Merge pull request #1376 from jmchilton/py3_0

More Python 3 fixes.

lib/galaxy/objectstore/pulsar.py

@@ -1,6 +1,10 @@
 from __future__ import absolute_import  # Need to import pulsar_client absolutely.
 from ..objectstore import ObjectStore
-from pulsar.client.manager import ObjectStoreClientManager
+
+try:
+    from pulsar.client.manager import ObjectStoreClientManager
+except ImportError:
+    ObjectStoreClientManager = None
 
 
 class PulsarObjectStore(ObjectStore):
@@ -61,6 +65,8 @@ class PulsarObjectStore(ObjectStore):
         pass
 
     def __build_pulsar_client(self, config_xml):
+        if ObjectStoreClientManager is None:
+            raise Exception("Pulsar client code not available, cannot use this module.")
         url = config_xml.get("url")
         private_token = config_xml.get("private_token", None)
         transport = config_xml.get("transport", None)

lib/galaxy/tools/parser/output_objects.py

@@ -2,7 +2,7 @@ from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.odict import odict
 
 
-class ToolOutputBase( object, Dictifiable ):
+class ToolOutputBase( Dictifiable, object ):
 
     def __init__( self, name, label=None, filters=None, hidden=False ):
         super( ToolOutputBase, self ).__init__()

lib/galaxy/tools/toolbox/base.py

@@ -7,7 +7,7 @@ import tempfile
 
 from sqlalchemy import and_
 from markupsafe import escape
-from urlparse import urlparse
+from six.moves.urllib.parse import urlparse
 
 from galaxy.util.dictifiable import Dictifiable
 
@@ -36,7 +36,7 @@ from galaxy.web.form_builder import SelectField
 log = logging.getLogger( __name__ )
 
 
-class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
+class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
     """
     Abstract container for managing a ToolPanel - containing tools and
     workflows optionally in labelled sections.

lib/galaxy/tools/toolbox/panel.py

@@ -40,7 +40,7 @@ class HasPanelItems:
             yield (panel_key, panel_type, panel_value)
 
 
-class ToolSection( object, Dictifiable, HasPanelItems ):
+class ToolSection( Dictifiable, HasPanelItems, object ):
     """
     A group of tools with similar type/purpose that will be displayed as a
     group in the user interface.
@@ -84,7 +84,7 @@ class ToolSection( object, Dictifiable, HasPanelItems ):
         return self.elems
 
 
-class ToolSectionLabel( object, Dictifiable ):
+class ToolSectionLabel( Dictifiable, object ):
     """
     A label for a set of tools that can be displayed above groups of tools
     and sections in the user interface
@@ -104,7 +104,7 @@ class ToolSectionLabel( object, Dictifiable ):
         return super( ToolSectionLabel, self ).to_dict()
 
 
-class ToolPanelElements( odict, HasPanelItems ):
+class ToolPanelElements( HasPanelItems, odict ):
     """ Represents an ordered dictionary of tool entries - abstraction
     used both by tool panel itself (normal and integrated) and its sections.
     """

lib/galaxy/util/__init__.py

@@ -27,6 +27,7 @@ from six.moves.urllib import parse as urlparse
 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
@@ -43,6 +44,13 @@ from xml.etree import ElementTree, ElementInclude
 from .inflection import Inflector, English
 inflector = Inflector(English)
 
+if PY3:
+    def list_map(f, input):
+        return list(map(f, input))
+else:
+    list_map = map
+
+
 log = logging.getLogger(__name__)
 _lock = threading.RLock()
 
@@ -145,7 +153,8 @@ def unique_id(KEY_SIZE=128):
     >>> len(set(ids))
     1000
     """
-    return md5(str( random.getrandbits( KEY_SIZE ) )).hexdigest()
+    random_bits = text_type(random.getrandbits(KEY_SIZE)).encode("UTF-8")
+    return md5(random_bits).hexdigest()
 
 
 def parse_xml( fname ):
@@ -418,7 +427,7 @@ def sanitize_text( text, valid_characters=valid_chars, character_map=mapped_char
     and lists of strings; non-string entities will be cast to strings.
     """
     if isinstance( text, list ):
-        return map( lambda x: sanitize_text( x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character ), text )
+        return list_map( lambda x: sanitize_text( x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character ), text )
     if not isinstance( text, string_types ):
         text = smart_str( text )
     return _sanitize_text_helper( text, valid_characters=valid_characters, character_map=character_map )
@@ -457,7 +466,7 @@ def sanitize_param( value, valid_characters=valid_chars, character_map=mapped_ch
     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 )
+        return list_map( lambda x: sanitize_text( x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character ), value )
     else:
         raise Exception('Unknown parameter type (%s)' % ( type( value ) ))
 

lib/galaxy/util/expressions.py

@@ -5,14 +5,11 @@ For the moment this depends on python's eval. In the future it should be
 replaced with a "safe" parser.
 """
 
-try:
-    from UserDict import DictMixin as AbstractMapping
-except ImportError:
-    # PY3
-    from collections import MutableMapping as AbstractMapping
+from collections import MutableMapping
+from itertools import chain
 
 
-class ExpressionContext( object, AbstractMapping ):
+class ExpressionContext( MutableMapping ):
     def __init__( self, dict, parent=None ):
         """
         Create a new expression context that looks for values in the
@@ -21,6 +18,18 @@ class ExpressionContext( object, AbstractMapping ):
         self.dict = dict
         self.parent = parent
 
+    def __delitem__(self, key):
+        if key in self.dict:
+            del self.dict[key]
+        elif self.parent is not None and key in self.parent:
+            del self.parent[key]
+
+    def __iter__(self):
+        return chain(iter(self.dict), iter(self.parent or []))
+
+    def __len__(self):
+        return len(self.dict) + len(self.parent or [])
+
     def __getitem__( self, key ):
         if key in self.dict:
             return self.dict[key]

lib/galaxy/util/object_wrapper.py

@@ -74,7 +74,7 @@ __WRAP_MAPPINGS__ = ( dict, UserDict, )
 
 # Define the set of characters that are not sanitized, and define a set of mappings for those that are.
 # characters that are valid
-VALID_CHARACTERS = set( string.letters + string.digits + " -=_.()/+*^,:?!@" )
+VALID_CHARACTERS = set( string.ascii_letters + string.digits + " -=_.()/+*^,:?!@" )
 
 # characters that are allowed but need to be escaped
 CHARACTER_MAP = { '>': '__gt__',

lib/galaxy/util/topsort.py

@@ -37,7 +37,12 @@ many methods to help analyze and break the cycles.  This requires
 a good deal more code than topsort itself!
 """
 from galaxy.util.odict import odict as OrderedDict
-from exceptions import Exception
+from six import PY3
+if PY3:
+    def list_filter(f, lst):
+        return list(filter(f, lst))
+else:
+    list_filter = filter
 
 
 class CycleError(Exception):
@@ -159,8 +164,8 @@ def topsort(pairlist):
     numpreds, successors = _numpreds_and_successors_from_pairlist(pairlist)
 
     # suck up everything without a predecessor
-    answer = filter(lambda x, numpreds=numpreds: numpreds[x] == 0,
-                    numpreds.keys())
+    answer = list_filter(lambda x, numpreds=numpreds: numpreds[x] == 0,
+                         numpreds.keys())
 
     # for everything in answer, knock down the pred count on
     # its successors; note that answer grows *in* the loop

test/unit/test_objectstore.py

@@ -2,10 +2,7 @@ import os
 from shutil import rmtree
 from string import Template
 from tempfile import mkdtemp
-try:
-    from galaxy import objectstore
-except ImportError:
-    from lwr import objectstore
+from galaxy import objectstore
 from contextlib import contextmanager
 
 DISK_TEST_CONFIG = """<?xml version="1.0"?>
@@ -26,22 +23,22 @@ def test_disk_store():
         # Write empty dataset 2 in second backend, ensure it is empty and
         # exists.
         empty_dataset = MockDataset(2)
-        directory.write(b"", "files1/000/dataset_2.dat")
+        directory.write("", "files1/000/dataset_2.dat")
         assert object_store.exists(empty_dataset)
         assert object_store.empty(empty_dataset)
 
         # Write non-empty dataset in backend 1, test it is not emtpy & exists.
         hello_world_dataset = MockDataset(3)
-        directory.write(b"Hello World!", "files1/000/dataset_3.dat")
+        directory.write("Hello World!", "files1/000/dataset_3.dat")
         assert object_store.exists(hello_world_dataset)
         assert not object_store.empty(hello_world_dataset)
 
         # Test get_data
         data = object_store.get_data(hello_world_dataset)
-        assert data == b"Hello World!"
+        assert data == "Hello World!"
 
         data = object_store.get_data(hello_world_dataset, start=1, count=6)
-        assert data == b"ello W"
+        assert data == "ello W"
 
         # Test Size
 
@@ -60,13 +57,13 @@ def test_disk_store():
         output_dataset = MockDataset(4)
         output_real_path = os.path.join(directory.temp_directory, "files1", "000", "dataset_4.dat")
         assert not os.path.exists(output_real_path)
-        output_working_path = directory.write(b"NEW CONTENTS", "job_working_directory1/example_output")
+        output_working_path = directory.write("NEW CONTENTS", "job_working_directory1/example_output")
         object_store.update_from_file(output_dataset, file_name=output_working_path, create=True)
         assert os.path.exists(output_real_path)
 
         # Test delete
         to_delete_dataset = MockDataset(5)
-        to_delete_real_path = directory.write(b"content to be deleted!", "files1/000/dataset_5.dat")
+        to_delete_real_path = directory.write("content to be deleted!", "files1/000/dataset_5.dat")
         assert object_store.exists(to_delete_dataset)
         assert object_store.delete(to_delete_dataset)
         assert not object_store.exists(to_delete_dataset)