Merge pull request #6722 from nsoranzo/fix_warnings

Small mixed fixes

contrib/nagios/check_galaxy.py

@@ -73,7 +73,7 @@ tc.agent("Mozilla/5.0 (compatible; check_galaxy/0.2)")
 tc.config('use_tidy', 0)
 
 
-class Browser:
+class Browser(object):
     def __init__(self):
         self.server = server
         self.handler = handler

lib/galaxy/authnz/psa_authnz.py

@@ -230,7 +230,7 @@ class Strategy(BaseStrategy):
         return self.backend.continue_pipeline(*args, **kwargs)
 
 
-class Storage:
+class Storage(object):
     user = UserAuthnzToken
     nonce = PSANonce
     association = PSAAssociation

lib/galaxy/tools/toolbox/base.py

@@ -714,7 +714,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
 
     def __watch_directory(self, directory, elems, integrated_elems, load_panel_dict, recursive, force_watch=False):
 
-        def quick_load(tool_file, async=True):
+        def quick_load(tool_file, async_load=True):
             try:
                 tool = self.load_tool(tool_file)
                 self.__add_tool(tool, load_panel_dict, elems)
@@ -722,7 +722,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 key = 'tool_%s' % str(tool.id)
                 integrated_elems[key] = tool
 
-                if async:
+                if async_load:
                     self._load_tool_panel()
                     self._save_integrated_tool_panel()
                 return tool.id
@@ -739,7 +739,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             if os.path.isdir(child_path) and recursive:
                 self.__watch_directory(child_path, elems, integrated_elems, load_panel_dict, recursive)
             elif self._looks_like_a_tool(child_path):
-                quick_load(child_path, async=False)
+                quick_load(child_path, async_load=False)
                 tool_loaded = True
         if (tool_loaded or force_watch) and self._tool_watcher:
             self._tool_watcher.watch_directory(directory, quick_load)

lib/galaxy/tools/util/maf_utilities.py

@@ -731,7 +731,7 @@ def get_attributes_from_fasta_header(header):
 
 
 def iter_fasta_alignment(filename):
-    class fastaComponent:
+    class fastaComponent(object):
         def __init__(self, species, text=""):
             self.species = species
             self.text = text

lib/galaxy/tools/verify/interactor.py

@@ -265,7 +265,7 @@ class GalaxyInteractorApi(object):
             output_id = output_data
         return output_id
 
-    def stage_data_async(self, test_data, history_id, tool_id, async=True):
+    def stage_data_async(self, test_data, history_id, tool_id):
         fname = test_data['fname']
         tool_input = {
             "file_type": test_data['ftype'],

lib/galaxy/tools/wrappers.py

@@ -120,7 +120,7 @@ class SelectToolParameterWrapper(ToolParameterValueWrapper):
     attributes are accessible.
     """
 
-    class SelectToolParameterFieldWrapper:
+    class SelectToolParameterFieldWrapper(object):
         """
         Provide access to any field by name or index for this particular value.
         Only applicable for dynamic_options selects, which have more than simple 'options' defined (name, value, selected).
@@ -182,7 +182,7 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
     attributes are accessible.
     """
 
-    class MetadataWrapper:
+    class MetadataWrapper(object):
         """
         Wraps a Metadata Collection to return MetadataParameters wrapped
         according to the metadata spec. Methods implemented to match behavior

lib/galaxy/util/streamball.py

@@ -33,7 +33,7 @@ class StreamBall(object):
     def stream(self, environ, start_response):
         response_write = start_response(self.wsgi_status, self.wsgi_headeritems)
 
-        class tarfileobj:
+        class tarfileobj(object):
             def write(self, *args, **kwargs):
                 response_write(*args, **kwargs)
         tf = tarfile.open(mode=self.mode, fileobj=tarfileobj())

lib/galaxy/util/xml_macros.py

@@ -141,7 +141,7 @@ def _expand_macro(element, expand_el, macros, tokens):
     # require this parent_map data structure but elementtree does not
     # track parents or recongnize .find('..').
     # TODO fix this now that we're not using elementtree
-    parent_map = dict((c, p) for p in element.getiterator() for c in p)
+    parent_map = dict((c, p) for p in element.iter() for c in p)
     _xml_replace(expand_el, expanded_elements, parent_map)
 
 
@@ -150,7 +150,7 @@ def _expand_yield_statements(macro_def, expand_el):
 
     expand_el_children = list(expand_el)
     macro_def_parent_map = \
-        dict((c, p) for macro_def_el in macro_def for p in macro_def_el.getiterator() for c in p)
+        dict((c, p) for macro_def_el in macro_def for p in macro_def_el.iter() for c in p)
 
     for yield_el in yield_els:
         _xml_replace(yield_el, expand_el_children, macro_def_parent_map)

lib/galaxy/web/framework/base.py

@@ -369,7 +369,7 @@ class Request(webob.Request):
         Create a new request wrapping the WSGI environment `environ`
         """
         #  self.environ = environ
-        webob.Request.__init__(self, environ, charset='utf-8', decode_param_names=False)
+        webob.Request.__init__(self, environ, charset='utf-8')
     # Properties that are computed and cached on first use
 
     @lazy_property

pytest.ini

@@ -1,6 +1,7 @@
 [pytest]
 addopts = --doctest-continue-on-failure
 log_level = DEBUG
+python_classes =
 python_paths = lib
 markers =
   data_manager: marks test as a data_manager test

scripts/api/library_upload_dir.py

@@ -8,7 +8,7 @@ import sys
 from bioblend import galaxy
 
 
-class Uploader:
+class Uploader(object):
 
     def __init__(self, url, api, library_id, folder_id, should_link,
                  non_local):

scripts/apply_tags.py

@@ -6,7 +6,7 @@ import time
 from bioblend.galaxy import GalaxyInstance
 
 
-class ApplyTagsHistory:
+class ApplyTagsHistory(object):
 
     @classmethod
     def __init__(self, galaxy_url, galaxy_api_key, history_id=None):

scripts/check_galaxy.py

@@ -107,7 +107,7 @@ tc.agent("Mozilla/5.0 (compatible; check_galaxy/0.1)")
 tc.config('use_tidy', 0)
 
 
-class Browser:
+class Browser(object):
 
     def __init__(self):
         self.server = server

scripts/grt/export.py

@@ -48,7 +48,7 @@ def kw_metrics(job):
     }
 
 
-class Sanitization:
+class Sanitization(object):
 
     def __init__(self, sanitization_config, model, sa_session):
         self.sanitization_config = sanitization_config

scripts/loc_files/create_all_fasta_loc.py

@@ -205,11 +205,11 @@ def __main__():
     loc_path = None
     tree = parse(options.data_table_xml)
     tables = tree.getroot()
-    for table in tables.getiterator():
+    for table in tables.iter():
         name = table.attrib.get('name')
         if name == options.data_table_name:
             cols = None
-            for node in table.getiterator():
+            for node in table.iter():
                 if node.tag == 'columns':
                     cols = node.text
                 elif node.tag == 'file':

scripts/microbes/util.py

@@ -7,7 +7,7 @@ assert sys.version_info[:2] >= (2, 4)
 
 
 # genbank_to_bed
-class Region:
+class Region(object):
     def __init__(self):
         self.qualifiers = {}
         self.start = None
@@ -37,7 +37,7 @@ class Region:
                     self.end = end
 
 
-class GenBankFeatureParser:
+class GenBankFeatureParser(object):
     """Parses Features from Single Locus GenBank file"""
     def __init__(self, fh, features_list=[]):
         self.fh = fh

test/base/api.py

@@ -19,7 +19,7 @@ from .interactor import TestCaseGalaxyInteractor as BaseInteractor
 from .testcase import FunctionalTestCase
 
 
-class UsesApiTestCaseMixin:
+class UsesApiTestCaseMixin(object):
 
     def _api_url(self, path, params=None, use_key=None, use_admin_key=None):
         if not params:

test/base/populators.py

@@ -140,7 +140,7 @@ def _raise_skip_if(check):
 
 # Deprecated mixin, use dataset populator instead.
 # TODO: Rework existing tests to target DatasetPopulator in a setup method instead.
-class TestsDatasets:
+class TestsDatasets(object):
 
     def _new_dataset(self, history_id, content='TestData123', **kwds):
         return DatasetPopulator(self.galaxy_interactor).new_dataset(history_id, content=content, **kwds)
@@ -1087,7 +1087,7 @@ def wait_on_state(state_func, desc="state", skip_states=["running", "queued", "n
         raise TimeoutAssertionError("%s Current response containing state [%s]." % (str(e), response.json()))
 
 
-class GiPostGetMixin:
+class GiPostGetMixin(object):
     """Mixin for adapting Galaxy testing populators helpers to bioblend."""
 
     def _get(self, route, data={}):

test/galaxy_selenium/has_driver.py

@@ -14,7 +14,7 @@ from selenium.webdriver.support.ui import WebDriverWait
 UNSPECIFIED_TIMEOUT = object()
 
 
-class HasDriver:
+class HasDriver(object):
     TimeoutException = TimeoutException
 
     def assert_xpath(self, xpath):

test/integration/test_job_environments.py

@@ -24,7 +24,7 @@ JobEnviromentProperties = collections.namedtuple("JobEnvironmentProperties", [
 ])
 
 
-class RunsEnvironmentJobs:
+class RunsEnvironmentJobs(object):
 
     def _run_and_get_environment_properties(self, tool_id="job_environment_default"):
         with self.dataset_populator.test_history() as history_id:

test/selenium_tests/framework.py

@@ -431,7 +431,7 @@ class SharedStateSeleniumTestCase(SeleniumTestCase):
         """Override this to setup shared data for tests that gets initialized only once."""
 
 
-class UsesHistoryItemAssertions:
+class UsesHistoryItemAssertions(object):
 
     def assert_item_peek_includes(self, hid, expected):
         item_body = self.history_panel_item_component(hid=hid)
@@ -508,7 +508,7 @@ def get_remote_driver():
     )
 
 
-class SeleniumSessionGetPostMixin:
+class SeleniumSessionGetPostMixin(object):
     """Mixin for adapting Galaxy testing populators helpers to Selenium session backed bioblend."""
 
     def _get(self, route, data={}):

test/unit/tools/test_evaluation.py

@@ -194,7 +194,7 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
             kwds["working_directory"] = self.test_directory
         if "new_file_path" not in kwds:
             kwds["new_file_path"] = self.app.config.new_file_path
-        self.evaluator.set_compute_environment(TestComputeEnviornment(**kwds))
+        self.evaluator.set_compute_environment(TestComputeEnvironment(**kwds))
         assert "exec_before_job" in self.tool.hooks_called
 
     def _setup_test_bwa_job(self):
@@ -218,7 +218,7 @@ class MockHistoryDatasetAssociation(HistoryDatasetAssociation):
         super(MockHistoryDatasetAssociation, self).__init__(**kwds)
 
 
-class TestComputeEnviornment(SimpleComputeEnvironment):
+class TestComputeEnvironment(SimpleComputeEnvironment):
 
     def __init__(
         self,
@@ -256,7 +256,7 @@ class TestComputeEnviornment(SimpleComputeEnvironment):
         if self._path_rewriter:
             return self._path_rewriter
         else:
-            return super(TestComputeEnviornment, self).unstructured_path_rewriter()
+            return super(TestComputeEnvironment, self).unstructured_path_rewriter()
 
     def tool_directory(self):
         return TEST_TOOL_DIRECTORY

tools/filters/join.py

@@ -20,7 +20,7 @@ from galaxy.util import stringify_dictionary_keys
 from galaxy.util.bunch import Bunch
 
 
-class OffsetList:
+class OffsetList(object):
     def __init__(self, filesize=0, fmt=None):
         self.file = tempfile.NamedTemporaryFile('w+b')
         if fmt:
@@ -146,7 +146,7 @@ class SortedOffsets(OffsetList):
 
 
 # indexed set of offsets, index is built on demand
-class OffsetIndex:
+class OffsetIndex(object):
     def __init__(self, filename, column, split=None, index_depth=3):
         self.filename = filename
         self.file = open(filename, 'r')
@@ -239,7 +239,7 @@ class OffsetIndex:
                 first_char = identifier[0]
 
 
-class BufferedIndex:
+class BufferedIndex(object):
     def __init__(self, filename, column, split=None, buffer=1000000, index_depth=3):
         self.index = OffsetIndex(filename, column, split, index_depth)
         self.buffered_offsets = {}

tools/filters/sff_extract.py

@@ -1180,7 +1180,7 @@ def read_ssaha_data(ssahadata_fh):
 #
 ##########################################################################
 
-class Fasta:
+class Fasta(object):
     def __init__(self, name, sequence):
         self.name = name
         self.sequence = sequence

tools/phenotype_association/senatag.py

@@ -37,7 +37,7 @@ debug_flag = False
 
 
 @total_ordering
-class node:
+class node(object):
     def __init__(self, name):
         self.name = name
         self.edges = []
@@ -65,7 +65,7 @@ class node:
         return self.name
 
 
-class graph:
+class graph(object):
     def __init__(self):
         self.nodes = {}
 

tools/stats/aggregate_scores_in_intervals.py

@@ -25,7 +25,7 @@ from bx.cookbook import doc_optparse
 from galaxy.util.ucsc import UCSCLimitException, UCSCOutWrapper
 
 
-class PositionalScoresOnDisk:
+class PositionalScoresOnDisk(object):
     fmt = 'f'
     fmt_size = struct.calcsize(fmt)
     default_value = float('nan')