added atc support for proflex backend (#702)

Co-authored-by: Rick Wierenga <rick_wierenga@icloud.com>

Author: xbtu2

pylabrobot/thermocycling/__init__.py

@@ -1,20 +1,7 @@
-"""This module contains the thermocycling related classes and functions."""
-
 from .backend import ThermocyclerBackend
 from .chatterbox import ThermocyclerChatterboxBackend
 from .opentrons import OpentronsThermocyclerModuleV1, OpentronsThermocyclerModuleV2
 from .opentrons_backend import OpentronsThermocyclerBackend
-from .proflex import ProflexBackend
 from .standard import Step
+from .thermo_fisher import *
 from .thermocycler import Thermocycler
-
-__all__ = [
-  "ThermocyclerBackend",
-  "ThermocyclerChatterboxBackend",
-  "Thermocycler",
-  "ProflexBackend",
-  "Step",
-  "OpentronsThermocyclerBackend",
-  "OpentronsThermocyclerModuleV1",
-  "OpentronsThermocyclerModuleV2",
-]

pylabrobot/thermocycling/thermo_fisher/__init__.py

@@ -0,0 +1,2 @@
+from .atc import ATCBackend
+from .proflex import ProflexBackend

pylabrobot/thermocycling/thermo_fisher/atc.py

@@ -0,0 +1,19 @@
+from pylabrobot.thermocycling.thermo_fisher.thermo_fisher_thermocycler import (
+  ThermoFisherThermocyclerBackend,
+)
+
+
+class ATCBackend(ThermoFisherThermocyclerBackend):
+  async def close_lid(self):
+    if self.bid != "31":
+      raise NotImplementedError("Lid control is only available for BID 31 (ATC)")
+    res = await self.send_command({"cmd": "lidclose"}, response_timeout=20, read_once=False)
+    if self._parse_scpi_response(res)["status"] != "OK":
+      raise ValueError("Failed to close lid")
+
+  async def open_lid(self):
+    if self.bid != "31":
+      raise NotImplementedError("Lid control is only available for BID 31 (ATC)")
+    res = await self.send_command({"cmd": "lidopen"}, response_timeout=20, read_once=False)
+    if self._parse_scpi_response(res)["status"] != "OK":
+      raise ValueError("Failed to open lid")

pylabrobot/thermocycling/thermo_fisher/proflex.py

@@ -0,0 +1,11 @@
+from pylabrobot.thermocycling.thermo_fisher.thermo_fisher_thermocycler import (
+  ThermoFisherThermocyclerBackend,
+)
+
+
+class ProflexBackend(ThermoFisherThermocyclerBackend):
+  async def open_lid(self):
+    raise NotImplementedError("Open lid command is not implemented for Proflex thermocycler")
+
+  async def close_lid(self):
+    raise NotImplementedError("Close lid command is not implemented for Proflex thermocycler")

pylabrobot/thermocycling/proflex_tests.py …mocycling/thermo_fisher/proflex_tests.pypylabrobot/thermocycling/proflex_tests.py renamed to pylabrobot/thermocycling/thermo_fisher/proflex_tests.py pylabrobot/thermocycling/proflex_tests.py renamed to pylabrobot/thermocycling/thermo_fisher/proflex_tests.py

@@ -2,8 +2,8 @@
 import unittest
 import unittest.mock
 
-from pylabrobot.thermocycling.proflex import ProflexBackend
 from pylabrobot.thermocycling.standard import Protocol, Stage, Step
+from pylabrobot.thermocycling.thermo_fisher.proflex import ProflexBackend
 
 
 class TestProflexBackend(unittest.IsolatedAsyncioTestCase):
@@ -168,7 +168,7 @@ async def test_run_protocol(self):
     -cover= 105
     -mode= Fast
     -coverEnabled= On
-    -notes= 
+    -notes=\x20
     </multiline.write>
     """
       ).strip()

pylabrobot/thermocycling/proflex.py …rmo_fisher/thermo_fisher_thermocycler.pypylabrobot/thermocycling/proflex.py renamed to pylabrobot/thermocycling/thermo_fisher/thermo_fisher_thermocycler.py pylabrobot/thermocycling/proflex.py renamed to pylabrobot/thermocycling/thermo_fisher/thermo_fisher_thermocycler.py

@@ -4,16 +4,16 @@
 import logging
 import re
 import xml.etree.ElementTree as ET
+from abc import ABCMeta
 from base64 import b64decode
 from dataclasses import dataclass
 from typing import Any, Dict, List, Optional, cast
 from xml.dom import minidom
 
 from pylabrobot.io import Socket
+from pylabrobot.thermocycling.backend import ThermocyclerBackend
 from pylabrobot.thermocycling.standard import LidStatus, Protocol, Stage, Step
 
-from .backend import ThermocyclerBackend
-
 
 def _generate_run_info_files(
   protocol: Protocol,
@@ -203,7 +203,7 @@ def stage_to_scpi(stage: Stage, stage_index: int, stage_name_prefix: str) -> dic
   return data
 
 
-class ProflexBackend(ThermocyclerBackend):
+class ThermoFisherThermocyclerBackend(ThermocyclerBackend, metaclass=ABCMeta):
   """Backend for Proflex thermocycler."""
 
   def __init__(self, ip: str, port: int = 7000, shared_secret: bytes = b"f4ct0rymt55"):
@@ -401,8 +401,11 @@ async def _load_num_blocks_and_type(self):
     elif self.bid == "13":
       self._num_blocks = 3
       self.num_temp_zones = 2
+    elif self.bid == "31":
+      self._num_blocks = 1
+      self.num_temp_zones = 1
     else:
-      raise NotImplementedError("Only BID 12 and 13 are supported")
+      raise NotImplementedError("Only BID 31, 12 and 13 are supported")
 
   async def is_block_running(self, block_id: int) -> bool:
     run_name = await self.get_run_name(block_id=block_id)
@@ -778,7 +781,7 @@ async def get_run_info(self, protocol: Protocol, block_id: int) -> "RunProgress"
     run_name = await self.get_run_name(block_id=block_id)
     if not progress:
       self.logger.info("Protocol completed")
-      return ProflexBackend.RunProgress(
+      return ThermoFisherThermocyclerBackend.RunProgress(
         running=False,
         stage="completed",
         elapsed_time=await self.get_elapsed_run_time_from_log(run_name=run_name),
@@ -788,7 +791,7 @@ async def get_run_info(self, protocol: Protocol, block_id: int) -> "RunProgress"
     if progress["RunTitle"] == "-":
       await self._read_response(timeout=5)
       self.logger.info("Protocol completed")
-      return ProflexBackend.RunProgress(
+      return ThermoFisherThermocyclerBackend.RunProgress(
         running=False,
         stage="completed",
         elapsed_time=await self.get_elapsed_run_time_from_log(run_name=run_name),
@@ -797,7 +800,7 @@ async def get_run_info(self, protocol: Protocol, block_id: int) -> "RunProgress"
 
     if progress["Stage"] == "POSTRun":
       self.logger.info("Protocol in POSTRun")
-      return ProflexBackend.RunProgress(
+      return ThermoFisherThermocyclerBackend.RunProgress(
         running=True,
         stage="POSTRun",
         elapsed_time=await self.get_elapsed_run_time_from_log(run_name=run_name),
@@ -820,7 +823,7 @@ async def get_run_info(self, protocol: Protocol, block_id: int) -> "RunProgress"
             break
           await asyncio.sleep(5)
         self.logger.info("Infinite hold")
-        return ProflexBackend.RunProgress(
+        return ThermoFisherThermocyclerBackend.RunProgress(
           running=False,
           stage="infinite_hold",
           elapsed_time=time_elapsed,
@@ -829,7 +832,7 @@ async def get_run_info(self, protocol: Protocol, block_id: int) -> "RunProgress"
 
     self.logger.info(f"Elapsed time: {time_elapsed}")
     self.logger.info(f"Remaining time: {remaining_time}")
-    return ProflexBackend.RunProgress(
+    return ThermoFisherThermocyclerBackend.RunProgress(
       running=True,
       stage=progress["Stage"],
       elapsed_time=time_elapsed,
@@ -852,12 +855,6 @@ async def setup(
       await self.set_block_idle_temp(temp=block_idle_temp, block_id=block_index)
       await self.set_cover_idle_temp(temp=cover_idle_temp, block_id=block_index)
 
-  async def open_lid(self):
-    raise NotImplementedError("Open lid command is not implemented for Proflex thermocycler")
-
-  async def close_lid(self):
-    raise NotImplementedError("Close lid command is not implemented for Proflex thermocycler")
-
   async def deactivate_lid(self, block_id: Optional[int] = None):
     assert block_id is not None, "block_id must be specified"
     return await self.set_cover_idle_temp(temp=105, control_enabled=False, block_id=block_id)