From 7b6ae4f162194a4c6ad61c34513ace638f0e6e62 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 2 Mar 2018 12:36:46 +0000
Subject: [PATCH] Unit tests for run module
---
tests/test_run.py | 140 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 140 insertions(+)
create mode 100644 tests/test_run.py
diff --git a/tests/test_run.py b/tests/test_run.py
new file mode 100644
index 000000000..5e3904622
--- /dev/null
+++ b/tests/test_run.py
@@ -0,0 +1,140 @@
+#!/usr/bin/env python
+#
+# test_run.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import os.path as op
+import os
+import textwrap
+
+# python 3
+try: from unittest import mock
+# python 2
+except ImportError: import mock
+
+import pytest
+
+import fsl.utils.tempdir as tempdir
+from fsl.utils.platform import platform as fslplatform
+import fsl.utils.run as run
+
+from . import make_random_image
+
+
+def test_run():
+
+ test_script = textwrap.dedent("""
+ #!/bin/bash
+
+ echo "standard output - arguments: $@"
+ echo "standard error" >&2
+ exit {}
+ """).strip()
+
+ with tempdir.tempdir():
+
+ # return code == 0
+ with open('script.sh', 'wt') as f:
+ f.write(test_script.format(0))
+ os.chmod('script.sh', 0o755)
+
+ expstdout = "standard output - arguments: 1 2 3"
+ expstderr = "standard error"
+
+ # test:
+ # - single string
+ # - packed sequence
+ # - unpacked sequence
+ assert run.run('./script.sh 1 2 3').strip() == expstdout
+ assert run.run(('./script.sh', '1', '2', '3')) == expstdout
+ assert run.run(*('./script.sh', '1', '2', '3')) == expstdout
+
+ # test stdout/stderr
+ stdout, stderr = run.run('./script.sh 1 2 3', err=True)
+ assert stdout.strip() == expstdout
+ assert stderr.strip() == expstderr
+
+ # test return code
+ stdout, ret = run.run('./script.sh 1 2 3', ret=True)
+ assert stdout.strip() == expstdout
+ assert ret == 0
+ stdout, stderr, ret = run.run('./script.sh 1 2 3', err=True, ret=True)
+ assert stdout.strip() == expstdout
+ assert stderr.strip() == expstderr
+ assert ret == 0
+
+ # return code != 0
+ with open('./script.sh', 'wt') as f:
+ f.write(test_script.format(255))
+ os.chmod('./script.sh', 0o755)
+
+ with pytest.raises(RuntimeError):
+ run.run('./script.sh 1 2 3')
+
+ stdout, ret = run.run('./script.sh 1 2 3', ret=True)
+ assert stdout.strip() == expstdout
+ assert ret == 255
+
+
+def test_dryrun():
+
+ test_script = textwrap.dedent("""
+ #!/bin/bash
+ touch foo
+ """).strip()
+
+ with tempdir.tempdir():
+ with open('./script.sh', 'wt') as f:
+ f.write(test_script)
+ os.chmod('./script.sh', 0o755)
+
+ run.run('./script.sh')
+ assert op.exists('foo')
+
+ os.remove('foo')
+
+ with run.dryrun():
+ run.run('./script.sh')
+
+ assert not op.exists('foo')
+
+
+# test runfsl with/without $FSLDIR
+def test_runfsl():
+
+ test_script = textwrap.dedent("""
+ #!/bin/bash
+ echo $@
+ exit 0
+ """).strip()
+
+ old_fsldir = fslplatform.fsldir
+
+ try:
+ with tempdir.tempdir():
+
+ make_random_image('image.nii.gz')
+
+ # no FSLDIR - should error
+ fslplatform.fsldir = None
+ with pytest.raises(run.FSLNotPresent):
+ run.runfsl('fslhd image')
+
+
+ # FSLDIR/bin exists - should be good
+ fsldir = op.abspath('./fsl')
+ fslhd = op.join(fsldir, 'bin', 'fslhd')
+ os.makedirs(op.join(fsldir, 'bin'))
+ with open(fslhd, 'wt') as f:
+ f.write(test_script)
+ os.chmod(fslhd, 0o777)
+
+ fslplatform.fsldir = fsldir
+ path = op.pathsep.join((fsldir, os.environ['PATH']))
+ with mock.patch.dict(os.environ, {'PATH' : path}):
+ assert run.runfsl('fslhd image').strip() == 'image'
+ finally:
+ fslplatform.fsldir = old_fsldir
--
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