adding warning when default docker container is used on Windows

Author: kapilkd13

cwltool/draft2tool.py

@@ -28,13 +28,24 @@
                       _logger_validation_warnings, compute_checksums,
                       normalizeFilesDirs, shortname, uniquename)
 from .stdfsaccess import StdFsAccess
-from .utils import aslist, docker_windows_path_adjust, convert_pathsep_to_unix
+from .utils import aslist, docker_windows_path_adjust, convert_pathsep_to_unix, windows_default_container_id, onWindows
 from six.moves import map
 
 ACCEPTLIST_EN_STRICT_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
 ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")  # Accept anything
 ACCEPTLIST_RE = ACCEPTLIST_EN_STRICT_RE
+DEFAULT_CONTAINER_MSG="""We are on Microsoft Windows and not all components of this CWL description have a
+container specified. This means that these steps will be executed in the default container, 
+which is %s.
 
+Note, this could affect portability if this CWL description relies on non-POSIX features
+or commands in this container. For best results add the following to your CWL
+description's hints section:
+
+hints:
+  DockerRequirement:
+    dockerPull: %s
+"""
 
 _logger = logging.getLogger("cwltool")
 
@@ -189,6 +200,8 @@ def makeJobRunner(self, use_container=True):  # type: (Optional[bool]) -> JobBas
                         "dockerPull": default_container
                     })
                     dockerReq = self.requirements[0]
+                    if default_container == windows_default_container_id and use_container and onWindows():
+                        _logger.warning(DEFAULT_CONTAINER_MSG%(windows_default_container_id, windows_default_container_id))
 
         if dockerReq and use_container:
             return DockerCommandLineJob()

cwltool/main.py

@@ -39,7 +39,7 @@
 from .software_requirements import DependenciesConfiguration, get_container_from_software_requirements, SOFTWARE_REQUIREMENTS_ENABLED
 from .stdfsaccess import StdFsAccess
 from .update import ALLUPDATES, UPDATES
-from .utils import onWindows
+from .utils import onWindows, windows_default_container_id
 from ruamel.yaml.comments import Comment, CommentedSeq, CommentedMap
 
 
@@ -712,7 +712,7 @@ def main(argsl=None,  # type: List[str]
         # If On windows platform, A default Docker Container is Used if not explicitely provided by user
         if onWindows() and not args.default_container:
             # This docker image is a minimal alpine image with bash installed(size 6 mb). source: https://github.com/frol/docker-alpine-bash
-            args.default_container = "frolvlad/alpine-bash"
+            args.default_container = windows_default_container_id
 
         # If caller provided custom arguments, it may be not every expected
         # option is set, so fill in no-op defaults to avoid crashing when

cwltool/utils.py

@@ -10,6 +10,7 @@
 from six.moves import zip_longest
 from typing import Any,Callable, Dict, List, Tuple, Text, Union
 
+windows_default_container_id = "frolvlad/alpine-bash"
 
 def aslist(l):  # type: (Any) -> List[Any]
     if isinstance(l, list):