diff options
| -rw-r--r-- | scripts/process_rqtl2_bundle.py | 4 | ||||
| -rw-r--r-- | scripts/rqtl2/entry.py | 7 | ||||
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 5 | ||||
| -rw-r--r-- | scripts/rqtl2/install_phenos.py | 5 | ||||
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 2 |
5 files changed, 19 insertions, 4 deletions
diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py index 4efc3e0..8b7a0fb 100644 --- a/scripts/process_rqtl2_bundle.py +++ b/scripts/process_rqtl2_bundle.py @@ -94,7 +94,9 @@ def process_bundle(dbconn: mdb.Connection, if has_geno_file(thejob): logger.info("Processing geno files.") genoexit = install_genotypes( + rconn, dbconn, + f"{rprefix}:{jobid}", argparse.Namespace( speciesid=meta["speciesid"], populationid=meta["populationid"], @@ -110,7 +112,9 @@ def process_bundle(dbconn: mdb.Connection, if has_pheno_file(thejob): phenoexit = install_pheno_files( + rconn, dbconn, + f"{rprefix}:{jobid}", argparse.Namespace( speciesid=meta["speciesid"], platformid=meta["platformid"], diff --git a/scripts/rqtl2/entry.py b/scripts/rqtl2/entry.py index 48d89fb..327ed2c 100644 --- a/scripts/rqtl2/entry.py +++ b/scripts/rqtl2/entry.py @@ -16,7 +16,10 @@ from scripts.redis_logger import setup_redis_logger def build_main( args: Namespace, - run_fn: Callable[[Connection, Namespace, logging.Logger], int], + run_fn: Callable[ + [Redis, Connection, str, Namespace, logging.Logger], + int + ], loggername: str ) -> Callable[[],int]: """Build a function to be used as an entry-point for scripts.""" @@ -45,7 +48,7 @@ def build_main( logger.error("File not found: '%s'.", args.rqtl2bundle) return 2 - returncode = run_fn(dbconn, args, logger) + returncode = run_fn(rconn, dbconn, fqjobid, args, logger) if returncode == 0: rconn.hset(fqjobid, "status", "completed:success") return returncode diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index 20a19da..8762655 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -7,6 +7,7 @@ from functools import reduce from typing import Iterator, Optional from logging import Logger, getLogger +from redis import Redis import MySQLdb as mdb from MySQLdb.cursors import DictCursor @@ -185,8 +186,10 @@ def cross_reference_genotypes( cursor.executemany(insertquery, insertparams) return cursor.rowcount -def install_genotypes(#pylint: disable=[too-many-arguments, too-many-locals] +def install_genotypes(#pylint: disable=[too-many-locals] + rconn: Redis,#pylint: disable=[unused-argument] dbconn: mdb.Connection, + fullyqualifiedjobid: str,#pylint: disable=[unused-argument] args: argparse.Namespace, logger: Logger = getLogger(__name__) ) -> int: diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py index a6e9fb2..9059cd6 100644 --- a/scripts/rqtl2/install_phenos.py +++ b/scripts/rqtl2/install_phenos.py @@ -6,6 +6,7 @@ from zipfile import ZipFile from functools import reduce from logging import Logger, getLogger +from redis import Redis import MySQLdb as mdb from MySQLdb.cursors import DictCursor @@ -95,8 +96,10 @@ def cross_reference_probeset_data(dbconn: mdb.Connection, } for row in dataids)) return cursor.rowcount -def install_pheno_files(#pylint: disable=[too-many-arguments, too-many-locals] +def install_pheno_files(#pylint: disable=[too-many-locals] + rconn: Redis,#pylint: disable=[unused-argument] dbconn: mdb.Connection, + fullyqualifiedjobid: str,#pylint: disable=[unused-argument] args: argparse.Namespace, logger: Logger = getLogger()) -> int: """Load data in `pheno` files and other related files into the database.""" diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 4f55e40..12b1803 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -324,7 +324,9 @@ def fullyqualifiedkey( return f"{prefix}:{rest}" def run_qc(# pylint: disable=[too-many-locals] + rconn: Redis, dbconn: mdb.Connection, + fullyqualifiedjobid: str, args: Namespace, logger: Logger ) -> int: |