cope with unmovable files from Docker+IWDR

Author: mr-c

MANIFEST.in

@@ -1,3 +1,4 @@
+include README.rst
 include MANIFEST.in
 include LICENSE.txt
 include *requirements.txt

cwltool/job.py

@@ -163,7 +163,10 @@ def relink_initialworkdir(
                 host_outdir, vol.target[len(container_outdir) + 1 :]
             )
             if os.path.islink(host_outdir_tgt) or os.path.isfile(host_outdir_tgt):
-                os.remove(host_outdir_tgt)
+                try:
+                    os.remove(host_outdir_tgt)
+                except PermissionError:
+                    pass
             elif os.path.isdir(host_outdir_tgt) and not vol.resolved.startswith("_:"):
                 shutil.rmtree(host_outdir_tgt)
             if onWindows():
@@ -175,7 +178,10 @@ def relink_initialworkdir(
                 elif vol.type in ("Directory", "WritableDirectory"):
                     copytree_with_merge(vol.resolved, host_outdir_tgt)
             elif not vol.resolved.startswith("_:"):
-                os.symlink(vol.resolved, host_outdir_tgt)
+                try:
+                    os.symlink(vol.resolved, host_outdir_tgt)
+                except FileExistsError:
+                    pass
 
 
 class JobBase(HasReqsHints, metaclass=ABCMeta):

cwltool/update.py

@@ -149,7 +149,9 @@ def v1_2_0dev1todev2(doc, loader, baseuri):  # pylint: disable=unused-argument
     return (doc, "v1.2.0-dev2")
 
 
-def v1_2_0dev2todev3(doc: Any, loader: Loader, baseuri: str) -> Tuple[Any, str]:  # pylint: disable=unused-argument
+def v1_2_0dev2todev3(
+    doc: Any, loader: Loader, baseuri: str
+) -> Tuple[Any, str]:  # pylint: disable=unused-argument
     """Public updater for v1.2.0-dev2 to v1.2.0-dev3"""
     doc = copy.deepcopy(doc)
 

tests/iwdr_dir_literal_real_file.cwl

@@ -0,0 +1,23 @@
+class: CommandLineTool
+cwlVersion: v1.0
+
+requirements:
+  DockerRequirement:
+      dockerPull: debian:stable-slim
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing: |
+      ${
+         return [{"class": "Directory",
+                  "basename": "subdir",
+                  "listing": [ inputs.example ]
+                  }]}
+
+inputs:
+  example: File
+
+outputs:
+  same:
+   type: File
+   outputBinding:
+     glob: subdir/$(inputs.example.basename)

tests/test_iwdr.py

@@ -30,6 +30,18 @@ def test_empty_file_creation():
     assert err_code == 0
 
 
+@needs_docker
+def test_directory_literal_with_real_inputs_inside():
+    """Cope with unmoveable files in the output directory created by Docker+IWDR."""
+    err_code, _, _ = get_main_output(
+        [
+            get_data("tests/iwdr_dir_literal_real_file.cwl"),
+            "--example={}".format(get_data("tests/__init__.py")),
+        ]
+    )
+    assert err_code == 0
+
+
 @needs_docker
 def test_iwdr_permutations():
     saved_tempdir = tempfile.tempdir