aboutsummaryrefslogtreecommitdiff
path: root/scripts
diff options
context:
space:
mode:
authorFrederick Muriuki Muriithi2024-10-24 15:57:27 -0500
committerFrederick Muriuki Muriithi2024-10-24 15:58:13 -0500
commit6fb2834489888937842d761cbbc7c2992a4f5a0d (patch)
treea2d4d76c563a9bf1a057016daa880c65a833631e /scripts
parenta52401e7191850c4a6542da1af5f2b2769312871 (diff)
downloadgn-uploader-6fb2834489888937842d761cbbc7c2992a4f5a0d.tar.gz
Parse entire namespace object rather than individual values.
Diffstat (limited to 'scripts')
-rw-r--r--scripts/process_rqtl2_bundle.py19
-rw-r--r--scripts/rqtl2/install_genotypes.py9
-rw-r--r--scripts/rqtl2/install_phenos.py9
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)