Merge branch 'edge' into feat_app-historicalprotocolrun

.eslintrc.js

@@ -101,7 +101,6 @@ module.exports = {
         '@typescript-eslint/no-floating-promises': 'warn',
         '@typescript-eslint/no-unnecessary-type-assertion': 'warn',
         '@typescript-eslint/no-unnecessary-boolean-literal-compare': 'warn',
-        '@typescript-eslint/no-unsafe-argument': 'warn',
         '@typescript-eslint/consistent-indexed-object-style': 'warn',
         '@typescript-eslint/ban-types': 'warn',
         '@typescript-eslint/non-nullable-type-assertion-style': 'warn',
@@ -126,11 +125,13 @@ module.exports = {
         '**/__fixtures__/**.@(js|ts|tsx)',
         '**/fixtures/**.@(js|ts|tsx)',
         'scripts/*.@(js|ts|tsx)',
+        '**/**test.@(js|ts|tsx)',
       ],
       rules: {
         '@typescript-eslint/consistent-type-assertions': 'off',
         '@typescript-eslint/no-var-requires': 'off',
         '@typescript-eslint/explicit-function-return-type': 'off',
+        '@typescript-eslint/no-unsafe-argument': 'off',
         '@typescript-eslint/no-confusing-void-expression': 'warn',
         'node/handle-callback-err': 'off',
       },

.github/workflows/components-test-build-deploy.yaml

@@ -169,6 +169,10 @@ jobs:
           AWS_DEFAULT_REGION: us-east-2
         run: |
           aws s3 sync ./dist s3://opentrons-components/${{ env.OT_BRANCH}} --acl public-read
+      - name: 'Set generated URL'
+        run: |
+          echo 'Created component storybook for [${{ env.OT_BRANCH }}](https://s3-us-west-2.amazonaws.com/opentrons-components/${{ env.OT_BRANCH }}/index.html?path=/)' >> $GITHUB_STEP_SUMMARY
+          echo 'Created component storybook for https://s3-us-west-2.amazonaws.com/opentrons-components/${{ env.OT_BRANCH }}/index.html?path=/'
 
   publish-components:
     name: 'publish components package to npm'

.github/workflows/js-check.yaml

@@ -75,12 +75,12 @@ jobs:
           make setup-js
         # Use the if to run all the lint checks even of some fail
         shell: bash
-      - name: 'lint js'
-        if: always() && steps.setup-js.outcome == 'success'
-        run: make lint-js
       - name: 'typechecks'
         if: always() && steps.setup-js.outcome == 'success'
         run: make check-js
+      - name: 'lint js'
+        if: always() && steps.setup-js.outcome == 'success'
+        run: make lint-js
       - name: 'circular deps'
         if: always() && steps.setup-js.outcome == 'success'
         run: make circular-dependencies-js

.storybook/preview.jsx

@@ -3,6 +3,15 @@ import { I18nextProvider } from 'react-i18next'
 import { GlobalStyle } from '../app/src/atoms/GlobalStyle'
 import { i18n } from '../app/src/i18n'
 
+global.APP_SHELL_REMOTE = {
+  ipcRenderer: {
+    on: (topic, cb) => {},
+    invoke: (callname, args) => {},
+    send:  (message, payload) => {}
+  },
+}
+global._PKG_VERSION_ = '0.0.0-storybook'
+
 export const customViewports = {
   onDeviceDisplay: {
     name: 'Touchscreen',
@@ -12,6 +21,27 @@ export const customViewports = {
       height: '600px',
     },
   },
+  desktopMinWidth: {
+    // retains a 4:3 aspect ratio... minHeight is not set so the user
+    // could drag the app up to a thin strip, but that's not terribly
+    // useful for viewing designs
+    name: 'Desktop Minimum Width',
+    type: 'desktop',
+    styles: {
+      width: '600px',
+      height: '450px'
+    }
+  },
+  desktopSmall: {
+    // A size typically used in figma app backgrounds, useful for viewing
+    // larger components in context
+    name: 'Desktop Typical Small',
+    type: 'desktop',
+    styles: {
+      width: '1024px',
+      height: '700px'
+    }
+  }
 }
 
 export const parameters = {

Makefile

@@ -219,7 +219,7 @@ lint-js: lint-js-eslint lint-js-prettier
 
 .PHONY: lint-js-eslint
 lint-js-eslint:
-	yarn eslint --quiet=$(quiet) --ignore-pattern "node_modules/" --cache ".*.@(js|ts|tsx)" "**/*.@(js|ts|tsx)"
+	yarn eslint --quiet=$(quiet) --ignore-pattern "node_modules/" ".*.@(js|ts|tsx)" "**/*.@(js|ts|tsx)"
 
 .PHONY: lint-js-prettier
 lint-js-prettier:

abr-testing/abr_testing/automation/jira_tool.py

@@ -178,6 +178,13 @@ def get_jira_users(self, storage_directory: str) -> str:
             print("JSON decoding error occurred.")
         return file_path
 
+    def get_project_components(self, project_id: str) -> List[Dict[str, str]]:
+        """Get list of components on JIRA board."""
+        component_url = f"{self.url}/rest/api/3/project/{project_id}/components"
+        response = requests.get(component_url, headers=self.headers, auth=self.auth)
+        components_list = response.json()
+        return components_list
+
 
 if __name__ == "__main__":
     """Create ticket for specified robot."""

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -9,6 +9,21 @@
 import subprocess
 import sys
 import json
+import re
+
+
+def match_error_to_component(
+    project_id: str, error_message: str, components: List[str]
+) -> List[str]:
+    """Match error to component based on error message."""
+    project_components = ticket.get_project_components(project_id)
+    component_names = [proj_comp["name"] for proj_comp in project_components]
+    for component in component_names:
+        pattern = re.compile(component, re.IGNORECASE)
+        matches = pattern.findall(error_message)
+        if matches:
+            components.append(component)
+    return components
 
 
 def get_user_id(user_file_path: str, assignee_name: str) -> str:
@@ -76,9 +91,10 @@ def get_robot_state(
     )
     module_data = response.json()
     for module in module_data["data"]:
-        print(module)
         description[module["moduleType"]] = module
     components = ["Flex-RABR"]
+    components = match_error_to_component("RABR", reported_string, components)
+    print(components)
     whole_description_str = (
         "{"
         + "\n".join("{!r}: {!r},".format(k, v) for k, v in description.items())
@@ -116,6 +132,8 @@ def get_run_error_info_from_robot(
     failure_level = "Level " + str(error_level) + " Failure"
 
     components = [failure_level, "Flex-RABR"]
+    components = match_error_to_component("RABR", error_type, components)
+    print(components)
     affects_version = results["API_Version"]
     parent = results.get("robot_name", "")
     print(parent)
@@ -211,8 +229,8 @@ def get_run_error_info_from_robot(
     except requests.exceptions.InvalidURL:
         print("Invalid IP address.")
         sys.exit()
-    one_run = error_runs[-1]  # Most recent run with error.
     if len(run_or_other) < 1:
+        one_run = error_runs[-1]  # Most recent run with error.
         (
             summary,
             robot,
@@ -234,7 +252,7 @@ def get_run_error_info_from_robot(
         ip, storage_directory
     )
     file_paths = read_robot_logs.get_logs(storage_directory, ip)
-    print(f"Making ticket for run: {one_run} on robot {robot}.")
+    print(f"Making ticket for {summary}.")
     # TODO: make argument or see if I can get rid of with using board_id.
     project_key = "RABR"
     parent_key = project_key + "-" + robot[-1]

abr-testing/abr_testing/data_collection/read_robot_logs.py

@@ -383,6 +383,9 @@ def get_error_info(file_results: Dict[str, Any]) -> Tuple[int, str, str, str, st
         error_str = 0
     if error_str > 1:
         error_type = run_command_error["error"].get("errorType", "")
+        if error_type == "PythonException":
+            # Reassign error_type to be more descriptive
+            error_type = run_command_error["detail"].split(":")[0]
         error_code = run_command_error["error"].get("errorCode", "")
         try:
             # Instrument Error

api/docs/v2/new_examples.rst

@@ -397,7 +397,7 @@ Opentrons electronic pipettes can do some things that a human cannot do with a p
 
                 p300.return_tip()
 
-Notice here how Python's :py:class:`slice` functionality (in the code sample as ``[:4]``) lets us select the first five wells of the well plate only. Also, in Python, a range of numbers is *exclusive* of the end value and counting starts at 0, not 1. For the Corning 96-well plate used here, this means well A1=0, B1=1, C1=2, and so on to the last well used, which is E1=4. See also, the :ref:`tutorial-commands` section of the Tutorial.
+Notice here how Python's :py:class:`slice` functionality (in the code sample as ``[:5]``) lets us select the first five wells of the well plate only. Also, in Python, a range of numbers is *exclusive* of the end value and counting starts at 0, not 1. For the USA Scientific 12-well reservoir used here, this means well A1=0, A2=1, A3=2, and so on to the last well used, which is A5=4. See also, the :ref:`tutorial-commands` section of the Tutorial.
 
 Dilution
 ========

api/src/opentrons/cli/analyze.py

@@ -5,6 +5,7 @@
 from contextlib import contextmanager
 from dataclasses import dataclass
 from datetime import datetime, timezone
+from enum import Enum
 from pathlib import Path
 from pydantic import BaseModel
 from typing import (
@@ -48,6 +49,7 @@
     Liquid,
     StateSummary,
 )
+from opentrons.protocol_engine.protocol_engine import code_in_error_tree
 
 from opentrons_shared_data.robot.dev_types import RobotType
 
@@ -302,6 +304,19 @@ async def _analyze(
     if not outputs:
         return return_code
 
+    if len(analysis.state_summary.errors) > 0:
+        if any(
+            code_in_error_tree(
+                root_error=error, code=ErrorCodes.RUNTIME_PARAMETER_VALUE_REQUIRED
+            )
+            for error in analysis.state_summary.errors
+        ):
+            result = AnalysisResult.PARAMETER_VALUE_REQUIRED
+        else:
+            result = AnalysisResult.NOT_OK
+    else:
+        result = AnalysisResult.OK
+
     results = AnalyzeResults.construct(
         createdAt=datetime.now(tz=timezone.utc),
         files=[
@@ -313,6 +328,7 @@ async def _analyze(
             if isinstance(protocol_source.config, JsonProtocolConfig)
             else PythonConfig.construct(apiVersion=protocol_source.config.api_version)
         ),
+        result=result,
         metadata=protocol_source.metadata,
         robotType=protocol_source.robot_type,
         runTimeParameters=analysis.parameters,
@@ -365,6 +381,26 @@ class PythonConfig(BaseModel):
     apiVersion: APIVersion
 
 
+class AnalysisResult(str, Enum):
+    """Result of a completed protocol analysis.
+
+    The result indicates whether the protocol is expected to run successfully.
+
+    Properties:
+        OK: No problems were found during protocol analysis.
+        NOT_OK: Problems were found during protocol analysis. Inspect
+            `analysis.errors` for error occurrences.
+        PARAMETER_VALUE_REQUIRED: A value is required to be set for a parameter
+            in order for the protocol to be analyzed/run. The absence of this does not
+            inherently mean there are no parameters, as there may be defaults for all
+            or unset parameters are not referenced or handled via try/except clauses.
+    """
+
+    OK = "ok"
+    NOT_OK = "not-ok"
+    PARAMETER_VALUE_REQUIRED = "parameter-value-required"
+
+
 class AnalyzeResults(BaseModel):
     """Results of a protocol analysis.
 
@@ -381,6 +417,7 @@ class AnalyzeResults(BaseModel):
     metadata: Dict[str, Any]
 
     # Fields that should match robot-server:
+    result: AnalysisResult
     robotType: RobotType
     runTimeParameters: List[RunTimeParameter]
     commands: List[Command]

api/src/opentrons/config/defaults_ot3.py

@@ -24,7 +24,6 @@
 
 DEFAULT_LIQUID_PROBE_SETTINGS: Final[LiquidProbeSettings] = LiquidProbeSettings(
     starting_mount_height=100,
-    max_z_distance=40,
     mount_speed=10,
     plunger_speed=5,
     sensor_threshold_pascals=40,
@@ -335,7 +334,6 @@ def _build_default_liquid_probe(
         starting_mount_height=from_conf.get(
             "starting_mount_height", default.starting_mount_height
         ),
-        max_z_distance=from_conf.get("max_z_distance", default.max_z_distance),
         mount_speed=from_conf.get("mount_speed", default.mount_speed),
         plunger_speed=from_conf.get("plunger_speed", default.plunger_speed),
         sensor_threshold_pascals=from_conf.get(

api/src/opentrons/config/types.py

@@ -132,7 +132,6 @@ class ZSenseSettings:
 @dataclass
 class LiquidProbeSettings:
     starting_mount_height: float
-    max_z_distance: float
     mount_speed: float
     plunger_speed: float
     sensor_threshold_pascals: float

api/src/opentrons/hardware_control/backends/ot3controller.py

@@ -191,7 +191,7 @@
     PipetteOverpressureError,
     FirmwareUpdateRequiredError,
     FailedGripperPickupError,
-    LiquidNotFoundError,
+    PipetteLiquidNotFoundError,
     CommunicationError,
     PythonException,
     UnsupportedHardwareCommand,
@@ -1412,7 +1412,7 @@ async def liquid_probe(
             or positions[head_node].move_ack
             == MoveCompleteAck.complete_without_condition
         ):
-            raise LiquidNotFoundError(
+            raise PipetteLiquidNotFoundError(
                 "Liquid not found during probe.",
                 {
                     str(node_to_axis(node)): str(point.motor_position)

api/src/opentrons/hardware_control/ot3api.py

@@ -52,7 +52,7 @@
     GripperNotPresentError,
     InvalidActuator,
     FirmwareUpdateFailedError,
-    LiquidNotFoundError,
+    PipetteLiquidNotFoundError,
 )
 
 from .util import use_or_initialize_loop, check_motion_bounds
@@ -2594,7 +2594,8 @@ def _get_probe_distances(
 
     async def liquid_probe(
         self,
-        mount: OT3Mount,
+        mount: Union[top_types.Mount, OT3Mount],
+        max_z_dist: float,
         probe_settings: Optional[LiquidProbeSettings] = None,
         probe: Optional[InstrumentProbeType] = None,
     ) -> float:
@@ -2605,7 +2606,7 @@ async def liquid_probe(
         reading from the pressure sensor.
 
         If the move is completed without the specified threshold being triggered, a
-        LiquidNotFoundError error will be thrown.
+        PipetteLiquidNotFoundError error will be thrown.
 
         Otherwise, the function will stop moving once the threshold is triggered,
         and return the position of the
@@ -2622,21 +2623,21 @@ async def liquid_probe(
         if not probe_settings:
             probe_settings = self.config.liquid_sense
 
-        pos = await self.gantry_position(mount, refresh=True)
+        pos = await self.gantry_position(checked_mount, refresh=True)
         probe_start_pos = pos._replace(z=probe_settings.starting_mount_height)
-        await self.move_to(mount, probe_start_pos)
-        total_z_travel = probe_settings.max_z_distance
+        await self.move_to(checked_mount, probe_start_pos)
+        total_z_travel = max_z_dist
         z_travels = self._get_probe_distances(
             checked_mount,
             total_z_travel,
             probe_settings.plunger_speed,
             probe_settings.mount_speed,
         )
-        error: Optional[LiquidNotFoundError] = None
+        error: Optional[PipetteLiquidNotFoundError] = None
         for z_travel in z_travels:
 
             if probe_settings.aspirate_while_sensing:
-                await self._move_to_plunger_bottom(mount, rate=1.0)
+                await self._move_to_plunger_bottom(checked_mount, rate=1.0)
             else:
                 # find the ideal travel distance by multiplying the plunger speed
                 # by the time it will take to complete the z move.
@@ -2656,17 +2657,17 @@ async def liquid_probe(
                 await self._move(target_pos, speed=speed, acquire_lock=True)
             try:
                 height = await self._liquid_probe_pass(
-                    mount,
+                    checked_mount,
                     probe_settings,
                     probe if probe else InstrumentProbeType.PRIMARY,
                     z_travel,
                 )
                 # if we made it here without an error we found the liquid
                 error = None
                 break
-            except LiquidNotFoundError as lnfe:
+            except PipetteLiquidNotFoundError as lnfe:
                 error = lnfe
-        await self.move_to(mount, probe_start_pos)
+        await self.move_to(checked_mount, probe_start_pos)
         if error is not None:
             # if we never found an liquid raise an error
             raise error