Rename file validation script

As preparation for building a new generic worker script, this commit
renames the file validation script from 'worker.py' to
'validate_file.py' so as to ensure the name conforms better to what
the script does.

1 files changed, 0 insertions, 121 deletions

diff --git a/scripts/worker.py b/scripts/worker.py
deleted file mode 100644
index c6e989f..0000000
--- a/scripts/worker.py
+++ /dev/null
@@ -1,121 +0,0 @@
-"""External worker script"""
-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()