Unit tests for run module

tests/test_run.py

+#!/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