final fixes

Author: mr-c

cwltool/job.py

@@ -498,7 +498,7 @@ def create_file_and_add_volume(self,
             os.makedirs(dirname, 0o0755)
         with open(host_outdir_tgt or new_file, "wb") as file_literal:
             file_literal.write(contents.encode("utf-8"))
-        if new_file:
+        if not host_outdir_tgt:
             self.append_volume(runtime, new_file, volume.target,
                                writable=writable)
         if writable:

tests/test_secrets.py

@@ -6,10 +6,7 @@
 from cwltool.main import main
 from .util import (get_data, needs_docker, needs_singularity,
                    windows_needs_docker)
-if sys.version_info[0] < 3:
-    from io import BytesIO as TextIO
-else:
-    from io import StringIO as TextIO
+from io import StringIO
 
 
 @pytest.fixture
@@ -47,18 +44,18 @@ def test_secrets(factory, expected, secrets):
 
 @needs_docker
 def test_secret_workflow_log():
-    stream = TextIO()
+    stream = StringIO()
     tmpdir = tempfile.mkdtemp()
-    main(["--debug", "--outdir", tmpdir, get_data("tests/wf/secret_wf.cwl"),
-          "--pw", "Hoopla!"],
+    main(["--debug", "--enable-ext", "--outdir", tmpdir,
+          get_data("tests/wf/secret_wf.cwl"), "--pw", "Hoopla!"],
          stderr=stream)
 
     shutil.rmtree(tmpdir)
     assert "Hoopla!" not in stream.getvalue()
 
 @needs_singularity
 def test_secret_workflow_log_singularity():
-    stream = TextIO()
+    stream = StringIO()
     tmpdir = tempfile.mkdtemp()
     main(["--debug", "--outdir", tmpdir, "--singularity",
           get_data("tests/wf/secret_wf.cwl"), "--pw", "Hoopla!"],
@@ -67,11 +64,11 @@ def test_secret_workflow_log_singularity():
     shutil.rmtree(tmpdir)
     assert "Hoopla!" not in stream.getvalue()
 
-@windows_needs_docker
+@needs_docker
 def test_secret_workflow_log_override():
-    stream = TextIO()
+    stream = StringIO()
     tmpdir = tempfile.mkdtemp()
-    main(["--debug", "--outdir", tmpdir, "--overrides",
+    main(["--debug", "--outdir", tmpdir, "--enable-ext", "--overrides",
           get_data("tests/wf/override-no-secrets.yml"),
           get_data("tests/wf/secret_wf.cwl"), "--pw", "Hoopla!"],
          stderr=stream)