except Exception as e:
log.error( 'The response id "%s" does not match the request id "%s"' % ( response['id'], id ) )
return False, response
return True, response
lib/galaxy/util/multi_byte.py
+3 -1
View File
@@ -1,10 +1,12 @@
import wchartype
from six import text_type
def is_multi_byte( chars ):
for char in chars:
try:
char = unicode( char )
char = text_type( char )
except UnicodeDecodeError:
# Probably binary
return False
lib/galaxy/util/object_wrapper.py
+8 -2
View File
@@ -11,7 +11,9 @@ from types import ( NoneType, NotImplementedType, EllipsisType, FunctionType, Me
BuiltinFunctionType, BuiltinMethodType, ModuleType, XRangeType, SliceType, TracebackType, FrameType,
BufferType, DictProxyType, GetSetDescriptorType, MemberDescriptorType )
from UserDict import UserDict
import sys
from .dictobj import cmp
from galaxy.util import sanitize_lists_to_string as _sanitize_lists_to_string
log = logging.getLogger( __name__ )
@@ -57,6 +59,10 @@ CHARACTER_MAP = { '>': '__gt__',
INVALID_CHARACTER = "X"
if sys.version_info > (3, 0):
# __coerce__ doesn't do anything under Python anyway.
coerce = lambda x, y: x
def sanitize_lists_to_string( values, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP, invalid_character=INVALID_CHARACTER ):
return _sanitize_lists_to_string( values, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character )
@@ -110,7 +116,7 @@ def wrap_with_safe_string( value, no_wrap_classes=None ):
else:
try:
wrapped_class = type( wrapped_class_name, ( safe_class, wrapped_class, ), {} )
except TypeError, e:
except TypeError as e:
# Fail-safe for when a class cannot be dynamically subclassed.
log.warning( "Unable to create dynamic subclass for %s, %s: %s", type( value), value, e )
wrapped_class = type( wrapped_class_name, ( safe_class, ), {} )
@@ -162,7 +168,7 @@ class SafeStringWrapper( object ):
# that will be used when other + this (this + other is handled by __add__)
try:
return super( SafeStringWrapper, cls ).__new__( cls, sanitize_lists_to_string( arg[0], valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP ) )
except Exception, e:
except Exception as e:
log.warning( "Could not provide an argument to %s.__new__: %s; will try without arguments.", cls, e )
return super( SafeStringWrapper, cls ).__new__( cls )
lib/galaxy/util/pastescript/loadwsgi.py
-2
View File
@@ -28,7 +28,6 @@ def print_(template, *args, **kwargs):
sys.stdout.writelines(template)
if sys.version_info < (3, 0):
basestring = basestring
from ConfigParser import ConfigParser
from urllib import unquote
iteritems = lambda d: d.iteritems()
@@ -37,7 +36,6 @@ if sys.version_info < (3, 0):
def reraise(t, e, tb):
exec('raise t, e, tb', dict(t=t, e=e, tb=tb))
else:
basestring = str
from configparser import ConfigParser
from urllib.parse import unquote
iteritems = lambda d: d.items()
lib/galaxy/util/pastescript/serve.py
+52 -50
View File
@@ -16,6 +16,8 @@
# code here, stripping out uneeded functionality.
# All top level imports from each package moved here and organized
from __future__ import print_function
import ConfigParser
import atexit
import errno
@@ -359,20 +361,20 @@ class Command(object):
class NotFoundCommand(Command):
def run(self, args):
print ('Command %r not known (you may need to run setup.py egg_info)'
% self.command_name)
print('Command %r not known (you may need to run setup.py egg_info)'
% self.command_name)
commands = list()
commands.sort()
if not commands:
print 'No commands registered.'
print 'Have you installed Paste Script?'
print '(try running python setup.py develop)'
print('No commands registered.')
print('Have you installed Paste Script?')
print('(try running python setup.py develop)')
return 2
print 'Known commands:'
print('Known commands:')
longest = max([len(n) for n, c in commands])
for name, command in commands:
print ' %s %s' % (self.pad(name, length=longest),
command.load().summary)
print(' %s %s' % (self.pad(name, length=longest),
command.load().summary))
return 2
@@ -536,7 +538,7 @@ class ServeCommand(Command):
if os.environ.get(self._reloader_environ_key):
from paste import reloader
if self.verbose > 1:
print 'Running reloading file monitor'
print('Running reloading file monitor')
reloader.install(int(self.options.reload_interval))
if self.requires_config_file:
reloader.watch_file(self.args[0])
@@ -553,7 +555,7 @@ class ServeCommand(Command):
if cmd == 'restart' or cmd == 'stop':
result = self.stop_daemon()
if result:
print "Could not stop daemon"
print("Could not stop daemon")
# It's ok to continue trying to restart if stop_daemon returns
# a 1, otherwise shortcut and return.
if cmd == 'restart' and result != 1:
@@ -588,7 +590,7 @@ class ServeCommand(Command):
if self.options.log_file:
try:
writeable_log_file = open(self.options.log_file, 'a')
except IOError, ioe:
except IOError as ioe:
msg = 'Error: Unable to write to log file: %s' % ioe
raise BadCommand(msg)
writeable_log_file.close()
@@ -597,7 +599,7 @@ class ServeCommand(Command):
if self.options.pid_file:
try:
writeable_pid_file = open(self.options.pid_file, 'a')
except IOError, ioe:
except IOError as ioe:
msg = 'Error: Unable to write to pid file: %s' % ioe
raise BadCommand(msg)
writeable_pid_file.close()
@@ -605,9 +607,9 @@ class ServeCommand(Command):
if getattr(self.options, 'daemon', False):
try:
self.daemonize()
except DaemonizeException, ex:
except DaemonizeException as ex:
if self.verbose > 0:
print str(ex)
print(str(ex))
return
if (self.options.monitor_restart and not
@@ -641,20 +643,20 @@ class ServeCommand(Command):
msg = 'Starting server in PID %i.' % os.getpid()
else:
msg = 'Starting server.'
print msg
print(msg)
def serve():
try:
server(app)
except (SystemExit, KeyboardInterrupt), e:
except (SystemExit, KeyboardInterrupt) as e:
if self.verbose > 1:
raise
if str(e):
msg = ' ' + str(e)
else:
msg = ''
print 'Exiting%s (-v to see traceback)' % msg
except AttributeError, e:
print('Exiting%s (-v to see traceback)' % msg)
except AttributeError as e:
# Capturing bad error response from paste
if str(e) == "'WSGIThreadPoolServer' object has no attribute 'thread_pool'":
import socket
@@ -665,7 +667,7 @@ class ServeCommand(Command):
if jython_monitor:
# JythonMonitor has to be ran from the main thread
threading.Thread(target=serve).start()
print 'Starting Jython file monitor'
print('Starting Jython file monitor')
jython_monitor.periodic_reload()
else:
serve()
@@ -678,7 +680,7 @@ class ServeCommand(Command):
% (pid, self.options.pid_file))
if self.verbose > 0:
print 'Entering daemon mode'
print('Entering daemon mode')
pid = os.fork()
if pid:
# The forked process also has a handle on resources, so we
@@ -717,7 +719,7 @@ class ServeCommand(Command):
def record_pid(self, pid_file):
pid = os.getpid()
if self.verbose > 1:
print 'Writing PID %s to %s' % (pid, pid_file)
print('Writing PID %s to %s' % (pid, pid_file))
f = open(pid_file, 'w')
f.write(str(pid))
f.close()
@@ -726,19 +728,19 @@ class ServeCommand(Command):
def stop_daemon(self):
pid_file = self.options.pid_file or 'paster.pid'
if not os.path.exists(pid_file):
print 'No PID file exists in %s' % pid_file
print('No PID file exists in %s' % pid_file)
return 1
pid = read_pidfile(pid_file)
if not pid:
print "Not a valid PID file in %s" % pid_file
print("Not a valid PID file in %s" % pid_file)
return 1
pid = live_pidfile(pid_file)
if not pid:
print "PID in %s is not valid (deleting)" % pid_file
print("PID in %s is not valid (deleting)" % pid_file)
try:
os.unlink(pid_file)
except (OSError, IOError), e:
print "Could not delete: %s" % e
except (OSError, IOError) as e:
print("Could not delete: %s" % e)
return 2
return 1
for j in range(10):
@@ -748,7 +750,7 @@ class ServeCommand(Command):
os.kill(pid, signal.SIGTERM)
time.sleep(1)
else:
print "failed to kill web process %s" % pid
print("failed to kill web process %s" % pid)
return 3
if os.path.exists(pid_file):
os.unlink(pid_file)
@@ -757,17 +759,17 @@ class ServeCommand(Command):
def show_status(self):
pid_file = self.options.pid_file or 'paster.pid'
if not os.path.exists(pid_file):
print 'No PID file %s' % pid_file
print('No PID file %s' % pid_file)
return 1
pid = read_pidfile(pid_file)
if not pid:
print 'No PID in file %s' % pid_file
print('No PID in file %s' % pid_file)
return 1
pid = live_pidfile(pid_file)
if not pid:
print 'PID %s in %s is not running' % (pid, pid_file)
print('PID %s in %s is not running' % (pid, pid_file))
return 1
print 'Server running in PID %s' % pid
print('Server running in PID %s' % pid)
return 0
def restart_with_reloader(self):
@@ -776,9 +778,9 @@ class ServeCommand(Command):
def restart_with_monitor(self, reloader=False):
if self.verbose > 0:
if reloader:
print 'Starting subprocess with file monitor'
print('Starting subprocess with file monitor')
else:
print 'Starting subprocess with monitor parent'
print('Starting subprocess with monitor parent')
while 1:
args = [self.quote_first_command_arg(sys.executable)] + sys.argv
new_environ = os.environ.copy()
@@ -794,7 +796,7 @@ class ServeCommand(Command):
exit_code = proc.wait()
proc = None
except KeyboardInterrupt:
print '^C caught in monitor process'
print('^C caught in monitor process')
if self.verbose > 1:
raise
return 1
@@ -813,7 +815,7 @@ class ServeCommand(Command):
if exit_code != 3:
return exit_code
if self.verbose > 0:
print '-' * 20, 'Restarting', '-' * 20
print('-' * 20, 'Restarting', '-' * 20)
def change_user_group(self, user, group):
if not user and not group:
@@ -846,8 +848,8 @@ class ServeCommand(Command):
gid = entry.pw_gid
uid = entry.pw_uid
if self.verbose > 0:
print 'Changing user to %s:%s (%s:%s)' % (
user, group or '(unknown)', uid, gid)
print('Changing user to %s:%s (%s:%s)' % (
user, group or '(unknown)', uid, gid))
if hasattr(os, 'initgroups'):
os.initgroups(user, gid)
else:
@@ -907,7 +909,7 @@ def live_pidfile(pidfile):
try:
os.kill(int(pid), 0)
return pid
except OSError, e:
except OSError as e:
if e.errno == errno.EPERM:
return pid
return None
@@ -943,26 +945,26 @@ def _remove_pid_file(written_pid, filename, verbosity):
pass
else:
if pid_in_file != current_pid:
print "PID file %s contains %s, not expected PID %s" % (
filename, pid_in_file, current_pid)
print("PID file %s contains %s, not expected PID %s" % (
filename, pid_in_file, current_pid))
return
if verbosity > 0:
print "Removing PID file %s" % filename
print("Removing PID file %s" % filename)
try:
os.unlink(filename)
return
except OSError, e:
except OSError as e:
# Record, but don't give traceback
print "Cannot remove PID file: %s" % e
print("Cannot remove PID file: %s" % e)
# well, at least lets not leave the invalid PID around...
try:
f = open(filename, 'w')
f.write('')
f.close()
except OSError, e:
print 'Stale PID left in file: %s (%e)' % (filename, e)
except OSError as e:
print('Stale PID left in file: %s (%e)' % (filename, e))
else:
print 'Stale PID removed'
print('Stale PID removed')
def ensure_port_cleanup(bound_addresses, maxtries=30, sleeptime=2):
@@ -988,7 +990,7 @@ def _cleanup_ports(bound_addresses, maxtries=30, sleeptime=2):
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
try:
sock.connect(bound_address)
except socket.error, e:
except socket.error as e:
if e.args[0] != errno.ECONNREFUSED:
raise
break
@@ -1049,7 +1051,7 @@ def run(args=None):
if options.do_help:
args = ['help'] + args
if not args:
print 'Usage: %s COMMAND' % sys.argv[0]
print('Usage: %s COMMAND' % sys.argv[0])
args = ['help']
command_name = args[0]
if command_name not in commands:
@@ -1063,7 +1065,7 @@ def invoke(command, command_name, options, args):
try:
runner = command(command_name)
exit_code = runner.run(args)
except BadCommand, e:
print e.message
except BadCommand as e:
print(e.message)
exit_code = e.exit_code
sys.exit(exit_code)
lib/galaxy/util/sanitize_html.py
+5 -1
View File
@@ -5,6 +5,10 @@ HTML Sanitizer (ripped from feedparser)
import re
import sgmllib
from six import unichr
from six import text_type as unicode
# reversable htmlentitydefs mappings for Python 2.2
try:
from htmlentitydefs import name2codepoint, codepoint2name
@@ -370,7 +374,7 @@ class _HTMLSanitizer(_BaseHTMLProcessor):
# declare xlink namespace, if needed
if self.mathmlOK or self.svgOK:
if filter(lambda (n, v): n.startswith('xlink:'), attrs):
if filter(lambda n, v: n.startswith('xlink:'), attrs):
if not ('xmlns:xlink', 'http://www.w3.org/1999/xlink') in attrs:
attrs.append(('xmlns:xlink', 'http://www.w3.org/1999/xlink'))
lib/galaxy/util/validation.py
+5 -3
View File
@@ -5,18 +5,20 @@ TODO: Refactor BaseController references to similar methods to use this module.
from galaxy import exceptions
from galaxy.util.sanitize_html import sanitize_html
from six import string_types, text_type
def validate_and_sanitize_basestring( key, val ):
if not isinstance( val, basestring ):
if not isinstance( val, string_types ):
raise exceptions.RequestParameterInvalidException( '%s must be a string or unicode: %s'
% ( key, str( type( val ) ) ) )
return unicode( sanitize_html( val, 'utf-8', 'text/html' ), 'utf-8' )
return text_type( sanitize_html( val, 'utf-8', 'text/html' ), 'utf-8' )
def validate_and_sanitize_basestring_list( key, val ):
try:
assert isinstance( val, list )
return [ unicode( sanitize_html( t, 'utf-8', 'text/html' ), 'utf-8' ) for t in val ]
return [ text_type( sanitize_html( t, 'utf-8', 'text/html' ), 'utf-8' ) for t in val ]
except ( AssertionError, TypeError ):
raise exceptions.RequestParameterInvalidException( '%s must be a list of strings: %s'
% ( key, str( type( val ) ) ) )
tox.ini
+7 -1
View File
@@ -1,5 +1,5 @@
[tox]
envlist = py27-lint, py26-lint, py27-unit, py26-unit, qunit, mako-count, web-controller-line-count
envlist = py27-lint, py26-lint, py27-unit, py26-unit, qunit, mako-count, web-controller-line-count, py34-lint
skipsdist = True
@@ -13,6 +13,12 @@ commands = bash .ci/flake8_wrapper.sh
whitelist_externals = bash
deps = flake8
[testenv:py34-lint]
commands = bash .ci/flake8_py3_wrapper.sh
whitelist_externals = bash
deps = flake8
[testenv:py27-unit]
commands = bash run_tests.sh --skip-venv -u
whitelist_externals = bash