From 3738b75f9c43c808976867c0c339ba9b125e964c Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 27 May 2018 18:24:23 +0100
Subject: [PATCH] TEST: Unit test for fsldir/fsldevdir/fsl_prefix
---
tests/test_run.py | 48 ++++++++++++++++++++++++++++++++++++++---------
1 file changed, 39 insertions(+), 9 deletions(-)
diff --git a/tests/test_run.py b/tests/test_run.py
index c12e2e714..5a79d2d52 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -8,6 +8,7 @@
import os.path as op
import os
+import shutil
import textwrap
# python 3
@@ -161,11 +162,13 @@ def test_runfsl():
test_script = textwrap.dedent("""
#!/bin/bash
- echo $@
+ echo {}
exit 0
""").strip()
- old_fsldir = fslplatform.fsldir
+ old_fsldir = fslplatform.fsldir
+ old_fsldevdir = fslplatform.fsldevdir
+
try:
with tempdir.tempdir():
@@ -173,24 +176,51 @@ def test_runfsl():
make_random_image('image.nii.gz')
# no FSLDIR - should error
- fslplatform.fsldir = None
+ fslplatform.fsldir = None
+ fslplatform.fsldevdir = None
with pytest.raises(run.FSLNotPresent):
- run.runfsl('fslhd image')
+ run.runfsl('fslhd')
# 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)
+ f.write(test_script.format('fsldir'))
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'
+ assert run.runfsl('fslhd').strip() == 'fsldir'
+
+ # FSLDEVDIR should take precedence
+ fsldevdir = './fsldev'
+ fslhd = op.join(fsldevdir, 'bin', 'fslhd')
+ shutil.copytree(fsldir, fsldevdir)
+ with open(fslhd, 'wt') as f:
+ f.write(test_script.format('fsldevdir'))
+
+ fslplatform.fsldevdir = fsldevdir
+ fslplatform.fsldir = None
+ assert run.runfsl('fslhd').strip() == 'fsldevdir'
+
+ # FSL_PREFIX should override all
+ override = './override'
+ fslhd = op.join(override, 'fslhd')
+ os.makedirs(override)
+ with open(fslhd, 'wt') as f:
+ f.write(test_script.format('override'))
+ os.chmod(fslhd, 0o777)
+
+
+ fslplatform.fsldir = None
+ fslplatform.fsldevdir = None
+ run.FSL_PREFIX = override
+ assert run.runfsl('fslhd').strip() == 'override'
+
finally:
- fslplatform.fsldir = old_fsldir
+ fslplatform.fsldir = old_fsldir
+ fslplatform.fsldevdir = old_fsldevdir
+ run.FSL_PREFIX = None
def mock_submit(cmd, **kwargs):
--
GitLab