X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/70f1b69fe1f0567483afc182e47fe717756b8bd1..6599088b45103087b4be743fd51a8330e694e57f:/sdk/cwl/tests/test_submit.py?ds=sidebyside

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index f65a82bca6..14ae7b9f8f 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -1,43 +1,52 @@
-import arvados
-import arvados.keep
-import arvados.collection
-import arvados_cwl
 import copy
 import cStringIO
 import functools
 import hashlib
+import json
+import logging
 import mock
 import sys
 import unittest
-import json
-import logging
+
+import arvados
+import arvados.collection
+import arvados_cwl
+import arvados_cwl.runner
+import arvados.keep
 
 from .matcher import JsonDiffMatcher
+from .mock_discovery import get_rootDesc
 
+_rootDesc = None
 
 def stubs(func):
     @functools.wraps(func)
     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
     @mock.patch("arvados.collection.KeepClient")
+    @mock.patch("arvados.keep.KeepClient")
     @mock.patch("arvados.events.subscribe")
-    def wrapped(self, events, keep_client, keepdocker, *args, **kwargs):
+    def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs):
         class Stubs:
             pass
         stubs = Stubs()
         stubs.events = events
         stubs.keepdocker = keepdocker
-        stubs.keep_client = keep_client
+
 
         def putstub(p, **kwargs):
             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
-        stubs.keep_client().put.side_effect = putstub
-        stubs.keep_client.put.side_effect = putstub
+        keep_client1().put.side_effect = putstub
+        keep_client1.put.side_effect = putstub
+        keep_client2().put.side_effect = putstub
+        keep_client2.put.side_effect = putstub
 
+        stubs.keep_client = keep_client2
         stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
         stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
 
-
         stubs.api = mock.MagicMock()
+        stubs.api._rootDesc = get_rootDesc()
+
         stubs.api.users().current().execute.return_value = {
             "uuid": stubs.fake_user_uuid,
         }
@@ -89,7 +98,8 @@ def stubs(func):
         }
         stubs.expect_job_spec = {
             'runtime_constraints': {
-                'docker_image': 'arvados/jobs'
+                'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+                'min_ram_mb_per_node': 1024
             },
             'script_parameters': {
                 'x': {
@@ -116,27 +126,32 @@ def stubs(func):
             },
             'repository': 'arvados',
             'script_version': 'master',
+            'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
             'script': 'cwl-runner'
         }
         stubs.pipeline_component = stubs.expect_job_spec.copy()
         stubs.expect_pipeline_instance = {
             'name': 'submit_wf.cwl',
             'state': 'RunningOnServer',
+            'owner_uuid': None,
             "components": {
                 "cwl-runner": {
-                    'runtime_constraints': {'docker_image': 'arvados/jobs'},
+                    'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
                     'script_parameters': {
-                        'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
-                        'x': {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt'},
-                        'z': {'basename': 'anonymous', 'class': 'Directory',
+                        'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
+                        'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt'}},
+                        'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
                               'listing': [
                                   {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
-                              ]},
-                        'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl'
+                              ]}},
+                        'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl',
+                        'arv:enable_reuse': True
                     },
                     'repository': 'arvados',
                     'script_version': 'master',
-                    'script': 'cwl-runner'
+                    'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
+                    'script': 'cwl-runner',
+                    'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
                 }
             }
         }
@@ -166,29 +181,44 @@ def stubs(func):
                     '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:99999999999999999999999999999994+99/blorp.txt'},
+                        'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
+                            {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+                        ]}
+                    },
+                    'kind': 'json'
                 }
             },
             'state': 'Committed',
-            'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
-            'command': ['arvados-cwl-runner', '--local', '--api=containers', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
+            'owner_uuid': None,
+            'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'],
             'name': 'submit_wf.cwl',
-            'container_image': '99999999999999999999999999999993+99',
+            'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
             'output_path': '/var/spool/cwl',
             'cwd': '/var/spool/cwl',
             'runtime_constraints': {
                 'API': True,
                 'vcpus': 1,
-                'ram': 268435456
-            }
+                'ram': 1024*1024*1024
+            },
+            "properties": {}
         }
 
         stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
         stubs.api.workflows().create().execute.return_value = {
             "uuid": stubs.expect_workflow_uuid,
         }
+        def update_mock(**kwargs):
+            stubs.updated_uuid = kwargs.get('uuid')
+            return mock.DEFAULT
+        stubs.api.workflows().update.side_effect = update_mock
+        stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
+            "uuid": stubs.updated_uuid,
+        }
 
         return func(self, stubs, *args, **kwargs)
     return wrapped
@@ -212,13 +242,12 @@ class TestSubmit(unittest.TestCase):
                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
                 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
-                'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+                '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',
-                            'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
                             'replication_desired': None,
                             'name': 'New collection'
             }, ensure_unique_name=True),
@@ -226,18 +255,125 @@ class TestSubmit(unittest.TestCase):
             mock.call(body={
                 'manifest_text':
                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
-                'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+                'owner_uuid': None,
                 'name': '#',
             }, ensure_unique_name=True),
             mock.call().execute()])
 
         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
-        expect_pipeline["owner_uuid"] = stubs.fake_user_uuid
+        stubs.api.pipeline_instances().create.assert_called_with(
+            body=expect_pipeline)
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_pipeline_uuid + '\n')
+
+
+    @mock.patch("time.sleep")
+    @stubs
+    def test_submit_no_reuse(self, stubs, tm):
+        capture_stdout = cStringIO.StringIO()
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--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)
+        stubs.api.pipeline_instances().create.assert_called_with(
+            body=JsonDiffMatcher(expect_pipeline))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_pipeline_uuid + '\n')
+
+
+    @mock.patch("time.sleep")
+    @stubs
+    def test_submit_runner_ram(self, stubs, tm):
+        capture_stdout = cStringIO.StringIO()
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
+             "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"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
+
+        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')
+
+
+    @mock.patch("time.sleep")
+    @stubs
+    def test_submit_invalid_runner_ram(self, stubs, tm):
+        capture_stdout = cStringIO.StringIO()
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            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"
+
+        capture_stdout = cStringIO.StringIO()
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--debug", "--output-name", output_name,
+             "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:output_name"] = output_name
+
+        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')
+
+
+    @mock.patch("time.sleep")
+    @stubs
+    def test_submit_pipeline_name(self, stubs, tm):
+        capture_stdout = cStringIO.StringIO()
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--debug", "--name=hello job 123",
+             "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["name"] = "hello job 123"
+
+        expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
         stubs.api.pipeline_instances().create.assert_called_with(
             body=expect_pipeline)
         self.assertEqual(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"
+
+        capture_stdout = cStringIO.StringIO()
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
+             "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:output_tags"] = output_tags
+
+        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')
+
     @mock.patch("time.sleep")
     @stubs
     def test_submit_with_project_uuid(self, stubs, tm):
@@ -253,7 +389,7 @@ 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):
@@ -274,13 +410,12 @@ class TestSubmit(unittest.TestCase):
                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
                 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
-                'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+                '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',
-                            'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
                             'name': 'New collection',
                             'replication_desired': None,
             }, ensure_unique_name=True),
@@ -288,37 +423,335 @@ class TestSubmit(unittest.TestCase):
             mock.call(body={
                 'manifest_text':
                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
-                'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+                'owner_uuid': None,
                 'name': '#',
             }, ensure_unique_name=True),
             mock.call().execute()])
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
-        expect_container["owner_uuid"] = stubs.fake_user_uuid
         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_no_reuse(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
+                 "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', '--no-log-timestamps',
+                                                  '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
+
+        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')
 
-class TestCreateTemplate(unittest.TestCase):
     @stubs
-    def test_create(self, stubs):
-        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+    def test_submit_container_output_name(self, stubs):
+        output_name = "test_output_name"
 
         capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
+                 "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', '--no-log-timestamps',
+                                                  "--output-name="+output_name, '--enable-reuse',
+                                                  '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
+        stubs.expect_container_spec["output_name"] = output_name
+
+        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_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", "--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["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+                                                  "--output-tags="+output_tags, '--enable-reuse',
+                                                  '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
 
+        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_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("")
+
+        stubs.expect_container_spec["runtime_constraints"]["ram"] = 2048*1024*1024
+
+        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')
+
+    @mock.patch("arvados.collection.CollectionReader")
+    @mock.patch("time.sleep")
+    @stubs
+    def test_submit_file_keepref(self, stubs, tm, collectionReader):
+        capture_stdout = cStringIO.StringIO()
         exited = arvados_cwl.main(
-            ["--create-template", "--debug",
-             "--project-uuid", project_uuid,
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+             "tests/wf/submit_keepref_wf.cwl"],
             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)
+    @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(
+            ["--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)
+
+        expect_container = {
+            'priority': 1,
+            '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',
+            'owner_uuid': None,
+            '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',
+                        '--enable-reuse', '/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
+            },
+            "properties": {}
+        }
+
+        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("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': 1,
+            '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',
+                    'json': {
+                        'cwlVersion': 'v1.0',
+                        '$graph': [
+                            {
+                                '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'
+                            }, {
+                                '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': []
+                            }
+                        ]
+                    }
+                },
+                '/var/lib/cwl/cwl.input.json': {
+                    'content': {
+                        'x': 'XxX'
+                    },
+                    'kind': 'json'
+                }
+            }, 'state': 'Committed',
+            'owner_uuid': None,
+            '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',
+                        '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+            'cwd': '/var/spool/cwl',
+            'runtime_constraints': {
+                'API': True,
+                'vcpus': 1,
+                'ram': 1073741824
+            },
+            "properties": {
+                "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
+            }
+        }
+
+        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("")
+
+        stubs.expect_container_spec["name"] = "hello container 123"
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        stubs.api.container_requests().create.assert_called_with(
+            body=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"
+
+        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))
+
+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,
@@ -336,6 +769,26 @@ class TestCreateTemplate(unittest.TestCase):
             '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,
@@ -350,7 +803,80 @@ class TestCreateTemplate(unittest.TestCase):
                          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 = open("tests/wf/expect_packed.cwl").read()
+
     @stubs
     def test_create(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
@@ -359,6 +885,7 @@ class TestCreateWorkflow(unittest.TestCase):
 
         exited = arvados_cwl.main(
             ["--create-workflow", "--debug",
+             "--api=containers",
              "--project-uuid", project_uuid,
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             capture_stdout, sys.stderr, api_client=stubs.api)
@@ -367,16 +894,13 @@ class TestCreateWorkflow(unittest.TestCase):
         stubs.api.pipeline_templates().create.refute_called()
         stubs.api.container_requests().create.refute_called()
 
-        with open("tests/wf/expect_packed.cwl") as f:
-            expect_workflow = f.read()
-
         body = {
             "workflow": {
                 "owner_uuid": project_uuid,
                 "name": "submit_wf.cwl",
                 "description": "",
-                "definition": expect_workflow
-                }
+                "definition": self.expect_workflow,
+            }
         }
         stubs.api.workflows().create.assert_called_with(
             body=JsonDiffMatcher(body))
@@ -385,12 +909,112 @@ class TestCreateWorkflow(unittest.TestCase):
                          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()
+        logging.getLogger('arvados.cwl-runner').addHandler(
+            logging.StreamHandler(capture_stderr))
+
+        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))
+
+    @stubs
+    def test_update(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--update-workflow", self.existing_workflow_uuid,
+             "--debug",
+             "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": "submit_wf.cwl",
+                "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_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')
+
+
 class TestTemplateInputs(unittest.TestCase):
     expect_template = {
         "components": {
             "inputs_test.cwl": {
                 'runtime_constraints': {
-                    'docker_image': 'arvados/jobs',
+                    'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+                    'min_ram_mb_per_node': 1024
                 },
                 'script_parameters': {
                     'cwl:tool':
@@ -426,6 +1050,7 @@ class TestTemplateInputs(unittest.TestCase):
                 },
                 'repository': 'arvados',
                 'script_version': 'master',
+                'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
                 'script': 'cwl-runner',
             },
         },
@@ -435,29 +1060,23 @@ 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)
 
-        expect_template = copy.deepcopy(self.expect_template)
-        expect_template["owner_uuid"] = stubs.fake_user_uuid
-
         stubs.api.pipeline_templates().create.assert_called_with(
-            body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+            body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
 
     @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)
 
-        self.expect_template["owner_uuid"] = stubs.fake_user_uuid
-
         expect_template = copy.deepcopy(self.expect_template)
-        expect_template["owner_uuid"] = stubs.fake_user_uuid
         params = expect_template[
             "components"]["inputs_test.cwl"]["script_parameters"]
         params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'