Update and apply ruff refactorings

ruff 0.280.0 has a bug that would turn the imports guarded by `if
TYPE_CHECKING` into their non-string variant, which would break the
runtime. So we can't merge 23.1 into dev without this.

lib/galaxy/datatypes/sequence.py

@@ -175,7 +175,7 @@ def do_slow_split(cls, input_datasets, subdir_generator_function, split_params):
     def do_fast_split(cls, input_datasets, toc_file_datasets, subdir_generator_function, split_params):
         data = json.load(open(toc_file_datasets[0].file_name))
         sections = data["sections"]
-        total_sequences = int(0)
+        total_sequences = 0
         for section in sections:
             total_sequences += int(section["sequences"])
         sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params)
@@ -247,7 +247,7 @@ def get_split_commands_with_toc(
         sections = toc_file["sections"]
         result = []
 
-        current_sequence = int(0)
+        current_sequence = 0
         i = 0
         # skip to the section that contains my starting sequence
         while i < len(sections) and start_sequence >= current_sequence + int(sections[i]["sequences"]):

lib/galaxy/dependencies/pinned-lint-requirements.txt

@@ -5,6 +5,6 @@ importlib-metadata==4.2.0
 mccabe==0.7.0
 pycodestyle==2.9.1
 pyflakes==2.5.0
-ruff==0.0.280
+ruff==0.0.283
 typing_extensions==4.7.1
 zipp==3.15.0

lib/galaxy/managers/citations.py

@@ -152,12 +152,10 @@ def to_bibtex(self):
                 log.exception("Failed to fetch bibtex for DOI %s", self.__doi)
 
         if self.raw_bibtex is DoiCitation.BIBTEX_UNSET:
-            return """@MISC{{{doi},
-                DOI = {{{doi}}},
+            return f"""@MISC{{{self.__doi},
+                DOI = {{{self.__doi}}},
                 note = {{Failed to fetch BibTeX for DOI.}}
-            }}""".format(
-                doi=self.__doi
-            )
+            }}"""
         else:
             return self.raw_bibtex
 

lib/galaxy/managers/cloud.py

@@ -86,7 +86,7 @@ def configure_provider(provider, credentials):
             if len(missing_credentials) > 0:
                 raise RequestParameterMissingException(
                     "The following required key(s) are missing from the provided "
-                    "credentials object: {}".format(missing_credentials)
+                    f"credentials object: {missing_credentials}"
                 )
             session_token = credentials.get("SessionToken")
             config = {"aws_access_key": access, "aws_secret_key": secret, "aws_session_token": session_token}
@@ -107,7 +107,7 @@ def configure_provider(provider, credentials):
             if len(missing_credentials) > 0:
                 raise RequestParameterMissingException(
                     "The following required key(s) are missing from the provided "
-                    "credentials object: {}".format(missing_credentials)
+                    f"credentials object: {missing_credentials}"
                 )
 
             config = {
@@ -145,7 +145,7 @@ def configure_provider(provider, credentials):
             if len(missing_credentials) > 0:
                 raise RequestParameterMissingException(
                     "The following required key(s) are missing from the provided "
-                    "credentials object: {}".format(missing_credentials)
+                    f"credentials object: {missing_credentials}"
                 )
             config = {
                 "os_username": username,
@@ -161,8 +161,8 @@ def configure_provider(provider, credentials):
             connection = CloudProviderFactory().create_provider(ProviderList.GCP, config)
         else:
             raise RequestParameterInvalidException(
-                "Unrecognized provider '{}'; the following are the supported "
-                "providers: {}.".format(provider, SUPPORTED_PROVIDERS.keys())
+                f"Unrecognized provider '{provider}'; the following are the supported "
+                f"providers: {SUPPORTED_PROVIDERS.keys()}."
             )
 
         # The authorization-assertion mechanism of Cloudbridge assumes a user has an elevated privileges,

lib/galaxy/objectstore/pithos.py

@@ -320,10 +320,7 @@ def _size(self, obj, **kwargs) -> int:
             try:
                 return os.path.getsize(self._get_cache_path(path))
             except OSError as ex:
-                log.warning(
-                    "Could not get size of file {path} in local cache,"
-                    "will try Pithos. Error: {err}".format(path=path, err=ex)
-                )
+                log.warning(f"Could not get size of file {path} in local cache," f"will try Pithos. Error: {ex}")
         try:
             file = self.pithos.get_object_info(path)
         except ClientError as ce:
@@ -406,10 +403,7 @@ def _update_from_file(self, obj, **kwargs):
         if kwargs.get("create"):
             self._create(obj, **kwargs)
         if not self._exists(obj, **kwargs):
-            raise ObjectNotFound(
-                "objectstore.update_from_file, object does not exist: {obj}, "
-                "kwargs: {kwargs}".format(obj=obj, kwargs=kwargs)
-            )
+            raise ObjectNotFound(f"objectstore.update_from_file, object does not exist: {obj}, " f"kwargs: {kwargs}")
 
         path = self._construct_path(obj, **kwargs)
         cache_path = self._get_cache_path(path)

lib/galaxy/queues.py

@@ -23,8 +23,7 @@ def all_control_queues_for_declare(application_stack):
     """
     # Get all active processes and construct queues for each process
     process_names = (
-        "{p.server_name}@{p.hostname}".format(p=p)
-        for p in application_stack.app.database_heartbeat.get_active_processes()
+        f"{p.server_name}@{p.hostname}" for p in application_stack.app.database_heartbeat.get_active_processes()
     )
     return [Queue(f"control.{server_name}", galaxy_exchange, routing_key="control.*") for server_name in process_names]
 

lib/galaxy/tool_util/deps/brew_exts.py

@@ -160,14 +160,14 @@ def __init__(self, command, stdout, stderr):
         self.stdout = stdout
         self.stderr = stderr
         self.message = (
-            "Failed to execute command-line {}, stderr was:\n"
+            f"Failed to execute command-line {command}, stderr was:\n"
             "-------->>begin stderr<<--------\n"
-            "{}\n"
+            f"{stderr}\n"
             "-------->>end stderr<<--------\n"
             "-------->>begin stdout<<--------\n"
-            "{}\n"
+            f"{stdout}\n"
             "-------->>end stdout<<--------\n"
-        ).format(command, stderr, stdout)
+        )
 
     def __str__(self):
         return self.message

lib/galaxy/util/__init__.py

@@ -544,7 +544,7 @@ def pretty_print_time_interval(time=False, precise=False, utc=False):
         now = datetime.utcnow()
     else:
         now = datetime.now()
-    if type(time) is int:
+    if isinstance(time, (int, float)):
         diff = now - datetime.fromtimestamp(time)
     elif isinstance(time, datetime):
         diff = now - time

lib/galaxy/util/commands.py

@@ -155,14 +155,14 @@ def __init__(self, command, stdout, stderr, returncode):
         self.stderr = stderr
         self.returncode = returncode
         self.message = (
-            "Failed to execute command-line {}, stderr was:\n"
+            f"Failed to execute command-line {command}, stderr was:\n"
             "-------->>begin stderr<<--------\n"
-            "{}\n"
+            f"{stderr}\n"
             "-------->>end stderr<<--------\n"
             "-------->>begin stdout<<--------\n"
-            "{}\n"
+            f"{stdout}\n"
             "-------->>end stdout<<--------\n"
-        ).format(command, stderr, stdout)
+        )
 
     def __str__(self):
         """Return a verbose error message indicating the command problem."""

lib/galaxy/webapps/base/webapp.py

@@ -147,7 +147,7 @@ def build_apispec(self):
             methods = []
             if rule.conditions:
                 m = rule.conditions.get("method", [])
-                methods = type(m) is str and [m] or m
+                methods = [m] if isinstance(m, str) else m
             # Find the controller class
             if controller not in self.api_controllers:
                 # Only happens when removing a controller after porting to FastAPI.

lib/galaxy/webapps/galaxy/api/cloudauthz.py

@@ -124,8 +124,7 @@ def create(self, trans, payload, **kwargs):
         if not isinstance(config, dict):
             log.debug(msg_template.format(f"invalid config type `{type(config)}`, expect `dict`"))
             raise RequestParameterInvalidException(
-                "Invalid type for the required `config` variable; expect `dict` "
-                "but received `{}`.".format(type(config))
+                "Invalid type for the required `config` variable; expect `dict` " f"but received `{type(config)}`."
             )
         if authn_id:
             try:

lib/galaxy/webapps/galaxy/api/library_contents.py

@@ -371,9 +371,9 @@ def _upload_library_dataset(self, trans, folder_id: int, **kwd):
                 trans, folder_id=folder.id, replace_dataset=replace_dataset, **kwd
             )
             if created_outputs_dict:
-                if type(created_outputs_dict) == str:
+                if isinstance(created_outputs_dict, str):
                     return 400, created_outputs_dict
-                elif type(created_outputs_dict) == tuple:
+                elif isinstance(created_outputs_dict, tuple):
                     return created_outputs_dict[0], created_outputs_dict[1]
                 return 200, created_outputs_dict
             else:

lib/galaxy/webapps/galaxy/api/users.py

@@ -1087,7 +1087,7 @@ def set_toolbox_filters(self, trans, id, payload=None, **kwd):
             for prefixed_name in payload:
                 if prefixed_name.startswith(filter_type):
                     filter_selection = payload.get(prefixed_name)
-                    if type(filter_selection) != bool:
+                    if not isinstance(filter_selection, bool):
                         raise exceptions.RequestParameterInvalidException(
                             "Please specify the filter selection as boolean value."
                         )

lib/galaxy/webapps/galaxy/controllers/authnz.py

@@ -101,9 +101,9 @@ def callback(self, trans, provider, idphint=None, **kwargs):
                 " Error message: {}".format(provider, user, kwargs.get("error", "None"))
             )
             return trans.show_error_message(
-                "Failed to handle authentication callback from {}. "
+                f"Failed to handle authentication callback from {provider}. "
                 "Please try again, and if the problem persists, contact "
-                "the Galaxy instance admin".format(provider)
+                "the Galaxy instance admin"
             )
         try:
             success, message, (redirect_url, user) = trans.app.authnz_manager.callback(

lib/galaxy_test/api/test_drs.py

@@ -130,7 +130,7 @@ def test_exception_handling_schema(self):
         for method in HTTP_METHODS:
             api_url = self._url_join(f"ga4gh/drs/v1/objects/{drs_id}/access/fakeid")
             error_response = method(api_url)
-            assert type(error_response.status_code) == int
+            assert isinstance(error_response.status_code, int)
             assert error_response.status_code == 404
             error_as_dict = error_response.json()
             assert "status_code" in error_as_dict

scripts/api/common.py

@@ -109,7 +109,7 @@ def display(api_key, url, return_formatted=True):
         print("------------------")
         for k, v in r.items():
             print(f"{k}: {v}")
-    elif type(r) == str:
+    elif isinstance(r, str):
         print(r)
     else:
         print("response is unknown type: %s" % type(r))

test/integration/test_cli_runners.py

@@ -43,7 +43,7 @@ def start_ssh_docker(container_name, jobs_directory, port=10022, image="agaveapi
         "--rm",
         "--privileged",  # for torque
         "-v",
-        "{jobs_directory}:{jobs_directory}".format(jobs_directory=jobs_directory),
+        f"{jobs_directory}:{jobs_directory}",
         "-v",
         f"{ssh_keys.public_key_file}:/home/testuser/.ssh/authorized_keys",
         "--ulimit",

test/unit/config/test_load_config.py

@@ -47,10 +47,10 @@ def test_load_config_from_schema(mock_init):
     assert config.property5 is None
     assert config.property6 is None
 
-    assert type(config.property1) is str
-    assert type(config.property2) is int
-    assert type(config.property3) is float
-    assert type(config.property4) is bool
+    assert isinstance(config.property1, str)
+    assert isinstance(config.property2, int)
+    assert isinstance(config.property3, float)
+    assert isinstance(config.property4, bool)
 
 
 def test_update_raw_config_from_kwargs(mock_init):
@@ -64,10 +64,10 @@ def test_update_raw_config_from_kwargs(mock_init):
     assert config._raw_config["property5"] is None  # no change
     assert config._raw_config["property6"] is None  # no change
 
-    assert type(config._raw_config["property1"]) is str
-    assert type(config._raw_config["property2"]) is int
-    assert type(config._raw_config["property3"]) is float
-    assert type(config._raw_config["property4"]) is bool
+    assert isinstance(config._raw_config["property1"], str)
+    assert isinstance(config._raw_config["property2"], int)
+    assert isinstance(config._raw_config["property3"], float)
+    assert isinstance(config._raw_config["property4"], bool)
 
 
 def test_update_raw_config_from_string_kwargs(mock_init):
@@ -80,10 +80,10 @@ def test_update_raw_config_from_string_kwargs(mock_init):
     assert config._raw_config["property3"] == 2.0  # updated
     assert config._raw_config["property4"] is False  # updated
 
-    assert type(config._raw_config["property1"]) is str
-    assert type(config._raw_config["property2"]) is int
-    assert type(config._raw_config["property3"]) is float
-    assert type(config._raw_config["property4"]) is bool
+    assert isinstance(config._raw_config["property1"], str)
+    assert isinstance(config._raw_config["property2"], int)
+    assert isinstance(config._raw_config["property3"], float)
+    assert isinstance(config._raw_config["property4"], bool)
 
 
 def test_update_raw_config_from_kwargs_with_none(mock_init):
@@ -111,7 +111,7 @@ def test_update_raw_config_from_kwargs_falsy_not_none(mock_init):
     config = BaseAppConfiguration(property1=0)
 
     assert config._raw_config["property1"] == "0"  # updated
-    assert type(config._raw_config["property1"]) is str  # and converted to str
+    assert isinstance(config._raw_config["property1"], str)  # and converted to str
 
 
 def test_unset_renamed_option_set_by_old_option(mock_init, monkeypatch):

test/unit/config/test_schema.py

@@ -60,10 +60,10 @@ def mock_init(self, stream):
     assert schema.defaults["property5"] is None
     assert schema.defaults["property6"] is None
 
-    assert type(schema.defaults["property1"]) is str
-    assert type(schema.defaults["property2"]) is int
-    assert type(schema.defaults["property3"]) is float
-    assert type(schema.defaults["property4"]) is bool
+    assert isinstance(schema.defaults["property1"], str)
+    assert isinstance(schema.defaults["property2"], int)
+    assert isinstance(schema.defaults["property3"], float)
+    assert isinstance(schema.defaults["property4"], bool)
 
     assert len(schema.reloadable_options) == 2
     assert "property2" in schema.reloadable_options