Add input_required flag to main().

When false, command line parameters that provide workflow inputs are
always optional.  This makes it possible to pass the executor an
incomplete input object.  This is desirable if the executor is going
to do something other than run the workflow.

Author: Peter Amstutz

cwltool/argparser.py

@@ -390,14 +390,16 @@ class DirectoryAppendAction(FSAppendAction):
 
 
 def add_argument(toolparser, name, inptype, records, description="",
-                 default=None):
+                 default=None, input_required=True):
     # type: (argparse.ArgumentParser, Text, Any, List[Text], Text, Any) -> None
     if len(name) == 1:
         flag = "-"
     else:
         flag = "--"
 
-    required = default is None
+    # if input_required is false, don't make the command line
+    # parameter required.
+    required = default is None and input_required
     if isinstance(inptype, MutableSequence):
         if inptype[0] == "null":
             required = False
@@ -458,7 +460,7 @@ def add_argument(toolparser, name, inptype, records, description="",
         default=default, **typekw)
 
 
-def generate_parser(toolparser, tool, namemap, records):
+def generate_parser(toolparser, tool, namemap, records, input_required=True):
     # type: (argparse.ArgumentParser, Process, Dict[Text, Text], List[Text]) -> argparse.ArgumentParser
     toolparser.add_argument("job_order", nargs="?", help="Job input json file")
     namemap["job_order"] = "job_order"
@@ -469,6 +471,6 @@ def generate_parser(toolparser, tool, namemap, records):
         inptype = inp["type"]
         description = inp.get("doc", "")
         default = inp.get("default", None)
-        add_argument(toolparser, name, inptype, records, description, default)
+        add_argument(toolparser, name, inptype, records, description, default, input_required)
 
     return toolparser

cwltool/main.py

@@ -281,14 +281,15 @@ def init_job_order(job_order_object,        # type: Optional[MutableMapping[Text
                    relative_deps=False,     # type: bool
                    make_fs_access=StdFsAccess,  # type: Callable[[Text], StdFsAccess]
                    input_basedir="",        # type: Text
-                   secret_store=None        # type: SecretStore
+                   secret_store=None,       # type: SecretStore
+                   input_required=True      # type: bool
                   ):  # type: (...) -> MutableMapping[Text, Any]
     secrets_req, _ = process.get_requirement("http://commonwl.org/cwltool#Secrets")
     if job_order_object is None:
         namemap = {}  # type: Dict[Text, Text]
         records = []  # type: List[Text]
         toolparser = generate_parser(
-            argparse.ArgumentParser(prog=args.workflow), process, namemap, records)
+            argparse.ArgumentParser(prog=args.workflow), process, namemap, records, input_required)
         if args.tool_help:
             toolparser.print_help()
             exit(0)
@@ -485,7 +486,8 @@ def main(argsl=None,                   # type: List[str]
          custom_schema_callback=None,  # type: Callable[[], None]
          executor=None,                # type: Callable[..., Tuple[Dict[Text, Any], Text]]
          loadingContext=None,          # type: LoadingContext
-         runtimeContext=None           # type: RuntimeContext
+         runtimeContext=None,          # type: RuntimeContext
+         input_required=True         # type: bool
         ):  # type: (...) -> int
     if not stdout:  # force UTF-8 even if the console is configured differently
         if (hasattr(sys.stdout, "encoding")  # type: ignore
@@ -789,7 +791,8 @@ def my_represent_none(self, data):  # pylint: disable=unused-argument
                 relative_deps=args.relative_deps,
                 make_fs_access=runtimeContext.make_fs_access,
                 input_basedir=input_basedir,
-                secret_store=runtimeContext.secret_store)
+                secret_store=runtimeContext.secret_store,
+                input_required=input_required)
         except SystemExit as err:
             return err.code