Skunk command annotations for step grouping

api/src/opentrons/cli/analyze.py

@@ -426,3 +426,4 @@ class AnalyzeResults(BaseModel):
     modules: List[LoadedModule]
     liquids: List[Liquid]
     errors: List[ErrorOccurrence]
+    commandAnnotations: List[Any]

api/src/opentrons/protocol_reader/file_identifier.py

@@ -2,7 +2,7 @@
 
 import json
 from dataclasses import dataclass
-from typing import Any, Dict, Sequence, Union, Optional
+from typing import Any, Dict, List, Sequence, Union, Optional
 
 import anyio
 
@@ -45,6 +45,8 @@ class IdentifiedJsonMain:
     metadata: Metadata
     """The protocol metadata extracted from this file."""
 
+    command_annotations: List[Any]
+
 
 @dataclass(frozen=True)
 class IdentifiedPythonMain:
@@ -62,6 +64,8 @@ class IdentifiedPythonMain:
     metadata: Metadata
     """The protocol metadata extracted from this file."""
 
+    command_annotations: List[Any]
+
 
 @dataclass(frozen=True)
 class IdentifiedLabwareDefinition:
@@ -203,6 +207,7 @@ def _analyze_json_protocol(
         metadata = json_contents["metadata"]
         schema_version = json_contents["schemaVersion"]
         robot_type = json_contents["robot"]["model"]
+        command_annotations = json_contents.get("commandAnnotations", [])
     except KeyError as e:
         raise FileIdentificationError(
             message=error_message,
@@ -218,6 +223,9 @@ def _analyze_json_protocol(
             message=error_message, detail={"kind": "json-metadata-not-object"}
         )
 
+    if not isinstance(command_annotations, list):
+        raise FileIdentificationError(error_message)
+
     if not isinstance(schema_version, int):
         raise FileIdentificationError(
             message=error_message,
@@ -239,6 +247,7 @@ def _analyze_json_protocol(
         schema_version=schema_version,
         robot_type=robot_type,
         metadata=metadata,
+        command_annotations=command_annotations,
     )
 
 
@@ -281,4 +290,5 @@ def _analyze_python_protocol(
         metadata=parsed.metadata or {},
         robot_type=parsed.robot_type,
         api_level=parsed.api_level,
+        command_annotations=[],
     )

api/src/opentrons/protocol_reader/protocol_reader.py

@@ -101,6 +101,7 @@ async def save(
             config=self._map_config(role_analysis),
             robot_type=role_analysis.main_file.robot_type,
             metadata=role_analysis.main_file.metadata,
+            command_annotations=role_analysis.main_file.command_annotations,
         )
 
     async def read_saved(
@@ -167,6 +168,7 @@ async def read_saved(
             config=self._map_config(role_analysis),
             robot_type=role_analysis.main_file.robot_type,
             metadata=role_analysis.main_file.metadata,
+            command_annotations=role_analysis.main_file.command_annotations,
         )
 
     @staticmethod

api/src/opentrons/protocol_reader/protocol_source.py

@@ -122,3 +122,4 @@ class ProtocolSource:
     metadata: Metadata
     robot_type: RobotType
     config: ProtocolConfig
+    command_annotations: List[Any]

app-shell/src/protocol-editor-ui.ts

@@ -0,0 +1,83 @@
+// sets up the main window ui
+import { app, shell, BrowserWindow, ipcMain } from 'electron'
+import path from 'path'
+
+import { getConfig } from './config'
+import { createLogger } from './log'
+import {
+  PROTOCOLS_DIRECTORY_PATH,
+  analyzeProtocolByKey,
+  getProtocolSourceJSON,
+  overwriteProtocol,
+} from './protocol-storage/file-system'
+
+const protocolEditorUiConfig = getConfig('protocolEditorUi')
+const log = createLogger('protocolEditorUi')
+
+const WINDOW_OPTS = {
+  show: false,
+  useContentSize: true,
+  width: protocolEditorUiConfig.width,
+  minWidth: protocolEditorUiConfig.minWidth,
+  height: protocolEditorUiConfig.height,
+  // allow webPreferences to be set at launchtime from config
+  webPreferences: Object.assign(
+    {
+      preload: path.join(__dirname, './preload.js'),
+      nodeIntegration: false,
+      // TODO: remove this by using electron contextBridge to specify
+      // exact, argument-sanitation-involved methods instead of just
+      // binding the entire ipcRenderer in. This is necessary because
+      // as of electron 12, contextIsolation defaults to true.
+      contextIsolation: false,
+    },
+    protocolEditorUiConfig.webPreferences
+  ),
+}
+
+const protocolEditorPath =
+  protocolEditorUiConfig.url.protocol === 'file:'
+    ? path.join(app.getAppPath(), protocolEditorUiConfig.url.path)
+    : protocolEditorUiConfig.url.path
+
+export function createProtocolEditorUi(srcFilePath: string): BrowserWindow {
+  log.debug('Creating protocol editor window', { options: WINDOW_OPTS })
+
+  const subWindow = new BrowserWindow(WINDOW_OPTS).once('ready-to-show', () => {
+    log.debug('Protocol Editor window ready to show')
+    subWindow.show()
+  })
+  const protocolEditorUrl = `${protocolEditorUiConfig.url.protocol}//${protocolEditorPath}`
+
+  log.info(`Loading ${protocolEditorUrl}`)
+  // eslint-disable-next-line @typescript-eslint/no-floating-promises
+  subWindow.loadURL(protocolEditorUrl)
+
+  // open new windows (<a target="_blank" ...) in browser windows
+  subWindow.webContents.setWindowOpenHandler(({ url }) => {
+    log.debug('Opening external link', { url })
+    // event.preventDefault()
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    shell.openExternal(url)
+    return { action: 'deny' }
+  })
+
+  subWindow.webContents.once('dom-ready', () => {
+    const protocolSourceJSON = getProtocolSourceJSON(srcFilePath)
+    protocolSourceJSON.then(json => {
+      subWindow.webContents.send('open-protocol-in-designer', json)
+      ipcMain.once(
+        'save-protocol-file-to-filesystem',
+        (_event, fileName, fileData) => {
+          overwriteProtocol(srcFilePath, fileName, fileData).then(() => {
+            const { protocolKey } =
+              /.*\/(?<protocolKey>.*)\/src.*/.exec(srcFilePath)?.groups ?? {}
+            return analyzeProtocolByKey(protocolKey, PROTOCOLS_DIRECTORY_PATH)
+          })
+        }
+      )
+    })
+  })
+
+  return subWindow
+}

app/Makefile

@@ -6,8 +6,10 @@ SHELL := bash
 # add node_modules/.bin to PATH
 PATH := $(shell cd .. && yarn bin):$(PATH)
 
-# dev server port
+# app dev server port
 PORT ?= 5173
+# protocol editor dev server port
+PD_PORT ?= 5178
 
 # Path of source package
 SRC_PATH = app
@@ -54,6 +56,7 @@ dist:
 .PHONY: dev
 dev: export NODE_ENV := development
 dev: export PORT := $(PORT)
+dev: export PD_PORT := $(PD_PORT)
 dev:
 	concurrently --no-color --kill-others --names "server,shell" \
 		"$(MAKE) dev-server OPENTRONS_PROJECT=$(OPENTRONS_PROJECT)" \

app/src/App/DesktopApp.tsx

@@ -32,6 +32,7 @@ import { IncompatibleModuleTakeover } from '../organisms/IncompatibleModule'
 import { OPENTRONS_USB } from '../redux/discovery'
 import { appShellRequestor } from '../redux/shell/remote'
 import { useRobot, useIsFlex } from '../organisms/Devices/hooks'
+import { ProtocolTimeline } from '../pages/Protocols/ProtocolDetails/ProtocolTimeline'
 import { PortalRoot as ModalPortalRoot } from './portal'
 import { DesktopAppFallback } from './DesktopAppFallback'
 
@@ -58,6 +59,12 @@ export const DesktopApp = (): JSX.Element => {
       name: 'Protocol Details',
       path: '/protocols/:protocolKey',
     },
+    {
+      Component: ProtocolTimeline,
+      exact: true,
+      name: 'Protocol Timeline',
+      path: '/protocols/:protocolKey/timeline',
+    },
     {
       Component: Labware,
       name: 'Labware',

app/src/assets/localization/en/app_settings.json

@@ -1,6 +1,7 @@
 {
   "__dev_internal__forceHttpPolling": "Poll all network requests instead of using MQTT",
   "__dev_internal__protocolStats": "Protocol Stats",
+  "__dev_internal__protocolTimeline": "Protocol Timeline",
   "__dev_internal__enableRunNotes": "Display Notes During a Protocol Run",
   "__dev_internal__enableQuickTransfer": "Enable Quick Transfer",
   "__dev_internal__enableCsvFile": "Enable CSV File",

app/src/assets/localization/en/protocol_details.json

@@ -22,6 +22,7 @@
   "extension_mount": "extension mount",
   "file_required": "File required",
   "go_to_labware_definition": "Go to labware definition",
+  "go_to_timeline": "Go to timeline",
   "gripper_pick_up_count_description": "individual move labware commands that use the gripper.",
   "gripper_pick_up_count": "Grip Count",
   "hardware": "hardware",

app/src/assets/localization/en/protocol_list.json

@@ -2,6 +2,8 @@
   "csv_file_required": "CSV file required for analysis. Add the CSV during run setup.",
   "delete_protocol_message": " and its run history will be permanently deleted.",
   "delete_this_protocol": "Delete this protocol?",
+  "edit": "edit",
+  "go_to_timeline": "Go to timeline",
   "last_updated_at": "Updated {{date}}",
   "left_mount": "left mount",
   "loading_data": "Loading data...",

app/src/molecules/Command/MoveLabwareCommandText.tsx

@@ -3,6 +3,7 @@ import { GRIPPER_WASTE_CHUTE_ADDRESSABLE_AREA } from '@opentrons/shared-data'
 import { getLabwareName } from './utils'
 import { getLabwareDisplayLocation } from './utils/getLabwareDisplayLocation'
 import { getFinalLabwareLocation } from './utils/getFinalLabwareLocation'
+
 import type {
   MoveLabwareRunTimeCommand,
   RobotType,

app/src/molecules/Command/PipettingCommandText.tsx

@@ -91,6 +91,13 @@ export const PipettingCommandText = ({
         flow_rate: flowRate,
       })
     }
+    case 'moveToWell': {
+      return t('move_to_well', {
+        well_name: wellName,
+        labware: getLabwareName(analysis, labwareId),
+        labware_location: displayLocation,
+      })
+    }
     case 'dropTip': {
       const loadedLabware = getLoadedLabware(commandTextData, labwareId)
       const labwareDefinitions = getLabwareDefinitionsFromCommands(

app/src/molecules/Command/utils/getCommandTextData.ts

@@ -1,12 +1,16 @@
 import type { LegacyGoodRunData } from '@opentrons/api-client'
 import type {
   CompletedProtocolAnalysis,
+  ProtocolAnalysisOutput,
   RunTimeCommand,
 } from '@opentrons/shared-data'
 import type { CommandTextData } from '../types'
 
 export function getCommandTextData(
-  protocolData: CompletedProtocolAnalysis | LegacyGoodRunData,
+  protocolData:
+    | CompletedProtocolAnalysis
+    | LegacyGoodRunData
+    | ProtocolAnalysisOutput,
   protocolCommands?: RunTimeCommand[]
 ): CommandTextData {
   const { pipettes, labware, modules, liquids } = protocolData

app/src/molecules/Command/utils/getLabwareDisplayLocation.ts

@@ -22,11 +22,11 @@ export function getLabwareDisplayLocation(
   if (location === 'offDeck') {
     return t('off_deck')
   } else if ('slotName' in location) {
-    return isOnDevice
+    return isOnDevice === true
       ? location.slotName
       : t('slot', { slot_name: location.slotName })
   } else if ('addressableAreaName' in location) {
-    return isOnDevice
+    return isOnDevice === true
       ? location.addressableAreaName
       : t('slot', { slot_name: location.addressableAreaName })
   } else if ('moduleId' in location) {
@@ -39,7 +39,7 @@ export function getLabwareDisplayLocation(
         commandTextData,
         location.moduleId
       )
-      return isOnDevice
+      return isOnDevice === true
         ? `${getModuleDisplayName(moduleModel)}, ${slotName}`
         : t('module_in_slot', {
             count: getOccludedSlotCountForModule(