diff options
| -rw-r--r-- | scripts/process_rqtl2_bundle.py | 19 | ||||
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 9 | ||||
| -rw-r--r-- | scripts/rqtl2/install_phenos.py | 9 |
3 files changed, 19 insertions, 18 deletions
diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py index 20cfd3b..ade9862 100644 --- a/scripts/process_rqtl2_bundle.py +++ b/scripts/process_rqtl2_bundle.py @@ -2,6 +2,7 @@ import sys import uuid import json +import argparse import traceback from typing import Any from pathlib import Path @@ -94,10 +95,11 @@ def process_bundle(dbconn: mdb.Connection, logger.info("Processing geno files.") genoexit = install_genotypes( dbconn, - meta["speciesid"], - meta["populationid"], - meta["geno-dataset-id"], - Path(meta["rqtl2-bundle-file"]), + argparse.Namespace( + speciesid=meta["speciesid"], + populationid=meta["populationid"], + datasetid=meta["geno-dataset-id"], + rqtl2bundle=Path(meta["rqtl2-bundle-file"])), logger) if genoexit != 0: raise Exception("Processing 'geno' file failed.") @@ -109,10 +111,11 @@ def process_bundle(dbconn: mdb.Connection, if has_pheno_file(thejob): phenoexit = install_pheno_files( dbconn, - meta["speciesid"], - meta["platformid"], - meta["probe-dataset-id"], - Path(meta["rqtl2-bundle-file"]), + argparse.Namespace( + speciesid=meta["speciesid"], + platformid=meta["platformid"], + dataset_id=meta["probe-dataset-id"], + rqtl2bundle=Path(meta["rqtl2-bundle-file"])), logger) if phenoexit != 0: raise Exception("Processing 'pheno' file failed.") diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index abc3f07..20a19da 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -1,7 +1,7 @@ """Load genotypes from R/qtl2 bundle into the database.""" import sys +import argparse import traceback -from pathlib import Path from zipfile import ZipFile from functools import reduce from typing import Iterator, Optional @@ -187,13 +187,12 @@ def cross_reference_genotypes( def install_genotypes(#pylint: disable=[too-many-arguments, too-many-locals] dbconn: mdb.Connection, - speciesid: int, - populationid: int, - datasetid: int, - rqtl2bundle: Path, + args: argparse.Namespace, logger: Logger = getLogger(__name__) ) -> int: """Load any existing genotypes into the database.""" + (speciesid, populationid, datasetid, rqtl2bundle) = ( + args.speciesid, args.populationid, args.datasetid, args.rqtl2bundle) count = 0 with ZipFile(str(rqtl2bundle.absolute()), "r") as zfile: try: diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py index e96742f..a6e9fb2 100644 --- a/scripts/rqtl2/install_phenos.py +++ b/scripts/rqtl2/install_phenos.py @@ -1,7 +1,7 @@ """Load pheno from R/qtl2 bundle into the database.""" import sys +import argparse import traceback -from pathlib import Path from zipfile import ZipFile from functools import reduce from logging import Logger, getLogger @@ -97,12 +97,11 @@ def cross_reference_probeset_data(dbconn: mdb.Connection, def install_pheno_files(#pylint: disable=[too-many-arguments, too-many-locals] dbconn: mdb.Connection, - speciesid: int, - platformid: int, - datasetid: int, - rqtl2bundle: Path, + args: argparse.Namespace, logger: Logger = getLogger()) -> int: """Load data in `pheno` files and other related files into the database.""" + (speciesid, platformid, datasetid, rqtl2bundle) = ( + args.speciesid, args.platformid, args.datasetid, args.rqtl2bundle) with ZipFile(str(rqtl2bundle), "r") as zfile: try: rqc.validate_bundle(zfile) |