more

pioreactor/background_jobs/base.py

@@ -1131,11 +1131,13 @@ def sneak_in(ads_interval, post_delay, pre_delay) -> None:
             self._action_to_do_before_od_reading()
 
         # this could fail in the following way:
-        # in the same experiment, the od_reading fails catastrophically so that the ADC attributes are never
-        # cleared. Later, this job starts, and it will pick up the _old_ ADC attributes.
+        # in the same experiment, the od_reading fails catastrophically so that the settings are never
+        # cleared. Later, this job starts, and it will pick up the _old_ settings.
         with JobManager() as jm:
-            ads_start_time = jm.get_setting_from_running_job("od_reading", "first_od_obs_time")
             ads_interval = jm.get_setting_from_running_job("od_reading", "interval")
+            ads_start_time = jm.get_setting_from_running_job(
+                "od_reading", "first_od_obs_time", block=True
+            )  # this is populated later in the job...
 
         # get interval, and confirm that the requirements are possible: post_delay + pre_delay <= ADS interval - (od reading duration)
         if not (ads_interval - self.OD_READING_DURATION > (post_delay + pre_delay)):

pioreactor/background_jobs/stirring.py

@@ -291,7 +291,8 @@ def action_to_do_after_od_reading(self):
         # self.poll_and_update_dc()
 
     def initialize_dodging_operation(self):
-        self.set_duty_cycle(0)  # stop stirring
+        self._estimate_duty_cycle = 0
+        self.set_duty_cycle(self._estimate_duty_cycle)
         self.rpm_check_repeated_thread = RepeatedTimer(
             1_000,
             lambda *args: None,
@@ -551,8 +552,7 @@ def start_stirring(
         experiment=experiment,
         rpm_calculator=rpm_calculator,
     )
-    if not stirrer.currently_dodging_od:
-        stirrer.start_stirring()
+    stirrer.start_stirring()
     return stirrer
 
 

pioreactor/utils/__init__.py

@@ -603,22 +603,27 @@ def upsert_setting(self, job_id: JobMetadataKey, setting: str, value: Any) -> No
         self.conn.commit()
         return
 
-    def get_setting_from_running_job(self, job_name: str, setting: str) -> Any:
-        if not self.is_job_running(job_name):
+    def get_setting_from_running_job(self, job_name: str, setting: str, block=False) -> Any:
+        if not block and not self.is_job_running(job_name):
             raise JobNotRunningError(f"Job {job_name} is not running.")
 
-        select_query = """
-            SELECT value
-                FROM pio_job_published_settings s
-                JOIN pio_job_metadata m ON s.job_id = m.id
-            WHERE job_name=(?) and setting=(?) and is_running=1"""
-        self.cursor.execute(select_query, (job_name, setting))
-        result = self.cursor.fetchone()  # returns None if not found
-        if result is not None:
-            return result[0]
-        else:
-            # TODO: could also be that the setting was wrong...
-            raise NameError(f"Setting {setting} was not found.")
+        result = None
+        while result is None:
+            select_query = """
+                SELECT value
+                    FROM pio_job_published_settings s
+                    JOIN pio_job_metadata m ON s.job_id = m.id
+                WHERE job_name=(?) and setting=(?) and is_running=1"""
+            self.cursor.execute(select_query, (job_name, setting))
+            result = self.cursor.fetchone()  # returns None if not found
+
+            if result is not None:
+                return result[0]
+            else:
+                if block:
+                    continue
+                else:
+                    raise NameError(f"Setting {setting} was not found.")
 
     def set_not_running(self, job_id: JobMetadataKey) -> None:
         update_query = "UPDATE pio_job_metadata SET is_running=0, ended_at=STRFTIME('%Y-%m-%dT%H:%M:%f000Z', 'NOW') WHERE id=(?)"