Merge pull request #1489 from nsoranzo/flake8_fixes

Fix all E731 "errors".

lib/galaxy/model/__init__.py

@@ -1398,7 +1398,6 @@ class History( object, Dictifiable, UsesAnnotations, HasName ):
         assert db_session is not None
         query = db_session.query( content_class ).filter( content_class.table.c.history_id == self.id )
         query = query.order_by( content_class.table.c.hid.asc() )
-        python_filter = None
         deleted = galaxy.util.string_as_bool_or_none( kwds.get( 'deleted', None ) )
         if deleted is not None:
             query = query.filter( content_class.deleted == deleted )
@@ -1411,11 +1410,8 @@ class History( object, Dictifiable, UsesAnnotations, HasName ):
             if len(ids) < max_in_filter_length:
                 query = query.filter( content_class.id.in_(ids) )
             else:
-                python_filter = lambda content: content.id in ids
-        if python_filter:
-            return ifilter(python_filter, query)
-        else:
-            return query
+                query = ifilter(lambda content: content.id in ids, query)
+        return query
 
     def __collection_contents_iter( self, **kwds ):
         return self.__filter_contents( HistoryDatasetCollectionAssociation, **kwds )

lib/galaxy/model/custom_types.py

@@ -232,7 +232,8 @@ def total_size(o, handlers={}, verbose=False):
 
     Recipe from:  https://code.activestate.com/recipes/577504-compute-memory-footprint-of-an-object-and-its-cont/
     """
-    dict_handler = lambda d: chain.from_iterable(d.items())
+    def dict_handler(d):
+        return chain.from_iterable(d.items())
     all_handlers = { tuple: iter,
                      list: iter,
                      deque: iter,

lib/galaxy/tools/parameters/basic.py

@@ -754,7 +754,8 @@ class BaseURLToolParameter( HiddenToolParameter ):
         return d
 
 
-DEFAULT_VALUE_MAP = lambda x: x
+def DEFAULT_VALUE_MAP(x):
+    return x
 
 
 def parse_dynamic_options(param, input_source):
@@ -1873,9 +1874,11 @@ class DataToolParameter( BaseDataToolParameter ):
 
     def _get_select_dataset_collection_fields( self, history, dataset_matcher, multiple=False, suffix="|__collection_multirun__", reduction=False ):
         if not reduction:
-            value_modifier = lambda x: x
+            def value_modifier(x):
+                return x
         else:
-            value_modifier = lambda value: "__collection_reduce__|%s" % value
+            def value_modifier(value):
+                return "__collection_reduce__|%s" % value
 
         value = dataset_matcher.value
         if value is not None:

lib/galaxy/tools/parser/output_actions.py

@@ -593,7 +593,9 @@ def parse_cast_attribute( cast ):
     elif cast == 'str':
         cast = str
     else:
-        cast = lambda x: x  # return value as-is
+        # return value as-is
+        def cast(x):
+            return x
     return cast
 
 

lib/galaxy/tools/test.py

@@ -1,13 +1,15 @@
+import logging
 import os
 import os.path
 import galaxy.tools.parameters.basic
 import galaxy.tools.parameters.grouping
 from galaxy.util import string_as_bool
+
 try:
     from nose.tools import nottest
 except ImportError:
-    nottest = lambda x: x
-import logging
+    def nottest(x):
+        return x
 
 log = logging.getLogger( __name__ )
 
@@ -74,11 +76,15 @@ class ToolTestBuilder( object ):
                 query_value = test_param.checked
             else:
                 query_value = _process_bool_param_value( test_param, declared_value )
-            matches_declared_value = lambda case_value: _process_bool_param_value( test_param, case_value ) == query_value
+
+            def matches_declared_value(case_value):
+                return _process_bool_param_value( test_param, case_value ) == query_value
         elif isinstance(test_param, galaxy.tools.parameters.basic.SelectToolParameter):
             if declared_value is not None:
                 # Test case supplied explicit value to check against.
-                matches_declared_value = lambda case_value: case_value == declared_value
+
+                def matches_declared_value(case_value):
+                    return case_value == declared_value
             elif test_param.static_options:
                 # No explicit value in test case, not much to do if options are dynamic but
                 # if static options are available can find the one specified as default or
@@ -90,7 +96,9 @@ class ToolTestBuilder( object ):
                     first_option = test_param.static_options[0]
                     first_option_value = first_option[1]
                     default_option = first_option_value
-                matches_declared_value = lambda case_value: case_value == default_option
+
+                def matches_declared_value(case_value):
+                    return case_value == default_option
             else:
                 # No explicit value for this param and cannot determine a
                 # default - give up. Previously this would just result in a key

lib/galaxy/tools/toolbox/panel.py

@@ -53,10 +53,11 @@ class ToolSection( Dictifiable, HasPanelItems, object ):
     def __init__( self, item=None ):
         """ Build a ToolSection from an ElementTree element or a dictionary.
         """
-        f = lambda item, val: item is not None and item.get( val ) or ''
-        self.name = f( item, 'name' )
-        self.id = f( item, 'id' )
-        self.version = f( item, 'version' )
+        if item is None:
+            item = dict()
+        self.name = item.get('name') or ''
+        self.id = item.get('id') or ''
+        self.version = item.get('version') or ''
         self.elems = ToolPanelElements()
 
     def copy( self ):

lib/galaxy/tools/wrappers.py

@@ -12,9 +12,12 @@ log = getLogger( __name__ )
 # remote ComputeEnvironments (such as one used by Pulsar) determine what values to
 # rewrite or transfer...
 PATH_ATTRIBUTES = [ "path" ]
+
+
 # ... by default though - don't rewrite anything (if no ComputeEnviornment
 # defined or ComputeEnvironment doesn't supply a rewriter).
-DEFAULT_PATH_REWRITER = lambda x: x
+def DEFAULT_PATH_REWRITER(x):
+    return x
 
 
 class ToolParameterValueWrapper( object ):

lib/galaxy/util/object_wrapper.py

@@ -94,7 +94,8 @@ INVALID_CHARACTER = "X"
 
 if sys.version_info > (3, 0):
     # __coerce__ doesn't do anything under Python anyway.
-    coerce = lambda x, y: x
+    def coerce(x, y):
+        return x
 
 
 def sanitize_lists_to_string( values, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP, invalid_character=INVALID_CHARACTER  ):

lib/galaxy/util/pastescript/loadwsgi.py

@@ -7,12 +7,13 @@ from __future__ import with_statement
 
 import inspect
 import os
-import sys
 import re
+import sys
 
 from galaxy.util.properties import NicerConfigParser
 
 import pkg_resources
+from six import iteritems
 
 __all__ = ['loadapp', 'loadserver', 'loadfilter', 'appconfig']
 
@@ -31,15 +32,11 @@ def print_(template, *args, **kwargs):
 
 if sys.version_info < (3, 0):
     from urllib import unquote
-    iteritems = lambda d: d.iteritems()
-    dictkeys = lambda d: d.keys()
 
     def reraise(t, e, tb):
         exec('raise t, e, tb', dict(t=t, e=e, tb=tb))
 else:
     from urllib.parse import unquote
-    iteritems = lambda d: d.items()
-    dictkeys = lambda d: list(d.keys())
 
     def reraise(t, e, tb):
         exec('raise e from tb', dict(e=e, tb=tb))
@@ -703,7 +700,7 @@ class EggLoader(_Loader):
                     dist.location,
                     ', '.join(_flatten(object_type.egg_protocols)),
                     ', '.join(_flatten([
-                        dictkeys(pkg_resources.get_entry_info(self.spec, prot, name) or {})
+                        list((pkg_resources.get_entry_info(self.spec, prot, name) or {}).keys())
                         for prot in protocol_options] or '(no entry points)'))))
         if len(possible) > 1:
             raise LookupError(

lib/galaxy/visualization/genomes.py

@@ -260,9 +260,12 @@ class Genomes( object ):
         # Add app keys to dbkeys.
 
         # If chrom_info is True, only include keys with len files (which contain chromosome info).
-        filter_fn = lambda b: True
         if chrom_info:
-            filter_fn = lambda b: b.len_file is not None
+            def filter_fn(b):
+                return b.len_file is not None
+        else:
+            def filter_fn(b):
+                return True
 
         dbkeys.extend( [ ( genome.description, genome.key ) for key, genome in self.genomes.items() if filter_fn( genome ) ] )
 

lib/galaxy/web/framework/openid_manager.py

@@ -15,7 +15,8 @@ except ImportError:
     oidutil = None
 
     class FakeConsumer( object ):
-        __getattr__ = lambda x, y: None
+        def __getattr__(x, y):
+            return None
     consumer = FakeConsumer()
 
 

setup.cfg

@@ -5,5 +5,4 @@
 # 203 whitespace before ':'
 # 402 module level import not at top of file # TODO, we would like to improve this.
 # 501 is line length
-# E731 is inline assigned lambdas -- #TODO this should be revisited to see if we want to change our usage.
-ignore = E128,E201,E202,E203,E501,E402,E731
+ignore = E128,E201,E202,E203,E501,E402

test/api/helpers.py

@@ -416,11 +416,15 @@ class BaseDatasetCollectionPopulator( object ):
         # 2-tuples of form (name, dataset_content).
         if contents and isinstance(contents[0], tuple):
             hdas = self.__datasets( history_id, count=count, contents=[c[1] for c in contents] )
-            hda_to_identifier = lambda ( i, hda ): dict( name=contents[i][0], src="hda", id=hda[ "id" ] )
+
+            def hda_to_identifier(i, hda):
+                return dict(name=contents[i][0], src="hda", id=hda["id"])
         else:
             hdas = self.__datasets( history_id, count=count, contents=contents )
-            hda_to_identifier = lambda ( i, hda ): dict( name="data%d" % ( i + 1 ), src="hda", id=hda[ "id" ] )
-        element_identifiers = map( hda_to_identifier, enumerate( hdas ) )
+
+            def hda_to_identifier(i, hda):
+                return dict(name="data%d" % (i + 1), src="hda", id=hda["id"])
+        element_identifiers = [hda_to_identifier(i, hda) for (i, hda) in enumerate(hdas)]
         return element_identifiers
 
     def __create( self, payload ):

test/casperjs/casperjs_runner.py

@@ -200,15 +200,12 @@ class CasperJSTestCase( unittest.TestCase ):
         """Converts the headless' error from JSON into a more informative
         python HeadlessJSJavascriptError.
         """
-        get_error = lambda d: d[ 'errors' ][0]
-        get_msg = lambda err: err[ 'msg' ]
-        get_trace = lambda err: err[ 'backtrace' ]
         try:
             # assume it's json and located in errors (and first)
             js_test_results = json.loads( stdout_output )
-            last_error = get_error( js_test_results )
-            err_string = ( "%s\n%s" % ( get_msg( last_error ),
-                           self.browser_backtrace_to_string( get_trace( last_error ) ) ) )
+            last_error = js_test_results['errors'][0]
+            err_string = ( "%s\n%s" % ( last_error['msg'],
+                           self.browser_backtrace_to_string( last_error['backtrace'] ) ) )
 
         # if we couldn't parse json from what's returned on the error, dump stdout
         except ValueError, val_err:

test/functional/test_toolbox.py

@@ -1,3 +1,4 @@
+import logging
 import new
 import sys
 from base.twilltestcase import TwillTestCase
@@ -6,11 +7,12 @@ from base.interactor import build_interactor, stage_data_in_history, RunToolExce
 from base.instrument import register_job_data
 from galaxy.tools import DataManagerTool
 from galaxy.util import bunch
-import logging
+
 try:
     from nose.tools import nottest
 except ImportError:
-    nottest = lambda x: x
+    def nottest(x):
+        return x
 
 log = logging.getLogger( __name__ )
 

test/unit/tools/test_execution.py

@@ -146,10 +146,10 @@ class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.Uses
         collection = galaxy.model.DatasetCollection(
             collection_type=collection_type,
         )
-        to_element = lambda hda: galaxy.model.DatasetCollectionElement(
-            collection=collection,
-            element=hda,
-        )
+
+        def to_element(hda):
+            return galaxy.model.DatasetCollectionElement(collection=collection,
+                                                         element=hda)
         elements = map(to_element, hdas)
         if collection_type == "list:paired":
             paired_collection = galaxy.model.DatasetCollection(