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-rw-r--r--scripts/validate_file.py121
1 files changed, 121 insertions, 0 deletions
diff --git a/scripts/validate_file.py b/scripts/validate_file.py
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+++ b/scripts/validate_file.py
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+"""External worker script that checks file for correctness"""
+import os
+import sys
+import traceback
+from typing import Callable
+from zipfile import ZipFile, is_zipfile
+
+import jsonpickle
+from redis import Redis
+from redis.exceptions import ConnectionError # pylint: disable=[redefined-builtin]
+
+from quality_control.utils import make_progress_calculator
+from quality_control.parsing import FileType, strain_names, collect_errors
+from .qc import cli_argument_parser
+
+
+def make_progress_indicator(
+ redis_connection: Redis, job_id: str,
+ progress_calc_fn: Callable) -> Callable:
+ """Make function that will compute the progress and update redis"""
+ def __indicator__(linenumber, linetext):
+ progress = progress_calc_fn(linenumber, linetext)
+ redis_connection.hset(name=job_id, mapping=progress._asdict())
+
+ return progress
+
+ return __indicator__
+
+def cli_args_valid(args):
+ "Check that the command-line arguments are provided and correct"
+ if not os.path.exists(args.filepath):
+ print(f"The file '{args.filepath}' does not exist.", file=sys.stderr)
+ return None
+
+ if not os.path.exists(args.strainsfile):
+ print(f"The file '{args.strainsfile}' does not exist.", file=sys.stderr)
+ return None
+
+ try:
+ conn = Redis.from_url(args.redisurl) # pylint: disable=[unused-variable]
+ except ConnectionError as conn_err: # pylint: disable=[unused-variable]
+ print(traceback.format_exc(), file=sys.stderr)
+ return None
+
+ return args
+
+def process_cli_arguments():
+ """Setup command-line parser"""
+ parser = cli_argument_parser()
+ parser.prog = "worker"
+ parser.add_argument(
+ "redisurl", default="redis:///", help="URL to the redis server")
+ parser.add_argument("job_id", help="The id of the job being processed")
+
+ return cli_args_valid(parser.parse_args())
+
+def stream_error(redis_conn, job_id, error):
+ """Update redis with the most current error(s) found"""
+ errors = jsonpickle.decode(
+ redis_conn.hget(job_id, key="errors") or jsonpickle.encode(tuple()))
+ redis_conn.hset(
+ job_id, key="errors", value=jsonpickle.encode(errors + (error,)))
+
+def make_user_aborted(redis_conn, job_id):
+ """Mkae function that checks whether the user aborted the process"""
+ def __aborted__():
+ user_aborted = bool(int(
+ redis_conn.hget(name=job_id, key="user_aborted") or "0"))
+ if user_aborted:
+ redis_conn.hset(name=job_id, key="status", value="aborted")
+
+ return user_aborted
+ return __aborted__
+
+def get_zipfile_size(filepath):
+ "Compute size of given zipfile"
+ with ZipFile(filepath, "r") as zfile:
+ return zfile.infolist()[0].file_size
+
+def main():
+ "entry point to the script"
+ args = process_cli_arguments()
+ if args is None:
+ print("Quiting due to errors!", file=sys.stderr)
+ return 1
+
+ with Redis.from_url(args.redisurl) as redis_conn:
+ progress_calculator = make_progress_calculator(
+ get_zipfile_size(args.filepath) if is_zipfile(args.filepath)
+ else os.stat(args.filepath).st_size)
+ progress_indicator = make_progress_indicator(
+ redis_conn, args.job_id, progress_calculator)
+ count = args.count
+ filepath = args.filepath
+ filetype = (
+ FileType.AVERAGE if args.filetype == "average"
+ else FileType.STANDARD_ERROR)
+ strains = strain_names(args.strainsfile)
+
+ redis_conn.hset(
+ name=args.job_id, key="status", value="Processing")
+ redis_conn.hset(
+ name=args.job_id, key="message", value="Collecting errors")
+
+ error_count = 0
+ for error in collect_errors(
+ filepath, filetype, strains, progress_indicator,
+ make_user_aborted(redis_conn, args.job_id)):
+ stream_error(redis_conn, args.job_id, error)
+
+ if count > 0:
+ error_count = error_count + 1
+ if error_count >= count:
+ break
+
+ redis_conn.hset(name=args.job_id, key="status", value="success")
+
+ return 0
+
+if __name__ == "__main__":
+ main()