Fix new B018 errors raised by ruff 0.0.260

Author: nsoranzo

lib/galaxy/jobs/__init__.py

@@ -1257,7 +1257,7 @@ def get_special():
             self.app.interactivetool_manager.create_interactivetool(job, self.tool, self.interactivetools)
 
         # Ensure galaxy_lib_dir is set in case there are any later chdirs
-        self.galaxy_lib_dir
+        self.galaxy_lib_dir  # noqa: B018
         if self.tool.requires_galaxy_python_environment or self.remote_command_line:
             # These tools (upload, metadata, data_source) may need access to the datatypes registry.
             self.app.datatypes_registry.to_xml_file(os.path.join(self.working_directory, "registry.xml"))
@@ -1387,7 +1387,7 @@ def fail(
         # self.get_destination_configuration() below accesses self.job_destination and will just cause
         # JobMappingException to be raised again.
         try:
-            self.job_destination
+            self.job_destination  # noqa: B018
         except JobMappingException as exc:
             log.debug(
                 "(%s) fail(): Job destination raised JobMappingException('%s'), caching fake '__fail__' "
@@ -2602,7 +2602,7 @@ def prepare(self, compute_environment=None):
             self.extra_filenames.extend(extra_filenames)
 
         # Ensure galaxy_lib_dir is set in case there are any later chdirs
-        self.galaxy_lib_dir
+        self.galaxy_lib_dir  # noqa: B018
 
         # We need command_line persisted to the db in order for Galaxy to re-queue the job
         # if the server was stopped and restarted before the job finished

lib/galaxy/jobs/runners/pbs.py

@@ -104,7 +104,7 @@ def __init__(self, app, nworkers):
 
         # Set the default server during startup
         self.__default_pbs_server = None
-        self.default_pbs_server  # this is a method with a property decorator, so this causes the default server to be set
+        self.default_pbs_server  # noqa: B018 this is a method with a property decorator, so this causes the default server to be set
 
         # Proceed with general initialization
         super().__init__(app, nworkers)

lib/galaxy/tools/cache.py

@@ -146,7 +146,7 @@ def __init__(self):
     def assert_hashes_initialized(self):
         if not self._hashes_initialized:
             for tool_hash in self._hash_by_tool_paths.values():
-                tool_hash.hash
+                tool_hash.hash  # noqa: B018
             self._hashes_initialized = True
 
     def cleanup(self):
@@ -261,7 +261,7 @@ def __init__(self, path, modtime=None, lazy_hash=False):
         self.modtime = modtime or os.path.getmtime(path)
         self._tool_hash = None
         if not lazy_hash:
-            self.hash
+            self.hash  # noqa: B018
 
     @property
     def hash(self):

lib/galaxy/tools/parameters/dynamic_options.py

@@ -570,7 +570,7 @@ def load_from_parameter(from_parameter, transform_lines=None):
         self._tool_data_table = None
         self.elem = elem
         self.column_elem = elem.find("column")
-        self.tool_data_table  # Need to touch tool data table once to populate self.columns
+        self.tool_data_table  # noqa: B018 Need to touch tool data table once to populate self.columns
 
         # Options are defined by parsing tabular text data from a data file
         # on disk, a dataset, or the value of another parameter

lib/galaxy/workflow/run_request.py

@@ -502,9 +502,8 @@ def add_parameter(name: str, value: str, type: WorkflowRequestInputParameter.typ
         workflow_invocation.step_states.append(step_state)
 
         if step.type == "subworkflow":
-            step.workflow_outputs
-            assert step.subworkflow
-            subworkflow: Workflow = step.subworkflow
+            subworkflow = step.subworkflow
+            assert subworkflow
             effective_outputs: Optional[List[EffectiveOutput]] = None
             if run_config.preferred_intermediate_object_store_id or run_config.preferred_outputs_object_store_id:
                 step_outputs = step.workflow_outputs

lib/galaxy_test/base/decorators.py

@@ -50,9 +50,7 @@ def using_requirement(tag: KnownRequirementT):
 
 def _attach_requirements(method, tag: KnownRequirementT):
     requirement = f"requires_{tag}"
-    try:
-        method.__required_galaxy_features
-    except AttributeError:
+    if not hasattr(method, "__required_galaxy_features"):
         method.__required_galaxy_features = []
     method.__required_galaxy_features.append(tag)
     getattr(pytest.mark, requirement)(method)

lib/tool_shed/util/repository_content_util.py

@@ -30,7 +30,6 @@ def upload_tar(
         message = "{} Invalid paths were: {}".format(" ".join(check_results.errors), ", ".join(check_results.invalid))
         return False, message, [], "", undesirable_dirs_removed, undesirable_files_removed
     else:
-        repository.hg_repo
         repo_dir = repository.repo_path(trans.app)
         if upload_point is not None:
             full_path = os.path.abspath(os.path.join(repo_dir, upload_point))

scripts/microbes/harvest_bacteria.py

@@ -137,7 +137,7 @@ def scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url):
                     results = None
                     time.sleep(1)  # Throttle Connection
             if results is None:
-                "URL COMPLETELY FAILED TO LOAD:", url
+                print("URL COMPLETELY FAILED TO LOAD:", url)
                 return
 
             # do special processing for each file type:
@@ -246,7 +246,7 @@ def __main__():
         # get ftp contents
         ftp_contents = get_ftp_contents(ftp_url)
         if ftp_contents is None:
-            "FTP COMPLETELY FAILED TO LOAD", "org:", org_num, "ftp:", ftp_url
+            print("FTP COMPLETELY FAILED TO LOAD", "org:", org_num, "ftp:", ftp_url)
         else:
             for refseq in chroms:
                 scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url)

test/unit/app/tools/test_toolbox.py

@@ -384,14 +384,14 @@ def test_writes_integrate_tool_panel(self):
         self._add_config("""<toolbox><tool file="tool.xml" /></toolbox>""")
 
         self.assert_integerated_tool_panel(exists=False)
-        self.toolbox
+        self.toolbox  # noqa: B018
         self.assert_integerated_tool_panel(exists=True)
 
     def test_groups_tools_in_section(self):
         self._init_tool()
         self._setup_two_versions_in_config(section=True)
         self._setup_two_versions()
-        self.toolbox
+        self.toolbox  # noqa: B018
         self.__verify_two_test_tools()
 
         # Assert only newer version of the tool loaded into the panel.
@@ -602,7 +602,7 @@ def __verify_get_tool_for_default_lineage(self):
     def __setup_shed_tool_conf(self):
         self._add_config("""<toolbox tool_path="."></toolbox>""")
 
-        self.toolbox  # create toolbox
+        self.toolbox  # noqa: B018 create toolbox
         assert not self.reindexed
 
         os.remove(self.integrated_tool_panel_path)

test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py

@@ -131,7 +131,6 @@ def test_plugin_load(self):
         assert not vis2.serves_templates
 
         mock_app_dir.remove()
-        template_cache_dir
 
     def test_script_entry(self):
         """"""

test/unit/data/test_dataset_materialization.py

@@ -320,8 +320,8 @@ def _ensure_relations_attached_and_expunge(deferred_hda: HistoryDatasetAssociati
     # make sure everything needed is in session (sources, hashes, and metadata)...
     # point here is exercise deferred_hda.history throws a detached error.
     [s.hashes for s in deferred_hda.dataset.sources]
-    deferred_hda.dataset.hashes
-    deferred_hda._metadata
+    deferred_hda.dataset.hashes  # noqa: B018
+    deferred_hda._metadata  # noqa: B018
     sa_session = fixture_context.sa_session
     sa_session.expunge_all()
 

test/unit/data/test_galaxy_mapping.py

@@ -753,7 +753,7 @@ def test_flush_refreshes(self):
         assert "id" in inspect(galaxy_model_object_new).unloaded
 
         # Verify a targeted flush prevent expiring unrelated objects.
-        galaxy_model_object_new.id
+        galaxy_model_object_new.id  # noqa: B018
         assert "id" not in inspect(galaxy_model_object_new).unloaded
         session.flush(model.GalaxySession())
         assert "id" not in inspect(galaxy_model_object_new).unloaded

test/unit/util/test_unittest.py

@@ -19,8 +19,8 @@ def test_setUp(self):
 
     def test_assertRaises(self):
         with self.assertRaises(ZeroDivisionError):
-            1 / 0
+            1 / 0  # noqa: B018
 
     def test_assertRaisesRegex(self):
         with self.assertRaisesRegex(ZeroDivisionError, "^division .* zero"):
-            1 / 0
+            1 / 0  # noqa: B018

tools/data_source/upload.py

@@ -123,9 +123,7 @@ def add_file(dataset, registry, output_path: str) -> Dict[str, str]:
     # auto_decompress is a request flag that can be swapped off to prevent Galaxy from automatically
     # decompressing archive files before sniffing.
     auto_decompress = dataset.get("auto_decompress", True)
-    try:
-        dataset.file_type
-    except AttributeError:
+    if not hasattr(dataset, "file_type"):
         raise UploadProblemException("Unable to process uploaded file, missing file_type parameter.")
 
     if dataset.type == "url":

tools/filters/sff_extract.py

@@ -47,7 +47,7 @@
 linkerlengths = {}  # type: ignore
 
 # set to true if something really fishy is going on with the sequences
-stern_warning = True
+stern_warning = False
 
 
 def read_bin_fragment(struct_def, fileh, offset=0, data=None, byte_padding=None):
@@ -983,7 +983,7 @@ def check_for_dubious_startseq(seqcheckstore, sffname, seqdata):
         for shortseq, count in seqdict.items():
             if float(count) / len(seqcheckstore) >= 0.5:
                 foundinloop = True
-                stern_warning
+                stern_warning = True
                 foundproblem = "\n" + "*" * 80
                 foundproblem += "\nWARNING: "
                 foundproblem += "weird sequences in file " + sffname + "\n\n"