Merge branch 'edge' into opentrons-ai-client-review

abr-testing/abr_testing/automation/google_drive_tool.py

@@ -56,6 +56,8 @@ def list_folder(self, delete: Any = False, folder: bool = False) -> Set[str]:
                     else ""  # type: ignore
                     if self.parent_folder
                     else None,
+                    supportsAllDrives=True,
+                    includeItemsFromAllDrives=True,
                     pageSize=1000,
                     fields="nextPageToken, files(id, name, mimeType)",
                     pageToken=page_token,

abr-testing/abr_testing/data_collection/abr_google_drive.py

@@ -37,12 +37,13 @@ def create_data_dictionary(
     plate: str,
     accuracy: Any,
     hellma_plate_standards: List[Dict[str, Any]],
-) -> Tuple[List[List[Any]], List[str], List[List[Any]], List[str]]:
+) -> Tuple[List[List[Any]], List[str], List[List[Any]], List[str], List[List[Any]]]:
     """Pull data from run files and format into a dictionary."""
     runs_and_robots: List[Any] = []
     runs_and_lpc: List[Dict[str, Any]] = []
     headers: List[str] = []
     headers_lpc: List[str] = []
+    list_of_heights: List[List[Any]] = [[], [], [], [], [], [], [], []]
     for filename in os.listdir(storage_directory):
         file_path = os.path.join(storage_directory, filename)
         if file_path.endswith(".json"):
@@ -120,6 +121,9 @@ def create_data_dictionary(
                 plate_reader_dict = read_robot_logs.plate_reader_commands(
                     file_results, hellma_plate_standards
                 )
+                list_of_heights = read_robot_logs.liquid_height_commands(
+                    file_results, list_of_heights
+                )
                 notes = {"Note1": "", "Jira Link": issue_url}
                 plate_measure = {
                     "Plate Measured": plate,
@@ -155,7 +159,13 @@ def create_data_dictionary(
     print(f"Number of runs read: {num_of_runs_read}")
     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
+    return (
+        transposed_runs_and_robots,
+        headers,
+        transposed_runs_and_lpc,
+        headers_lpc,
+        list_of_heights,
+    )
 
 
 def run(
@@ -173,7 +183,8 @@ def run(
         credentials_path, google_sheet_name, 0
     )
     # Get run ids on google sheet
-    run_ids_on_gs = set(google_sheet.get_column(2))
+    run_ids_on_gs: Set[str] = set(google_sheet.get_column(2))
+
     # Get robots on google sheet
     # Uploads files that are not in google drive directory
     google_drive.upload_missing_files(storage_directory)
@@ -191,6 +202,7 @@ def run(
         headers,
         transposed_runs_and_lpc,
         headers_lpc,
+        list_of_heights,
     ) = create_data_dictionary(
         missing_runs_from_gs,
         storage_directory,
@@ -201,7 +213,15 @@ def run(
     )
     start_row = google_sheet.get_index_row() + 1
     google_sheet.batch_update_cells(transposed_runs_and_robots, "A", start_row, "0")
-
+    # Record Liquid Heights Found
+    google_sheet_ldf = google_sheets_tool.google_sheet(
+        credentials_path, google_sheet_name, 2
+    )
+    google_sheet_ldf.get_row(1)
+    start_row_lhd = google_sheet_ldf.get_index_row() + 1
+    google_sheet_ldf.batch_update_cells(
+        list_of_heights, "A", start_row_lhd, "2075262446"
+    )
     # Add LPC to google sheet
     google_sheet_lpc = google_sheets_tool.google_sheet(credentials_path, "ABR-LPC", 0)
     start_row_lpc = google_sheet_lpc.get_index_row() + 1

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -602,6 +602,7 @@ def get_run_error_info_from_robot(
             headers,
             runs_and_lpc,
             headers_lpc,
+            list_of_heights,
         ) = abr_google_drive.create_data_dictionary(
             run_id,
             error_folder_path,
@@ -614,6 +615,15 @@ def get_run_error_info_from_robot(
         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")
+        # Record Liquid Heights Found
+        google_sheet_ldf = google_sheets_tool.google_sheet(
+            credentials_path, google_sheet_name, 4
+        )
+        start_row_lhd = google_sheet_ldf.get_index_row() + 1
+        google_sheet_ldf.batch_update_cells(
+            list_of_heights, "A", start_row_lhd, "1795535088"
+        )
+        print("wrote liquid heights found.")
         # Add LPC to google sheet
         google_sheet_lpc = google_sheets_tool.google_sheet(
             credentials_path, "ABR-LPC", 0

abr-testing/abr_testing/data_collection/read_robot_logs.py

@@ -213,6 +213,42 @@ def instrument_commands(
     return pipette_dict
 
 
+def liquid_height_commands(
+    file_results: Dict[str, Any], all_heights_list: List[List[Any]]
+) -> List[List[Any]]:
+    """Record found liquid heights during a protocol."""
+    commandData = file_results.get("commands", "")
+    robot = file_results.get("robot_name", "")
+    run_id = file_results.get("run_id", "")
+    for command in commandData:
+        commandType = command["commandType"]
+        if commandType == "comment":
+            result = command["params"].get("message", "")
+            try:
+                result_str = "'" + result.split("result: {")[1] + "'"
+                entries = result_str.split(", (")
+                comment_time = command["completedAt"]
+                for entry in entries:
+                    height = float(entry.split(": ")[1].split("'")[0].split("}")[0])
+                    labware_type = str(
+                        entry.split(",")[0].replace("'", "").replace("(", "")
+                    )
+                    well_location = str(entry.split(", ")[1].split(" ")[0])
+                    slot_location = str(entry.split("slot ")[1].split(")")[0])
+                    labware_name = str(entry.split("of ")[1].split(" on")[0])
+                    all_heights_list[0].append(robot)
+                    all_heights_list[1].append(run_id)
+                    all_heights_list[2].append(comment_time)
+                    all_heights_list[3].append(labware_type)
+                    all_heights_list[4].append(labware_name)
+                    all_heights_list[5].append(slot_location)
+                    all_heights_list[6].append(well_location)
+                    all_heights_list[7].append(height)
+            except (IndexError, ValueError):
+                continue
+    return all_heights_list
+
+
 def plate_reader_commands(
     file_results: Dict[str, Any], hellma_plate_standards: List[Dict[str, Any]]
 ) -> Dict[str, object]:

abr-testing/abr_testing/data_collection/single_run_log_reader.py

@@ -34,6 +34,7 @@
         header,
         runs_and_lpc,
         lpc_headers,
+        list_of_heights,
     ) = abr_google_drive.create_data_dictionary(
         run_ids_in_storage,
         run_log_file_path,
@@ -42,6 +43,7 @@
         "",
         hellma_plate_standards=file_values,
     )
+    print("list_of_heights not recorded.")
     transposed_list = list(zip(*runs_and_robots))
     # Adds Run to local csv
     sheet_location = os.path.join(run_log_file_path, "saved_data.csv")

abr-testing/abr_testing/protocols/active_protocols/11_Dynabeads_IP_Flex_96well_RIT.py

@@ -125,7 +125,7 @@ def run(ctx: ProtocolContext) -> None:
         "Wash": [{"well": wash, "volume": 750.0}],
         "Samples": [{"well": samples, "volume": 250.0}],
     }
-    flattened_wells = helpers.find_liquid_height_of_loaded_liquids(
+    helpers.find_liquid_height_of_loaded_liquids(
         ctx, liquid_vols_and_wells, p1000_single
     )
 
@@ -268,5 +268,6 @@ def discard(vol3: float, start: List[Well]) -> None:
         ctx.delay(minutes=MAG_DELAY_MIN)
         transfer_plate_to_plate(ELUTION_VOL * 1.1, working_cols, final_cols, 6)
         temp.deactivate()
-    flattened_wells.append(waste)
-    helpers.find_liquid_height_of_all_wells(ctx, p1000_single, flattened_wells)
+    end_wells_to_probe = [reagent_res["A1"], reagent_res["B1"], reagent_res["C1"]]
+    end_wells_to_probe.extend(wash_res.wells())
+    helpers.find_liquid_height_of_all_wells(ctx, p1000_single, end_wells_to_probe)

abr-testing/abr_testing/protocols/active_protocols/12_KAPA HyperPlus Library Prep.py

@@ -451,6 +451,10 @@ def tiptrack(rack: int, reuse_col: Optional[int], reuse: bool = False) -> None:
                 )
                 p200.pick_up_tip()
 
+    tiptrack(tip50, None, reuse=False)
+    p50.return_tip()
+    helpers.find_liquid_height_of_loaded_liquids(ctx, liquid_vols_and_wells, p50)
+
     def TipSwap(tipvol: int) -> None:
         """Tip swap."""
         if tipvol == 50:
@@ -1203,18 +1207,11 @@ def lib_cleanup_2() -> None:
         # Set Block Temp for Final Plate
         tc_mod.set_block_temperature(4)
 
-    tiptrack(tip50, None, reuse=False)
-    p50.return_tip()
-    probed_wells = helpers.find_liquid_height_of_loaded_liquids(
-        ctx, liquid_vols_and_wells, p50
-    )
-
     unused_lids, used_lids = Fragmentation(unused_lids, used_lids)
     unused_lids, used_lids = end_repair(unused_lids, used_lids)
     unused_lids, used_lids = index_ligation(unused_lids, used_lids)
     lib_cleanup()
     unused_lids, used_lids = lib_amplification(unused_lids, used_lids)
     lib_cleanup_2()
-    probed_wells.append(waste1_res)
-    probed_wells.append(waste2_res)
-    helpers.find_liquid_height_of_all_wells(ctx, p50, probed_wells)
+    end_probed_wells = [waste1_res, waste2_res]
+    helpers.find_liquid_height_of_all_wells(ctx, p50, end_probed_wells)

abr-testing/abr_testing/protocols/active_protocols/8_Illumina and Plate Reader.py

@@ -77,6 +77,7 @@ def plate_reader_actions(
     """Plate reader single and multi wavelength readings."""
     wavelengths = [450, 650]
     # Single Wavelength Readings
+    plate_reader.close_lid()
     for wavelength in wavelengths:
         plate_reader.initialize("single", [wavelength], reference_wavelength=wavelength)
         plate_reader.open_lid()
@@ -156,14 +157,13 @@ def run(protocol: ProtocolContext) -> None:
     p50 = protocol.load_instrument(
         "flex_8channel_50", "right", tip_racks=[tiprack_50_1, tiprack_50_2]
     )
-
-    plate_reader_actions(protocol, plate_reader, hellma_plate)
     # reagent
     AMPure = reservoir["A1"]
     SMB = reservoir["A2"]
 
     EtOH = reservoir["A4"]
     RSB = reservoir["A5"]
+
     Liquid_trash_well_1 = reservoir["A9"]
     Liquid_trash_well_2 = reservoir["A10"]
     Liquid_trash_well_3 = reservoir["A11"]
@@ -181,6 +181,8 @@ def run(protocol: ProtocolContext) -> None:
     ET2 = reagent_plate.wells_by_name()["A5"]
     PPC = reagent_plate.wells_by_name()["A6"]
     EPM = reagent_plate.wells_by_name()["A7"]
+    # Load Liquids
+    plate_reader_actions(protocol, plate_reader, hellma_plate)
 
     # tip and sample tracking
     if COLUMNS == 1:

abr-testing/abr_testing/protocols/active_protocols/9_Magmax_RNA_Cells_Flex.py

@@ -172,9 +172,7 @@ def run(ctx: ProtocolContext) -> None:
         "Stop": [{"well": stopreaction, "volume": stop_vol}],
     }
 
-    flattened_list_of_wells = helpers.find_liquid_height_of_loaded_liquids(
-        ctx, liquid_vols_and_wells, m1000
-    )
+    helpers.find_liquid_height_of_loaded_liquids(ctx, liquid_vols_and_wells, m1000)
 
     m1000.flow_rate.aspirate = 50
     m1000.flow_rate.dispense = 150
@@ -556,5 +554,6 @@ def elute(vol: float) -> None:
         )
     elute(elution_vol)
 
-    flattened_list_of_wells.append(waste_reservoir["A1"])
-    helpers.find_liquid_height_of_all_wells(ctx, m1000, flattened_list_of_wells)
+    end_list_of_wells_to_probe = [waste_reservoir["A1"], res1["A1"]]
+    end_list_of_wells_to_probe.extend(elution_samples_m)
+    helpers.find_liquid_height_of_all_wells(ctx, m1000, end_list_of_wells_to_probe)

abr-testing/abr_testing/tools/abr_scale.py

@@ -149,6 +149,7 @@ def get_most_recent_run_and_record(
         headers,
         runs_and_lpc,
         headers_lpc,
+        list_of_heights,
     ) = abr_google_drive.create_data_dictionary(
         most_recent_run_id,
         storage_directory,
@@ -163,6 +164,15 @@ def get_most_recent_run_and_record(
     start_row = google_sheet_abr_data.get_index_row() + 1
     google_sheet_abr_data.batch_update_cells(runs_and_robots, "A", start_row, "0")
     print("Wrote run to ABR-run-data")
+    # Add liquid height detection to abr sheet
+    google_sheet_ldf = google_sheets_tool.google_sheet(
+        credentials_path, "ABR-run-data", 4
+    )
+    start_row_lhd = google_sheet_ldf.get_index_row() + 1
+    google_sheet_ldf.batch_update_cells(
+        list_of_heights, "A", start_row_lhd, "1795535088"
+    )
+    print("Wrote found liquid heights to ABR-run-data")
     # Add LPC to google sheet
     google_sheet_lpc = google_sheets_tool.google_sheet(
         credentials_path, "ABR-LPC", tab_number=0