new svgs

Author: CamDavidsonPilon

core/pioreactor/actions/self_test.py

@@ -386,6 +386,7 @@ def test_positive_correlation_between_temperature_and_heating(
         tc._update_heater(0)
         measured_correlation = round(correlation(dcs, measured_pcb_temps), 2)
         logger.debug(f"Correlation between temp sensor and heating: {measured_correlation}")
+        logger.debug(f"{measured_pcb_temps=}\n{dcs=}")
         assert (
             measured_correlation > 0.9
         ), f"Temp and DC% correlation was not high enough {dcs=}, {measured_pcb_temps=}"

core/pioreactor/calibrations/protocols/pump_duration_based.py

@@ -220,7 +220,7 @@ class IntroConfirm3(SessionStep):
     def render(self, ctx: SessionContext) -> CalibrationStep:
         step = steps.info(
             "Keep hardware safe",
-            "Move the vial and output end of the tubing away from the Pioreactor hardware.",
+            "Keep the vial and tubing away from the Pioreactor hardware during this protocol",
         )
         step.metadata = {
             "image": {
@@ -323,7 +323,31 @@ def advance(self, ctx: SessionContext) -> SessionStep | None:
         dc = ctx.inputs.float("dc", minimum=0, maximum=100, default=100.0)
         ctx.data["hz"] = hz
         ctx.data["dc"] = dc
-        return PrimePumpDuration()
+        return TubingIntoWater()
+
+
+class TubingIntoWater(SessionStep):
+    step_id = "tubing_into_water"
+
+    def render(self, ctx: SessionContext) -> CalibrationStep:
+        pump_device = _get_pump_device(ctx)
+        step = steps.info(
+            f"Place tubing ends in water ({pump_device})",
+            "Place both ends of the tubing into the larger container of water before priming.",
+        )
+        step.metadata = {
+            "image": {
+                "src": "/static/svgs/tubing-ends-in-water.svg",
+                "alt": "Place both ends of the tubing into the larger water container.",
+                "caption": "Both tubing ends should sit below the water line.",
+            }
+        }
+        return step
+
+    def advance(self, ctx: SessionContext) -> SessionStep | None:
+        if ctx.inputs.has_inputs:
+            return PrimePumpDuration()
+        return None
 
 
 class PrimePumpDuration(SessionStep):
@@ -351,7 +375,7 @@ def render(self, ctx: SessionContext) -> CalibrationStep:
         tracer_duration = float(ctx.data.get("tracer_duration_s", 1.0))
         step = steps.action(
             "Tracer run",
-            f"Running the pump for {tracer_duration:.2f} seconds. While running, hold the tube above the vial. Please measure the volume expelled.",
+            f"Running the pump for {tracer_duration:.2f} seconds. While running, hold the tube above the vial. Please measure the volume expelled. Ready?",
         )
         step.metadata = {
             "image": {
@@ -404,7 +428,7 @@ def render(self, ctx: SessionContext) -> CalibrationStep:
         duration = float(durations[test_index])
         step = steps.action(
             "Dispense",
-            f"Next: running the pump for {duration:.2f} seconds. Please measure the volume expelled.",
+            f"Next: running the pump for {duration:.2f} seconds. Please measure the volume expelled. Ready?",
         )
         if results:
             step.metadata = {
@@ -514,6 +538,7 @@ def advance(self, ctx: SessionContext) -> SessionStep | None:
     IntroConfirm1.step_id: IntroConfirm1,
     IntroConfirm2.step_id: IntroConfirm2,
     IntroConfirm3.step_id: IntroConfirm3,
+    TubingIntoWater.step_id: TubingIntoWater,
     NameInput.step_id: NameInput,
     NameOverwriteConfirm.step_id: NameOverwriteConfirm,
     VolumeTargets.step_id: VolumeTargets,

core/pioreactor/web/static/asset-manifest.json

@@ -1,7 +1,7 @@
 {
   "files": {
     "main.css": "/static/static/css/main.9c7a48b7.css",
-    "main.js": "/static/static/js/main.796aa6ca.js",
+    "main.js": "/static/static/js/main.5fd7351c.js",
     "static/media/pioreactor_cloud.webp": "/static/static/media/pioreactor_cloud.b15b29e435797dc69d76.webp",
     "static/media/roboto-all-500-normal.woff": "/static/static/media/roboto-all-500-normal.0ab669b7a0d19b178f57.woff",
     "static/media/roboto-all-700-normal.woff": "/static/static/media/roboto-all-700-normal.a457fde362a540fcadff.woff",
@@ -30,10 +30,10 @@
     "static/media/roboto-greek-ext-700-normal.woff2": "/static/static/media/roboto-greek-ext-700-normal.bd9854c751441ccc1a70.woff2",
     "index.html": "/static/index.html",
     "main.9c7a48b7.css.map": "/static/static/css/main.9c7a48b7.css.map",
-    "main.796aa6ca.js.map": "/static/static/js/main.796aa6ca.js.map"
+    "main.5fd7351c.js.map": "/static/static/js/main.5fd7351c.js.map"
   },
   "entrypoints": [
     "static/css/main.9c7a48b7.css",
-    "static/js/main.796aa6ca.js"
+    "static/js/main.5fd7351c.js"
   ]
 }

core/pioreactor/web/static/index.html

@@ -1 +1 @@
-<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Pioreactor"/><link rel="apple-touch-icon" href="/static/logo192.png"/><link rel="manifest" href="/static/manifest.json"/><script defer="defer" src="/static/static/js/main.796aa6ca.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>
+<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Pioreactor"/><link rel="apple-touch-icon" href="/static/logo192.png"/><link rel="manifest" href="/static/manifest.json"/><script defer="defer" src="/static/static/js/main.5fd7351c.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>