Python3: test/unit/

mariabernard · Jun 29, 2016 · 9a97a29 · 9a97a29
1 parent 40f85f2
commit 9a97a29
Show file tree

Hide file tree

Showing 12 changed files with 104 additions and 129 deletions.
diff --git a/.ci/py3_sources.txt b/.ci/py3_sources.txt
@@ -69,26 +69,7 @@ scripts/cleanup_datasets/update_metadata.py
 scripts/data_libraries/build_whoosh_index.py
 scripts/db_shell.py
 scripts/drmaa_external_runner.py
-test/api/helpers.py
-test/api/test_datasets.py
-test/api/test_tool_data.py
-test/api/test_workflow_extraction.py
-test/api/test_workflows.py
-test/api/test_workflows_from_yaml.py
-test/base/
-test/casperjs/
-test/functional/
-test/integration/
-test/manual/
-test/shed_functional/base/twilltestcase.py
-test/shed_functional/functional_tests.py
-test/unit/datatypes/dataproviders/test_base_dataproviders.py
-test/unit/datatypes/dataproviders/test_line_dataproviders.py
-test/unit/managers/base.py
-test/unit/managers/test_DatasetManager.py
-test/unit/test_galaxy_mapping.py
-test/unit/tools/test_actions.py
-test/unit/workflows/test_run_parameters.py
+test/
 tool_list.py
 tools/data_source/
 tools/evolution/

diff --git a/test/unit/managers/test_HDAManager.py b/test/unit/managers/test_HDAManager.py
@@ -1,22 +1,20 @@
 # -*- coding: utf-8 -*-
-import os
 import imp
+import os
 import unittest
 
 test_utils = imp.load_source( 'test_utils',
     os.path.join( os.path.dirname( __file__), '../unittest_utils/utility.py' ) )
 
 import sqlalchemy
+from six import string_types
 
-from galaxy import model
-from galaxy import exceptions
-
-from base import BaseTestCase
-
-from galaxy.managers.histories import HistoryManager
-from galaxy.managers.datasets import DatasetManager
+from galaxy import exceptions, model
 from galaxy.managers import hdas
+from galaxy.managers.datasets import DatasetManager
+from galaxy.managers.histories import HistoryManager
 
+from .base import BaseTestCase
 
 # =============================================================================
 default_password = '123456'
@@ -429,11 +427,11 @@ def test_serializers( self ):
         self.assertIsInstance( serialized[ 'dataset' ], dict )
         self.assertEncodedId( serialized[ 'dataset_id' ] )
         self.assertUUID( serialized[ 'uuid' ] )
-        self.assertIsInstance( serialized[ 'file_name' ], basestring )
-        self.assertIsInstance( serialized[ 'extra_files_path' ], basestring )
+        self.assertIsInstance( serialized[ 'file_name' ], string_types )
+        self.assertIsInstance( serialized[ 'extra_files_path' ], string_types )
         self.assertIsInstance( serialized[ 'size' ], int )
         self.assertIsInstance( serialized[ 'file_size' ], int )
-        self.assertIsInstance( serialized[ 'nice_size' ], basestring )
+        self.assertIsInstance( serialized[ 'nice_size' ], string_types )
         # TODO: these should be tested w/copy
         self.assertNullableEncodedId( serialized[ 'copied_from_history_dataset_association_id'] )
         self.assertNullableEncodedId( serialized[ 'copied_from_library_dataset_dataset_association_id'] )
@@ -443,8 +441,8 @@ def test_serializers( self ):
         self.assertIsInstance( serialized[ 'meta_files' ], list )
         self.assertNullableEncodedId( serialized[ 'parent_id'] )
         self.assertEqual( serialized[ 'designation' ], None )
-        self.assertIsInstance( serialized[ 'genome_build' ], basestring )
-        self.assertIsInstance( serialized[ 'data_type' ], basestring )
+        self.assertIsInstance( serialized[ 'genome_build' ], string_types )
+        self.assertIsInstance( serialized[ 'data_type' ], string_types )
 
         # hda
         self.assertEncodedId( serialized[ 'history_id' ] )
@@ -469,9 +467,9 @@ def test_serializers( self ):
         self.assertEqual( serialized[ 'api_type' ], 'file' )
         self.assertEqual( serialized[ 'type' ], 'file' )
 
-        self.assertIsInstance( serialized[ 'url' ], basestring )
+        self.assertIsInstance( serialized[ 'url' ], string_types )
         self.assertIsInstance( serialized[ 'urls' ], dict )
-        self.assertIsInstance( serialized[ 'download_url' ], basestring )
+        self.assertIsInstance( serialized[ 'download_url' ], string_types )
 
         self.log( 'serialized should jsonify well' )
         self.assertIsJsonifyable( serialized )
@@ -579,7 +577,7 @@ def test_deserialize_visible( self ):
     def test_deserialize_genome_build( self ):
         hda = self._create_vanilla_hda()
 
-        self.assertIsInstance( hda.dbkey, basestring )
+        self.assertIsInstance( hda.dbkey, string_types )
         self.log( 'should deserialize to "?" from None' )
         self.hda_deserializer.deserialize( hda, { 'genome_build': None } )
         self.assertEqual( hda.dbkey, '?' )

diff --git a/test/unit/managers/test_HDCAManager.py b/test/unit/managers/test_HDCAManager.py
@@ -6,8 +6,8 @@
 test_utils = imp.load_source( 'test_utils',
     os.path.join( os.path.dirname( __file__), '../unittest_utils/utility.py' ) )
 
-from base import BaseTestCase
-from base import CreatesCollectionsMixin
+from .base import BaseTestCase
+from .base import CreatesCollectionsMixin
 
 from galaxy.managers.histories import HistoryManager
 from galaxy.managers.datasets import DatasetManager
@@ -72,7 +72,7 @@ def set_up_managers( self ):
     def test_views( self ):
         serializer = self.hdca_serializer
         item = self._create_list_hdca([
-            dict( name=( "hda-{0}".format( i ) ), hid=i ) for i in xrange( 5 )
+            dict( name=( "hda-{0}".format( i ) ), hid=i ) for i in range( 5 )
         ])
 
         self.log( 'should have a summary view' )
@@ -99,7 +99,7 @@ def test_views( self ):
     def test_views_and_keys( self ):
         serializer = self.hdca_serializer
         item = self._create_list_hdca([
-            dict( name=( "hda-{0}".format( i ) ), hid=i ) for i in xrange( 5 )
+            dict( name=( "hda-{0}".format( i ) ), hid=i ) for i in range( 5 )
         ])
         summary_plus_key = [ 'elements' ]
         only_keys = [ 'id', 'populated_state_message' ]

diff --git a/test/unit/managers/test_HistoryContentsManager.py b/test/unit/managers/test_HistoryContentsManager.py
@@ -1,28 +1,23 @@
 # -*- coding: utf-8 -*-
 """
 """
-import os
+import datetime
 import imp
-import unittest
+import os
 import random
-import datetime
+import unittest
 
 test_utils = imp.load_source( 'test_utils',
     os.path.join( os.path.dirname( __file__), '../unittest_utils/utility.py' ) )
 
-from sqlalchemy import true
-from sqlalchemy import false
-from sqlalchemy import desc
+from sqlalchemy import column, desc, false, true
 from sqlalchemy.sql import text
-from sqlalchemy import column
-
-from base import BaseTestCase
-from base import CreatesCollectionsMixin
 
+from galaxy.managers import collections, hdas, history_contents
 from galaxy.managers.histories import HistoryManager
-from galaxy.managers import hdas
-from galaxy.managers import collections
-from galaxy.managers import history_contents
+
+from .base import BaseTestCase
+from .base import CreatesCollectionsMixin
 
 default_password = '123456'
 user2_data = dict( email='[email protected]', username='user2', password=default_password )
@@ -62,10 +57,10 @@ def test_contents( self ):
         self.assertEqual( [], list( self.contents_manager.contents( history ) ) )
 
         self.log( "calling contents on an history with hdas should return those in order of their hids" )
-        hdas = [ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 3 ) ]
+        hdas = [ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 3 ) ]
         random.shuffle( hdas )
         ordered_hda_contents = list( self.contents_manager.contents( history ) )
-        self.assertEqual( map( lambda hda: hda.hid, ordered_hda_contents ), [ 1, 2, 3 ] )
+        self.assertEqual( [hda.hid for hda in ordered_hda_contents], [ 1, 2, 3 ] )
 
         self.log( "calling contents on an history with both hdas and collections should return both" )
         hdca = self.add_list_collection_to_history( history, hdas )
@@ -80,7 +75,7 @@ def test_contained( self ):
         self.assertEqual( [], list( self.contents_manager.contained( history ) ) )
 
         self.log( "calling contained on an history with both hdas and collections should return only hdas" )
-        hdas = [ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 3 ) ]
+        hdas = [ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 3 ) ]
         self.add_list_collection_to_history( history, hdas )
         self.assertEqual( list( self.contents_manager.contained( history ) ), hdas )
 
@@ -92,7 +87,7 @@ def test_subcontainers( self ):
         self.assertEqual( [], list( self.contents_manager.subcontainers( history ) ) )
 
         self.log( "calling subcontainers on an history with both hdas and collections should return only collections" )
-        hdas = [ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 3 ) ]
+        hdas = [ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 3 ) ]
         hdca = self.add_list_collection_to_history( history, hdas )
         subcontainers = list( self.contents_manager.subcontainers( history ) )
         self.assertEqual( subcontainers, [ hdca ] )
@@ -101,9 +96,9 @@ def test_limit_and_offset( self ):
         user2 = self.user_manager.create( **user2_data )
         history = self.history_manager.create( name='history', user=user2 )
         contents = []
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 3 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 3 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[:3] ) )
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 4, 6 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 4, 6 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[4:6] ) )
 
         # _subquery = self.contents_manager._contents_common_query( self.contents_manager.subcontainer_class, history.id )
@@ -130,9 +125,9 @@ def test_orm_filtering( self ):
         user2 = self.user_manager.create( **user2_data )
         history = self.history_manager.create( name='history', user=user2 )
         contents = []
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 3 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 3 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[:3] ) )
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 4, 6 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 4, 6 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[4:6] ) )
 
         self.log( "should allow filter on deleted" )
@@ -207,9 +202,9 @@ def test_order_by( self ):
         user2 = self.user_manager.create( **user2_data )
         history = self.history_manager.create( name='history', user=user2 )
         contents = []
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 3 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 3 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[:3] ) )
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 4, 6 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 4, 6 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[4:6] ) )
 
         self.log( "should default to hid order_by" )
@@ -240,9 +235,9 @@ def test_update_time_filter( self ):
         user2 = self.user_manager.create( **user2_data )
         history = self.history_manager.create( name='history', user=user2 )
         contents = []
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 3 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 3 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[:3] ) )
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 4, 6 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 4, 6 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[4:6] ) )
 
         self.log( "should allow filtering by update_time" )
@@ -264,9 +259,9 @@ def test_filtered_counting( self ):
         user2 = self.user_manager.create( **user2_data )
         history = self.history_manager.create( name='history', user=user2 )
         contents = []
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 3 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 3 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[:3] ) )
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 4, 6 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 4, 6 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[4:6] ) )
 
         self.log( "should show correct count with filters" )
@@ -292,9 +287,9 @@ def test_type_id( self ):
         user2 = self.user_manager.create( **user2_data )
         history = self.history_manager.create( name='history', user=user2 )
         contents = []
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 3 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 3 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[:3] ) )
-        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in xrange( 4, 6 ) ])
+        contents.extend([ self.add_hda_to_history( history, name=( 'hda-' + str( x ) ) ) for x in range( 4, 6 ) ])
         contents.append( self.add_list_collection_to_history( history, contents[4:6] ) )
 
         self.log( "should be able to use eq and in with hybrid type_id" )

diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py
@@ -1,28 +1,24 @@
 # -*- coding: utf-8 -*-
 """
 """
-import os
 import imp
+import os
 import unittest
 
 test_utils = imp.load_source( 'test_utils',
     os.path.join( os.path.dirname( __file__), '../unittest_utils/utility.py' ) )
 import galaxy_mock
 
 import sqlalchemy
+from six import string_types
 from sqlalchemy import true
 
-from galaxy import model
-from galaxy import exceptions
-
-from base import BaseTestCase
+from galaxy import exceptions, model
+from galaxy.managers import base, hdas
+from galaxy.managers.histories import (HistoryDeserializer, HistoryFilters,
+                                       HistoryManager, HistorySerializer)
 
-from galaxy.managers import base
-from galaxy.managers.histories import HistoryManager
-from galaxy.managers.histories import HistorySerializer
-from galaxy.managers.histories import HistoryDeserializer
-from galaxy.managers.histories import HistoryFilters
-from galaxy.managers import hdas
+from .base import BaseTestCase
 
 default_password = '123456'
 user2_data = dict( email='[email protected]', username='user2', password=default_password )
@@ -260,7 +256,7 @@ def test_sharable( self ):
             len( self.history_manager.get_share_assocs( item1 ) ), 1 )
         self.assertEqual(
             len( self.history_manager.get_share_assocs( item1, user=non_owner ) ), 1 )
-        self.assertIsInstance( item1.slug, basestring )
+        self.assertIsInstance( item1.slug, string_types )
 
         self.log( "should be able to unshare with specific users" )
         share_assoc = self.history_manager.unshare_with( item1, non_owner )
@@ -491,7 +487,7 @@ def test_history_serializers( self ):
 
         self.log( 'everything serialized should be of the proper type' )
         self.assertIsInstance( serialized[ 'size' ], int )
-        self.assertIsInstance( serialized[ 'nice_size' ], basestring )
+        self.assertIsInstance( serialized[ 'nice_size' ], string_types )
 
         self.log( 'serialized should jsonify well' )
         self.assertIsJsonifyable( serialized )
@@ -560,7 +556,7 @@ def test_contents( self ):
         self.assertEqual( serialized[ 'state_details' ][ 'ok' ], 1 )
         self.assertIsInstance( serialized[ 'state_ids' ][ 'ok' ], list )
         self.assertIsInstance( serialized[ 'hdas' ], list )
-        self.assertIsInstance( serialized[ 'hdas' ][0], basestring )
+        self.assertIsInstance( serialized[ 'hdas' ][0], string_types )
 
         serialized = self.history_serializer.serialize( history1, [ 'contents' ] )
         self.assertHasKeys( serialized[ 'contents' ][0], [ 'id', 'name', 'peek', 'create_time' ])

diff --git a/test/unit/managers/test_UserManager.py b/test/unit/managers/test_UserManager.py
@@ -1,21 +1,20 @@
 # -*- coding: utf-8 -*-
 """
 """
-import os
 import imp
+import os
 import unittest
 
 test_utils = imp.load_source( 'test_utils',
     os.path.join( os.path.dirname( __file__), '../unittest_utils/utility.py' ) )
 
 import sqlalchemy
+from six import string_types
 
-from galaxy import model
-from galaxy import exceptions
+from galaxy import exceptions, model
+from galaxy.managers import histories, users
 
-from base import BaseTestCase
-from galaxy.managers import users
-from galaxy.managers import histories
+from .base import BaseTestCase
 
 
 # =============================================================================
@@ -114,7 +113,7 @@ def test_api_keys( self ):
 
         self.log( "should be able to generate and retrieve valid api key" )
         user2_api_key = self.user_manager.create_api_key( user2 )
-        self.assertIsInstance( user2_api_key, basestring )
+        self.assertIsInstance( user2_api_key, string_types )
         self.assertEqual( self.user_manager.valid_api_key( user2 ).key, user2_api_key )
 
         self.log( "should return the most recent (i.e. most valid) api key" )
@@ -179,7 +178,7 @@ def test_serializers( self ):
         # self.assertIsInstance( serialized[ 'active' ], bool )
         self.assertIsInstance( serialized[ 'is_admin' ], bool )
         self.assertIsInstance( serialized[ 'total_disk_usage' ], float )
-        self.assertIsInstance( serialized[ 'nice_total_disk_usage' ], basestring )
+        self.assertIsInstance( serialized[ 'nice_total_disk_usage' ], string_types )
         self.assertIsInstance( serialized[ 'quota_percent' ], ( type( None ), float ) )
         self.assertIsInstance( serialized[ 'tags_used' ], list )
         self.assertIsInstance( serialized[ 'has_requests' ], bool )
@@ -209,7 +208,7 @@ def test_anonymous( self ):
         self.assertEqual( serialized[ 'id' ], None )
         self.log( 'everything serialized should be of the proper type' )
         self.assertIsInstance( serialized[ 'total_disk_usage' ], float )
-        self.assertIsInstance( serialized[ 'nice_total_disk_usage' ], basestring )
+        self.assertIsInstance( serialized[ 'nice_total_disk_usage' ], string_types )
         self.assertIsInstance( serialized[ 'quota_percent' ], ( type( None ), float ) )
 
         self.log( 'serialized should jsonify well' )