Make timeout configurable as per review feedback

emap-setup/emap_runner/runner.py

@@ -1,4 +1,5 @@
 import argparse
+from datetime import timedelta
 
 from pathlib import Path
 from typing import Any
@@ -100,8 +101,15 @@ def create_parser() -> Parser:
         default=False,
         action="store_true",
     )
+    validation_parser.add_argument(
+        "--timeout",
+        type=lambda h: timedelta(hours=float(h)),
+        metavar="HOURS",
+        help="Max time to wait for the validation run to finish",
+        default=timedelta(hours=10),
+    )
 
-    # add use-FOO and no-use-FOO options for enabling/disabling various services in validation
+    # flags for enabling/disabling various services in validation
     add_boolean_optional_action(validation_parser, "hl7-reader", True, "the main HL7 ADT reader")
     add_boolean_optional_action(validation_parser, "hoover", True, "the hoover service")
     add_boolean_optional_action(validation_parser, "waveform", False, "waveform reader")
@@ -212,6 +220,7 @@ def validation(self) -> ValidationRunner:
             use_hl7_reader=self.args.use_hl7_reader,
             use_hoover=self.args.use_hoover,
             use_waveform=self.args.use_waveform,
+            timeout=self.args.timeout,
         )
         runner.run()
         return runner

emap-setup/emap_runner/validation/validation_runner.py

@@ -13,14 +13,14 @@ class ValidationRunnerException(EMAPRunnerException):
 
 
 class ValidationRunner:
-    timeout = timedelta(hours=10)
     wait_secs = 120
     final_wait_secs = 600
 
     def __init__(
         self,
         docker_runner: "DockerRunner",
         time_window: "TimeWindow",
+        timeout: timedelta,
         should_build: bool = True,
         use_hl7_reader: bool = True,
         use_hoover: bool = True,
@@ -35,6 +35,7 @@ def __init__(
 
         self.docker = docker_runner
         self.time_window = time_window
+        self.timeout = timeout
 
     def run(self) -> None:
         """Run a validation run pipeline by constructing services and waiting
@@ -180,11 +181,11 @@ def _wait_for_queue_to_empty(self) -> None:
         while self._has_populated_queues:
             time.sleep(ValidationRunner.wait_secs)
             elapsed_time = timedelta(seconds=time.monotonic() - start_time_monotonic)
-            if elapsed_time > ValidationRunner.timeout:
+            if elapsed_time > self.timeout:
                 self._save_logs_and_stop()
                 raise ValidationRunnerException(
                     f"Waiting for queue timed out. Elapsed time "
-                    f"({elapsed_time}) > timeout ({ValidationRunner.timeout})"
+                    f"({elapsed_time}) > timeout ({self.timeout})"
                 )
 
         # exits too keenly from databaseExtracts queue, adding in a wait period

emap-setup/tests/test_runner.py

@@ -92,6 +92,7 @@ def test_time_window_is_set():
     runner = ValidationRunner(
         docker_runner=DockerRunner(project_dir=Path.cwd(), config=config),
         time_window=TimeWindow(start_date="today", end_date="7 days ago"),
+        timeout=timedelta(minutes=3),
     )
 
     mkdir("config")
@@ -149,7 +150,7 @@ def test_validation_source_arguments_set_correct_runner_attributes(args_list,
     ])
 def test_validation_timeout(num_trues, timeout_seconds, expect_raises):
     parser = create_parser()
-    args = parser.parse_args(["validation", "--use-waveform"])
+    args = parser.parse_args(["validation", "--use-waveform", "--timeout", str(timeout_seconds / 3600)])
     global_config = GlobalConfiguration(config_path_all)
 
     # simulate having to go through the check and wait loop a variable number of times
@@ -162,7 +163,7 @@ def inner_mock_has_populated_queues():
             return call_count <= num_trues
         return inner_mock_has_populated_queues
 
-    with patch.multiple(ValidationRunner, timeout=timedelta(seconds=timeout_seconds), wait_secs=0.6, final_wait_secs=0):
+    with patch.multiple(ValidationRunner, wait_secs=0.6, final_wait_secs=0):
         with patch.object(ValidationRunner, '_run_emap', new_callable=MagicMock) as run_emap:
             with patch.object(ValidationRunner, '_has_populated_queues', new_callable=PropertyMock) as populated_queues:
                 with patch.object(ValidationRunner, '_save_logs_and_stop', new_callable=MagicMock) as stop: