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feat(api): define & execute v3 json protocols #3312

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merged 9 commits into from
Apr 9, 2019
Merged

feat(api): define & execute v3 json protocols #3312

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899a642
feat(api): define & execute v3 json protocols
IanLondon Apr 5, 2019
2b08a48
add tests
IanLondon Apr 8, 2019
519bf65
split out v1 vs v3 execution code
IanLondon Apr 8, 2019
db4c2e2
fixup typo
IanLondon Apr 8, 2019
e59529c
move json dispatch fixtures to files; do not use Dict.get on required…
IanLondon Apr 8, 2019
a9fa1fa
type cleanup; move trough def to fixture json
IanLondon Apr 8, 2019
6505a6b
use dispatcher map for v3 executor
IanLondon Apr 8, 2019
03c41c9
cleanup re: Laura PR comments
IanLondon Apr 8, 2019
e082c6d
delete extra space
IanLondon Apr 9, 2019
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269 changes: 39 additions & 230 deletions api/src/opentrons/protocol_api/execute.py
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Original file line number Diff line number Diff line change
@@ -1,14 +1,11 @@
import inspect
import itertools
import logging
import traceback
import sys
from typing import Any, Callable, Dict, Optional
from typing import Any, Callable, Dict

from .contexts import ProtocolContext, InstrumentContext
from .back_compat import BCLabware
from . import labware
from opentrons.types import Point, Location
from .contexts import ProtocolContext
from . import execute_v1, execute_v3
from opentrons import config

MODULE_LOG = logging.getLogger(__name__)
Expand Down Expand Up @@ -111,227 +108,25 @@ def _run_python(proto: Any, context: ProtocolContext):
raise ExceptionInProtocolError(e, tb, str(e), frame.lineno)


def load_pipettes_from_json(
ctx: ProtocolContext,
protocol: Dict[Any, Any]) -> Dict[str, InstrumentContext]:
pipette_data = protocol.get('pipettes', {})
pipettes_by_id = {}
for pipette_id, props in pipette_data.items():
model = props.get('model')
mount = props.get('mount')

# TODO: Ian 2018-11-06 remove this fallback to 'model' when
# backwards-compatability for JSON protocols with versioned
# pipettes is dropped (next JSON protocol schema major bump)
name = props.get('name')
if not name:
name = model.split('_v')[0]

instr = ctx.load_instrument(name, mount)

pipettes_by_id[pipette_id] = instr

return pipettes_by_id


def load_labware_from_json(
ctx: ProtocolContext,
protocol: Dict[Any, Any]) -> Dict[str, labware.Labware]:
data = protocol.get('labware', {})
loaded_labware = {}
bc = BCLabware(ctx)
for labware_id, props in data.items():
slot = props.get('slot')
model = props.get('model')
if slot == '12':
if model == 'fixed-trash':
# pass in the pre-existing fixed-trash
loaded_labware[labware_id] = ctx.fixed_trash
else:
raise RuntimeError(
"Nothing but the fixed trash may be loaded in slot 12; "
"this protocol attempts to load a {} there."
.format(model))
else:
loaded_labware[labware_id] = bc.load(
model, slot, label=props.get('display-name'))

return loaded_labware


def _get_well(loaded_labware: Dict[str, labware.Labware],
params: Dict[str, Any]):
labwareId = params['labware']
well = params['well']
plate = loaded_labware.get(labwareId)
if not plate:
raise ValueError(
'Command tried to use labware "{}", but that ID does not exist '
'in protocol\'s "labware" section'.format(labwareId))
return plate.wells_by_index()[well]


def _get_bottom_offset(command_type: str,
params: Dict[str, Any],
default_values: Dict[str, float]) -> Optional[float]:
# default offset from bottom for aspirate/dispense commands
offset_default = default_values.get(
'{}-mm-from-bottom'.format(command_type))

# optional command-specific value, fallback to default
offset_from_bottom = params.get(
'offsetFromBottomMm', offset_default)

return offset_from_bottom


def _get_location_with_offset(loaded_labware: Dict[str, labware.Labware],
command_type: str,
params: Dict[str, Any],
default_values: Dict[str, float]) -> Location:
well = _get_well(loaded_labware, params)

# Never move to the bottom of the fixed trash
if 'fixedTrash' in labware.quirks_from_any_parent(well):
return well.top()

offset_from_bottom = _get_bottom_offset(
command_type, params, default_values)

bot = well.bottom()
if offset_from_bottom:
with_offs = bot.move(Point(z=offset_from_bottom))
else:
with_offs = bot
MODULE_LOG.debug("offset from bottom for {}: {}->{}"
.format(command_type, bot, with_offs))
return with_offs


# TODO (Ian 2018-08-22) once Pipette has more sensible way of managing
# flow rate value (eg as an argument in aspirate/dispense fns), remove this
def _set_flow_rate(
pipette_name, pipette, command_type, params, default_values):
"""
Set flow rate in uL/mm, to value obtained from command's params,
or if unspecified in command params, then from protocol's "default-values".
"""
default_aspirate = default_values.get(
'aspirate-flow-rate', {}).get(pipette_name)

default_dispense = default_values.get(
'dispense-flow-rate', {}).get(pipette_name)

flow_rate_param = params.get('flow-rate')

if flow_rate_param is not None:
if command_type == 'aspirate':
pipette.flow_rate = {
'aspirate': flow_rate_param,
'dispense': default_dispense
}
return
if command_type == 'dispense':
pipette.flow_rate = {
'aspirate': default_aspirate,
'dispense': flow_rate_param
}
return

pipette.flow_rate = {
'aspirate': default_aspirate,
'dispense': default_dispense
}


def dispatch_json(context: ProtocolContext, # noqa(C901)
protocol_data: Dict[Any, Any],
instruments: Dict[str, InstrumentContext],
labware: Dict[str, labware.Labware]):
subprocedures = [
p.get('subprocedure', [])
for p in protocol_data.get('procedure', [])]

default_values = protocol_data.get('default-values', {})
flat_subs = itertools.chain.from_iterable(subprocedures)

for command_item in flat_subs:
command_type = command_item.get('command')
params = command_item.get('params', {})
pipette = instruments.get(params.get('pipette'))
protocol_pipette_data = protocol_data\
.get('pipettes', {})\
.get(params.get('pipette'), {})
pipette_name = protocol_pipette_data.get('name')

if (not pipette_name):
# TODO: Ian 2018-11-06 remove this fallback to 'model' when
# backwards-compatability for JSON protocols with versioned
# pipettes is dropped (next JSON protocol schema major bump)
pipette_name = protocol_pipette_data.get('model')

if command_type == 'delay':
wait = params.get('wait')
if wait is None:
raise ValueError('Delay cannot be null')
elif wait is True:
message = params.get('message', 'Pausing until user resumes')
context.pause(msg=message)
else:
context.delay(seconds=wait)

elif command_type == 'blowout':
well = _get_well(labware, params)
pipette.blow_out(well) # type: ignore

elif command_type == 'pick-up-tip':
well = _get_well(labware, params)
pipette.pick_up_tip(well) # type: ignore

elif command_type == 'drop-tip':
well = _get_well(labware, params)
pipette.drop_tip(well) # type: ignore

elif command_type == 'aspirate':
location = _get_location_with_offset(
labware, 'aspirate', params, default_values)
volume = params['volume']
_set_flow_rate(
pipette_name, pipette, command_type, params, default_values)
pipette.aspirate(volume, location) # type: ignore

elif command_type == 'dispense':
location = _get_location_with_offset(
labware, 'dispense', params, default_values)
volume = params['volume']
_set_flow_rate(
pipette_name, pipette, command_type, params, default_values)
pipette.dispense(volume, location) # type: ignore

elif command_type == 'touch-tip':
well = _get_well(labware, params)
offset = default_values.get('touch-tip-mm-from-top', -1)
pipette.touch_tip(location, v_offset=offset) # type: ignore

elif command_type == 'move-to-slot':
slot = params.get('slot')
if slot not in [str(s+1) for s in range(12)]:
raise ValueError('Invalid "slot" for "move-to-slot": {}'
.format(slot))
slot_obj = context.deck.position_for(slot)

offset = params.get('offset', {})
offsetPoint = Point(
offset.get('x', 0),
offset.get('y', 0),
offset.get('z', 0))

pipette.move_to( # type: ignore
slot_obj.move(offsetPoint),
force_direct=params.get('force-direct'),
minimum_z_height=params.get('minimum-z-height'))
else:
MODULE_LOG.warning("Bad command type {}".format(command_type))
def get_protocol_schema_version(protocol_json: Dict[Any, Any]) -> int:
# v3 and above uses `schemaVersion: integer`
version = protocol_json.get('schemaVersion')
if None is not version:
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Could you change this to either:

if protocol_json.get('schemaVersion'):
    return protocol_json.get('schemaVersion')

or:

version = protocol_json.get('schemaVersion')
if version:
    return version

return version
# v1 uses 1.x.x and v2 uses 2.x.x
legacyKebabVersion = protocol_json.get('protocol-schema')
# No minor/patch schemas ever were released,
# do not permit protocols with nonexistent schema versions to load
if (legacyKebabVersion == '1.0.0'):
return 1
if (legacyKebabVersion == '2.0.0'):
return 2
if (legacyKebabVersion is not None):
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Same here:

if legacyKebabVersion:

Also may want to change format to if/elif as that's normally used for conditional checking

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pylint yells at you if you do

if:
  return
else:
  other stuff

I personally disagree but if that's what the linter says that's what the linter says

raise RuntimeError(('No such schema version: "{}". Did you mean ' +
'"1.0.0" or "2.0.0"?').format(legacyKebabVersion))
raise RuntimeError(
'Could not determine schema version for protocol. ' +
'Make sure there is a version number under "schemaVersion"')


def run_protocol(protocol_code: Any = None,
Expand Down Expand Up @@ -364,8 +159,22 @@ def run_protocol(protocol_code: Any = None,
if None is not protocol_code:
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Same here for checking whether a variable is populated (if protocol_code)

_run_python(protocol_code, true_context)
elif None is not protocol_json:
lw = load_labware_from_json(true_context, protocol_json)
ins = load_pipettes_from_json(true_context, protocol_json)
dispatch_json(true_context, protocol_json, ins, lw)
protocol_version = get_protocol_schema_version(protocol_json)
if (protocol_version) > 3:
raise RuntimeError('JSON Protocol version {} is not yet supported \
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May fail lint; \ is not required inside braces, you can do

raise RuntimError('Json Protocol version {} is not yet supported'
                              'in this version of the API')

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make -C api lint is working for me as-is but would you prefer this?

raise RuntimeError((
                'JSON Protocol version {} is not yet ' +
                'supported in this version of the API')
                .format(protocol_version))

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You can also do this fancy new thing (similar to javascript evaluated strings)

f'Json Protocol version {protocol_version} is not yet supported in this version of the API' if you don't want to use format

in this version of the API'.format(protocol_version))

if (protocol_version >= 3):
ins = execute_v3.load_pipettes_from_json(
true_context, protocol_json)
lw = execute_v3.load_labware_from_json_defs(
true_context, protocol_json)
execute_v3.dispatch_json(true_context, protocol_json, ins, lw)
else:
ins = execute_v1.load_pipettes_from_json(
true_context, protocol_json)
lw = execute_v1.load_labware_from_json_loadnames(
true_context, protocol_json)
execute_v1.dispatch_json(true_context, protocol_json, ins, lw)
else:
raise RuntimeError("run_protocol must have either code or json")
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