From aaff8b8ac968bce9821d6fef22b1296247a9df09 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Thu, 24 Feb 2022 13:46:34 +0530
Subject: gn3: Explicitly specify UTF-8 to be the file encoding.

When the encoding is not specified explicitly, the system default encoding is
used. This is not recommended.

* gn3/computations/ctl.py (call_ctl_script),
gn3/computations/gemma.py (generate_pheno_txt_file),
gn3/computations/parsers.py (parse_genofile),
gn3/computations/partial_correlations.py (partial_correlations_fast),
gn3/computations/rqtl.py (process_rqtl_output, process_perm_output),
gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script),
gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file
encoding.
*
tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file),
tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test
for call to open with encoding='utf-8' argument.
---
 tests/unit/computations/test_gemma.py | 2 +-
 tests/unit/computations/test_wgcna.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'tests')

diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py
index b36a93e..137c95c 100644
--- a/tests/unit/computations/test_gemma.py
+++ b/tests/unit/computations/test_gemma.py
@@ -22,7 +22,7 @@ class TestGemma(unittest.TestCase):
             self.assertEqual(_file, ("/tmp/gn2/phenotype_"
                                      "P7y6QWnwBPedSZdL0+m/GQ.txt"))
         open_mock.assert_called_with(("/tmp/gn2/phenotype_"
-                                      "P7y6QWnwBPedSZdL0+m/GQ.txt"), "w")
+                                      "P7y6QWnwBPedSZdL0+m/GQ.txt"), "w", encoding="utf-8")
         open_mock.return_value.write.assert_has_calls([
             mock.call("NA\n"),
             mock.call("NA\n"),
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index 3130374..a9108b0 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -166,7 +166,7 @@ class TestWgcna(TestCase):
                 expected_input)
 
             file_handler.assert_called_once_with(
-                "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json", 'w')
+                "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json", 'w', encoding='utf-8')
 
             self.assertEqual(
                 results, "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json")
-- 
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