update scripts

CamDavidsonPilon · CamDavidsonPilon · commit 665df8de5032 · 2026-01-14T11:55:09.000-05:00
diff --git a/core/pioreactor/web/static/asset-manifest.json b/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.8cc982bf.js",
+    "main.js": "/static/static/js/main.c7c3634a.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.8cc982bf.js.map": "/static/static/js/main.8cc982bf.js.map"
+    "main.c7c3634a.js.map": "/static/static/js/main.c7c3634a.js.map"
   },
   "entrypoints": [
     "static/css/main.9c7a48b7.css",
-    "static/js/main.8cc982bf.js"
+    "static/js/main.c7c3634a.js"
   ]
 }
diff --git a/core/pioreactor/web/static/index.html b/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.8cc982bf.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.c7c3634a.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>
diff --git a/core/pioreactor/web/static/static/js/main.c7c3634a.js b/core/pioreactor/web/static/static/js/main.c7c3634a.js
diff --git a/core/pioreactor/web/static/static/js/main.c7c3634a.js.LICENSE.txt b/core/pioreactor/web/static/static/js/main.c7c3634a.js.LICENSE.txt
diff --git a/core/pioreactor/web/static/static/js/main.c7c3634a.js.map b/core/pioreactor/web/static/static/js/main.c7c3634a.js.map
diff --git a/core/pioreactor/web/static/svgs/calibration-complete.svg b/core/pioreactor/web/static/svgs/calibration-complete.svg
@@ -1,7 +1,7 @@
 <svg width="240" height="240" viewBox="0 0 200 200" xmlns="http://www.w3.org/2000/svg">
   <title>calibration complete</title>
   <g stroke="#111111" stroke-linecap="round" stroke-linejoin="round">
-    <circle cx="100" cy="106" r="62" fill="none" stroke-width="4" />
+    <circle cx="100" cy="106" r="62" fill="#f6f5ef" stroke-width="4" />
     <path
       d="M170 26 L176 44 L194 50 L176 56 L170 74 L164 56 L146 50 L164 44 Z"
       fill="#f7f1c7"
diff --git a/core/pioreactor/web/static/svgs/place-blank-arrow-pioreactor.svg b/core/pioreactor/web/static/svgs/place-blank-arrow-pioreactor.svg
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 360 200">
+  <g transform="translate(-12 -6) scale(1.1)">
+    <g style="color:#616161">
+      <g transform="translate(75 70) scale(2.6)" stroke="currentColor" stroke-width="1.2" fill="none">
+        <rect x="0.95" y="11.2" width="9.4" height="7.8" rx="0.6" ry="0.6" fill="#e0d0b5" stroke="none" />
+        <rect x="3.1" y="17.2" width="4.9" height="0.9" rx="0.4" fill="currentColor" stroke="none" />
+        <path
+          d="M0.17 5.96L0.14 19.44H11.17V5.81L0.18 5.97Z"
+          stroke-linecap="round"
+          stroke-linejoin="round"
+        />
+        <line x1="7.14" y1="0.00" x2="7.14" y2="12.94" />
+        <line x1="4" y1="-0.00" x2="4" y2="14.94" />
+        <rect
+          x="0.86"
+          y="0.5"
+          width="9.61"
+          height="3.0"
+          fill="currentColor"
+          stroke="currentColor"
+          stroke-linejoin="round"
+        />
+      </g>
+
+      <g fill="none" stroke="currentColor" stroke-width="3.2" stroke-linecap="round" stroke-linejoin="round">
+        <line x1="140" y1="100" x2="200" y2="100" />
+        <polyline points="192,94 200,100 192,106" />
+      </g>
+
+      <g transform="translate(230 70) scale(2.6)" stroke="currentColor" stroke-width="1.2" fill="none" fill-rule="evenodd">
+        <path d="M1.4,18.9 L1.4,14.7 L0,14.7 L0,11.2 L2.799,11.2 L2.8,0 L14,0 L13.999,11.2 L16.8,11.2 L16.8,14.7 L15.399,14.7 L15.4,18.9 L1.4,18.9 Z" />
+        <circle cx="8.4" cy="13.3" r="2.1" />
+      </g>
+    </g>
+  </g>
+</svg>
diff --git a/core/pioreactor/web/static/svgs/place-standard-arrow-pioreactor.svg b/core/pioreactor/web/static/svgs/place-standard-arrow-pioreactor.svg
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 360 200">
+  <g transform="translate(-12 -6) scale(1.1)">
+    <g style="color:#616161">
+      <g transform="translate(75 70) scale(2.6)" stroke="currentColor" stroke-width="1.2" fill="none">
+        <rect x="0.95" y="11.2" width="9.4" height="7.8" rx="0.6" ry="0.6" fill="#d9c4a3" stroke="none" />
+        <circle cx="3.1" cy="13.6" r="0.45" fill="#c3a074" stroke="none" />
+        <circle cx="6.4" cy="15.2" r="0.45" fill="#c3a074" stroke="none" />
+        <circle cx="8.4" cy="13.2" r="0.45" fill="#c3a074" stroke="none" />
+        <rect x="3.1" y="17.2" width="4.9" height="0.9" rx="0.4" fill="currentColor" stroke="none" />
+        <path
+          d="M0.17 5.96L0.14 19.44H11.17V5.81L0.18 5.97Z"
+          stroke-linecap="round"
+          stroke-linejoin="round"
+        />
+        <line x1="7.14" y1="0.00" x2="7.14" y2="12.94" />
+        <line x1="4" y1="-0.00" x2="4" y2="14.94" />
+        <rect
+          x="0.86"
+          y="0.5"
+          width="9.61"
+          height="3.0"
+          fill="currentColor"
+          stroke="currentColor"
+          stroke-linejoin="round"
+        />
+      </g>
+
+      <g fill="none" stroke="currentColor" stroke-width="3.2" stroke-linecap="round" stroke-linejoin="round">
+        <line x1="140" y1="100" x2="200" y2="100" />
+        <polyline points="192,94 200,100 192,106" />
+      </g>
+
+      <g transform="translate(230 70) scale(2.6)" stroke="currentColor" stroke-width="1.2" fill="none" fill-rule="evenodd">
+        <path d="M1.4,18.9 L1.4,14.7 L0,14.7 L0,11.2 L2.799,11.2 L2.8,0 L14,0 L13.999,11.2 L16.8,11.2 L16.8,14.7 L15.399,14.7 L15.4,18.9 L1.4,18.9 Z" />
+        <circle cx="8.4" cy="13.3" r="2.1" />
+      </g>
+    </g>
+  </g>
+</svg>
diff --git a/core/pioreactor/web/static/svgs/prepare-vial-arrow-pioreactor-compact.svg b/core/pioreactor/web/static/svgs/prepare-vial-arrow-pioreactor-compact.svg
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 500 300">
+  <g transform="translate(-150 -70) scale(2.3)">
+    <g style="color:#616161">
+    <g transform="translate(75 70) scale(2.6)" stroke="currentColor" stroke-width="1.2" fill="none">
+      <rect x="0.95" y="11.2" width="9.4" height="7.8" rx="0.6" ry="0.6" fill="#9fd7f4" stroke="none" />
+      <rect x="3.2" y="17.3" width="4.8" height="0.9" rx="0.4" fill="currentColor" stroke="none" />
+      <path
+        d="M0.17 5.96L0.14 19.44H11.17V5.81L0.18 5.97Z"
+        stroke-linecap="round"
+        stroke-linejoin="round"
+      />
+      <line x1="7.14" y1="0.00" x2="7.14" y2="12.94" />
+      <line x1="4" y1="-0.00" x2="4" y2="14.94" />
+      <rect
+        x="0.86"
+        y="0.5"
+        width="9.61"
+        height="3.0"
+        fill="currentColor"
+        stroke="currentColor"
+        stroke-linejoin="round"
+      />
+    </g>
+
+    <g fill="none" stroke="currentColor" stroke-width="3.2" stroke-linecap="round" stroke-linejoin="round">
+      <line x1="140" y1="100" x2="200" y2="100" />
+      <polyline points="192,94 200,100 192,106" />
+    </g>
+
+    <g transform="translate(230 70) scale(2.6)" stroke="currentColor" stroke-width="1.2" fill="none" fill-rule="evenodd">
+      <path d="M1.4,18.9 L1.4,14.7 L0,14.7 L0,11.2 L2.799,11.2 L2.8,0 L14,0 L13.999,11.2 L16.8,11.2 L16.8,14.7 L15.399,14.7 L15.4,18.9 L1.4,18.9 Z" />
+      <circle cx="8.4" cy="13.3" r="2.1" />
+    </g>
+    </g>
+  </g>
+</svg>
diff --git a/core/pioreactor/web/static/svgs/pump-measure-volume.svg b/core/pioreactor/web/static/svgs/pump-measure-volume.svg
@@ -27,7 +27,7 @@
       />
       <line x1="1.7" y1="2.4" x2="9.6" y2="2.4" stroke="currentColor" />
       <line x1="1.6" y1="4.0" x2="9.7" y2="4.5" stroke="currentColor" />
-      <rect x="1.1" y="18.0" width="9.0" height="0.8" fill="#9fd7f4" stroke="none" />
+      <rect x="1.1" y="18.0" width="9.0" height="1.0" fill="#9fd7f4" stroke="none" />
     </g>
 
     <!-- Out tube above droplets -->
@@ -53,7 +53,7 @@
 
 
   </g>
-  <g style="color:#616161" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round" stroke-linejoin="round">
+  <g style="color:#616161" fill="none" stroke="currentColor" stroke-width="1.4" stroke-linecap="round" stroke-linejoin="round">
     <text x="194" y="32" font-size="12" font-family="Menlo,Consolas,system-ui" fill="currentColor">Out</text>
   </g>
 </svg>
diff --git a/core/pioreactor/web/static/svgs/tubing-ends-in-water.svg b/core/pioreactor/web/static/svgs/tubing-ends-in-water.svg
@@ -2,7 +2,7 @@
 <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 360 200">
   <g style="color:#616161" fill="none" stroke="currentColor" stroke-width="3.2" stroke-linecap="round" stroke-linejoin="round">
     <!-- Water container -->
-    <path d="M110 60V170H250V60" />
+    <path d="M110 80V170H250V80" />
     <rect x="118" y="120" width="124" height="44" fill="#9fd7f4" stroke="none" />
 
     <!-- Peristaltic pump -->
@@ -12,13 +12,13 @@
     <circle cx="190" cy="46" r="4" />
 
     <!-- Tubing into water -->
-    <path d="M168 52C150 70 140 88 140 132" />
-    <path d="M192 52C210 70 220 88 220 132" />
+    <path d="M160 52C150 70 140 88 140 132" />
+    <path d="M200 52C210 70 220 88 220 132" />
     <circle cx="140" cy="132" r="4" fill="currentColor" stroke="none" />
     <circle cx="220" cy="132" r="4" fill="currentColor" stroke="none" />
   </g>
-  <g style="color:#616161" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round" stroke-linejoin="round">
-    <text x="150" y="92" font-size="12" font-family="Menlo,Consolas,system-ui" fill="currentColor">In</text>
-    <text x="218" y="92" font-size="12" font-family="Menlo,Consolas,system-ui" fill="currentColor">Out</text>
+  <g style="color:#616161" fill="none" stroke="currentColor" stroke-width="1.30" stroke-linecap="round" stroke-linejoin="round">
+    <text x="151" y="92" font-size="12" font-family="Menlo,Consolas,system-ui" fill="currentColor">In</text>
+    <text x="219" y="92" font-size="12" font-family="Menlo,Consolas,system-ui" fill="currentColor">Out</text>
   </g>
 </svg>
diff --git a/core/update_scripts/upcoming/05_od.yaml b/core/update_scripts/upcoming/05_od.yaml
@@ -0,0 +1,13 @@
+---
+chart_key: optical_density
+data_source: od_readings # SQL table
+title: Optical density
+mqtt_topic: [od_reading/od1, od_reading/od2, od_reading/od3, od_reading/od4]
+source: app
+payload_key: od
+y_axis_label: Reading
+interpolation: stepAfter
+lookback: parseFloat(config['ui.overview.settings']['raw_od_lookback_hours'])
+fixed_decimals: 3
+y_axis_domain: [0.001, 0.05] # good default for near 0 OD, but will break out after growth.
+down_sample: true
diff --git a/core/update_scripts/upcoming/update.sh b/core/update_scripts/upcoming/update.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+
+set -xeu
+
+export LC_ALL=C
+
+DOT_PIOREACTOR=/home/pioreactor/.pioreactor
+CONFIG="$DOT_PIOREACTOR/config.ini"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+HOSTNAME=$(hostname)
+LEADER_HOSTNAME=$(crudini --get "$CONFIG" cluster.topology leader_hostname)
+
+if [ "$HOSTNAME" = "$LEADER_HOSTNAME" ]; then
+    sudo -u pioreactor mkdir -p "$DOT_PIOREACTOR/ui/charts"
+    sudo -u pioreactor cp -f "$SCRIPT_DIR"/05_od.yaml "$DOT_PIOREACTOR/ui/charts/05_od.yaml"
+fi
+
+sudo -u pioreactor mkdir -p "$DOT_PIOREACTOR/hardware/models/pioreactor_20ml_XR/1.5"
+cat <<'EOF' | sudo -u pioreactor tee "$DOT_PIOREACTOR/hardware/models/pioreactor_20ml_XR/1.5/adc.yaml" >/dev/null
+pd1:
+  driver: ads1114
+  address: 0x49
+  channel: 0
+pd2:
+  driver: ads1114
+  address: 0x4a
+  channel: 0
+pd3:
+  driver: ads1114
+  address: 0x4b
+  channel: 0
+pd4:
+  driver: ads1114
+  address: 0x48
+  channel: 0
+EOF
+
+sudo -u pioreactor mkdir -p "$DOT_PIOREACTOR/hardware/models/pioreactor_40ml_XR/1.5"
+cat <<'EOF' | sudo -u pioreactor tee "$DOT_PIOREACTOR/hardware/models/pioreactor_40ml_XR/1.5/adc.yaml" >/dev/null
+pd1:
+  driver: ads1114
+  address: 0x49
+  channel: 0
+pd2:
+  driver: ads1114
+  address: 0x4a
+  channel: 0
+pd3:
+  driver: ads1114
+  address: 0x4b
+  channel: 0
+pd4:
+  driver: ads1114
+  address: 0x48
+  channel: 0
+EOF
+
+sudo -u pioreactor python "$SCRIPT_DIR"/od_calibration_device_migration.py
diff --git a/frontend/public/svgs/tubing-ends-in-water.svg b/frontend/public/svgs/tubing-ends-in-water.svg
@@ -2,7 +2,7 @@
 <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 360 200">
   <g style="color:#616161" fill="none" stroke="currentColor" stroke-width="3.2" stroke-linecap="round" stroke-linejoin="round">
     <!-- Water container -->
-    <path d="M110 60V170H250V60" />
+    <path d="M110 80V170H250V80" />
     <rect x="118" y="120" width="124" height="44" fill="#9fd7f4" stroke="none" />
 
     <!-- Peristaltic pump -->
@@ -12,13 +12,13 @@
     <circle cx="190" cy="46" r="4" />
 
     <!-- Tubing into water -->
-    <path d="M168 52C150 70 140 88 140 132" />
-    <path d="M192 52C210 70 220 88 220 132" />
+    <path d="M160 52C150 70 140 88 140 132" />
+    <path d="M200 52C210 70 220 88 220 132" />
     <circle cx="140" cy="132" r="4" fill="currentColor" stroke="none" />
     <circle cx="220" cy="132" r="4" fill="currentColor" stroke="none" />
   </g>
-  <g style="color:#616161" fill="none" stroke="currentColor" stroke-width="1.4" stroke-linecap="round" stroke-linejoin="round">
-    <text x="150" y="92" font-size="12" font-family="Menlo,Consolas,system-ui" fill="currentColor">In</text>
-    <text x="218" y="92" font-size="12" font-family="Menlo,Consolas,system-ui" fill="currentColor">Out</text>
+  <g style="color:#616161" fill="none" stroke="currentColor" stroke-width="1.30" stroke-linecap="round" stroke-linejoin="round">
+    <text x="151" y="92" font-size="12" font-family="Menlo,Consolas,system-ui" fill="currentColor">In</text>
+    <text x="219" y="92" font-size="12" font-family="Menlo,Consolas,system-ui" fill="currentColor">Out</text>
   </g>
 </svg>
diff --git a/frontend/src/Protocols.jsx b/frontend/src/Protocols.jsx
@@ -10,6 +10,7 @@ import Divider from "@mui/material/Divider";
 import FormControl from "@mui/material/FormControl";
 import FormLabel from "@mui/material/FormLabel";
 import Grid from "@mui/material/Grid";
+import AlertTitle from "@mui/material/AlertTitle";
 import MenuItem from "@mui/material/MenuItem";
 import Select from "@mui/material/Select";
 import Snackbar from "@mui/material/Snackbar";
@@ -46,6 +47,9 @@ function ProtocolCard({
 
         <Box sx={{ mt: 2 }}>
           <RequirementsAlert>
+            <AlertTitle>
+              Requires:
+            </AlertTitle>
             <Box>
               <Box component="ul" sx={{ mt: 0, mb: 0, pl: 2 }}>
               {requirements.map((item) => (
diff --git a/frontend/src/components/RequirementsAlert.jsx b/frontend/src/components/RequirementsAlert.jsx
@@ -1,7 +1,5 @@
 import React from "react";
 import Alert from "@mui/material/Alert";
-import AlertTitle from "@mui/material/AlertTitle";
-import VialIcon from "./VialIcon";
 
 function RequirementsAlert(props) {
   const { sx, children, ...rest } = props;
@@ -20,7 +18,7 @@ function RequirementsAlert(props) {
   const combinedSx = Array.isArray(sx) ? [baseSx, ...sx] : [baseSx, sx];
 
   return (
-    <Alert severity="info" sx={combinedSx} {...rest}>
+    <Alert severity="info"  sx={combinedSx} {...rest}>
       {children}
     </Alert>
   );
diff --git a/frontend/src/components/SelfTestDialog.jsx b/frontend/src/components/SelfTestDialog.jsx
@@ -151,13 +151,13 @@ export default function SelfTestDialog({client, disabled, experiment, unit, labe
           <Typography variant="body2" component="p" gutterBottom>
             Perform a check of the heating & temperature sensor, LEDs & photodiodes, and stirring.
           </Typography>
-          <RequirementsAlert>
+          <RequirementsAlert sx={{mb: 2, pb: 0}}>
             Add a closed vial, half-filled with water, and stirbar into the Pioreactor.
             <Box
               component="img"
               src="/static/svgs/prepare-vial-arrow-pioreactor-compact.svg"
               alt="Prepare vial"
-              sx={{width: "150px", display: "block", mb: 1, mx: "auto"}}
+              sx={{width: "150px", display: "block", mb: 0, mx: "auto"}}
             />
           </RequirementsAlert>
 

Original file line number	Diff line number	Diff line change
`@@ -1 +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.8cc982bf.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>
	`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.c7c3634a.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>