fix(robot-server): save custom tiprack def on robot during tip length…

… cal (#7231)

* fix(robot-server): save custom tiprack def on robot during tip length cal

* remove log statements

* add missing module

* fix lint error

* add tests

api/src/opentrons/calibration_storage/get.py

@@ -4,6 +4,7 @@
 labware calibration from its designated file location.
 """
 import itertools
+import json
 import typing
 from typing_extensions import Literal
 
@@ -282,3 +283,22 @@ def get_all_pipette_offset_calibrations() \
                         source=_get_calibration_source(data),
                         status=_get_calibration_status(data)))
     return all_calibrations
+
+
+def get_custom_tiprack_definition_for_tlc(labware_uri: str) -> 'LabwareDefinition':
+    """
+    Return the custom tiprack definition saved in the custom tiprack directory
+    during tip length calibration
+    """
+    custom_tiprack_dir = config.get_custom_tiprack_def_path()
+    custom_tiprack_path = custom_tiprack_dir / f'{labware_uri}.json'
+    try:
+        with open(custom_tiprack_path, 'rb') as f:
+            return json.loads(f.read().decode('utf-8'))
+    except FileNotFoundError:
+        raise FileNotFoundError(
+            f'Custom tiprack {labware_uri} not found in the custom tiprack'
+            'directory on the robot. Please recalibrate tip length and '
+            'pipette offset with this tiprack before performing calibration '
+            'health check.'
+        )

api/src/opentrons/calibration_storage/modify.py

@@ -11,6 +11,7 @@
 from opentrons import config
 from opentrons.types import Mount, Point
 
+from opentrons.protocols.api_support.constants import OPENTRONS_NAMESPACE
 from opentrons.util.helpers import utc_now
 
 from . import (
@@ -140,10 +141,24 @@ def create_tip_length_data(
         'uri': labware_uri
     }
 
+    if not definition.get('namespace') == OPENTRONS_NAMESPACE:
+        _save_custom_tiprack_definition(labware_uri, definition)
+
     data = {labware_hash + parent: tip_length_data}
     return data
 
 
+def _save_custom_tiprack_definition(
+        labware_uri: str, definition: 'LabwareDefinition'):
+    namespace, load_name, version = labware_uri.split('/')
+    custom_tr_dir_path = config.get_custom_tiprack_def_path()
+    custom_namespace_dir = custom_tr_dir_path/f'{namespace}/{load_name}'
+    custom_namespace_dir.mkdir(parents=True, exist_ok=True)
+
+    custom_tr_def_path = custom_namespace_dir/f'{version}.json'
+    io.save_to_file(custom_tr_def_path, definition)
+
+
 def _helper_offset_data_format(filepath: str, delta: Point) -> dict:
     if not Path(filepath).is_file():
         calibration_data = {

api/src/opentrons/config/__init__.py

@@ -201,7 +201,13 @@ class ConfigElement(NamedTuple):
                   'Pipette Calibration Directory',
                   Path('robot') / 'pipettes',
                   ConfigElementType.DIR,
-                  'The dir where pipette calibration is stored')
+                  'The dir where pipette calibration is stored'),
+    ConfigElement('custom_tiprack_dir',
+                  'Custom Tiprack Directory',
+                  Path('tip_lengths') / 'custom_tiprack_definitions',
+                  ConfigElementType.DIR,
+                  'The dir where custom tiprack definitions for tip length '
+                  'calibration are stored')
 )
 #: The available configuration file elements to modify. All of these can be
 #: changed by editing opentrons.json, where the keys are the name elements,
@@ -506,3 +512,7 @@ def get_opentrons_path(path_name: str) -> Path:
 
 def get_tip_length_cal_path():
     return get_opentrons_path('tip_length_calibration_dir')
+
+
+def get_custom_tiprack_def_path():
+    return get_opentrons_path('custom_tiprack_dir')

api/tests/opentrons/protocol_api/test_offsets.py

@@ -20,6 +20,7 @@
 
 MOCK_HASH = 'mock_hash'
 PIPETTE_ID = 'pipette_id'
+URI = 'custom/minimal_labware_def/1'
 
 minimalLabwareDef = {
     "metadata": {
@@ -62,7 +63,7 @@
         "yDimension": 2.0,
         "zDimension": 3.0
     },
-    "namespace": "opentrons",
+    "namespace": "custom",
     "version": 1
 }
 
@@ -78,6 +79,11 @@ def tlc_path(pip_id):
         / '{}.json'.format(pip_id)
 
 
+def custom_tiprack_path(uri):
+    return config.get_custom_tiprack_def_path() \
+        / '{}.json'.format(uri)
+
+
 def mock_hash_labware(labware_def):
     return MOCK_HASH
 
@@ -95,6 +101,19 @@ def clear_calibration(monkeypatch):
         pass
 
 
+@pytest.fixture
+def clear_custom_tiprack_dir(monkeypatch):
+    try:
+        os.remove(custom_tiprack_path(URI))
+    except FileNotFoundError:
+        pass
+    yield
+    try:
+        os.remove(custom_tiprack_path(URI))
+    except FileNotFoundError:
+        pass
+
+
 @pytest.fixture
 def clear_tlc_calibration(monkeypatch):
     try:
@@ -139,7 +158,7 @@ def test_json_datetime_encoder():
     assert decoded == original
 
 
-def test_create_tip_length_calibration_data(monkeypatch):
+def test_create_tip_length_calibration_data(monkeypatch, clear_custom_tiprack_dir):
 
     fake_time = utc_now()
 
@@ -157,15 +176,18 @@ def test_create_tip_length_calibration_data(monkeypatch):
             'lastModified': fake_time,
             'source': cs_types.SourceType.user,
             'status': {'markedBad': False},
-            'uri': 'opentrons/minimal_labware_def/1'
+            'uri': URI
         }
     }
+    assert not os.path.exists(custom_tiprack_path(URI))
     result = modify.create_tip_length_data(
         minimalLabwareDef, parent, tip_length)
     assert result == expected_data
+    assert os.path.exists(custom_tiprack_path(URI))
 
 
-def test_save_tip_length_calibration_data(monkeypatch, clear_tlc_calibration):
+def test_save_tip_length_calibration_data(monkeypatch,
+                                          clear_tlc_calibration):
     assert not os.path.exists(tlc_path(PIPETTE_ID))
 
     test_data = {
@@ -239,7 +261,7 @@ def test_load_tip_length_calibration_data(monkeypatch, clear_tlc_calibration):
         source=cs_types.SourceType.user,
         status=cs_types.CalibrationStatus(markedBad=False),
         tiprack=MOCK_HASH,
-        uri='opentrons/minimal_labware_def/1',
+        uri='custom/minimal_labware_def/1',
         last_modified=test_data[MOCK_HASH]['lastModified']
     )
     assert result == expected
@@ -256,9 +278,9 @@ def test_clear_tip_length_calibration_data(monkeypatch):
         }
         json.dump(test_offset, offset_file)
 
-    assert len(os.listdir(calpath)) > 0
+    assert len([f for f in os.listdir(calpath) if f.endswith('.json')]) > 0
     delete.clear_tip_length_calibration()
-    assert len(os.listdir(calpath)) == 0
+    assert len([f for f in os.listdir(calpath) if f.endswith('.json')]) == 0
 
 
 def test_schema_shape(monkeypatch, clear_calibration):

robot-server/robot_server/robot/calibration/check/user_flow.py

@@ -12,6 +12,7 @@
 from opentrons.hardware_control import (
     ThreadManager, CriticalPoint, Pipette, robot_calibration, util)
 from opentrons.protocol_api import labware
+from opentrons.protocols.api_support.constants import OPENTRONS_NAMESPACE
 from opentrons.config import feature_flags as ff
 from opentrons.protocols.geometry.deck import Deck
 
@@ -311,13 +312,18 @@ def _get_tip_length_from_pipette(
             return None
         details = helpers.details_from_uri(pip_offset.uri)
         position = self._deck.position_for(TIPRACK_SLOT)
-        tiprack = labware.load(load_name=details.load_name,
-                               namespace=details.namespace,
-                               version=details.version,
-                               parent=position)
+        if details.namespace == OPENTRONS_NAMESPACE:
+            tiprack = labware.load(load_name=details.load_name,
+                                   namespace=details.namespace,
+                                   version=details.version,
+                                   parent=position)
+            tiprack_def = tiprack._implementation.get_definition()
+        else:
+            tiprack_def = get.get_custom_tiprack_definition_for_tlc(
+                pip_offset.uri)
         return get.load_tip_length_calibration(
             pipette.pipette_id,
-            tiprack._implementation.get_definition(),
+            tiprack_def,
             '')
 
     def _check_valid_calibrations(self):
@@ -402,6 +408,12 @@ def _get_tr_lw(tip_rack_def: Optional['LabwareDefinition'],
             try:
                 details \
                      = helpers.details_from_uri(existing_calibration.uri)
+                if not details.namespace == OPENTRONS_NAMESPACE:
+                    tiprack_def = get.get_custom_tiprack_definition_for_tlc(
+                        existing_calibration.uri)
+                    return labware.load_from_definition(
+                        definition=tiprack_def,
+                        parent=position)
                 return labware.load(load_name=details.load_name,
                                     namespace=details.namespace,
                                     version=details.version,

robot-server/tests/conftest.py

@@ -228,3 +228,66 @@ def _get_labware_fixture(fixture_name):
             return json.loads(f.read().decode('utf-8'))
 
     return _get_labware_fixture
+
+
+@pytest.fixture
+def custom_tiprack_def():
+    return {
+        "metadata": {
+            "displayName": "minimal labware"
+        },
+        "cornerOffsetFromSlot": {
+            "x": 10,
+            "y": 10,
+            "z": 5
+        },
+        "parameters": {
+            "isTiprack": True,
+            "tipLength": 55.3,
+            "tipOverlap": 2.8,
+            "loadName": "minimal_labware_def"
+        },
+        "ordering": [["A1"], ["A2"]],
+        "wells": {
+            "A1": {
+                "depth": 40,
+                "totalLiquidVolume": 100,
+                "diameter": 30,
+                "x": 0,
+                "y": 0,
+                "z": 0,
+                "shape": "circular"
+            },
+            "A2": {
+                "depth": 40,
+                "totalLiquidVolume": 100,
+                "diameter": 30,
+                "x": 10,
+                "y": 0,
+                "z": 0,
+                "shape": "circular"
+            }
+        },
+        "dimensions": {
+            "xDimension": 1.0,
+            "yDimension": 2.0,
+            "zDimension": 3.0
+        },
+        "namespace": "custom",
+        "version": 1
+    }
+
+
+@pytest.fixture
+def clear_custom_tiprack_def_dir():
+    tiprack_path = config.get_custom_tiprack_def_path() \
+        / 'custom/minimal_labware_def/1.json'
+    try:
+        os.remove(tiprack_path)
+    except FileNotFoundError:
+        pass
+    yield
+    try:
+        os.remove(tiprack_path)
+    except FileNotFoundError:
+        pass

robot-server/tests/robot/calibration/check/test_user_flow.py

@@ -4,7 +4,7 @@
 import pytest
 from opentrons.hardware_control import pipette
 from opentrons.types import Mount, Point
-from opentrons.calibration_storage import get, types as CSTypes
+from opentrons.calibration_storage import get, modify, types as CSTypes
 from opentrons.config import robot_configs
 from opentrons.config.pipette_config import load
 
@@ -140,6 +140,14 @@ def build_mock_stored_pipette_offset(kind='normal'):
                 uri='opentrons/opentrons_96_filtertiprack_200ul/1',
                 source=CSTypes.SourceType.user,
                 status=CSTypes.CalibrationStatus(markedBad=False)))
+    elif kind == 'custom_tiprack':
+        return MagicMock(
+            return_value=CSTypes.PipetteOffsetByPipetteMount(
+                offset=[0, 1, 2],
+                tiprack='tiprack-id',
+                uri='custom/minimal_labware_def/1',
+                source=CSTypes.SourceType.user,
+                status=CSTypes.CalibrationStatus(markedBad=False)))
     else:
         return MagicMock(return_value=None)
 
@@ -155,6 +163,16 @@ def build_mock_stored_tip_length(kind='normal'):
             status=CSTypes.CalibrationStatus(markedBad=False),
             uri='path/to_my_labware/1')
         return MagicMock(return_value=tip_length)
+    elif kind == 'custom_tiprack':
+        tip_length = CSTypes.TipLengthCalibration(
+            tip_length=30,
+            pipette='fake id',
+            tiprack='fake_hash',
+            last_modified='some time',
+            source=CSTypes.SourceType.user,
+            status=CSTypes.CalibrationStatus(markedBad=False),
+            uri='custom/minimal_labware_def/1')
+        return MagicMock(return_value=tip_length)
     else:
         return MagicMock(return_value=None)
 
@@ -201,6 +219,33 @@ def test_load_labware(mock_hw):
         assert len(uf.get_required_labware()) == 2
 
 
+def test_load_custom_tiprack(mock_hw,
+                             custom_tiprack_def,
+                             clear_custom_tiprack_def_dir):
+    # save custom tiprack definition to custom tiprack directory
+    modify._save_custom_tiprack_definition(
+        'custom/minimal_labware_def/1',
+        custom_tiprack_def
+    )
+    # load a labware with calibrations
+    with patch.object(
+            get,
+            'get_robot_deck_attitude',
+            new=build_mock_deck_calibration()),\
+            patch.object(
+                get,
+                'load_tip_length_calibration',
+                new=build_mock_stored_tip_length('custom_tiprack')),\
+            patch.object(
+                get, 'get_pipette_offset',
+                new=build_mock_stored_pipette_offset('custom_tiprack')):
+        uf = CheckCalibrationUserFlow(
+            hardware=mock_hw, has_calibration_block=True)
+        assert uf.active_tiprack._implementation.get_display_name() ==\
+            'minimal labware on 8'
+        assert len(uf.get_required_labware()) == 2
+
+
 def test_bad_calibration(mock_hw):
     with pytest.raises(RobotServerError):
         CheckCalibrationUserFlow(hardware=mock_hw)