From 7785049a64dc3f1b2d9d07a31f43b8cc5527214b Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 19 Sep 2022 09:58:37 +0300
Subject: Provide fixtures for test. Fix error to pass test.

Provide the following (empty) files to be used for the test
* wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
* wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt

Rework the paths in
`wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py`
such that they point to the files added above for testing.

Do not require that the phenotype file exists in
`wqflask/wqflask/marker_regression/gemma_mapping.py` before attempting
the mapping.
---
 .../unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt   | 0
 .../unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt   | 0
 wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py | 7 +++++--
 3 files changed, 5 insertions(+), 2 deletions(-)
 create mode 100644 wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
 create mode 100644 wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt

(limited to 'wqflask/tests')

diff --git a/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt b/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
new file mode 100644
index 00000000..e69de29b
diff --git a/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt b/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt
new file mode 100644
index 00000000..e69de29b
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index 43051828..24400b33 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -1,4 +1,5 @@
 # test for wqflask/marker_regression/gemma_mapping.py
+import os
 import unittest
 import random
 from unittest import mock
@@ -40,7 +41,8 @@ class TestGemmaMapping(unittest.TestCase):
     @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
     @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug")
     @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR",
+                os.path.join(os.path.dirname(__file__), "user/data"))
     @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
     @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
     @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file")
@@ -64,7 +66,8 @@ class TestGemmaMapping(unittest.TestCase):
         mock_os.path.isfile.return_value = True
         mock_gen_covar.return_value = None
         mock_choice.return_value = "R"
-        mock_flat_files.return_value = "/home/genotype/bimbam"
+        mock_flat_files.return_value = os.path.join(
+            os.path.dirname(__file__), "genotype/bimbam")
         mock_parse_loco.return_value = []
         results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
         ], vals=[], covariates="", use_loco=True)
-- 
cgit v1.2.3