Ensure that files copied for update are writable.

Author: Peter Amstutz

cwltool/job.py

@@ -21,7 +21,7 @@
 from .builder import Builder
 from .docker_id import docker_vm_id
 from .errors import WorkflowException
-from .pathmapper import PathMapper
+from .pathmapper import PathMapper, ensure_writable
 from .process import (UnsupportedRequirement, empty_subtree, get_feature,
                       stageFiles)
 from .utils import bytes2str_in_dicts
@@ -113,7 +113,7 @@ def relink_initialworkdir(pathmapper, host_outdir, container_outdir, inplace_upd
                 shutil.rmtree(host_outdir_tgt)
             if onWindows():
                 if vol.type in ("File", "WritableFile"):
-                    shutil.copy(vol.resolved,host_outdir_tgt)
+                    shutil.copy(vol.resolved, host_outdir_tgt)
                 elif vol.type in ("Directory", "WritableDirectory"):
                     copytree_with_merge(vol.resolved, host_outdir_tgt)
             else:
@@ -332,6 +332,7 @@ def add_volumes(self, pathmapper, runtime):
                     runtime.append(u"--volume=%s:%s:rw" % (docker_windows_path_adjust(vol.resolved), docker_windows_path_adjust(vol.target)))
                 else:
                     shutil.copy(vol.resolved, host_outdir_tgt)
+                    ensure_writable(host_outdir_tgt)
             elif vol.type == "WritableDirectory":
                 if vol.resolved.startswith("_:"):
                     os.makedirs(vol.target, 0o0755)
@@ -340,6 +341,7 @@ def add_volumes(self, pathmapper, runtime):
                         runtime.append(u"--volume=%s:%s:rw" % (docker_windows_path_adjust(vol.resolved), docker_windows_path_adjust(vol.target)))
                     else:
                         shutil.copytree(vol.resolved, host_outdir_tgt)
+                        ensure_writable(host_outdir_tgt)
             elif vol.type == "CreateFile":
                 if host_outdir_tgt:
                     with open(host_outdir_tgt, "wb") as f:

cwltool/pathmapper.py

@@ -168,6 +168,24 @@ def downloadHttpFile(httpurl):
     r.close()
     return f.name
 
+def ensure_writable(path):
+    if os.path.isdir(path):
+        for root, dirs, files in os.walk(path):
+            for name in files:
+                j = os.path.join(root, name)
+                st = os.stat(j)
+                mode = stat.S_IMODE(st.st_mode)
+                os.chmod(j, mode|stat.S_IWUSR)
+            for name in dirs:
+                j = os.path.join(root, name)
+                st = os.stat(j)
+                mode = stat.S_IMODE(st.st_mode)
+                os.chmod(j, mode|stat.S_IWUSR)
+    else:
+        st = os.stat(path)
+        mode = stat.S_IMODE(st.st_mode)
+        os.chmod(path, mode|stat.S_IWUSR)
+
 class PathMapper(object):
     """Mapping of files from relative path provided in the file to a tuple of
     (absolute local path, absolute container path)

cwltool/process.py

@@ -34,7 +34,8 @@
 from .builder import Builder
 from .errors import UnsupportedRequirement, WorkflowException
 from .pathmapper import (PathMapper, adjustDirObjs, get_listing,
-                         normalizeFilesDirs, visit_class, trim_listing)
+                         normalizeFilesDirs, visit_class, trim_listing,
+                         ensure_writable)
 from .stdfsaccess import StdFsAccess
 from .utils import aslist, get_feature, copytree_with_merge, onWindows
 
@@ -230,15 +231,17 @@ def stageFiles(pm, stageFunc=None, ignoreWritable=False, symLink=True):
             os.makedirs(p.target, 0o0755)
         elif p.type == "WritableFile" and not ignoreWritable:
             shutil.copy(p.resolved, p.target)
+            ensure_writable(p.target)
         elif p.type == "WritableDirectory" and not ignoreWritable:
             if p.resolved.startswith("_:"):
                 os.makedirs(p.target, 0o0755)
             else:
                 shutil.copytree(p.resolved, p.target)
+                ensure_writable(p.target)
         elif p.type == "CreateFile":
             with open(p.target, "wb") as n:
                 n.write(p.resolved.encode("utf-8"))
-
+            ensure_writable(p.target)
 
 def collectFilesAndDirs(obj, out):
     # type: (Union[Dict[Text, Any], List[Dict[Text, Any]]], List[Dict[Text, Any]]) -> None