diff options
Diffstat (limited to 'scripts/process_rqtl2_bundle.py')
| -rw-r--r-- | scripts/process_rqtl2_bundle.py | 26 |
1 files changed, 15 insertions, 11 deletions
diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py index 7b114cf..1b26264 100644 --- a/scripts/process_rqtl2_bundle.py +++ b/scripts/process_rqtl2_bundle.py @@ -27,12 +27,12 @@ def safe_json_decode(value: str) -> Any: except json.decoder.JSONDecodeError: return value -def parse_job(rconn: Redis, jobid: uuid.UUID) -> dict: +def parse_job(rconn: Redis, rprefix: str, jobid: uuid.UUID) -> dict: """Load and parse job from Redis""" return { key: safe_json_decode(value) for key, value - in jobs.job(rconn, jobid).items() + in jobs.job(rconn, rprefix, jobid).items() } def has_geno_file(job: dict) -> bool: @@ -51,14 +51,15 @@ def percent_completion(geno: float, pheno: float) -> float: def process_bundle(dbconn: mdb.Connection, rconn: Redis, + rprefix: str, jobid: uuid.UUID, logger: Logger) -> int: """Process the R/qtl2 bundle.""" try: - thejob = parse_job(rconn, jobid) + thejob = parse_job(rconn, rprefix, jobid) meta = thejob["bundle-metadata"] - rconn.hset(str(jobid), "geno-percent", "0") - rconn.hset(str(jobid), "pheno-percent", "0") + rconn.hset(jobs.job_key(rprefix, jobid), "geno-percent", "0") + rconn.hset(jobs.job_key(rprefix, jobid), "pheno-percent", "0") if has_geno_file(thejob): logger.info("Processing geno files.") @@ -74,7 +75,7 @@ def process_bundle(dbconn: mdb.Connection, logger.debug( "geno file processing completed successfully. (ExitCode: %s)", genoexit) - rconn.hset(str(jobid), "geno-percent", "100") + rconn.hset(jobs.job_key(rprefix, jobid), "geno-percent", "100") if has_pheno_file(thejob): phenoexit = install_pheno_files( @@ -89,7 +90,7 @@ def process_bundle(dbconn: mdb.Connection, logger.debug( "pheno file processing completed successfully. (ExitCode: %s)", phenoexit) - rconn.hset(str(jobid), "pheno-percent", "100") + rconn.hset(jobs.job_key(rprefix, jobid), "pheno-percent", "100") return 0 except jobs.JobNotFound as exc: @@ -113,14 +114,17 @@ if __name__ == "__main__": logger.addHandler(StreamHandler(stream=sys.stderr)) logger.setLevel("DEBUG") - jobid = args.jobid + fqjobid = jobs.job_key(args.redisprefix, args.jobid) with (database_connection(args.databaseuri) as dbconn, Redis.from_url(args.redisuri, decode_responses=True) as rconn): logger.addHandler(setup_redis_logger( - rconn, jobid, f"{str(jobid)}:log-messages", args.redisexpiry)) + rconn, fqjobid, f"{fqjobid}:log-messages", + args.redisexpiry)) - exitcode = process_bundle(dbconn, rconn, args.jobid, logger) - rconn.hset(str(args.jobid), "percent", "100") + exitcode = process_bundle( + dbconn, rconn, args.redisprefix, args.jobid, logger) + rconn.hset( + jobs.job_key(args.redisprefix, args.jobid), "percent", "100") return exitcode sys.exit(main()) |