Merge branch 'edge' into chore_update-vitest-and-related-packages

.storybook/main.js

@@ -2,6 +2,7 @@ module.exports = {
   stories: [
     '../components/**/*.stories.@(js|jsx|ts|tsx)',
     '../app/**/*.stories.@(js|jsx|ts|tsx)',
+    '../protocol-designer/**/*.stories.@(js|jsx|ts|tsx)',
     '../opentrons-ai-client/**/*.stories.@(js|jsx|ts|tsx)',
   ],
 

.storybook/preview.jsx

@@ -7,7 +7,7 @@ global.APP_SHELL_REMOTE = {
   ipcRenderer: {
     on: (topic, cb) => {},
     invoke: (callname, args) => {},
-    send:  (message, payload) => {}
+    send: (message, payload) => {},
   },
 }
 global._PKG_VERSION_ = '0.0.0-storybook'
@@ -29,8 +29,8 @@ export const customViewports = {
     type: 'desktop',
     styles: {
       width: '600px',
-      height: '450px'
-    }
+      height: '450px',
+    },
   },
   desktopSmall: {
     // A size typically used in figma app backgrounds, useful for viewing
@@ -39,9 +39,9 @@ export const customViewports = {
     type: 'desktop',
     styles: {
       width: '1024px',
-      height: '700px'
-    }
-  }
+      height: '700px',
+    },
+  },
 }
 
 export const parameters = {
@@ -50,7 +50,14 @@ export const parameters = {
   options: {
     storySort: {
       method: 'alphabetical',
-      order: ['Design Tokens', 'Library', 'App', 'ODD', 'AI'],
+      order: [
+        'Design Tokens',
+        'Library',
+        'App',
+        'ODD',
+        'Protocol-Designer',
+        'AI',
+      ],
     },
   },
 }

abr-testing/abr_testing/automation/google_sheets_tool.py

@@ -57,7 +57,7 @@ def open_worksheet(self, tab_number: int) -> Any:
     def create_worksheet(self, title: str) -> Optional[str]:
         """Create a worksheet with tab name. Existing spreadsheet needed."""
         try:
-            new_sheet = self.spread_sheet.add_worksheet(title, rows="2500", cols="40")
+            new_sheet = self.spread_sheet.add_worksheet(title, rows="2500", cols="60")
             return new_sheet.id
         except gspread.exceptions.APIError:
             print("Sheet already exists.")

abr-testing/abr_testing/automation/jira_tool.py

@@ -170,17 +170,20 @@ def create_ticket(
 
     def post_attachment_to_ticket(self, issue_id: str, attachment_path: str) -> None:
         """Adds attachments to ticket."""
-        # TODO: Ensure that file is actually uploaded.
-        file = {"file": open(attachment_path, "rb")}
-        JSON_headers = {"Accept": "application/json"}
+        file = {
+            "file": (attachment_path, open(attachment_path, "rb"), "application-type")
+        }
+        JSON_headers = {"Accept": "application/json", "X-Atlassian-Token": "no-check"}
+        attachment_url = f"{self.url}/rest/api/3/issue/{issue_id}/attachments"
         try:
-            response = requests.post(
-                f"{self.url}/rest/api/3/issue/{issue_id}/attachments",
+            response = requests.request(
+                "POST",
+                attachment_url,
                 headers=JSON_headers,
                 auth=self.auth,
                 files=file,
             )
-            print(response)
+            print(f"File: {attachment_path} posted to ticket {issue_id}.")
         except json.JSONDecodeError:
             error_message = str(response.content)
             print(f"JSON decoding error occurred. Response content: {error_message}.")
@@ -256,9 +259,9 @@ def get_project_components(self, project_id: str) -> List[Dict[str, str]]:
         components_list = response.json()
         return components_list
 
-    def comment(self, content_list: List[Dict[str, Any]], issue_url: str) -> None:
+    def comment(self, content_list: List[Dict[str, Any]], issue_key: str) -> None:
         """Leave comment on JIRA Ticket."""
-        comment_url = issue_url + "/comment"
+        comment_url = f"{self.url}/rest/api/3/issue/{issue_key}/comment"
         payload = json.dumps(
             {
                 "body": {
@@ -272,6 +275,29 @@ def comment(self, content_list: List[Dict[str, Any]], issue_url: str) -> None:
             "POST", comment_url, data=payload, headers=self.headers, auth=self.auth
         )
 
+    def format_jira_comment(self, comment_info: Any) -> List[Dict[str, Any]]:
+        """Formats a string input to work with the "comment" function."""
+        content_list: List = []
+        line_1 = {
+            "type": "paragraph",
+            "content": [{"type": "text", "text": comment_info}],
+        }
+        content_list.insert(0, line_1)
+        return content_list
+
+    def get_ticket(self) -> str:
+        """Gets and confirms jira ticket number."""
+        while True:
+            issue_key = input("Ticket Key: ")
+            url = f"{self.url}/rest/api/3/issue/{issue_key}"
+            headers = {"Accept": "application/json"}
+            response = requests.request("GET", url, headers=headers, auth=self.auth)
+            if str(response) == "<Response [200]>":
+                break
+            else:
+                print("Please input a valid JIRA Key")
+        return issue_key
+
 
 if __name__ == "__main__":
     """Create ticket for specified robot."""

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -200,7 +200,7 @@ def read_each_log(folder_path: str, issue_url: str) -> None:
                         "content": [{"type": "text", "text": message}],
                     }
                     content_list.insert(0, line_1)
-                    ticket.comment(content_list, issue_url)
+                    ticket.comment(content_list, issue_key)
             no_word_found_message = (
                 f"Key words '{not_found_words} were not found in {file_name}."
             )
@@ -209,7 +209,7 @@ def read_each_log(folder_path: str, issue_url: str) -> None:
                 "content": [{"type": "text", "text": no_word_found_message}],
             }
             content_list.append(no_word_found_dict)
-            ticket.comment(content_list, issue_url)
+            ticket.comment(content_list, issue_key)
 
 
 def match_error_to_component(
@@ -383,21 +383,26 @@ def get_run_error_info_from_robot(
                 errored_labware_dict["Slot"] = labware["location"].get("slotName", "")
                 errored_labware_dict["Labware Type"] = labware.get("definitionUri", "")
                 offset_id = labware.get("offsetId", "")
-                for lpc in lpc_dict:
-                    if lpc.get("id", "") == offset_id:
-                        errored_labware_dict["X"] = lpc["vector"].get("x", "")
-                        errored_labware_dict["Y"] = lpc["vector"].get("y", "")
-                        errored_labware_dict["Z"] = lpc["vector"].get("z", "")
-                        errored_labware_dict["Module"] = lpc["location"].get(
-                            "moduleModel", ""
-                        )
-                        errored_labware_dict["Adapter"] = lpc["location"].get(
-                            "definitionUri", ""
-                        )
-
-                        lpc_message = compare_lpc_to_historical_data(
-                            errored_labware_dict, parent, storage_directory
-                        )
+                if offset_id == "":
+                    labware_slot = errored_labware_dict["Slot"]
+                    lpc_message = f"The current LPC coords found at {labware_slot} are (0, 0, 0). \
+Please confirm with the ABR-LPC sheet and re-LPC."
+                else:
+                    for lpc in lpc_dict:
+                        if lpc.get("id", "") == offset_id:
+                            errored_labware_dict["X"] = lpc["vector"].get("x", "")
+                            errored_labware_dict["Y"] = lpc["vector"].get("y", "")
+                            errored_labware_dict["Z"] = lpc["vector"].get("z", "")
+                            errored_labware_dict["Module"] = lpc["location"].get(
+                                "moduleModel", ""
+                            )
+                            errored_labware_dict["Adapter"] = lpc["location"].get(
+                                "definitionUri", ""
+                            )
+
+                            lpc_message = compare_lpc_to_historical_data(
+                                errored_labware_dict, parent, storage_directory
+                            )
 
     description["protocol_step"] = protocol_step
     description["right_mount"] = results.get("right", "No attachment")
@@ -535,15 +540,12 @@ def get_run_error_info_from_robot(
         affects_version,
         parent_key,
     )
-
     # Link Tickets
     to_link = ticket.match_issues(all_issues, summary)
     ticket.link_issues(to_link, issue_key)
-
     # OPEN TICKET
     issue_url = ticket.open_issue(issue_key)
     # MOVE FILES TO ERROR FOLDER.
-
     error_files = [saved_file_path_calibration, run_log_file_path] + file_paths
     error_folder_path = os.path.join(storage_directory, issue_key)
     os.makedirs(error_folder_path, exist_ok=True)
@@ -555,8 +557,11 @@ def get_run_error_info_from_robot(
             shutil.move(source_file, destination_file)
         except shutil.Error:
             continue
-    # OPEN FOLDER DIRECTORY
-    subprocess.Popen(["explorer", error_folder_path])
+    # POST FILES TO TICKET
+    list_of_files = os.listdir(error_folder_path)
+    for file in list_of_files:
+        file_to_attach = os.path.join(error_folder_path, file)
+        ticket.post_attachment_to_ticket(issue_key, file_to_attach)
     # ADD ERROR COMMENTS TO TICKET
     read_each_log(error_folder_path, raw_issue_url)
     # WRITE ERRORED RUN TO GOOGLE SHEET
@@ -601,3 +606,5 @@ def get_run_error_info_from_robot(
         google_sheet_lpc.batch_update_cells(runs_and_lpc, "A", start_row_lpc, "0")
     else:
         print("Ticket created.")
+    # Open folder directory incase uploads to ticket were incomplete
+    subprocess.Popen(["explorer", error_folder_path])

api-client/src/dataFiles/getCsvFile.ts

@@ -0,0 +1,12 @@
+import { GET, request } from '../request'
+
+import type { CsvFileDataResponse } from './types'
+import type { ResponsePromise } from '../request'
+import type { HostConfig } from '../types'
+
+export function getCsvFile(
+  config: HostConfig,
+  fileId: string
+): ResponsePromise<CsvFileDataResponse> {
+  return request<CsvFileDataResponse>(GET, `/dataFiles/${fileId}`, null, config)
+}

api-client/src/dataFiles/index.ts

@@ -1,3 +1,4 @@
+export { getCsvFile } from './getCsvFile'
 export { getCsvFileRaw } from './getCsvFileRaw'
 export { uploadCsvFile } from './uploadCsvFile'
 

api-client/src/dataFiles/types.ts

@@ -13,10 +13,12 @@ export interface CsvFileData {
   name: string
 }
 
-export interface UploadedCsvFileResponse {
+export interface CsvFileDataResponse {
   data: CsvFileData
 }
 
+export type UploadedCsvFileResponse = CsvFileDataResponse
+
 export interface UploadedCsvFilesResponse {
   data: CsvFileData[]
 }

api-client/src/protocols/index.ts

@@ -9,5 +9,3 @@ export { getProtocolIds } from './getProtocolIds'
 export { getProtocols } from './getProtocols'
 
 export * from './types'
-export * from './utils'
-export * from './__fixtures__'

api-client/src/runs/commands/getRunCommandErrors.ts

@@ -0,0 +1,19 @@
+import { GET, request } from '../../request'
+
+import type { ResponsePromise } from '../../request'
+import type { HostConfig } from '../../types'
+import type { GetCommandsParams, RunCommandErrors } from '../types'
+
+export function getRunCommandErrors(
+  config: HostConfig,
+  runId: string,
+  params: GetCommandsParams
+): ResponsePromise<RunCommandErrors> {
+  return request<RunCommandErrors>(
+    GET,
+    `/runs/${runId}/commandErrors`,
+    null,
+    config,
+    params
+  )
+}

api-client/src/runs/commands/types.ts

@@ -1,10 +1,15 @@
-import type { RunTimeCommand } from '@opentrons/shared-data'
+import type { RunTimeCommand, RunCommandError } from '@opentrons/shared-data'
 
 export interface GetCommandsParams {
   cursor: number | null // the index of the command at the center of the window
   pageLength: number // the number of items to include
 }
 
+export interface RunCommandErrors {
+  data: RunCommandError[]
+  meta: GetCommandsParams & { totalLength: number }
+}
+
 // NOTE: this incantation allows us to omit a key from each item in a union distributively
 // this means we can, for example, maintain the associated commandType and params after the Omit is applied
 type DistributiveOmit<T, K extends keyof T> = T extends any ? Omit<T, K> : never

api-client/src/runs/index.ts

@@ -9,6 +9,7 @@ export { getCommand } from './commands/getCommand'
 export { getCommands } from './commands/getCommands'
 export { getCommandsAsPreSerializedList } from './commands/getCommandsAsPreSerializedList'
 export { createRunAction } from './createRunAction'
+export { getRunCommandErrors } from './commands/getRunCommandErrors'
 export * from './createLabwareOffset'
 export * from './createLabwareDefinition'
 export * from './constants'

api-client/src/runs/types.ts

@@ -54,11 +54,11 @@ export interface LegacyGoodRunData {
   modules: LoadedModule[]
   protocolId?: string
   labwareOffsets?: LabwareOffset[]
-  runTimeParameters: RunTimeParameter[]
 }
 
 export interface KnownGoodRunData extends LegacyGoodRunData {
   ok: true
+  runTimeParameters: RunTimeParameter[]
 }
 
 export interface KnownInvalidRunData extends LegacyGoodRunData {

api/docs/v2/basic_commands/liquids.rst

@@ -258,3 +258,38 @@ This example aspirates enough air to fill the remaining volume in a pipette::
 
 .. versionadded:: 2.0
 
+.. _detect-liquid-presence:
+
+Detect Liquids
+==============
+
+The :py:meth:`.InstrumentContext.detect_liquid_presence` method tells a Flex pipette to check for liquid in a well. It returns ``True`` if the pressure sensors in the pipette detect a liquid and ``False`` if the sensors do not. 
+
+Aspiration isn't required to use ``detect_liquid_presence()``. This is a standalone method that can be called when you want the robot to record the presence or absence of a liquid. When ``detect_liquid_presence()`` finds an empty well it won't raise an error or stop your protocol.
+
+A potential use of liquid detection is to try aspirating from another well if the first well is found to contain no liquid.
+
+.. code-block:: python
+    
+    if pipette.detect_liquid_presence(reservoir["A1"]):
+        pipette.aspirate(100, reservoir["A1"])
+    else:
+        pipette.aspirate(100, reservoir["A2"])
+
+.. versionadded:: 2.20
+
+.. _require-liquid-presence:
+
+Require Liquids
+===============
+
+The :py:meth:`.InstrumentContext.require_liquid_presence` method tells a Flex pipette to check for `and require` liquid in a well. 
+
+Aspiration isn't required to use ``require_liquid_presence()``. This is a standalone method that can be called when you want the robot to react to a missing liquid or empty well. When ``require_liquid_presence()`` finds an empty well, it raises an error and pauses the protocol to let you resolve the problem. See also :ref:`lpd`.
+
+.. code-block:: python
+
+    pipette.require_liquid_presence(reservoir["A1"])
+    pipette.aspirate(100, reservoir["A1"])  # only occurs if liquid found
+
+.. versionadded:: 2.20

api/docs/v2/conf.py

@@ -99,7 +99,7 @@
 # use rst_prolog to hold the subsitution
 # update the apiLevel value whenever a new minor version is released
 rst_prolog = f"""
-.. |apiLevel| replace:: 2.19
+.. |apiLevel| replace:: 2.20
 .. |release| replace:: {release}
 """
 
@@ -445,7 +445,7 @@
     ("py:class", r".*protocol_api\.config.*"),
     ("py:class", r".*opentrons_shared_data.*"),
     ("py:class", r".*protocol_api._parameters.Parameters.*"),
-    ("py:class", r".*AbsorbanceReaderContext"),  # shh it's a secret (for now)
+    ("py:class", r".*AbsorbanceReaderContext"), 
 	("py:class", r".*RobotContext"),  # shh it's a secret (for now)
     ("py:class", r'.*AbstractLabware|APIVersion|LabwareLike|LoadedCoreMap|ModuleTypes|NoneType|OffDeckType|ProtocolCore|WellCore'),  # laundry list of not fully qualified things
 ]

api/docs/v2/new_pipette.rst

@@ -18,11 +18,7 @@ Pages in this section of the documentation cover:
 
     - :ref:`Loading pipettes <loading-pipettes>` into your protocol.
     - :ref:`Pipette characteristics <pipette-characteristics>`, such as how fast they can move liquid and how they move around the deck.
-    - The :ref:`partial tip pickup <partial-tip-pickup>` configuration for the Flex 96-Channel Pipette, which uses only 8 channels for pipetting. Full and partial tip pickup can be combined in a single protocol.
+    - :ref:`Partial tip pickup <partial-tip-pickup>` configurations for multi-channel pipettes. Full and partial tip pickup configurations can be combined in a single protocol.
     - The :ref:`volume modes <pipette-volume-modes>` of Flex 50 µL pipettes, which must operate in low-volume mode to accurately dispense very small volumes of liquid. 
 
 For information about liquid handling, see :ref:`v2-atomic-commands` and :ref:`v2-complex-commands`.
-
-
-
-