New/adjusted unit tests for run(submit=True) and cmd/fslwrapper(submit=True)

tests/test_run.py

@@ -15,6 +15,7 @@ try:  from unittest import mock
 # python 2
 except ImportError: import mock
 
+import six
 import pytest
 
 import fsl.utils.tempdir                  as tempdir
@@ -22,7 +23,7 @@ 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, mockFSLDIR
+from . import make_random_image, mockFSLDIR, touch
 
 
 def test_run():
@@ -142,16 +143,25 @@ def test_runfsl():
         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 mock_submit(cmd, **kwargs):
+    if isinstance(cmd, six.string_types):
+        name = cmd.split()[0]
+    else:
+        name = cmd[0]
+
+    name = op.basename(name)
+
+    jid = '12345'
+    output = run.run(cmd)
+
+    with open('{}.o{}'.format(name, jid), 'wt') as f:
+        f.write(output)
+
+    with open('{}.e{}'.format(name, jid), 'wt') as f:
+        for k, v in kwargs.items():
+            f.write('{}: {}\n'.format(k, v))
+
+    return (jid,)
 
 
 def test_run_submit():
@@ -167,16 +177,30 @@ def test_run_submit():
     exit 0
     """).strip()
 
-    with tempdir.tempdir(), mockFSLDIR():
+    with tempdir.tempdir(), \
+         mockFSLDIR(), \
+         mock.patch('fsl.utils.fslsub.submit', mock_submit):
 
         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')
+        stdout, stderr = fslsub.output(jid)
 
         assert stdout.strip() == 'test_script running'
         assert stderr.strip() == ''
+
+        kwargs = {'name' : 'abcde', 'ram' : '4GB'}
+
+        jid = run.run('fsltest', submit=kwargs)[0]
+
+        assert jid == '12345'
+
+        stdout, stderr = fslsub.output(jid)
+
+        experr = '\n'.join(['{}: {}'.format(k, v) for k, v in kwargs.items()])
+
+        assert stdout.strip() == 'test_script running'
+        assert stderr.strip() == experr

tests/test_wrapperutils.py

@@ -8,6 +8,10 @@
 import os.path as op
 import            os
 import            shlex
+import            textwrap
+
+try: from unittest import mock
+except ImportError: import mock
 
 import pytest
 
@@ -16,10 +20,12 @@ import nibabel as nib
 
 import fsl.utils.tempdir         as tempdir
 import fsl.utils.run             as run
+import fsl.utils.fslsub          as fslsub
 import fsl.wrappers.wrapperutils as wutils
 
 
 from . import mockFSLDIR
+from .test_run import mock_submit
 
 
 def test_applyArgStyle():
@@ -310,7 +316,6 @@ def test_cmdwrapper():
         assert func(1, 2)[0] == 'func 1 2'
 
 
-
 def test_fslwrapper():
     @wutils.fslwrapper
     def func(a, b):
@@ -319,3 +324,73 @@ def test_fslwrapper():
     with run.dryrun(), mockFSLDIR() as fsldir:
         expected = '{} 1 2'.format(op.join(fsldir, 'bin', 'func'))
         assert func(1, 2)[0] == expected
+
+
+_test_script = textwrap.dedent("""
+#!/usr/bin/env bash
+echo "test_script running: $1 $2"
+exit 0
+""").strip()
+
+
+def _test_script_func(a, b):
+    return ['test_script', str(a), str(b)]
+
+
+def test_cmdwrapper_submit():
+
+    test_func = wutils.cmdwrapper(_test_script_func)
+    newpath = op.pathsep.join(('.', os.environ['PATH']))
+
+    with tempdir.tempdir(), \
+         mock.patch('fsl.utils.fslsub.submit', mock_submit), \
+         mock.patch.dict(os.environ, {'PATH' : newpath}):
+
+        with open('test_script', 'wt') as f:
+            f.write(_test_script)
+        os.chmod('test_script', 0o755)
+
+        jid = test_func(1, 2, submit=True)
+
+        assert jid == ('12345',)
+
+        stdout, stderr = fslsub.output('12345')
+
+        assert stdout.strip() == 'test_script running: 1 2'
+        assert stderr.strip() == ''
+
+
+def test_fslwrapper_submit():
+
+    test_func = wutils.fslwrapper(_test_script_func)
+
+    with mockFSLDIR() as fsldir, \
+         mock.patch('fsl.utils.fslsub.submit', mock_submit):
+
+        test_file = op.join(fsldir, 'bin', 'test_script')
+
+        with open(test_file, 'wt') as f:
+            f.write(_test_script)
+        os.chmod(test_file, 0o755)
+
+        jid = test_func(1, 2, submit=True)
+
+        assert jid == ('12345',)
+
+        stdout, stderr = fslsub.output('12345')
+
+        assert stdout.strip() == 'test_script running: 1 2'
+        assert stderr.strip() == ''
+
+        kwargs = {'name' : 'abcde', 'ram' : '4GB'}
+
+        jid = test_func(1, 2, submit=kwargs)
+
+        assert jid == ('12345',)
+
+        stdout, stderr = fslsub.output('12345')
+
+        experr = '\n'.join(['{}: {}'.format(k, v) for k, v in kwargs.items()])
+
+        assert stdout.strip() == 'test_script running: 1 2'
+        assert stderr.strip() == experr