diff options
| -rw-r--r-- | scripts/load_phenotypes_to_db.py | 8 |
1 files changed, 7 insertions, 1 deletions
diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py index b78c648..980aa94 100644 --- a/scripts/load_phenotypes_to_db.py +++ b/scripts/load_phenotypes_to_db.py @@ -3,6 +3,7 @@ import json import logging import argparse from pathlib import Path +from zipfile import ZipFile from typing import Any, Union from MySQLdb.cursors import Cursor, DictCursor @@ -243,7 +244,12 @@ def load_data(conn, job): conn, int(_job_metadata.get("publicationid", "0"))) or {"Id": 0} # 2. Save all new phenotypes: # -> return phenotype IDs - _control_data = rqtl.control_data(job["job-metadata"]["bundle-file"]) + bundle = Path(_job_metadata["bundle_file"]) + _control_data = rqtl2.control_data(bundle) + logger.info("Extracting the zipped bundle of files.") + _outdir = Path(bundle.parent, f"bundle_{bundle.stem}") + with ZipFile(str(bundle), "r") as zfile: + _files = rqtl2.extract(zfile, _outdir) logger.info("Saving basic phenotype data.") _phenos = save_phenotypes(cursor, _control_data) |