Merge branch 'edge' into EXEC-553-desktop-wire-up-are-you-sure-you-wa…

…nt-to-cancel

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

@@ -207,6 +207,7 @@ jobs:
     needs: [determine-build-type]
     if: needs.determine-build-type.outputs.variants != '[]'
     strategy:
+      fail-fast: false
       matrix:
         os: ['windows-2022', 'ubuntu-22.04', 'macos-latest']
         variant: ${{fromJSON(needs.determine-build-type.outputs.variants)}}

abr-testing/abr_testing/data_collection/abr_google_drive.py

@@ -76,13 +76,13 @@ def create_data_dictionary(
                 start_time = datetime.strptime(
                     file_results.get("startedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
                 )
-                adjusted_start_time = start_time - timedelta(hours=5)
+                adjusted_start_time = start_time - timedelta(hours=4)
                 start_date = str(adjusted_start_time.date())
                 start_time_str = str(adjusted_start_time).split("+")[0]
                 complete_time = datetime.strptime(
                     file_results.get("completedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
                 )
-                adjusted_complete_time = complete_time - timedelta(hours=5)
+                adjusted_complete_time = complete_time - timedelta(hours=4)
                 complete_time_str = str(adjusted_complete_time).split("+")[0]
                 run_time = complete_time - start_time
                 run_time_min = run_time.total_seconds() / 60

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -1,16 +1,105 @@
 """Create ticket for robot with error."""
-from typing import List, Tuple, Any, Dict
+from typing import List, Tuple, Any, Dict, Optional
 from abr_testing.data_collection import read_robot_logs, abr_google_drive, get_run_logs
 import requests
 import argparse
 from abr_testing.automation import jira_tool, google_sheets_tool, google_drive_tool
 import shutil
 import os
 import subprocess
+from datetime import datetime, timedelta
 import sys
 import json
 import re
 import pandas as pd
+from statistics import mean, StatisticsError
+
+
+def compare_current_trh_to_average(
+    robot: str,
+    start_time: Any,
+    end_time: Optional[Any],
+    protocol_name: str,
+    storage_directory: str,
+) -> str:
+    """Get average temp/rh for errored run and compare to average."""
+    # Connect to ABR ambient conditions sheet
+    credentials_path = os.path.join(storage_directory, "credentials.json")
+    temprh_data_sheet = google_sheets_tool.google_sheet(
+        credentials_path, "ABR Ambient Conditions", 0
+    )
+    headers = temprh_data_sheet.get_row(1)
+    all_trh_data = temprh_data_sheet.get_all_data(expected_headers=headers)
+    # Connect to ABR-run-data sheet
+    abr_data = google_sheets_tool.google_sheet(credentials_path, "ABR-run-data", 0)
+    headers = abr_data.get_row(1)
+    all_run_data = abr_data.get_all_data(expected_headers=headers)
+    # Find average conditions of errored time period
+    df_all_trh = pd.DataFrame(all_trh_data)
+    # Convert timestamps to datetime objects
+    df_all_trh["Timestamp"] = pd.to_datetime(
+        df_all_trh["Timestamp"], format="mixed", utc=True
+    ).dt.tz_localize(None)
+    # Ensure start_time is timezone-naive
+    start_time = start_time.replace(tzinfo=None)
+    relevant_temp_rhs = df_all_trh[
+        (df_all_trh["Robot"] == robot) & (df_all_trh["Timestamp"] >= start_time)
+    ]
+    try:
+        avg_temp = round(mean(relevant_temp_rhs["Temp (oC)"]), 2)
+        avg_rh = round(mean(relevant_temp_rhs["Relative Humidity (%)"]), 2)
+    except StatisticsError:
+        # If there is one value assign it as the average.
+        if len(relevant_temp_rhs["Temp (oC)"]) == 1:
+            avg_temp = relevant_temp_rhs["Temp (oC)"][0]
+            avg_rh = relevant_temp_rhs["Relative Humidity (%)"][0]
+        else:
+            avg_temp = None
+            avg_rh = None
+    # Get AVG t/rh of runs w/ same robot & protocol newer than 3 wks old with no errors
+    weeks_ago_3 = start_time - timedelta(weeks=3)
+    df_all_run_data = pd.DataFrame(all_run_data)
+    df_all_run_data["Start_Time"] = pd.to_datetime(
+        df_all_run_data["Start_Time"], format="mixed", utc=True
+    ).dt.tz_localize(None)
+    df_all_run_data["Errors"] = pd.to_numeric(df_all_run_data["Errors"])
+    df_all_run_data["Average Temp (oC)"] = pd.to_numeric(
+        df_all_run_data["Average Temp (oC)"]
+    )
+    common_filters = (
+        (df_all_run_data["Robot"] == robot)
+        & (df_all_run_data["Start_Time"] >= weeks_ago_3)
+        & (df_all_run_data["Start_Time"] <= start_time)
+        & (df_all_run_data["Errors"] < 1)
+        & (df_all_run_data["Average Temp (oC)"] > 1)
+    )
+
+    if protocol_name == "":
+        relevant_run_data = df_all_run_data[common_filters]
+    else:
+        relevant_run_data = df_all_run_data[
+            common_filters & (df_all_run_data["Protocol_Name"] == protocol_name)
+        ]
+    # Calculate means of historical data
+    try:
+        historical_avg_temp = round(
+            mean(relevant_run_data["Average Temp (oC)"].astype(float)), 2
+        )
+        historical_avg_rh = round(
+            mean(relevant_run_data["Average RH(%)"].astype(float)), 2
+        )
+    except StatisticsError:
+        historical_avg_temp = None
+        historical_avg_rh = None
+    # Formats TEMP/RH message for ticket.
+    temp_rh_message = (
+        f"{len(relevant_run_data)} runs with temp/rh data for {robot} running {protocol_name}."
+        f" AVG TEMP (deg C): {historical_avg_temp}. AVG RH (%): {historical_avg_rh}."
+        f" AVG TEMP of ERROR: {avg_temp}. AVG RH of ERROR: {avg_rh}."
+    )
+    # Print out comparison string.
+    print(temp_rh_message)
+    return temp_rh_message
 
 
 def compare_lpc_to_historical_data(
@@ -42,9 +131,9 @@ def compare_lpc_to_historical_data(
     current_x = round(labware_dict["X"], 2)
     current_y = round(labware_dict["Y"], 2)
     current_z = round(labware_dict["Z"], 2)
-    avg_x = round(sum(x_float) / len(x_float), 2)
-    avg_y = round(sum(y_float) / len(y_float), 2)
-    avg_z = round(sum(z_float) / len(z_float), 2)
+    avg_x = round(mean(x_float), 2)
+    avg_y = round(mean(y_float), 2)
+    avg_z = round(mean(z_float), 2)
 
     # Formats LPC message for ticket.
     lpc_message = (
@@ -195,6 +284,15 @@ def get_robot_state(
     components = ["Flex-RABR"]
     components = match_error_to_component("RABR", reported_string, components)
     print(components)
+    end_time = datetime.now()
+    print(end_time)
+    start_time = end_time - timedelta(hours=2)
+    print(start_time)
+    # Get current temp/rh compared to historical data
+    temp_rh_string = compare_current_trh_to_average(
+        parent, start_time, end_time, "", storage_directory
+    )
+    description["Robot Temp and RH Comparison"] = temp_rh_string
     whole_description_str = (
         "{"
         + "\n".join("{!r}: {!r},".format(k, v) for k, v in description.items())
@@ -242,6 +340,23 @@ def get_run_error_info_from_robot(
     description["protocol_name"] = results["protocol"]["metadata"].get(
         "protocolName", ""
     )
+    # Get start and end time of run
+    start_time = datetime.strptime(
+        results.get("startedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
+    )
+    adjusted_start_time = start_time - timedelta(hours=4)
+    complete_time = datetime.strptime(
+        results.get("completedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
+    )
+    adjusted_complete_time = complete_time - timedelta(hours=4)
+    # Get average temp and rh of robot and protocol the error occurred on.
+    temp_rh_comparison = compare_current_trh_to_average(
+        parent,
+        adjusted_start_time,
+        adjusted_complete_time,
+        description["protocol_name"],
+        storage_directory,
+    )
     # Get LPC coordinates of labware of failure
     lpc_dict = results["labwareOffsets"]
     labware_dict = results["labware"]
@@ -280,6 +395,7 @@ def get_run_error_info_from_robot(
     if len(lpc_message) < 1:
         lpc_message = "No LPC coordinates found in relation to error."
     description["LPC Comparison"] = lpc_message
+    description["Robot Temp and RH Comparison"] = temp_rh_comparison
     all_modules = abr_google_drive.get_modules(results)
     whole_description = {**description, **all_modules}
     whole_description_str = (
@@ -352,6 +468,7 @@ def get_run_error_info_from_robot(
     email = args.email[0]
     board_id = args.board_id[0]
     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)
@@ -384,7 +501,6 @@ def get_run_error_info_from_robot(
     saved_file_path_calibration, calibration = read_robot_logs.get_calibration_offsets(
         ip, storage_directory
     )
-    file_paths = read_robot_logs.get_logs(storage_directory, ip)
 
     print(f"Making ticket for {summary}.")
     # TODO: make argument or see if I can get rid of with using board_id.

abr-testing/abr_testing/data_collection/read_robot_logs.py

@@ -569,23 +569,32 @@ def get_calibration_offsets(
 
 def get_logs(storage_directory: str, ip: str) -> List[str]:
     """Get Robot logs."""
-    log_types = ["api.log", "server.log", "serial.log", "touchscreen.log"]
+    log_types: List[Dict[str, Any]] = [
+        {"log type": "api.log", "records": 1000},
+        {"log type": "server.log", "records": 10000},
+        {"log type": "serial.log", "records": 10000},
+        {"log type": "touchscreen.log", "records": 1000},
+    ]
     all_paths = []
     for log_type in log_types:
         try:
+            log_type_name = log_type["log type"]
+            print(log_type_name)
+            log_records = int(log_type["records"])
+            print(log_records)
             response = requests.get(
-                f"http://{ip}:31950/logs/{log_type}",
-                headers={"log_identifier": log_type},
-                params={"records": 5000},
+                f"http://{ip}:31950/logs/{log_type_name}",
+                headers={"log_identifier": log_type_name},
+                params={"records": log_records},
             )
             response.raise_for_status()
             log_data = response.text
-            log_name = ip + "_" + log_type.split(".")[0] + ".log"
+            log_name = ip + "_" + log_type_name.split(".")[0] + ".log"
             file_path = os.path.join(storage_directory, log_name)
             with open(file_path, mode="w", encoding="utf-8") as file:
                 file.write(log_data)
         except RuntimeError:
-            print(f"Request exception. Did not save {log_type}")
+            print(f"Request exception. Did not save {log_type_name}")
             continue
         all_paths.append(file_path)
     # Get weston.log using scp

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[d8cb88b3b2][Flex_S_v2_16_P1000_96_TC_PartialTipPickupSingle].json

@@ -3535,7 +3535,7 @@
   "errors": [
     {
       "createdAt": "TIMESTAMP",
-      "detail": "ValueError [line 16]: Nozzle layout configuration of style SINGLE is currently unsupported.",
+      "detail": "ValueError [line 16]: Nozzle layout configuration of style SINGLE is unsupported in API Versions lower than 2.20.",
       "errorCode": "4000",
       "errorInfo": {},
       "errorType": "ExceptionInProtocolError",
@@ -3544,10 +3544,10 @@
       "wrappedErrors": [
         {
           "createdAt": "TIMESTAMP",
-          "detail": "ValueError: Nozzle layout configuration of style SINGLE is currently unsupported.",
+          "detail": "ValueError: Nozzle layout configuration of style SINGLE is unsupported in API Versions lower than 2.20.",
           "errorCode": "4000",
           "errorInfo": {
-            "args": "('Nozzle layout configuration of style SINGLE is currently unsupported.',)",
+            "args": "('Nozzle layout configuration of style SINGLE is unsupported in API Versions lower than 2.20.',)",
             "class": "ValueError",
             "traceback": "  File \"/usr/local/lib/python3.10/site-packages/opentrons/protocols/execution/execute_python.py\", line N, in exec_run\n    exec(\"run(__context)\", new_globs)\n\n  File \"<string>\", line N, in <module>\n\n  File \"Flex_S_v2_16_P1000_96_TC_PartialTipPickupSingle.py\", line N, in run\n\n  File \"/usr/local/lib/python3.10/site-packages/opentrons/protocols/api_support/util.py\", line N, in _check_version_wrapper\n    return decorated_obj(*args, **kwargs)\n\n  File \"/usr/local/lib/python3.10/site-packages/opentrons/protocol_api/instrument_context.py\", line N, in configure_nozzle_layout\n    raise ValueError(\n"
           },

api-client/src/dataFiles/uploadCsvFile.ts

@@ -8,11 +8,18 @@ export function uploadCsvFile(
   config: HostConfig,
   data: FileData
 ): ResponsePromise<UploadedCsvFileResponse> {
-  return request<UploadedCsvFileResponse>(
+  let formData
+
+  if (typeof data !== 'string') {
+    formData = new FormData()
+    formData.append('file', data)
+  } else {
+    formData = data
+  }
+  return request<UploadedCsvFileResponse, FormData | string>(
     POST,
     '/dataFiles',
-    null,
-    config,
-    data
+    formData,
+    config
   )
 }

api-client/src/protocols/createProtocol.ts

@@ -2,14 +2,18 @@ import { POST, request } from '../request'
 import type { ResponsePromise } from '../request'
 import type { HostConfig } from '../types'
 import type { Protocol } from './types'
-import type { RunTimeParameterCreateData } from '../runs'
+import type {
+  RunTimeParameterValuesCreateData,
+  RunTimeParameterFilesCreateData,
+} from '../runs'
 
 export function createProtocol(
   config: HostConfig,
   files: File[],
   protocolKey?: string,
   protocolKind?: string,
-  runTimeParameterValues?: RunTimeParameterCreateData
+  runTimeParameterValues?: RunTimeParameterValuesCreateData,
+  runTimeParameterFiles?: RunTimeParameterFilesCreateData
 ): ResponsePromise<Protocol> {
   const formData = new FormData()
   files.forEach(file => {
@@ -22,6 +26,11 @@ export function createProtocol(
       'runTimeParameterValues',
       JSON.stringify(runTimeParameterValues)
     )
+  if (runTimeParameterFiles != null)
+    formData.append(
+      'runTimeParameterFiles',
+      JSON.stringify(runTimeParameterFiles)
+    )
 
   return request<Protocol, FormData>(POST, '/protocols', formData, config)
 }

api-client/src/protocols/createProtocolAnalysis.ts

@@ -3,21 +3,27 @@ import { POST, request } from '../request'
 import type { ProtocolAnalysisSummary } from '@opentrons/shared-data'
 import type { ResponsePromise } from '../request'
 import type { HostConfig } from '../types'
-import type { RunTimeParameterCreateData } from '../runs'
+import type {
+  RunTimeParameterFilesCreateData,
+  RunTimeParameterValuesCreateData,
+} from '../runs'
 
 interface CreateProtocolAnalysisData {
-  runTimeParameterValues: RunTimeParameterCreateData
+  runTimeParameterValues: RunTimeParameterValuesCreateData
+  runTimeParameterFiles: RunTimeParameterFilesCreateData
   forceReAnalyze: boolean
 }
 
 export function createProtocolAnalysis(
   config: HostConfig,
   protocolKey: string,
-  runTimeParameterValues?: RunTimeParameterCreateData,
+  runTimeParameterValues?: RunTimeParameterValuesCreateData,
+  runTimeParameterFiles?: RunTimeParameterFilesCreateData,
   forceReAnalyze?: boolean
 ): ResponsePromise<ProtocolAnalysisSummary[]> {
   const data = {
     runTimeParameterValues: runTimeParameterValues ?? {},
+    runTimeParameterFiles: runTimeParameterFiles ?? {},
     forceReAnalyze: forceReAnalyze ?? false,
   }
   const response = request<

api-client/src/protocols/getCsvFiles.ts

@@ -1,5 +1,3 @@
-import { v4 as uuidv4 } from 'uuid'
-
 // import { GET, request } from '../request'
 
 // import type { ResponsePromise } from '../request'
@@ -25,18 +23,16 @@ export function getCsvFiles(
   config: HostConfig,
   protocolId: string
 ): Promise<{ data: UploadedCsvFilesResponse }> {
-  const fileIdOne = uuidv4()
-  const fileIdTwo = uuidv4()
   const stub = {
     data: {
       files: [
         {
-          id: fileIdOne,
+          id: '1',
           createdAt: '2024-06-07T19:19:56.268029+00:00',
           name: 'rtp_mock_file1.csv',
         },
         {
-          id: fileIdTwo,
+          id: '2',
           createdAt: '2024-06-17T19:19:56.268029+00:00',
           name: 'rtp_mock_file2.csv',
         },