R interface tests

Author: Terf

nipype/interfaces/tests/test_r.py

@@ -0,0 +1,100 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+import os
+
+import pytest
+import nipype.interfaces.r as r
+
+r_cmd = r.get_r_command()
+no_r = r_cmd is None
+if not no_r:
+    r.RCommand.set_default_r_cmd(r_cmd)
+
+
+def clean_workspace_and_get_default_script_file():
+    # Make sure things are clean.
+    default_script_file = r.RInputSpec().script_file
+    if os.path.exists(default_script_file):
+        os.remove(
+            default_script_file
+        )  # raise Exception('Default script file needed for tests; please remove %s!' % default_script_file)
+    return default_script_file
+
+
+@pytest.mark.skipif(no_r, reason="R is not available")
+def test_cmdline():
+    default_script_file = clean_workspace_and_get_default_script_file()
+
+    ri = r.RCommand(script="1 + 1", script_file="testscript", rfile=False)
+
+    assert ri.cmdline == r_cmd + (
+        ' -e "1 + 1"'
+    )
+
+    assert ri.inputs.script == "1 + 1"
+    assert ri.inputs.script_file == "testscript"
+    assert not os.path.exists(ri.inputs.script_file), "scriptfile should not exist"
+    assert not os.path.exists(
+        default_script_file
+    ), "default scriptfile should not exist."
+
+@pytest.mark.skipif(no_r, reason="R is not available")
+def test_r_init():
+    default_script_file = clean_workspace_and_get_default_script_file()
+
+    assert r.RCommand._cmd == "R"
+    assert r.RCommand.input_spec == r.RInputSpec
+
+    assert r.RCommand().cmd == r_cmd
+    rc = r.RCommand(r_cmd="foo_m")
+    assert rc.cmd == "foo_m"
+
+
+@pytest.mark.skipif(no_r, reason="R is not available")
+def test_run_interface(tmpdir):
+    default_script_file = clean_workspace_and_get_default_script_file()
+
+    rc = r.RCommand(r_cmd="foo_m")
+    assert not os.path.exists(default_script_file), "scriptfile should not exist 1."
+    with pytest.raises(ValueError):
+        rc.run()  # script is mandatory
+    assert not os.path.exists(default_script_file), "scriptfile should not exist 2."
+    if os.path.exists(default_script_file):  # cleanup
+        os.remove(default_script_file)
+
+    rc.inputs.script = "a=1;"
+    assert not os.path.exists(default_script_file), "scriptfile should not exist 3."
+    with pytest.raises(IOError):
+        rc.run()  # foo_m is not an executable
+    assert os.path.exists(default_script_file), "scriptfile should exist 3."
+    if os.path.exists(default_script_file):  # cleanup
+        os.remove(default_script_file)
+
+    cwd = tmpdir.chdir()
+
+    # bypasses ubuntu dash issue
+    rc = r.RCommand(script="foo;", rfile=True)
+    assert not os.path.exists(default_script_file), "scriptfile should not exist 4."
+    with pytest.raises(RuntimeError):
+        rc.run()
+    assert os.path.exists(default_script_file), "scriptfile should exist 4."
+    if os.path.exists(default_script_file):  # cleanup
+        os.remove(default_script_file)
+
+    # bypasses ubuntu dash issue
+    res = r.RCommand(script="a=1;", rfile=True).run()
+    assert res.runtime.returncode == 0
+    assert os.path.exists(default_script_file), "scriptfile should exist 5."
+    cwd.chdir()
+
+
+@pytest.mark.skipif(no_r, reason="R is not available")
+def test_set_rcmd():
+    default_script_file = clean_workspace_and_get_default_script_file()
+
+    ri = r.RCommand()
+    ri.set_default_r_cmd("foo")
+    assert not os.path.exists(default_script_file), "scriptfile should not exist."
+    assert ri._default_r_cmd == "foo"
+    ri.set_default_r_cmd(r_cmd)