From 6b2c56dc064adc20e1f97404ae1a7223f5e1552b Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 8 Oct 2017 16:04:47 -0500
Subject: [PATCH] Add in test for utils.
---
workflow/tests/test_utils.py | 53 ++++++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
create mode 100644 workflow/tests/test_utils.py
diff --git a/workflow/tests/test_utils.py b/workflow/tests/test_utils.py
new file mode 100644
index 0000000..159c9bb
--- /dev/null
+++ b/workflow/tests/test_utils.py
@@ -0,0 +1,53 @@
+#!/usr/bin/env python3
+
+import pytest
+import shutil
+import shlex
+import utils
+
+
+@pytest.fixture
+def steps():
+ steps = []
+ return steps
+
+
+@pytest.fixture
+def steps_1(steps):
+ design_file = "test_data/design_ENCSR238SGC_SE.txt"
+ step = [
+ "grep H3K4me1 %s " % (design_file)]
+ return step
+
+
+@pytest.fixture
+def steps_2(steps_1):
+ steps_1.extend([
+ "cut -f7"
+ ])
+ return steps_1
+
+
+def test_run_one_step(steps_1, capsys):
+ check_output = 'ENCSR238SGC\tlimb\tH3K4me1\tNone\t1\tENCSR687ALB\tENCFF833BLU.fastq.gz'.encode('UTF-8')
+ out, err = utils.run_pipe(steps_1)
+ output, errors = capsys.readouterr()
+ assert "first step shlex to stdout" in output
+ assert check_output in out
+
+
+def test_run_two_step(steps_2, capsys):
+ check_output = 'ENCFF833BLU.fastq.gz\nENCFF646LXU.fastq.gz'.encode('UTF-8')
+ out, err = utils.run_pipe(steps_2)
+ output, errors = capsys.readouterr()
+ assert "intermediate step 2 shlex to stdout" in output
+ assert check_output in out
+
+
+def test_run_last_step_file(steps_2, capsys, tmpdir):
+ check_output = 'ENCFF833BLU.fastq.gz\nENCFF646LXU.fastq.gz'
+ tmp_outfile = tmpdir.join('output.txt')
+ out, err = utils.run_pipe(steps_2, tmp_outfile.strpath)
+ output, errors = capsys.readouterr()
+ assert "last step shlex" in output
+ assert check_output in tmp_outfile.read()
--
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