[ARVADOS] created: 13c27ef91fc2516bdcdee94ba1ff2f08361dc51d

[Git user]

        at  13c27ef91fc2516bdcdee94ba1ff2f08361dc51d (commit)


commit 13c27ef91fc2516bdcdee94ba1ff2f08361dc51d
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jan 25 13:20:28 2017 -0500

    10812: Fix bug and add test that docker dependencies are found and uploaded.

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index ef01b7f..49047fa 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -123,7 +123,8 @@ 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 +133,9 @@ 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 +193,8 @@ 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
 
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 31d7c2b..bbff612 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -233,9 +233,10 @@ def stubs(func):
 
 
 class TestSubmit(unittest.TestCase):
+    @mock.patch("arvados_cwl.runner.arv_docker_get_image")
     @mock.patch("time.sleep")
     @stubs
-    def test_submit(self, stubs, tm):
+    def test_submit(self, stubs, tm, arvdock):
         capture_stdout = cStringIO.StringIO()
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=jobs", "--debug",
@@ -260,6 +261,11 @@ class TestSubmit(unittest.TestCase):
             }), ensure_unique_name=True),
             mock.call().execute()])
 
+        arvdock.assert_has_calls([
+            mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
+            mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
+        ])
+
         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
         stubs.api.pipeline_instances().create.assert_called_with(
             body=JsonDiffMatcher(expect_pipeline))

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hooks/post-receive
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