Faster and cleaner set creation

lib/galaxy/containers/__init__.py

@@ -47,7 +47,7 @@ class ContainerPort(namedtuple('ContainerPort', ('port', 'protocol', 'hostaddr',
 
 class ContainerVolume(with_metaclass(ABCMeta, object)):
 
-    valid_modes = frozenset(["ro", "rw"])
+    valid_modes = frozenset({"ro", "rw"})
 
     def __init__(self, path, host_path=None, mode=None):
         self.path = path

lib/galaxy/datatypes/binary.py

@@ -1738,7 +1738,7 @@ class GAFASQLite(SQlite):
 
     def sniff(self, filename):
         if super(IdpDB, self).sniff(filename):
-            table_names = frozenset(['gene', 'gene_family', 'gene_family_member', 'meta', 'transcript'])
+            table_names = frozenset({'gene', 'gene_family', 'gene_family_member', 'meta', 'transcript'})
             return self.sniff_table_names(filename, table_names)
         return False
 

lib/galaxy/datatypes/dataproviders/dataset.py

@@ -652,7 +652,7 @@ class SamtoolsDataProvider(line.RegexLineDataProvider):
         # strip out any user supplied bash switch formating -> string of option chars
         #   then compress to single option string of unique, VALID flags with prefixed bash switch char '-'
         options_string = options_string.strip('- ')
-        validated_flag_list = set([flag for flag in options_string if flag in self.FLAGS_WO_ARGS])
+        validated_flag_list = {flag for flag in options_string if flag in self.FLAGS_WO_ARGS}
 
         # if sam add -S
         # TODO: not the best test in the world...

lib/galaxy/job_metrics/collectl/processes.py

@@ -147,7 +147,7 @@ class CollectlProcessSummarizer(object):
     def __init__(self, pid, statistics):
         self.pid = pid
         self.statistics = statistics
-        self.columns_of_interest = set([s[1] for s in statistics])
+        self.columns_of_interest = {s[1] for s in statistics}
         self.tree_statistics = collections.defaultdict(stats.StatisticsTracker)
         self.process_accum_statistics = collections.defaultdict(stats.StatisticsTracker)
         self.interval_count = 0
@@ -206,7 +206,7 @@ class CollectlProcessSummarizer(object):
         return process_rows
 
     def __all_child_pids(self, rows, pid):
-        pids_in_process_tree = set([str(self.pid)])
+        pids_in_process_tree = {str(self.pid)}
         added = True
         while added:
             added = False

lib/galaxy/jobs/handler.py

@@ -96,10 +96,10 @@ class JobHandlerQueue(Monitors):
         self.__initialize_job_grabbing()
 
     def __initialize_job_grabbing(self):
-        grabbable_methods = set([
+        grabbable_methods = {
             HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION,
             HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED,
-        ])
+        }
         try:
             method = [m for m in self.app.job_config.handler_assignment_methods if m in grabbable_methods][0]
         except IndexError:

lib/galaxy/jobs/runners/drmaa.py

@@ -29,7 +29,7 @@ log = logging.getLogger(__name__)
 
 __all__ = ('DRMAAJobRunner',)
 
-RETRY_EXCEPTIONS_LOWER = frozenset(['invalidjobexception', 'internalexception'])
+RETRY_EXCEPTIONS_LOWER = frozenset({'invalidjobexception', 'internalexception'})
 
 
 class DRMAAJobRunner(AsynchronousJobRunner):

lib/galaxy/managers/base.py

@@ -551,7 +551,7 @@ class ModelSerializer(HasAModelManager):
         #   this allows us to: 'mention' the key without adding the default serializer
         # TODO: we may want to eventually error if a key is requested
         #   that is in neither serializable_keyset or serializers
-        self.serializable_keyset = set([])
+        self.serializable_keyset = set()
         # a map of dictionary keys to the functions (often lambdas) that create the values for those keys
         self.serializers = {}
         # add subclass serializers defined there
@@ -719,7 +719,7 @@ class ModelDeserializer(HasAModelManager):
         self.app = app
 
         self.deserializers = {}
-        self.deserializable_keyset = set([])
+        self.deserializable_keyset = set()
         self.add_deserializers()
         # a sub object that can validate incoming values
         self.validate = validator or ModelValidator(self.app)

lib/galaxy/managers/pages.py

@@ -228,11 +228,11 @@ class PageContentProcessor(HTMLParser, object):
     For now, processor renders embedded objects.
     """
     bare_ampersand = re.compile(r"&(?!#\d+;|#x[0-9a-fA-F]+;|\w+;)")
-    elements_no_end_tag = set([
+    elements_no_end_tag = {
         'area', 'base', 'basefont', 'br', 'col', 'command', 'embed', 'frame',
         'hr', 'img', 'input', 'isindex', 'keygen', 'link', 'meta', 'param',
         'source', 'track', 'wbr'
-    ])
+    }
 
     def __init__(self, trans, render_embed_html_fn):
         HTMLParser.__init__(self)

lib/galaxy/managers/sharable.py

@@ -427,7 +427,7 @@ class SharableModelDeserializer(base.ModelDeserializer,
         unencoded_ids = [self.app.security.decode_id(id_) for id_ in val]
         new_users_shared_with = set(self.manager.user_manager.by_ids(unencoded_ids))
         current_shares = self.manager.get_share_assocs(item)
-        currently_shared_with = set([share.user for share in current_shares])
+        currently_shared_with = {share.user for share in current_shares}
 
         needs_adding = new_users_shared_with - currently_shared_with
         for user in needs_adding:

lib/galaxy/managers/workflows.py

@@ -942,7 +942,7 @@ class WorkflowContentsManager(UsesAnnotations):
 
             # Encode input connections as dictionary
             input_conn_dict = {}
-            unique_input_names = set([conn.input_name for conn in input_connections])
+            unique_input_names = {conn.input_name for conn in input_connections}
             for input_name in unique_input_names:
                 input_conn_dicts = []
                 for conn in input_connections:
@@ -1133,7 +1133,7 @@ class WorkflowContentsManager(UsesAnnotations):
         steps_by_external_id[external_id] = step
         if 'workflow_outputs' in step_dict:
             workflow_outputs = step_dict['workflow_outputs']
-            found_output_names = set([])
+            found_output_names = set()
             for workflow_output in workflow_outputs:
                 # Allow workflow outputs as list of output_names for backward compatibility.
                 if not isinstance(workflow_output, dict):

lib/galaxy/model/__init__.py

@@ -2170,7 +2170,7 @@ class Dataset(StorableObject, RepresentById):
     )
     ready_states = tuple(set(states.__dict__.values()) - set(non_ready_states))
     valid_input_states = tuple(
-        set(states.__dict__.values()) - set([states.ERROR, states.DISCARDED])
+        set(states.__dict__.values()) - {states.ERROR, states.DISCARDED}
     )
     terminal_states = (
         states.OK,

lib/galaxy/model/tags.py

@@ -50,7 +50,7 @@ class TagHandler(object):
 
     def remove_tags_from_list(self, user, item, tag_to_remove_list):
         tag_to_remove_set = set(tag_to_remove_list)
-        tags_set = set([_.strip() for _ in self.get_tags_str(item.tags).split(',')])
+        tags_set = {_.strip() for _ in self.get_tags_str(item.tags).split(',')}
         if item.tags:
             tags_set -= tag_to_remove_set
         return self.set_tags_from_list(user, item, tags_set)

lib/galaxy/queue_worker.py

@@ -274,7 +274,7 @@ def reload_tour(app, **kwargs):
 
 
 def __job_rule_module_names(app):
-    rules_module_names = set(['galaxy.jobs.rules'])
+    rules_module_names = {'galaxy.jobs.rules'}
     if app.job_config.dynamic_params is not None:
         module_name = app.job_config.dynamic_params.get('rules_module')
         if module_name:

lib/galaxy/tool_shed/galaxy_install/install_manager.py

@@ -925,7 +925,7 @@ class InstallRepositoryManager(object):
                 self.update_tool_shed_repository_status(tool_shed_repository,
                                                         self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES)
                 new_tools = [self.app.toolbox._tools_by_id.get(tool_d['guid'], None) for tool_d in metadata['tools']]
-                new_requirements = set([tool.requirements.packages for tool in new_tools if tool])
+                new_requirements = {tool.requirements.packages for tool in new_tools if tool}
                 [self._view.install_dependencies(r) for r in new_requirements]
                 dependency_manager = self.app.toolbox.dependency_manager
                 if dependency_manager.cached:

lib/galaxy/tool_util/cwl/representation.py

@@ -109,7 +109,7 @@ def type_representation_from_name(type_representation_name):
 
 
 def type_descriptions_for_field_types(field_types):
-    type_representation_names = set([])
+    type_representation_names = set()
     for field_type in field_types:
         if isinstance(field_type, dict) and field_type.get("type"):
             field_type = field_type.get("type")

lib/galaxy/tool_util/deps/mulled/mulled_build.py

@@ -130,7 +130,7 @@ def get_affected_packages(args):
     hours = args.diff_hours
     cmd = ['git', 'log', '--diff-filter=ACMRTUXB', '--name-only', '--pretty=""', '--since="%s hours ago"' % hours]
     changed_files = subprocess.check_output(cmd, cwd=recipes_dir).strip().split('\n')
-    pkg_list = set([x for x in changed_files if x.startswith('recipes/') and x.endswith('meta.yaml')])
+    pkg_list = {x for x in changed_files if x.startswith('recipes/') and x.endswith('meta.yaml')}
     for pkg in pkg_list:
         if pkg and os.path.exists(os.path.join(recipes_dir, pkg)):
             yield (get_pkg_name(args, pkg), get_tests(args, pkg))

lib/galaxy/tool_util/deps/resolvers/conda.py

@@ -151,7 +151,7 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
             all_resolved = [r for r in all_resolved if r.dependency_type]
         if not all_resolved:
             return None
-        environments = set([os.path.basename(dependency.environment_path) for dependency in all_resolved])
+        environments = {os.path.basename(dependency.environment_path) for dependency in all_resolved}
         return self.uninstall_environments(environments)
 
     def uninstall_environments(self, environments):

lib/galaxy/tools/__init__.py

@@ -263,7 +263,7 @@ class ToolBox(BaseGalaxyToolBox):
 
     @property
     def all_requirements(self):
-        reqs = set([req for _, tool in self.tools() for req in tool.tool_requirements])
+        reqs = {req for _, tool in self.tools() for req in tool.tool_requirements}
         return [r.to_dict() for r in reqs]
 
     @property

lib/galaxy/tools/actions/upload_common.py

@@ -82,7 +82,7 @@ def validate_url(url, ip_whitelist):
     #   AF_* family: It will resolve to AF_INET or AF_INET6, getaddrinfo(3) doesn't even mention AF_UNIX,
     #   socktype: We don't care if a stream/dgram/raw protocol
     #   protocol: we don't care if it is tcp or udp.
-    addrinfo_results = set([info[4][0] for info in addrinfo])
+    addrinfo_results = {info[4][0] for info in addrinfo}
     # There may be multiple (e.g. IPv4 + IPv6 or DNS round robin). Any one of these
     # could resolve to a local addresses (and could be returned by chance),
     # therefore we must check them all.

lib/galaxy/util/__init__.py

@@ -921,8 +921,8 @@ def parse_resource_parameters(resource_param_file):
 
 
 # asbool implementation pulled from PasteDeploy
-truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1'])
-falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
+truthy = frozenset({'true', 'yes', 'on', 'y', 't', '1'})
+falsy = frozenset({'false', 'no', 'off', 'n', 'f', '0'})
 
 
 def asbool(obj):

lib/galaxy/visualization/plugins/interactive_environments.py

@@ -28,13 +28,13 @@ from galaxy.util.bunch import Bunch
 
 IS_OS_X = _platform == "darwin"
 CONTAINER_NAME_PREFIX = 'gie_'
-ENV_OVERRIDE_CAPITALIZE = frozenset([
+ENV_OVERRIDE_CAPITALIZE = frozenset({
     'notebook_username',
     'notebook_password',
     'dataset_hid',
     'dataset_filename',
     'additional_ids',
-])
+})
 
 log = logging.getLogger(__name__)
 

lib/galaxy/web_stack/__init__.py

@@ -228,10 +228,10 @@ class UWSGIApplicationStack(MessageApplicationStack):
     Note that mules will use this as their stack class even though they start with the "webless" loading point.
     """
     name = 'uWSGI'
-    prohibited_middleware = frozenset([
+    prohibited_middleware = frozenset({
         'wrap_in_static',
         'EvalException',
-    ])
+    })
     transport_class = UWSGIFarmMessageTransport
     log_filter_class = UWSGILogFilter
     log_format = '%(name)s %(levelname)s %(asctime)s [p:%(process)s,w:%(worker_id)s,m:%(mule_id)s] [%(threadName)s] %(message)s'

lib/galaxy/webapps/galaxy/api/datatypes.py

@@ -68,7 +68,7 @@ class DatatypesController(BaseAPIController):
                     visit_bases(types, base)
             for c in classes:
                 n = c.__module__ + "." + c.__name__
-                types = set([n])
+                types = {n}
                 visit_bases(types, c)
                 class_to_classes[n] = dict((t, True) for t in types)
             return dict(ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes)

lib/galaxy/webapps/galaxy/api/histories.py

@@ -234,7 +234,7 @@ class HistoriesController(BaseAPIController, ExportsHistoryMixin, ImportsHistory
         the history.
         """
         history = self.manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history)
-        tool_ids = set([])
+        tool_ids = set()
         for dataset in history.datasets:
             job = dataset.creating_job
             if not job:

lib/galaxy/webapps/galaxy/api/tool_dependencies.py

@@ -246,7 +246,7 @@ class ToolDependenciesAPIController(BaseAPIController):
         """
         tools_by_id = trans.app.toolbox.tools_by_id.copy()
         tool_ids = payload.get("tool_ids")
-        requirements = set([tools_by_id[tid].tool_requirements for tid in tool_ids])
+        requirements = {tools_by_id[tid].tool_requirements for tid in tool_ids}
         install_kwds = {}
         for source in [payload, kwds]:
             if 'include_containers' in source:
@@ -280,7 +280,7 @@ class ToolDependenciesAPIController(BaseAPIController):
         """
         tools_by_id = trans.app.toolbox.tools_by_id.copy()
         tool_ids = payload.get("tool_ids")
-        requirements = set([tools_by_id[tid].tool_requirements for tid in tool_ids])
+        requirements = {tools_by_id[tid].tool_requirements for tid in tool_ids}
         install_kwds = {}
         for source in [payload, kwds]:
             if 'include_containers' in source:

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -302,7 +302,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         :param use_cached_job:               If set to True galaxy will attempt to find previously executed steps for all workflow steps with the exact same parameter combinations
                                              and will copy the outputs of the previously executed step.
         """
-        ways_to_create = set([
+        ways_to_create = {
             'archive_source',
             'workflow_id',
             'installed_repository_file',
@@ -310,7 +310,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             'from_path',
             'shared_workflow_id',
             'workflow',
-        ])
+        }
 
         if len(ways_to_create.intersection(payload)) == 0:
             message = "One parameter among - %s - must be specified" % ", ".join(ways_to_create)

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -1602,7 +1602,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
             # install the dependencies for the tools in the selected_tool_ids list
             if not isinstance(selected_tool_ids, list):
                 selected_tool_ids = [selected_tool_ids]
-            requirements = set([tools_by_id[tid].tool_requirements for tid in selected_tool_ids])
+            requirements = {tools_by_id[tid].tool_requirements for tid in selected_tool_ids}
             if install_dependencies:
                 [view.install_dependencies(r) for r in requirements]
             elif uninstall_dependencies:

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -1003,7 +1003,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             elif target_history_ids:
                 if not isinstance(target_history_ids, list):
                     target_history_ids = target_history_ids.split(",")
-                target_history_ids = list(set([self.decode_id(h) for h in target_history_ids if h]))
+                target_history_ids = list({self.decode_id(h) for h in target_history_ids if h})
             else:
                 target_history_ids = []
         done_msg = error_msg = ""

test/unit/jobs/test_rule_helper.py

@@ -77,22 +77,22 @@ def test_choose_one_unhashed():
     rule_helper = __rule_helper()
 
     # Random choices if hash not set.
-    chosen_ones = set([])
+    chosen_ones = set()
     __do_a_bunch(lambda: chosen_ones.add(rule_helper.choose_one(['a', 'b'])))
 
-    assert chosen_ones == set(['a', 'b'])
+    assert chosen_ones == {'a', 'b'}
 
 
 def test_choose_one_hashed():
     rule_helper = __rule_helper()
 
     # Hashed, so all choosen ones should be the same...
-    chosen_ones = set([])
+    chosen_ones = set()
     __do_a_bunch(lambda: chosen_ones.add(rule_helper.choose_one(['a', 'b'], hash_value=1234)))
     assert len(chosen_ones) == 1
 
     # ... also can verify hashing on strings
-    chosen_ones = set([])
+    chosen_ones = set()
     __do_a_bunch(lambda: chosen_ones.add(rule_helper.choose_one(['a', 'b'], hash_value="i am a string")))
 
     assert len(chosen_ones) == 1

test/unit/test_containers.py

@@ -5,4 +5,4 @@ def test_dummy():
     t = galaxy.containers.parse_containers_config('')
     assert t == {'_default_': {'type': 'docker'}}
     s = galaxy.containers.docker_model.DockerAttributeContainer()
-    assert s.members == frozenset([])
+    assert s.members == frozenset()

test/unit/tool_util/test_tool_deps.py

@@ -140,7 +140,7 @@ def test_tool_requirements():
     assert tool_requirements_ab == ToolRequirements([REQUIREMENT_B, REQUIREMENT_A])
     assert tool_requirements_ab == ToolRequirements([REQUIREMENT_B, REQUIREMENT_A, REQUIREMENT_A])
     assert tool_requirements_ab != tool_requirements_b
-    assert len(set([tool_requirements_ab, tool_requirements_ab_dup])) == 1
+    assert len({tool_requirements_ab, tool_requirements_ab_dup}) == 1
 
 
 def test_module_dependency_resolver():

tools/phenotype_association/pagetag.py

@@ -94,7 +94,7 @@ def annotate_locus(input, minorallelefrequency, snpsfile):
         genotypes = v.values()
         alleles = [y for x in genotypes for y in x]
         alleleset = list(set(alleles))
-        alleleset = list(set(alleles) - set(["N", "X"]))
+        alleleset = list(set(alleles) - {'N', 'X'})
 
         if len(alleleset) == 2:
             genotypevec = ""