13111: Merge branch 'master' into 13111-webdav-projects

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

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 2ca63cfe5048a62f0a1853e2aca06be865ea1fd4..053c99502bf06e0c5829b67a4563bfd7544b8c1a 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -13,8 +13,7 @@ from StringIO import StringIO
 
 from schema_salad.sourceline import SourceLine
 
-import cwltool.draft2tool
-from cwltool.draft2tool import CommandLineTool
+from cwltool.command_line_tool import CommandLineTool
 import cwltool.workflow
 from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname
 from cwltool.load_tool import fetch_document
@@ -161,7 +160,7 @@ def upload_docker(arvrunner, tool):
     if isinstance(tool, CommandLineTool):
         (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
         if docker_req:
-            if docker_req.get("dockerOutputDirectory"):
+            if docker_req.get("dockerOutputDirectory") and arvrunner.work_api != "containers":
                 # TODO: can be supported by containers API, but not jobs API.
                 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
                     "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
@@ -317,7 +316,8 @@ class Runner(object):
     def __init__(self, runner, tool, job_order, enable_reuse,
                  output_name, output_tags, submit_runner_ram=0,
                  name=None, on_error=None, submit_runner_image=None,
-                 intermediate_output_ttl=0, merged_map=None):
+                 intermediate_output_ttl=0, merged_map=None, priority=None,
+                 secret_store=None):
         self.arvrunner = runner
         self.tool = tool
         self.job_order = job_order
@@ -337,6 +337,8 @@ class Runner(object):
         self.on_error = on_error
         self.jobs_image = submit_runner_image or "arvados/jobs:"+__version__
         self.intermediate_output_ttl = intermediate_output_ttl
+        self.priority = priority
+        self.secret_store = secret_store
 
         if submit_runner_ram:
             self.submit_runner_ram = submit_runner_ram