Release v1.2.3 (#640)

- Add post stiffness display under plate barcode display. - Add biphasic stim check. - Update itles of live view screens. - Handle network errors when logging in. - Fix dropdown overflow styling. - Barcode change warning now displays in the correct position. - Barcode change while stimulating now correctly requires another stim configuration check before restarting stimulation. - Can no longer manually edit barcodes while stimulating.
CuriBio · Apr 30, 2024 · 4cbbeee · 4cbbeee
1 parent 2903c00
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,12 +1,34 @@
 Changelog for Mantarray Desktop App
 ===================================
 
-1.2.2 (unreleased)
+1.2.3 (unreleased)
 ------------------
 
 Added:
 ^^^^^^
-- Ability to view changelog.
+- Post stiffness display under plate barcode display.
+- Biphasic stim check.
+
+Changed:
+^^^^^^^^
+- Titles of live view screens.
+
+Fixed:
+^^^^^^
+- Handle network errors when logging in.
+- Dropdown overflow styling.
+- Barcode change warning now displays in the correct position.
+- Barcode change while stimulating now correctly requires another stim configuration check before restarting stimulation.
+- Can no longer manually edit barcodes while stimulating.
+
+
+1.2.2 (2024-02-06)
+------------------
+
+Added:
+^^^^^^
+- User-defined metadata can be included in recording files.
+- Ability to view MA controller changelog.
 
 Changed:
 ^^^^^^^^

diff --git a/controller/src/mantarray_desktop_app/constants.py b/controller/src/mantarray_desktop_app/constants.py
@@ -399,6 +399,7 @@ class StimulatorCircuitStatuses(IntEnum):
     OPEN = 1
     SHORT = 2
     ERROR = 3
+    NOT_CHECKED = 4
 
 
 class StimProtocolStatuses(IntEnum):

diff --git a/controller/src/mantarray_desktop_app/main_process/process_monitor.py b/controller/src/mantarray_desktop_app/main_process/process_monitor.py
@@ -517,10 +517,12 @@ def _check_and_handle_instrument_comm_to_main_queue(self) -> None:
             elif command == "start_stim_checks":
                 key = "stimulator_circuit_statuses"
                 stimulator_circuit_statuses = communication[key]
-                self._values_to_share_to_server[key] = stimulator_circuit_statuses
-                self._queue_websocket_message(
-                    {"data_type": key, "data_json": json.dumps(stimulator_circuit_statuses)}
-                )
+                status_combined = {
+                    well_idx: list(StimulatorCircuitStatuses)[max(statuses.values()) + 1].name.lower()
+                    for well_idx, statuses in stimulator_circuit_statuses.items()
+                }
+                self._values_to_share_to_server[key] = status_combined
+                self._queue_websocket_message({"data_type": key, "data_json": json.dumps(status_combined)})
         elif communication_type == "board_connection_status_change":
             board_idx = communication["board_index"]
             self._values_to_share_to_server["in_simulation_mode"] = not communication["is_connected"]

diff --git a/controller/src/mantarray_desktop_app/main_process/server.py b/controller/src/mantarray_desktop_app/main_process/server.py
@@ -396,6 +396,8 @@ def login_user() -> Response:
         auth_response = validate_user_credentials(request.args)
     except LoginFailedError as e:
         return Response(json.dumps(str(e)), status=f"401 {repr(e)}")
+    except requests.exceptions.ConnectionError:  # pragma: no cover
+        return Response(json.dumps({"err": "network"}), mimetype="application/json")
 
     queue_command_to_main(
         {

diff --git a/controller/src/mantarray_desktop_app/simulators/mc_simulator.py b/controller/src/mantarray_desktop_app/simulators/mc_simulator.py
@@ -498,7 +498,7 @@ def _process_main_module_command(self, comm_from_pc: bytes) -> None:
             # Tanner (4/8/22): currently assuming that stim checks will take a negligible amount of time
             for module_readings in self._adc_readings:
                 status = convert_adc_readings_to_circuit_status(*module_readings)
-                response_body += struct.pack("<HHB", *module_readings, status)
+                response_body += struct.pack("<HHB", *module_readings, status) * 2
         elif packet_type == SERIAL_COMM_SET_SAMPLING_PERIOD_PACKET_TYPE:
             response_body += self._update_sampling_period(comm_from_pc)
         elif packet_type == SERIAL_COMM_START_DATA_STREAMING_PACKET_TYPE:

diff --git a/controller/src/mantarray_desktop_app/sub_processes/mc_comm.py b/controller/src/mantarray_desktop_app/sub_processes/mc_comm.py
@@ -83,7 +83,6 @@
 from ..constants import SERIAL_COMM_STOP_STIM_PACKET_TYPE
 from ..constants import STIM_COMPLETE_SUBPROTOCOL_IDX
 from ..constants import STIM_MODULE_ID_TO_WELL_IDX
-from ..constants import StimulatorCircuitStatuses
 from ..constants import STM_VID
 from ..exceptions import FirmwareAndSoftwareNotCompatibleError
 from ..exceptions import FirmwareGoingDormantError
@@ -851,16 +850,22 @@ def _process_comm_from_instrument(self, packet_type: int, packet_payload: bytes)
             elif prev_command["command"] == "start_stim_checks":
                 stimulator_check_dict = convert_stimulator_check_bytes_to_dict(response_data)
 
-                stimulator_circuit_statuses: Dict[int, str] = {}
-                adc_readings: Dict[int, Tuple[int, int]] = {}
-
-                for module_id, (adc8, adc9, status_int) in enumerate(zip(*stimulator_check_dict.values())):
+                stimulator_circuit_statuses: Dict[int, Dict[str, str]] = {}
+                adc_readings: Dict[int, Dict[str, Tuple[int, int]]] = {}
+
+                for module_id, (
+                    adc8_pos,
+                    adc9_pos,
+                    status_int_pos,
+                    adc8_neg,
+                    adc9_neg,
+                    status_int_neg,
+                ) in enumerate(zip(*stimulator_check_dict.values())):
                     well_idx = STIM_MODULE_ID_TO_WELL_IDX[module_id]
                     if well_idx not in prev_command["well_indices"]:
                         continue
-                    status_str = list(StimulatorCircuitStatuses)[status_int + 1].name.lower()
-                    stimulator_circuit_statuses[well_idx] = status_str
-                    adc_readings[well_idx] = (adc8, adc9)
+                    stimulator_circuit_statuses[well_idx] = {"pos": status_int_pos, "neg": status_int_neg}
+                    adc_readings[well_idx] = {"pos": (adc8_pos, adc9_pos), "neg": (adc8_neg, adc9_neg)}
 
                 prev_command["stimulator_circuit_statuses"] = stimulator_circuit_statuses
                 prev_command["adc_readings"] = adc_readings

diff --git a/controller/src/mantarray_desktop_app/utils/serial_comm.py b/controller/src/mantarray_desktop_app/utils/serial_comm.py
@@ -83,11 +83,7 @@ def _get_checksum_bytes(packet: bytes) -> bytes:
     return crc32(packet).to_bytes(SERIAL_COMM_CHECKSUM_LENGTH_BYTES, byteorder="little")
 
 
-def create_data_packet(
-    timestamp: int,
-    packet_type: int,
-    packet_payload: bytes = bytes(0),
-) -> bytes:
+def create_data_packet(timestamp: int, packet_type: int, packet_payload: bytes = bytes(0)) -> bytes:
     """Create a data packet to send to the PC."""
     packet_base = convert_to_timestamp_bytes(timestamp) + bytes([packet_type])
     packet_remainder_size = len(packet_base) + len(packet_payload) + SERIAL_COMM_CHECKSUM_LENGTH_BYTES
@@ -104,10 +100,7 @@ def create_data_packet(
 
 def validate_checksum(comm_from_pc: bytes) -> bool:
     expected_checksum = crc32(comm_from_pc[:-SERIAL_COMM_CHECKSUM_LENGTH_BYTES])
-    actual_checksum = int.from_bytes(
-        comm_from_pc[-SERIAL_COMM_CHECKSUM_LENGTH_BYTES:],
-        byteorder="little",
-    )
+    actual_checksum = int.from_bytes(comm_from_pc[-SERIAL_COMM_CHECKSUM_LENGTH_BYTES:], byteorder="little")
     return actual_checksum == expected_checksum
 
 
@@ -225,15 +218,16 @@ def get_serial_comm_timestamp() -> int:
 
 
 def convert_stimulator_check_bytes_to_dict(stimulator_check_bytes: bytes) -> Dict[str, List[int]]:
-    stimulator_checks_as_ints = struct.unpack("<" + "HHB" * 24, stimulator_check_bytes)
+    stimulator_checks_as_ints = struct.unpack("<" + "HHB" * 24 * 2, stimulator_check_bytes)
     # convert to lists of adc8, adc9, and status where the index of each list is the module id. Only creating an array here to reshape easily
     stimulator_checks_list = (
         np.array(stimulator_checks_as_ints, copy=False)
-        .reshape((3, len(stimulator_checks_as_ints) // 3), order="F")
+        .reshape((6, len(stimulator_checks_as_ints) // 6), order="F")
         .tolist()
     )
     stimulator_checks_dict = {
-        key: stimulator_checks_list[i] for i, key in enumerate(["adc8", "adc9", "status"])
+        key: stimulator_checks_list[i]
+        for i, key in enumerate(["adc8_pos", "adc9_pos", "status_pos", "adc8_neg", "adc9_neg", "status_neg"])
     }
     return stimulator_checks_dict
 

diff --git a/controller/tests/mc_comm/test_stimulation.py b/controller/tests/mc_comm/test_stimulation.py
@@ -18,7 +18,6 @@
 from mantarray_desktop_app.constants import SERIAL_COMM_CHECKSUM_LENGTH_BYTES
 from mantarray_desktop_app.constants import SERIAL_COMM_PAYLOAD_INDEX
 from mantarray_desktop_app.constants import STIM_MODULE_ID_TO_WELL_IDX
-from mantarray_desktop_app.constants import StimulatorCircuitStatuses
 from mantarray_desktop_app.simulators import mc_simulator
 from mantarray_desktop_app.utils.serial_comm import convert_adc_readings_to_circuit_status
 from mantarray_desktop_app.utils.stimulation import get_subprotocol_dur_us
@@ -52,11 +51,7 @@
 ]
 
 
-def set_stimulation_protocols(
-    mc_fixture,
-    simulator,
-    stim_info,
-):
+def set_stimulation_protocols(mc_fixture, simulator, stim_info):
     mc_process = mc_fixture["mc_process"]
     from_main_queue = mc_fixture["board_queues"][0][0]
     to_main_queue = mc_fixture["board_queues"][0][1]
@@ -132,12 +127,11 @@ def test_McCommunicationProcess__processes_start_stim_checks_command__and_sends_
     for well_idx in test_well_indices:
         well_readings = adc_readings[well_idx]
         status_int = convert_adc_readings_to_circuit_status(*well_readings)
-        status = list(StimulatorCircuitStatuses)[status_int + 1].name.lower()
-        stimulator_circuit_statuses[well_idx] = status
+        stimulator_circuit_statuses[well_idx] = {"pos": status_int, "neg": status_int}
     assert msg_to_main["stimulator_circuit_statuses"] == stimulator_circuit_statuses
 
     assert msg_to_main["adc_readings"] == {
-        well_idx: adc_reading
+        well_idx: {"pos": adc_reading, "neg": adc_reading}
         for well_idx, adc_reading in enumerate(adc_readings)
         if well_idx in test_well_indices
     }
@@ -304,13 +298,7 @@ def test_McCommunicationProcess__handles_stimulation_status_comm_from_instrument
                 "protocol_id": "A",
                 "stimulation_type": "C",
                 "run_until_stopped": False,
-                "subprotocols": [
-                    {
-                        "type": "loop",
-                        "num_iterations": 1,
-                        "subprotocols": [test_subprotocol],
-                    }
-                ],
+                "subprotocols": [{"type": "loop", "num_iterations": 1, "subprotocols": [test_subprotocol]}],
             }
         ],
         "protocol_assignments": {
@@ -389,11 +377,7 @@ def test_McCommunicationProcess__handles_stimulation_status_comm_from_instrument
                 "stimulation_type": "V",
                 "run_until_stopped": False,
                 "subprotocols": [
-                    {
-                        "type": "loop",
-                        "num_iterations": 1,
-                        "subprotocols": [test_subprotocol] * 2,
-                    }
+                    {"type": "loop", "num_iterations": 1, "subprotocols": [test_subprotocol] * 2}
                 ],
             }
         ],
@@ -518,13 +502,7 @@ def test_McCommunicationProcess__handles_stimulation_status_comm_from_instrument
                 "protocol_id": "A",
                 "stimulation_type": "C",
                 "run_until_stopped": False,
-                "subprotocols": [
-                    {
-                        "type": "loop",
-                        "num_iterations": 1,
-                        "subprotocols": [test_subprotocol],
-                    }
-                ],
+                "subprotocols": [{"type": "loop", "num_iterations": 1, "subprotocols": [test_subprotocol]}],
             }
         ],
         "protocol_assignments": {
@@ -640,11 +618,7 @@ def test_McCommunicationProcess__protocols_can_be_updated_and_stimulation_can_be
                 "stimulation_type": "C",
                 "run_until_stopped": False,
                 "subprotocols": [
-                    {
-                        "type": "loop",
-                        "num_iterations": 1,
-                        "subprotocols": [test_first_subprotocol],
-                    }
+                    {"type": "loop", "num_iterations": 1, "subprotocols": [test_first_subprotocol]}
                 ],
             }
         ],
@@ -721,24 +695,14 @@ def test_McCommunicationProcess__stim_packets_sent_to_file_writer_after_restarti
                 "protocol_id": "A",
                 "stimulation_type": "C",
                 "run_until_stopped": True,
-                "subprotocols": [
-                    {
-                        "type": "loop",
-                        "num_iterations": 1,
-                        "subprotocols": [test_subprotocol],
-                    }
-                ],
+                "subprotocols": [{"type": "loop", "num_iterations": 1, "subprotocols": [test_subprotocol]}],
             },
             {
                 "protocol_id": "B",
                 "stimulation_type": "C",
                 "run_until_stopped": True,
                 "subprotocols": [
-                    {
-                        "type": "loop",
-                        "num_iterations": 1,
-                        "subprotocols": [get_random_stim_pulse()],
-                    }
+                    {"type": "loop", "num_iterations": 1, "subprotocols": [get_random_stim_pulse()]}
                 ],
             },
         ],

diff --git a/controller/tests/process_monitor/test_process_monitor.py b/controller/tests/process_monitor/test_process_monitor.py
@@ -1935,8 +1935,18 @@ def test_MantarrayProcessesMonitor__passes_stim_status_check_results_from_mc_com
     queue_to_server_ws = test_process_manager.queue_container.to_websocket
 
     test_wells = range(randint(0, 3), randint(20, 24))
-    possible_stim_statuses = [member.name.lower() for member in StimulatorCircuitStatuses]
-    stim_check_results = {well_idx: choice(possible_stim_statuses) for well_idx in test_wells}
+    stim_check_results = {
+        well_idx: {
+            "pos": choice(list(StimulatorCircuitStatuses)),
+            "neg": choice(list(StimulatorCircuitStatuses)),
+        }
+        for well_idx in test_wells
+    }
+
+    combined_results = {
+        well_idx: list(StimulatorCircuitStatuses)[max(res["pos"], res["neg"]) + 1].name.lower()
+        for well_idx, res in stim_check_results.items()
+    }
 
     # values in this dict don't matter, just the keys
     adc_readings = {well_idx: None for well_idx in test_wells}
@@ -1956,13 +1966,13 @@ def test_MantarrayProcessesMonitor__passes_stim_status_check_results_from_mc_com
         copy.deepcopy(test_comm), instrument_comm_to_main
     )
     invoke_process_run_and_check_errors(monitor_thread)
-    assert shared_values_dict["stimulator_circuit_statuses"] == stim_check_results
+    assert shared_values_dict["stimulator_circuit_statuses"] == combined_results
 
     confirm_queue_is_eventually_of_size(queue_to_server_ws, 1)
     ws_message = queue_to_server_ws.get(timeout=QUEUE_CHECK_TIMEOUT_SECONDS)
     assert ws_message == {
         "data_type": "stimulator_circuit_statuses",
-        "data_json": json.dumps(stim_check_results),
+        "data_json": json.dumps(combined_results),
     }
 
     # convert all well idxs to well names