Merge branch 'edge' into EXEC-655-store-commands-error-list-in-db

Opentrons · Nov 20, 2024 · 5af324e · 5af324e
2 parents 11aa280 + 54a4017
commit 5af324e
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diff --git a/.github/workflows/analyses-snapshot-test.yaml b/.github/workflows/analyses-snapshot-test.yaml
@@ -45,12 +45,13 @@ jobs:
     timeout-minutes: 15
     runs-on: ubuntu-latest
     env:
+      BASE_IMAGE_NAME: opentrons-python-base:3.10
       ANALYSIS_REF: ${{ github.event.inputs.ANALYSIS_REF || github.head_ref || 'edge' }}
       SNAPSHOT_REF: ${{ github.event.inputs.SNAPSHOT_REF || github.head_ref || 'edge' }}
       # If we're running because of workflow_dispatch, use the user input to decide
       # whether to open a PR on failure. Otherwise, there is no user input,
       # so we only open a PR if the PR has the label 'gen-analyses-snapshot-pr'
-      OPEN_PR_ON_FAILURE: ${{ (github.event_name == 'workflow_dispatch' && github.events.inputs.OPEN_PR_ON_FAILURE) || ((github.event_name != 'workflow_dispatch') && (contains(github.event.pull_request.labels.*.name, 'gen-analyses-snapshot-pr'))) }}
+      OPEN_PR_ON_FAILURE: ${{ (github.event_name == 'workflow_dispatch' && github.event.inputs.OPEN_PR_ON_FAILURE) || ((github.event_name != 'workflow_dispatch') && (contains(github.event.pull_request.labels.*.name, 'gen-analyses-snapshot-pr'))) }}
       PR_TARGET_BRANCH: ${{ github.event.pull_request.base.ref || 'not a pr'}}
     steps:
       - name: Checkout Repository
@@ -71,9 +72,24 @@ jobs:
             echo "Analyses snapshots match ${{ env.PR_TARGET_BRANCH }} snapshots."
           fi
 
-      - name: Docker Build
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build base image
+        id: build_base_image
+        uses: docker/build-push-action@v6
+        with:
+          context: analyses-snapshot-testing/citools
+          file: analyses-snapshot-testing/citools/Dockerfile.base
+          push: false
+          load: true
+          tags: ${{ env.BASE_IMAGE_NAME }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Build analysis image
         working-directory: analyses-snapshot-testing
-        run: make build-opentrons-analysis
+        run: make build-opentrons-analysis BASE_IMAGE_NAME=${{ env.BASE_IMAGE_NAME }} ANALYSIS_REF=${{ env.ANALYSIS_REF }} CACHEBUST=${{ github.run_number }}
 
       - name: Set up Python 3.13
         uses: actions/setup-python@v5
@@ -112,8 +128,8 @@ jobs:
           commit-message: 'fix(analyses-snapshot-testing): heal analyses snapshots'
           title: 'fix(analyses-snapshot-testing): heal ${{ env.ANALYSIS_REF }} snapshots'
           body: 'This PR was requested on the PR https://github.com/${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
-          branch: 'analyses-snapshot-testing/${{ env.ANALYSIS_REF }}-from-${{ env.SNAPSHOT_REF}}'
-          base: ${{ env.SNAPSHOT_REF}}
+          branch: 'analyses-snapshot-testing/${{ env.ANALYSIS_REF }}-from-${{ env.SNAPSHOT_REF }}'
+          base: ${{ env.SNAPSHOT_REF }}
 
       - name: Comment on feature PR
         if: always() && steps.create_pull_request.outcome == 'success' && github.event_name == 'pull_request'
@@ -135,5 +151,5 @@ jobs:
           commit-message: 'fix(analyses-snapshot-testing): heal ${{ env.ANALYSIS_REF }} snapshots'
           title: 'fix(analyses-snapshot-testing): heal ${{ env.ANALYSIS_REF }} snapshots'
           body: 'The ${{ env.ANALYSIS_REF }} overnight analyses snapshot test is failing. This PR was opened to alert us to the failure.'
-          branch: 'analyses-snapshot-testing/${{ env.ANALYSIS_REF }}-from-${{ env.SNAPSHOT_REF}}'
-          base: ${{ env.SNAPSHOT_REF}}
+          branch: 'analyses-snapshot-testing/${{ env.ANALYSIS_REF }}-from-${{ env.SNAPSHOT_REF }}'
+          base: ${{ env.SNAPSHOT_REF }}
diff --git a/abr-testing/abr_testing/data_collection/abr_google_drive.py b/abr-testing/abr_testing/data_collection/abr_google_drive.py
@@ -48,7 +48,11 @@ def create_data_dictionary(
         file_path = os.path.join(storage_directory, filename)
         if file_path.endswith(".json"):
             with open(file_path) as file:
-                file_results = json.load(file)
+                try:
+                    file_results = json.load(file)
+                except json.decoder.JSONDecodeError:
+                    print(f"Skipped file {file_path} bc no data.")
+                    continue
         else:
             continue
         if not isinstance(file_results, dict):

diff --git a/abr-testing/abr_testing/data_collection/get_run_logs.py b/abr-testing/abr_testing/data_collection/get_run_logs.py
@@ -17,7 +17,7 @@ def get_run_ids_from_robot(ip: str) -> Set[str]:
             f"http://{ip}:31950/runs", headers={"opentrons-version": "3"}
         )
         run_data = response.json()
-        run_list = run_data["data"]
+        run_list = run_data.get("data", "")
     except requests.exceptions.RequestException:
         print(f"Could not connect to robot with IP {ip}")
         run_list = []

diff --git a/abr-testing/abr_testing/protocols/active_protocols/10_ZymoBIOMICS_Magbead_DNA_Cells_Flex.py b/abr-testing/abr_testing/protocols/active_protocols/10_ZymoBIOMICS_Magbead_DNA_Cells_Flex.py
@@ -94,7 +94,6 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
         bind_time_1 = bind_time_2 = wash_time = 0.25
         drybeads = 0.5
         lysis_rep_1 = lysis_rep_2 = bead_reps_2 = 1
-    PK_vol = 20.0
     bead_vol = 25.0
     starting_vol = lysis_vol + sample_vol
     binding_buffer_vol = bind_vol + bead_vol
@@ -137,7 +136,7 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
     """
     lysis_ = res1.wells()[0]
     binding_buffer = res1.wells()[1:4]
-    bind2_res = res1.wells()[4:6]
+    bind2_res = res1.wells()[4:8]
     wash1 = res1.wells()[6:8]
     elution_solution = res1.wells()[-1]
     wash2 = res2.wells()[:6]
@@ -149,16 +148,12 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
     samps = sample_plate.wells()[: (8 * num_cols)]
 
     liquid_vols_and_wells: Dict[str, List[Dict[str, Well | List[Well] | float]]] = {
-        "Lysis": [{"well": lysis_, "volume": lysis_vol}],
-        "PK": [{"well": lysis_, "volume": PK_vol}],
-        "Beads": [{"well": binding_buffer, "volume": bead_vol}],
-        "Binding": [{"well": binding_buffer, "volume": bind_vol}],
-        "Binding 2": [{"well": bind2_res, "volume": bind2_vol}],
-        "Wash 1": [{"well": wash1_vol, "volume": wash1}],
-        "Wash 2": [{"well": wash2_vol, "volume": wash2}],
-        "Wash 3": [{"well": wash3_vol, "volume": wash3}],
-        "Final Elution": [{"well": elution_solution, "volume": elution_vol}],
-        "Samples": [{"well": samps, "volume": 0}],
+        "Lysis and PK": [{"well": lysis_, "volume": 12320.0}],
+        "Beads and Binding": [{"well": binding_buffer, "volume": 11875.0}],
+        "Binding 2": [{"well": bind2_res, "volume": 13500.0}],
+        "Final Elution": [{"well": elution_solution, "volume": 52000}],
+        "Samples": [{"well": samps, "volume": 0.0}],
+        "Reagents": [{"well": res2.wells(), "volume": 9000.0}],
     }
     flattened_list_of_wells = helpers.find_liquid_height_of_loaded_liquids(
         ctx, liquid_vols_and_wells, m1000

diff --git a/abr-testing/abr_testing/protocols/active_protocols/1_Simple Normalize Long Right.py b/abr-testing/abr_testing/protocols/active_protocols/1_Simple Normalize Long Right.py
@@ -121,8 +121,6 @@ def run(protocol: ProtocolContext) -> None:
         style=SINGLE, start="H1", tip_racks=[tiprack_x_1, tiprack_x_2, tiprack_x_3]
     )
     helpers.find_liquid_height_of_all_wells(protocol, p1000, wells)
-    tiprack_x_1.reset()
-
     sample_quant_csv = """
     sample_plate_1, Sample_well,DYE,DILUENT
     sample_plate_1,A1,0,100

diff --git a/abr-testing/abr_testing/protocols/helpers.py b/abr-testing/abr_testing/protocols/helpers.py
@@ -14,7 +14,6 @@
     ThermocyclerContext,
     TemperatureModuleContext,
 )
-
 from typing import List, Union, Dict
 from opentrons.hardware_control.modules.types import ThermocyclerStep
 from opentrons_shared_data.errors.exceptions import PipetteLiquidNotFoundError
@@ -225,6 +224,31 @@ def create_hs_speed_parameter(parameters: ParameterContext) -> None:
     )
 
 
+def create_tc_compatible_labware_parameter(parameters: ParameterContext) -> None:
+    """Create parameter for labware type compatible with thermocycler."""
+    parameters.add_str(
+        variable_name="labware_tc_compatible",
+        display_name="Labware Type for Thermocycler",
+        description="labware compatible with thermocycler.",
+        default="biorad_96_wellplate_200ul_pcr",
+        choices=[
+            {
+                "display_name": "Armadillo_200ul",
+                "value": "armadillo_96_wellplate_200ul_pcr_full_skirt",
+            },
+            {"display_name": "Bio-Rad_200ul", "value": "biorad_96_wellplate_200ul_pcr"},
+            {
+                "display_name": "NEST_100ul",
+                "value": "nest_96_wellplate_100ul_pcr_full_skirt",
+            },
+            {
+                "display_name": "Opentrons_200ul",
+                "value": "opentrons_96_wellplate_200ul_pcr_full_skirt",
+            },
+        ],
+    )
+
+
 # FUNCTIONS FOR COMMON MODULE SEQUENCES
 
 

diff --git a/abr-testing/abr_testing/protocols/liquid_setups/10_ZymoBIOMICS Magbead Liquid Setup.py b/abr-testing/abr_testing/protocols/liquid_setups/10_ZymoBIOMICS Magbead Liquid Setup.py
@@ -29,23 +29,35 @@ def run(protocol: protocol_api.ProtocolContext) -> None:
     res1 = protocol.load_labware("nest_12_reservoir_15ml", "C3", "R1")
     res2 = protocol.load_labware("nest_12_reservoir_15ml", "B3", "R2")
 
-    lysis_and_pk = (3200 + 320) / 8
-    beads_and_binding = (275 + 6600) / 8
-    binding2 = 5500 / 8
-    wash1 = 5500 / 8
-    final_elution = 2100 / 8
+    lysis_and_pk = 12320 / 8
+    beads_and_binding = 11875 / 8
+    binding2 = 13500 / 8
     wash2 = 9000 / 8
-    wash3 = 9000 / 8
+    wash2_list = [wash2] * 12
     # Fill up Plates
     # Res1
     p1000.transfer(
-        volume=[lysis_and_pk, beads_and_binding, binding2, wash1, final_elution],
+        volume=[
+            lysis_and_pk,
+            beads_and_binding,
+            beads_and_binding,
+            beads_and_binding,
+            binding2,
+            binding2,
+            binding2,
+            binding2,
+            binding2,
+        ],
         source=source_reservoir["A1"].bottom(z=0.2),
         dest=[
             res1["A1"].top(),
             res1["A2"].top(),
+            res1["A3"].top(),
+            res1["A4"].top(),
             res1["A5"].top(),
+            res1["A6"].top(),
             res1["A7"].top(),
+            res1["A8"].top(),
             res1["A12"].top(),
         ],
         blow_out=True,
@@ -54,9 +66,9 @@ def run(protocol: protocol_api.ProtocolContext) -> None:
     )
     # Res2
     p1000.transfer(
-        volume=[wash2, wash3],
+        volume=wash2_list,
         source=source_reservoir["A1"],
-        dest=[res2["A1"].top(), res2["A7"].top()],
+        dest=res2.wells(),
         blow_out=True,
         blowout_location="source well",
         trash=False,

diff --git a/...testing/abr_testing/protocols/liquid_setups/7_HDQ DNA Bacteria Extraction Liquid Setup.py b/...testing/abr_testing/protocols/liquid_setups/7_HDQ DNA Bacteria Extraction Liquid Setup.py
@@ -35,15 +35,23 @@ def run(protocol: protocol_api.ProtocolContext) -> None:
     res1 = protocol.load_labware("nest_12_reservoir_15ml", "D2", "reagent reservoir 1")
     # Label Reservoirs
     well1 = res1["A1"].top()
+    well2 = res1["A2"].top()
     well3 = res1["A3"].top()
     well4 = res1["A4"].top()
+    well5 = res1["A5"].top()
+    well6 = res1["A6"].top()
     well7 = res1["A7"].top()
+    well8 = res1["A8"].top()
+    well9 = res1["A9"].top()
     well10 = res1["A10"].top()
-
+    well11 = res1["A11"].top()
+    well12 = res1["A12"].top()
     # Volumes
     wash = 600
-    al_and_pk = 468
-    beads_and_binding = 552
+    binding = 320
+    beads = 230
+    pk = 230
+    lysis = 230
 
     # Sample Plate
     p1000.transfer(
@@ -65,9 +73,41 @@ def run(protocol: protocol_api.ProtocolContext) -> None:
     )
     # Res 1
     p1000.transfer(
-        volume=[beads_and_binding, al_and_pk, wash, wash, wash],
+        volume=[
+            binding,
+            beads,
+            binding,
+            beads,
+            lysis,
+            pk,
+            wash,
+            wash,
+            wash,
+            wash,
+            wash,
+            wash,
+            wash,
+            wash,
+            wash,
+        ],
         source=source_reservoir["A1"].bottom(z=0.5),
-        dest=[well1, well3, well4, well7, well10],
+        dest=[
+            well1,
+            well1,
+            well2,
+            well2,
+            well3,
+            well3,
+            well4,
+            well5,
+            well6,
+            well7,
+            well8,
+            well9,
+            well10,
+            well11,
+            well12,
+        ],
         blowout=True,
         blowout_location="source well",
         trash=False,