Apply github/super-linter@v4 diffs

files/galaxy_jwd.py

@@ -165,9 +165,7 @@ def main():
     backends = parse_object_store(object_store_conf)
 
     # Add pulsar staging directory (runner: pulsar_embedded) to backends
-    backends["pulsar_embedded"] = get_pulsar_staging_dir(
-        galaxy_pulsar_app_conf
-    )
+    backends["pulsar_embedded"] = get_pulsar_staging_dir(galaxy_pulsar_app_conf)
 
     # Connect to Galaxy database
     db = Database(
@@ -181,9 +179,7 @@ def main():
     if args.operation == "get":
         job_id = args.job_id
         object_store_id, job_runner_name = db.get_job_info(job_id)
-        jwd_path = decode_path(
-            job_id, [object_store_id], backends, job_runner_name
-        )
+        jwd_path = decode_path(job_id, [object_store_id], backends, job_runner_name)
 
         # Check
         if jwd_path:
@@ -200,8 +196,7 @@ def main():
         # Check if the given Galaxy log directory exists
         if not os.path.isdir(galaxy_log_dir):
             raise ValueError(
-                f"The given Galaxy log directory {galaxy_log_dir} does not"
-                f"exist"
+                f"The given Galaxy log directory {galaxy_log_dir} does not" f"exist"
             )
 
         # Set variables
@@ -299,7 +294,7 @@ def parse_object_store(object_store_conf: str) -> dict:
     """
     if object_store_conf.endswith(".xml"):
         return parse_object_store_xml(object_store_conf)
-    if object_store_conf.split('.')[-1] in ('yml', 'yaml'):
+    if object_store_conf.split(".")[-1] in ("yml", "yaml"):
         return parse_object_store_yaml(object_store_conf)
     raise ValueError("Invalid object store configuration file extension")
 
@@ -321,11 +316,11 @@ def parse_object_store_yaml(object_store_conf: str) -> dict:
     with open(object_store_conf, "r") as f:
         data = yaml.safe_load(f)
     backends = {}
-    for backend in data['backends']:
-        backend_id = backend['id']
+    for backend in data["backends"]:
+        backend_id = backend["id"]
         backends[backend_id] = {}
         # Get the extra_dir's path for each backend if type is "job_work"
-        if 'extra_dirs' in backend:
+        if "extra_dirs" in backend:
             for extra_dir in backend["extra_dirs"]:
                 if extra_dir.get("type") == "job_work":
                     backends[backend_id] = extra_dir["path"]
@@ -390,8 +385,7 @@ def decode_path(
         jwd_path = f"{backends_dict['pulsar_embedded']}/{job_id}"
     else:
         jwd_path = (
-            f"{backends_dict[metadata[0]]}/"
-            f"0{job_id[0:2]}/{job_id[2:5]}/{job_id}"
+            f"{backends_dict[metadata[0]]}/" f"0{job_id[0:2]}/{job_id[2:5]}/{job_id}"
         )
 
     # Validate that the path is a JWD

files/walle.py

@@ -329,9 +329,7 @@ def collect_files_in_a_directory(
                     continue
                 file = pathlib.Path(os.path.join(root, filename))
                 file_stat = file.stat()
-                if not file_in_size_range(
-                    file_stat, args.min_size, args.max_size
-                ):
+                if not file_in_size_range(file_stat, args.min_size, args.max_size):
                     logger.debug(f"File {file} not in size range")
                 elif not file_accessed_in_range(file_stat, args.since):
                     logger.debug(f"File {file} not in access date range")
@@ -472,7 +470,9 @@ def scan_file_for_malware(
     sha1 = None
     for malware in lib:
         if malware.crc32 == crc32:
-            logger.debug(f"File {file} CRC32 matches {malware.program} {malware.version}")
+            logger.debug(
+                f"File {file} CRC32 matches {malware.program} {malware.version}"
+            )
             if sha1 is None:
                 sha1 = digest_file_sha1(chunksize, file)
             if malware.sha1 == sha1:
@@ -485,9 +485,11 @@ def scan_file_for_malware(
 
 
 def report_matching_malware(job: Job, malware: Malware, path: pathlib.Path) -> str:
-    return (f"Job user: {job.user_name} Job ID: {job.galaxy_id}"
-            f"{malware.malware_class} {malware.program} {malware.version}"
-            f" {path}")
+    return (
+        f"Job user: {job.user_name} Job ID: {job.galaxy_id}"
+        f"{malware.malware_class} {malware.program} {malware.version}"
+        f" {path}"
+    )
 
 
 def construct_malware_list(malware_yaml: dict) -> [Malware]:
@@ -619,27 +621,23 @@ def kill_job(job: Job, debug=False):
     serial_args = [
         [
             GXADMIN_PATH,
-            'mutate',
-            'fail-job',
+            "mutate",
+            "fail-job",
             str(job.galaxy_id),
-            '--commit',
+            "--commit",
         ],
         [
             GXADMIN_PATH,
-            'mutate',
-            'fail-terminal-datasets',
-            '--commit',
+            "mutate",
+            "fail-terminal-datasets",
+            "--commit",
         ],
     ]
     for args in serial_args:
         if debug:
             logger.debug(f"COMMAND: {' '.join(args)}")
         try:
-            result = subprocess.run(
-                args,
-                check=True,
-                capture_output=True,
-                text=True)
+            result = subprocess.run(args, check=True, capture_output=True, text=True)
             if debug:
                 if result.stdout:
                     logger.debug(f"COMMAND STDOUT:\n{result.stdout}")
@@ -662,7 +660,7 @@ def evaluate_match_for_deletion(
     args = make_parser().parse_args()
     logging.basicConfig(
         level=logging.DEBUG if args.debug else logging.INFO,
-        format='%(asctime)s - %(levelname)s - %(message)s'
+        format="%(asctime)s - %(levelname)s - %(message)s",
     )
     logger.info("Starting scan...")
     jwd_getter = JWDGetter()