diff options
Diffstat (limited to 'scripts/process_rqtl2_bundle.py')
| -rw-r--r-- | scripts/process_rqtl2_bundle.py | 25 |
1 files changed, 16 insertions, 9 deletions
diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py index 20cfd3b..8b7a0fb 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 @@ -10,6 +11,7 @@ from logging import Logger, getLogger, StreamHandler import MySQLdb as mdb from redis import Redis +from gn_libs.mysqldb import database_connection from functional_tools import take @@ -18,7 +20,6 @@ import r_qtl.r_qtl2_qc as rqc import r_qtl.exceptions as rqe from uploader import jobs -from uploader.db_utils import database_connection from uploader.check_connections import check_db, check_redis from scripts.cli_parser import init_cli_parser @@ -93,11 +94,14 @@ def process_bundle(dbconn: mdb.Connection, if has_geno_file(thejob): logger.info("Processing geno files.") genoexit = install_genotypes( + rconn, dbconn, - meta["speciesid"], - meta["populationid"], - meta["geno-dataset-id"], - Path(meta["rqtl2-bundle-file"]), + f"{rprefix}:{jobid}", + 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.") @@ -108,11 +112,14 @@ def process_bundle(dbconn: mdb.Connection, if has_pheno_file(thejob): phenoexit = install_pheno_files( + rconn, dbconn, - meta["speciesid"], - meta["platformid"], - meta["probe-dataset-id"], - Path(meta["rqtl2-bundle-file"]), + f"{rprefix}:{jobid}", + 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.") |