Merge branch 'edge' into E2E_Transfer_and_Command_update

analyses-snapshot-testing/README.md

@@ -86,3 +86,20 @@ You have the option to specify one or many protocols to run the analyses on. Thi
 ### Updating the snapshots locally
 
 - `make snapshot-test-update-local` - this target builds the base image, builds the local code into the base image, then runs the analyses battery against the image you just created, updating the snapshots by passing the `--update-snapshots` flag to the test
+
+### Add some protocols to the analyses battery
+
+> The below instructions avoid needing docker and executing snapshot tests locally.
+
+1. create new protocol file(s) in the [files/protocols](./files/protocols) directory following the naming convention in [files/README.md](./files/README.md)
+1. add the protocol(s) to the [protocols.py](./automation/data/protocols.py)
+1. `make format` (make sure you have followed setup instructions)
+1. commit and push your branch
+1. open a PR and add the label `gen-analyses-snapshot-pr`
+1. when the snapshot fails because your new protocols don't have snapshots a PR will be created that heals.
+1. merge the healing PR if the snapshots are as expected
+1. get a review and merge! 🎉 now your protocols are a part of the test
+
+### Add a protocol with overrides to the analyses battery
+
+> TODO when we have a more straight forward example

analyses-snapshot-testing/automation/data/protocols.py

@@ -708,6 +708,48 @@ class Protocols:
         file_extension="py",
         robot="Flex",
     )
+    # analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_no_trash.py
+    Flex_X_v2_21_plate_reader_no_trash: Protocol = Protocol(
+        file_stem="Flex_X_v2_21_plate_reader_no_trash",
+        file_extension="py",
+        robot="Flex",
+    )
+    # analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_wrong_plate.py
+    Flex_X_v2_21_plate_reader_wrong_plate: Protocol = Protocol(
+        file_stem="Flex_X_v2_21_plate_reader_wrong_plate",
+        file_extension="py",
+        robot="Flex",
+    )
+    # analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_wrong_plate2.py
+    Flex_X_v2_21_plate_reader_wrong_plate2: Protocol = Protocol(
+        file_stem="Flex_X_v2_21_plate_reader_wrong_plate2",
+        file_extension="py",
+        robot="Flex",
+    )
+    # analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_bad_slot.py
+    Flex_X_v2_21_plate_reader_bad_slot: Protocol = Protocol(
+        file_stem="Flex_X_v2_21_plate_reader_bad_slot",
+        file_extension="py",
+        robot="Flex",
+    )
+    # analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_no_close_lid.py
+    Flex_X_v2_21_plate_reader_no_close_lid: Protocol = Protocol(
+        file_stem="Flex_X_v2_21_plate_reader_no_close_lid",
+        file_extension="py",
+        robot="Flex",
+    )
+    # analyses-snapshot-testing/files/protocols/Flex_S_v2_21_tc_lids_happy_path.py
+    Flex_S_v2_21_tc_lids_happy_path: Protocol = Protocol(
+        file_stem="Flex_S_v2_21_tc_lids_happy_path",
+        file_extension="py",
+        robot="Flex",
+    )
+    # analyses-snapshot-testing/files/protocols/Flex_X_v2_21_tc_lids_wrong_target.py
+    Flex_X_v2_21_tc_lids_wrong_target: Protocol = Protocol(
+        file_stem="Flex_X_v2_21_tc_lids_wrong_target",
+        file_extension="py",
+        robot="Flex",
+    )
 
     OT2_X_v2_18_None_None_duplicateRTPVariableName: Protocol = Protocol(
         file_stem="OT2_X_v2_18_None_None_duplicateRTPVariableName",

analyses-snapshot-testing/files/protocols/Flex_S_v2_21_tc_lids_happy_path.py

@@ -0,0 +1,99 @@
+from typing import List, Dict, Any, Optional
+from opentrons.protocol_api import ProtocolContext, Labware
+
+metadata = {"protocolName": "Opentrons Flex Deck Riser with TC Lids Test"}
+requirements = {"robotType": "Flex", "apiLevel": "2.21"}
+
+
+"""
+Setup:
+ - 1-5x lids are stacked in deck D2
+ - Thermocycler installed
+
+Run:
+ - For each lid in the stack (1-5x)
+   - Move lid in D2 to Thermocycler
+     - Remove top-most lid
+     - PAUSE, wait for tester to press continue
+   - Move lid from Thermocycler to new slot C2
+     - Stacked onto any previously placed lids
+"""
+
+LID_STARTING_SLOT = "B2"
+LID_ENDING_SLOT = "C2"
+LID_COUNT = 3
+LID_DEFINITION = "opentrons_tough_pcr_auto_sealing_lid"
+LID_BOTTOM_DEFINITION = "opentrons_tough_pcr_auto_sealing_lid"
+DECK_RISER_NAME = "opentrons_flex_deck_riser"
+USING_THERMOCYCLER = True
+
+OFFSET_DECK = {
+    "pick-up": {"x": 0, "y": 0, "z": 0},
+    "drop": {"x": 0, "y": 0, "z": 0},
+}
+OFFSET_THERMOCYCLER = {
+    "pick-up": {"x": 0, "y": 0, "z": 0},
+    "drop": {"x": 0, "y": 0, "z": 0},
+}
+
+
+def _move_labware_with_offset_and_pause(
+    protocol: ProtocolContext,
+    labware: Labware,
+    destination: Any,
+    pick_up_offset: Optional[Dict[str, float]] = None,
+    drop_offset: Optional[Dict[str, float]] = None,
+) -> None:
+    protocol.move_labware(
+        labware,
+        destination,
+        use_gripper=True,
+        pick_up_offset=pick_up_offset,
+        drop_offset=drop_offset,
+    )
+
+
+def run(protocol: ProtocolContext):
+    # SETUP
+    deck_riser_adapter = protocol.load_adapter(DECK_RISER_NAME, "B2")
+
+    lids: List[Labware] = [deck_riser_adapter.load_labware(LID_BOTTOM_DEFINITION)]
+    for i in range(LID_COUNT - 1):
+        lids.append(lids[-1].load_labware(LID_DEFINITION))
+    lids.reverse()  # NOTE: reversing to more easily loop through lids from top-to-bottom
+    if USING_THERMOCYCLER:
+        # TODO: confirm if we need to load 96-well adapter onto Thermocycler
+        thermocycler = protocol.load_module("thermocyclerModuleV2")
+        thermocycler.open_lid()
+        plate_in_cycler = thermocycler.load_labware("armadillo_96_wellplate_200ul_pcr_full_skirt")
+    else:
+        plate_in_cycler = None
+
+    # RUN
+    prev_moved_lid: Optional[Labware] = None
+    for lid in lids:
+
+        if USING_THERMOCYCLER:
+            _move_labware_with_offset_and_pause(
+                protocol,
+                lid,
+                plate_in_cycler,
+                pick_up_offset=OFFSET_DECK["pick-up"],
+                drop_offset=OFFSET_THERMOCYCLER["drop"],
+            )
+            _move_labware_with_offset_and_pause(
+                protocol,
+                lid,
+                prev_moved_lid if prev_moved_lid else LID_ENDING_SLOT,
+                pick_up_offset=OFFSET_THERMOCYCLER["pick-up"],
+                drop_offset=OFFSET_DECK["drop"],
+            )
+        else:
+            _move_labware_with_offset_and_pause(
+                protocol,
+                lid,
+                prev_moved_lid if prev_moved_lid else LID_ENDING_SLOT,
+                pick_up_offset=OFFSET_DECK["pick-up"],
+                drop_offset=OFFSET_DECK["drop"],
+            )
+        prev_moved_lid = lid

analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_bad_slot.py

@@ -0,0 +1,22 @@
+from typing import cast
+from opentrons import protocol_api
+from opentrons.protocol_api.module_contexts import AbsorbanceReaderContext
+
+from opentrons import protocol_api
+from opentrons.protocol_api import SINGLE, ALL
+
+requirements = {"robotType": "Flex", "apiLevel": "2.21"}
+metadata = {"protocolName": "plate_reader bad slot"}
+
+
+def run(protocol: protocol_api.ProtocolContext):
+    partial_rack = protocol.load_labware(load_name="opentrons_flex_96_tiprack_1000ul", location="D3")
+    trash = protocol.load_trash_bin("A3")
+    instrument = protocol.load_instrument(instrument_name="flex_8channel_1000", mount="right")
+    instrument.configure_nozzle_layout(style=SINGLE, start="H1", tip_racks=[partial_rack])
+
+    plate_1 = protocol.load_labware("nest_96_wellplate_200ul_flat", "D1")
+    mod = protocol.load_module("absorbanceReaderV1", "C1")
+    mod.open_lid()
+    protocol.move_labware(plate_1, mod, use_gripper=True)
+    mod.close_lid()

analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_no_close_lid.py

@@ -0,0 +1,88 @@
+from typing import cast
+from opentrons import protocol_api
+from opentrons.protocol_api.module_contexts import AbsorbanceReaderContext
+
+# metadata
+metadata = {
+    "protocolName": "Absorbance Reader no close lid",
+    "author": "Platform Expansion",
+}
+
+requirements = {
+    "robotType": "Flex",
+    "apiLevel": "2.21",
+}
+
+
+# protocol run function
+def run(protocol: protocol_api.ProtocolContext):
+    mod = cast(AbsorbanceReaderContext, protocol.load_module("absorbanceReaderV1", "D3"))
+    plate = protocol.load_labware("nest_96_wellplate_200ul_flat", "C2")
+    tiprack_1000 = protocol.load_labware(load_name="opentrons_flex_96_tiprack_50ul", location="B2")
+    trash_labware = protocol.load_trash_bin("B3")
+    instrument = protocol.load_instrument("flex_8channel_50", "right", tip_racks=[tiprack_1000])
+
+    # pick up tip and perform action
+    instrument.pick_up_tip(tiprack_1000.wells_by_name()["A1"])
+    instrument.aspirate(30, plate.wells_by_name()["A1"])
+    instrument.dispense(30, plate.wells_by_name()["B1"])
+    instrument.return_tip()
+
+    # Initialize to a single wavelength with reference wavelength
+    # Issue: Make sure there is no labware here or youll get an error
+    # mod.close_lid()
+    mod.initialize("single", [600], 450)
+
+    # NOTE: CANNOT INITIALIZE WITH THE LID OPEN
+
+    # Remove the Plate Reader lid using the Gripper.
+    mod.open_lid()
+    protocol.move_labware(plate, mod, use_gripper=True)
+    mod.close_lid()
+
+    # Take a reading and show the resulting absorbance values.
+    # Issue: cant read before you initialize or you an get an error
+    result = mod.read()
+    msg = f"single: {result}"
+    protocol.comment(msg=msg)
+    protocol.pause(msg=msg)
+
+    # Initialize to multiple wavelengths
+    protocol.pause(msg="Perform Multi Read")
+    mod.open_lid()
+    protocol.move_labware(plate, "C2", use_gripper=True)
+
+    mod.close_lid()
+
+    # mod.initialize('multi', [450, 570, 600])
+    mod.initialize("multi", [450, 600])
+    # Open the lid and move the labware into the reader
+    mod.open_lid()
+    protocol.move_labware(plate, mod, use_gripper=True)
+
+    # pick up tip and perform action on labware inside plate reader
+    instrument.pick_up_tip(tiprack_1000.wells_by_name()["A1"])
+    instrument.aspirate(30, plate.wells_by_name()["A1"])
+    instrument.dispense(30, plate.wells_by_name()["B1"])
+    instrument.return_tip()
+
+    mod.close_lid()
+
+    # Take reading
+    result = mod.read()
+    msg = f"multi: {result}"
+    protocol.comment(msg=msg)
+    protocol.pause(msg=msg)
+
+    # Take a reading and save to csv
+    protocol.pause(msg="Perform Read and Save to CSV")
+    result = mod.read(export_filename="plate_reader_csv.csv")
+    msg = f"csv: {result}"
+    protocol.pause(msg=msg)
+
+    # Place the Plate Reader lid back on using the Gripper.
+    mod.open_lid()
+    protocol.move_labware(plate, "C2", use_gripper=True)
+    mod.close_lid()
+
+    mod.read(export_filename="csv_name.csv")

analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_no_trash.py

@@ -0,0 +1,24 @@
+from typing import cast
+from opentrons import protocol_api
+from opentrons.protocol_api.module_contexts import AbsorbanceReaderContext
+
+from opentrons import protocol_api
+from opentrons.protocol_api import SINGLE, ALL
+
+requirements = {"robotType": "Flex", "apiLevel": "2.21"}
+metadata = {"protocolName": "plate_reader no trash"}
+
+
+def run(protocol: protocol_api.ProtocolContext):
+    partial_rack = protocol.load_labware(load_name="opentrons_flex_96_tiprack_1000ul", location="D2")
+    trash = protocol.load_trash_bin("A3")
+    instrument = protocol.load_instrument(instrument_name="flex_8channel_1000", mount="right")
+    instrument.configure_nozzle_layout(style=SINGLE, start="H1", tip_racks=[partial_rack])
+
+    plate_1 = protocol.load_labware("nest_96_wellplate_200ul_flat", "C1")
+
+    mod = protocol.load_module("absorbanceReaderV1", "B3")
+
+    mod.open_lid()
+    protocol.move_labware(plate_1, mod, use_gripper=True)
+    protocol.move_labware(plate_1, trash, use_gripper=True)

analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_wrong_plate.py

@@ -0,0 +1,24 @@
+from typing import cast
+from opentrons import protocol_api
+from opentrons.protocol_api.module_contexts import AbsorbanceReaderContext
+
+from opentrons import protocol_api
+from opentrons.protocol_api import SINGLE, ALL
+
+requirements = {"robotType": "Flex", "apiLevel": "2.21"}
+metadata = {"protocolName": "plate_reader wrong plate"}
+
+
+def run(protocol: protocol_api.ProtocolContext):
+    partial_rack = protocol.load_labware(load_name="opentrons_flex_96_tiprack_1000ul", location="D2")
+    trash = protocol.load_trash_bin("A3")
+    instrument = protocol.load_instrument(instrument_name="flex_8channel_1000", mount="right")
+    instrument.configure_nozzle_layout(style=SINGLE, start="H1", tip_racks=[partial_rack])
+
+    plate_1 = protocol.load_labware("corning_12_wellplate_6.9ml_flat", "C2")
+
+    mod = protocol.load_module("absorbanceReaderV1", "B3")
+
+    mod.open_lid()
+    protocol.move_labware(plate_1, mod, use_gripper=True)
+    protocol.move_labware(plate_1, trash, use_gripper=True)

analyses-snapshot-testing/files/protocols/Flex_X_v2_21_plate_reader_wrong_plate2.py

@@ -0,0 +1,24 @@
+from typing import cast
+from opentrons import protocol_api
+from opentrons.protocol_api.module_contexts import AbsorbanceReaderContext
+
+from opentrons import protocol_api
+from opentrons.protocol_api import SINGLE, ALL
+
+requirements = {"robotType": "Flex", "apiLevel": "2.21"}
+metadata = {"protocolName": "plate_reader wrong plate"}
+
+
+def run(protocol: protocol_api.ProtocolContext):
+    partial_rack = protocol.load_labware(load_name="opentrons_flex_96_tiprack_1000ul", location="D2")
+    trash = protocol.load_trash_bin("A3")
+    instrument = protocol.load_instrument(instrument_name="flex_8channel_1000", mount="right")
+    instrument.configure_nozzle_layout(style=SINGLE, start="H1", tip_racks=[partial_rack])
+
+    plate_1 = protocol.load_labware("thermoscientificnunc_96_wellplate_2000ul", "C2")
+
+    mod = protocol.load_module("absorbanceReaderV1", "B3")
+
+    mod.open_lid()
+    protocol.move_labware(plate_1, mod, use_gripper=True)
+    protocol.move_labware(plate_1, trash, use_gripper=True)

analyses-snapshot-testing/files/protocols/Flex_X_v2_21_tc_lids_wrong_target.py

@@ -0,0 +1,26 @@
+from typing import List, Dict, Any, Optional
+from opentrons.protocol_api import ProtocolContext, Labware
+
+metadata = {"Stacking a deep well plate on its adapter "}
+requirements = {"robotType": "Flex", "apiLevel": "2.21"}
+
+
+def run(protocol: ProtocolContext):
+    temp_mod = protocol.load_module(module_name="temperature module gen2", location="D1")
+    LID_COUNT = 5
+    LID_DEFINITION = "opentrons_tough_pcr_auto_sealing_lid"
+    LID_BOTTOM_DEFINITION = "opentrons_tough_pcr_auto_sealing_lid"
+    adapter = temp_mod.load_adapter("opentrons_96_deep_well_temp_mod_adapter")
+    stack = protocol.load_labware("nest_96_wellplate_2ml_deep", "A1")
+    deck_riser_adapter = protocol.load_adapter("opentrons_flex_deck_riser", "B2")
+    protocol.move_labware(stack, adapter)
+    lids = [deck_riser_adapter.load_labware(LID_BOTTOM_DEFINITION, "D2")]
+    for i in range(LID_COUNT - 1):
+        lids.append(lids[-1].load_labware(LID_DEFINITION))
+    lids.reverse()  # NOTE: reversing to more easily loop through lids from top-to-bottom
+
+    protocol.move_labware(
+        lids[0],
+        stack,
+        use_gripper=True,
+    )