Merge branch 'edge' into plate_reader_csv_engine_file_provider

.github/workflows/analyses-snapshot-lint.yaml

@@ -27,7 +27,7 @@ jobs:
       - name: Setup Python
         uses: 'actions/setup-python@v5'
         with:
-          python-version: '3.13.0-rc.3'
+          python-version: '3.13.0'
           cache: 'pipenv'
           cache-dependency-path: analyses-snapshot-testing/Pipfile.lock
       - name: Setup

.github/workflows/analyses-snapshot-test.yaml

@@ -78,7 +78,7 @@ jobs:
       - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: '3.13.0-rc.3'
+          python-version: '3.13.0'
           cache: 'pipenv'
           cache-dependency-path: analyses-snapshot-testing/Pipfile.lock
 

abr-testing/abr_testing/automation/google_sheets_tool.py

@@ -172,7 +172,15 @@ def update_cell(
         self, sheet_title: str, row: int, column: int, single_data: Any
     ) -> Tuple[int, int, Any]:
         """Update ONE individual cell according to a row and column."""
-        self.spread_sheet.worksheet(sheet_title).update_cell(row, column, single_data)
+        try:
+            self.spread_sheet.worksheet(sheet_title).update_cell(
+                row, column, single_data
+            )
+        except gspread.exceptions.APIError:
+            t.sleep(30)
+            self.spread_sheet.worksheet(sheet_title).update_cell(
+                row, column, single_data
+            )
         return row, column, single_data
 
     def get_all_data(

abr-testing/abr_testing/data_collection/abr_google_drive.py

@@ -60,7 +60,7 @@ def create_data_dictionary(
             print(f"Run {run_id} is incomplete. Skipping run.")
             continue
         if run_id in runs_to_save:
-            print("started reading run.")
+            print(f"started reading run {run_id}.")
             robot = file_results.get("robot_name")
             protocol_name = file_results["protocol"]["metadata"].get("protocolName", "")
             software_version = file_results.get("API_Version", "")
@@ -114,7 +114,9 @@ def create_data_dictionary(
                 tc_dict = read_robot_logs.thermocycler_commands(file_results)
                 hs_dict = read_robot_logs.hs_commands(file_results)
                 tm_dict = read_robot_logs.temperature_module_commands(file_results)
-                pipette_dict = read_robot_logs.instrument_commands(file_results)
+                pipette_dict = read_robot_logs.instrument_commands(
+                    file_results, labware_name="opentrons_tough_pcr_auto_sealing_lid"
+                )
                 plate_reader_dict = read_robot_logs.plate_reader_commands(
                     file_results, hellma_plate_standards
                 )

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -526,7 +526,10 @@ def get_run_error_info_from_robot(
     # TODO: make argument or see if I can get rid of with using board_id.
     project_key = "RABR"
     print(robot)
-    parent_key = project_key + "-" + robot.split("ABR")[1]
+    try:
+        parent_key = project_key + "-" + robot.split("ABR")[1]
+    except IndexError:
+        parent_key = ""
 
     # Grab all previous issues
     all_issues = ticket.issues_on_board(project_key)

abr-testing/abr_testing/data_collection/read_robot_logs.py

@@ -9,7 +9,7 @@
 from datetime import datetime
 import os
 from abr_testing.data_collection.error_levels import ERROR_LEVELS_PATH
-from typing import List, Dict, Any, Tuple, Set
+from typing import List, Dict, Any, Tuple, Set, Optional
 import time as t
 import json
 import requests
@@ -107,7 +107,44 @@ def count_command_in_run_data(
     return total_command, avg_time
 
 
-def instrument_commands(file_results: Dict[str, Any]) -> Dict[str, float]:
+def identify_labware_ids(
+    file_results: Dict[str, Any], labware_name: Optional[str]
+) -> List[str]:
+    """Determine what type of labware is being picked up."""
+    if labware_name:
+        labwares = file_results.get("labware", "")
+        list_of_labware_ids = []
+        if len(labwares) > 1:
+            for labware in labwares:
+                load_name = labware["loadName"]
+                if load_name == labware_name:
+                    labware_id = labware["id"]
+                    list_of_labware_ids.append(labware_id)
+    return list_of_labware_ids
+
+
+def match_pipette_to_action(
+    command_dict: Dict[str, Any],
+    commandTypes: List[str],
+    right_pipette: Optional[str],
+    left_pipette: Optional[str],
+) -> Tuple[int, int]:
+    """Match pipette id to id in command."""
+    right_pipette_add = 0
+    left_pipette_add = 0
+    for command in commandTypes:
+        command_type = command_dict["commandType"]
+        command_pipette = command_dict.get("pipetteId", "")
+        if command_type == command and command_pipette == right_pipette:
+            right_pipette_add = 1
+        elif command_type == command and command_pipette == left_pipette:
+            left_pipette_add = 1
+    return left_pipette_add, right_pipette_add
+
+
+def instrument_commands(
+    file_results: Dict[str, Any], labware_name: Optional[str]
+) -> Dict[str, float]:
     """Count number of pipette and gripper commands per run."""
     pipettes = file_results.get("pipettes", "")
     commandData = file_results.get("commands", "")
@@ -120,38 +157,44 @@ def instrument_commands(file_results: Dict[str, Any]) -> Dict[str, float]:
     right_pipette_id = ""
     left_pipette_id = ""
     gripper_pickups = 0.0
+    gripper_labware_of_interest = 0.0
     avg_liquid_probe_time_sec = 0.0
+    list_of_labware_ids = identify_labware_ids(file_results, labware_name)
     # Match pipette mount to id
     for pipette in pipettes:
         if pipette["mount"] == "right":
             right_pipette_id = pipette["id"]
         elif pipette["mount"] == "left":
             left_pipette_id = pipette["id"]
     for command in commandData:
-        commandType = command["commandType"]
-        # Count tip pick ups
-        if commandType == "pickUpTip":
-            if command["params"].get("pipetteId", "") == right_pipette_id:
-                right_tip_pick_up += 1
-            elif command["params"].get("pipetteId", "") == left_pipette_id:
-                left_tip_pick_up += 1
+        # Count pick ups
+        single_left_pickup, single_right_pickup = match_pipette_to_action(
+            command, ["pickUpTip"], right_pipette_id, left_pipette_id
+        )
+        right_tip_pick_up += single_right_pickup
+        left_tip_pick_up += single_left_pickup
         # Count aspirates
-        elif commandType == "aspirate":
-            if command["params"].get("pipetteId", "") == right_pipette_id:
-                right_aspirate += 1
-            elif command["params"].get("pipetteId", "") == left_pipette_id:
-                left_aspirate += 1
+        single_left_aspirate, single_right_aspirate = match_pipette_to_action(
+            command, ["aspirate"], right_pipette_id, left_pipette_id
+        )
+        right_aspirate += single_right_aspirate
+        left_aspirate += single_left_aspirate
         # count dispenses/blowouts
-        elif commandType == "dispense" or commandType == "blowout":
-            if command["params"].get("pipetteId", "") == right_pipette_id:
-                right_dispense += 1
-            elif command["params"].get("pipetteId", "") == left_pipette_id:
-                left_dispense += 1
-        elif (
+        single_left_dispense, single_right_dispense = match_pipette_to_action(
+            command, ["blowOut", "dispense"], right_pipette_id, left_pipette_id
+        )
+        right_dispense += single_right_dispense
+        left_dispense += single_left_dispense
+        # count gripper actions
+        commandType = command["commandType"]
+        if (
             commandType == "moveLabware"
             and command["params"]["strategy"] == "usingGripper"
         ):
             gripper_pickups += 1
+            labware_moving = command["params"]["labwareId"]
+            if labware_moving in list_of_labware_ids:
+                gripper_labware_of_interest += 1
     liquid_probes, avg_liquid_probe_time_sec = count_command_in_run_data(
         commandData, "liquidProbe", True
     )
@@ -163,6 +206,7 @@ def instrument_commands(file_results: Dict[str, Any]) -> Dict[str, float]:
         "Right Pipette Total Aspirates": right_aspirate,
         "Right Pipette Total Dispenses": right_dispense,
         "Gripper Pick Ups": gripper_pickups,
+        f"Gripper Pick Ups of {labware_name}": gripper_labware_of_interest,
         "Total Liquid Probes": liquid_probes,
         "Average Liquid Probe Time (sec)": avg_liquid_probe_time_sec,
     }
@@ -178,11 +222,12 @@ def plate_reader_commands(
     initialize_count: int = 0
     read = "no"
     final_result = {}
-    # Count Number of Reads
+    read_num = 0
+    # Count Number of Reads per measure mode
     read_count, avg_read_time = count_command_in_run_data(
         commandData, "absorbanceReader/read", True
     )
-    # Count Number of Initializations
+    # Count Number of Initializations per measure mode
     initialize_count, avg_initialize_time = count_command_in_run_data(
         commandData, "absorbanceReader/initialize", True
     )
@@ -198,28 +243,37 @@ def plate_reader_commands(
             read = "yes"
         elif read == "yes" and commandType == "comment":
             result = command["params"].get("message", "")
-            wavelength = result.split("result: {")[1].split(":")[0]
-            wavelength_str = wavelength + ": "
-            rest_of_string = result.split(wavelength_str)[1][:-1]
-            result_dict = eval(rest_of_string)
-            result_ndarray = plate_reader.convert_read_dictionary_to_array(result_dict)
-            for item in hellma_plate_standards:
-                wavelength_of_interest = item["wavelength"]
-                if str(wavelength) == str(wavelength_of_interest):
-                    error_cells = plate_reader.check_byonoy_data_accuracy(
-                        result_ndarray, item, False
-                    )
-                    if len(error_cells[0]) > 0:
-                        percent = (96 - len(error_cells)) / 96 * 100
-                        for cell in error_cells:
-                            print("FAIL: Cell " + str(cell) + " out of accuracy spec.")
-                    else:
-                        percent = 100
-                        print(
-                            f"PASS: {wavelength_of_interest} meet accuracy specification"
+            formatted_result = result.split("result: ")[1]
+            result_dict = eval(formatted_result)
+            result_dict_keys = list(result_dict.keys())
+            if len(result_dict_keys) > 1:
+                read_type = "multi"
+            else:
+                read_type = "single"
+            for wavelength in result_dict_keys:
+                one_wavelength_dict = result_dict.get(wavelength)
+                result_ndarray = plate_reader.convert_read_dictionary_to_array(
+                    one_wavelength_dict
+                )
+                for item in hellma_plate_standards:
+                    wavelength_of_interest = item["wavelength"]
+                    if str(wavelength) == str(wavelength_of_interest):
+                        error_cells = plate_reader.check_byonoy_data_accuracy(
+                            result_ndarray, item, False
                         )
-                    final_result[wavelength] = percent
-                    input("###########################")
+                        if len(error_cells[0]) > 0:
+                            percent = (96 - len(error_cells)) / 96 * 100
+                            for cell in error_cells:
+                                print(
+                                    "FAIL: Cell " + str(cell) + " out of accuracy spec."
+                                )
+                        else:
+                            percent = 100
+                            print(
+                                f"PASS: {wavelength_of_interest} meet accuracy specification"
+                            )
+                        final_result[read_type, wavelength, read_num] = percent
+                        read_num += 1
             read = "no"
     plate_dict = {
         "Plate Reader # of Reads": read_count,
@@ -372,7 +426,10 @@ def thermocycler_commands(file_results: Dict[str, Any]) -> Dict[str, float]:
             or commandType == "thermocycler/closeLid"
         ):
             lid_engagements += 1
-        if commandType == "thermocycler/setTargetBlockTemperature":
+        if (
+            commandType == "thermocycler/setTargetBlockTemperature"
+            and command["status"] != "queued"
+        ):
             block_temp = command["params"]["celsius"]
             block_temp_changes += 1
             block_on_time = datetime.strptime(
@@ -502,7 +559,10 @@ def get_error_info(file_results: Dict[str, Any]) -> Dict[str, Any]:
         error_code = error_details.get("errorCode", "")
         error_instrument = error_details.get("detail", "")
     # Determine error level
-    error_level = error_levels.get(error_code, "4")
+    if end_run_errors > 0:
+        error_level = error_levels.get(error_code, "4")
+    else:
+        error_level = ""
     # Create dictionary with all error descriptions
     error_dict = {
         "Total Recoverable Error(s)": total_recoverable_errors,

abr-testing/protocol_simulation/__init__.py

@@ -0,0 +1 @@
+"""The package holding code for simulating protocols."""