feat(api): Mark calibrations as bad when determined they exceed thres…

…hold

closes #6730

api/src/opentrons/calibration_storage/get.py

@@ -18,7 +18,7 @@
 
 
 def _format_calibration_type(
-        data: 'CalibrationDict') -> local_types.CalibrationTypes:
+        data: 'CalibrationDict') -> local_types.LabwareCalibrationTypes:
     offset = local_types.OffsetData(
         value=data['default']['offset'],
         last_modified=data['default']['lastModified']
@@ -27,7 +27,7 @@ def _format_calibration_type(
     # the labware calibraiton file. We should
     # have a follow-up PR to grab tip lengths
     # based on the loaded pips + labware
-    return local_types.CalibrationTypes(
+    return local_types.LabwareCalibrationTypes(
             offset=offset,
             tip_length=local_types.TipLengthData())
 

api/src/opentrons/calibration_storage/modify.py

@@ -8,7 +8,8 @@
 from pathlib import Path
 
 from opentrons import config
-from opentrons.types import Mount
+from opentrons.types import Mount, Point
+
 from opentrons.util.helpers import utc_now
 
 from . import (
@@ -22,7 +23,7 @@
         TipLengthCalibration, PipTipLengthCalibration,
         DeckCalibrationData, PipetteCalibrationData, CalibrationStatusDict)
     from opentrons_shared_data.labware.dev_types import LabwareDefinition
-    from opentrons.types import Point
+    from opentrons.protocol_api.labware import Labware
 
 
 def _add_to_index_offset_file(parent: str, slot: str, uri: str, lw_hash: str):
@@ -76,7 +77,7 @@ def add_existing_labware_to_index_file(
 def save_labware_calibration(
         labware_path: local_types.StrPath,
         definition: 'LabwareDefinition',
-        delta: 'Point',
+        delta: Point,
         slot: str = '',
         parent: str = ''):
     """
@@ -106,7 +107,9 @@ def save_labware_calibration(
 def create_tip_length_data(
         definition: 'LabwareDefinition',
         parent: str,
-        length: float) -> 'PipTipLengthCalibration':
+        length: float,
+        cal_status: typing.Optional[local_types.CalibrationStatus] = None
+        ) -> 'PipTipLengthCalibration':
     """
     Function to correctly format tip length data.
 
@@ -121,22 +124,25 @@ def create_tip_length_data(
     # assert labware._is_tiprack, \
     #     'cannot save tip length for non-tiprack labware'
     labware_hash = helpers.hash_labware_def(definition)
-    status: 'CalibrationStatusDict' =\
-        helpers.convert_to_dict(  # type: ignore
-            local_types.CalibrationStatus())
+    if cal_status:
+        status = cal_status
+    else:
+        status = local_types.CalibrationStatus()
+    status_dict: 'CalibrationStatusDict' =\
+        helpers.convert_to_dict(status)  # type: ignore
 
     tip_length_data: 'TipLengthCalibration' = {
         'tipLength': length,
         'lastModified': utc_now(),
         'source': local_types.SourceType.user,
-        'status': status
+        'status': status_dict
     }
 
     data = {labware_hash + parent: tip_length_data}
     return data
 
 
-def _helper_offset_data_format(filepath: str, delta: 'Point') -> dict:
+def _helper_offset_data_format(filepath: str, delta: Point) -> dict:
     if not Path(filepath).is_file():
         calibration_data = {
             "default": {
@@ -197,20 +203,25 @@ def save_robot_deck_attitude(
         transform: local_types.AttitudeMatrix,
         pip_id: typing.Optional[str],
         lw_hash: typing.Optional[str],
-        source: local_types.SourceType = None):
+        source: local_types.SourceType = None,
+        cal_status: typing.Optional[local_types.CalibrationStatus] = None):
     robot_dir = config.get_opentrons_path('robot_calibration_dir')
     robot_dir.mkdir(parents=True, exist_ok=True)
     gantry_path = robot_dir/'deck_calibration.json'
-    status: 'CalibrationStatusDict' = \
-        helpers.convert_to_dict(  # type: ignore
-            local_types.CalibrationStatus())
+    if cal_status:
+        status = cal_status
+    else:
+        status = local_types.CalibrationStatus()
+    status_dict: 'CalibrationStatusDict' =\
+        helpers.convert_to_dict(status)  # type: ignore
+
     gantry_dict: 'DeckCalibrationData' = {
         'attitude': transform,
         'pipette_calibrated_with': pip_id,
         'last_modified': utc_now(),
         'tiprack': lw_hash,
         'source': source or local_types.SourceType.user,
-        'status': status
+        'status': status_dict
     }
     io.save_to_file(gantry_path, gantry_dict)
 
@@ -233,23 +244,60 @@ def _add_to_pipette_offset_index_file(pip_id: str, mount: Mount):
 
 
 def save_pipette_calibration(
-        offset: 'Point',
+        offset: Point,
         pip_id: str, mount: Mount,
-        tiprack_hash: str, tiprack_uri: str):
+        tiprack_hash: str, tiprack_uri: str,
+        cal_status: typing.Optional[local_types.CalibrationStatus] = None):
     pip_dir = config.get_opentrons_path(
         'pipette_calibration_dir') / mount.name.lower()
     pip_dir.mkdir(parents=True, exist_ok=True)
-    status: 'CalibrationStatusDict' =\
-        helpers.convert_to_dict(  # type: ignore
-            local_types.CalibrationStatus())
+    if cal_status:
+        status = cal_status
+    else:
+        status = local_types.CalibrationStatus()
+    status_dict: 'CalibrationStatusDict' =\
+        helpers.convert_to_dict(status)  # type: ignore
     offset_path = pip_dir/f'{pip_id}.json'
     offset_dict: 'PipetteCalibrationData' = {
         'offset': [offset.x, offset.y, offset.z],
         'tiprack': tiprack_hash,
         'uri': tiprack_uri,
         'last_modified': utc_now(),
         'source': local_types.SourceType.user,
-        'status': status
+        'status': status_dict
     }
     io.save_to_file(offset_path, offset_dict)
     _add_to_pipette_offset_index_file(pip_id, mount)
+
+
+def mark_bad(
+        calibration: typing.Union[
+            local_types.DeckCalibration,
+            local_types.PipetteOffsetCalibration,
+            typing.Tuple[float, str, 'Labware']],
+        source_marked_bad: local_types.SourceType):
+    status = local_types.CalibrationStatus(
+        markedBad=True, source=source_marked_bad, markedAt=utc_now())
+    if isinstance(calibration, local_types.DeckCalibration):
+        save_robot_deck_attitude(
+            transform=calibration.attitude,
+            pip_id=calibration.pipette_calibrated_with,
+            lw_hash=calibration.tiprack,
+            source=calibration.source,
+            cal_status=status)
+    elif isinstance(calibration, local_types.PipetteOffsetCalibration):
+        save_pipette_calibration(
+            offset=Point(*calibration.offset),
+            pip_id=calibration.pipette,
+            mount=Mount.string_to_mount(calibration.mount),
+            tiprack_hash=calibration.tiprack,
+            tiprack_uri=calibration.uri,
+            cal_status=status)
+    else:
+        tip_length, pipette_id, tiprack = calibration
+        tip_length_dict = create_tip_length_data(
+            definition=tiprack._implementation.get_definition(),
+            parent=tiprack.parent,
+            length=tip_length,
+            cal_status=status)
+        save_tip_length_calibration(pipette_id, tip_length_dict)

api/src/opentrons/calibration_storage/types.py

@@ -75,7 +75,7 @@ class ParentOptions:
 
 
 @dataclass
-class CalibrationTypes:
+class LabwareCalibrationTypes:
     """
     Class to categorize what calibration
     data might be stored for a labware.
@@ -90,7 +90,7 @@ class CalibrationInformation:
     Class to store important calibration
     info for labware.
     """
-    calibration: CalibrationTypes
+    calibration: LabwareCalibrationTypes
     parent: ParentOptions
     labware_id: str
     uri: str
@@ -119,7 +119,7 @@ class DeckCalibration:
 @dataclass
 class PipetteOffsetByPipetteMount:
     """
-    Class to store pipette offset without pipette and monut info
+    Class to store pipette offset without pipette and mount info
     """
     offset: PipetteOffset
     source: SourceType

api/src/opentrons/types.py

@@ -119,6 +119,13 @@ class Mount(enum.Enum):
     def __str__(self):
         return self.name
 
+    @classmethod
+    def string_to_mount(cls, mount: str) -> 'Mount':
+        if mount == 'right':
+            return cls.RIGHT
+        else:
+            return cls.LEFT
+
 
 class TransferTipPolicy(enum.Enum):
     ONCE = enum.auto()