more validation stuff

Opentrons · Dec 5, 2024 · dcd9257 · dcd9257
1 parent 2170735
commit dcd9257
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Showing 37 changed files with 66 additions and 47 deletions.
diff --git a/api/src/opentrons/protocol_engine/commands/absorbance_reader/initialize.py b/api/src/opentrons/protocol_engine/commands/absorbance_reader/initialize.py
@@ -22,7 +22,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class InitializeParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/absorbance_reader/read.py b/api/src/opentrons/protocol_engine/commands/absorbance_reader/read.py
@@ -24,7 +24,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 ReadAbsorbanceCommandType = Literal["absorbanceReader/read"]

diff --git a/api/src/opentrons/protocol_engine/commands/calibration/calibrate_gripper.py b/api/src/opentrons/protocol_engine/commands/calibration/calibrate_gripper.py
@@ -24,7 +24,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class CalibrateGripperParamsJaw(Enum):  # noqa: D101

diff --git a/api/src/opentrons/protocol_engine/commands/command.py b/api/src/opentrons/protocol_engine/commands/command.py
@@ -65,7 +65,7 @@ class CommandIntent(str, enum.Enum):
 
 
 def _pop_default(s: Dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class BaseCommandCreate(

diff --git a/api/src/opentrons/protocol_engine/commands/configure_for_volume.py b/api/src/opentrons/protocol_engine/commands/configure_for_volume.py
@@ -19,7 +19,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class ConfigureForVolumeParams(PipetteIdMixin):

diff --git a/api/src/opentrons/protocol_engine/commands/dispense.py b/api/src/opentrons/protocol_engine/commands/dispense.py
@@ -41,7 +41,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class DispenseParams(

diff --git a/api/src/opentrons/protocol_engine/commands/dispense_in_place.py b/api/src/opentrons/protocol_engine/commands/dispense_in_place.py
@@ -34,7 +34,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class DispenseInPlaceParams(PipetteIdMixin, DispenseVolumeMixin, FlowRateMixin):

diff --git a/api/src/opentrons/protocol_engine/commands/drop_tip.py b/api/src/opentrons/protocol_engine/commands/drop_tip.py
@@ -40,7 +40,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class DropTipParams(PipetteIdMixin):

diff --git a/api/src/opentrons/protocol_engine/commands/drop_tip_in_place.py b/api/src/opentrons/protocol_engine/commands/drop_tip_in_place.py
@@ -28,7 +28,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class DropTipInPlaceParams(PipetteIdMixin):

diff --git a/api/src/opentrons/protocol_engine/commands/heater_shaker/wait_for_temperature.py b/api/src/opentrons/protocol_engine/commands/heater_shaker/wait_for_temperature.py
@@ -18,7 +18,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class WaitForTemperatureParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/home.py b/api/src/opentrons/protocol_engine/commands/home.py
@@ -21,7 +21,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class HomeParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/liquid_probe.py b/api/src/opentrons/protocol_engine/commands/liquid_probe.py
@@ -49,7 +49,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 LiquidProbeCommandType = Literal["liquidProbe"]
@@ -375,9 +375,9 @@ class TryLiquidProbe(
     params: TryLiquidProbeParams
     result: Optional[TryLiquidProbeResult]
 
-    _ImplementationCls: Type[
+    _ImplementationCls: Type[TryLiquidProbeImplementation] = (
         TryLiquidProbeImplementation
-    ] = TryLiquidProbeImplementation
+    )
 
 
 class LiquidProbeCreate(BaseCommandCreate[LiquidProbeParams]):

diff --git a/api/src/opentrons/protocol_engine/commands/load_labware.py b/api/src/opentrons/protocol_engine/commands/load_labware.py
@@ -32,7 +32,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class LoadLabwareParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/load_liquid_class.py b/api/src/opentrons/protocol_engine/commands/load_liquid_class.py
@@ -22,7 +22,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class LoadLiquidClassParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/load_module.py b/api/src/opentrons/protocol_engine/commands/load_module.py
@@ -27,7 +27,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class LoadModuleParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/load_pipette.py b/api/src/opentrons/protocol_engine/commands/load_pipette.py
@@ -31,7 +31,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class LoadPipetteParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/move_labware.py b/api/src/opentrons/protocol_engine/commands/move_labware.py
@@ -53,7 +53,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 # Extra buffer on top of minimum distance to move to the right

diff --git a/api/src/opentrons/protocol_engine/commands/move_to_addressable_area_for_drop_tip.py b/api/src/opentrons/protocol_engine/commands/move_to_addressable_area_for_drop_tip.py
@@ -35,7 +35,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class MoveToAddressableAreaForDropTipParams(PipetteIdMixin, MovementMixin):

diff --git a/api/src/opentrons/protocol_engine/commands/movement_common.py b/api/src/opentrons/protocol_engine/commands/movement_common.py
@@ -28,7 +28,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class WellLocationMixin(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/robot/close_gripper_jaw.py b/api/src/opentrons/protocol_engine/commands/robot/close_gripper_jaw.py
@@ -21,7 +21,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class closeGripperJawParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/robot/move_axes_relative.py b/api/src/opentrons/protocol_engine/commands/robot/move_axes_relative.py
@@ -26,7 +26,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class MoveAxesRelativeParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/robot/move_axes_to.py b/api/src/opentrons/protocol_engine/commands/robot/move_axes_to.py
@@ -25,7 +25,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class MoveAxesToParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/robot/move_to.py b/api/src/opentrons/protocol_engine/commands/robot/move_to.py
@@ -26,7 +26,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class MoveToParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/save_position.py b/api/src/opentrons/protocol_engine/commands/save_position.py
@@ -19,7 +19,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class SavePositionParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/temperature_module/wait_for_temperature.py b/api/src/opentrons/protocol_engine/commands/temperature_module/wait_for_temperature.py
@@ -17,7 +17,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class WaitForTemperatureParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py b/api/src/opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py
@@ -23,7 +23,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class ProfileStep(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/thermocycler/run_profile.py b/api/src/opentrons/protocol_engine/commands/thermocycler/run_profile.py
@@ -20,7 +20,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class RunProfileStepParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/thermocycler/set_target_block_temperature.py b/api/src/opentrons/protocol_engine/commands/thermocycler/set_target_block_temperature.py
@@ -18,7 +18,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class SetTargetBlockTemperatureParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/touch_tip.py b/api/src/opentrons/protocol_engine/commands/touch_tip.py
@@ -38,7 +38,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class TouchTipParams(PipetteIdMixin, WellLocationMixin):

diff --git a/api/src/opentrons/protocol_engine/commands/unsafe/unsafe_drop_tip_in_place.py b/api/src/opentrons/protocol_engine/commands/unsafe/unsafe_drop_tip_in_place.py
@@ -25,7 +25,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class UnsafeDropTipInPlaceParams(PipetteIdMixin):

diff --git a/api/src/opentrons/protocol_engine/commands/verify_tip_presence.py b/api/src/opentrons/protocol_engine/commands/verify_tip_presence.py
@@ -20,7 +20,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class VerifyTipPresenceParams(PipetteIdMixin):

diff --git a/api/src/opentrons/protocol_engine/commands/wait_for_duration.py b/api/src/opentrons/protocol_engine/commands/wait_for_duration.py
@@ -17,7 +17,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class WaitForDurationParams(BaseModel):

diff --git a/api/src/opentrons/protocol_engine/commands/wait_for_resume.py b/api/src/opentrons/protocol_engine/commands/wait_for_resume.py
@@ -19,7 +19,7 @@
 
 
 def _remove_default(s: dict[str, Any]) -> None:
-    s.pop("default")
+    s.pop("default", None)
 
 
 class WaitForResumeParams(BaseModel):

diff --git a/api/src/opentrons/protocols/labware.py b/api/src/opentrons/protocols/labware.py
@@ -2,10 +2,10 @@
 
 import logging
 import json
-
 from pathlib import Path
 from typing import Any, AnyStr, Dict, Optional, Union
 
+from pydantic_core import from_json
 import jsonschema  # type: ignore
 
 from opentrons_shared_data import load_shared_data, get_shared_data_root
@@ -103,7 +103,7 @@ def save_definition(
 
 
 def verify_definition(
-    contents: Union[AnyStr, LabwareDefinition, Dict[str, Any]]
+    contents: Union[AnyStr, LabwareDefinition, Dict[str, Any]],
 ) -> LabwareDefinition:
     """Verify that an input string is a labware definition and return it.
 
@@ -114,14 +114,23 @@ def verify_definition(
     :raises jsonschema.ValidationError: If the definition is not valid.
     :returns: The parsed definition
     """
-    schema_body = load_shared_data("labware/schemas/2.json").decode("utf-8")
-    labware_schema_v2 = json.loads(schema_body)
+    schemata_by_version = {
+        2: from_json(load_shared_data("labware/schemas/2.json").decode("utf-8")),
+        3: from_json(load_shared_data("labware/schemas/3.json").decode("utf-8")),
+    }
 
     if isinstance(contents, dict):
         to_return = contents
     else:
-        to_return = json.loads(contents)
-    jsonschema.validate(to_return, labware_schema_v2)
+        to_return = from_json(contents)
+    try:
+        schema = schemata_by_version[to_return.get("schemaVersion", None)]
+    except KeyError:
+        raise RuntimeError(
+            f'Invalid or unknown labware schema version {to_return.get("schemaVersion", None)}'
+        )
+    jsonschema.validate(to_return, schema)
+
     # we can type ignore this because if it passes the jsonschema it has
     # the correct structure
     return to_return  # type: ignore[return-value]
@@ -176,7 +185,6 @@ def _get_labware_definition_from_bundle(
 def _get_standard_labware_definition(
     load_name: str, namespace: Optional[str] = None, version: Optional[int] = None
 ) -> LabwareDefinition:
-
     if version is None:
         checked_version = 1
     else: