X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/7360ecf9c5bd593834c45b1ad60bf0b6ac30d05e..a9a4f7d43340f4f317fb041c93b9aa9c1b6e51c8:/sdk/cwl/tests/test_submit.py

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index a1ace717bb..61892bf2a4 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -6,6 +6,7 @@ from future import standard_library
 standard_library.install_aliases()
 from builtins import object
 from builtins import str
+from future.utils import viewvalues
 
 import copy
 import io
@@ -16,8 +17,19 @@ import logging
 import mock
 import sys
 import unittest
+import cwltool.process
+import re
 
-from io import BytesIO, StringIO
+from io import BytesIO
+
+# StringIO.StringIO and io.StringIO have different behavior write() is
+# called with both python2 (byte) strings and unicode strings
+# (specifically there's some logging in cwltool that causes trouble).
+# This isn't a problem on python3 because all string are unicode.
+if sys.version_info[0] < 3:
+    from StringIO import StringIO
+else:
+    from io import StringIO
 
 import arvados
 import arvados.collection
@@ -55,10 +67,10 @@ def stubs(func):
 
         stubs.keep_client = keep_client2
         stubs.docker_images = {
-            "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")],
-            "debian:8": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")],
-            "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")],
-            "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")],
+            "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", {})],
+            "debian:buster-slim": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", {})],
+            "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", {})],
+            "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", {})],
         }
         def kd(a, b, image_name=None, image_tag=None):
             return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
@@ -74,6 +86,8 @@ def stubs(func):
 
         stubs.api = mock.MagicMock()
         stubs.api._rootDesc = get_rootDesc()
+        stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
+        stubs.api._rootDesc["revision"] = "20210628"
 
         stubs.api.users().current().execute.return_value = {
             "uuid": stubs.fake_user_uuid,
@@ -82,6 +96,11 @@ def stubs(func):
         stubs.api.containers().current().execute.return_value = {
             "uuid": stubs.fake_container_uuid,
         }
+        stubs.api.config()["StorageClasses"].items.return_value = {
+            "default": {
+                "Default": True
+            }
+        }.items()
 
         class CollectionExecute(object):
             def __init__(self, exe):
@@ -101,7 +120,7 @@ def stubs(func):
             return CollectionExecute(created_collections[uuid])
 
         def collection_getstub(created_collections, uuid):
-            for v in created_collections.values():
+            for v in viewvalues(created_collections):
                 if uuid in (v["uuid"], v["portable_data_hash"]):
                     return CollectionExecute(v)
 
@@ -111,6 +130,11 @@ def stubs(func):
                 "portable_data_hash": "99999999999999999999999999999998+99",
                 "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
             },
+            "99999999999999999999999999999997+99": {
+                "uuid": "",
+                "portable_data_hash": "99999999999999999999999999999997+99",
+                "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt"
+            },
             "99999999999999999999999999999994+99": {
                 "uuid": "",
                 "portable_data_hash": "99999999999999999999999999999994+99",
@@ -284,8 +308,8 @@ def stubs(func):
             'secret_mounts': {},
             'state': 'Committed',
             'command': ['arvados-cwl-runner', '--local', '--api=containers',
-                        '--no-log-timestamps', '--disable-validate',
-                        '--eval-timeout=20', '--thread-count=1',
+                        '--no-log-timestamps', '--disable-validate', '--disable-color',
+                        '--eval-timeout=20', '--thread-count=0',
                         '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
             'name': 'submit_wf.cwl',
@@ -297,7 +321,7 @@ def stubs(func):
                 'vcpus': 1,
                 'ram': (1024+256)*1024*1024
             },
-            'use_existing': True,
+            'use_existing': False,
             'properties': {},
             'secret_mounts': {}
         }
@@ -319,115 +343,11 @@ def stubs(func):
 
 
 class TestSubmit(unittest.TestCase):
-    @mock.patch("arvados_cwl.arvdocker.arv_docker_get_image")
-    @mock.patch("time.sleep")
-    @stubs
-    def test_submit(self, stubs, tm, arvdock):
-        def get_image(api_client, dockerRequirement, pull_image, project_uuid):
-            if dockerRequirement["dockerPull"] == 'arvados/jobs:'+arvados_cwl.__version__:
-                return '999999999999999999999999999999d3+99'
-            elif dockerRequirement["dockerPull"] == "debian:8":
-                return '999999999999999999999999999999d4+99'
-        arvdock.side_effect = get_image
-
-        exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--api=jobs", "--debug",
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
-        stubs.api.collections().create.assert_has_calls([
-            mock.call(body=JsonDiffMatcher({
-                'manifest_text':
-                '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
-                'replication_desired': None,
-                'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
-            }), ensure_unique_name=False),
-            mock.call(body=JsonDiffMatcher({
-                'manifest_text':
-                '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
-                'replication_desired': None,
-                'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
-            }), ensure_unique_name=False),
-            mock.call(body=JsonDiffMatcher({
-                'manifest_text':
-                ". 68089141fbf7e020ac90a9d6a575bc8f+1312 0:1312: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, {"class": "DockerRequirement", "dockerPull": "debian:8", 'http://arvados.org/cwl#dockerCollectionPDH': '999999999999999999999999999999d4+99'}, 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))
-        self.assertEqual(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_uuid + '\n')
-        self.assertEqual(exited, 0)
-
-    @mock.patch("time.sleep")
-    @stubs
-    def test_submit_no_reuse(self, stubs, tm):
-        exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
-        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(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_uuid + '\n')
-        self.assertEqual(exited, 0)
-
-    @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):
-        exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
-        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=JsonDiffMatcher(expect_pipeline))
-        self.assertEqual(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_uuid + '\n')
-        self.assertEqual(exited, 0)
-
-    @mock.patch("time.sleep")
-    @stubs
-    def test_submit_runner_ram(self, stubs, tm):
-        exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
-        expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
-        expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
+    def setUp(self):
+        cwltool.process._names = set()
+        arvados_cwl.arvdocker.arv_docker_clear_cache()
 
-        stubs.api.pipeline_instances().create.assert_called_with(
-            body=JsonDiffMatcher(expect_pipeline))
-        self.assertEqual(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_uuid + '\n')
-        self.assertEqual(exited, 0)
 
     @mock.patch("time.sleep")
     @stubs
@@ -438,80 +358,9 @@ class TestSubmit(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 1)
 
-    @mock.patch("time.sleep")
-    @stubs
-    def test_submit_output_name(self, stubs, tm):
-        output_name = "test_output_name"
-
-        exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--debug", "--output-name", output_name,
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
-        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=JsonDiffMatcher(expect_pipeline))
-        self.assertEqual(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_uuid + '\n')
-        self.assertEqual(exited, 0)
 
-    @mock.patch("time.sleep")
     @stubs
-    def test_submit_pipeline_name(self, stubs, tm):
-        exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--debug", "--name=hello job 123",
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-        self.assertEqual(exited, 0)
-
-        expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
-        expect_pipeline["name"] = "hello job 123"
-
-        stubs.api.pipeline_instances().create.assert_called_with(
-            body=JsonDiffMatcher(expect_pipeline))
-        self.assertEqual(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_uuid + '\n')
-
-    @mock.patch("time.sleep")
-    @stubs
-    def test_submit_output_tags(self, stubs, tm):
-        output_tags = "tag0,tag1,tag2"
-
-        exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            stubs.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:output_tags"] = output_tags
-
-        stubs.api.pipeline_instances().create.assert_called_with(
-            body=JsonDiffMatcher(expect_pipeline))
-        self.assertEqual(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_uuid + '\n')
-
-    @mock.patch("time.sleep")
-    @stubs
-    def test_submit_with_project_uuid(self, stubs, tm):
-        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
-        exited = arvados_cwl.main(
-            ["--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)
-        self.assertEqual(exited, 0)
-
-        expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
-        expect_pipeline["owner_uuid"] = project_uuid
-        stubs.api.pipeline_instances().create.assert_called_with(
-            body=JsonDiffMatcher(expect_pipeline))
-
-    @stubs
-    def test_submit_container(self, stubs):        
+    def test_submit_container(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug",
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
@@ -520,16 +369,17 @@ class TestSubmit(unittest.TestCase):
         stubs.api.collections().create.assert_has_calls([
             mock.call(body=JsonDiffMatcher({
                 'manifest_text':
-                '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
+                '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
                 'replication_desired': None,
-                'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+                'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
             }), ensure_unique_name=False),
             mock.call(body=JsonDiffMatcher({
                 'manifest_text':
-                '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
+                '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
                 'replication_desired': None,
-                'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
-            }), ensure_unique_name=False)])
+                'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+            }), ensure_unique_name=False),
+            ])
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         stubs.api.container_requests().create.assert_called_with(
@@ -538,6 +388,19 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
+
+    @stubs
+    def test_submit_container_tool(self, stubs):
+        # test for issue #16139
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+                "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
     @stubs
     def test_submit_container_no_reuse(self, stubs):
         exited = arvados_cwl.main(
@@ -548,8 +411,8 @@ class TestSubmit(unittest.TestCase):
         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=1',
+            '--no-log-timestamps', '--disable-validate', '--disable-color',
+            '--eval-timeout=20', '--thread-count=0',
             '--disable-reuse', "--collection-cache-size=256",
             '--debug', '--on-error=continue',
             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -558,7 +421,7 @@ class TestSubmit(unittest.TestCase):
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
         self.assertEqual(stubs.capture_stdout.getvalue(),
-                         stubs.expect_container_request_uuid + '\n') 
+                         stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
     @stubs
@@ -572,8 +435,8 @@ class TestSubmit(unittest.TestCase):
         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=1',
+            '--no-log-timestamps', '--disable-validate', '--disable-color',
+            '--eval-timeout=20', '--thread-count=0',
             '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
         expect_container["use_existing"] = False
@@ -584,7 +447,7 @@ class TestSubmit(unittest.TestCase):
                 "enableReuse": False,
             },
         ]
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
             "arv": "http://arvados.org/cwl#",
             "cwltool": "http://commonwl.org/cwltool#"
         }
@@ -601,11 +464,11 @@ class TestSubmit(unittest.TestCase):
             ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- 
+
         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=1',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
                                        '--debug', '--on-error=stop',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -619,7 +482,7 @@ class TestSubmit(unittest.TestCase):
     @stubs
     def test_submit_container_output_name(self, stubs):
         output_name = "test_output_name"
-  
+
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
@@ -627,8 +490,8 @@ class TestSubmit(unittest.TestCase):
 
         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=1',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
                                        "--output-name="+output_name, '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -641,7 +504,7 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(exited, 0)
 
     @stubs
-    def test_submit_storage_classes(self, stubs):     
+    def test_submit_storage_classes(self, stubs):
         exited = arvados_cwl.main(
             ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
@@ -649,8 +512,8 @@ class TestSubmit(unittest.TestCase):
 
         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=1',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256", "--debug",
                                        "--storage-classes=foo", '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -661,11 +524,35 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @mock.patch("arvados_cwl.task_queue.TaskQueue")
+    @stubs
+    def test_submit_multiple_storage_classes(self, stubs):
+        exited = arvados_cwl.main(
+            ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
+                                       '--enable-reuse', "--collection-cache-size=256", "--debug",
+                                       "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--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(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
+    @mock.patch("cwltool.task_queue.TaskQueue")
     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
-    @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
+    @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
     @stubs
     def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+        final_output_c = arvados.collection.Collection()
+        make_output.return_value = ({},final_output_c)
+
         def set_final_output(job_order, output_callback, runtimeContext):
             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
             return []
@@ -674,16 +561,20 @@ class TestSubmit(unittest.TestCase):
         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)
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
         make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
         self.assertEqual(exited, 0)
 
-    @mock.patch("arvados_cwl.task_queue.TaskQueue")
+    @mock.patch("cwltool.task_queue.TaskQueue")
     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
-    @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
+    @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
     @stubs
     def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+        final_output_c = arvados.collection.Collection()
+        make_output.return_value = ({},final_output_c)
+        stubs.api.config().get.return_value = {"default": {"Default": True}}
+
         def set_final_output(job_order, output_callback, runtimeContext):
             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
             return []
@@ -692,11 +583,32 @@ class TestSubmit(unittest.TestCase):
         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)
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
         make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
         self.assertEqual(exited, 0)
 
+    @mock.patch("cwltool.task_queue.TaskQueue")
+    @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
+    @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
+    @stubs
+    def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
+        final_output_c = arvados.collection.Collection()
+        make_output.return_value = ({},final_output_c)
+
+        def set_final_output(job_order, output_callback, runtimeContext):
+            output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+            return []
+        job.side_effect = set_final_output
+
+        exited = arvados_cwl.main(
+            ["--debug", "--local",
+                "tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+        self.assertEqual(exited, 0)
+
     @stubs
     def test_submit_container_output_ttl(self, stubs):
         exited = arvados_cwl.main(
@@ -706,8 +618,8 @@ class TestSubmit(unittest.TestCase):
 
         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=1',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256", '--debug',
                                        '--on-error=continue',
                                        "--intermediate-output-ttl=3600",
@@ -725,12 +637,12 @@ class TestSubmit(unittest.TestCase):
             ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
-            
+
 
         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=1',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
                                        '--debug', '--on-error=continue',
                                        "--trash-intermediate",
@@ -753,8 +665,8 @@ class TestSubmit(unittest.TestCase):
 
         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=1',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
                                        "--output-tags="+output_tags, '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -785,6 +697,7 @@ class TestSubmit(unittest.TestCase):
     @mock.patch("time.sleep")
     @stubs
     def test_submit_file_keepref(self, stubs, tm, collectionReader):
+        collectionReader().exists.return_value = True
         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug",
@@ -830,8 +743,8 @@ class TestSubmit(unittest.TestCase):
             'name': 'expect_arvworkflow.cwl#main',
             'container_image': '999999999999999999999999999999d3+99',
             'command': ['arvados-cwl-runner', '--local', '--api=containers',
-                        '--no-log-timestamps', '--disable-validate',
-                        '--eval-timeout=20', '--thread-count=1',
+                        '--no-log-timestamps', '--disable-validate', '--disable-color',
+                        '--eval-timeout=20', '--thread-count=0',
                         '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
                         '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
             'cwd': '/var/spool/cwl',
@@ -840,7 +753,7 @@ class TestSubmit(unittest.TestCase):
                 'vcpus': 1,
                 'ram': 1342177280
             },
-            'use_existing': True,
+            'use_existing': False,
             'properties': {},
             'secret_mounts': {}
         }
@@ -851,28 +764,6 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @mock.patch("arvados.collection.CollectionReader")
-    @mock.patch("time.sleep")
-    @stubs
-    def test_submit_jobs_keepref(self, stubs, tm, reader):
-        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"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
-        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))
-        self.assertEqual(exited, 0)
-
     @mock.patch("time.sleep")
     @stubs
     def test_submit_arvworkflow(self, stubs, tm):
@@ -923,7 +814,7 @@ class TestSubmit(unittest.TestCase):
                                 ],
                                 'requirements': [
                                     {
-                                        'dockerPull': 'debian:8',
+                                        'dockerPull': 'debian:buster-slim',
                                         'class': 'DockerRequirement',
                                         "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
                                     }
@@ -947,8 +838,8 @@ class TestSubmit(unittest.TestCase):
             'name': 'a test workflow',
             'container_image': "999999999999999999999999999999d3+99",
             'command': ['arvados-cwl-runner', '--local', '--api=containers',
-                        '--no-log-timestamps', '--disable-validate',
-                        '--eval-timeout=20', '--thread-count=1',
+                        '--no-log-timestamps', '--disable-validate', '--disable-color',
+                        '--eval-timeout=20', '--thread-count=0',
                         '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
             'cwd': '/var/spool/cwl',
@@ -957,7 +848,7 @@ class TestSubmit(unittest.TestCase):
                 'vcpus': 1,
                 'ram': 1342177280
             },
-            'use_existing': True,
+            'use_existing': False,
             'properties': {
                 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
             },
@@ -1003,6 +894,7 @@ class TestSubmit(unittest.TestCase):
     @stubs
     def test_submit_container_project(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
@@ -1011,8 +903,8 @@ class TestSubmit(unittest.TestCase):
         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=1",
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       "--eval-timeout=20", "--thread-count=0",
                                        '--enable-reuse', "--collection-cache-size=256", '--debug',
                                        '--on-error=continue',
                                        '--project-uuid='+project_uuid,
@@ -1033,8 +925,8 @@ class TestSubmit(unittest.TestCase):
 
         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=1',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=60.0', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
                                        '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -1054,8 +946,8 @@ class TestSubmit(unittest.TestCase):
 
         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=1',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=500",
                                        '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -1076,7 +968,7 @@ class TestSubmit(unittest.TestCase):
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
-                                       '--no-log-timestamps', '--disable-validate',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=20',
                                        '--enable-reuse', "--collection-cache-size=256",
                                        '--debug', '--on-error=continue',
@@ -1088,22 +980,6 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
-    def test_submit_job_runner_image(self, stubs):
-        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"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
-
-        stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "999999999999999999999999999999d5+99"
-
-        expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
-        stubs.api.pipeline_instances().create.assert_called_with(
-            body=JsonDiffMatcher(expect_pipeline))
-        self.assertEqual(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_uuid + '\n')
-        self.assertEqual(exited, 0)
-
     @stubs
     def test_submit_container_runner_image(self, stubs):
         exited = arvados_cwl.main(
@@ -1158,12 +1034,12 @@ class TestSubmit(unittest.TestCase):
                 "keep_cache": 512
             }
         ]
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
             "arv": "http://arvados.org/cwl#",
         }
         expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
-                        '--no-log-timestamps', '--disable-validate',
-                        '--eval-timeout=20', '--thread-count=1',
+                        '--no-log-timestamps', '--disable-validate', '--disable-color',
+                        '--eval-timeout=20', '--thread-count=0',
                         '--enable-reuse', "--collection-cache-size=512", '--debug', '--on-error=continue',
                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
@@ -1186,6 +1062,7 @@ class TestSubmit(unittest.TestCase):
         arvrunner.project_uuid = ""
         api.return_value = mock.MagicMock()
         arvrunner.api = api.return_value
+        arvrunner.runtimeContext.match_local_docker = False
         arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
                                                                         "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
                                                                         "link_class": "docker_image_repo+tag",
@@ -1227,8 +1104,9 @@ class TestSubmit(unittest.TestCase):
                 "--api=containers",
                 "--no-log-timestamps",
                 "--disable-validate",
+                "--disable-color",
                 "--eval-timeout=20",
-                '--thread-count=1',
+                '--thread-count=0',
                 "--enable-reuse",
                 "--collection-cache-size=256",
                 '--debug',
@@ -1251,9 +1129,6 @@ class TestSubmit(unittest.TestCase):
                     "content": {
                         "$graph": [
                             {
-                                "$namespaces": {
-                                    "cwltool": "http://commonwl.org/cwltool#"
-                                },
                                 "arguments": [
                                     "md5sum",
                                     "example.conf"
@@ -1277,7 +1152,10 @@ class TestSubmit(unittest.TestCase):
                                 "outputs": [
                                     {
                                         "id": "#secret_job.cwl/out",
-                                        "type": "stdout"
+                                        "type": "File",
+                                        "outputBinding": {
+                                              "glob": "hashed_example.txt"
+                                        }
                                     }
                                 ],
                                 "stdout": "hashed_example.txt",
@@ -1298,7 +1176,7 @@ class TestSubmit(unittest.TestCase):
                                 "hints": [
                                     {
                                         "class": "DockerRequirement",
-                                        "dockerPull": "debian:8",
+                                        "dockerPull": "debian:buster-slim",
                                         "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
                                     },
                                     {
@@ -1339,6 +1217,9 @@ class TestSubmit(unittest.TestCase):
                                 ]
                             }
                         ],
+                        "$namespaces": {
+                            "cwltool": "http://commonwl.org/cwltool#"
+                        },
                         "cwlVersion": "v1.0"
                     },
                     "kind": "json"
@@ -1368,7 +1249,7 @@ class TestSubmit(unittest.TestCase):
                 }
             },
             "state": "Committed",
-            "use_existing": True
+            "use_existing": False
         }
 
         stubs.api.container_requests().create.assert_called_with(
@@ -1379,6 +1260,7 @@ class TestSubmit(unittest.TestCase):
 
     @stubs
     def test_submit_request_uuid(self, stubs):
+        stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
         stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
 
         stubs.api.container_requests().update().execute.return_value = {
@@ -1393,7 +1275,7 @@ class TestSubmit(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
         stubs.api.container_requests().update.assert_called_with(
-            uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec), cluster_id="zzzzz")
+            uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
         self.assertEqual(stubs.capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
@@ -1424,132 +1306,224 @@ class TestSubmit(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
         self.assertEqual(exited, 1)
 
-
-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'
+    def test_submit_validate_project_uuid(self, stubs):
+        # Fails with bad cluster prefix
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzb-j7d0g-zzzzzzzzzzzzzzz",
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+        self.assertEqual(exited, 1)
 
+        # Project lookup fails
+        stubs.api.groups().get().execute.side_effect = Exception("Bad project")
         exited = arvados_cwl.main(
-            ["--create-workflow", "--debug",
-             "--api=jobs",
-             "--project-uuid", project_uuid,
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-j7d0g-zzzzzzzzzzzzzzx",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+        self.assertEqual(exited, 1)
 
-        stubs.api.pipeline_instances().create.refute_called()
-        stubs.api.jobs().create.refute_called()
+        # It should work this time because it is looking up a user (and only group is stubbed out to fail)
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-tpzed-zzzzzzzzzzzzzzx",
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+        self.assertEqual(exited, 0)
 
-        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)
 
+    @mock.patch("arvados.collection.CollectionReader")
+    @stubs
+    def test_submit_uuid_inputs(self, stubs, collectionReader):
+        collectionReader().exists.return_value = True
+        collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
+        def list_side_effect(**kwargs):
+            m = mock.MagicMock()
+            if "count" in kwargs:
+                m.execute.return_value = {"items": [
+                    {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999998+99"}
+                ]}
+            else:
+                m.execute.return_value = {"items": []}
+            return m
+        stubs.api.collections().list.side_effect = list_side_effect
+
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
+        expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
+        expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
+
+        stubs.api.collections().list.assert_has_calls([
+            mock.call(count='none',
+                      filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz']]],
+                      select=['uuid', 'portable_data_hash'])])
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
         self.assertEqual(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_template_uuid + '\n')
+                         stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
     @stubs
-    def test_create_name(self, stubs):
-        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+    def test_submit_mismatched_uuid_inputs(self, stubs):
+        def list_side_effect(**kwargs):
+            m = mock.MagicMock()
+            if "count" in kwargs:
+                m.execute.return_value = {"items": [
+                    {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999997+99"}
+                ]}
+            else:
+                m.execute.return_value = {"items": []}
+            return m
+        stubs.api.collections().list.side_effect = list_side_effect
+
+        for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"):
+            capture_stderr = StringIO()
+            cwltool_logger = logging.getLogger('cwltool')
+            stderr_logger = logging.StreamHandler(capture_stderr)
+            cwltool_logger.addHandler(stderr_logger)
+
+            try:
+                exited = arvados_cwl.main(
+                    ["--submit", "--no-wait", "--api=containers", "--debug",
+                        "tests/wf/submit_wf.cwl", infile],
+                    stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+                self.assertEqual(exited, 1)
+                self.assertRegex(
+                    re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()),
+                    r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99")
+            finally:
+                cwltool_logger.removeHandler(stderr_logger)
+
+    @mock.patch("arvados.collection.CollectionReader")
+    @stubs
+    def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
+        collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
+        capture_stderr = StringIO()
+
+        cwltool_logger = logging.getLogger('cwltool')
+        stderr_logger = logging.StreamHandler(capture_stderr)
+        cwltool_logger.addHandler(stderr_logger)
 
         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"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
+            stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
-        stubs.api.pipeline_instances().create.refute_called()
-        stubs.api.jobs().create.refute_called()
+        try:
+            self.assertEqual(exited, 1)
+            self.assertRegex(
+                capture_stderr.getvalue(),
+                r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found")
+        finally:
+            cwltool_logger.removeHandler(stderr_logger)
 
-        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
+    def test_submit_set_process_properties(self, stubs):
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+                "tests/wf/submit_wf_process_properties.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["name"] = "submit_wf_process_properties.cwl"
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+            {
+                "class": "http://arvados.org/cwl#ProcessProperties",
+                "processProperties": [
+                    {"propertyName": "baz",
+                     "propertyValue": "$(inputs.x.basename)"},
+                    {"propertyName": "foo",
+                     "propertyValue": "bar"},
+                    {"propertyName": "quux",
+                     "propertyValue": {
+                         "q1": 1,
+                         "q2": 2
+                     }
+                    }
+                ],
+            }
+        ]
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
+            "arv": "http://arvados.org/cwl#"
+        }
+
+        expect_container["properties"] = {
+            "baz": "blorp.txt",
+            "foo": "bar",
+            "quux": {
+                "q1": 1,
+                "q2": 2
+            }
         }
-        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(stubs.capture_stdout.getvalue(),
-                         stubs.expect_pipeline_template_uuid + '\n')
+                         stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
-    def test_update_name(self, stubs):
-        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 
+    @stubs
+    def test_submit_enable_preemptible(self, stubs):
         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"],
-            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
-        stubs.api.pipeline_instances().create.refute_called()
-        stubs.api.jobs().create.refute_called()
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
+                        '--no-log-timestamps', '--disable-validate', '--disable-color',
+                        '--eval-timeout=20', '--thread-count=0',
+                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                                       '--enable-preemptible',
+                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
-        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)
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
+    @stubs
+    def test_submit_disable_preemptible(self, stubs):
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
+                        '--no-log-timestamps', '--disable-validate', '--disable-color',
+                        '--eval-timeout=20', '--thread-count=0',
+                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                                       '--disable-preemptible',
+                        '/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(stubs.capture_stdout.getvalue(),
-                         self.existing_template_uuid + '\n')
+                         stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
-        
+
 
 class TestCreateWorkflow(unittest.TestCase):
     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
     expect_workflow = StripYAMLComments(
-        open("tests/wf/expect_packed.cwl").read())
+        open("tests/wf/expect_upload_packed.cwl").read().rstrip())
+
+    def setUp(self):
+        cwltool.process._names = set()
+        arvados_cwl.arvdocker.arv_docker_clear_cache()
 
     @stubs
     def test_create(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
 
         exited = arvados_cwl.main(
             ["--create-workflow", "--debug",
@@ -1579,6 +1553,7 @@ class TestCreateWorkflow(unittest.TestCase):
     @stubs
     def test_create_name(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
 
         exited = arvados_cwl.main(
             ["--create-workflow", "--debug",
@@ -1606,24 +1581,6 @@ class TestCreateWorkflow(unittest.TestCase):
                          stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
-    def test_incompatible_api(self, stubs):
-        capture_stderr = io.StringIO()
-        acr_logger = logging.getLogger('arvados.cwl-runner')
-        stderr_logger = logging.StreamHandler(capture_stderr)
-        acr_logger.addHandler(stderr_logger)
-
-        exited = arvados_cwl.main(
-            ["--update-workflow", self.existing_workflow_uuid,
-             "--api=jobs",
-             "--debug",
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            sys.stderr, sys.stderr, api_client=stubs.api)
-        self.assertEqual(exited, 1)
-        self.assertRegexpMatches(
-            capture_stderr.getvalue(),
-            "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
-        acr_logger.removeHandler(stderr_logger)
 
     @stubs
     def test_update(self, stubs):
@@ -1672,6 +1629,7 @@ class TestCreateWorkflow(unittest.TestCase):
     @stubs
     def test_create_collection_per_tool(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
 
         exited = arvados_cwl.main(
             ["--create-workflow", "--debug",
@@ -1681,7 +1639,7 @@ class TestCreateWorkflow(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
         toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
-        expect_workflow = StripYAMLComments(open(toolfile).read())
+        expect_workflow = StripYAMLComments(open(toolfile).read().rstrip())
 
         body = {
             "workflow": {
@@ -1698,81 +1656,40 @@ class TestCreateWorkflow(unittest.TestCase):
                          stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-class TestTemplateInputs(unittest.TestCase):
-    expect_template = {
-        "components": {
-            "inputs_test.cwl": {
-                'runtime_constraints': {
-                    'docker_image': '999999999999999999999999999999d3+99',
-                    'min_ram_mb_per_node': 1024
-                },
-                'script_parameters': {
-                    'cwl:tool':
-                    'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main',
-                    'optionalFloatInput': None,
-                    'fileInput': {
-                        'type': 'File',
-                        'dataclass': 'File',
-                        'required': True,
-                        'title': "It's a file; we expect to find some characters in it.",
-                        'description': 'If there were anything further to say, it would be said here,\nor here.'
-                    },
-                    'floatInput': {
-                        'type': 'float',
-                        'dataclass': 'number',
-                        'required': True,
-                        'title': 'Floats like a duck',
-                        'default': 0.1,
-                        'value': 0.1,
-                    },
-                    'optionalFloatInput': {
-                        'type': ['null', 'float'],
-                        'dataclass': 'number',
-                        'required': False,
-                    },
-                    'boolInput': {
-                        'type': 'boolean',
-                        'dataclass': 'boolean',
-                        'required': True,
-                        'title': 'True or false?',
-                    },
-                },
-                'repository': 'arvados',
-                'script_version': 'master',
-                'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
-                'script': 'cwl-runner',
-            },
-        },
-        "name": "inputs_test.cwl",
-    }
-
     @stubs
-    def test_inputs_empty(self, stubs):
+    def test_create_with_imports(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
+
         exited = arvados_cwl.main(
-            ["--create-template",
-             "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
+            ["--create-workflow", "--debug",
+             "--api=containers",
+             "--project-uuid", project_uuid,
+             "tests/wf/feddemo/feddemo.cwl"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
-        stubs.api.pipeline_templates().create.assert_called_with(
-            body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
+        stubs.api.pipeline_templates().create.refute_called()
+        stubs.api.container_requests().create.refute_called()
 
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
     @stubs
-    def test_inputs(self, stubs):
+    def test_create_with_no_input(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
+
         exited = arvados_cwl.main(
-            ["--create-template",
-             "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
+            ["--create-workflow", "--debug",
+             "--api=containers",
+             "--project-uuid", project_uuid,
+             "tests/wf/revsort/revsort.cwl"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
-        expect_template = copy.deepcopy(self.expect_template)
-        params = expect_template[
-            "components"]["inputs_test.cwl"]["script_parameters"]
-        params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
-        params["cwl:tool"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main'
-        params["floatInput"]["value"] = 1.234
-        params["boolInput"]["value"] = True
+        stubs.api.pipeline_templates().create.refute_called()
+        stubs.api.container_requests().create.refute_called()
 
-        stubs.api.pipeline_templates().create.assert_called_with(
-            body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)