whitespace fixes

app/bookkeeping/query.py

@@ -204,9 +204,9 @@ async def find_task(request) -> JSONResponse:
     study_filter = request.query_params.get("study_filter", "false")
     filter_term = ""
     if search_term:
-        filter_term = (f"""and ((tag_accessionnumber ilike '{search_term}%') """ +
-                       f"""or (tag_patientid ilike '{search_term}%') """ +
-                       f"""or (tag_patientname ilike '%{search_term}%'))""")
+        filter_term = (f"""and ((tag_accessionnumber ilike '{search_term}%') """
+                       + f"""or (tag_patientid ilike '{search_term}%') """
+                       + f"""or (tag_patientname ilike '%{search_term}%'))""")
 
     study_filter_term = ""
     if study_filter == "true":

app/common/event_types.py

@@ -69,7 +69,7 @@ class task_event(StringEnum):
     REMOVE = auto()
     PROCESS_MODULE_BEGIN = auto()
     PROCESS_MODULE_COMPLETE = auto()
-    
+
 
 class severity(Enum):
     """Severity level associated to the mercure events."""

app/common/helper.py

@@ -33,7 +33,7 @@ def validate_folders(config) -> Tuple[bool, str]:
                 print(f"Created directory: {folder}")
             except Exception:
                 return False, f"Folder {folder} does not exist."
-            
+
         if not os.access(folder, os.R_OK | os.W_OK):
             return False, f"No read/write access to {folder}"
     return True, ""
@@ -212,7 +212,7 @@ class FileLock:
     """Helper class that implements a file lock. The lock file will be removed also from the destructor so that
     no spurious lock files remain if exceptions are raised."""
     lockCreated = False
-    
+
     def __init__(self, path_for_lockfile: Path):
         self.lockfile = path_for_lockfile
         # TODO: Handle case if lock file cannot be created

app/common/notification.py

@@ -87,7 +87,7 @@ def parse_payload(
         **context,
     }
     return Template(payload_parsed).render(context)
-    
+
 
 def send_webhook(url: str, payload: str) -> None:
     if not url:

app/common/types.py

@@ -33,7 +33,7 @@ class Target(BaseModel, Compat):
     @property
     def short_description(self) -> str:
         return ""
-    
+
     @classmethod
     def __get_validators__(cls):
         # one or more validators may be yielded which will be called in the
@@ -121,7 +121,7 @@ class RsyncTarget(Target):
     host: str
     password: Optional[str]
     run_on_complete: bool = False
-    
+
     @property
     def short_description(self) -> str:
         return f"{self.host}:{self.folder}"
@@ -254,7 +254,7 @@ class DicomDestination(BaseModel):
 class DicomRetrieveConfig(BaseModel):
     dicom_nodes: List[DicomNodeBase] = []
     destination_folders: List[DicomDestination] = []
-    
+
 
 class Config(BaseModel, Compat):
     appliance_name: str

app/dispatch/dispatcher.py

@@ -202,7 +202,7 @@ def main(args=sys.argv[1:]) -> None:
             config.mercure.influxdb_bucket,
             "mercure." + appliance_name + ".dispatcher." + instance_name
         )
-    
+
     logger.info(f"Dispatching folder: {config.mercure.outgoing_folder}")
     dispatcher_lockfile = Path(config.mercure.outgoing_folder + "/" + mercure_names.HALT)
 

app/dispatch/send.py

@@ -188,7 +188,7 @@ def execute(
     if len(current_status) != len(dispatch_info.target_name):
         current_status = {target_item: TaskDispatchStatus(state="waiting", time=get_now_str())
                           for target_item in dispatch_info.target_name}
-     
+
     for target_item in dispatch_info.target_name:
         if current_status[target_item] and current_status[target_item].state != "complete":  # type: ignore
 

app/dispatch/target_types/base.py

@@ -25,7 +25,7 @@ class ProgressInfo():
 class TargetHandler(Generic[TargetTypeVar]):
     test_template = "targets/base-test.html"
     can_pull = False
-    
+
     def __init__(self):
         pass
 
@@ -45,7 +45,7 @@ def send_to_target(
 
     class NoSuchTagException(Exception):
         pass
-    
+
     def get_from_target(self, target: TargetTypeVar, accession: str,
                         search_filters: Dict[str, List[str]], destination_path: str) -> Generator[ProgressInfo, None, None]:
         raise Exception()
@@ -57,7 +57,7 @@ def find_from_target(self, target: TargetTypeVar, accession: str, search_filters
             if not tag_for_keyword(t):
                 raise TargetHandler.NoSuchTagException(f"Invalid search filter: no such tag '{t}'")
         return []
-    
+
     def handle_error(self, e, command) -> None:
         pass
 

app/dispatch/target_types/builtin.py

@@ -64,7 +64,7 @@ def find_from_target(self, target: DicomTarget, accession: str, search_filters:
             return c.findscu(accession, search_filters)
         except DicomClientCouldNotFind:
             return []
-        
+
     def get_from_target(self, target: DicomTarget, accession: str,
                         search_filters: Dict[str, List[str]], destination_path: str) -> Generator[ProgressInfo, None, None]:
         config.read_config()

app/dispatch/target_types/dicomweb.py

@@ -27,7 +27,7 @@ class DicomWebTargetHandler(TargetHandler[DicomWebTarget]):
     icon = "fa-share-alt"
     display_name = "DICOMweb"
     can_pull = True
-    
+
     def create_client(self, target: DicomWebTarget) -> Union[DICOMfileClient, DICOMwebClient]:
         session = None
         headers = None
@@ -39,7 +39,7 @@ def create_client(self, target: DicomWebTarget) -> Union[DICOMfileClient, DICOMw
                 # Todo: store the db elsewhere if we don't have write access to this folder
                 # This also makes it possible to run tests under pyfakefs since it can't patch sqlite3
                 return DICOMfileClient(url=target.url, in_memory=True, update_db=True)
-          
+
         if target.http_user and target.http_password:
             session = create_session_from_user_pass(username=target.http_user, password=target.http_password)
         elif target.access_token:
@@ -71,15 +71,15 @@ def find_from_target(self, target: DicomWebTarget, accession: str, search_filter
                 break
         else:
             use_filters.update({k: v[0] for k, v in search_filters.items()})
-        
+
         metadata = client.search_for_series(search_filters=use_filters, get_remaining=True,
                                             fields=['StudyInstanceUID',
                                                     'SeriesInstanceUID',
                                                     'NumberOfSeriesRelatedInstances',
                                                     'StudyDescription', 'SeriesDescription'] + list(search_filters.keys()))
         meta_datasets = [pydicom.Dataset.from_json(ds) for ds in metadata]
         result = []
-        
+
         # In case the server didn't filter as strictly as we expected it to, filter again
         for d in meta_datasets:
             for filter in search_filters:

app/process/process_series.py

@@ -134,11 +134,11 @@ def decode_task_json(json_string: Optional[str]) -> Any:
     else:
         logger.error("No docker tag supplied")
         return False
-      
+
     runtime = {}
     if config.mercure.processing_runtime:
         runtime = dict(runtime=config.mercure.processing_runtime)
-        
+
     additional_volumes: Dict[str, Dict[str, str]] = decode_task_json(module.additional_volumes)
     module_environment = decode_task_json(module.environment)
     mercure_environment = dict(MERCURE_IN_DIR=container_in_dir, MERCURE_OUT_DIR=container_out_dir)
@@ -163,7 +163,7 @@ def decode_task_json(json_string: Optional[str]) -> Any:
         raise Exception(f"Docker tag {docker_tag} not found, aborting.") from None
     except (json.decoder.JSONDecodeError, KeyError):
         raise Exception("Failed to parse MONAI app manifest.")
-    
+
     module.requires_root = module.requires_root or image_is_monai_map
 
     # Merge the two dictionaries
@@ -267,7 +267,7 @@ def decode_task_json(json_string: Optional[str]) -> Any:
             logs = helper.localize_log_timestamps(logs, config)
             if not config.mercure.processing_logs.discard_logs:
                 monitor.send_process_logs(task.id, task_processing.module_name, logs)
-            
+
             logger.info(logs)
         logger.info("=== MODULE OUTPUT - END ==========================================")
 
@@ -277,8 +277,8 @@ def decode_task_json(json_string: Optional[str]) -> Any:
             if (datetime.now() - docker_pull_throttle.get("busybox:stable-musl",
                                                           datetime.fromisocalendar(1, 1, 1))
                 ).total_seconds() > 86400:  # noqa: 125
-                    docker_client.images.pull("busybox:stable-musl")  # noqa: E117
-                    docker_pull_throttle["busybox:stable_musl"] = datetime.now()
+                docker_client.images.pull("busybox:stable-musl")  # noqa: E117
+                docker_pull_throttle["busybox:stable_musl"] = datetime.now()
         except Exception:
             logger.exception("could not pull busybox")
 
@@ -499,7 +499,7 @@ async def process_series(folder: Path) -> None:
                 monitor.send_task_event(
                     monitor.task_event.PROCESS_COMPLETE, task_id, file_count_complete, "", "Processing job complete"
                 )
-                
+
                 # If dispatching not needed, then trigger the completion notification (for docker/systemd)
                 if not needs_dispatching:
                     monitor.send_task_event(monitor.task_event.COMPLETE, task_id, 0, "", "Task complete")
@@ -530,7 +530,7 @@ async def process_series(folder: Path) -> None:
                     trigger_notification(task, mercure_events.ERROR)
     return
 
-        
+
 def push_input_task(input_folder: Path, output_folder: Path):
     task_json = output_folder / "task.json"
     if not task_json.exists():

app/routing/route_series.py

@@ -366,7 +366,7 @@ def push_serieslevel_routing(
                         targets.append(rule_definition.get("target"))
                 else:
                     targets = rule_definition.get("target")
-            
+
             for target in targets:
                 if not selected_targets.get(target):
                     selected_targets[target] = [current_rule]
@@ -622,7 +622,7 @@ def remove_series(task_id: str, file_list: List[str], series_UID: str) -> bool:
         except Exception:
             logger.error(f"Error while removing file {entry}", task_id)  # handle_error
             return False
- 
+
     monitor.send_task_event(monitor.task_event.REMOVE, task_id, len(file_list), "", "Removed duplicate files")
 
     return True

app/webinterface/dashboards/query/jobs.py

@@ -136,7 +136,7 @@ def move_to_destination(path: str, destination: Optional[str], job_id: str,
             (dest_folder / ".complete").touch()
             lock.free()
             return
-        
+
         config.read_config()
         moved_files = []
         try:
@@ -167,7 +167,7 @@ def move_to_destination(path: str, destination: Optional[str], job_id: str,
 class CheckAccessionsTask(ClassBasedRQTask):
     type: str = "check_accessions"
     _queue: str = rq_fast_queue.name
-    
+
     def execute(self, *, accessions: List[str], node: Union[DicomTarget, DicomWebTarget],
                 search_filters: Dict[str, List[str]] = {}):
         """
@@ -211,7 +211,7 @@ def get_accession(cls, job_id, accession: str, node: Union[DicomTarget, DicomWeb
     def execute(self, *, accession: str, node: Union[DicomTarget, DicomWebTarget],
                 search_filters: Dict[str, List[str]], path: str, force_rule: Optional[str] = None):
         logger.info(f"Getting ACC {accession}")
-        
+
         def error_handler(reason) -> None:
             logger.error(reason)
             if not job_parent:
@@ -262,13 +262,13 @@ def error_handler(reason) -> None:
                     except Exception as e:
                         error_handler(f"Failure during move to destination of accession {accession}: {e}")
                         raise
-                        
+
                 job_parent.get_meta()  # there is technically a race condition here...
                 job_parent.meta['completed'] += 1
                 job_parent.meta['progress'] = (f"{job_parent.meta['started'] } /"
                                                f" {job_parent.meta['completed'] } / {job_parent.meta['total']}")
                 job_parent.save_meta()  # type: ignore
-            
+
         except Exception as e:
             error_handler(f"Failure with accession {accession}: {e}")
             raise
@@ -325,7 +325,7 @@ def execute(self, *, accessions, subjobs, path: str, destination: Optional[str],
 class QueryPipeline():
     job: Job
     connection: Redis
-    
+
     def __init__(self, job: Union[Job, str], connection: Redis = redis):
         self.connection = connection
         if isinstance(job, str):
@@ -482,19 +482,19 @@ def get_status(self) -> JobStatus:
 
     def get_meta(self) -> Any:
         return cast(dict, self.job.get_meta())
-        
+
     @property
     def meta(self) -> typing.Dict:
         return cast(dict, self.job.meta)
-    
+
     @property
     def is_failed(self) -> bool:
         return cast(bool, self.job.is_failed)
 
     @property
     def is_finished(self) -> bool:
         return cast(bool, self.job.is_finished)
-    
+
     @property
     def is_paused(self) -> bool:
         return cast(bool, self.meta.get("paused", False))
@@ -510,15 +510,15 @@ def kwargs(self) -> typing.Dict:
         except rq.exceptions.DeserializationError:
             logger.info(f"Failed to deserialize job kwargs: {self.job.data}")
             raise
-    
+
     @property
     def result(self) -> Any:
         return self.job.result
-    
+
     @property
     def created_at(self) -> datetime:
         return cast(datetime, self.job.created_at)
-    
+
     @property
     def enqueued_at(self) -> datetime:
         return cast(datetime, self.job.enqueued_at)
@@ -546,5 +546,5 @@ def get_all(cls, type: str = "batch", connection: Redis = redis) -> Generator['Q
             job_ids.add(j_id)
 
         jobs = (Job.fetch(j_id, connection) for j_id in job_ids)
-        
+
         return (QueryPipeline(j, connection) for j in jobs if j and j.get_meta().get("type") == type)