From f1855a2bec72934f1d819474906b91ff7ef229f1 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 19 Apr 2018 14:29:42 +0100
Subject: [PATCH] New unit test for run(submit=True). Not going to test fslsub
right now, as it will probably change.
---
tests/__init__.py | 13 +++++++++++--
tests/test_run.py | 48 ++++++++++++++++++++++++++++++++++++++++++++---
2 files changed, 56 insertions(+), 5 deletions(-)
diff --git a/tests/__init__.py b/tests/__init__.py
index 723ed0f1d..57794123f 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -21,6 +21,10 @@ import nibabel as nib
from six import StringIO
+
+try: from unittest import mock
+except ImportError: import mock
+
import fsl.data.image as fslimage
from fsl.utils.tempdir import tempdir
from fsl.utils.platform import platform as fslplatform
@@ -37,9 +41,14 @@ def mockFSLDIR():
try:
with tempdir() as td:
fsldir = op.join(td, 'fsl')
- os.makedirs(fsldir)
+ bindir = op.join(fsldir, 'bin')
+ os.makedirs(bindir)
fslplatform.fsldir = fsldir
- yield fsldir
+
+ path = op.pathsep.join((bindir, os.environ['PATH']))
+
+ with mock.patch.dict(os.environ, {'PATH': path}):
+ yield fsldir
finally:
fslplatform.fsldir = oldval
diff --git a/tests/test_run.py b/tests/test_run.py
index 5e3904622..849fff60e 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -20,8 +20,9 @@ import pytest
import fsl.utils.tempdir as tempdir
from fsl.utils.platform import platform as fslplatform
import fsl.utils.run as run
+import fsl.utils.fslsub as fslsub
-from . import make_random_image
+from . import make_random_image, mockFSLDIR
def test_run():
@@ -58,7 +59,9 @@ def test_run():
assert stderr.strip() == expstderr
# test return code
- stdout, ret = run.run('./script.sh 1 2 3', ret=True)
+ res = run.run('./script.sh 1 2 3', ret=True)
+ print(res)
+ stdout, ret = res
assert stdout.strip() == expstdout
assert ret == 0
stdout, stderr, ret = run.run('./script.sh 1 2 3', err=True, ret=True)
@@ -123,7 +126,6 @@ def test_runfsl():
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')
@@ -138,3 +140,43 @@ def test_runfsl():
assert run.runfsl('fslhd image').strip() == 'image'
finally:
fslplatform.fsldir = old_fsldir
+
+
+mock_fsl_sub = textwrap.dedent("""
+#!/usr/bin/env bash
+jid=12345
+cmd=$1
+name=`basename $cmd`
+$cmd > "$name".o"$jid"
+touch "$name".e"$jid"
+echo $jid
+exit 0
+""").strip()
+
+
+def test_run_submit():
+
+ def mkexec(path, contents):
+ with open(path, 'wt') as f:
+ f.write(contents)
+ os.chmod(path, 0o755)
+
+ test_script = textwrap.dedent("""
+ #!/usr/bin/env bash
+ echo test_script running
+ exit 0
+ """).strip()
+
+ with tempdir.tempdir(), mockFSLDIR():
+
+ mkexec(op.expandvars('$FSLDIR/bin/fsltest'), test_script)
+ mkexec(op.expandvars('$FSLDIR/bin/fsl_sub'), mock_fsl_sub)
+
+ jid = run.run('fsltest', submit=True)[0]
+
+ assert jid == '12345'
+
+ stdout, stderr = fslsub.output(jid, 'fsltest')
+
+ assert stdout.strip() == 'test_script running'
+ assert stderr.strip() == ''
--
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