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

…hold (#6918)

api/src/opentrons/calibration_storage/get.py

@@ -13,12 +13,11 @@
     file_operators as io, helpers, migration, modify)
 if typing.TYPE_CHECKING:
     from opentrons_shared_data.labware.dev_types import LabwareDefinition
-    from .dev_types import (
-        TipLengthCalibration, CalibrationIndexDict, CalibrationDict)
+    from .dev_types import CalibrationIndexDict, CalibrationDict
 
 
 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 +26,7 @@ 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())
 
@@ -77,12 +76,19 @@ def get_all_calibrations() -> typing.List[local_types.CalibrationInformation]:
 
 def _get_tip_length_data(
         pip_id: str, labware_hash: str, labware_load_name: str
-) -> 'TipLengthCalibration':
+) -> local_types.TipLengthCalibration:
     try:
         pip_tip_length_path = config.get_tip_length_cal_path()/f'{pip_id}.json'
-        tip_length_data =\
+        tip_rack_data =\
             io.read_cal_file(str(pip_tip_length_path))
-        return tip_length_data[labware_hash]
+        tip_length_info = tip_rack_data[labware_hash]
+        return local_types.TipLengthCalibration(
+            tip_length=tip_length_info['tipLength'],
+            pipette=pip_id,
+            tiprack=labware_hash,
+            last_modified=tip_length_info['lastModified'],
+            source=_get_calibration_source(tip_length_info),
+            status=_get_calibration_status(tip_length_info))
     except (FileNotFoundError, KeyError):
         raise local_types.TipLengthCalNotFound(
             f'Tip length of {labware_load_name} has not been '
@@ -118,7 +124,7 @@ def get_labware_calibration(
 def load_tip_length_calibration(
         pip_id: str,
         definition: 'LabwareDefinition',
-        parent: str) -> 'TipLengthCalibration':
+        parent: str) -> local_types.TipLengthCalibration:
     """
     Function used to grab the current tip length associated
     with a particular tiprack.

api/src/opentrons/calibration_storage/modify.py

@@ -7,8 +7,10 @@
 import typing
 from pathlib import Path
 
+from dataclasses import asdict
 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 +24,6 @@
         TipLengthCalibration, PipTipLengthCalibration,
         DeckCalibrationData, PipetteCalibrationData, CalibrationStatusDict)
     from opentrons_shared_data.labware.dev_types import LabwareDefinition
-    from opentrons.types import Point
 
 
 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: 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: 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 +244,57 @@ 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: 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)
+
+
+@typing.overload
+def mark_bad(
+    calibration: local_types.DeckCalibration,
+    source_marked_bad: local_types.SourceType
+    ) -> local_types.DeckCalibration: ...
+
+
+@typing.overload
+def mark_bad(
+    calibration: local_types.PipetteOffsetCalibration,
+    source_marked_bad: local_types.SourceType
+    ) -> local_types.PipetteOffsetCalibration: ...
+
+
+@typing.overload
+def mark_bad(
+    calibration: local_types.TipLengthCalibration,
+    source_marked_bad: local_types.SourceType
+    ) -> local_types.TipLengthCalibration: ...
+
+
+def mark_bad(calibration, source_marked_bad: local_types.SourceType):
+    caldict = asdict(calibration)
+    # remove current status key
+    del caldict['status']
+    status = local_types.CalibrationStatus(
+        markedBad=True, source=source_marked_bad, markedAt=utc_now())
+    return type(calibration)(**caldict, status=status)

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/legacy_api/containers/__init__.py

@@ -1,7 +1,6 @@
 from collections import OrderedDict
 import itertools
 import logging
-from typing import TYPE_CHECKING
 from opentrons.config import CONFIG
 from opentrons.data_storage import database
 from opentrons.util.vector import Vector
@@ -23,11 +22,9 @@
     get,
     helpers as cal_helpers,
     file_operators as io,
+    types as cal_types,
     modify)
 
-if TYPE_CHECKING:
-    from opentrons.calibration_storage.dev_types import TipLengthCalibration
-
 
 __all__ = [
     'Deck',
@@ -290,7 +287,7 @@ def load_new_labware_def(definition):
 
 
 def load_tip_length_calibration(
-        pip_id: str, location) -> 'TipLengthCalibration':
+        pip_id: str, location) -> cal_types.TipLengthCalibration:
     placeable, _ = unpack_location(location)
     lw = placeable.get_parent()
     return get._get_tip_length_data(

api/src/opentrons/protocol_api/instrument_context.py

@@ -1567,6 +1567,6 @@ def _build_length_from_overlap() -> float:
             return get.load_tip_length_calibration(
                 self.hw_pipette['pipette_id'],
                 tiprack._implementation.get_definition(),
-                parent)['tipLength']
+                parent).tip_length
         except TipLengthCalNotFound:
             return _build_length_from_overlap()

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()

api/tests/opentrons/protocol_api/test_context.py

@@ -856,7 +856,14 @@ def test_tip_length_for_caldata(loop, monkeypatch, use_new_calibration):
     instr = ctx.load_instrument('p20_single_gen2', 'left')
     tiprack = ctx.load_labware('geb_96_tiprack_10ul', '1')
     mock_tip_length = mock.Mock()
-    mock_tip_length.return_value = {'tipLength': 2}
+    mock_tip_length.return_value =\
+        cs_types.TipLengthCalibration(
+            tip_length=2,
+            pipette='fake id',
+            tiprack='fake_hash',
+            last_modified='some time',
+            source=cs_types.SourceType.user,
+            status=cs_types.CalibrationStatus(markedBad=False))
     monkeypatch.setattr(get, 'load_tip_length_calibration', mock_tip_length)
     instr._tip_length_for.cache_clear()
     assert instr._tip_length_for(tiprack) == 2

api/tests/opentrons/protocol_api/test_offsets.py

@@ -238,8 +238,15 @@ def test_load_tip_length_calibration_data(monkeypatch, clear_tlc_calibration):
     modify.save_tip_length_calibration(PIPETTE_ID, test_data)
     result = get.load_tip_length_calibration(
         PIPETTE_ID, minimalLabwareDef, parent)
-
-    assert result == test_data[MOCK_HASH]
+    expected = cs_types.TipLengthCalibration(
+        tip_length=tip_length,
+        pipette=PIPETTE_ID,
+        source=cs_types.SourceType.user,
+        status=cs_types.CalibrationStatus(markedBad=False),
+        tiprack=MOCK_HASH,
+        last_modified=test_data[MOCK_HASH]['lastModified']
+    )
+    assert result == expected
 
 
 def test_clear_tip_length_calibration_data(monkeypatch):

app/src/components/CheckCalibration/ResultsSummary.js

@@ -48,7 +48,12 @@ const LOOKING_FOR_DATA = 'Looking for your detailed calibration data?'
 const DOWNLOAD_SUMMARY = 'Download JSON summary'
 
 export function ResultsSummary(props: CalibrationPanelProps): React.Node {
-  const { comparisonsByPipette, instruments, cleanUpAndExit } = props
+  const {
+    comparisonsByPipette,
+    instruments,
+    checkBothPipettes,
+    cleanUpAndExit,
+  } = props
 
   if (!comparisonsByPipette || !instruments) {
     return null
@@ -93,7 +98,10 @@ export function ResultsSummary(props: CalibrationPanelProps): React.Node {
     },
   }
 
-  const deckCalibrationResult = comparisonsByPipette.first.deck?.status ?? null
+  const getDeckCalibration = checkBothPipettes
+    ? comparisonsByPipette.second.deck?.status
+    : comparisonsByPipette.first.deck?.status
+  const deckCalibrationResult = getDeckCalibration ?? null
 
   return (
     <>