Merge branch 'edge' into papi_try_liquid_probe

Resolve conflicts in api/tests/opentrons/protocol_api/core/engine/test_instrument_core.py.

Author: SyntaxColoring

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -1,5 +1,5 @@
 """Create ticket for robot with error."""
-from typing import List, Tuple, Any, Dict
+from typing import List, Tuple, Any, Dict, Optional
 from abr_testing.data_collection import read_robot_logs, abr_google_drive, get_run_logs
 import requests
 import argparse
@@ -18,7 +18,7 @@
 def compare_current_trh_to_average(
     robot: str,
     start_time: Any,
-    end_time: Any,
+    end_time: Optional[Any],
     protocol_name: str,
     storage_directory: str,
 ) -> str:
@@ -38,27 +38,29 @@ def compare_current_trh_to_average(
     df_all_trh = pd.DataFrame(all_trh_data)
     # Convert timestamps to datetime objects
     df_all_trh["Timestamp"] = pd.to_datetime(
-        df_all_trh["Timestamp"], format="mixed"
+        df_all_trh["Timestamp"], format="mixed", utc=True
     ).dt.tz_localize(None)
     # Ensure start_time is timezone-naive
     start_time = start_time.replace(tzinfo=None)
-    end_time = end_time.replace(tzinfo=None)
     relevant_temp_rhs = df_all_trh[
-        (df_all_trh["Robot"] == robot)
-        & (df_all_trh["Timestamp"] >= start_time)
-        & (df_all_trh["Timestamp"] <= end_time)
+        (df_all_trh["Robot"] == robot) & (df_all_trh["Timestamp"] >= start_time)
     ]
     try:
         avg_temp = round(mean(relevant_temp_rhs["Temp (oC)"]), 2)
         avg_rh = round(mean(relevant_temp_rhs["Relative Humidity (%)"]), 2)
     except StatisticsError:
-        avg_temp = None
-        avg_rh = None
+        # If there is one value assign it as the average.
+        if len(relevant_temp_rhs["Temp (oC)"]) == 1:
+            avg_temp = relevant_temp_rhs["Temp (oC)"][0]
+            avg_rh = relevant_temp_rhs["Relative Humidity (%)"][0]
+        else:
+            avg_temp = None
+            avg_rh = None
     # Get AVG t/rh of runs w/ same robot & protocol newer than 3 wks old with no errors
     weeks_ago_3 = start_time - timedelta(weeks=3)
     df_all_run_data = pd.DataFrame(all_run_data)
     df_all_run_data["Start_Time"] = pd.to_datetime(
-        df_all_run_data["Start_Time"], format="mixed"
+        df_all_run_data["Start_Time"], format="mixed", utc=True
     ).dt.tz_localize(None)
     df_all_run_data["Errors"] = pd.to_numeric(df_all_run_data["Errors"])
     df_all_run_data["Average Temp (oC)"] = pd.to_numeric(
@@ -283,7 +285,9 @@ def get_robot_state(
     components = match_error_to_component("RABR", reported_string, components)
     print(components)
     end_time = datetime.now()
+    print(end_time)
     start_time = end_time - timedelta(hours=2)
+    print(start_time)
     # Get current temp/rh compared to historical data
     temp_rh_string = compare_current_trh_to_average(
         parent, start_time, end_time, "", storage_directory

api-client/src/dataFiles/uploadCsvFile.ts

@@ -8,11 +8,18 @@ export function uploadCsvFile(
   config: HostConfig,
   data: FileData
 ): ResponsePromise<UploadedCsvFileResponse> {
-  return request<UploadedCsvFileResponse>(
+  let formData
+
+  if (typeof data !== 'string') {
+    formData = new FormData()
+    formData.append('file', data)
+  } else {
+    formData = data
+  }
+  return request<UploadedCsvFileResponse, FormData | string>(
     POST,
     '/dataFiles',
-    null,
-    config,
-    data
+    formData,
+    config
   )
 }

api-client/src/protocols/createProtocol.ts

@@ -2,14 +2,18 @@ import { POST, request } from '../request'
 import type { ResponsePromise } from '../request'
 import type { HostConfig } from '../types'
 import type { Protocol } from './types'
-import type { RunTimeParameterCreateData } from '../runs'
+import type {
+  RunTimeParameterValuesCreateData,
+  RunTimeParameterFilesCreateData,
+} from '../runs'
 
 export function createProtocol(
   config: HostConfig,
   files: File[],
   protocolKey?: string,
   protocolKind?: string,
-  runTimeParameterValues?: RunTimeParameterCreateData
+  runTimeParameterValues?: RunTimeParameterValuesCreateData,
+  runTimeParameterFiles?: RunTimeParameterFilesCreateData
 ): ResponsePromise<Protocol> {
   const formData = new FormData()
   files.forEach(file => {
@@ -22,6 +26,11 @@ export function createProtocol(
       'runTimeParameterValues',
       JSON.stringify(runTimeParameterValues)
     )
+  if (runTimeParameterFiles != null)
+    formData.append(
+      'runTimeParameterFiles',
+      JSON.stringify(runTimeParameterFiles)
+    )
 
   return request<Protocol, FormData>(POST, '/protocols', formData, config)
 }

api-client/src/protocols/createProtocolAnalysis.ts

@@ -3,21 +3,27 @@ import { POST, request } from '../request'
 import type { ProtocolAnalysisSummary } from '@opentrons/shared-data'
 import type { ResponsePromise } from '../request'
 import type { HostConfig } from '../types'
-import type { RunTimeParameterCreateData } from '../runs'
+import type {
+  RunTimeParameterFilesCreateData,
+  RunTimeParameterValuesCreateData,
+} from '../runs'
 
 interface CreateProtocolAnalysisData {
-  runTimeParameterValues: RunTimeParameterCreateData
+  runTimeParameterValues: RunTimeParameterValuesCreateData
+  runTimeParameterFiles: RunTimeParameterFilesCreateData
   forceReAnalyze: boolean
 }
 
 export function createProtocolAnalysis(
   config: HostConfig,
   protocolKey: string,
-  runTimeParameterValues?: RunTimeParameterCreateData,
+  runTimeParameterValues?: RunTimeParameterValuesCreateData,
+  runTimeParameterFiles?: RunTimeParameterFilesCreateData,
   forceReAnalyze?: boolean
 ): ResponsePromise<ProtocolAnalysisSummary[]> {
   const data = {
     runTimeParameterValues: runTimeParameterValues ?? {},
+    runTimeParameterFiles: runTimeParameterFiles ?? {},
     forceReAnalyze: forceReAnalyze ?? false,
   }
   const response = request<

api-client/src/protocols/getCsvFiles.ts

@@ -1,5 +1,3 @@
-import { v4 as uuidv4 } from 'uuid'
-
 // import { GET, request } from '../request'
 
 // import type { ResponsePromise } from '../request'
@@ -25,18 +23,16 @@ export function getCsvFiles(
   config: HostConfig,
   protocolId: string
 ): Promise<{ data: UploadedCsvFilesResponse }> {
-  const fileIdOne = uuidv4()
-  const fileIdTwo = uuidv4()
   const stub = {
     data: {
       files: [
         {
-          id: fileIdOne,
+          id: '1',
           createdAt: '2024-06-07T19:19:56.268029+00:00',
           name: 'rtp_mock_file1.csv',
         },
         {
-          id: fileIdTwo,
+          id: '2',
           createdAt: '2024-06-17T19:19:56.268029+00:00',
           name: 'rtp_mock_file2.csv',
         },

api-client/src/runs/createRun.ts

@@ -5,13 +5,15 @@ import type { HostConfig } from '../types'
 import type {
   Run,
   LabwareOffsetCreateData,
-  RunTimeParameterCreateData,
+  RunTimeParameterValuesCreateData,
+  RunTimeParameterFilesCreateData,
 } from './types'
 
 export interface CreateRunData {
   protocolId?: string
   labwareOffsets?: LabwareOffsetCreateData[]
-  runTimeParameterValues?: RunTimeParameterCreateData
+  runTimeParameterValues?: RunTimeParameterValuesCreateData
+  runTimeParameterFiles?: RunTimeParameterFilesCreateData
 }
 
 export function createRun(

api-client/src/runs/types.ts

@@ -132,11 +132,12 @@ export interface LabwareOffsetCreateData {
   vector: VectorOffset
 }
 
-type RunTimeParameterValueType = string | number | boolean | { id: string }
-export type RunTimeParameterCreateData = Record<
+type RunTimeParameterValuesType = string | number | boolean | { id: string }
+export type RunTimeParameterValuesCreateData = Record<
   string,
-  RunTimeParameterValueType
+  RunTimeParameterValuesType
 >
+export type RunTimeParameterFilesCreateData = Record<string, string>
 
 export interface CommandData {
   data: RunTimeCommand

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

@@ -643,7 +643,7 @@ async def move(
                 origin=origin, target_list=[move_target]
             )
         except ZeroLengthMoveError as zme:
-            log.warning(f"Not moving because move was zero length {str(zme)}")
+            log.debug(f"Not moving because move was zero length {str(zme)}")
             return
         moves = movelist[0]
         log.info(f"move: machine {target} from {origin} requires {moves}")

api/src/opentrons/hardware_control/ot3api.py

@@ -2666,6 +2666,8 @@ async def liquid_probe(
             except PipetteLiquidNotFoundError as lnfe:
                 error = lnfe
             pos = await self.gantry_position(checked_mount, refresh=True)
+        await self.move_to(checked_mount, probe_start_pos + top_types.Point(z=2))
+        await self.prepare_for_aspirate(checked_mount)
         await self.move_to(checked_mount, probe_start_pos)
         if error is not None:
             # if we never found liquid raise an error

api/src/opentrons/protocol_api/core/engine/instrument.py

@@ -879,7 +879,7 @@ def liquid_probe_with_recovery(self, well_core: WellCore, loc: Location) -> None
         labware_id = well_core.labware_id
         well_name = well_core.get_name()
         well_location = WellLocation(
-            origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=0)
+            origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=2)
         )
         self._engine_client.execute_command(
             cmd.LiquidProbeParams(
@@ -898,7 +898,7 @@ def liquid_probe_without_recovery(
         labware_id = well_core.labware_id
         well_name = well_core.get_name()
         well_location = WellLocation(
-            origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=0)
+            origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=2)
         )
         result = self._engine_client.execute_command_without_recovery(
             cmd.LiquidProbeParams(

api/src/opentrons/protocol_api/protocol_context.py

@@ -246,10 +246,6 @@ def cleanup(self) -> None:
             self._unsubscribe_commands()
             self._unsubscribe_commands = None
 
-    def __del__(self) -> None:
-        if getattr(self, "_unsubscribe_commands", None):
-            self._unsubscribe_commands()  # type: ignore
-
     @property
     @requires_version(2, 0)
     def max_speeds(self) -> AxisMaxSpeeds:

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

@@ -143,7 +143,10 @@ async def execute(self, params: _CommonParams) -> _LiquidProbeExecuteReturn:
 
         try:
             z_pos = await self._pipetting.liquid_probe_in_place(
-                pipette_id=pipette_id, labware_id=labware_id, well_name=well_name
+                pipette_id=pipette_id,
+                labware_id=labware_id,
+                well_name=well_name,
+                well_location=params.wellLocation,
             )
         except PipetteLiquidNotFoundError as e:
             return DefinedErrorData(

api/src/opentrons/protocol_engine/execution/pipetting.py

@@ -13,7 +13,7 @@
     InvalidPushOutVolumeError,
     InvalidDispenseVolumeError,
 )
-
+from opentrons.protocol_engine.types import WellLocation
 
 # 1e-9 µL (1 femtoliter!) is a good value because:
 # * It's large relative to rounding errors that occur in practice in protocols. For
@@ -68,6 +68,7 @@ async def liquid_probe_in_place(
         pipette_id: str,
         labware_id: str,
         well_name: str,
+        well_location: WellLocation,
     ) -> float:
         """Detect liquid level."""
 
@@ -176,6 +177,7 @@ async def liquid_probe_in_place(
         pipette_id: str,
         labware_id: str,
         well_name: str,
+        well_location: WellLocation,
     ) -> float:
         """Detect liquid level."""
         hw_pipette = self._state_view.pipettes.get_hardware_pipette(
@@ -188,7 +190,8 @@ async def liquid_probe_in_place(
             pipette_id=pipette_id
         )
         z_pos = await self._hardware_api.liquid_probe(
-            mount=hw_pipette.mount, max_z_dist=well_depth - lld_min_height
+            mount=hw_pipette.mount,
+            max_z_dist=well_depth - lld_min_height + well_location.offset.z,
         )
         return float(z_pos)
 
@@ -290,6 +293,7 @@ async def liquid_probe_in_place(
         pipette_id: str,
         labware_id: str,
         well_name: str,
+        well_location: WellLocation,
     ) -> float:
         """Detect liquid level."""
         # TODO (pm, 6-18-24): return a value of worth if needed

api/src/opentrons/system/log_control.py

@@ -15,7 +15,11 @@
 MAX_RECORDS = 100000
 DEFAULT_RECORDS = 50000
 
-UNIT_SELECTORS = ["opentrons-robot-server", "opentrons-robot-app"]
+UNIT_SELECTORS = [
+    "opentrons-robot-server",
+    "opentrons-update-server",
+    "opentrons-robot-app",
+]
 SERIAL_SPECIAL = "ALL_SERIAL"
 SERIAL_SELECTORS = [
     "opentrons-api-serial",

api/tests/opentrons/hardware_control/test_ot3_api.py

@@ -835,7 +835,7 @@ async def test_liquid_probe(
         )
         fake_max_z_dist = 10.0
         await ot3_hardware.liquid_probe(mount, fake_max_z_dist, fake_settings_aspirate)
-        mock_move_to_plunger_bottom.assert_called_once()
+        mock_move_to_plunger_bottom.call_count == 2
         mock_liquid_probe.assert_called_once_with(
             mount,
             3.0,
@@ -910,7 +910,7 @@ async def test_multi_liquid_probe(
         await ot3_hardware.liquid_probe(
             OT3Mount.LEFT, fake_max_z_dist, fake_settings_aspirate
         )
-        assert mock_move_to_plunger_bottom.call_count == 3
+        assert mock_move_to_plunger_bottom.call_count == 4
         mock_liquid_probe.assert_called_with(
             OT3Mount.LEFT,
             plunger_positions.bottom - plunger_positions.top,
@@ -986,8 +986,8 @@ async def _fake_pos_update_and_raise(
         await ot3_hardware.liquid_probe(
             OT3Mount.LEFT, fake_max_z_dist, fake_settings_aspirate
         )
-    # assert that it went through 3 passes
-    assert mock_move_to_plunger_bottom.call_count == 3
+    # assert that it went through 3 passes and then prepared to aspirate
+    assert mock_move_to_plunger_bottom.call_count == 4
 
 
 @pytest.mark.parametrize(

api/tests/opentrons/protocol_api/core/engine/test_instrument_core.py

@@ -1374,7 +1374,7 @@ def test_liquid_probe_without_recovery(
             cmd.LiquidProbeParams(
                 pipetteId=subject.pipette_id,
                 wellLocation=WellLocation(
-                    origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=0)
+                    origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=2)
                 ),
                 wellName=well_core.get_name(),
                 labwareId=well_core.labware_id,
@@ -1402,7 +1402,7 @@ def test_liquid_probe_with_recovery(
             cmd.LiquidProbeParams(
                 pipetteId=subject.pipette_id,
                 wellLocation=WellLocation(
-                    origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=0)
+                    origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=2.0)
                 ),
                 wellName=well_core.get_name(),
                 labwareId=well_core.labware_id,