X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/9b0654adfffaac018395de29f6e441b843d46e85..6fe8e52020d421797306e5c6536afbcee761510a:/sdk/cwl/tests/test_submit.py

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 61a52c4e69..cd46251300 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 import copy
 import cStringIO
 import functools
@@ -14,9 +18,11 @@ import arvados_cwl
 import arvados_cwl.runner
 import arvados.keep
 
-from .matcher import JsonDiffMatcher
+from .matcher import JsonDiffMatcher, StripYAMLComments
 from .mock_discovery import get_rootDesc
 
+import ruamel.yaml as yaml
+
 _rootDesc = None
 
 def stubs(func):
@@ -32,7 +38,6 @@ def stubs(func):
         stubs.events = events
         stubs.keepdocker = keepdocker
 
-
         def putstub(p, **kwargs):
             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
         keep_client1().put.side_effect = putstub
@@ -51,33 +56,43 @@ def stubs(func):
             "uuid": stubs.fake_user_uuid,
         }
         stubs.api.collections().list().execute.return_value = {"items": []}
-        stubs.api.collections().create().execute.side_effect = ({
-            "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
-            "portable_data_hash": "99999999999999999999999999999991+99",
-            "manifest_text": ""
-        }, {
-            "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
-            "portable_data_hash": "99999999999999999999999999999992+99",
-            "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"
-        },
-        {
-            "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4",
-            "portable_data_hash": "99999999999999999999999999999994+99",
-            "manifest_text": ""
-        },
-        {
-            "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz5",
-            "portable_data_hash": "99999999999999999999999999999995+99",
-            "manifest_text": ""
-        },
-        {
-            "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz6",
-            "portable_data_hash": "99999999999999999999999999999996+99",
-            "manifest_text": ""
+
+        class CollectionExecute(object):
+            def __init__(self, exe):
+                self.exe = exe
+            def execute(self, num_retries=None):
+                return self.exe
+
+        def collection_createstub(created_collections, body, ensure_unique_name=None):
+            mt = body["manifest_text"]
+            uuid = "zzzzz-4zz18-zzzzzzzzzzzzzz%d" % len(created_collections)
+            pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
+            created_collections[uuid] = {
+                "uuid": uuid,
+                "portable_data_hash": pdh,
+                "manifest_text": mt
+            }
+            return CollectionExecute(created_collections[uuid])
+
+        def collection_getstub(created_collections, uuid):
+            for v in created_collections.itervalues():
+                if uuid in (v["uuid"], v["portable_data_hash"]):
+                    return CollectionExecute(v)
+
+        created_collections = {
+            "99999999999999999999999999999998+99": {
+                "uuid": "",
+                "portable_data_hash": "99999999999999999999999999999998+99",
+                "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
+            },
+            "99999999999999999999999999999994+99": {
+                "uuid": "",
+                "portable_data_hash": "99999999999999999999999999999994+99",
+                "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
+            }
         }
-        )
-        stubs.api.collections().get().execute.return_value = {
-            "portable_data_hash": "99999999999999999999999999999993+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"}
+        stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
+        stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
 
         stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         stubs.api.jobs().create().execute.return_value = {
@@ -104,7 +119,7 @@ def stubs(func):
             'script_parameters': {
                 'x': {
                     'basename': 'blorp.txt',
-                    'location': 'keep:99999999999999999999999999999994+99/blorp.txt',
+                    'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
                     'class': 'File'
                 },
                 'y': {
@@ -121,11 +136,11 @@ def stubs(func):
                     }],
                     'class': 'Directory'
                 },
-                'cwl:tool':
-                '99999999999999999999999999999991+99/wf/submit_wf.cwl'
+                'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main'
             },
             'repository': 'arvados',
-            'script_version': arvados_cwl.__version__,
+            'script_version': 'master',
+            'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
             'script': 'cwl-runner'
         }
         stubs.pipeline_component = stubs.expect_job_spec.copy()
@@ -138,16 +153,28 @@ def stubs(func):
                     'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
                     'script_parameters': {
                         'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
-                        'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt'}},
+                        'x': {"value": {
+                            'basename': 'blorp.txt',
+                            'class': 'File',
+                            'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+                            "size": 16
+                        }},
                         'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
                               'listing': [
-                                  {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+                                  {
+                                      'basename': 'renamed.txt',
+                                      'class': 'File', 'location':
+                                      'keep:99999999999999999999999999999998+99/file1.txt'
+                                  }
                               ]}},
-                        'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl',
-                        'arv:enable_reuse': True
+                        'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
+                        'arv:debug': True,
+                        'arv:enable_reuse': True,
+                        'arv:on_error': 'continue'
                     },
                     'repository': 'arvados',
-                    'script_version': arvados_cwl.__version__,
+                    'script_version': 'master',
+                    'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
                     'script': 'cwl-runner',
                     'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
                 }
@@ -164,29 +191,54 @@ def stubs(func):
         stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
         stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
 
+        with open("tests/wf/submit_wf_packed.cwl") as f:
+            expect_packed_workflow = yaml.round_trip_load(f)
+
         stubs.expect_container_spec = {
-            'priority': 1,
+            'priority': 500,
             'mounts': {
                 '/var/spool/cwl': {
                     'writable': True,
                     'kind': 'collection'
                 },
-                '/var/lib/cwl/workflow': {
-                    'portable_data_hash': '99999999999999999999999999999991+99',
-                    'kind': 'collection'
+                '/var/lib/cwl/workflow.json': {
+                    'content': expect_packed_workflow,
+                    'kind': 'json'
                 },
                 'stdout': {
                     'path': '/var/spool/cwl/cwl.output.json',
                     'kind': 'file'
                 },
-                '/var/lib/cwl/job/cwl.input.json': {
-                    'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json',
-                    'kind': 'collection'
+                '/var/lib/cwl/cwl.input.json': {
+                    'kind': 'json',
+                    'content': {
+                        'y': {
+                            'basename': '99999999999999999999999999999998+99',
+                            'location': 'keep:99999999999999999999999999999998+99',
+                            'class': 'Directory'},
+                        'x': {
+                            'basename': u'blorp.txt',
+                            'class': 'File',
+                            'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+                            "size": 16
+                        },
+                        'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
+                            {'basename': 'renamed.txt',
+                             'class': 'File',
+                             'location': 'keep:99999999999999999999999999999998+99/file1.txt'
+                            }
+                        ]}
+                    },
+                    'kind': 'json'
                 }
             },
+            'secret_mounts': {},
             'state': 'Committed',
-            'owner_uuid': None,
-            'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
+            'command': ['arvados-cwl-runner', '--local', '--api=containers',
+                        '--no-log-timestamps', '--disable-validate',
+                        '--eval-timeout=20', '--thread-count=4',
+                        '--enable-reuse', '--debug', '--on-error=continue',
+                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
             'name': 'submit_wf.cwl',
             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
             'output_path': '/var/spool/cwl',
@@ -195,7 +247,10 @@ def stubs(func):
                 'API': True,
                 'vcpus': 1,
                 'ram': 1024*1024*1024
-            }
+            },
+            'use_existing': True,
+            'properties': {},
+            'secret_mounts': {}
         }
 
         stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
@@ -215,44 +270,45 @@ 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", "--debug",
+            ["--submit", "--no-wait", "--api=jobs", "--debug",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             capture_stdout, sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
 
         stubs.api.collections().create.assert_has_calls([
-            mock.call(),
-            mock.call(body={
+            mock.call(body=JsonDiffMatcher({
                 'manifest_text':
-                './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
-                '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
-                'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
-                'owner_uuid': None,
-                'name': 'submit_wf.cwl',
-            }, ensure_unique_name=True),
-            mock.call().execute(),
-            mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
-                            '0:0:blub.txt 0:0:submit_tool.cwl\n',
-                            'replication_desired': None,
-                            'name': 'New collection'
-            }, ensure_unique_name=True),
-            mock.call().execute(num_retries=4),
-            mock.call(body={
+                '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
+                'replication_desired': None,
+                'name': 'submit_tool.cwl dependencies',
+            }), ensure_unique_name=True),
+            mock.call(body=JsonDiffMatcher({
                 'manifest_text':
                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
-                'owner_uuid': None,
-                'name': '#',
-            }, ensure_unique_name=True),
-            mock.call().execute()])
+                'replication_desired': None,
+                'name': 'submit_wf.cwl input',
+            }), ensure_unique_name=True),
+            mock.call(body=JsonDiffMatcher({
+                'manifest_text':
+                '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n',
+                'replication_desired': None,
+                'name': 'submit_wf.cwl',
+            }), ensure_unique_name=True)        ])
+
+        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=expect_pipeline)
+            body=JsonDiffMatcher(expect_pipeline))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_pipeline_uuid + '\n')
 
@@ -262,16 +318,44 @@ class TestSubmit(unittest.TestCase):
     def test_submit_no_reuse(self, stubs, tm):
         capture_stdout = cStringIO.StringIO()
         exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--debug", "--disable-reuse",
+            ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             capture_stdout, sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
 
-        stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
+        expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+        expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
+        expect_pipeline["properties"] = {"run_options": {"enable_job_reuse": False}}
+
+        stubs.api.pipeline_instances().create.assert_called_with(
+            body=JsonDiffMatcher(expect_pipeline))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_pipeline_uuid + '\n')
+
+    @stubs
+    def test_error_when_multiple_storage_classes_specified(self, stubs):
+        storage_classes = "foo,bar"
+        exited = arvados_cwl.main(
+                ["--debug", "--storage-classes", storage_classes,
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                sys.stdin, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 1)
+
+    @mock.patch("time.sleep")
+    @stubs
+    def test_submit_on_error(self, stubs, tm):
+        capture_stdout = cStringIO.StringIO()
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
 
         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+        expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
+
         stubs.api.pipeline_instances().create.assert_called_with(
-            body=expect_pipeline)
+            body=JsonDiffMatcher(expect_pipeline))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_pipeline_uuid + '\n')
 
@@ -286,11 +370,11 @@ class TestSubmit(unittest.TestCase):
             capture_stdout, sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
 
-        stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
-
         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+        expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
+
         stubs.api.pipeline_instances().create.assert_called_with(
-            body=expect_pipeline)
+            body=JsonDiffMatcher(expect_pipeline))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_pipeline_uuid + '\n')
 
@@ -317,11 +401,11 @@ class TestSubmit(unittest.TestCase):
             capture_stdout, sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
 
-        stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
-
         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+        expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
+
         stubs.api.pipeline_instances().create.assert_called_with(
-            body=expect_pipeline)
+            body=JsonDiffMatcher(expect_pipeline))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_pipeline_uuid + '\n')
 
@@ -336,11 +420,11 @@ class TestSubmit(unittest.TestCase):
             capture_stdout, sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
 
-        stubs.expect_pipeline_instance["name"] = "hello job 123"
-
         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+        expect_pipeline["name"] = "hello job 123"
+
         stubs.api.pipeline_instances().create.assert_called_with(
-            body=expect_pipeline)
+            body=JsonDiffMatcher(expect_pipeline))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_pipeline_uuid + '\n')
 
@@ -356,11 +440,11 @@ class TestSubmit(unittest.TestCase):
             capture_stdout, sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
 
-        stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
-
         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+        expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
+
         stubs.api.pipeline_instances().create.assert_called_with(
-            body=expect_pipeline)
+            body=JsonDiffMatcher(expect_pipeline))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_pipeline_uuid + '\n')
 
@@ -370,7 +454,7 @@ class TestSubmit(unittest.TestCase):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 
         exited = arvados_cwl.main(
-            ["--submit", "--no-wait",
+            ["--submit", "--no-wait", "--debug",
              "--project-uuid", project_uuid,
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             sys.stdout, sys.stderr, api_client=stubs.api)
@@ -379,7 +463,7 @@ class TestSubmit(unittest.TestCase):
         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
         expect_pipeline["owner_uuid"] = project_uuid
         stubs.api.pipeline_instances().create.assert_called_with(
-            body=expect_pipeline)
+            body=JsonDiffMatcher(expect_pipeline))
 
     @stubs
     def test_submit_container(self, stubs):
@@ -394,33 +478,22 @@ class TestSubmit(unittest.TestCase):
             logging.exception("")
 
         stubs.api.collections().create.assert_has_calls([
-            mock.call(),
-            mock.call(body={
+            mock.call(body=JsonDiffMatcher({
                 'manifest_text':
-                './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
-                '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
-                'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
-                'owner_uuid': None,
-                'name': 'submit_wf.cwl',
-            }, ensure_unique_name=True),
-            mock.call().execute(),
-            mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
-                            '0:0:blub.txt 0:0:submit_tool.cwl\n',
-                            'name': 'New collection',
-                            'replication_desired': None,
-            }, ensure_unique_name=True),
-            mock.call().execute(num_retries=4),
-            mock.call(body={
+                '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
+                'replication_desired': None,
+                'name': 'submit_tool.cwl dependencies',
+            }), ensure_unique_name=True),
+            mock.call(body=JsonDiffMatcher({
                 'manifest_text':
                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
-                'owner_uuid': None,
-                'name': '#',
-            }, ensure_unique_name=True),
-            mock.call().execute()])
+                'replication_desired': None,
+                'name': 'submit_wf.cwl input',
+            }), ensure_unique_name=True)])
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         stubs.api.container_requests().create.assert_called_with(
-            body=expect_container)
+            body=JsonDiffMatcher(expect_container))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
 
@@ -436,11 +509,78 @@ class TestSubmit(unittest.TestCase):
         except:
             logging.exception("")
 
-        stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = [
+            'arvados-cwl-runner', '--local', '--api=containers',
+            '--no-log-timestamps', '--disable-validate',
+            '--eval-timeout=20', '--thread-count=4',
+            '--disable-reuse', '--debug', '--on-error=continue',
+            '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+        expect_container["use_existing"] = False
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
+    @stubs
+    def test_submit_container_reuse_disabled_by_workflow(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+             "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
+            capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+        self.assertEqual(exited, 0)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = [
+            'arvados-cwl-runner', '--local', '--api=containers',
+            '--no-log-timestamps', '--disable-validate',
+            '--eval-timeout=20', '--thread-count=4',
+            '--disable-reuse', '--debug', '--on-error=continue',
+            '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+        expect_container["use_existing"] = False
+        expect_container["name"] = "submit_wf_no_reuse.cwl"
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+            {
+                "class": "http://arvados.org/cwl#ReuseRequirement",
+                "enableReuse": False,
+            },
+        ]
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+            "arv": "http://arvados.org/cwl#",
+            "cwltool": "http://commonwl.org/cwltool#"
+        }
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
+    @stubs
+    def test_submit_container_on_error(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate',
+                                       '--eval-timeout=20', '--thread-count=4',
+                                       '--enable-reuse', '--debug', '--on-error=stop',
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
         stubs.api.container_requests().create.assert_called_with(
-            body=expect_container)
+            body=JsonDiffMatcher(expect_container))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
 
@@ -458,176 +598,934 @@ class TestSubmit(unittest.TestCase):
         except:
             logging.exception("")
 
-        stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate',
+                                       '--eval-timeout=20', '--thread-count=4',
+                                       '--enable-reuse',
+                                       "--output-name="+output_name, '--debug', '--on-error=continue',
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+        expect_container["output_name"] = output_name
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+    @stubs
+    def test_submit_storage_classes(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate',
+                                       '--eval-timeout=20', '--thread-count=4',
+                                       '--enable-reuse', "--debug",
+                                       "--storage-classes=foo", '--on-error=continue',
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
         stubs.api.container_requests().create.assert_called_with(
-            body=expect_container)
+            body=JsonDiffMatcher(expect_container))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
 
+    @mock.patch("arvados_cwl.task_queue.TaskQueue")
+    @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
+    @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None))
     @stubs
-    def test_submit_container_output_tags(self, stubs):
-        output_tags = "tag0,tag1,tag2"
+    def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+        def set_final_output(job_order, output_callback, runtimeContext):
+            output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+            return []
+        job.side_effect = set_final_output
+
+        try:
+            exited = arvados_cwl.main(
+                ["--debug", "--local", "--storage-classes=foo",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+
+    @mock.patch("arvados_cwl.task_queue.TaskQueue")
+    @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
+    @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None))
+    @stubs
+    def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+        def set_final_output(job_order, output_callback, runtimeContext):
+            output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+            return []
+        job.side_effect = set_final_output
+
+        try:
+            exited = arvados_cwl.main(
+                ["--debug", "--local",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
 
+        make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+
+    @stubs
+    def test_submit_container_output_ttl(self, stubs):
         capture_stdout = cStringIO.StringIO()
         try:
             exited = arvados_cwl.main(
-                ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
             self.assertEqual(exited, 0)
         except:
             logging.exception("")
 
-        stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
-
         expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate',
+                                       '--eval-timeout=20', '--thread-count=4',
+                                       '--enable-reuse', '--debug', '--on-error=continue',
+                                       "--intermediate-output-ttl=3600",
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
         stubs.api.container_requests().create.assert_called_with(
-            body=expect_container)
+            body=JsonDiffMatcher(expect_container))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
 
     @stubs
-    def test_submit_container_runner_ram(self, stubs):
+    def test_submit_container_trash_intermediate(self, stubs):
         capture_stdout = cStringIO.StringIO()
         try:
             exited = arvados_cwl.main(
-                ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
             self.assertEqual(exited, 0)
         except:
             logging.exception("")
 
-        stubs.expect_container_spec["runtime_constraints"]["ram"] = 2048*1024*1024
-
         expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate',
+                                       '--eval-timeout=20', '--thread-count=4',
+                                       '--enable-reuse', '--debug', '--on-error=continue',
+                                       "--trash-intermediate",
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
         stubs.api.container_requests().create.assert_called_with(
-            body=expect_container)
+            body=JsonDiffMatcher(expect_container))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
 
     @stubs
-    def test_submit_container_name(self, stubs):
+    def test_submit_container_output_tags(self, stubs):
+        output_tags = "tag0,tag1,tag2"
+
         capture_stdout = cStringIO.StringIO()
         try:
             exited = arvados_cwl.main(
-                ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
             self.assertEqual(exited, 0)
         except:
             logging.exception("")
 
-        stubs.expect_container_spec["name"] = "hello container 123"
-
         expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate',
+                                       '--eval-timeout=20', '--thread-count=4',
+                                       '--enable-reuse',
+                                       "--output-tags="+output_tags, '--debug', '--on-error=continue',
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
         stubs.api.container_requests().create.assert_called_with(
-            body=expect_container)
+            body=JsonDiffMatcher(expect_container))
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
 
-    @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
-    @mock.patch("cwltool.docker.get_image")
-    @mock.patch("arvados.api")
-    def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
-        arvrunner = mock.MagicMock()
-        arvrunner.project_uuid = ""
-        api.return_value = mock.MagicMock()
-        arvrunner.api = api.return_value
-        arvrunner.api.links().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0},
-                                                            {"items": [], "items_available": 0, "offset": 0},
-                                                            {"items": [], "items_available": 0, "offset": 0},
-                                                            {"items": [{"created_at": "",
-                                                                        "head_uuid": "",
-                                                                        "link_class": "docker_image_hash",
-                                                                        "name": "123456",
-                                                                        "owner_uuid": "",
-                                                                        "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
-                                                            {"items": [], "items_available": 0, "offset": 0},
-                                                            {"items": [{"created_at": "",
-                                                                        "head_uuid": "",
-                                                                        "link_class": "docker_image_repo+tag",
-                                                                        "name": "arvados/jobs:"+arvados_cwl.__version__,
-                                                                        "owner_uuid": "",
-                                                                        "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
-                                                            {"items": [{"created_at": "",
-                                                                        "head_uuid": "",
-                                                                        "link_class": "docker_image_hash",
-                                                                        "name": "123456",
-                                                                        "owner_uuid": "",
-                                                                        "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}                                                            ,
-        )
-        find_one_image_hash.return_value = "123456"
+    @stubs
+    def test_submit_container_runner_ram(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
 
-        arvrunner.api.collections().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0},
-                                                                  {"items": [{"uuid": "",
-                                                                              "owner_uuid": "",
-                                                                              "manifest_text": "",
-                                                                              "properties": ""
-                                                                          }], "items_available": 1, "offset": 0},
-                                                                  {"items": [{"uuid": ""}], "items_available": 1, "offset": 0})
-        arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
-        self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, arvados_cwl.runner.arvados_jobs_image(arvrunner))
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["runtime_constraints"]["ram"] = 2048*1024*1024
 
-class TestCreateTemplate(unittest.TestCase):
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+    @mock.patch("arvados.collection.CollectionReader")
+    @mock.patch("time.sleep")
     @stubs
-    def test_create(self, stubs):
-        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+    def test_submit_file_keepref(self, stubs, tm, collectionReader):
+        capture_stdout = cStringIO.StringIO()
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+             "tests/wf/submit_keepref_wf.cwl"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
 
+    @mock.patch("arvados.collection.CollectionReader")
+    @mock.patch("time.sleep")
+    @stubs
+    def test_submit_keepref(self, stubs, tm, reader):
         capture_stdout = cStringIO.StringIO()
 
+        with open("tests/wf/expect_arvworkflow.cwl") as f:
+            reader().open().__enter__().read.return_value = f.read()
+
         exited = arvados_cwl.main(
-            ["--create-workflow", "--debug",
-             "--project-uuid", project_uuid,
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+             "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
             capture_stdout, sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
 
-        stubs.api.pipeline_instances().create.refute_called()
-        stubs.api.jobs().create.refute_called()
-
-        expect_component = copy.deepcopy(stubs.expect_job_spec)
-        expect_component['script_parameters']['x'] = {
-            'dataclass': 'File',
-            'required': True,
-            'type': 'File',
-            'value': '99999999999999999999999999999994+99/blorp.txt',
-        }
-        expect_component['script_parameters']['y'] = {
-            'dataclass': 'Collection',
-            'required': True,
-            'type': 'Directory',
-            'value': '99999999999999999999999999999998+99',
-        }
-        expect_component['script_parameters']['z'] = {
-            'dataclass': 'Collection',
-            'required': True,
-            'type': 'Directory',
-        }
-        expect_template = {
-            "components": {
-                "submit_wf.cwl": expect_component,
+        expect_container = {
+            'priority': 500,
+            'mounts': {
+                '/var/spool/cwl': {
+                    'writable': True,
+                    'kind': 'collection'
+                },
+                'stdout': {
+                    'path': '/var/spool/cwl/cwl.output.json',
+                    'kind': 'file'
+                },
+                '/var/lib/cwl/workflow': {
+                    'portable_data_hash': '99999999999999999999999999999994+99',
+                    'kind': 'collection'
+                },
+                '/var/lib/cwl/cwl.input.json': {
+                    'content': {
+                        'x': 'XxX'
+                    },
+                    'kind': 'json'
+                }
+            }, 'state': 'Committed',
+            'output_path': '/var/spool/cwl',
+            'name': 'expect_arvworkflow.cwl#main',
+            'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
+            'command': ['arvados-cwl-runner', '--local', '--api=containers',
+                        '--no-log-timestamps', '--disable-validate',
+                        '--eval-timeout=20', '--thread-count=4',
+                        '--enable-reuse', '--debug', '--on-error=continue',
+                        '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
+            'cwd': '/var/spool/cwl',
+            'runtime_constraints': {
+                'API': True,
+                'vcpus': 1,
+                'ram': 1073741824
             },
-            "name": "submit_wf.cwl",
-            "owner_uuid": project_uuid,
+            'use_existing': True,
+            'properties': {},
+            'secret_mounts': {}
         }
-        stubs.api.pipeline_templates().create.assert_called_with(
-            body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
         self.assertEqual(capture_stdout.getvalue(),
-                         stubs.expect_pipeline_template_uuid + '\n')
-
+                         stubs.expect_container_request_uuid + '\n')
 
-class TestCreateWorkflow(unittest.TestCase):
-    existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
-    expect_workflow = open("tests/wf/expect_packed.cwl").read()
 
+    @mock.patch("arvados.collection.CollectionReader")
+    @mock.patch("time.sleep")
     @stubs
-    def test_create(self, stubs):
-        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
+    def test_submit_jobs_keepref(self, stubs, tm, reader):
+        capture_stdout = cStringIO.StringIO()
+
+        with open("tests/wf/expect_arvworkflow.cwl") as f:
+            reader().open().__enter__().read.return_value = f.read()
+
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=jobs", "--debug",
+             "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+        expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
+        del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
+        del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
+        expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
+        expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
+        stubs.api.pipeline_instances().create.assert_called_with(
+            body=JsonDiffMatcher(expect_pipeline))
+
+    @mock.patch("time.sleep")
+    @stubs
+    def test_submit_arvworkflow(self, stubs, tm):
+        capture_stdout = cStringIO.StringIO()
+
+        with open("tests/wf/expect_arvworkflow.cwl") as f:
+            stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
+
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+             "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        expect_container = {
+            'priority': 500,
+            'mounts': {
+                '/var/spool/cwl': {
+                    'writable': True,
+                    'kind': 'collection'
+                },
+                'stdout': {
+                    'path': '/var/spool/cwl/cwl.output.json',
+                    'kind': 'file'
+                },
+                '/var/lib/cwl/workflow.json': {
+                    'kind': 'json',
+                    'content': {
+                        'cwlVersion': 'v1.0',
+                        '$graph': [
+                            {
+                                'id': '#main',
+                                'inputs': [
+                                    {'type': 'string', 'id': '#main/x'}
+                                ],
+                                'steps': [
+                                    {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
+                                     'run': '#submit_tool.cwl',
+                                     'id': '#main/step1',
+                                     'out': []}
+                                ],
+                                'class': 'Workflow',
+                                'outputs': []
+                            },
+                            {
+                                'inputs': [
+                                    {
+                                        'inputBinding': {'position': 1},
+                                        'type': 'string',
+                                        'id': '#submit_tool.cwl/x'}
+                                ],
+                                'requirements': [
+                                    {'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
+                                ],
+                                'id': '#submit_tool.cwl',
+                                'outputs': [],
+                                'baseCommand': 'cat',
+                                'class': 'CommandLineTool'
+                            }
+                        ]
+                    }
+                },
+                '/var/lib/cwl/cwl.input.json': {
+                    'content': {
+                        'x': 'XxX'
+                    },
+                    'kind': 'json'
+                }
+            }, 'state': 'Committed',
+            'output_path': '/var/spool/cwl',
+            'name': 'a test workflow',
+            'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
+            'command': ['arvados-cwl-runner', '--local', '--api=containers',
+                        '--no-log-timestamps', '--disable-validate',
+                        '--eval-timeout=20', '--thread-count=4',
+                        '--enable-reuse', '--debug', '--on-error=continue',
+                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+            'cwd': '/var/spool/cwl',
+            'runtime_constraints': {
+                'API': True,
+                'vcpus': 1,
+                'ram': 1073741824
+            },
+            'use_existing': True,
+            'properties': {
+                "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
+            },
+            'secret_mounts': {}
+        }
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
+    @stubs
+    def test_submit_container_name(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["name"] = "hello container 123"
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
+    @stubs
+    def test_submit_container_project(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["owner_uuid"] = project_uuid
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate',
+                                       "--eval-timeout=20", "--thread-count=4",
+                                       '--enable-reuse', '--debug', '--on-error=continue',
+                                       '--project-uuid='+project_uuid,
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+    @stubs
+    def test_submit_container_eval_timeout(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate',
+                                       '--eval-timeout=60.0', '--thread-count=4',
+                                       '--enable-reuse', '--debug', '--on-error=continue',
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
+    @stubs
+    def test_submit_container_thread_count(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate',
+                                       '--eval-timeout=20', '--thread-count=20',
+                                       '--enable-reuse', '--debug', '--on-error=continue',
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
+    @stubs
+    def test_submit_job_runner_image(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
+
+        expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+        stubs.api.pipeline_instances().create.assert_called_with(
+            body=JsonDiffMatcher(expect_pipeline))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_pipeline_uuid + '\n')
+
+    @stubs
+    def test_submit_container_runner_image(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+    @stubs
+    def test_submit_priority(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        stubs.expect_container_spec["priority"] = 669
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
+    @stubs
+    def test_submit_wf_runner_resources(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug",
+                 "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["runtime_constraints"] = {
+            "API": True,
+            "vcpus": 2,
+            "ram": 2000 * 2**20
+        }
+        expect_container["name"] = "submit_wf_runner_resources.cwl"
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+            {
+                "class": "http://arvados.org/cwl#WorkflowRunnerResources",
+                "coresMin": 2,
+                "ramMin": 2000
+            }
+        ]
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+            "arv": "http://arvados.org/cwl#",
+        }
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
+    @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
+    @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
+    @mock.patch("arvados.api")
+    def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
+        arvrunner = mock.MagicMock()
+        arvrunner.project_uuid = ""
+        api.return_value = mock.MagicMock()
+        arvrunner.api = api.return_value
+        arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
+                                                                        "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+                                                                        "link_class": "docker_image_repo+tag",
+                                                                        "name": "arvados/jobs:"+arvados_cwl.__version__,
+                                                                        "owner_uuid": "",
+                                                                        "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
+                                                            {"items": [{"created_at": "",
+                                                                        "head_uuid": "",
+                                                                        "link_class": "docker_image_hash",
+                                                                        "name": "123456",
+                                                                        "owner_uuid": "",
+                                                                        "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
+        )
+        find_one_image_hash.return_value = "123456"
+
+        arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+                                                                              "owner_uuid": "",
+                                                                              "manifest_text": "",
+                                                                              "properties": ""
+                                                                          }], "items_available": 1, "offset": 0},)
+        arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
+        self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
+                         arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
+
+    @stubs
+    def test_submit_secrets(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug",
+                 "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+
+        expect_container = {
+            "command": [
+                "arvados-cwl-runner",
+                "--local",
+                "--api=containers",
+                "--no-log-timestamps",
+                "--disable-validate",
+                "--eval-timeout=20",
+                '--thread-count=4',
+                "--enable-reuse",
+                '--debug',
+                "--on-error=continue",
+                "/var/lib/cwl/workflow.json#main",
+                "/var/lib/cwl/cwl.input.json"
+            ],
+            "container_image": "arvados/jobs:"+arvados_cwl.__version__,
+            "cwd": "/var/spool/cwl",
+            "mounts": {
+                "/var/lib/cwl/cwl.input.json": {
+                    "content": {
+                        "pw": {
+                            "$include": "/secrets/s0"
+                        }
+                    },
+                    "kind": "json"
+                },
+                "/var/lib/cwl/workflow.json": {
+                    "content": {
+                        "$graph": [
+                            {
+                                "$namespaces": {
+                                    "cwltool": "http://commonwl.org/cwltool#"
+                                },
+                                "arguments": [
+                                    "md5sum",
+                                    "example.conf"
+                                ],
+                                "class": "CommandLineTool",
+                                "hints": [
+                                    {
+                                        "class": "http://commonwl.org/cwltool#Secrets",
+                                        "secrets": [
+                                            "#secret_job.cwl/pw"
+                                        ]
+                                    }
+                                ],
+                                "id": "#secret_job.cwl",
+                                "inputs": [
+                                    {
+                                        "id": "#secret_job.cwl/pw",
+                                        "type": "string"
+                                    }
+                                ],
+                                "outputs": [
+                                    {
+                                        "id": "#secret_job.cwl/out",
+                                        "type": "stdout"
+                                    }
+                                ],
+                                "stdout": "hashed_example.txt",
+                                "requirements": [
+                                    {
+                                        "class": "InitialWorkDirRequirement",
+                                        "listing": [
+                                            {
+                                                "entry": "username: user\npassword: $(inputs.pw)\n",
+                                                "entryname": "example.conf"
+                                            }
+                                        ]
+                                    }
+                                ]
+                            },
+                            {
+                                "class": "Workflow",
+                                "hints": [
+                                    {
+                                        "class": "DockerRequirement",
+                                        "dockerPull": "debian:8"
+                                    },
+                                    {
+                                        "class": "http://commonwl.org/cwltool#Secrets",
+                                        "secrets": [
+                                            "#main/pw"
+                                        ]
+                                    }
+                                ],
+                                "id": "#main",
+                                "inputs": [
+                                    {
+                                        "id": "#main/pw",
+                                        "type": "string"
+                                    }
+                                ],
+                                "outputs": [
+                                    {
+                                        "id": "#main/out",
+                                        "outputSource": "#main/step1/out",
+                                        "type": "File"
+                                    }
+                                ],
+                                "steps": [
+                                    {
+                                        "id": "#main/step1",
+                                        "in": [
+                                            {
+                                                "id": "#main/step1/pw",
+                                                "source": "#main/pw"
+                                            }
+                                        ],
+                                        "out": [
+                                            "#main/step1/out"
+                                        ],
+                                        "run": "#secret_job.cwl"
+                                    }
+                                ]
+                            }
+                        ],
+                        "cwlVersion": "v1.0"
+                    },
+                    "kind": "json"
+                },
+                "/var/spool/cwl": {
+                    "kind": "collection",
+                    "writable": True
+                },
+                "stdout": {
+                    "kind": "file",
+                    "path": "/var/spool/cwl/cwl.output.json"
+                }
+            },
+            "name": "secret_wf.cwl",
+            "output_path": "/var/spool/cwl",
+            "priority": 500,
+            "properties": {},
+            "runtime_constraints": {
+                "API": True,
+                "ram": 1073741824,
+                "vcpus": 1
+            },
+            "secret_mounts": {
+                "/secrets/s0": {
+                    "content": "blorp",
+                    "kind": "text"
+                }
+            },
+            "state": "Committed",
+            "use_existing": True
+        }
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+    @stubs
+    def test_submit_request_uuid(self, stubs):
+        stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
+
+        stubs.api.container_requests().update().execute.return_value = {
+            "uuid": stubs.expect_container_request_uuid,
+            "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
+            "state": "Queued"
+        }
+
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        stubs.api.container_requests().update.assert_called_with(
+            uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
+class TestCreateTemplate(unittest.TestCase):
+    existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
+
+    def _adjust_script_params(self, expect_component):
+        expect_component['script_parameters']['x'] = {
+            'dataclass': 'File',
+            'required': True,
+            'type': 'File',
+            'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+        }
+        expect_component['script_parameters']['y'] = {
+            'dataclass': 'Collection',
+            'required': True,
+            'type': 'Directory',
+            'value': '99999999999999999999999999999998+99',
+        }
+        expect_component['script_parameters']['z'] = {
+            'dataclass': 'Collection',
+            'required': True,
+            'type': 'Directory',
+        }
+
+    @stubs
+    def test_create(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--create-workflow", "--debug",
+             "--api=jobs",
+             "--project-uuid", project_uuid,
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        stubs.api.pipeline_instances().create.refute_called()
+        stubs.api.jobs().create.refute_called()
+
+        expect_component = copy.deepcopy(stubs.expect_job_spec)
+        self._adjust_script_params(expect_component)
+        expect_template = {
+            "components": {
+                "submit_wf.cwl": expect_component,
+            },
+            "name": "submit_wf.cwl",
+            "owner_uuid": project_uuid,
+        }
+        stubs.api.pipeline_templates().create.assert_called_with(
+            body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_pipeline_template_uuid + '\n')
+
+
+    @stubs
+    def test_create_name(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--create-workflow", "--debug",
+             "--project-uuid", project_uuid,
+             "--api=jobs",
+             "--name", "testing 123",
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        stubs.api.pipeline_instances().create.refute_called()
+        stubs.api.jobs().create.refute_called()
+
+        expect_component = copy.deepcopy(stubs.expect_job_spec)
+        self._adjust_script_params(expect_component)
+        expect_template = {
+            "components": {
+                "testing 123": expect_component,
+            },
+            "name": "testing 123",
+            "owner_uuid": project_uuid,
+        }
+        stubs.api.pipeline_templates().create.assert_called_with(
+            body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_pipeline_template_uuid + '\n')
+
+
+    @stubs
+    def test_update_name(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--update-workflow", self.existing_template_uuid,
+             "--debug",
+             "--project-uuid", project_uuid,
+             "--api=jobs",
+             "--name", "testing 123",
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        stubs.api.pipeline_instances().create.refute_called()
+        stubs.api.jobs().create.refute_called()
+
+        expect_component = copy.deepcopy(stubs.expect_job_spec)
+        self._adjust_script_params(expect_component)
+        expect_template = {
+            "components": {
+                "testing 123": expect_component,
+            },
+            "name": "testing 123",
+            "owner_uuid": project_uuid,
+        }
+        stubs.api.pipeline_templates().create.refute_called()
+        stubs.api.pipeline_templates().update.assert_called_with(
+            body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
+
+        self.assertEqual(capture_stdout.getvalue(),
+                         self.existing_template_uuid + '\n')
+
+
+class TestCreateWorkflow(unittest.TestCase):
+    existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
+    expect_workflow = StripYAMLComments(
+        open("tests/wf/expect_packed.cwl").read())
+
+    @stubs
+    def test_create(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
         capture_stdout = cStringIO.StringIO()
 
         exited = arvados_cwl.main(
@@ -655,6 +1553,39 @@ class TestCreateWorkflow(unittest.TestCase):
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_workflow_uuid + '\n')
 
+
+    @stubs
+    def test_create_name(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--create-workflow", "--debug",
+             "--api=containers",
+             "--project-uuid", project_uuid,
+             "--name", "testing 123",
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        stubs.api.pipeline_templates().create.refute_called()
+        stubs.api.container_requests().create.refute_called()
+
+        body = {
+            "workflow": {
+                "owner_uuid": project_uuid,
+                "name": "testing 123",
+                "description": "",
+                "definition": self.expect_workflow,
+            }
+        }
+        stubs.api.workflows().create.assert_called_with(
+            body=JsonDiffMatcher(body))
+
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_workflow_uuid + '\n')
+
     @stubs
     def test_incompatible_api(self, stubs):
         capture_stderr = cStringIO.StringIO()
@@ -697,6 +1628,62 @@ class TestCreateWorkflow(unittest.TestCase):
                          self.existing_workflow_uuid + '\n')
 
 
+    @stubs
+    def test_update_name(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--update-workflow", self.existing_workflow_uuid,
+             "--debug", "--name", "testing 123",
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        body = {
+            "workflow": {
+                "name": "testing 123",
+                "description": "",
+                "definition": self.expect_workflow,
+            }
+        }
+        stubs.api.workflows().update.assert_called_with(
+            uuid=self.existing_workflow_uuid,
+            body=JsonDiffMatcher(body))
+        self.assertEqual(capture_stdout.getvalue(),
+                         self.existing_workflow_uuid + '\n')
+
+
+    @stubs
+    def test_create_collection_per_tool(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--create-workflow", "--debug",
+             "--api=containers",
+             "--project-uuid", project_uuid,
+             "tests/collection_per_tool/collection_per_tool.cwl"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
+        expect_workflow = StripYAMLComments(open(toolfile).read())
+
+        body = {
+            "workflow": {
+                "owner_uuid": project_uuid,
+                "name": "collection_per_tool.cwl",
+                "description": "",
+                "definition": expect_workflow,
+            }
+        }
+        stubs.api.workflows().create.assert_called_with(
+            body=JsonDiffMatcher(body))
+
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_workflow_uuid + '\n')
+
 class TestTemplateInputs(unittest.TestCase):
     expect_template = {
         "components": {
@@ -707,8 +1694,7 @@ class TestTemplateInputs(unittest.TestCase):
                 },
                 'script_parameters': {
                     'cwl:tool':
-                    '99999999999999999999999999999991+99/'
-                    'wf/inputs_test.cwl',
+                    '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main',
                     'optionalFloatInput': None,
                     'fileInput': {
                         'type': 'File',
@@ -738,7 +1724,8 @@ class TestTemplateInputs(unittest.TestCase):
                     },
                 },
                 'repository': 'arvados',
-                'script_version': arvados_cwl.__version__,
+                'script_version': 'master',
+                'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
                 'script': 'cwl-runner',
             },
         },
@@ -748,7 +1735,7 @@ class TestTemplateInputs(unittest.TestCase):
     @stubs
     def test_inputs_empty(self, stubs):
         exited = arvados_cwl.main(
-            ["--create-template", "--no-wait",
+            ["--create-template",
              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
@@ -759,7 +1746,7 @@ class TestTemplateInputs(unittest.TestCase):
     @stubs
     def test_inputs(self, stubs):
         exited = arvados_cwl.main(
-            ["--create-template", "--no-wait",
+            ["--create-template",
              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
@@ -767,7 +1754,8 @@ class TestTemplateInputs(unittest.TestCase):
         expect_template = copy.deepcopy(self.expect_template)
         params = expect_template[
             "components"]["inputs_test.cwl"]["script_parameters"]
-        params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
+        params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
+        params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main'
         params["floatInput"]["value"] = 1.234
         params["boolInput"]["value"] = True