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-rw-r--r--qc_app/upload/rqtl2.py1
-rw-r--r--r_qtl/r_qtl2_qc.py16
-rw-r--r--scripts/rqtl2/install_genotypes.py3
-rw-r--r--scripts/rqtl2/install_phenos.py3
-rw-r--r--tests/r_qtl/test_r_qtl2_qc.py3
5 files changed, 13 insertions, 13 deletions
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 2d032f8..73d91ec 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -18,7 +18,6 @@ from flask import (
current_app as app)
from r_qtl import r_qtl2
-from r_qtl import errors as rqe
from r_qtl import r_qtl2_qc as rqc
from r_qtl.errors import InvalidFormat
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index 261d300..853c34b 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -7,23 +7,23 @@ from r_qtl import errors as rqe
from r_qtl import r_qtl2 as rqtl2
from r_qtl.r_qtl2 import __FILE_TYPES__
-def bundle_files_list(zfile, cdata: dict) -> tuple[str]:
+def bundle_files_list(cdata: dict) -> tuple[str, ...]:
"""Retrieve files listed in control file."""
def __merge__(alist: tuple[str, ...], member: Union[str, Sequence[str]]) -> tuple[str, ...]:
if isinstance(cdata[member], str):
return alist + (cdata[member],)
return alist + tuple(cdata[member])
- fileslist = tuple()
- fileslist = reduce(__merge__,
- (key for key in cdata.keys() if key in __FILE_TYPES__),
- tuple())
+ fileslist: tuple[str, ...] = reduce(
+ __merge__,
+ (key for key in cdata.keys() if key in __FILE_TYPES__),
+ tuple())
if "file" in cdata.get("sex", {}):
sexfile = cdata["sex"]["file"]
fileslist = fileslist + (
(sexfile,) if isinstance(sexfile, str) else tuple(sexfile))
-
+
if "file" in cdata.get("cross_info", {}):
crossinfofile = cdata["cross_info"]["file"]
fileslist = fileslist + (
@@ -32,7 +32,7 @@ def bundle_files_list(zfile, cdata: dict) -> tuple[str]:
return fileslist
-def missing_files(zfile: ZipFile) -> tuple[str]:
+def missing_files(zfile: ZipFile) -> tuple[str, ...]:
"""
Retrieve a list of files listed in the control file that do not exist in the
bundle.
@@ -45,7 +45,7 @@ def missing_files(zfile: ZipFile) -> tuple[str]:
return True
return tuple(filter(__missing_p__,
- bundle_files_list(zfile, rqtl2.control_data(zfile))))
+ bundle_files_list(rqtl2.control_data(zfile))))
def validate_bundle(zfile: ZipFile):
"""Ensure the R/qtl2 bundle is valid."""
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index bfe17b8..7f3f65a 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -11,6 +11,7 @@ import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
from r_qtl import r_qtl2 as rqtl2
+from r_qtl import r_qtl2_qc as rqc
from functional_tools import take
@@ -166,7 +167,7 @@ def install_genotypes(#pylint: disable=[too-many-arguments, too-many-locals]
with ZipFile(str(rqtl2bundle.absolute()), "r") as zfile:
try:
logger.info("Validating bundle")
- rqtl2.validate_bundle(zfile)
+ rqc.validate_bundle(zfile)
logger.info("Bundle validated successfully.")
logger.info(("Loading genotypes. This could take a while. "
"Please be patient."))
diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
index a6cdacc..95745d7 100644
--- a/scripts/rqtl2/install_phenos.py
+++ b/scripts/rqtl2/install_phenos.py
@@ -14,6 +14,7 @@ from scripts.rqtl2.cli_parser import add_common_arguments
from scripts.cli_parser import init_cli_parser, add_global_data_arguments
from r_qtl import r_qtl2 as rqtl2
+from r_qtl import r_qtl2_qc as rqc
from functional_tools import take
@@ -102,7 +103,7 @@ def install_pheno_files(#pylint: disable=[too-many-arguments, too-many-locals]
"""Load data in `pheno` files and other related files into the database."""
with ZipFile(str(rqtl2bundle), "r") as zfile:
try:
- rqtl2.validate_bundle(zfile)
+ rqc.validate_bundle(zfile)
logger.info("R/qtl2 bundle validated successfully.")
cdata = rqtl2.control_data(zfile)
diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py
index 5fcccf5..9b19ae2 100644
--- a/tests/r_qtl/test_r_qtl2_qc.py
+++ b/tests/r_qtl/test_r_qtl2_qc.py
@@ -47,8 +47,7 @@ def test_bundle_files_list(filepath, expected):
THEN: verify that ALL files listed in the control file are returned.
"""
with ZipFile(Path(filepath).absolute(), "r") as zfile:
- assert qc.bundle_files_list(
- zfile, rqtl2.control_data(zfile)) == expected
+ assert qc.bundle_files_list(rqtl2.control_data(zfile)) == expected
@pytest.mark.unit_test
@pytest.mark.parametrize(