Merge branch 'edge' into chore_no-unsafe-argument

.storybook/preview.jsx

@@ -3,6 +3,15 @@ import { I18nextProvider } from 'react-i18next'
 import { GlobalStyle } from '../app/src/atoms/GlobalStyle'
 import { i18n } from '../app/src/i18n'
 
+global.APP_SHELL_REMOTE = {
+  ipcRenderer: {
+    on: (topic, cb) => {},
+    invoke: (callname, args) => {},
+    send:  (message, payload) => {}
+  },
+}
+global._PKG_VERSION_ = '0.0.0-storybook'
+
 export const customViewports = {
   onDeviceDisplay: {
     name: 'Touchscreen',

api-client/src/dataFiles/index.ts

@@ -0,0 +1,3 @@
+export { uploadCsvFile } from './uploadCsvFile'
+
+export * from './types'

api-client/src/dataFiles/types.ts

@@ -0,0 +1,24 @@
+/**
+ * Represents the parameters for uploading a CSV file.
+ *
+ * @interface UploadCsvFileParams
+ * @property {File | string} [fileData] - File object for Desktop app and string for USB drive on ODD
+ */
+
+export type FileData = File | string
+
+interface CsvFileData {
+  id: string
+  createdAt: string
+  name: string
+}
+
+export interface UploadedCsvFileResponse {
+  data: CsvFileData
+}
+
+export interface UploadedCsvFilesResponse {
+  data: {
+    files: CsvFileData[]
+  }
+}

api-client/src/dataFiles/uploadCsvFile.ts

@@ -0,0 +1,36 @@
+import { v4 as uuidv4 } from 'uuid'
+// import { POST, request } from '../request'
+
+// import type { ResponsePromise } from '../request'
+import type { HostConfig } from '../types'
+import type { FileData /** UploadedCsvFileResponse */ } from './types'
+
+// export function uploadCsvFile(
+//   config: HostConfig,
+//   data FileData
+// ): ResponsePromise<UploadedCsvFileResponse> {
+//   return request<UploadedCsvFileResponse>(
+//     POST,
+//     '/dataFiles',
+//     null,
+//     config,
+//     data
+//   )
+// }
+
+// ToDo (kk:06/14/2024) remove when activate the above code
+export function uploadCsvFile(
+  config: HostConfig,
+  data: FileData
+  // Note (kk: 06/14/2024) temporary using any for useUploadCsvFileMutation
+): Promise<any> {
+  const fileId = uuidv4()
+  const stub = {
+    data: {
+      id: fileId,
+      createdAt: '2024-06-07T19:19:56.268029+00:00',
+      name: 'rtp_mock_file.csv',
+    },
+  }
+  return Promise.resolve(stub)
+}

api-client/src/index.ts

@@ -1,5 +1,6 @@
 // api client entry point
 export * from './calibration'
+export * from './dataFiles'
 export * from './deck_configuration'
 export * from './health'
 export * from './instruments'

api-client/src/protocols/getCsvFiles.ts

@@ -0,0 +1,47 @@
+import { v4 as uuidv4 } from 'uuid'
+
+// import { GET, request } from '../request'
+
+// import type { ResponsePromise } from '../request'
+import type { HostConfig } from '../types'
+import type { UploadedCsvFilesResponse } from '../dataFiles/types'
+
+/**
+export function getCsvFiles(
+  config: HostConfig,
+  protocolId: string
+): ResponsePromise<UploadCsvFilesResponse> {
+  return request<UploadCsvFilesResponse>(
+    GET,
+    `/protocols/${protocolId}/dataFiles`,
+    null,
+    config
+  )
+}
+   */
+
+// ToDo (kk:06/14/2024) remove when activate the above code
+export function getCsvFiles(
+  config: HostConfig,
+  protocolId: string
+): Promise<{ data: UploadedCsvFilesResponse }> {
+  const fileIdOne = uuidv4()
+  const fileIdTwo = uuidv4()
+  const stub = {
+    data: {
+      files: [
+        {
+          id: fileIdOne,
+          createdAt: '2024-06-07T19:19:56.268029+00:00',
+          name: 'rtp_mock_file1.csv',
+        },
+        {
+          id: fileIdTwo,
+          createdAt: '2024-06-17T19:19:56.268029+00:00',
+          name: 'rtp_mock_file2.csv',
+        },
+      ],
+    },
+  }
+  return Promise.resolve({ data: stub })
+}

api-client/src/protocols/index.ts

@@ -1,11 +1,12 @@
+export { createProtocol } from './createProtocol'
+export { createProtocolAnalysis } from './createProtocolAnalysis'
+export { deleteProtocol } from './deleteProtocol'
+export { getCsvFiles } from './getCsvFiles'
 export { getProtocol } from './getProtocol'
 export { getProtocolAnalyses } from './getProtocolAnalyses'
 export { getProtocolAnalysisAsDocument } from './getProtocolAnalysisAsDocument'
-export { deleteProtocol } from './deleteProtocol'
-export { createProtocol } from './createProtocol'
-export { createProtocolAnalysis } from './createProtocolAnalysis'
-export { getProtocols } from './getProtocols'
 export { getProtocolIds } from './getProtocolIds'
+export { getProtocols } from './getProtocols'
 
 export * from './types'
 export * from './utils'

api/docs/v2/new_examples.rst

@@ -397,7 +397,7 @@ Opentrons electronic pipettes can do some things that a human cannot do with a p
 
                 p300.return_tip()
 
-Notice here how Python's :py:class:`slice` functionality (in the code sample as ``[:4]``) lets us select the first five wells of the well plate only. Also, in Python, a range of numbers is *exclusive* of the end value and counting starts at 0, not 1. For the Corning 96-well plate used here, this means well A1=0, B1=1, C1=2, and so on to the last well used, which is E1=4. See also, the :ref:`tutorial-commands` section of the Tutorial.
+Notice here how Python's :py:class:`slice` functionality (in the code sample as ``[:5]``) lets us select the first five wells of the well plate only. Also, in Python, a range of numbers is *exclusive* of the end value and counting starts at 0, not 1. For the USA Scientific 12-well reservoir used here, this means well A1=0, A2=1, A3=2, and so on to the last well used, which is A5=4. See also, the :ref:`tutorial-commands` section of the Tutorial.
 
 Dilution
 ========

api/src/opentrons/config/defaults_ot3.py

@@ -24,7 +24,6 @@
 
 DEFAULT_LIQUID_PROBE_SETTINGS: Final[LiquidProbeSettings] = LiquidProbeSettings(
     starting_mount_height=100,
-    max_z_distance=40,
     mount_speed=10,
     plunger_speed=5,
     sensor_threshold_pascals=40,
@@ -335,7 +334,6 @@ def _build_default_liquid_probe(
         starting_mount_height=from_conf.get(
             "starting_mount_height", default.starting_mount_height
         ),
-        max_z_distance=from_conf.get("max_z_distance", default.max_z_distance),
         mount_speed=from_conf.get("mount_speed", default.mount_speed),
         plunger_speed=from_conf.get("plunger_speed", default.plunger_speed),
         sensor_threshold_pascals=from_conf.get(

api/src/opentrons/config/types.py

@@ -132,7 +132,6 @@ class ZSenseSettings:
 @dataclass
 class LiquidProbeSettings:
     starting_mount_height: float
-    max_z_distance: float
     mount_speed: float
     plunger_speed: float
     sensor_threshold_pascals: float

api/src/opentrons/hardware_control/backends/ot3controller.py

@@ -191,7 +191,7 @@
     PipetteOverpressureError,
     FirmwareUpdateRequiredError,
     FailedGripperPickupError,
-    LiquidNotFoundError,
+    PipetteLiquidNotFoundError,
     CommunicationError,
     PythonException,
     UnsupportedHardwareCommand,
@@ -1412,7 +1412,7 @@ async def liquid_probe(
             or positions[head_node].move_ack
             == MoveCompleteAck.complete_without_condition
         ):
-            raise LiquidNotFoundError(
+            raise PipetteLiquidNotFoundError(
                 "Liquid not found during probe.",
                 {
                     str(node_to_axis(node)): str(point.motor_position)

api/src/opentrons/hardware_control/ot3api.py

@@ -52,7 +52,7 @@
     GripperNotPresentError,
     InvalidActuator,
     FirmwareUpdateFailedError,
-    LiquidNotFoundError,
+    PipetteLiquidNotFoundError,
 )
 
 from .util import use_or_initialize_loop, check_motion_bounds
@@ -2594,7 +2594,8 @@ def _get_probe_distances(
 
     async def liquid_probe(
         self,
-        mount: OT3Mount,
+        mount: Union[top_types.Mount, OT3Mount],
+        max_z_dist: float,
         probe_settings: Optional[LiquidProbeSettings] = None,
         probe: Optional[InstrumentProbeType] = None,
     ) -> float:
@@ -2605,7 +2606,7 @@ async def liquid_probe(
         reading from the pressure sensor.
 
         If the move is completed without the specified threshold being triggered, a
-        LiquidNotFoundError error will be thrown.
+        PipetteLiquidNotFoundError error will be thrown.
 
         Otherwise, the function will stop moving once the threshold is triggered,
         and return the position of the
@@ -2622,21 +2623,21 @@ async def liquid_probe(
         if not probe_settings:
             probe_settings = self.config.liquid_sense
 
-        pos = await self.gantry_position(mount, refresh=True)
+        pos = await self.gantry_position(checked_mount, refresh=True)
         probe_start_pos = pos._replace(z=probe_settings.starting_mount_height)
-        await self.move_to(mount, probe_start_pos)
-        total_z_travel = probe_settings.max_z_distance
+        await self.move_to(checked_mount, probe_start_pos)
+        total_z_travel = max_z_dist
         z_travels = self._get_probe_distances(
             checked_mount,
             total_z_travel,
             probe_settings.plunger_speed,
             probe_settings.mount_speed,
         )
-        error: Optional[LiquidNotFoundError] = None
+        error: Optional[PipetteLiquidNotFoundError] = None
         for z_travel in z_travels:
 
             if probe_settings.aspirate_while_sensing:
-                await self._move_to_plunger_bottom(mount, rate=1.0)
+                await self._move_to_plunger_bottom(checked_mount, rate=1.0)
             else:
                 # find the ideal travel distance by multiplying the plunger speed
                 # by the time it will take to complete the z move.
@@ -2656,17 +2657,17 @@ async def liquid_probe(
                 await self._move(target_pos, speed=speed, acquire_lock=True)
             try:
                 height = await self._liquid_probe_pass(
-                    mount,
+                    checked_mount,
                     probe_settings,
                     probe if probe else InstrumentProbeType.PRIMARY,
                     z_travel,
                 )
                 # if we made it here without an error we found the liquid
                 error = None
                 break
-            except LiquidNotFoundError as lnfe:
+            except PipetteLiquidNotFoundError as lnfe:
                 error = lnfe
-        await self.move_to(mount, probe_start_pos)
+        await self.move_to(checked_mount, probe_start_pos)
         if error is not None:
             # if we never found an liquid raise an error
             raise error

api/src/opentrons/hardware_control/protocols/liquid_handler.py

@@ -171,3 +171,16 @@ async def drop_tip(
                                 the ejector shroud after a drop.
         """
         ...
+
+    async def liquid_probe(
+        self,
+        mount: MountArgType,
+        max_z_dist: float,
+    ) -> float:
+        """Search for and return liquid level height using this pipette
+        at the current location.
+
+        mount : Mount.LEFT or Mount.RIGHT
+        max_z_dist : maximum depth to probe for liquid
+        """
+        ...

api/src/opentrons/protocol_engine/commands/__init__.py

@@ -325,6 +325,14 @@
     VerifyTipPresenceCommandType,
 )
 
+from .liquid_probe import (
+    LiquidProbe,
+    LiquidProbeParams,
+    LiquidProbeCreate,
+    LiquidProbeResult,
+    LiquidProbeCommandType,
+)
+
 __all__ = [
     # command type unions
     "Command",
@@ -566,4 +574,10 @@
     "VerifyTipPresenceParams",
     "VerifyTipPresenceResult",
     "VerifyTipPresenceCommandType",
+    # liquid probe command bundle
+    "LiquidProbe",
+    "LiquidProbeParams",
+    "LiquidProbeCreate",
+    "LiquidProbeResult",
+    "LiquidProbeCommandType",
 ]