Add errored runs to abr tracking sheet (#14845)

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# Overview

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Use this section to describe your pull-request at a high level. If the
PR addresses any open issues, please tag the issues here.
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Improved ABR Error Data Collection

# Test Plan

Tested code on multiple robots.

# Changelog

Added function to download robot logs
Added lines of code to move error documents (run log, calibration log,
robot logs) into folder named after ticket.
Adds robot run to ABR sheet and links JIRA ticket
Added extra lines to abr_scale to read scale more often
Edited ABR calibration script to ensure duplicate calibrations are not
added.

# Review requests

Is 5000 lines of recording enough to capture robot error if script is
run immediately?
Is there any manipulation to robot logs that can be down to make error
analysis more efficient.

# Risk assessment

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abr-testing/abr_testing/automation/google_drive_tool.py

@@ -25,7 +25,6 @@ def __init__(self, credentials: Any, folder_name: str, email: str) -> None:
         self.drive_service = build("drive", "v3", credentials=self.credentials)
         self.parent_folder = folder_name
         self.email = email
-        self.folder = self.open_folder()
 
     def list_folder(self, delete: Any = False) -> Set[str]:
         """List folders and files in Google Drive."""

abr-testing/abr_testing/automation/google_sheets_tool.py

@@ -2,6 +2,7 @@
 import gspread  # type: ignore[import]
 import socket
 import httplib2
+from datetime import datetime
 from oauth2client.service_account import ServiceAccountCredentials  # type: ignore[import]
 from typing import Dict, List, Any, Set, Tuple
 
@@ -57,6 +58,12 @@ def write_to_row(self, data: List) -> None:
         """Write data into a row in a List[] format."""
         try:
             self.row_index += 1
+            data = [
+                item.strftime("%Y/%m/%d %H:%M:%S")
+                if isinstance(item, datetime)
+                else item
+                for item in data
+            ]
             self.worksheet.insert_row(data, index=self.row_index)
         except socket.gaierror:
             pass

abr-testing/abr_testing/automation/jira_tool.py

@@ -5,7 +5,7 @@
 import json
 import webbrowser
 import argparse
-from typing import List, Tuple
+from typing import List
 
 
 class JiraTicket:
@@ -41,11 +41,12 @@ def issues_on_board(self, board_id: str) -> List[str]:
             issue_ids.append(issue_id)
         return issue_ids
 
-    def open_issue(self, issue_key: str) -> None:
+    def open_issue(self, issue_key: str) -> str:
         """Open issue on web browser."""
         url = f"{self.url}/browse/{issue_key}"
         print(f"Opening at {url}.")
         webbrowser.open(url)
+        return url
 
     def create_ticket(
         self,
@@ -58,7 +59,7 @@ def create_ticket(
         components: list,
         affects_versions: str,
         robot: str,
-    ) -> Tuple[str, str]:
+    ) -> str:
         """Create ticket."""
         data = {
             "fields": {
@@ -94,13 +95,15 @@ def create_ticket(
             response_str = str(response.content)
             issue_url = response.json().get("self")
             issue_key = response.json().get("key")
+            print(f"issue key {issue_key}")
+            print(f"issue url{issue_url}")
             if issue_key is None:
                 print("Error: Could not create issue. No key returned.")
         except requests.exceptions.HTTPError:
             print(f"HTTP error occurred. Response content: {response_str}")
         except json.JSONDecodeError:
             print(f"JSON decoding error occurred. Response content: {response_str}")
-        return issue_url, issue_key
+        return issue_key
 
     def post_attachment_to_ticket(self, issue_id: str, attachment_path: str) -> None:
         """Adds attachments to ticket."""

abr-testing/abr_testing/data_collection/abr_calibration_logs.py

@@ -1,5 +1,5 @@
 """Get Calibration logs from robots."""
-from typing import Dict, Any, List
+from typing import Dict, Any, List, Union
 import argparse
 import os
 import json
@@ -16,15 +16,18 @@ def check_for_duplicates(
     col_2: int,
     row: List[str],
     headers: List[str],
-) -> List[str]:
+) -> Union[List[str], None]:
     """Check google sheet for duplicates."""
     serials = google_sheet.get_column(col_1)
     modify_dates = google_sheet.get_column(col_2)
-    for serial, modify_date in zip(serials, modify_dates):
-        if row[col_1 - 1] == serial and row[col_2 - 1] == modify_date:
-            print(f"Skipped row{row}. Already on Google Sheet.")
-            continue
-    read_robot_logs.write_to_sheets(sheet_location, google_sheet, row, headers)
+    # check for complete calibration.
+    if len(row[-1]) > 0:
+        for serial, modify_date in zip(serials, modify_dates):
+            if row[col_1 - 1] == serial and row[col_2 - 1] == modify_date:
+                print(f"Skipped row for instrument {serial}. Already on Google Sheet.")
+                return None
+        read_robot_logs.write_to_sheets(sheet_location, google_sheet, row, headers)
+        print(f"Writing calibration for: {serial}")
     return row
 
 
@@ -64,6 +67,7 @@ def upload_calibration_offsets(
             instrument_row,
             instrument_headers,
         )
+
     # MODULE SHEET
     if len(calibration.get("Modules", "")) > 0:
         module_headers = (
@@ -198,13 +202,19 @@ def upload_calibration_offsets(
     except FileNotFoundError:
         print(f"Add .json file with robot IPs to: {storage_directory}.")
         sys.exit()
+
     if ip_or_all == "ALL":
         ip_address_list = ip_file["ip_address_list"]
         for ip in ip_address_list:
-            saved_file_path, calibration = read_robot_logs.get_calibration_offsets(
-                ip, storage_directory
-            )
-            upload_calibration_offsets(calibration, storage_directory)
+            print(ip)
+            try:
+                saved_file_path, calibration = read_robot_logs.get_calibration_offsets(
+                    ip, storage_directory
+                )
+                upload_calibration_offsets(calibration, storage_directory)
+            except Exception:
+                print(f"ERROR: Failed to read IP address: {ip}")
+                continue
     else:
         saved_file_path, calibration = read_robot_logs.get_calibration_offsets(
             ip_or_all, storage_directory

abr-testing/abr_testing/data_collection/abr_google_drive.py

@@ -6,7 +6,7 @@
 import gspread  # type: ignore[import]
 from datetime import datetime, timedelta
 from abr_testing.data_collection import read_robot_logs
-from typing import Set, Dict, Any, Tuple, List
+from typing import Set, Dict, Any, Tuple, List, Union
 from abr_testing.automation import google_drive_tool, google_sheets_tool
 
 
@@ -30,7 +30,9 @@ def get_modules(file_results: Dict[str, str]) -> Dict[str, Any]:
 
 
 def create_data_dictionary(
-    runs_to_save: Set[str], storage_directory: str
+    runs_to_save: Union[Set[str], str],
+    storage_directory: str,
+    issue_url: str,
 ) -> Tuple[Dict[Any, Dict[str, Any]], List]:
     """Pull data from run files and format into a dictionary."""
     runs_and_robots = {}
@@ -41,7 +43,7 @@ def create_data_dictionary(
                 file_results = json.load(file)
         else:
             continue
-        run_id = file_results.get("run_id")
+        run_id = file_results.get("run_id", "NaN")
         if run_id in runs_to_save:
             robot = file_results.get("robot_name")
             protocol_name = file_results["protocol"]["metadata"].get("protocolName", "")
@@ -56,6 +58,7 @@ def create_data_dictionary(
                 error_instrument,
                 error_level,
             ) = read_robot_logs.get_error_info(file_results)
+
             all_modules = get_modules(file_results)
 
             start_time_str, complete_time_str, start_date, run_time_min = (
@@ -103,13 +106,14 @@ def create_data_dictionary(
                 tc_dict = read_robot_logs.thermocycler_commands(file_results)
                 hs_dict = read_robot_logs.hs_commands(file_results)
                 tm_dict = read_robot_logs.temperature_module_commands(file_results)
-                notes = {"Note1": "", "Note2": ""}
+                notes = {"Note1": "", "Jira Link": issue_url}
                 row_2 = {**row, **all_modules, **notes, **hs_dict, **tm_dict, **tc_dict}
                 headers = list(row_2.keys())
                 runs_and_robots[run_id] = row_2
             else:
-                os.remove(file_path)
-                print(f"Run ID: {run_id} has a run time of 0 minutes. Run removed.")
+                continue
+                # os.remove(file_path)
+                # print(f"Run ID: {run_id} has a run time of 0 minutes. Run removed.")
     return runs_and_robots, headers
 
 
@@ -168,6 +172,14 @@ def create_data_dictionary(
     except gspread.exceptions.APIError:
         print("ERROR: Check google sheet name. Check credentials file.")
         sys.exit()
+    try:
+        google_sheet_lpc = google_sheets_tool.google_sheet(
+            credentials_path, "ABR-LPC", 0
+        )
+        print("Connected to google sheet ABR-LPC")
+    except gspread.exceptions.APIError:
+        print("ERROR: Check google sheet name. Check credentials file.")
+        sys.exit()
     run_ids_on_gs = google_sheet.get_column(2)
     run_ids_on_gs = set(run_ids_on_gs)
 
@@ -181,7 +193,7 @@ def create_data_dictionary(
     )
     # Add missing runs to google sheet
     runs_and_robots, headers = create_data_dictionary(
-        missing_runs_from_gs, storage_directory
+        missing_runs_from_gs, storage_directory, ""
     )
     read_robot_logs.write_to_local_and_google_sheet(
         runs_and_robots, storage_directory, google_sheet_name, google_sheet, headers

abr-testing/abr_testing/data_collection/abr_lpc.py

@@ -0,0 +1 @@
+"""Get Unique LPC Values from Run logs."""

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -3,7 +3,13 @@
 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
+from abr_testing.automation import jira_tool, google_sheets_tool, google_drive_tool
+import shutil
+import os
+import subprocess
+import json
+import sys
+import gspread  # type: ignore[import]
 
 
 def get_error_runs_from_robot(ip: str) -> List[str]:
@@ -44,7 +50,6 @@ def get_error_info_from_robot(
     # JIRA Ticket Fields
     failure_level = "Level " + str(error_level) + " Failure"
     components = [failure_level, "Flex-RABR"]
-    components = ["Flex-RABR"]
     affects_version = results["API_Version"]
     parent = results.get("robot_name", "")
     print(parent)
@@ -140,18 +145,19 @@ def get_error_info_from_robot(
         affects_version,
         components,
         whole_description_str,
-        saved_file_path,
+        run_log_file_path,
     ) = get_error_info_from_robot(ip, one_run, storage_directory)
     # get calibration data
     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 run: {one_run} on robot {robot}.")
     # TODO: make argument or see if I can get rid of with using board_id.
     project_key = "RABR"
     parent_key = project_key + "-" + robot[-1]
-    issues_ids = ticket.issues_on_board(board_id)
-    issue_url, issue_key = ticket.create_ticket(
+    # CREATE TICKET
+    issue_key = ticket.create_ticket(
         summary,
         whole_description_str,
         project_key,
@@ -162,6 +168,51 @@ def get_error_info_from_robot(
         affects_version,
         parent_key,
     )
-    ticket.open_issue(issue_key)
-    ticket.post_attachment_to_ticket(issue_key, saved_file_path)
-    ticket.post_attachment_to_ticket(issue_key, saved_file_path_calibration)
+    # 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, str("RABR-238"))
+    os.makedirs(error_folder_path, exist_ok=True)
+    for source_file in error_files:
+        destination_file = os.path.join(
+            error_folder_path, os.path.basename(source_file)
+        )
+        shutil.move(source_file, destination_file)
+    # OPEN FOLDER DIRECTORY
+    subprocess.Popen(["explorer", error_folder_path])
+    # CONNECT TO GOOGLE DRIVE
+    credentials_path = os.path.join(storage_directory, "credentials.json")
+    google_sheet_name = "ABR-run-data"
+    try:
+        google_drive = google_drive_tool.google_drive(
+            credentials_path,
+            "1Cvej0eadFOTZr9ILRXJ0Wg65ymOtxL4m",
+            "[email protected]",
+        )
+        print("Connected to google drive.")
+    except json.decoder.JSONDecodeError:
+        print(
+            "Credential file is damaged. Get from https://console.cloud.google.com/apis/credentials"
+        )
+        sys.exit()
+    # CONNECT TO GOOGLE SHEET
+    try:
+        google_sheet = google_sheets_tool.google_sheet(
+            credentials_path, google_sheet_name, 0
+        )
+        print(f"Connected to google sheet: {google_sheet_name}")
+    except gspread.exceptions.APIError:
+        print("ERROR: Check google sheet name. Check credentials file.")
+        sys.exit()
+    # WRITE ERRORED RUN TO GOOGLE SHEET
+    error_run_log = os.path.join(error_folder_path, os.path.basename(run_log_file_path))
+    google_drive.upload_file(error_run_log)
+    run_id = os.path.basename(error_run_log).split("_")[1].split(".")[0]
+    runs_and_robots, headers = abr_google_drive.create_data_dictionary(
+        run_id, error_folder_path, issue_url
+    )
+    read_robot_logs.write_to_local_and_google_sheet(
+        runs_and_robots, storage_directory, google_sheet_name, google_sheet, headers
+    )
+    print("Wrote run to ABR-run-data")