Added feature to pull python protocol file from specifed robot with r…

…un error, as well as additional error handling

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -11,11 +11,34 @@
 import sys
 import json
 import re
+from pathlib import Path
 import pandas as pd
 from statistics import mean, StatisticsError
 from abr_testing.tools import plate_reader
 
 
+def retrieve_protocol_file(
+    protocol_id: str,
+    robot_ip: str,
+    storage: str,
+) -> Path | str:
+    """Find and copy protocol file on robot with error."""
+    protocol_dir = f"/var/lib/opentrons-robot-server/7.1/protocols/{protocol_id}"
+
+    print(f"FILE TO FIND: {protocol_dir}/{protocol_id}")
+    # Download protocol and supporting files
+    save_dir = Path(f"{storage}/protocol_errors")
+
+    command = ["scp", "-r", f"root@{robot_ip}:{protocol_dir}", save_dir]
+    try:
+        subprocess.run(command, check=True)  # type: ignore
+        print("File transfer successful!")
+        return save_dir
+    except subprocess.CalledProcessError as e:
+        print(f"Error during file transfer: {e}")
+    return ""
+
+
 def compare_current_trh_to_average(
     robot: str,
     start_time: Any,
@@ -38,9 +61,13 @@ def compare_current_trh_to_average(
     # 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)
+    print(f'TIMESTAMP: {df_all_trh["Timestamp"]}')
+    try:
+        df_all_trh["Timestamp"] = pd.to_datetime(
+            df_all_trh["Timestamp"], format="mixed", utc=True
+        ).dt.tz_localize(None)
+    except Exception:
+        print(f'The following timestamp is invalid: {df_all_trh["Timestamp"]}')
     # Ensure start_time is timezone-naive
     start_time = start_time.replace(tzinfo=None)
     relevant_temp_rhs = df_all_trh[
@@ -245,20 +272,23 @@ def get_user_id(user_file_path: str, assignee_name: str) -> str:
     return assignee_id
 
 
-def get_error_runs_from_robot(ip: str) -> List[str]:
+def get_error_runs_from_robot(ip: str) -> Tuple[List[str], List[str]]:
     """Get runs that have errors from robot."""
     error_run_ids = []
+    protocol_ids = []
     response = requests.get(
         f"http://{ip}:31950/runs", headers={"opentrons-version": "3"}
     )
     run_data = response.json()
     run_list = run_data.get("data", [])
     for run in run_list:
         run_id = run["id"]
+        protocol_id = run["protocolId"]
         num_of_errors = len(run["errors"])
         if not run["current"] and num_of_errors > 0:
             error_run_ids.append(run_id)
-    return error_run_ids
+            protocol_ids.append(protocol_id)
+    return (error_run_ids, protocol_ids)
 
 
 def get_robot_state(
@@ -335,7 +365,7 @@ def get_robot_state(
 
 
 def get_run_error_info_from_robot(
-    ip: str, one_run: str, storage_directory: str
+    ip: str, one_run: str, storage_directory: str, protocol_found: bool
 ) -> Tuple[str, str, str, List[str], List[str], str, str]:
     """Get error information from robot to fill out ticket."""
     description = dict()
@@ -369,6 +399,8 @@ def get_run_error_info_from_robot(
     description["protocol_name"] = results["protocol"]["metadata"].get(
         "protocolName", ""
     )
+
+    description["protocol_found_on_robot"] = protocol_found
     # Get start and end time of run
     start_time = datetime.strptime(
         results.get("startedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
@@ -511,12 +543,19 @@ def get_run_error_info_from_robot(
     users_file_path = ticket.get_jira_users(storage_directory)
     assignee_id = get_user_id(users_file_path, assignee)
     run_log_file_path = ""
+    protocol_found = False
     try:
-        error_runs = get_error_runs_from_robot(ip)
+        error_runs, protocol_ids = get_error_runs_from_robot(ip)
     except requests.exceptions.InvalidURL:
         print("Invalid IP address.")
         sys.exit()
     if len(run_or_other) < 1:
+        protocol_files_path = retrieve_protocol_file(
+            protocol_ids[-1], ip, storage_directory
+        )
+        if protocol_files_path:
+            protocol_found = True
+
         one_run = error_runs[-1]  # Most recent run with error.
         (
             summary,
@@ -526,7 +565,9 @@ def get_run_error_info_from_robot(
             labels,
             whole_description_str,
             run_log_file_path,
-        ) = get_run_error_info_from_robot(ip, one_run, storage_directory)
+        ) = get_run_error_info_from_robot(
+            ip, one_run, storage_directory, protocol_found
+        )
     else:
         (
             summary,
@@ -566,8 +607,14 @@ def get_run_error_info_from_robot(
     # OPEN TICKET
     issue_url = ticket.open_issue(issue_key)
     # MOVE FILES TO ERROR FOLDER.
+    print(protocol_files_path)
     error_files = [saved_file_path_calibration, run_log_file_path] + file_paths
-    error_folder_path = os.path.join(storage_directory, issue_key)
+
+    if protocol_files_path:
+        for file in os.listdir(protocol_files_path):
+            error_files.append(os.path.join(protocol_files_path, file))
+
+    error_folder_path = os.path.join(storage_directory, "issue_key")
     os.makedirs(error_folder_path, exist_ok=True)
     for source_file in error_files:
         try: