Changing TaskQueue constructor to accept the kill_switch threading.Event as an argument rather than an entire RuntimeContext, per @mr-c

Author: AlexTate

cwltool/executors.py

@@ -102,6 +102,7 @@ def check_for_abstract_op(tool: CWLObjectType) -> None:
         runtime_context.mutation_manager = MutationManager()
         runtime_context.toplevel = True
         runtime_context.workflow_eval_lock = threading.Condition(threading.RLock())
+        runtime_context.kill_switch = threading.Event()
 
         job_reqs: Optional[list[CWLObjectType]] = None
         if "https://w3id.org/cwl/cwl#requirements" in job_order_object:
@@ -439,9 +440,13 @@ def run_jobs(
         logger: logging.Logger,
         runtime_context: RuntimeContext,
     ) -> None:
+        if runtime_context.kill_switch is None:
+            runtime_context.kill_switch = threading.Event()
+
         self.taskqueue: TaskQueue = TaskQueue(
-            threading.Lock(), int(math.ceil(self.max_cores)), runtime_context
+            threading.Lock(), int(math.ceil(self.max_cores)), runtime_context.kill_switch
         )
+
         try:
             jobiter = process.job(job_order_object, self.output_callback, runtime_context)
 

cwltool/task_queue.py

@@ -7,7 +7,6 @@
 import threading
 from typing import Callable, Optional
 
-from .context import RuntimeContext
 from .errors import WorkflowKillSwitch
 from .loghandler import _logger
 
@@ -35,7 +34,7 @@ class TaskQueue:
     in_flight: int = 0
     """The number of tasks in the queue."""
 
-    def __init__(self, lock: threading.Lock, thread_count: int, runtime_context: RuntimeContext):
+    def __init__(self, lock: threading.Lock, thread_count: int, kill_switch: threading.Event):
         """Create a new task queue using the specified lock and number of threads."""
         self.thread_count = thread_count
         self.task_queue: queue.Queue[Optional[Callable[[], None]]] = queue.Queue(
@@ -44,11 +43,7 @@ def __init__(self, lock: threading.Lock, thread_count: int, runtime_context: Run
         self.task_queue_threads = []
         self.lock = lock
         self.error: Optional[BaseException] = None
-
-        if runtime_context.kill_switch is None:
-            self.kill_switch = runtime_context.kill_switch = threading.Event()
-        else:
-            self.kill_switch = runtime_context.kill_switch
+        self.kill_switch = kill_switch
 
         for _r in range(0, self.thread_count):
             t = threading.Thread(target=self._task_queue_func)