Detect references to /var/spool/cwl

Author: mr-c

cwltool/load_tool.py

@@ -13,7 +13,7 @@
         Text, Tuple, Union, cast)
 
 import requests.sessions
-from six import itervalues, string_types
+from six import iteritems, itervalues, string_types
 from six.moves import urllib
 
 import schema_salad.schema as schema
@@ -220,6 +220,33 @@ def validate_document(document_loader,  # type: Loader
 
         workflowobj = fetch_document(uri, fetcher_constructor=fetcher_constructor)[1]
 
+    def var_spool_cwl_detector(obj,           # type: Union[Mapping, Iterable, Text]
+                               item=None,     # type: Optional[Any]
+                               obj_key=None,  # type: Optional[Any]
+                              ):              # type: (...)->None
+        """ Detects any textual reference to /var/spool/cwl. """
+        if isinstance(obj, string_types):
+            if "var/spool/cwl" in obj:
+                message = SourceLine(
+                    item=item, key=obj_key, raise_type=Text,
+                    include_traceback=_logger.isEnabledFor(logging.DEBUG)).makeError(
+                        "Non-portable reference to /var/spool/cwl found: "
+                        "'{}'.\n Replace with /var/spool/cwl/ with "
+                        "$(runtime.outdir).".format(obj))
+                if not strict:
+                    _logger.warning(message)
+                else:
+                    raise ValidationException(message)
+            else:
+                return
+        elif isinstance(obj, Mapping):
+            for key, value in iteritems(obj):
+                var_spool_cwl_detector(value, obj, key)
+        elif isinstance(obj, Iterable):
+            for element in obj:
+                var_spool_cwl_detector(element, obj, None)
+    var_spool_cwl_detector(workflowobj)
+
     fileuri = urllib.parse.urldefrag(uri)[0]
     if "cwlVersion" not in workflowobj:
         if metadata and 'cwlVersion' in metadata:

tests/non_portable.cwl

@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: debian
+  InitialWorkDirRequirement:
+    listing:
+      - class: File
+        basename: hi.txt
+        contents: Hello, World!
+
+inputs: []
+
+baseCommand:
+ - cat
+ - /var/spool/cwl/hi.txt
+
+stdout: result.txt
+
+outputs:
+  result: stdout