Merge branch '11493-cwl-six' refs #11493

[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 ef01b7f68466776426b853bce8bb8aa95a79b926..1c10fe8196aba940495934169d559bb756cfda31 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -3,7 +3,6 @@ import urlparse
 from functools import partial
 import logging
 import json
-import re
 import subprocess
 
 from StringIO import StringIO
@@ -30,8 +29,6 @@ from . import done
 
 logger = logging.getLogger('arvados.cwl-runner')
 
-cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r".*")
-
 def trim_listing(obj):
     """Remove 'listing' field from Directory objects that are keep references.
 
@@ -123,7 +120,8 @@ def upload_dependencies(arvrunner, name, document_loader,
 
 
 def upload_docker(arvrunner, tool):
-    """Visitor which uploads Docker images referenced in CommandLineTool objects."""
+    """Uploads Docker images used in CommandLineTool objects."""
+
     if isinstance(tool, CommandLineTool):
         (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
         if docker_req:
@@ -132,6 +130,9 @@ def upload_docker(arvrunner, tool):
                 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
                     "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
             arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid)
+    elif isinstance(tool, cwltool.workflow.Workflow):
+        for s in tool.steps:
+            upload_docker(arvrunner, s.embedded_tool)
 
 def packed_workflow(arvrunner, tool):
     """Create a packed workflow.
@@ -189,7 +190,8 @@ def upload_job_order(arvrunner, name, tool, job_order):
 
 def upload_workflow_deps(arvrunner, tool):
     # Ensure that Docker images needed by this workflow are available
-    tool.visit(partial(upload_docker, arvrunner))
+
+    upload_docker(arvrunner, tool)
 
     document_loader = tool.doc_loader