Merge pull request #1169 from common-workflow-language/argparser-require

Add input_required flag to main().

Author: mr-c

cwltool/argparser.py

@@ -394,14 +394,16 @@ class DirectoryAppendAction(FSAppendAction):
 
 
 def add_argument(toolparser, name, inptype, records, description="",
-                 default=None):
-    # type: (argparse.ArgumentParser, Text, Any, List[Text], Text, Any) -> None
+                 default=None, input_required=True):
+    # type: (argparse.ArgumentParser, Text, Any, List[Text], Text, Any, bool) -> 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
@@ -462,8 +464,8 @@ def add_argument(toolparser, name, inptype, records, description="",
         default=default, **typekw)
 
 
-def generate_parser(toolparser, tool, namemap, records):
-    # type: (argparse.ArgumentParser, Process, Dict[Text, Text], List[Text]) -> argparse.ArgumentParser
+def generate_parser(toolparser, tool, namemap, records, input_required=True):
+    # type: (argparse.ArgumentParser, Process, Dict[Text, Text], List[Text], bool) -> argparse.ArgumentParser
     toolparser.add_argument("job_order", nargs="?", help="Job input json file")
     namemap["job_order"] = "job_order"
 
@@ -473,6 +475,6 @@ 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

@@ -285,14 +285,15 @@ 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: Optional[SecretStore]
+                   secret_store=None,       # type: Optional[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)
@@ -490,7 +491,8 @@ def main(argsl=None,                   # type: Optional[List[str]]
          custom_schema_callback=None,  # type: Optional[Callable[[], None]]
          executor=None,                # type: Optional[JobExecutor]
          loadingContext=None,          # type: Optional[LoadingContext]
-         runtimeContext=None           # type: Optional[RuntimeContext]
+         runtimeContext=None,          # type: Optional[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")
@@ -795,7 +797,8 @@ 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
 

tests/test_toolargparse.py

@@ -1,12 +1,14 @@
 import os
+import sys
 from tempfile import NamedTemporaryFile
+from io import BytesIO, StringIO
 
 import pytest
 from cwltool.main import main
+import cwltool.executors
 
 from .util import get_data, needs_docker
 
-
 script_a = '''
 #!/usr/bin/env cwl-runner
 cwlVersion: v1.0
@@ -94,3 +96,43 @@ def test_argparse(name, script_contents, params, tmpdir):
     finally:
         if script and script.name and os.path.exists(script.name):
             os.unlink(script.name)
+
+
+class NoopJobExecutor(cwltool.executors.JobExecutor):
+    def run_jobs(self,
+                 process,           # type: Process
+                 job_order_object,  # type: Dict[Text, Any]
+                 logger,            # type: logging.Logger
+                 runtime_context     # type: RuntimeContext
+                ):  # type: (...) -> None
+        pass
+
+    def execute(self,
+                process,           # type: Process
+                job_order_object,  # type: Dict[Text, Any]
+                runtime_context,   # type: RuntimeContext
+                logger=None,       # type: logging.Logger
+               ):  # type: (...) -> Tuple[Optional[Union[Dict[Text, Any], List[Dict[Text, Any]]]], Text]
+        return {}, "success"
+
+def test_dont_require_inputs():
+    if sys.version_info[0] < 3:
+        stream = BytesIO()
+    else:
+        stream = StringIO()
+
+    script = None
+    try:
+        script = NamedTemporaryFile(mode='w', delete=False)
+        script.write(script_a)
+        script.close()
+
+        assert main(argsl=["--debug", script.name, "--input", script.name], executor=NoopJobExecutor(), stdout=stream) == 0
+        assert main(argsl=["--debug", script.name], executor=NoopJobExecutor(), stdout=stream) == 2
+        assert main(argsl=["--debug", script.name], executor=NoopJobExecutor(), input_required=False, stdout=stream) == 0
+
+    except SystemExit as err:
+        assert err.code == 0, name
+    finally:
+        if script and script.name and os.path.exists(script.name):
+            os.unlink(script.name)