Merge branch 'edge' into app_384-well-selection

.github/workflows/hardware-testing.yaml

@@ -9,6 +9,9 @@ on:
     paths:
       - 'Makefile'
       - 'hardware-testing/**'
+      - 'api/**'
+      - 'shared-data/**'
+      - 'hardware/**'
       - '.github/workflows/hardware-testing.yaml'
       - '.github/actions/python/**'
     branches:

abr-testing/abr_testing/automation/google_sheets_tool.py

@@ -6,7 +6,7 @@
 import sys
 from datetime import datetime
 from oauth2client.service_account import ServiceAccountCredentials  # type: ignore[import]
-from typing import Dict, List, Any, Set, Tuple
+from typing import Dict, List, Any, Set, Tuple, Optional
 
 """Google Sheets Tool.
 
@@ -48,13 +48,14 @@ def open_worksheet(self, tab_number: int) -> Any:
         """Open individual worksheet within a googlesheet."""
         return self.spread_sheet.get_worksheet(tab_number)
 
-    def create_worksheet(self, title: str) -> None:
+    def create_worksheet(self, title: str) -> Optional[str]:
         """Create a worksheet with tab name. Existing spreadsheet needed."""
         try:
-            new_sheet = self.spread_sheet.add_worksheet(title, rows="2000", cols="26")
+            new_sheet = self.spread_sheet.add_worksheet(title, rows="2500", cols="40")
             return new_sheet.id
         except gspread.exceptions.APIError:
             print("Sheet already exists.")
+            return new_sheet.id
 
     def write_header(self, header: List) -> None:
         """Write Header to first row if not present."""
@@ -108,17 +109,55 @@ def batch_delete_rows(self, row_indices: List[int]) -> None:
         self.spread_sheet.batch_update(body=delete_body)
 
     def batch_update_cells(
-        self, sheet_title: str, data: List[List[str]], start_column: str, start_row: int
+        self,
+        data: List[List[Any]],
+        start_column: str,
+        start_row: int,
+        sheet_id: str,
     ) -> None:
         """Writes to multiple cells at once in a specific sheet."""
-        sheet = self.spread_sheet.worksheet(sheet_title)
-        for idx, values in enumerate(data):
-            column = chr(ord(start_column) + idx)  # Convert index to column letter
-            location = f"{column}{start_row}:{column}{start_row + len(values) - 1}"
-            cells_to_update = sheet.range(location)
-            for cell, value in zip(cells_to_update, values):
-                cell.value = value
-            sheet.update_cells(cells_to_update)
+
+        def column_letter_to_index(column_letter: str) -> int:
+            """Convert a column letter (e.g., 'A') to a 1-based column index (e.g., 1)."""
+            index = 0
+            for char in column_letter.upper():
+                index = index * 26 + (ord(char) - ord("A") + 1)
+            return index
+
+        requests = []
+        user_entered_value: Dict[str, Any] = {}
+        start_column_index = column_letter_to_index(start_column) - 1
+
+        for col_offset, col_values in enumerate(data):
+            column_index = start_column_index + col_offset
+            # column_letter = index_to_column_letter(column_index)
+            for row_offset, value in enumerate(col_values):
+                row_index = start_row + row_offset
+                try:
+                    float_value = float(value)
+                    user_entered_value = {"numberValue": float_value}
+                except ValueError:
+                    user_entered_value = {"stringValue": str(value)}
+                requests.append(
+                    {
+                        "updateCells": {
+                            "range": {
+                                "sheetId": sheet_id,
+                                "startRowIndex": row_index - 1,
+                                "endRowIndex": row_index,
+                                "startColumnIndex": column_index,
+                                "endColumnIndex": column_index + 1,
+                            },
+                            "rows": [
+                                {"values": [{"userEnteredValue": user_entered_value}]}
+                            ],
+                            "fields": "userEnteredValue",
+                        }
+                    }
+                )
+
+        body = {"requests": requests}
+        self.spread_sheet.batch_update(body=body)
 
     def update_cell(
         self, sheet_title: str, row: int, column: int, single_data: Any
@@ -135,13 +174,13 @@ def get_column(self, column_number: int) -> Set[str]:
         """Get all values in column."""
         return self.worksheet.col_values(column_number)
 
-    def get_cell(self, cell: str) -> Any:
+    def get_cell(self, sheet_title: str, cell: str) -> Any:
         """Get cell value with location ex: 'A1'."""
-        return self.worksheet.acell(cell).value
+        return self.spread_sheet.worksheet(sheet_title).acell(cell).value
 
-    def get_single_col_range(self, range: str) -> List:
+    def get_single_col_range(self, sheet_name: str, range: str) -> List:
         """Get cell values from one column range."""
-        values_range = self.worksheet.range(range)
+        values_range = self.spread_sheet.worksheet(sheet_name).range(range)
         return [cell.value for cell in values_range]
 
     def get_index_row(self) -> int:
@@ -214,7 +253,7 @@ def create_line_chart(
                                 "overlayPosition": {
                                     "anchorCell": {
                                         "sheetId": sheet_id,
-                                        "rowIndex": 1,
+                                        "rowIndex": 15,
                                         "columnIndex": col_position,
                                     }
                                 }

abr-testing/abr_testing/data_collection/abr_google_drive.py

@@ -32,10 +32,10 @@ def create_data_dictionary(
     runs_to_save: Union[Set[str], str],
     storage_directory: str,
     issue_url: str,
-) -> Tuple[Dict[str, Dict[str, Any]], List[str], Dict[str, Dict[str, Any]], List[str]]:
+) -> Tuple[List[List[Any]], List[str], List[List[Any]], List[str]]:
     """Pull data from run files and format into a dictionary."""
-    runs_and_robots: Dict[Any, Dict[str, Any]] = {}
-    runs_and_lpc: Dict[Any, Dict[str, Any]] = {}
+    runs_and_robots: List[Any] = []
+    runs_and_lpc: List[Dict[str, Any]] = []
     for filename in os.listdir(storage_directory):
         file_path = os.path.join(storage_directory, filename)
         if file_path.endswith(".json"):
@@ -119,14 +119,17 @@ def create_data_dictionary(
                     **tc_dict,
                 }
                 headers: List[str] = list(row_2.keys())
-                runs_and_robots[run_id] = row_2
+                # runs_and_robots[run_id] = row_2
+                runs_and_robots.append(list(row_2.values()))
                 # LPC Data Recording
                 runs_and_lpc, headers_lpc = read_robot_logs.lpc_data(
                     file_results, row_for_lpc, runs_and_lpc
                 )
             else:
                 continue
-    return runs_and_robots, headers, runs_and_lpc, headers_lpc
+    transposed_runs_and_robots = list(map(list, zip(*runs_and_robots)))
+    transposed_runs_and_lpc = list(map(list, zip(*runs_and_lpc)))
+    return transposed_runs_and_robots, headers, transposed_runs_and_lpc, headers_lpc
 
 
 if __name__ == "__main__":
@@ -183,14 +186,19 @@ def create_data_dictionary(
         run_ids_on_gd, run_ids_on_gs
     )
     # Add missing runs to google sheet
-    runs_and_robots, headers, runs_and_lpc, headers_lpc = create_data_dictionary(
-        missing_runs_from_gs, storage_directory, ""
-    )
-    read_robot_logs.write_to_local_and_google_sheet(
-        runs_and_robots, storage_directory, google_sheet_name, google_sheet, headers
-    )
+    (
+        transposed_runs_and_robots,
+        headers,
+        transposed_runs_and_lpc,
+        headers_lpc,
+    ) = create_data_dictionary(missing_runs_from_gs, storage_directory, "")
+
+    start_row = google_sheet.get_index_row() + 1
+    google_sheet.batch_update_cells(transposed_runs_and_robots, "A", start_row, "0")
+
     # Add LPC to google sheet
     google_sheet_lpc = google_sheets_tool.google_sheet(credentials_path, "ABR-LPC", 0)
-    read_robot_logs.write_to_local_and_google_sheet(
-        runs_and_lpc, storage_directory, "ABR-LPC", google_sheet_lpc, headers_lpc
+    start_row_lpc = google_sheet_lpc.get_index_row() + 1
+    google_sheet_lpc.batch_update_cells(
+        transposed_runs_and_lpc, "A", start_row_lpc, "0"
     )

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -47,6 +47,7 @@ def get_error_info_from_robot(
     ) = read_robot_logs.get_error_info(results)
     # JIRA Ticket Fields
     failure_level = "Level " + str(error_level) + " Failure"
+
     components = [failure_level, "Flex-RABR"]
     affects_version = results["API_Version"]
     parent = results.get("robot_name", "")
@@ -201,12 +202,11 @@ def get_error_info_from_robot(
         runs_and_lpc,
         headers_lpc,
     ) = abr_google_drive.create_data_dictionary(run_id, error_folder_path, issue_url)
-    read_robot_logs.write_to_local_and_google_sheet(
-        runs_and_robots, storage_directory, google_sheet_name, google_sheet, headers
-    )
+
+    start_row = google_sheet.get_index_row() + 1
+    google_sheet.batch_update_cells(runs_and_robots, "A", start_row, "0")
     print("Wrote run to ABR-run-data")
     # Add LPC to google sheet
     google_sheet_lpc = google_sheets_tool.google_sheet(credentials_path, "ABR-LPC", 0)
-    read_robot_logs.write_to_local_and_google_sheet(
-        runs_and_lpc, storage_directory, "ABR-LPC", google_sheet_lpc, headers_lpc
-    )
+    start_row_lpc = google_sheet_lpc.get_index_row() + 1
+    google_sheet_lpc.batch_update_cells(runs_and_lpc, "A", start_row_lpc, "0")

abr-testing/abr_testing/data_collection/read_robot_logs.py

@@ -18,11 +18,10 @@
 def lpc_data(
     file_results: Dict[str, Any],
     protocol_info: Dict[str, Any],
-    runs_and_lpc: Dict[str, Any],
-) -> Tuple[Dict[str, Dict[str, Any]], List[str]]:
+    runs_and_lpc: List[Dict[str, Any]],
+) -> Tuple[List[Dict[str, Any]], List[str]]:
     """Get labware offsets from one run log."""
     offsets = file_results.get("labwareOffsets", "")
-    n = 0
     # TODO: per UNIQUE slot AND LABWARE TYPE only keep the most recent LPC recording
     if len(offsets) > 0:
         unique_offsets: Dict[Any, Any] = {}
@@ -55,9 +54,7 @@ def lpc_data(
                     "Z": z_offset,
                 }
     for item in unique_offsets:
-        run_id = protocol_info["Run_ID"] + "_" + str(n)
-        runs_and_lpc[run_id] = unique_offsets[item]
-        n += 1
+        runs_and_lpc.append(unique_offsets[item].values())
     headers_lpc = list(unique_offsets[(slot, labware_type)].keys())
 
     return runs_and_lpc, headers_lpc
@@ -298,6 +295,7 @@ def create_abr_data_sheet(
 def get_error_info(file_results: Dict[str, Any]) -> Tuple[int, str, str, str, str]:
     """Determines if errors exist in run log and documents them."""
     error_levels = []
+    error_level = ""
     # Read error levels file
     with open(ERROR_LEVELS_PATH, "r") as error_file:
         error_levels = list(csv.reader(error_file))
@@ -328,6 +326,8 @@ def get_error_info(file_results: Dict[str, Any]) -> Tuple[int, str, str, str, st
         code_error = error[1]
         if code_error == error_code:
             error_level = error[4]
+    if len(error_level) < 1:
+        error_level = str(4)
 
     return num_of_errors, error_type, error_code, error_instrument, error_level
 

abr-testing/abr_testing/data_collection/single_run_log_reader.py

@@ -15,16 +15,8 @@
         nargs=1,
         help="Folder path that holds individual run logs of interest.",
     )
-    parser.add_argument(
-        "google_sheet_name",
-        metavar="GOOGLE_SHEET_NAME",
-        type=str,
-        nargs=1,
-        help="Google sheet name.",
-    )
     args = parser.parse_args()
     run_log_file_path = args.run_log_file_path[0]
-    google_sheet_name = args.google_sheet_name[0]
 
     try:
         credentials_path = os.path.join(run_log_file_path, "credentials.json")
@@ -41,16 +33,14 @@
     ) = abr_google_drive.create_data_dictionary(
         run_ids_in_storage, run_log_file_path, ""
     )
-    list_of_runs = list(runs_and_robots.keys())
+    transposed_list = list(zip(*runs_and_robots))
     # Adds Run to local csv
     sheet_location = os.path.join(run_log_file_path, "saved_data.csv")
     file_exists = os.path.exists(sheet_location) and os.path.getsize(sheet_location) > 0
     with open(sheet_location, "a", newline="") as f:
         writer = csv.writer(f)
         if not file_exists:
             writer.writerow(header)
-        for run in list_of_runs:
+        for run in transposed_list:
             # Add new row
-            row = runs_and_robots[run].values()
-            row_list = list(row)
-            writer.writerow(row_list)
+            writer.writerow(run)

api-client/src/modules/__fixtures__/index.ts

@@ -7,6 +7,7 @@ export const mockModulesResponse = [
     hasAvailableUpdate: false,
     moduleType: 'thermocyclerModuleType',
     moduleModel: 'thermocyclerModuleV1',
+    compatibleWithRobot: true,
     data: {
       status: 'holding at target',
       currentTemperature: 3.0,
@@ -31,6 +32,7 @@ export const mockModulesResponse = [
     hasAvailableUpdate: false,
     moduleType: 'heaterShakerModuleType',
     moduleModel: 'heaterShakerModuleV1',
+    compatibleWithRobot: true,
     data: {
       status: 'idle',
       labwareLatchStatus: 'idle_unknown',
@@ -55,6 +57,7 @@ export const mockModulesResponse = [
     hasAvailableUpdate: false,
     moduleType: 'temperatureModuleType',
     moduleModel: 'temperatureModuleV1',
+    compatibleWithRobot: true,
     data: {
       status: 'holding at target',
       currentTemperature: 3.0,
@@ -75,6 +78,7 @@ export const mockModulesResponse = [
     hasAvailableUpdate: false,
     moduleType: 'magneticModuleType',
     moduleModel: 'magneticModuleV1',
+    compatibleWithRobot: true,
     data: {
       status: 'engaged',
       engaged: true,
@@ -89,6 +93,29 @@ export const mockModulesResponse = [
   },
 ]
 
+export const mockUnknownModuleResponse = [
+  ...mockModulesResponse,
+  {
+    name: 'unknown',
+    displayName: 'UnknownModule',
+    moduleModel: 'unknownModule',
+    port: '/dev/unknown',
+    usbPort: {
+      port: 0,
+      hub: false,
+      portGroup: 'unknown',
+      path: '',
+    },
+    serial: 'dummySerialMD',
+    model: 'unknown_v1.1',
+    revision: 'unknown_v1.1',
+    fwVersion: 'dummyVersionMD',
+    hasAvailableUpdate: false,
+    status: 'engaged',
+    data: {},
+  },
+]
+
 export const v2MockModulesResponse = [
   {
     name: 'thermocycler',

api-client/src/modules/api-types.ts

@@ -36,6 +36,7 @@ export interface ApiBaseModule {
   firmwareVersion: string
   hasAvailableUpdate: boolean
   usbPort: PhysicalPort
+  compatibleWithRobot?: boolean
   moduleOffset?: ModuleOffset
 }
 

api/src/opentrons/config/defaults_ot3.py

@@ -25,7 +25,6 @@
 DEFAULT_LIQUID_PROBE_SETTINGS: Final[LiquidProbeSettings] = LiquidProbeSettings(
     starting_mount_height=100,
     max_z_distance=40,
-    min_z_distance=5,
     mount_speed=10,
     plunger_speed=5,
     sensor_threshold_pascals=40,
@@ -337,7 +336,6 @@ def _build_default_liquid_probe(
             "starting_mount_height", default.starting_mount_height
         ),
         max_z_distance=from_conf.get("max_z_distance", default.max_z_distance),
-        min_z_distance=from_conf.get("min_z_distance", default.min_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

@@ -130,7 +130,6 @@ class OutputOptions(int, Enum):
 class LiquidProbeSettings:
     starting_mount_height: float
     max_z_distance: float
-    min_z_distance: float
     mount_speed: float
     plunger_speed: float
     sensor_threshold_pascals: float