feat(abr-testing): add plate reader + tartrazine protocol (#16920)

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# Overview

Adds protocol that uses tartrazine and takes plate reader measurements

## Test Plan and Hands on Testing

- passed simulate test and runs on robot

## Changelog

- removed OT3 ABR Normalize with Tubes protocol
- added plate reader + tartrazine protocol

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---------

Co-authored-by: CaseyBatten <[email protected]>

abr-testing/abr_testing/data_collection/abr_google_drive.py

@@ -44,6 +44,7 @@ def create_data_dictionary(
     headers: List[str] = []
     headers_lpc: List[str] = []
     list_of_heights: List[List[Any]] = [[], [], [], [], [], [], [], []]
+    hellma_plate_orientation = False  # default hellma plate is not rotated.
     for filename in os.listdir(storage_directory):
         file_path = os.path.join(storage_directory, filename)
         if file_path.endswith(".json"):
@@ -67,6 +68,10 @@ def create_data_dictionary(
         if run_id in runs_to_save:
             print(f"started reading run {run_id}.")
             robot = file_results.get("robot_name")
+            parameters = file_results.get("runTimeParameters", "")
+            for parameter in parameters:
+                if parameter["displayName"] == "Hellma Plate Orientation":
+                    hellma_plate_orientation = bool(parameter["value"])
             protocol_name = file_results["protocol"]["metadata"].get("protocolName", "")
             software_version = file_results.get("API_Version", "")
             left_pipette = file_results.get("left", "")
@@ -123,7 +128,7 @@ def create_data_dictionary(
                     file_results, labware_name="opentrons_tough_pcr_auto_sealing_lid"
                 )
                 plate_reader_dict = read_robot_logs.plate_reader_commands(
-                    file_results, hellma_plate_standards
+                    file_results, hellma_plate_standards, hellma_plate_orientation
                 )
                 list_of_heights = read_robot_logs.liquid_height_commands(
                     file_results, list_of_heights

abr-testing/abr_testing/data_collection/read_robot_logs.py

@@ -250,7 +250,9 @@ def liquid_height_commands(
 
 
 def plate_reader_commands(
-    file_results: Dict[str, Any], hellma_plate_standards: List[Dict[str, Any]]
+    file_results: Dict[str, Any],
+    hellma_plate_standards: List[Dict[str, Any]],
+    orientation: bool,
 ) -> Dict[str, object]:
     """Plate Reader Command Counts."""
     commandData = file_results.get("commands", "")
@@ -279,38 +281,46 @@ def plate_reader_commands(
             read = "yes"
         elif read == "yes" and commandType == "comment":
             result = command["params"].get("message", "")
-            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
+            if "result:" in result:
+                plate_name = result.split("result:")[0]
+                formatted_result = result.split("result: ")[1]
+                print(formatted_result)
+                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"
+                if "hellma_plate" in plate_name:
+                    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
                         )
-                        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."
+                        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, orientation
                                 )
-                        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"
+                                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 spec."
+                                    )
+                                final_result[read_type, wavelength, read_num] = percent
+                                read_num += 1
+                else:
+                    final_result = result_dict
+                read = "no"
     plate_dict = {
         "Plate Reader # of Reads": read_count,
         "Plate Reader Avg Read Time (sec)": avg_read_time,

abr-testing/abr_testing/protocol_simulation/simulation_metrics.py

@@ -225,7 +225,11 @@ def parse_results_volume(
     else:
         print(f"Expected JSON object (dict) but got {type(json_data).__name__}.")
         commands = {}
-
+    hellma_plate_orientation = False
+    parameters = json_data.get("runTimeParameters", "")
+    for parameter in parameters:
+        if parameter["displayName"] == "Hellma Plate Orientation":
+            hellma_plate_orientation = bool(parameter["value"])
     start_time = datetime.fromisoformat(commands[0]["createdAt"])
     end_time = datetime.fromisoformat(commands[len(commands) - 1]["completedAt"])
     header = ["", "Protocol Name", "Date", "Time"]
@@ -283,7 +287,7 @@ def parse_results_volume(
         temp_module_dict = read_robot_logs.temperature_module_commands(json_data)
         thermo_cycler_dict = read_robot_logs.thermocycler_commands(json_data)
         plate_reader_dict = read_robot_logs.plate_reader_commands(
-            json_data, hellma_plate_standards
+            json_data, hellma_plate_standards, hellma_plate_orientation
         )
         instrument_dict = read_robot_logs.instrument_commands(
             json_data, labware_name=None
@@ -499,12 +503,12 @@ def check_params(protocol_path: str) -> str:
 def get_extra_files(protocol_file_path: str) -> tuple[str, List[Path]]:
     """Get supporting files for protocol simulation if needed."""
     params = check_params(protocol_file_path)
-    needs_files = input("Does your protocol utilize custom labware? (y/n): ")
+    needs_files = input("Does your protocol utilize custom labware? (Y/N): ")
     labware_files = []
-    if needs_files == "y":
+    if needs_files == "Y":
         num_labware = input("How many custom labware?: ")
         for labware_num in range(int(num_labware)):
-            path = input("Enter custom labware definition: ")
+            path = input("Enter custom labware definition path: ")
             labware_files.append(Path(path))
     return (params, labware_files)