diff options
Diffstat (limited to 'scripts/qc_on_rqtl2_bundle.py')
| -rw-r--r-- | scripts/qc_on_rqtl2_bundle.py | 24 |
1 files changed, 14 insertions, 10 deletions
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py index 40809b7..fc95d13 100644 --- a/scripts/qc_on_rqtl2_bundle.py +++ b/scripts/qc_on_rqtl2_bundle.py @@ -16,13 +16,13 @@ from redis import Redis from quality_control.errors import InvalidValue from quality_control.checks import decimal_points_error -from qc_app import jobs -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis +from uploader import jobs +from uploader.db_utils import database_connection +from uploader.check_connections import check_db, check_redis -from r_qtl import errors as rqe from r_qtl import r_qtl2 as rqtl2 from r_qtl import r_qtl2_qc as rqc +from r_qtl import exceptions as rqe from r_qtl import fileerrors as rqfe from scripts.process_rqtl2_bundle import parse_job @@ -105,7 +105,7 @@ def retrieve_errors_with_progress(rconn: Redis,#pylint: disable=[too-many-locals __update_processed__(value) rconn.hset(fqjobid, f"{filetype}-linecount", count) - except rqe.MissingFileError: + except rqe.MissingFileException: fname = cdata.get(filetype) yield rqfe.MissingFile(filetype, fname, ( f"The file '{fname}' does not exist in the bundle despite it being " @@ -133,7 +133,7 @@ def qc_geno_errors(rconn, fqjobid, _dburi, _speciesid, zfile, logger) -> bool: def fetch_db_geno_samples(conn: mdb.Connection, speciesid: int) -> tuple[str, ...]: """Fetch samples/cases/individuals from the database.""" - samples = set() + samples = set()# type: ignore[var-annotated] with conn.cursor() as cursor: cursor.execute("SELECT Name, Name2 from Strain WHERE SpeciesId=%s", (speciesid,)) @@ -191,12 +191,13 @@ def check_pheno_samples( return allerrors -def qc_pheno_errors(rconn, fqjobid, dburi, speciesid, zfile, logger) -> bool: +def qc_pheno_errors(# pylint: disable=[too-many-arguments] + rconn, fqjobid, dburi, speciesid, zfile, logger) -> bool: """Check for errors in `pheno` file(s).""" cdata = rqtl2.control_data(zfile) if "pheno" in cdata: logger.info("Checking for errors in the 'pheno' file…") - perrs = tuple() + perrs = tuple()# type: ignore[var-annotated] with database_connection(dburi) as dbconn: perrs = check_pheno_samples( dbconn, speciesid, zfile.filename, logger) + tuple( @@ -216,7 +217,8 @@ def qc_pheno_errors(rconn, fqjobid, dburi, speciesid, zfile, logger) -> bool: return False -def qc_phenose_errors(rconn, fqjobid, dburi, speciesid, zfile, logger) -> bool: +def qc_phenose_errors(# pylint: disable=[too-many-arguments] + rconn, fqjobid, _dburi, _speciesid, zfile, logger) -> bool: """Check for errors in `phenose` file(s).""" cdata = rqtl2.control_data(zfile) if "phenose" in cdata: @@ -258,7 +260,9 @@ def run_qc(rconn: Redis, if qc_missing_files(rconn, fqjobid, zfile, logger): return 1 - def with_zipfile(rconn, fqjobid, dbconn, speciesid, filename, logger, func): + def with_zipfile(# pylint: disable=[too-many-arguments] + rconn, fqjobid, dbconn, speciesid, filename, logger, func + ): with ZipFile(filename, "r") as zfile: return func(rconn, fqjobid, dbconn, speciesid, zfile, logger) |