From 949ea71eb721a3f5bdff3ba10f7dd7c70899d560 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 5 Feb 2024 12:11:43 +0300
Subject: Fix linting and type errors.

---
 qc_app/upload/rqtl2.py             |  1 -
 r_qtl/r_qtl2_qc.py                 | 16 ++++++++--------
 scripts/rqtl2/install_genotypes.py |  3 ++-
 scripts/rqtl2/install_phenos.py    |  3 ++-
 tests/r_qtl/test_r_qtl2_qc.py      |  3 +--
 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(
-- 
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