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License: MIT License

Python 98.11% Makefile 0.27% Shell 1.62%

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syssynbio zheins brandogw nb-e photocyte maraxen ezirayw drofish6390 eduardanicoletto vhu43 cnpem-emi amoghpj chris-krenz hicsail fynch-bio evolver-extensions josephrp

evolver's Issues

Consolidate evolver config and calibration config files

evolver_config.json contains:

{"ip": "192.168.1.37", "mac": "b8:27:eb:34:55:8a", "deviceName": "evolver-darwin"}

calibrations.json contains:

{"activeCalibration": {"temp": {"filename": "sample_tempcal.txt"}, "od": {"filename": "sample_odcal.txt"}}}

Could be consolidated into one file to simplify file structure

Communication issues with updated server code

I find this error when updating the code. Seems like there's still some thing I'm not setting up properly.

I'm currently using Master in both the DPU and Arduino branches.

od_135r,1000,_!

Traceback (most recent call last):
  File "/home/pi/evolver/evolver/evolver_server.py", line 246, in run_commands
    returned_data = serial_communication(command['param'], command['value'], command['type'])
  File "/home/pi/evolver/evolver/evolver_server.py", line 284, in serial_communication
    raise EvolverSerialError('Error: Response has incorrect address.\n\tExpected: ' + param + '\n\tFound:' + address)
evolver_server.EvolverSerialError: Error: Response has incorrect address.
	Expected: od_135
	Found:
od_90r,1000,_!
od_90b,32114,31657,31284,31869,31740,31508,
Traceback (most recent call last):
  File "/home/pi/evolver/evolver/evolver_server.py", line 246, in run_commands
    returned_data = serial_communication(command['param'], command['value'], command['type'])
  File "/home/pi/evolver/evolver/evolver_server.py", line 286, in serial_communication
    raise EvolverSerialError('Error: Response did not have valid serial communication termination string!\n\tExpected: ' +  evolver_conf['serial_end_incoming'] + '\n\tFound: ' + response[len(response) - 3:])
evolver_server.EvolverSerialError: Error: Response did not have valid serial communication termination string!
	Expected: end
	Found: 08,
od_ledr,2500,2500,2500,2500,2500,2500,2500,2500,2500,2500,2500,2500,2500,2500,2500,2500,_!
od_lede,2500,2500,2500,2500,
Traceback (most recent call last):
  File "/home/pi/evolver/evolver/evolver_server.py", line 246, in run_commands
    returned_data = serial_communication(command['param'], command['value'], command['type'])
  File "/home/pi/evolver/evolver/evolver_server.py", line 286, in serial_communication
    raise EvolverSerialError('Error: Response did not have valid serial communication termination string!\n\tExpected: ' +  evolver_conf['serial_end_incoming'] + '\n\tFound: ' + response[len(response) - 3:])
evolver_server.EvolverSerialError: Error: Response did not have valid serial communication termination string!
	Expected: end
	Found: 00,
stirr,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,_!

Traceback (most recent call last):
  File "/home/pi/evolver/evolver/evolver_server.py", line 246, in run_commands
    returned_data = serial_communication(command['param'], command['value'], command['type'])
  File "/home/pi/evolver/evolver/evolver_server.py", line 284, in serial_communication
    raise EvolverSerialError('Error: Response has incorrect address.\n\tExpected: ' + param + '\n\tFound:' + address)
evolver_server.EvolverSerialError: Error: Response has incorrect address.
	Expected: stir
	Found:
tempr,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,_!
tempb,1967,1948,1938,1935,
Traceback (most recent call last):
  File "/home/pi/evolver/evolver/evolver_server.py", line 246, in run_commands
    returned_data = serial_communication(command['param'], command['value'], command['type'])
  File "/home/pi/evolver/evolver/evolver_server.py", line 286, in serial_communication
    raise EvolverSerialError('Error: Response did not have valid serial communication termination string!\n\tExpected: ' +  evolver_conf['serial_end_incoming'] + '\n\tFound: ' + response[len(response) - 3:])
evolver_server.EvolverSerialError: Error: Response did not have valid serial communication termination string!
	Expected: end
	Found: 35,
Broadcasting data
{'data': {}, 'config': {'lxml': {'fields_expected_incoming': 17, 'fields_expected_outgoing': 17, 'recurring': False, 'value': ['4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095']}, 'od_135': {'fields_expected_incoming': 17, 'fields_expected_outgoing': 2, 'recurring': True, 'value': '1000'}, 'od_90': {'fields_expected_incoming': 17, 'fields_expected_outgoing': 2, 'recurring': True, 'value': '1000'}, 'od_led': {'fields_expected_incoming': 17, 'fields_expected_outgoing': 17, 'recurring': True, 'value': ['2500', '2500', '2500', '2500', '2500', '2500', '2500', '2500', '2500', '2500', '2500', '2500', '2500', '2500', '2500', '2500']}, 'pump': {'fields_expected_incoming': 49, 'fields_expected_outgoing': 49, 'recurring': False, 'value': None}, 'stir': {'fields_expected_incoming': 17, 'fields_expected_outgoing': 17, 'recurring': True, 'value': ['15', '15', '15', '15', '15', '15', '15', '15', '15', '15', '15', '15', '15', '15', '15', '15']}, 'temp': {'fields_expected_incoming': 17, 'fields_expected_outgoing': 17, 'recurring': True, 'value': ['4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095', '4095']}}}

Second aberrant broadcast from the server

Broadcast always is happening in pairs and one of the pairs has a different power level, from eVOLVER server

Add socket cloud functions

on_start
on_stop
on_pause
on_create
on_update

Noticed after doing a temperature calibration that the setup page was no longer updating values. Most likely caused by the broadcasting thread crashing due to serial communication issues with the server.

Add events for Arduino communication

Reformat parameters hardcoded lists

In evolver_server.py, the reformat_parameters function should be generalized

Add authentication token for cloud and dpu

Token for cloud communication should probably be set separately on the device, and integrate with HAPI auth (if possible). When creating a new device on the cloud, get a session token for it and input that through the touch screen of the evolver.
Token to communicate to DPU could be part of config file? Both evolver and DPU have to contain same token.

PyYAML yaml.load() deprecated

evolver/evolver/evolver.py

Line 25 in a3213d7

conf = yaml.load(ymlfile)

https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation

use: yaml.safe_load()

Server freezes during temp cal

During temperature calibration, during updating the temperature, the server freezes up. This is the output log from the server.

Output to arduino: xrNaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN, ! Received from arduino: temp2018,1980,1986,1997,1983,1961,1973,1972,1986,1954,1919,1956,1994,1957,1943,1969,end Output to arduino: we4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095, ! Received COMMAND Output to arduino: xr1517,1478,1484,1492,1481,1461,1472,1470,1485,1454,1419,1456,1492,1458,1442,1467, ! Error in running commands - relinquishing serial an integer is required (got type NoneType) Got command from BROADCAST Output to arduino: we4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095,4095, ! Error in running commands - relinquishing serial 'utf-8' codec can't decode byte 0xfe in position 0: invalid start byte Got command from BROADCAST

Fluidic commands not going through

When trying to send fluidic commands via the GUI. In this case, printed the value variable.

Received COMMAND
['13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '13', '0', '0', '0', '0', '0', '0', '0', '0', '0', '0', '0', '0', '0', '0', '0', '0']
13
Task exception was never retrieved
future: <Task finished coro=<AsyncServer._handle_event_internal() done, defined at /usr/local/lib/python3.6/site-packages/python_socketio-3.0.0-py3.6.egg/socketio/asyncio_server.py:296> exception=TypeError("'NoneType' object does not support item assignment",)>
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/python_socketio-3.0.0-py3.6.egg/socketio/asyncio_server.py", line 297, in _handle_event_internal
    r = await server._trigger_event(data[0], namespace, sid, *data[1:])
  File "/usr/local/lib/python3.6/site-packages/python_socketio-3.0.0-py3.6.egg/socketio/asyncio_server.py", line 325, in _trigger_event
    ret = await self.handlers[namespace][event](*args)
  File "/home/pi/evolver/evolver/evolver_server.py", line 51, in on_command
    evolver_conf['experimental_params'][param]['value'][i] = value[i]
TypeError: 'NoneType' object does not support item assignment
Received COMMAND

Dropped successive fluidic commands

If multiple fluidic commands are sent in rapid succession (say, at ~1 second intervals), some are currently (server version 1.1.1) being dropped. I have done limited testing, but I think in those cases the server send the previous command to the arduinos instead of the new one. The solution from the DPU side is to write the custom function so that all required fluidic events are collated and fired only once (which is how the example custom_script.py is written anyway).

Not sure what a good solution could be, apart from adopting a parsimonious approach at sending commands. Might be good to explicitly warn the users too (with a comment in the custom_script.py template).

Server log file should have time stamps

To be able to go to errors at specific times should they happen

Pump Calibration within GUI

New GUI react component for pump cals - entering numbers for flow rates for each pump, and how much time.

Add configuration file

IP addresses are currently hard-coded, and should be loaded from a config file.

Broadcast events don't run if immediate commands are sent frequently

The queue is cleared of all broadcast events when immediate commands come in right now. To fix this (1) Immediate commands clears all broadcast commands of only of the same class and (2) don't have broadcast events reset the timer

Server Crashing

xrNaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN, !
File "/home/pi/evolver/evolver/evolver_server.py", line 417, in broadcast
data = run_commands()
File "/home/pi/evolver/evolver/evolver_server.py", line 279, in run_commands
data = ping_arduino(config)
File "/home/pi/evolver/evolver/evolver_server.py", line 379, in ping_arduino
config_to_arduino(key, value, PARAM[key][0], ENDING_SEND, PARAM[key][2])
File "/home/pi/evolver/evolver/evolver_server.py", line 350, in config_to_arduino
SERIAL.write(bytes(output, 'UTF-8'))
File "/usr/local/lib/python3.6/site-packages/pyserial-3.4-py3.6.egg/serial/serialposix.py", line 537, in write
TypeError: an integer is required (got type NoneType)

Increase default delays on server for serial communication

Test with a long command to ensure it works.

Increase serial_timeout to 1.0

Increase time.sleep(x) to 0.1

serial_timeout is in conf.yml

time.sleep(x) in evolver_server.py. Move x into the conf file as serial_delay