Merge pull request #3177 from nsoranzo/flake8-import-order

Fix import order and Python3 compatibility for test/unit/

.ci/flake8_lint_include_list.txt

@@ -516,52 +516,64 @@ test/shed_functional/base/__init__.py
 test/shed_functional/functional/
 test/shed_functional/functional_tests.py
 test/shed_functional/__init__.py
-test/unit/dataset_collections/__init__.py
+test/unit/dataset_collections/
 test/unit/datatypes/dataproviders/__init__.py
+test/unit/datatypes/dataproviders/test_line_dataproviders.py
 test/unit/datatypes/__init__.py
 test/unit/datatypes/test_data.py
-test/unit/jobs/dynamic_tool_destination/__init__.py
-test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
-test/unit/jobs/dynamic_tool_destination/ymltests.py
+test/unit/jobs/dynamic_tool_destination/
 test/unit/jobs/__init__.py
+test/unit/jobs/test_command_factory.py
 test/unit/jobs/test_datasets.py
+test/unit/jobs/test_job_configuration.py
+test/unit/jobs/test_job_output_checker.py
+test/unit/jobs/test_mapper.py
+test/unit/jobs/test_rule_helper.py
 test/unit/jobs/test_rules/
 test/unit/jobs/test_runner_params.py
 test/unit/managers/__init__.py
+test/unit/managers/test_CollectionManager.py
+test/unit/managers/test_DatasetManager.py
 test/unit/managers/test_HDAManager.py
+test/unit/managers/test_HDCAManager.py
 test/unit/managers/test_HistoryContentsManager.py
-test/unit/managers/test_HistoryManager.py
 test/unit/managers/test_UserManager.py
 test/unit/shed_unit/__init__.py
 test/unit/shed_unit/test_fabric_util.py
+test/unit/shed_unit/test_td_common_util.py
+test/unit/test_galaxy_transactions.py
 test/unit/test_lazy_process.py
+test/unit/test_routes.py
 test/unit/test_security_helper.py
 test/unit/test_sockets.py
 test/unit/test_sqlite_utils.py
 test/unit/test_topsort.py
 test/unit/tools/filter_modules/
 test/unit/tools/__init__.py
-test/unit/tools/test_data_parameters.py
-test/unit/tools/test_tool_dependency_description.py
-test/unit/tools/test_tool_panel.py
+test/unit/tools/test_actions.py
+test/unit/tools/test_citations.py
+test/unit/tools/test_collect_primary_datasets.py
+test/unit/tools/test_conda_resolution.py
+test/unit/tools/test_dataset_matcher.py
+test/unit/tools/test_parameter_parsing.py
 test/unit/tools/test_parsing.py
+test/unit/tools/test_select_parameters.py
+test/unit/tools/test_toolbox_filters.py
+test/unit/tools/test_tool_dependency_description.py
 test/unit/tools/test_tool_deps.py
+test/unit/tools/test_tool_external_files.py
 test/unit/tools/test_tool_loader.py
-test/unit/tools/test_toolbox_filters.py
+test/unit/tools/test_tool_panel.py
 test/unit/tools/test_watcher.py
+test/unit/tools/test_wrappers.py
 test/unit/tools_support.py
-test/unit/unittest_utils/__init__.py
-test/unit/unittest_utils/utility.py
+test/unit/unittest_utils/
 test/unit/visualizations/__init__.py
 test/unit/visualizations/plugins/__init__.py
 test/unit/web/base/__init__.py
 test/unit/web/framework/__init__.py
 test/unit/web/__init__.py
-test/unit/workflows/__init__.py
-test/unit/workflows/test_extract_summary.py
-test/unit/workflows/test_modules.py
-test/unit/workflows/test_render.py
-test/unit/workflows/test_workflow_progress.py
+test/unit/workflows/
 test/unit/test_objectstore.py
 tool_list.py
 tools/

test/manual/workflows_scaling.py

@@ -20,7 +20,8 @@
 galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir))
 sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ]
 
-from api import helpers, yaml_to_workflow
+from api import helpers
+from api.workflows_format_2.converter import python_to_workflow
 
 LONG_TIMEOUT = 1000000000
 DESCRIPTION = "Script to exercise the workflow engine."
@@ -53,7 +54,7 @@ def main(argv=None):
 
     gi = _gi(args)
 
-    workflow = yaml_to_workflow.python_to_workflow(workflow_struct)
+    workflow = python_to_workflow(workflow_struct)
     workflow_info = gi.workflows.import_workflow_json(workflow)
     workflow_id = workflow_info["id"]
 

test/unit/dataset_collections/test_matching.py

@@ -1,7 +1,7 @@
 from galaxy.dataset_collections import (
-    type_description,
-    registry,
     matching,
+    registry,
+    type_description,
 )
 
 TYPE_REGISTRY = registry.DatasetCollectionTypesRegistry( None )
@@ -98,7 +98,7 @@ def list_instance( collection_type="list", elements=None, ids=None ):
     if not elements:
         if ids is None:
             ids = [ "data1", "data2" ]
-        elements = map(hda_element, ids)
+        elements = [hda_element(_) for _ in ids]
     list_collection_instance = collection_instance(
         collection_type=collection_type,
         elements=elements

test/unit/datatypes/dataproviders/test_base_dataproviders.py

@@ -2,20 +2,20 @@
 Unit tests for base DataProviders.
 .. seealso:: galaxy.datatypes.dataproviders.base
 """
-
+import logging
 import os.path
-import imp
+import sys
 import unittest
+
 from six import StringIO
 
-import logging
-log = logging.getLogger( __name__ )
+from galaxy.datatypes.dataproviders import base, exceptions
 
-test_utils = imp.load_source( 'test_utils',
-    os.path.join( os.path.dirname( __file__), '../../unittest_utils/utility.py' ) )
-import tempfilecache
+unit_root = os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) )
+sys.path.insert( 1, unit_root )
+from unittest_utils import tempfilecache, utility
 
-from galaxy.datatypes.dataproviders import base, exceptions
+log = logging.getLogger( __name__ )
 
 # TODO: fix imports there after dist and retry
 # TODO: fix off by ones in FilteredDataProvider counters
@@ -52,7 +52,7 @@ def tearDown( self ):
 
     def format_tmpfile_contents( self, contents=None ):
         contents = contents or self.default_file_contents
-        contents = test_utils.clean_multiline_string( contents )
+        contents = utility.clean_multiline_string( contents )
         log.debug( 'file contents:\n%s', contents )
         return contents
 
@@ -135,7 +135,7 @@ def test_readlines( self ):
     def test_stringio( self ):
         """should work with StringIO
         """
-        contents = test_utils.clean_multiline_string( """
+        contents = utility.clean_multiline_string( """
             One
             Two
             Three
@@ -297,7 +297,7 @@ class Test_MultiSourceDataProvider( BaseTestCase ):
     def contents_and_tmpfile( self, contents=None ):
         # TODO: hmmmm...
         contents = contents or self.default_file_contents
-        contents = test_utils.clean_multiline_string( contents )
+        contents = utility.clean_multiline_string( contents )
         return ( contents, self.tmpfiles.create_tmpfile( contents ) )
 
     def test_multiple_sources( self ):
@@ -323,7 +323,7 @@ def test_multiple_sources( self ):
                 Twelve! (<-- http://youtu.be/JZshZp-cxKg)
             """
         ]
-        contents = [ test_utils.clean_multiline_string( c ) for c in contents ]
+        contents = [ utility.clean_multiline_string( c ) for c in contents ]
         source_list = [ open( self.tmpfiles.create_tmpfile( c ) ) for c in contents ]
 
         provider = self.provider_class( source_list )
@@ -355,7 +355,7 @@ def test_multiple_compound_sources( self ):
                 Twelve! (<-- http://youtu.be/JZshZp-cxKg)
             """
         ]
-        contents = [ test_utils.clean_multiline_string( c ) for c in contents ]
+        contents = [ utility.clean_multiline_string( c ) for c in contents ]
         source_list = [ open( self.tmpfiles.create_tmpfile( c ) ) for c in contents ]
 
         def no_Fs( string ):

test/unit/datatypes/dataproviders/test_line_dataproviders.py

@@ -2,18 +2,14 @@
 Unit tests for base DataProviders.
 .. seealso:: galaxy.datatypes.dataproviders.base
 """
-
-import imp
-import unittest
-import os.path
 import logging
-log = logging.getLogger( __name__ )
+import unittest
 
-test_utils = imp.load_source( 'test_utils',
-    os.path.join( os.path.dirname( __file__), '../../unittest_utils/utility.py' ) )
+from galaxy.datatypes.dataproviders import line
 
 from . import test_base_dataproviders
-from galaxy.datatypes.dataproviders import line
+
+log = logging.getLogger( __name__ )
 
 
 # TODO: TestCase hierarchy is a bit of mess here.

test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py

@@ -1,16 +1,15 @@
 import logging
 import os
-import sys
-sys.path.append("")
 import unittest
-import mockGalaxy as mg
-import ymltests as yt
-import galaxy.jobs.dynamic_tool_destination as dt
 
-from galaxy.jobs.dynamic_tool_destination import map_tool_to_destination
 from testfixtures import log_capture
+
+import galaxy.jobs.dynamic_tool_destination as dt
+from galaxy.jobs.dynamic_tool_destination import map_tool_to_destination
 from galaxy.jobs.mapper import JobMappingException
 
+from . import mockGalaxy as mg
+from . import ymltests as yt
 
 theApp = mg.App( "waffles_default", "test_spec")
 script_dir = os.path.dirname(__file__)

test/unit/jobs/test_command_factory.py

@@ -1,6 +1,6 @@
 import os
-from os import getcwd
 import shutil
+from os import getcwd
 from tempfile import mkdtemp
 from unittest import TestCase
 

test/unit/jobs/test_job_configuration.py

@@ -4,8 +4,8 @@
 import tempfile
 import unittest
 
-from galaxy.util import bunch
 from galaxy.jobs import JobConfiguration
+from galaxy.util import bunch
 
 # File would be slightly more readable if contents were embedded directly, but
 # there are advantages to testing the documentation/examples.

test/unit/jobs/test_job_output_checker.py

@@ -1,9 +1,10 @@
 from unittest import TestCase
-from galaxy.util.bunch import Bunch
-from galaxy.jobs.output_checker import check_output
+
 from galaxy.jobs.error_level import StdioErrorLevel
-from galaxy.tools.parser.interface import ToolStdioRegex
+from galaxy.jobs.output_checker import check_output
 from galaxy.model import Job
+from galaxy.tools.parser.interface import ToolStdioRegex
+from galaxy.util.bunch import Bunch
 
 
 class OutputCheckerTestCase( TestCase ):

test/unit/jobs/test_job_wrapper.py

@@ -1,15 +1,18 @@
 import os
 from contextlib import contextmanager
-
 from unittest import TestCase
-from galaxy.model import Job
-from galaxy.model import Task
-from galaxy.model import User
-from galaxy.jobs import JobWrapper
-from galaxy.jobs import TaskWrapper
-from galaxy.util.bunch import Bunch
 
+from galaxy.jobs import (
+    JobWrapper,
+    TaskWrapper
+)
+from galaxy.model import (
+    Job,
+    Task,
+    User
+)
 from galaxy.tools import evaluation
+from galaxy.util.bunch import Bunch
 
 from tools_support import UsesApp
 

test/unit/jobs/test_mapper.py

@@ -1,16 +1,15 @@
 import uuid
 
-import jobs.test_rules
-
+from galaxy.jobs import JobDestination
 from galaxy.jobs.mapper import (
-    JobRunnerMapper,
     ERROR_MESSAGE_NO_RULE_FUNCTION,
     ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND,
+    JobRunnerMapper,
 )
-from galaxy.jobs import JobDestination
-
 from galaxy.util import bunch
 
+from . import test_rules
+
 WORKFLOW_UUID = uuid.uuid1().hex
 TOOL_JOB_DESTINATION = JobDestination()
 DYNAMICALLY_GENERATED_DESTINATION = JobDestination()
@@ -107,7 +106,7 @@ def __mapper( tool_job_destination=TOOL_JOB_DESTINATION ):
         {},
         job_config
     )
-    mapper.rules_module = jobs.test_rules
+    mapper.rules_module = test_rules
     return mapper
 
 

test/unit/jobs/test_rule_helper.py

@@ -1,10 +1,9 @@
 import uuid
 
-from galaxy.util import bunch
 from galaxy import model
-from galaxy.model import mapping
-
 from galaxy.jobs.rule_helper import RuleHelper
+from galaxy.model import mapping
+from galaxy.util import bunch
 
 USER_EMAIL_1 = "u1@example.com"
 USER_EMAIL_2 = "u2@example.com"

test/unit/jobs/test_runner_local.py

@@ -3,10 +3,10 @@
 import time
 from unittest import TestCase
 
-from galaxy.util import bunch
-from galaxy.jobs.runners import local
-from galaxy.jobs import metrics
 from galaxy import model
+from galaxy.jobs import metrics
+from galaxy.jobs.runners import local
+from galaxy.util import bunch
 
 from tools_support import (
     UsesApp,