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-rw-r--r--qc_app/samples.py2
-rw-r--r--quality_control/parsing.py4
-rw-r--r--scripts/insert_data.py3
-rw-r--r--scripts/qc.py8
-rw-r--r--scripts/rqtl2/install_genotypes.py2
-rw-r--r--scripts/rqtl2/install_phenos.py2
-rw-r--r--tests/qc/test_error_collection.py3
7 files changed, 11 insertions, 13 deletions
diff --git a/qc_app/samples.py b/qc_app/samples.py
index 8f56ee1..bf33715 100644
--- a/qc_app/samples.py
+++ b/qc_app/samples.py
@@ -18,7 +18,7 @@ from flask import (
render_template,
current_app as app)
-from quality_control.parsing import take
+from functional_tools import take
from qc_app import jobs
from qc_app.files import save_file
diff --git a/quality_control/parsing.py b/quality_control/parsing.py
index 5b21716..c545937 100644
--- a/quality_control/parsing.py
+++ b/quality_control/parsing.py
@@ -2,7 +2,7 @@
import collections
from enum import Enum
from functools import partial
-from typing import Tuple, Union, Iterable, Generator, Callable, Optional
+from typing import Tuple, Union, Generator, Callable, Optional
import quality_control.average as avg
from quality_control.file_utils import open_file
@@ -12,8 +12,6 @@ from quality_control.errors import (
from quality_control.headers import (
invalid_header, invalid_headings, duplicate_headings)
-from functional_tools import take
-
class FileType(Enum):
"""Enumerate the expected file types"""
AVERAGE = 1
diff --git a/scripts/insert_data.py b/scripts/insert_data.py
index 0ac3799..72fc897 100644
--- a/scripts/insert_data.py
+++ b/scripts/insert_data.py
@@ -11,7 +11,8 @@ import MySQLdb as mdb
from redis import Redis
from MySQLdb.cursors import DictCursor
-from quality_control.parsing import take
+from functional_tools import take
+
from quality_control.file_utils import open_file
from qc_app.db_utils import database_connection
from qc_app.check_connections import check_db, check_redis
diff --git a/scripts/qc.py b/scripts/qc.py
index 2057cd6..7d41d6c 100644
--- a/scripts/qc.py
+++ b/scripts/qc.py
@@ -5,13 +5,11 @@ import argparse
import mimetypes
from typing import Union, Callable
+from functional_tools import take
+
from quality_control.utils import make_progress_calculator
from quality_control.errors import InvalidValue, DuplicateHeading
-from quality_control.parsing import (
- take,
- FileType,
- strain_names,
- collect_errors)
+from quality_control.parsing import FileType, strain_names, collect_errors
def is_file_mime(filepath:str, mimetype:str) -> bool:
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 354bff0..77e7163 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -12,7 +12,7 @@ from MySQLdb.cursors import DictCursor
from r_qtl import r_qtl2 as rqtl2
-from quality_control.parsing import take
+from functional_tools import take
from scripts.rqtl2.entry import build_main
from scripts.cli_parser import init_cli_parser
diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
index b3d445b..4fdf428 100644
--- a/scripts/rqtl2/install_phenos.py
+++ b/scripts/rqtl2/install_phenos.py
@@ -15,7 +15,7 @@ from scripts.rqtl2.cli_parser import add_common_arguments
from r_qtl import r_qtl2 as rqtl2
-from quality_control.parsing import take
+from functional_tools import take
stderr_handler = logging.StreamHandler(stream=sys.stderr)
logger = logging.getLogger("install_phenos")
logger.addHandler(stderr_handler)
diff --git a/tests/qc/test_error_collection.py b/tests/qc/test_error_collection.py
index 25f5d01..962d2c5 100644
--- a/tests/qc/test_error_collection.py
+++ b/tests/qc/test_error_collection.py
@@ -2,7 +2,8 @@
import pytest
-from quality_control.parsing import take, FileType, collect_errors
+from functional_tools import take
+from quality_control.parsing import FileType, collect_errors
from quality_control.errors import (
InvalidValue, DuplicateHeading, InconsistentColumns)