Merge branch '13301-cwl-resource-scatter' closes #13301

[arvados.git] / sdk / cwl / arvados_cwl / __init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index e2607ce93ae855dcbf6f10943b2ab2148b401ca0..e4f5ceab7465cb17372466b265d417e02a6d4637 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -237,6 +237,8 @@ class ArvCwlRunner(object):
                     if not obj.get("dockerOutputDirectory").startswith('/'):
                         raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError(
                             "Option 'dockerOutputDirectory' must be an absolute path.")
+            if obj.get("class") == "http://commonwl.org/cwltool#Secrets" and self.work_api != "containers":
+                raise SourceLine(obj, "class", UnsupportedRequirement).makeError("Secrets not supported with --api=jobs")
             for v in obj.itervalues():
                 self.check_features(v)
         elif isinstance(obj, list):
@@ -354,7 +356,7 @@ class ArvCwlRunner(object):
         make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess,
                                                                  collection_cache=self.collection_cache)
         self.fs_access = make_fs_access(kwargs["basedir"])
-
+        self.secret_store = kwargs.get("secret_store")
 
         self.trash_intermediate = kwargs["trash_intermediate"]
         if self.trash_intermediate and self.work_api != "containers":
@@ -452,7 +454,8 @@ class ArvCwlRunner(object):
                                                 submit_runner_image=kwargs.get("submit_runner_image"),
                                                 intermediate_output_ttl=kwargs.get("intermediate_output_ttl"),
                                                 merged_map=merged_map,
-                                                priority=kwargs.get("priority"))
+                                                priority=kwargs.get("priority"),
+                                                secret_store=self.secret_store)
             elif self.work_api == "jobs":
                 runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"),
                                       self.output_name,
@@ -590,7 +593,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--print-dot", action="store_true",
                          help="Print workflow visualization in graphviz format and exit")
-    exgroup.add_argument("--version", action="store_true", help="Print version and exit")
+    exgroup.add_argument("--version", action="version", help="Print version and exit", version=versionstring())
     exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
 
     exgroup = parser.add_mutually_exclusive_group()
@@ -712,10 +715,6 @@ def main(args, stdout, stderr, api_client=None, keep_client=None):
     job_order_object = None
     arvargs = parser.parse_args(args)
 
-    if arvargs.version:
-        print versionstring()
-        return
-
     if arvargs.update_workflow:
         if arvargs.update_workflow.find('-7fd4e-') == 5:
             want_api = 'containers'