Use the walrus := operator!

Fixed by running
```
ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^tools/\|^.venv/' | xargs auto-walrus
make format
```

doc/parse_gx_xsd.py

@@ -107,8 +107,7 @@ def _build_tag(tag, hide_attributes):
                     assertions_buffer.write(f"#### ``{element.attrib['name']}``:\n\n{doc}\n\n")
             text = text.replace(line, assertions_buffer.getvalue())
     tag_help.write(text)
-    best_practices = _get_bp_link(annotation_el)
-    if best_practices:
+    if best_practices := _get_bp_link(annotation_el):
         tag_help.write("\n\n### Best Practices\n")
         tag_help.write(
             """

lib/galaxy/actions/library.py

@@ -224,8 +224,7 @@ def _get_path_paste_uploaded_datasets(self, trans, params, library_bunch, respon
         return uploaded_datasets, 200, None
 
     def _get_path_files_and_folders(self, params, preserve_dirs):
-        problem_response = self._check_path_paste_params(params)
-        if problem_response:
+        if problem_response := self._check_path_paste_params(params):
             return problem_response
         files_and_folders = []
         for line, path in self._paths_list(params):

lib/galaxy/app.py

@@ -839,8 +839,7 @@ def to_str(self, **kwd):
 
 class ExecutionTimerFactory:
     def __init__(self, config):
-        statsd_host = getattr(config, "statsd_host", None)
-        if statsd_host:
+        if statsd_host := getattr(config, "statsd_host", None):
             from galaxy.web.statsd_client import GalaxyStatsdClient
 
             self.galaxy_statsd_client: Optional[GalaxyStatsdClient] = GalaxyStatsdClient(

lib/galaxy/auth/__init__.py

@@ -123,8 +123,7 @@ def active_authenticators(self, email, username, password):
 
 def _get_allow_register(d):
     s = d.get("allow-register", True)
-    lower_s = str(s).lower()
-    if lower_s == "challenge":
+    if (lower_s := str(s).lower()) == "challenge":
         return lower_s
     else:
         return string_as_bool(s)

lib/galaxy/celery/__init__.py

@@ -101,8 +101,7 @@ def get_galaxy_app():
 
 @lru_cache(maxsize=1)
 def build_app():
-    kwargs = get_app_properties()
-    if kwargs:
+    if kwargs := get_app_properties():
         kwargs["check_migrate_databases"] = False
         kwargs["use_display_applications"] = False
         kwargs["use_converters"] = False

lib/galaxy/config/__init__.py

@@ -1170,7 +1170,6 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
         log_destination = kwargs.get("log_destination")
         log_rotate_size = size_to_bytes(unicodify(kwargs.get("log_rotate_size", 0)))
         log_rotate_count = int(kwargs.get("log_rotate_count", 0))
-        galaxy_daemon_log_destination = os.environ.get("GALAXY_DAEMON_LOG")
         if log_destination == "stdout":
             LOGGING_CONFIG_DEFAULT["handlers"]["console"] = {
                 "class": "logging.StreamHandler",
@@ -1189,7 +1188,7 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
                 "maxBytes": log_rotate_size,
                 "backupCount": log_rotate_count,
             }
-        if galaxy_daemon_log_destination:
+        if galaxy_daemon_log_destination := os.environ.get("GALAXY_DAEMON_LOG"):
             LOGGING_CONFIG_DEFAULT["handlers"]["files"] = {
                 "class": "logging.handlers.RotatingFileHandler",
                 "formatter": "stack",

lib/galaxy/config/config_manage.py

@@ -426,8 +426,7 @@ def _replace_file(args: Namespace, f: StringIO, app_desc: App, from_path: str, t
 def _build_sample_yaml(args: Namespace, app_desc: App) -> None:
     schema = app_desc.schema
     f = StringIO()
-    description = getattr(schema, "description", None)
-    if description:
+    if description := getattr(schema, "description", None):
         description = description.lstrip()
         as_comment = "\n".join(f"# {line}" for line in description.split("\n")) + "\n"
         f.write(as_comment)
@@ -517,8 +516,7 @@ def _warn(message: str) -> None:
 
 def _get_option_desc(option: Dict[str, Any]) -> str:
     desc = option["desc"]
-    parent_dir = option.get("path_resolves_to")
-    if parent_dir:
+    if parent_dir := option.get("path_resolves_to"):
         path_resolves = f"The value of this option will be resolved with respect to <{parent_dir}>."
         return f"{desc}\n{path_resolves}" if desc else path_resolves
     return desc

lib/galaxy/datatypes/dataproviders/base.py

@@ -56,8 +56,7 @@ def __new__(cls, name, base_classes, attributes):
             if base_settings:
                 settings.update(base_settings)
         # get settings defined in this class
-        new_settings = attributes.pop("settings", None)
-        if new_settings:
+        if new_settings := attributes.pop("settings", None):
             settings.update(new_settings)
         attributes["settings"] = settings
         return type.__new__(cls, name, base_classes, attributes)

lib/galaxy/datatypes/dataproviders/line.py

@@ -184,8 +184,7 @@ def __iter__(self):
         parent_gen = super().__iter__()
         yield from parent_gen
 
-        last_block = self.handle_last_block()
-        if last_block is not None:
+        if (last_block := self.handle_last_block()) is not None:
             self.num_data_returned += 1
             yield last_block
 

lib/galaxy/datatypes/display_applications/parameters.py

@@ -118,8 +118,7 @@ def _get_dataset_like_object(self, other_values):
         return data
 
     def get_value(self, other_values, dataset_hash, user_hash, trans):
-        data = self._get_dataset_like_object(other_values)
-        if data:
+        if data := self._get_dataset_like_object(other_values):
             return DisplayDataValueWrapper(data, self, other_values, dataset_hash, user_hash, trans)
         return None
 
@@ -165,8 +164,7 @@ def is_preparing(self, other_values):
         return False
 
     def ready(self, other_values):
-        value = self._get_dataset_like_object(other_values)
-        if value:
+        if value := self._get_dataset_like_object(other_values):
             if value.state == value.states.OK:
                 return True
             elif value.state == value.states.ERROR:

lib/galaxy/datatypes/isa.py

@@ -129,8 +129,7 @@ def _get_investigation(self, dataset: HasExtraFilesPath) -> Optional["Investigat
         We will use it to parse and access information from the archive."""
 
         investigation = None
-        main_file = self._get_main_file(dataset)
-        if main_file is not None:
+        if (main_file := self._get_main_file(dataset)) is not None:
             investigation = self._make_investigation_instance(main_file)
 
         return investigation

lib/galaxy/datatypes/registry.py

@@ -483,8 +483,7 @@ def load_datatype_sniffers(self, root, override=False, compressed_sniffers=None)
         distributed config) or contained within an installed Tool Shed repository.
         """
         sniffer_elem_classes = [e.attrib["type"] for e in self.sniffer_elems]
-        sniffers = root.find("sniffers")
-        if sniffers is not None:
+        if (sniffers := root.find("sniffers")) is not None:
             for elem in sniffers.findall("sniffer"):
                 # Keep a status of the process steps to enable stopping the process of handling the sniffer if necessary.
                 ok = True

lib/galaxy/files/sources/__init__.py

@@ -463,8 +463,7 @@ def _get_error_msg_for(rule_name: str) -> str:
 
 def uri_join(*args):
     # url_join doesn't work with non-standard scheme
-    arg0 = args[0]
-    if "://" in arg0:
+    if "://" in (arg0 := args[0]):
         scheme, path = arg0.split("://", 1)
         rval = f"{scheme}://{slash_join(path, *args[1:]) if path else slash_join(*args[1:])}"
     else:

lib/galaxy/files/sources/drs.py

@@ -64,8 +64,7 @@ def _write_from(self, target_path, native_path, user_context=None, opts: Optiona
         raise NotImplementedError()
 
     def score_url_match(self, url: str):
-        match = self._url_regex.match(url)
-        if match:
+        if match := self._url_regex.match(url):
             return match.span()[1]
         else:
             return 0

lib/galaxy/files/sources/http.py

@@ -85,8 +85,7 @@ def _serialization_props(self, user_context=None) -> HTTPFilesSourceProperties:
         return cast(HTTPFilesSourceProperties, effective_props)
 
     def score_url_match(self, url: str):
-        match = self._url_regex.match(url)
-        if match:
+        if match := self._url_regex.match(url):
             return match.span()[1]
         else:
             return 0

lib/galaxy/forms/forms.py

@@ -54,16 +54,14 @@ def from_elem(self, elem, form_definition_current=None):
         form_type = elem.get("type", None)
         # load layout
         layout = []
-        layouts_elem = elem.find("layout")
-        if layouts_elem:
+        if layouts_elem := elem.find("layout"):
             for layout_elem in layouts_elem.findall("grid"):
                 layout_name = layout_elem.get("name", None)
                 assert layout_name and layout_name not in layout, "Layout grid element requires a unique name."
                 layout.append(layout_name)
         # load fields
         fields = []
-        fields_elem = elem.find("fields")
-        if fields_elem is not None:
+        if (fields_elem := elem.find("fields")) is not None:
             for field_elem in fields_elem.findall("field"):
                 field_type = field_elem.get("type")
                 assert field_type in self.field_type_factories, f"Invalid form field type ( {field_type} )."

lib/galaxy/job_execution/actions/post.py

@@ -140,8 +140,7 @@ def execute_on_mapped_over(
             if step_input and hasattr(step_input, "name"):
                 input_names[input_key] = step_input.name
 
-        new_name = cls._gen_new_name(action, input_names, replacement_dict)
-        if new_name:
+        if new_name := cls._gen_new_name(action, input_names, replacement_dict):
             for name, step_output in step_outputs.items():
                 if action.output_name == "" or name == action.output_name:
                     step_output.name = new_name
@@ -248,8 +247,7 @@ def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state
             if has_collection and hasattr(has_collection, "name"):
                 input_names[input_assoc.name] = has_collection.name
 
-        new_name = cls._gen_new_name(action, input_names, replacement_dict)
-        if new_name:
+        if new_name := cls._gen_new_name(action, input_names, replacement_dict):
             for dataset_assoc in job.output_datasets:
                 if action.output_name == "" or dataset_assoc.name == action.output_name:
                     dataset_assoc.dataset.name = new_name

lib/galaxy/job_execution/output_collect.py

@@ -86,8 +86,7 @@ def permissions(self):
         return self._permissions
 
     def set_default_hda_permissions(self, primary_data):
-        permissions = self.permissions
-        if permissions is not UNSET:
+        if (permissions := self.permissions) is not UNSET:
             self._security_agent.set_all_dataset_permissions(primary_data.dataset, permissions, new=True, flush=False)
 
     def copy_dataset_permissions(self, init_from, primary_data):
@@ -672,9 +671,8 @@ def match(self, dataset_instance, filename, path=None, parent_paths=None):
         pattern = self._pattern_for_dataset(dataset_instance)
         if self.match_relative_path and parent_paths:
             filename = os.path.join(*parent_paths, filename)
-        re_match = re.match(pattern, filename)
         match_object = None
-        if re_match:
+        if re_match := re.match(pattern, filename):
             match_object = RegexCollectedDatasetMatch(re_match, self, filename, path=path)
         return match_object
 

lib/galaxy/job_execution/ports/view.py

@@ -25,8 +25,7 @@ def register_container_information(self, job_id, **kwd):
 
     # Copy/paste from JobFilesView - TODO: de-duplicate.
     def __authorize_job_access(self, encoded_job_id, **kwargs):
-        key = "job_key"
-        if key not in kwargs:
+        if (key := "job_key") not in kwargs:
             error_message = f"Job files action requires a valid '{key}'."
             raise ObjectAttributeMissingException(error_message)
 

lib/galaxy/job_metrics/instrumenters/cgroup.py

@@ -90,8 +90,7 @@ class CgroupPlugin(InstrumentPlugin):
     def __init__(self, **kwargs):
         self.verbose = asbool(kwargs.get("verbose", False))
         self.cgroup_mount = kwargs.get("cgroup_mount", "/sys/fs/cgroup")
-        params_str = kwargs.get("params", None)
-        if params_str:
+        if params_str := kwargs.get("params", None):
             params = [v.strip() for v in params_str.split(",")]
         else:
             params = list(TITLES.keys())

lib/galaxy/job_metrics/instrumenters/env.py

@@ -28,8 +28,7 @@ class EnvPlugin(InstrumentPlugin):
     default_safety = Safety.UNSAFE
 
     def __init__(self, **kwargs):
-        variables_str = kwargs.get("variables", None)
-        if variables_str:
+        if variables_str := kwargs.get("variables", None):
             self.variables = [v.strip() for v in variables_str.split(",")]
         else:
             self.variables = None

lib/galaxy/jobs/__init__.py

@@ -165,8 +165,7 @@ def job_config_xml_to_dict(config, root):
     config_dict["runners"] = runners
 
     # Parser plugins section populate 'runners' and 'dynamic' in config_dict.
-    plugins = root.find("plugins")
-    if plugins is not None:
+    if (plugins := root.find("plugins")) is not None:
         for plugin in ConfiguresHandlers._findall_with_required(plugins, "plugin", ("id", "type", "load")):
             if plugin.get("type") == "runner":
                 workers = plugin.get("workers", plugins.get("workers", JobConfiguration.DEFAULT_NWORKERS))
@@ -243,8 +242,7 @@ def job_config_xml_to_dict(config, root):
     resource_groups = {}
 
     # Parse resources...
-    resources = root.find("resources")
-    if resources is not None:
+    if (resources := root.find("resources")) is not None:
         default_resource_group = resources.get("default", None)
         if default_resource_group:
             resources_config_dict["default"] = default_resource_group
@@ -259,9 +257,8 @@ def job_config_xml_to_dict(config, root):
     config_dict["resources"] = resources_config_dict
 
     # Parse tool mappings
-    tools = root.find("tools")
     config_dict["tools"] = []
-    if tools is not None:
+    if (tools := root.find("tools")) is not None:
         for tool in tools.findall("tool"):
             # There can be multiple definitions with identical ids, but different params
             tool_mapping_conf = {}
@@ -275,8 +272,7 @@ def job_config_xml_to_dict(config, root):
             config_dict["tools"].append(tool_mapping_conf)
 
     limits_config = []
-    limits = root.find("limits")
-    if limits is not None:
+    if (limits := root.find("limits")) is not None:
         for limit in JobConfiguration._findall_with_required(limits, "limit", ("type",)):
             limit_dict = {}
             for key in ["type", "tag", "id", "window"]:
@@ -1237,8 +1233,7 @@ def prepare(self, compute_environment=None):
 
         def get_special():
             stmt = select(model.JobExportHistoryArchive).filter_by(job=job).limit(1)
-            jeha = self.sa_session.scalars(stmt).first()
-            if jeha:
+            if jeha := self.sa_session.scalars(stmt).first():
                 return jeha.fda
             stmt = select(model.GenomeIndexToolData).filter_by(job=job).limit(1)
             return self.sa_session.scalars(stmt).first()
@@ -1510,8 +1505,7 @@ def is_ready_for_resubmission(self, job=None):
         if job is None:
             job = self.get_job()
 
-        destination_params = job.destination_params
-        if "__resubmit_delay_seconds" in destination_params:
+        if "__resubmit_delay_seconds" in (destination_params := job.destination_params):
             delay = float(destination_params["__resubmit_delay_seconds"])
             if job.seconds_since_updated < delay:
                 return False
@@ -2408,8 +2402,7 @@ def container_monitor_command(self, container, **kwds):
     @property
     def user(self):
         job = self.get_job()
-        user_email = job.get_user_email()
-        if user_email:
+        if user_email := job.get_user_email():
             return user_email
         elif job.galaxy_session is not None:
             return f"anonymous@{job.galaxy_session.remote_addr.split()[-1]}"

lib/galaxy/jobs/command_factory.py

@@ -123,8 +123,7 @@ def build_command(
 
     __handle_remote_command_line_building(commands_builder, job_wrapper, for_pulsar=for_pulsar)
 
-    container_monitor_command = job_wrapper.container_monitor_command(container)
-    if container_monitor_command:
+    if container_monitor_command := job_wrapper.container_monitor_command(container):
         commands_builder.prepend_command(container_monitor_command)
 
     working_directory = remote_job_directory or job_wrapper.working_directory

lib/galaxy/jobs/handler.py

@@ -1231,8 +1231,7 @@ def stop(self, job, job_wrapper):
             from galaxy.celery import celery_app
 
             celery_app.control.revoke(job.job_runner_external_id)
-        job_runner_name = job.get_job_runner_name()
-        if job_runner_name is not None:
+        if (job_runner_name := job.get_job_runner_name()) is not None:
             runner_name = job_runner_name.split(":", 1)[0]
             log.debug(f"Stopping job {job_wrapper.get_id_tag()} in {runner_name} runner")
             try:

lib/galaxy/jobs/mapper.py

@@ -160,8 +160,7 @@ def __get_expand_function(self, destination):
         rules_module_name = destination.params.get("rules_module")
         rule_modules = self.__get_rule_modules_or_defaults(rules_module_name)
         expand_function = None
-        expand_function_name = destination.params.get("function")
-        if expand_function_name:
+        if expand_function_name := destination.params.get("function"):
             expand_function = self.__last_matching_function_in_modules(rule_modules, expand_function_name)
             if not expand_function:
                 message = ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND % expand_function_name

lib/galaxy/jobs/runners/__init__.py

@@ -217,8 +217,7 @@ def shutdown(self):
         for _ in range(len(self.work_threads)):
             self.work_queue.put((STOP_SIGNAL, None))
 
-        join_timeout = self.app.config.monitor_thread_join_timeout
-        if join_timeout > 0:
+        if (join_timeout := self.app.config.monitor_thread_join_timeout) > 0:
             log.info("Waiting up to %d seconds for job worker threads to shutdown...", join_timeout)
             start = time.time()
             # NOTE: threads that have already joined by now are not going to be logged