don't need to start stirring if od_statistics will do it anyways - ri…

…ght?
Pioreactor · Dec 18, 2024 · 11b9b4f · 11b9b4f
1 parent db28276
commit 11b9b4f
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Showing 4 changed files with 19 additions and 26 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,9 +2,11 @@
  - API to set clock time
  - new calibrations CLI
  - persistent storage is now on single sqlite3 database
+ - new "add log entry" dialog
  - deprecated `default` in background_jobs yaml fields.
    - [ ] test self-test
    - [ ] check back edits to stirring calibration
+   - [ ] cahnges to settings api
 
 ### 24.12.10
  - Hotfix for UI settings bug

diff --git a/pioreactor/actions/leader/export_experiment_data.py b/pioreactor/actions/leader/export_experiment_data.py
@@ -225,9 +225,10 @@ def export_experiment_data(
                 iloc_unit = None
 
             parition_to_writer_map: dict[tuple, Any] = {}
-
+            count = 0
             with ExitStack() as stack:
-                for i, row in enumerate(cursor, start=1):
+                for row in cursor:
+                    count += 1
                     rows_partition = (
                         row[iloc_experiment] if iloc_experiment is not None else "all_experiments",
                         row[iloc_unit] if iloc_unit is not None else "all_units",
@@ -245,10 +246,12 @@ def export_experiment_data(
 
                     parition_to_writer_map[rows_partition].writerow(row)
 
-                    if i % 1000 == 0:
-                        logger.debug(f"Exported {i} rows...")
+                    if count % 1000 == 0:
+                        logger.debug(f"Exported {count} rows...")
 
-            logger.debug(f"Exported {i} rows from {dataset_name}.")
+            logger.debug(f"Exported {count} rows from {dataset_name}.")
+            if count == 0:
+                logger.warning(f"No data present in {dataset_name}. Check database?")
 
             for filename in filenames:
                 path_to_file = Path(Path(output).parent / filename)

diff --git a/pioreactor/actions/od_blank.py b/pioreactor/actions/od_blank.py
@@ -174,17 +174,12 @@ def od_blank(
                     interval=1.5,
                     experiment=testing_experiment,  # use testing experiment to not pollute the database (and they would show up in the UI)
                     fake_data=whoami.is_testing_env(),
-                ) as od_stream, start_stirring(
-                    unit=unit,
-                    experiment=testing_experiment,
-                ) as st:
+                ) as od_stream:
                     # warm up OD reader
                     for count, _ in enumerate(od_stream, start=0):
                         if count == 5:
                             break
 
-                    st.block_until_rpm_is_close_to_target(timeout=30)
-
                     means, _ = od_statistics(
                         od_stream,
                         action_name,

diff --git a/pioreactor/structs.py b/pioreactor/structs.py
@@ -134,11 +134,7 @@ class Voltage(JSONPrintedStruct):
     voltage: pt.Voltage
 
 
-def to_calibration_tag(s: str) -> str:
-    return s.lower().removesuffix("calibration")
-
-
-class CalibrationBase(Struct, tag_field="calibration_type", tag=to_calibration_tag, kw_only=True):
+class CalibrationBase(Struct, tag_field="calibration_type", kw_only=True):
     calibration_name: str
     pioreactor_unit: str
     created_at: t.Annotated[datetime, Meta(tz=True)]
@@ -150,10 +146,10 @@ class CalibrationBase(Struct, tag_field="calibration_type", tag=to_calibration_t
 
     @property
     def calibration_type(self):
-        return to_calibration_tag(self.__class__.__name__)
+        return self.__struct_config__.tag
 
 
-class ODCalibration(CalibrationBase, kw_only=True):
+class ODCalibration(CalibrationBase, kw_only=True, tag="od"):
     ir_led_intensity: float
     angle: str
     pd_channel: str
@@ -163,7 +159,6 @@ class ODCalibration(CalibrationBase, kw_only=True):
     maximum_voltage: float
 
 
-
 class _PumpCalibration(CalibrationBase, kw_only=True):
     hz: t.Annotated[float, Meta(ge=0)]
     dc: t.Annotated[float, Meta(ge=0)]
@@ -192,19 +187,19 @@ def duration_to_ml(self, duration: pt.Seconds) -> pt.mL:
         return t.cast(pt.mL, duration * duration_ + bias_)
 
 
-class MediaPumpCalibration(_PumpCalibration, kw_only=True):
+class MediaPumpCalibration(_PumpCalibration, kw_only=True, tag="media_pump"):
     pass
 
 
-class AltMediaPumpCalibration(_PumpCalibration, kw_only=True):
+class AltMediaPumpCalibration(_PumpCalibration, kw_only=True, tag="alt_media_pump"):
     pass
 
 
-class WastePumpCalibration(_PumpCalibration, kw_only=True):
+class WastePumpCalibration(_PumpCalibration, kw_only=True, tag="waste_pump"):
     pass
 
 
-class StirringCalibration(CalibrationBase, kw_only=True):
+class StirringCalibration(CalibrationBase, kw_only=True, tag="stirring_pump"):
     pwm_hz: t.Annotated[float, Meta(ge=0)]
     voltage: float
     x: str = "DC %"
@@ -216,9 +211,7 @@ class StirringCalibration(CalibrationBase, kw_only=True):
 ]
 
 
-AnyPumpCalibration = t.Union[
-    MediaPumpCalibration, WastePumpCalibration, AltMediaPumpCalibration
-]
+AnyPumpCalibration = t.Union[MediaPumpCalibration, WastePumpCalibration, AltMediaPumpCalibration]
 
 
 class Log(JSONPrintedStruct):