fix some tests

Author: CamDavidsonPilon

core/pioreactor/background_jobs/od_reading.py

@@ -732,20 +732,25 @@ def _calibrate_signal(observed_voltage: pt.Voltage) -> pt.OD:
 
     def __call__(self, od_readings: structs.ODReadings) -> structs.CalibratedODReadings:
         od_readings = copy(od_readings)
+        calibrated_od_readings = structs.CalibratedODReadings(ods={}, timestamp=od_readings.timestamp)
+
         for channel in self.models:
             if channel in od_readings.ods:
                 raw_od = od_readings.ods[channel]
 
-                # check if everything is okay
+                # check if everything is okay - blows up if not.
                 self.verifiers[channel](raw_od)
 
-                od_readings.ods[channel] = structs.CalibratedODReading(
-                    **raw_od,
+                calibrated_od_readings.ods[channel] = structs.CalibratedODReading(
                     od=self.models[channel](raw_od.od),
                     calibration_name=self.models[channel].name,  # type: ignore
+                    channel=raw_od.channel,
+                    angle=raw_od.angle,
+                    timestamp=raw_od.timestamp,
+                    ir_led_intensity=raw_od.ir_led_intensity,
                 )
-        assert isinstance(od_readings, structs.CalibratedODReadings)
-        return od_readings
+        assert isinstance(calibrated_od_readings, structs.CalibratedODReadings)
+        return calibrated_od_readings
 
 
 class ODReader(BackgroundJob):

core/tests/test_dosing_automation.py

@@ -672,7 +672,7 @@ def test_throughput_calculator_manual_set() -> None:
 def test_execute_io_action() -> None:
     experiment = "test_execute_io_action"
 
-    with Silent(unit=unit, experiment=experiment, volume_ml=15.0, max_working_volume_ml=15.0) as ca:
+    with Silent(unit=unit, experiment=experiment, current_volume_ml=15.0, max_working_volume_ml=15.0) as ca:
         ca.execute_io_action(media_ml=0.50, alt_media_ml=0.35, waste_ml=0.50 + 0.35)
         pause()
         assert ca.media_throughput == 0.50
@@ -707,7 +707,7 @@ def test_execute_io_action() -> None:
 def test_execute_io_action2() -> None:
     experiment = "test_execute_io_action2"
 
-    with Silent(unit=unit, experiment=experiment, volume_ml=14.0) as ca:
+    with Silent(unit=unit, experiment=experiment, current_volume_ml=14.0) as ca:
         results = ca.execute_io_action(media_ml=1.25, alt_media_ml=0.01, waste_ml=1.26)
         pause()
         assert results["media_ml"] == 1.25
@@ -1143,7 +1143,7 @@ def test_chemostat_from_0_volume() -> None:
         unit,
         experiment,
         exchange_volume_ml=0.5,
-        volume_ml=0,
+        current_volume_ml=0,
     ) as chemostat:
         pause(n=25)
         assert chemostat.media_throughput == 0.5
@@ -1700,7 +1700,7 @@ def test_automation_will_pause_itself_if_pumping_goes_above_safety_threshold() -
         experiment=experiment,
         duration=0.05,
         exchange_volume_ml=0.5,
-        volume_ml=Chemostat.MAX_VIAL_VOLUME_TO_STOP - 0.05,
+        current_volume_ml=Chemostat.MAX_VIAL_VOLUME_TO_STOP - 0.05,
     ) as job:
         while job.state == "ready":
             pause()
@@ -1807,7 +1807,7 @@ def test_dosing_automation_initial_values_for_volumes():
         unit=unit,
         experiment=exp,
         alt_media_fraction=0.5,
-        volume_ml=10.0,
+        current_volume_ml=10.0,
         max_working_volume_ml=15.0,
     ) as ca:
         assert ca.current_volume_ml == 10.0
@@ -1821,7 +1821,7 @@ def test_dosing_automation_initial_values_for_volumes():
         unit=unit,
         experiment=exp,
         alt_media_fraction=None,
-        volume_ml=None,
+        current_volume_ml=None,
         max_working_volume_ml=16.0,
     ) as ca:
         assert ca.current_volume_ml == 11.0

core/tests/test_growth_rate_calculating.py

@@ -41,7 +41,7 @@ def create_od_raw_batched(channels, voltages: list[float], angles, timestamp: st
     for channel, voltage, angle in zip(channels, voltages, angles):
         assert int(channel) in (1, 2)
         readings.ods[channel] = structs.RawODReading(
-            od=voltage, angle=angle, timestamp=to_datetime(timestamp), channel=channel
+            od=voltage, angle=angle, timestamp=to_datetime(timestamp), channel=channel, ir_led_intensity=80
         )
 
     return readings
@@ -937,7 +937,11 @@ def test_baseline_shift_gets_absorbed(self) -> None:
                     )
                     publish(
                         f"pioreactor/{unit}/{experiment}/od_reading/od2",
-                        encode(structs.RawODReading(od=v, angle="90", timestamp=to_datetime(t), channel="2")),
+                        encode(
+                            structs.RawODReading(
+                                od=v, angle="90", timestamp=to_datetime(t), channel="2", ir_led_intensity=80
+                            )
+                        ),
                         retain=True,
                     )
                     time.sleep(0.5)
@@ -957,7 +961,11 @@ def test_baseline_shift_gets_absorbed(self) -> None:
                     )
                     publish(
                         f"pioreactor/{unit}/{experiment}/od_reading/od2",
-                        encode(structs.RawODReading(od=v, angle="90", timestamp=to_datetime(t), channel="2")),
+                        encode(
+                            structs.RawODReading(
+                                od=v, angle="90", timestamp=to_datetime(t), channel="2", ir_led_intensity=80
+                            )
+                        ),
                         retain=True,
                     )
                     time.sleep(0.5)
@@ -1006,7 +1014,11 @@ def test_massive_outlier_spike_gets_absorbed(self) -> None:
                     )
                     publish(
                         f"pioreactor/{unit}/{experiment}/od_reading/od2",
-                        encode(structs.RawODReading(od=v, angle="90", timestamp=to_datetime(t), channel="2")),
+                        encode(
+                            structs.RawODReading(
+                                od=v, angle="90", timestamp=to_datetime(t), channel="2", ir_led_intensity=80
+                            )
+                        ),
                         retain=True,
                     )
                     time.sleep(0.5)
@@ -1024,7 +1036,11 @@ def test_massive_outlier_spike_gets_absorbed(self) -> None:
                 )
                 publish(
                     f"pioreactor/{unit}/{experiment}/od_reading/od2",
-                    encode(structs.RawODReading(od=v, angle="90", timestamp=to_datetime(t), channel="2")),
+                    encode(
+                        structs.RawODReading(
+                            od=v, angle="90", timestamp=to_datetime(t), channel="2", ir_led_intensity=80
+                        )
+                    ),
                     retain=True,
                 )
                 time.sleep(0.5)
@@ -1046,7 +1062,11 @@ def test_massive_outlier_spike_gets_absorbed(self) -> None:
                     )
                     publish(
                         f"pioreactor/{unit}/{experiment}/od_reading/od2",
-                        encode(structs.RawODReading(od=v, angle="90", timestamp=to_datetime(t), channel="2")),
+                        encode(
+                            structs.RawODReading(
+                                od=v, angle="90", timestamp=to_datetime(t), channel="2", ir_led_intensity=80
+                            )
+                        ),
                         retain=True,
                     )
                     time.sleep(0.5)

core/tests/test_od_reading.py

@@ -595,7 +595,7 @@ def test_sin_regression_all_negative() -> None:
 
 
 def test_simple_API() -> None:
-    od_job = start_od_reading("90", "REF", interval=100_000, fake_data=True)
+    od_job = start_od_reading("90", "REF", interval=100_000, fake_data=True, calibration=False)
 
     for led_int in range(5, 70, 15):
         time.sleep(2)
@@ -1060,7 +1060,7 @@ def float_to_od_readings_struct(ch: pt.PdChannel, v: float) -> structs.ODReading
             timestamp=current_utc_datetime(),
             ods={
                 ch: structs.RawODReading(
-                    ir_led_intensity=80, od=v, angle="90", channel=ch, timestamp=current_utc_datetime()
+                    ir_led_intensity=70.0, od=v, angle="90", channel=ch, timestamp=current_utc_datetime()
                 )
             },
         )
@@ -1393,7 +1393,7 @@ def test_mandys_calibration() -> None:
 
 def test_setting_interval_after_starting() -> None:
     initial_interval = 2
-    with start_od_reading("90", "REF", interval=initial_interval, fake_data=True) as od:
+    with start_od_reading("90", "REF", interval=initial_interval, fake_data=True, calibration=False) as od:
         next(od)
         with catchtime() as c:
             next(od)

web/tests/test_app.py

@@ -401,7 +401,6 @@ def test_get_settings_api(client):
     with start_stirring(unit="unit1", experiment="exp1"):
         r = client.get("/api/workers/$broadcast/jobs/settings/job_name/stirring/experiments/exp1")
         # follow the task
-        print(r.json)
         r = client.get(r.json["result_url_path"])
         settings_per_unit = r.json["result"]
         assert settings_per_unit["unit2"] is None
@@ -410,7 +409,6 @@ def test_get_settings_api(client):
         # next api
         r = client.get("/api/workers/unit1/jobs/settings/job_name/stirring/experiments/exp1")
         # follow the task
-        print(r.json)
         r = client.get(r.json["result_url_path"])
         settings_per_unit = r.json["result"]
         assert settings_per_unit["unit1"]["settings"]["target_rpm"] == 500.0