remove default field; adding more http methods for broadcast; calibra…

…tion work

contrib/jobs/00_stirring.yaml

@@ -10,5 +10,4 @@ published_settings:
     label: Target stir RPM
     description: Modify the target RPM of stirring. This will effect the optical density reading. Too low and the stirring may completely stop. Too high and the resulting vortex may interfere with the optics.
     type: numeric
-    default: null
     display: true

contrib/jobs/03_temperature_automation.yaml

@@ -10,10 +10,8 @@ published_settings:
     unit: ℃
     label: Target temperature
     type: numeric
-    description: Change the target temperature. Lower bound is the ambient temperature, and upperbound is 50℃. Only used in when Thermostat automation is active.
-    default: null
+    description: Change the target temperature. Lower bound is the ambient temperature, and upper bound is 50℃. Only used in when Thermostat automation is active.
     display: true
   - key: automation_name
     type: string
     display: false
-    default: ""

contrib/jobs/04_dosing_automation.yaml

@@ -10,31 +10,26 @@ published_settings:
     unit: min
     label: Time between dosing
     type: numeric
-    default: null
     display: true
     description: Change how long to wait between dilutions. Typically between 0.5 and 60 minutes. Changing may immediately trigger a dosing event.
   - key: volume
     unit: mL
     label: Volume / dosing
     type: numeric
-    default: null
     display: true
     description: Change the volume per dilution. Typical values are between 0.0mL and 2.0mL.
   - key: target_normalized_od
     unit: AU
     label: Target nOD
     type: numeric
-    default: null
     display: true
     description: Change the target normalized optical density. Typical values are between 1.0 AU and 100.0 AU.
   - key: target_od
     unit: OD
     label: Target OD
     type: numeric
-    default: null
     display: true
     description: Change the target optical density. Only used if running "Turbidostat Targeting OD" automation.
   - key: automation_name
     type: string
     display: false
-    default: ""

contrib/jobs/05_leds.yaml

@@ -8,4 +8,3 @@ published_settings:
     label: LED intensity
     type: string
     display: true
-    default: ""

contrib/jobs/06_led_automation.yaml

@@ -9,4 +9,3 @@ published_settings:
   - key: automation_name
     type: string
     display: false
-    default: ""

contrib/jobs/13_pwms.yaml

@@ -8,4 +8,3 @@ published_settings:
     label: PWM intensity
     type: string
     display: true
-    default: ""

contrib/jobs/50_self_test.yaml

@@ -21,7 +21,6 @@ published_settings:
     type: boolean
   - key: correlations_between_pds_and_leds
     display: false
-    default: '[]'
     type: json
   - key: test_positive_correlation_between_rpm_and_stirring
     display: false
@@ -43,5 +42,4 @@ published_settings:
     type: boolean
   - key: all_tests_passed
     display: false
-    default: false
     type: boolean

contrib/jobs/background_job.yaml.example

@@ -10,12 +10,10 @@ published_settings:
     label: Stirring speed # human readable name
     description: This description is displayed with an editable field in Manage / Settings.
     type: numeric  # one of numeric, boolean, text
-    default: null
     display: true # true to display on the /Pioreactors card
   - key: something_else
     unit: lb
     label: Something else
     description: This description is displayed with an editable field in Manage / Settings.
     type: numeric # one of numeric, boolean, text
-    default: null
-    display: true # true to display on the /Pioreactors card
+    display: true # true to display on the /Pioreactors card

pioreactorui/__init__.py

@@ -105,14 +105,16 @@ def handle_server_error(e):
     return app
 
 
-def msg_to_JSON(msg: str, task: str, level: str) -> bytes:
+def msg_to_JSON(msg: str, task: str, level: str, timestamp: None | str = None) -> bytes:
+    if timestamp is None:
+        timestamp = datetime.now(timezone.utc).isoformat().replace("+00:00", "Z")
     return dumps(
         {
             "message": msg.strip(),
             "task": task,
             "source": "ui",
             "level": level,
-            "timestamp": datetime.now(timezone.utc).isoformat().replace("+00:00", "Z"),
+            "timestamp": timestamp,
         }
     )
 
@@ -157,8 +159,8 @@ def _get_app_db_connection():
     return db
 
 
-def _get_local_metadata_db_connection():
-    db = getattr(g, "_metadata_database", None)
+def _get_temp_local_metadata_db_connection():
+    db = getattr(g, "_local_metadata_database", None)
     if db is None:
         db = g._local_metadata_database = sqlite3.connect(
             f"{tempfile.gettempdir()}/local_intermittent_pioreactor_metadata.sqlite"
@@ -177,10 +179,10 @@ def query_app_db(
     return (rv[0] if rv else None) if one else rv
 
 
-def query_local_metadata_db(
+def query_temp_local_metadata_db(
     query: str, args=(), one: bool = False
 ) -> dict[str, t.Any] | list[dict[str, t.Any]] | None:
-    cur = _get_local_metadata_db_connection().execute(query, args)
+    cur = _get_temp_local_metadata_db_connection().execute(query, args)
     rv = cur.fetchall()
     cur.close()
     return (rv[0] if rv else None) if one else rv