Merge branch 'edge' into exec-201-strict-mypy-api

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="50")
             return new_sheet.id
         except gspread.exceptions.APIError:
             print("Sheet already exists.")

abr-testing/abr_testing/automation/jira_tool.py

@@ -23,25 +23,79 @@ def __init__(self, url: str, api_token: str, email: str) -> None:
             "Content-Type": "application/json",
         }
 
-    def issues_on_board(self, board_id: str) -> List[str]:
+    def issues_on_board(self, project_key: str) -> List[List[Any]]:
         """Print Issues on board."""
+        params = {"jql": f"project = {project_key}"}
         response = requests.get(
-            f"{self.url}/rest/agile/1.0/board/{board_id}/issue",
+            f"{self.url}/rest/api/3/search",
             headers=self.headers,
+            params=params,
             auth=self.auth,
         )
+
         response.raise_for_status()
         try:
             board_data = response.json()
             all_issues = board_data["issues"]
         except json.JSONDecodeError as e:
             print("Error decoding json: ", e)
+        # convert issue id's into array and have one key as
+        # the issue key and one be summary, return entire array
         issue_ids = []
         for i in all_issues:
             issue_id = i.get("id")
-            issue_ids.append(issue_id)
+            issue_summary = i["fields"].get("summary")
+            issue_ids.append([issue_id, issue_summary])
         return issue_ids
 
+    def match_issues(self, issue_ids: List[List[str]], ticket_summary: str) -> List:
+        """Matches related ticket ID's."""
+        to_link = []
+        error = ticket_summary.split("_")[3]
+        robot = ticket_summary.split("_")[0]
+        # for every issue see if both match, if yes then grab issue ID and add it to a list
+        for issue in issue_ids:
+            summary = issue[1]
+            try:
+                issue_error = summary.split("_")[3]
+                issue_robot = summary.split("_")[0]
+            except IndexError:
+                continue
+            issue_id = issue[0]
+            if robot == issue_robot and error == issue_error:
+                to_link.append(issue_id)
+        return to_link
+
+    def link_issues(self, to_link: list, ticket_key: str) -> None:
+        """Links relevant issues in Jira."""
+        for issue in to_link:
+            link_data = json.dumps(
+                {
+                    "inwardIssue": {"key": ticket_key},
+                    "outwardIssue": {"id": issue},
+                    "type": {"name": "Relates"},
+                }
+            )
+            try:
+                response = requests.post(
+                    f"{self.url}/rest/api/3/issueLink",
+                    headers=self.headers,
+                    auth=self.auth,
+                    data=link_data,
+                )
+                response.raise_for_status()
+            except requests.exceptions.HTTPError:
+                print(
+                    f"HTTP error occurred. Ticket ID {issue} was not linked. \
+                        Check user permissions and authentication credentials"
+                )
+            except requests.exceptions.ConnectionError:
+                print(f"Connection error occurred. Ticket ID {issue} was not linked.")
+            except json.JSONDecodeError:
+                print(
+                    f"JSON decoding error occurred. Ticket ID {issue} was not linked."
+                )
+
     def open_issue(self, issue_key: str) -> str:
         """Open issue on web browser."""
         url = f"{self.url}/browse/{issue_key}"
@@ -116,17 +170,18 @@ 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"}
         try:
             response = requests.post(
                 f"{self.url}/rest/api/3/issue/{issue_id}/attachments",
                 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}.")

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -481,7 +481,6 @@ def get_run_error_info_from_robot(
     reporter_id = args.reporter_id[0]
     file_paths = read_robot_logs.get_logs(storage_directory, ip)
     ticket = jira_tool.JiraTicket(url, api_token, email)
-    ticket.issues_on_board(board_id)
     users_file_path = ticket.get_jira_users(storage_directory)
     assignee_id = get_user_id(users_file_path, assignee)
     run_log_file_path = ""
@@ -519,6 +518,9 @@ def get_run_error_info_from_robot(
     print(robot)
     parent_key = project_key + "-" + robot.split("ABR")[1]
 
+    # Grab all previous issues
+    all_issues = ticket.issues_on_board(project_key)
+
     # TODO: read board to see if ticket for run id already exists.
     # CREATE TICKET
     issue_key, raw_issue_url = ticket.create_ticket(
@@ -533,10 +535,12 @@ 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)
@@ -548,8 +552,11 @@ 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
@@ -594,3 +601,5 @@ 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/getCsvFileRaw.ts

@@ -0,0 +1,17 @@
+import { GET, request } from '../request'
+
+import type { DownloadedCsvFileResponse } from './types'
+import type { ResponsePromise } from '../request'
+import type { HostConfig } from '../types'
+
+export function getCsvFileRaw(
+  config: HostConfig,
+  fileId: string
+): ResponsePromise<DownloadedCsvFileResponse> {
+  return request<DownloadedCsvFileResponse>(
+    GET,
+    `/dataFiles/${fileId}/download`,
+    null,
+    config
+  )
+}

api-client/src/dataFiles/index.ts

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

api-client/src/dataFiles/types.ts

@@ -18,7 +18,7 @@ export interface UploadedCsvFileResponse {
 }
 
 export interface UploadedCsvFilesResponse {
-  data: {
-    files: CsvFileData[]
-  }
+  data: CsvFileData[]
 }
+
+export type DownloadedCsvFileResponse = string

api-client/src/runs/index.ts

@@ -12,5 +12,7 @@ export { createRunAction } from './createRunAction'
 export * from './createLabwareOffset'
 export * from './createLabwareDefinition'
 export * from './constants'
+export * from './updateErrorRecoveryPolicy'
+
 export * from './types'
 export type { CreateRunData } from './createRun'

api-client/src/runs/types.ts

@@ -47,6 +47,7 @@ export interface LegacyGoodRunData {
   status: RunStatus
   actions: RunAction[]
   errors: RunError[]
+  hasEverEnteredErrorRecovery: boolean
   pipettes: LoadedPipette[]
   labware: LoadedLabware[]
   liquids: Liquid[]
@@ -146,3 +147,29 @@ export interface CommandData {
 // Although run errors are semantically different from command errors,
 // the server currently happens to use the exact same model for both.
 export type RunError = RunCommandError
+
+/**
+ * Error Policy
+ */
+
+export type IfMatchType = 'ignoreAndContinue' | 'failRun' | 'waitForRecovery'
+
+export interface ErrorRecoveryPolicy {
+  policyRules: Array<{
+    matchCriteria: {
+      command: {
+        commandType: RunTimeCommand['commandType']
+        error: {
+          errorType: RunCommandError['errorType']
+        }
+      }
+    }
+    ifMatch: IfMatchType
+  }>
+}
+
+export interface UpdateErrorRecoveryPolicyRequest {
+  data: ErrorRecoveryPolicy
+}
+
+export type UpdateErrorRecoveryPolicyResponse = Record<string, never>

api-client/src/runs/updateErrorRecoveryPolicy.ts

@@ -0,0 +1,48 @@
+import { PUT, request } from '../request'
+
+import type { HostConfig } from '../types'
+import type { ResponsePromise } from '../request'
+import type {
+  ErrorRecoveryPolicy,
+  IfMatchType,
+  UpdateErrorRecoveryPolicyRequest,
+  UpdateErrorRecoveryPolicyResponse,
+} from './types'
+import type { RunCommandError, RunTimeCommand } from '@opentrons/shared-data'
+
+export type RecoveryPolicyRulesParams = Array<{
+  commandType: RunTimeCommand['commandType']
+  errorType: RunCommandError['errorType']
+  ifMatch: IfMatchType
+}>
+
+export function updateErrorRecoveryPolicy(
+  config: HostConfig,
+  runId: string,
+  policyRules: RecoveryPolicyRulesParams
+): ResponsePromise<UpdateErrorRecoveryPolicyResponse> {
+  const policy = buildErrorRecoveryPolicyBody(policyRules)
+
+  return request<
+    UpdateErrorRecoveryPolicyResponse,
+    UpdateErrorRecoveryPolicyRequest
+  >(PUT, `/runs/${runId}/errorRecoveryPolicy`, { data: policy }, config)
+}
+
+function buildErrorRecoveryPolicyBody(
+  policyRules: RecoveryPolicyRulesParams
+): ErrorRecoveryPolicy {
+  return {
+    policyRules: policyRules.map(rule => ({
+      matchCriteria: {
+        command: {
+          commandType: rule.commandType,
+          error: {
+            errorType: rule.errorType,
+          },
+        },
+      },
+      ifMatch: rule.ifMatch,
+    })),
+  }
+}

api/docs/v2/conf.py

@@ -446,5 +446,6 @@
     ("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".*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/release-notes-internal.md

@@ -2,6 +2,16 @@ For more details about this release, please see the full [technical change log][
 
 [technical change log]: https://github.com/Opentrons/opentrons/releases
 
+## Internal Release 2.0.0-alpha.4
+
+This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only. There are no changes to `buildroot`, `ot3-firmware`, or `oe-core` since the last internal release.
+
+- [Opentrons changes since the latest stable release](https://github.com/Opentrons/opentrons/compare/[email protected])
+- [Opentrons changes since the last internal release](https://github.com/Opentrons/opentrons/compare/[email protected]@2.0.0-alpha.4)
+- [Flex changes since last stable release](https://github.com/Opentrons/oe-core/compare/[email protected])
+- [Flex firmware changes since last stable release](https://github.com/Opentrons/ot3-firmware/compare/v52...internal@v10)
+- [OT2 changes since last stable release](https://github.com/Opentrons/buildroot/compare/[email protected])
+
 ## Internal Release 2.0.0-alpha.3
 
 This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only.

api/release-notes.md

@@ -6,15 +6,23 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 
 ---
 
-## Opentrons Robot Software Changes in 7.4.0
+## Opentrons Robot Software Changes in 7.5.0
 
-Welcome to the v7.4.0 release of the Opentrons robot software!
+Welcome to the v7.5.0 release of the Opentrons robot software!
 
-This release adds support for the [Opentrons Flex HEPA/UV Module](https://opentrons.com/products/opentrons-flex-hepa-uv-module).
+### Hardware Support
+
+- [Opentrons Flex HEPA/UV Module](https://opentrons.com/products/opentrons-flex-hepa-uv-module)
+- Latest Flex Gripper model (serial numbers beginning `GRPV13`)
 
 ### Bug Fixes
 
 - Fixed certain string runtime parameter values being misinterpreted as an incorrect type.
+
+### Known Issue
+
+- The HEPA/UV Module's buttons may not respond properly after its safety shutoff is activated. This happens when the module is removed from the top of Flex while its lights are on. Power cycle the module to restore normal behavior. The module is safe to use even if you do not power cycle it.
+
 ---
 
 ## Opentrons Robot Software Changes in 7.3.1

api/src/opentrons/cli/analyze.py

@@ -275,6 +275,7 @@ async def _do_analyze(protocol_source: ProtocolSource) -> RunResult:
                 modules=[],
                 labwareOffsets=[],
                 liquids=[],
+                hasEverEnteredErrorRecovery=False,
             ),
             parameters=[],
         )