diff options
Diffstat (limited to 'scripts/process_rqtl2_bundle.py')
| -rw-r--r-- | scripts/process_rqtl2_bundle.py | 10 |
1 files changed, 7 insertions, 3 deletions
diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py index ade9862..e2ce420 100644 --- a/scripts/process_rqtl2_bundle.py +++ b/scripts/process_rqtl2_bundle.py @@ -11,6 +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 @@ -19,7 +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 @@ -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"], @@ -102,7 +104,7 @@ def process_bundle(dbconn: mdb.Connection, rqtl2bundle=Path(meta["rqtl2-bundle-file"])), logger) if genoexit != 0: - raise Exception("Processing 'geno' file failed.") + raise Exception("Processing 'geno' file failed.")# pylint: disable=[broad-exception-raised] logger.debug( "geno file processing completed successfully. (ExitCode: %s)", genoexit) @@ -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"], @@ -118,7 +122,7 @@ def process_bundle(dbconn: mdb.Connection, rqtl2bundle=Path(meta["rqtl2-bundle-file"])), logger) if phenoexit != 0: - raise Exception("Processing 'pheno' file failed.") + raise Exception("Processing 'pheno' file failed.")# pylint: disable=[broad-exception-raised] logger.debug( "pheno file processing completed successfully. (ExitCode: %s)", phenoexit) |