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authorArun Isaac2023-12-29 18:55:37 +0000
committerArun Isaac2023-12-29 19:01:46 +0000
commit204a308be0f741726b9a620d88fbc22b22124c81 (patch)
treeb3cf66906674020b530c844c2bb4982c8a0e2d39 /gn2/scripts/run_external.py
parent83062c75442160427b50420161bfcae2c5c34c84 (diff)
downloadgenenetwork2-204a308be0f741726b9a620d88fbc22b22124c81.tar.gz
Namespace all modules under gn2.
We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service.
Diffstat (limited to 'gn2/scripts/run_external.py')
-rw-r--r--gn2/scripts/run_external.py159
1 files changed, 159 insertions, 0 deletions
diff --git a/gn2/scripts/run_external.py b/gn2/scripts/run_external.py
new file mode 100644
index 00000000..297d17a1
--- /dev/null
+++ b/gn2/scripts/run_external.py
@@ -0,0 +1,159 @@
+"""
+Run jobs in external processes.
+"""
+
+import os
+import sys
+import shlex
+import argparse
+import traceback
+import subprocess
+from uuid import UUID
+from time import sleep
+from datetime import datetime
+from urllib.parse import urlparse
+from tempfile import TemporaryDirectory
+
+# import psutil
+from redis import Redis
+
+import gn2.jobs.jobs as jobs
+
+def print_help(args, parser):
+ print(parser.format_help())
+
+def UUID4(val):
+ return UUID(val)
+
+def redis_connection(parsed_url):
+ return Redis.from_url(
+ f"redis://{parsed_url.netloc}{parsed_url.path}", decode_responses=True)
+
+def update_status(redis_conn: Redis, job_id: UUID, value: str):
+ "Update the job's status."
+ redis_conn.hset(jobs.job_namespace(job_id), key="status", value=value)
+
+def __update_stdout_stderr__(
+ redis_conn: Redis, job_id: UUID, bytes_read: bytes, stream: str):
+ job = jobs.job(redis_conn, job_id)
+ if job.is_nothing():
+ raise jobs.NoSuchJob(job_id)
+
+ job = job.maybe({}, lambda x: x)
+ redis_conn.hset(
+ jobs.job_namespace(job_id), key=stream,
+ value=(job.get(stream, "") + bytes_read.decode("utf-8")))
+
+def set_stdout(redis_conn: Redis, job_id:UUID, bytes_read: bytes):
+ """Set the stdout value for the given job."""
+ job = jobs.job(redis_conn, job_id)
+ if job.is_nothing():
+ raise jobs.NoSuchJob(job_id)
+
+ job = job.maybe({}, lambda x: x)
+ redis_conn.hset(
+ jobs.job_namespace(job_id), key="stdout",
+ value=bytes_read.decode("utf-8"))
+
+def update_stdout(redis_conn: Redis, job_id:UUID, bytes_read: bytes):
+ """Update the stdout value for the given job."""
+ __update_stdout_stderr__(redis_conn, job_id, bytes_read, "stdout")
+
+def update_stderr(redis_conn: Redis, job_id:UUID, bytes_read: bytes):
+ """Update the stderr value for the given job."""
+ __update_stdout_stderr__(redis_conn, job_id, bytes_read, "stderr")
+
+def set_meta(redis_conn: Redis, job_id: UUID, meta_key: str, meta_val: str):
+ job = jobs.job(redis_conn, job_id)
+ if job.is_nothing():
+ raise jobs.NoSuchJob(job_id)
+
+ redis_conn.hset(jobs.job_namespace(job_id), key=meta_key, value=meta_val)
+
+def run_job(redis_conn: Redis, job_id: UUID):
+ """Run the job in an external process."""
+ print(f"THE ARGUMENTS TO RUN_JOB:\n\tConnection: {redis_conn}\n\tJob ID: {job_id}\n")
+
+ the_job = jobs.job(redis_conn, job_id)
+ if the_job.is_nothing():
+ raise jobs.NoSuchJob(job_id)
+
+ with TemporaryDirectory() as tmpdir:
+ stdout_file = f"{tmpdir}/{job_id}.stdout"
+ stderr_file = f"{tmpdir}/{job_id}.stderr"
+ with open(stdout_file, "w+b") as outfl, open(stderr_file, "w+b") as errfl:
+ with subprocess.Popen(
+ jobs.command(the_job), stdout=outfl,
+ stderr=errfl) as process:
+ while process.poll() is None:
+ update_status(redis_conn, job_id, "running")
+ update_stdout(redis_conn, job_id, outfl.read1())
+ sleep(1)
+
+ update_status(redis_conn, job_id, "completed")
+ with open(stdout_file, "rb") as outfl, open(stderr_file, "rb") as errfl:
+ set_stdout(redis_conn, job_id, outfl.read())
+ update_stderr(redis_conn, job_id, errfl.read())
+
+ os.remove(stdout_file)
+ os.remove(stderr_file)
+
+ returncode = process.returncode
+ set_meta(redis_conn, job_id, "completion-status",
+ ("success" if returncode == 0 else "error"))
+ set_meta(redis_conn, job_id, "return-code", returncode)
+ return process.returncode
+
+def run_job_parser(parent_parser):
+ parser = parent_parser.add_parser(
+ "run-job",
+ help="run job with given id")
+ parser.add_argument(
+ "job_id", type=UUID4, help="A string representing a UUID4 value.")
+ parser.set_defaults(
+ run=lambda conn, args, parser: run_job(conn, args.job_id))
+
+def add_subparsers(parent_parser, *subparser_fns):
+ sub_parsers = parent_parser.add_subparsers(
+ title="subcommands", description="valid subcommands", required=True)
+ for parser_fn in subparser_fns:
+ parser_fn(sub_parsers)
+ pass
+
+ return parent_parser
+
+def parse_cli_args():
+ parser = add_subparsers(argparse.ArgumentParser(
+ description=sys.modules[__name__].__doc__.strip()), run_job_parser)
+ parser.add_argument(
+ "--redis-uri", required=True,
+ help=(
+ "URI to use to connect to job management db."
+ "The URI should be of the form "
+ "'<scheme>://<user>:<passwd>@<host>:<port>/<path>'"),
+ type=urlparse)
+ return parser, parser.parse_args()
+
+def launch_manager():
+ parser, args = parse_cli_args()
+ with redis_connection(args.redis_uri) as conn:
+ try:
+ return args.run(conn, args, parser)
+ except Exception as nsj:
+ prev_msg = (
+ conn.hget(f"{jobs.JOBS_NAMESPACE}:manager", key="stderr") or "")
+ if bool(prev_msg):
+ prev_msg = f"{prev_msg}\n"
+
+ notfoundmsg = (
+ f"{prev_msg}"
+ f"{datetime.now().isoformat()}: {type(nsj).__name__}: {traceback.format_exc()}")
+ conn.hset(
+ f"{jobs.JOBS_NAMESPACE}:manager",
+ key="stderr",
+ value=notfoundmsg)
+
+if __name__ == "__main__":
+ def run():
+ sys.exit(launch_manager())
+ run()