Just add approve_timeout to the python script

ingest/Snakefile

@@ -25,7 +25,7 @@ COLUMN_MAPPING = config["column_mapping"]
 LOG_LEVEL = config.get("log_level", "INFO")
 NCBI_API_KEY = os.getenv("NCBI_API_KEY")
 FILTER_FASTA_HEADERS = config.get("filter_fasta_headers", None)
-APPROVE_TIMEOUT = config.get("approve_timeout", '1m')
+APPROVE_TIMEOUT = config.get("approve_timeout", '1') #time in minutes
 
 
 def rename_columns(input_file, output_file, mapping=COLUMN_MAPPING):
@@ -448,9 +448,10 @@ rule approve:
         approve_timeout=APPROVE_TIMEOUT,
     shell:
         """
-        timeout --preserve-status -s SIGTERM {params.approve_timeout} \
-            bash -c "python {input.script} \
+        python {input.script} \
             --mode approve \
             --config-file {input.config} \
-            --log-level {params.log_level}" \
+            --log-level {params.log_level} \
+            --approve-timeout {params.approve_timeout}
+        touch results/approved
         """

ingest/scripts/call_loculus.py

@@ -3,13 +3,15 @@
 import os
 from collections import defaultdict
 from dataclasses import dataclass
+from datetime import datetime, timedelta
 from http import HTTPMethod
 from pathlib import Path
 from time import sleep
 from typing import Any, Literal
 
 import click
 import jsonlines
+import pytz
 import requests
 import yaml
 
@@ -21,6 +23,8 @@
     datefmt="%H:%M:%S",
 )
 
+_start_time: datetime | None = None
+
 
 @dataclass
 class Config:
@@ -413,10 +417,18 @@ def get_submitted(config: Config):
     required=False,
     type=click.Path(exists=True),
 )
-def submit_to_loculus(metadata, sequences, mode, log_level, config_file, output, revoke_map):
+@click.option(
+    "--approve-timeout",
+    required=False,
+    type=int,
+)
+def submit_to_loculus(
+    metadata, sequences, mode, log_level, config_file, output, revoke_map, approve_timeout
+):
     """
     Submit data to Loculus.
     """
+    global _start_time
     logger.setLevel(log_level)
     logging.getLogger("requests").setLevel(logging.WARNING)
     logging.getLogger("urllib3").setLevel(logging.WARNING)
@@ -449,10 +461,14 @@ def record_factory(*args, **kwargs):
 
     if mode == "approve":
         while True:
+            if not _start_time:
+                _start_time = datetime.now(tz=pytz.utc)
             logger.info("Approving sequences")
             response = approve(config)
             logger.info(f"Approved: {len(response)} sequences")
             sleep(30)
+            if datetime.now(tz=pytz.utc) - timedelta(minutes=approve_timeout) > _start_time:
+                break
 
     if mode == "regroup-and-revoke":
         try: