feat(api): add module firmware update endpoint

Closes #1654

api/opentrons/drivers/mag_deck/driver.py

@@ -156,10 +156,9 @@ def __init__(self, config={}):
         self._plate_height = None
         self._mag_position = None
 
-    def connect(self, port=None, baudrate=MAG_DECK_BAUDRATE) -> str:
+    def connect(self, port=None) -> str:
         '''
         :param port: '/dev/modules/ttyn_magdeck'
-        :param baudrate: MAG_DECK_BAUDRATE or 1200 for dfu
         NOTE: Using the symlink above to connect makes sure that the robot
         connects/reconnects to the module even after a device
         reset/reconnection
@@ -168,7 +167,7 @@ def connect(self, port=None, baudrate=MAG_DECK_BAUDRATE) -> str:
             return ''
         try:
             self.disconnect()
-            self._connect_to_port(port, baudrate)
+            self._connect_to_port(port)
             self._wait_for_ack()    # verify the device is there
         except (SerialException, SerialNoResponse) as e:
             return str(e)
@@ -327,13 +326,13 @@ def _send_command(self, command, timeout=DEFAULT_MAG_DECK_TIMEOUT):
 
         return ret_code.strip()
 
-    def _connect_to_port(self, port=None, baudrate=MAG_DECK_BAUDRATE):
+    def _connect_to_port(self, port=None):
         try:
             mag_deck = environ.get('OT_MAG_DECK_ID')
             self._connection = serial_communication.connect(
                 device_name=mag_deck,
                 port=port,
-                baudrate=baudrate
+                baudrate=MAG_DECK_BAUDRATE
             )
         except SerialException:
             # if another process is using the port, pyserial raises an

api/opentrons/modules/__init__.py

@@ -84,11 +84,13 @@ def discover_and_connect():
 
 def enter_bootloader(module):
     """
-    Disconnect from current port, connect at 1200 baud and disconnect to
-    enter bootloader on a (possibly) different port. On disconnect, the
-    kernel could assign it a lower port number if available, or keep it on
-    the same port. So we check for changes in port assigned and use the
-    appropriate one
+    Using the driver method, enter bootloader mode of the atmega32u4. The bootloader mode opens a new port on the uC to
+    upload the hex file. After receiving a 'dfu' command, the firmware provides a 3-second window to close the
+    current port so as to do a clean switch to the bootloader port. The new port shows up as 'ttyn_bootloader' on the pi
+    Use this port to upload firmware
+    NOTE: Modules with old bootloader will have the bootloader port show up as a regular module port- 'ttyn_tempdeck'/
+    'ttyn_magdeck' with the port number being either different or same as the one that the module was originally on.
+    So we check for changes in ports and use the appropriate one
     """
     ports_before_dfu_mode = discover_ports()  # Required only for old bootloadr
 
@@ -107,10 +109,10 @@ def enter_bootloader(module):
 
 async def update_firmware(module, firmware_file_path, config_file_path, loop):
     """
-    Enter bootloader then run avrdude firmware upload command. The kernel
-    could assign the module a new port after the update (since the board is
-    automatically reset). Scan for such a port change and use the
-    appropriate port
+    Run avrdude firmware upload command. Switch back to normal module port
+
+    Note: For modules with old bootloader, the kernel could assign the module a new port after the update
+    (since the board is automatically reset). Scan for such a port change and use the appropriate port
     """
     # TODO: Make sure the module isn't in the middle of operation
 
@@ -124,7 +126,7 @@ async def update_firmware(module, firmware_file_path, config_file_path, loop):
         'baudrate': '57600',
         'firmware_file': firmware_file_path
     }
-    proc = await asyncio.create_subprocess_shell(
+    proc = await asyncio.create_subprocess_exec(
         'avrdude '
         '-C{config_file} '
         '-v -p{part_no} '
@@ -166,12 +168,12 @@ def port_on_mode_switch(ports_before_switch):
     return new_port
 
 
-def port_poll(has_old_bootloader, ports_before_switch=None):
+def port_poll(old_bootloader, ports_before_switch=None):
     """
     Checks for the bootloader port
     """
     new_port = ''
-    if has_old_bootloader:
+    if old_bootloader:
         new_port = port_on_mode_switch(ports_before_switch)
     else:
         discovered_ports = list(filter(

api/opentrons/modules/magdeck.py

@@ -1,15 +1,10 @@
-import logging
-
 from opentrons.drivers.mag_deck import MagDeck as MagDeckDriver
 from opentrons import commands
 
 LABWARE_ENGAGE_HEIGHT = {'biorad-hardshell-96-PCR': 18}    # mm
 MAX_ENGAGE_HEIGHT = 45  # mm from home position
 
 
-log = logging.getLogger(__name__)
-
-
 class MissingDevicePortError(Exception):
     pass