Don't create runtime_context.kill_switch by default

So that the runtime_context object can still be pickled.

Other cleanups

Author: mr-c

cwltool/context.py

@@ -183,7 +183,7 @@ def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
         self.select_resources: Optional[select_resources_callable] = None
         self.eval_timeout: float = 60
         self.postScatterEval: Optional[Callable[[CWLObjectType], Optional[CWLObjectType]]] = None
-        self.on_error: Union[Literal["stop"], Literal["continue"]] = "stop"
+        self.on_error: Union[Literal["stop"], Literal["continue"], Literal["kill"]] = "stop"
         self.strict_memory_limit: bool = False
         self.strict_cpu_limit: bool = False
         self.cidfile_dir: Optional[str] = None
@@ -200,7 +200,7 @@ def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
         self.default_stderr: Optional[Union[IO[bytes], TextIO]] = None
         self.validate_only: bool = False
         self.validate_stdout: Optional[Union[IO[bytes], TextIO, IO[str]]] = None
-        self.kill_switch = threading.Event()
+        self.kill_switch: Optional[threading.Event] = None
         super().__init__(kwargs)
         if self.tmp_outdir_prefix == "":
             self.tmp_outdir_prefix = self.tmpdir_prefix

cwltool/errors.py

@@ -17,9 +17,11 @@ class GraphTargetMissingException(WorkflowException):
 class WorkflowKillSwitch(Exception):
     """When processStatus != "success" and on-error=kill, raise this exception."""
 
-    def __init__(self, job_id, rcode):
+    def __init__(self, job_id: str, rcode: int) -> None:
+        """Record the job identifier and the error code."""
         self.job_id = job_id
         self.rcode = rcode
 
-    def __str__(self):
-        return f'[job {self.job_id}] activated kill switch with return code {self.rcode}'
+    def __str__(self) -> str:
+        """Represent this exception as a string."""
+        return f"[job {self.job_id}] activated kill switch with return code {self.rcode}"

cwltool/executors.py

@@ -477,7 +477,8 @@ def run_jobs(
                 self.wait_for_next_completion(runtime_context)
                 self.run_job(None, runtime_context)
         finally:
-            runtime_context.workflow_eval_lock.release()
+            if (lock := runtime_context.workflow_eval_lock) is not None:
+                lock.release()
             self.taskqueue.drain()
             self.taskqueue.join()
 

cwltool/job.py

@@ -231,7 +231,9 @@ def _execute(
         runtime: List[str],
         env: MutableMapping[str, str],
         runtimeContext: RuntimeContext,
-        monitor_function: Optional[Callable[["subprocess.Popen[str]"], None]] = None,
+        monitor_function: Optional[
+            Callable[["subprocess.Popen[str]", threading.Event], None]
+        ] = None,
     ) -> None:
         """Execute the tool, either directly or via script.
 
@@ -333,6 +335,10 @@ def stderr_stdout_log_path(
             builder: Optional[Builder] = getattr(self, "builder", None)
             if builder is not None:
                 job_script_contents = builder.build_job_script(commands)
+            if runtimeContext.kill_switch is None:
+                runtimeContext.kill_switch = kill_switch = threading.Event()
+            else:
+                kill_switch = runtimeContext.kill_switch
             rcode = _job_popen(
                 commands,
                 stdin_path=stdin_path,
@@ -341,7 +347,7 @@ def stderr_stdout_log_path(
                 env=env,
                 cwd=self.outdir,
                 make_job_dir=lambda: runtimeContext.create_outdir(),
-                kill_switch=runtimeContext.kill_switch,
+                kill_switch=kill_switch,
                 job_script_contents=job_script_contents,
                 timelimit=self.timelimit,
                 name=self.name,
@@ -547,7 +553,8 @@ def monitor_kill_switch() -> None:
             nonlocal ks_tm
             if kill_switch.is_set():
                 _logger.error("[job %s] terminating by kill switch", self.name)
-                if sproc.stdin: sproc.stdin.close()
+                if sproc.stdin:
+                    sproc.stdin.close()
                 sproc.terminate()
             else:
                 ks_tm = Timer(interval=1, function=monitor_kill_switch)

cwltool/task_queue.py

@@ -7,8 +7,8 @@
 import threading
 from typing import Callable, Optional
 
-from .loghandler import _logger
 from .errors import WorkflowKillSwitch
+from .loghandler import _logger
 
 
 class TaskQueue: