Check state of the jobs launched by autocloser

src/osa/job.py

@@ -702,6 +702,33 @@
     return sacct_output
 
 
+def get_closer_sacct_output(sacct_output) -> pd.DataFrame:
+    """
+    Fetch the information of jobs in the queue launched by AUTOCLOSER using the sacct 
+    SLURM output and store it in a pandas dataframe.
+
+    Returns
+    -------
+    queue_list: pd.DataFrame
+    """
+    sacct_output = pd.read_csv(sacct_output, names=FORMAT_SLURM)
+
+    # Keep only the jobs corresponding to AUTOCLOSER sequences
+    sacct_output = sacct_output[
+        (sacct_output["JobName"].str.contains("lstchain"))
+        | (sacct_output["JobName"].str.contains("provproces"))
+    ]
+
+    try:
+        sacct_output["JobID"] = sacct_output["JobID"].apply(lambda x: x.split("_")[0])
+        sacct_output["JobID"] = sacct_output["JobID"].str.strip(".batch").astype(int)
+
+    except AttributeError:
+        log.debug("No job info could be obtained from sacct")
+
+    return sacct_output
+
+
 def filter_jobs(job_info: pd.DataFrame, sequence_list: Iterable):
     """Filter the job info list to get the values of the jobs in the current queue."""
     sequences_info = pd.DataFrame([vars(seq) for seq in sequence_list])

src/osa/scripts/closer.py

@@ -8,14 +8,20 @@
 import shutil
 import subprocess
 import sys
+import time
 from datetime import datetime, timedelta
 from pathlib import Path
 from typing import Tuple, Iterable, List
 
 from osa import osadb
 from osa.configs import options
 from osa.configs.config import cfg
-from osa.job import are_all_jobs_correctly_finished, save_job_information
+from osa.job import (
+    are_all_jobs_correctly_finished, 
+    save_job_information, 
+    run_sacct, 
+    get_closer_sacct_output
+)
 from osa.nightsummary.extract import extract_runs, extract_sequences
 from osa.nightsummary.nightsummary import run_summary_table
 from osa.paths import destination_dir
@@ -169,6 +175,20 @@
     if not options.no_dl2:
         merge_files(seq_list, data_level="DL2")
 
+    time.sleep(300)
+
+    # Check if all jobs launched by autocloser finished correctly 
+    # before creating the NightFinished.txt file
+    n_max = 10
+    n = 0
+    while not all_closer_jobs_finished_correctly() & n <= n_max:
+        log.info(
+            "All jobs launched by autocloser did not finished correctly yet. "
+            "Checking again in 5 minutes..."
+        )
+        time.sleep(300)
+        n += 1
+
     if options.seqtoclose is None:
         database = cfg.get("database", "path")
         if database:
@@ -490,5 +510,15 @@
         log.debug("Simulate launching scripts")
 
 
+def all_closer_jobs_finished_correctly():
+    """Check if all the jobs launched by autocloser finished correctly."""
+    sacct_output = run_sacct()
+    jobs_closer = get_closer_sacct_output(sacct_output)
+    if len(jobs_closer[jobs_closer["State"]!="COMPLETED"])==0:
+        return True
+    else:
+        return False
+
+
 if __name__ == "__main__":
     main()