Merge pull request #13002 from nsoranzo/unnecessary_lists

lib/galaxy/authnz/custos_authnz.py

@@ -265,7 +265,7 @@ class CustosAuthnz(IdentityProvider):
 
     def _load_config_for_custos(self):
         self.config['well_known_oidc_config_uri'] = self._get_well_known_uri_from_url(self.config['provider'])
-        self.config['credential_url'] = '/'.join([self.config['url'].rstrip('/'), 'credentials'])
+        self.config['credential_url'] = f"{self.config['url'].rstrip('/')}/credentials"
         self._get_custos_credentials()
         # Set custos endpoints
         clientIdAndSec = f"{self.config['client_id']}:{self.config['client_secret']}"

lib/galaxy/datatypes/binary.py

@@ -2539,11 +2539,11 @@ class RDS(CompressedArchive):
         version = header_bytes[2:6]
         rversion = header_bytes[6:10]
         minrversion = header_bytes[10:14]
-        version = int("".join([str(_) for _ in version]))
+        version = int("".join(str(_) for _ in version))
         if version not in [2, 3]:
             raise Exception()
-        rversion = int("".join([str(_) for _ in rversion]))
-        minrversion = int("".join([str(_) for _ in minrversion]))
+        rversion = int("".join(str(_) for _ in rversion))
+        minrversion = int("".join(str(_) for _ in minrversion))
         version = ".".join(str(version))
         rversion = ".".join(str(rversion))
         minrversion = ".".join(str(minrversion))

lib/galaxy/datatypes/dataproviders/line.py

@@ -121,7 +121,7 @@ class RegexLineDataProvider(FilteredLineDataProvider):
         return line
 
     def filter_by_regex(self, line):
-        matches = any([regex.match(line) for regex in self.compiled_regex_list])
+        matches = any(regex.match(line) for regex in self.compiled_regex_list)
         if self.invert:
             return line if not matches else None
         return line if matches else None

lib/galaxy/datatypes/genetics.py

@@ -921,7 +921,7 @@ class GenotypeMatrix(LinkageStudies):
             return False
 
         try:
-            return all([int(sid) > 0 for sid in header_elems[1:]])
+            return all(int(sid) > 0 for sid in header_elems[1:])
         except ValueError:
             return False
 

lib/galaxy/datatypes/goldenpath.py

@@ -193,7 +193,7 @@ class AGPFile:
     @property
     def num_lines(self):
         """ Calculate the number of lines in the current state of the AGP file. """
-        return sum([len(self._comment_lines)] + [obj.num_lines for obj in self._objects])
+        return len(self._comment_lines) + sum(obj.num_lines for obj in self._objects)
 
     def iterate_objs(self):
         """ Iterate over the objects of the AGP file. """
@@ -238,7 +238,7 @@ class AGPObject:
         self.add_line(in_agp_line)
 
     def __str__(self):
-        return "\n".join([str(i) for i in self._agp_lines])
+        return "\n".join(str(i) for i in self._agp_lines)
 
     def __repr__(self):
         return f"AGP Object: {self.obj}"

lib/galaxy/jobs/runners/pulsar.py

@@ -652,7 +652,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
             # Following check is a hack for jobs started during 19.01 or earlier release
             # and finishing with a 19.05 code base. Eliminate the hack in 19.09 or later
             # along with hacks for legacy metadata compute strategy.
-            if not os.path.exists(job_metrics_directory) or not any(["__instrument" in f for f in os.listdir(job_metrics_directory)]):
+            if not os.path.exists(job_metrics_directory) or not any("__instrument" in f for f in os.listdir(job_metrics_directory)):
                 job_metrics_directory = job_wrapper.working_directory
             job_wrapper.finish(
                 stdout,

lib/galaxy/jobs/runners/util/job_script/__init__.py

@@ -86,7 +86,7 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
     >>> script.find('GALAXY_MEMORY_MB="32768"\\n') > 0
     True
     """
-    if any([param not in kwds for param in REQUIRED_TEMPLATE_PARAMS]):
+    if any(param not in kwds for param in REQUIRED_TEMPLATE_PARAMS):
         raise Exception("Failed to create job_script, a required parameter is missing.")
     job_instrumenter = kwds.get("job_instrumenter", None)
     if job_instrumenter:

lib/galaxy/selenium/navigates_galaxy.py

@@ -365,7 +365,7 @@ class NavigatesGalaxy(HasDriver):
 
         def history_has_hid(driver):
             hids = get_hids()
-            return any([h == hid for h in hids])
+            return any(h == hid for h in hids)
 
         timeout = self.timeout_for(wait_type=WAIT_TYPES.JOB_COMPLETION)
         try:
@@ -1698,7 +1698,7 @@ class NavigatesGalaxy(HasDriver):
         if contains is not None:
 
             if type(element) == list:
-                assert any([contains in el.text for el in element]), \
+                assert any(contains in el.text for el in element), \
                     f"{contains} was not found in {[el.text for el in element]}"
                 return
 

lib/galaxy/tool_util/linters/inputs.py

@@ -133,9 +133,9 @@ def lint_inputs(tool_xml, lint_ctx):
                 lint_ctx.error(f"Select parameter [{param_name}] contains multiple options elements")
 
             # lint statically defined options
-            if any(['value' not in option.attrib for option in select_options]):
+            if any('value' not in option.attrib for option in select_options):
                 lint_ctx.error(f"Select parameter [{param_name}] has option without value")
-            if any([option.text is None for option in select_options]):
+            if any(option.text is None for option in select_options):
                 lint_ctx.warn(f"Select parameter [{param_name}] has option without text")
             if len(set(select_options_text)) != len(select_options_text):
                 lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same text content")
@@ -225,7 +225,7 @@ def lint_inputs(tool_xml, lint_ctx):
 
     if datasource:
         for datasource_tag in ('display', 'uihints'):
-            if not any([param.tag == datasource_tag for param in inputs]):
+            if not any(param.tag == datasource_tag for param in inputs):
                 lint_ctx.info(f"{datasource_tag} tag usually present in data sources")
 
     if num_inputs:

lib/galaxy/tools/wrappers.py

@@ -567,7 +567,7 @@ class DatasetListWrapper(
         if not self._dataset_elements_cache.get(group):
             wrappers = []
             for element in self:
-                if any([t for t in element.tags if t.user_tname.lower() == 'group' and t.value.lower() == group]):
+                if any(t for t in element.tags if t.user_tname.lower() == 'group' and t.value.lower() == group):
                     wrappers.append(element)
             self._dataset_elements_cache[group] = wrappers
         return self._dataset_elements_cache[group]
@@ -652,7 +652,7 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         if not self._dataset_elements_cache.get(group):
             wrappers = []
             for element in self.collection.dataset_elements:
-                if any([t for t in element.dataset_instance.tags if t.user_tname.lower() == 'group' and t.value.lower() == group]):
+                if any(t for t in element.dataset_instance.tags if t.user_tname.lower() == 'group' and t.value.lower() == group):
                     wrappers.append(self._dataset_wrapper(element.element_object, identifier=element.element_identifier, **self.kwargs))
             self._dataset_elements_cache[group] = wrappers
         return self._dataset_elements_cache[group]

lib/galaxy/web/framework/middleware/remoteuser.py

@@ -172,10 +172,10 @@ class RemoteUser:
                 # requests.
                 pass
             elif environ[self.remote_user_header] in self.admin_users and \
-                    any([path_info.startswith(prefix) for prefix in admin_accessible_paths]):
+                    any(path_info.startswith(prefix) for prefix in admin_accessible_paths):
                 # If the user is an admin user, and any of the admin accessible paths match..., allow them to execute that action.
                 pass
-            elif any([path_info.startswith(prefix) for prefix in user_accessible_paths]):
+            elif any(path_info.startswith(prefix) for prefix in user_accessible_paths):
                 # If the user is allowed to access the path, pass
                 pass
             elif path_info == '/user' or path_info == '/user/':

lib/galaxy/web_stack/__init__.py

@@ -180,7 +180,7 @@ class ApplicationStack:
         return {}
 
     def has_base_pool(self, pool_name):
-        return self.has_pool(pool_name) or any([pool.startswith(f"{pool_name}.") for pool in self.configured_pools])
+        return self.has_pool(pool_name) or any(pool.startswith(f"{pool_name}.") for pool in self.configured_pools)
 
     def has_pool(self, pool_name):
         return pool_name in self.configured_pools

lib/galaxy/web_stack/handlers.py

@@ -124,7 +124,7 @@ class ConfiguresHandlers:
                 method = method.lower()
                 assert HANDLER_ASSIGNMENT_METHODS.has_value(method), \
                     "Invalid job handler assignment method '{}', must be one of: {}".format(
-                        method, ', '.join([h.value for h in HANDLER_ASSIGNMENT_METHODS]))
+                        method, ', '.join(h.value for h in HANDLER_ASSIGNMENT_METHODS))
                 try:
                     self.handler_assignment_methods.append(method)
                 except AttributeError:

lib/galaxy_test/api/test_dataset_collections.py

@@ -443,7 +443,7 @@ class DatasetCollectionApiTestCase(ApiTestCase):
         actual: List[str] = []
         for converter in converters.json():
             actual.append(converter["tool_id"])
-        assert sorted(actual) == sorted([])
+        assert actual == []
 
     def test_collection_tools_tag_propagation(self):
         elements = [{"src": "files", "tags": ["name:element_tag"]}]

lib/galaxy_test/base/populators.py

@@ -739,19 +739,19 @@ class BaseDatasetPopulator(BasePopulator):
     def get_history_dataset_source_transform_actions(self, history_id: str, **kwd) -> Set[str]:
         details = self.get_history_dataset_details(history_id, **kwd)
         if "sources" not in details:
-            return set([])
+            return set()
         sources = details["sources"]
         assert len(sources) <= 1  # We don't handle this use case yet.
         if len(sources) == 0:
-            return set([])
+            return set()
 
         source_0 = sources[0]
         assert "transform" in source_0
         transform = source_0["transform"]
         if transform is None:
-            return set([])
+            return set()
         assert isinstance(transform, list)
-        return set([t["action"] for t in transform])
+        return {t["action"] for t in transform}
 
     def get_history_dataset_details(self, history_id: str, **kwds) -> dict:
         dataset_id = self.__history_content_id(history_id, **kwds)

lib/galaxy_test/selenium/test_tool_form.py

@@ -163,7 +163,7 @@ class ToolFormTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         tbody_element = tool_parameters_table.find_element_by_css_selector("tbody")
         tds = tbody_element.find_elements_by_css_selector("td")
         assert tds
-        assert any([expected_value in td.text for td in tds])
+        assert any(expected_value in td.text for td in tds)
 
     def _run_environment_test_tool(self, inttest_value="42"):
         self.home()

scripts/cwl_conformance_to_test_cases.py

@@ -360,7 +360,7 @@ def main():
             raise Exception(f"No doc in test [{test_with_doc}]")
         del test_with_doc["doc"]
         cwl_test_def = yaml.dump(test_with_doc, default_flow_style=False)
-        cwl_test_def = "\n".join([f"            {line}" for line in cwl_test_def.splitlines()])
+        cwl_test_def = "\n".join(f"            {line}" for line in cwl_test_def.splitlines())
         label = conformance_test.get("label", str(i))
         tags = conformance_test.get("tags", [])
         is_red = label in red_tests_list

scripts/objectstore/copy_files_to_irods.py

@@ -257,7 +257,7 @@ def get_irods_resource(conn, objectid, object_store_id, irods_info):
         irods_tape_resc_cuttoff_dt = datetime.strptime(irods_tape_resc_cuttoff, "%m/%d/%Y")
 
         read_cursor = conn.cursor()
-        args = ('ok', objectid, objectid, tuple([object_store_id]), 'ok', objectid, objectid, tuple([object_store_id]))
+        args = ('ok', objectid, objectid, (object_store_id, ), 'ok', objectid, objectid, (object_store_id, ))
         read_cursor.execute(last_accessed_sql_statement, args)
         row = read_cursor.fetchone()
         if row is None:

test/integration/test_resolvers.py

@@ -93,7 +93,7 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
-        assert any([True for d in response if d['dependency_type'] == 'conda'])
+        assert any(True for d in response if d['dependency_type'] == 'conda')
         endpoint = "tools/%s/build_dependency_cache" % tool_id
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
@@ -105,7 +105,7 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
-        assert any([True for d in response if d['dependency_type'] == 'conda'])
+        assert any(True for d in response if d['dependency_type'] == 'conda')
         endpoint = "tools/%s/dependencies" % tool_id
         create_response = self._delete(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
@@ -131,7 +131,7 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
-        assert any([True for d in response if d['dependency_type'] == 'conda'])
+        assert any(True for d in response if d['dependency_type'] == 'conda')
         # Now that we know install was successfullt we can also doube check that the uninstall works
         self._uninstall_mulled_example_multi_1(resolver_type='conda')
 

test/manual/workflows_scaling.py

@@ -51,7 +51,7 @@ def main(argv=None):
     uuid = str(uuid4())
     workflow_struct = _workflow_struct(args, uuid)
 
-    has_input = any([s.get("type", "tool") == "input_collection" for s in workflow_struct])
+    has_input = any(s.get("type", "tool") == "input_collection" for s in workflow_struct)
     if not has_input:
         uuid = None
 

test/unit/app/authnz/test_custos_authnz.py

@@ -32,10 +32,10 @@ class CustosAuthnzTestCase(unittest.TestCase):
         return 'https://iam.scigap.org/auth'
 
     def _get_credential_url(self):
-        return '/'.join([self._get_idp_url(), 'credentials'])
+        return f"{self._get_idp_url()}/credentials"
 
     def _get_well_known_url(self):
-        return '/'.join([self._get_idp_url(), '.well-known/openid-configuration'])
+        return f"{self._get_idp_url()}/.well-known/openid-configuration"
 
     def setUp(self):
         self.orig_requests_get = requests.get

test/unit/shed_unit/test_td_common_util.py

@@ -66,7 +66,7 @@ def test_get_env_shell_file_paths_from_setup_environment_elem():
         # Verify new ones added.
         assert r_env_sh in all_env_paths
         # env_shell_file_paths includes everything
-        assert all([env in action_dict['env_shell_file_paths'] for env in all_env_paths])
+        assert all(env in action_dict['env_shell_file_paths'] for env in all_env_paths)
         # for every given repository there should be one env
         # file + the required_for_install_env_sh file
         assert len(action_dict['env_shell_file_paths']) == 3