sdk/cwl/tests/test_submit.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 import copy
   6 import cStringIO
   7 import functools
   8 import hashlib
   9 import json
  10 import logging
  11 import mock
  12 import sys
  13 import unittest
  14
  15 import arvados
  16 import arvados.collection
  17 import arvados_cwl
  18 import arvados_cwl.runner
  19 import arvados.keep
  20
  21 from .matcher import JsonDiffMatcher, StripYAMLComments
  22 from .mock_discovery import get_rootDesc
  23
  24 import ruamel.yaml as yaml
  25
  26 _rootDesc = None
  27
  28 def stubs(func):
  29     @functools.wraps(func)
  30     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  31     @mock.patch("arvados.collection.KeepClient")
  32     @mock.patch("arvados.keep.KeepClient")
  33     @mock.patch("arvados.events.subscribe")
  34     def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs):
  35         class Stubs:
  36             pass
  37         stubs = Stubs()
  38         stubs.events = events
  39         stubs.keepdocker = keepdocker
  40
  41         def putstub(p, **kwargs):
  42             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
  43         keep_client1().put.side_effect = putstub
  44         keep_client1.put.side_effect = putstub
  45         keep_client2().put.side_effect = putstub
  46         keep_client2.put.side_effect = putstub
  47
  48         stubs.keep_client = keep_client2
  49         stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  50         stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
  51
  52         stubs.api = mock.MagicMock()
  53         stubs.api._rootDesc = get_rootDesc()
  54
  55         stubs.api.users().current().execute.return_value = {
  56             "uuid": stubs.fake_user_uuid,
  57         }
  58         stubs.api.collections().list().execute.return_value = {"items": []}
  59
  60         class CollectionExecute(object):
  61             def __init__(self, exe):
  62                 self.exe = exe
  63             def execute(self, num_retries=None):
  64                 return self.exe
  65
  66         def collection_createstub(created_collections, body, ensure_unique_name=None):
  67             mt = body["manifest_text"]
  68             uuid = "zzzzz-4zz18-zzzzzzzzzzzzzz%d" % len(created_collections)
  69             pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
  70             created_collections[uuid] = {
  71                 "uuid": uuid,
  72                 "portable_data_hash": pdh,
  73                 "manifest_text": mt
  74             }
  75             return CollectionExecute(created_collections[uuid])
  76
  77         def collection_getstub(created_collections, uuid):
  78             for v in created_collections.itervalues():
  79                 if uuid in (v["uuid"], v["portable_data_hash"]):
  80                     return CollectionExecute(v)
  81
  82         created_collections = {
  83             "99999999999999999999999999999998+99": {
  84                 "uuid": "",
  85                 "portable_data_hash": "99999999999999999999999999999998+99",
  86                 "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
  87             }}
  88         stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
  89         stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
  90
  91         stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  92         stubs.api.jobs().create().execute.return_value = {
  93             "uuid": stubs.expect_job_uuid,
  94             "state": "Queued",
  95         }
  96
  97         stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
  98         stubs.api.container_requests().create().execute.return_value = {
  99             "uuid": stubs.expect_container_request_uuid,
 100             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
 101             "state": "Queued"
 102         }
 103
 104         stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
 105         stubs.api.pipeline_templates().create().execute.return_value = {
 106             "uuid": stubs.expect_pipeline_template_uuid,
 107         }
 108         stubs.expect_job_spec = {
 109             'runtime_constraints': {
 110                 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
 111                 'min_ram_mb_per_node': 1024
 112             },
 113             'script_parameters': {
 114                 'x': {
 115                     'basename': 'blorp.txt',
 116                     'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 117                     'class': 'File'
 118                 },
 119                 'y': {
 120                     'basename': '99999999999999999999999999999998+99',
 121                     'location': 'keep:99999999999999999999999999999998+99',
 122                     'class': 'Directory'
 123                 },
 124                 'z': {
 125                     'basename': 'anonymous',
 126                     "listing": [{
 127                         "basename": "renamed.txt",
 128                         "class": "File",
 129                         "location": "keep:99999999999999999999999999999998+99/file1.txt"
 130                     }],
 131                     'class': 'Directory'
 132                 },
 133                 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main'
 134             },
 135             'repository': 'arvados',
 136             'script_version': 'master',
 137             'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
 138             'script': 'cwl-runner'
 139         }
 140         stubs.pipeline_component = stubs.expect_job_spec.copy()
 141         stubs.expect_pipeline_instance = {
 142             'name': 'submit_wf.cwl',
 143             'state': 'RunningOnServer',
 144             'owner_uuid': None,
 145             "components": {
 146                 "cwl-runner": {
 147                     'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
 148                     'script_parameters': {
 149                         'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
 150                         'x': {"value": {
 151                             'basename': 'blorp.txt',
 152                             'class': 'File',
 153                             'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 154                             "nameext": ".txt",
 155                             "nameroot": "blorp"
 156                         }},
 157                         'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
 158                               'listing': [
 159                                   {
 160                                       'basename': 'renamed.txt',
 161                                       'class': 'File', 'location':
 162                                       'keep:99999999999999999999999999999998+99/file1.txt',
 163                                       "nameext": ".txt",
 164                                       "nameroot": "renamed"
 165                                   }
 166                               ]}},
 167                         'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
 168                         'arv:enable_reuse': True,
 169                         'arv:on_error': 'continue'
 170                     },
 171                     'repository': 'arvados',
 172                     'script_version': 'master',
 173                     'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
 174                     'script': 'cwl-runner',
 175                     'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
 176                 }
 177             }
 178         }
 179         stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
 180         stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
 181         stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
 182         stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
 183         stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
 184             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 185             "state": "Queued"
 186         }
 187         stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
 188         stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
 189
 190         with open("tests/wf/submit_wf_packed.cwl") as f:
 191             expect_packed_workflow = yaml.round_trip_load(f)
 192
 193         stubs.expect_container_spec = {
 194             'priority': 1,
 195             'mounts': {
 196                 '/var/spool/cwl': {
 197                     'writable': True,
 198                     'kind': 'collection'
 199                 },
 200                 '/var/lib/cwl/workflow.json': {
 201                     'content': expect_packed_workflow,
 202                     'kind': 'json'
 203                 },
 204                 'stdout': {
 205                     'path': '/var/spool/cwl/cwl.output.json',
 206                     'kind': 'file'
 207                 },
 208                 '/var/lib/cwl/cwl.input.json': {
 209                     'kind': 'json',
 210                     'content': {
 211                         'y': {
 212                             'basename': '99999999999999999999999999999998+99',
 213                             'location': 'keep:99999999999999999999999999999998+99',
 214                             'class': 'Directory'},
 215                         'x': {
 216                             'basename': u'blorp.txt',
 217                             'class': 'File',
 218                             'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 219                             "nameext": ".txt",
 220                             "nameroot": "blorp"
 221                         },
 222                         'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
 223                             {'basename': 'renamed.txt',
 224                              'class': 'File',
 225                              'location': 'keep:99999999999999999999999999999998+99/file1.txt',
 226                              "nameext": ".txt",
 227                              "nameroot": "renamed"
 228                             }
 229                         ]}
 230                     },
 231                     'kind': 'json'
 232                 }
 233             },
 234             'state': 'Committed',
 235             'owner_uuid': None,
 236             'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
 237                         '--enable-reuse', '--on-error=continue',
 238                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
 239             'name': 'submit_wf.cwl',
 240             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
 241             'output_path': '/var/spool/cwl',
 242             'cwd': '/var/spool/cwl',
 243             'runtime_constraints': {
 244                 'API': True,
 245                 'vcpus': 1,
 246                 'ram': 1024*1024*1024
 247             },
 248             "properties": {}
 249         }
 250
 251         stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
 252         stubs.api.workflows().create().execute.return_value = {
 253             "uuid": stubs.expect_workflow_uuid,
 254         }
 255         def update_mock(**kwargs):
 256             stubs.updated_uuid = kwargs.get('uuid')
 257             return mock.DEFAULT
 258         stubs.api.workflows().update.side_effect = update_mock
 259         stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
 260             "uuid": stubs.updated_uuid,
 261         }
 262
 263         return func(self, stubs, *args, **kwargs)
 264     return wrapped
 265
 266
 267 class TestSubmit(unittest.TestCase):
 268     @mock.patch("arvados_cwl.runner.arv_docker_get_image")
 269     @mock.patch("time.sleep")
 270     @stubs
 271     def test_submit(self, stubs, tm, arvdock):
 272         capture_stdout = cStringIO.StringIO()
 273         exited = arvados_cwl.main(
 274             ["--submit", "--no-wait", "--api=jobs", "--debug",
 275              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 276             capture_stdout, sys.stderr, api_client=stubs.api)
 277         self.assertEqual(exited, 0)
 278
 279         stubs.api.collections().create.assert_has_calls([
 280             mock.call(body=JsonDiffMatcher({
 281                 'manifest_text':
 282                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
 283                 'replication_desired': None,
 284                 'name': 'submit_tool.cwl dependencies',
 285             }), ensure_unique_name=True),
 286             mock.call(body=JsonDiffMatcher({
 287                 'manifest_text':
 288                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 289                 'replication_desired': None,
 290                 'name': 'submit_wf.cwl input',
 291             }), ensure_unique_name=True),
 292             mock.call(body=JsonDiffMatcher({
 293                 'manifest_text':
 294                 '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n',
 295                 'replication_desired': None,
 296                 'name': 'submit_wf.cwl',
 297             }), ensure_unique_name=True)        ])
 298
 299         arvdock.assert_has_calls([
 300             mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
 301             mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
 302         ])
 303
 304         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 305         stubs.api.pipeline_instances().create.assert_called_with(
 306             body=JsonDiffMatcher(expect_pipeline))
 307         self.assertEqual(capture_stdout.getvalue(),
 308                          stubs.expect_pipeline_uuid + '\n')
 309
 310
 311     @mock.patch("time.sleep")
 312     @stubs
 313     def test_submit_no_reuse(self, stubs, tm):
 314         capture_stdout = cStringIO.StringIO()
 315         exited = arvados_cwl.main(
 316             ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
 317              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 318             capture_stdout, sys.stderr, api_client=stubs.api)
 319         self.assertEqual(exited, 0)
 320
 321         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 322         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
 323
 324         stubs.api.pipeline_instances().create.assert_called_with(
 325             body=JsonDiffMatcher(expect_pipeline))
 326         self.assertEqual(capture_stdout.getvalue(),
 327                          stubs.expect_pipeline_uuid + '\n')
 328
 329     @mock.patch("time.sleep")
 330     @stubs
 331     def test_submit_on_error(self, stubs, tm):
 332         capture_stdout = cStringIO.StringIO()
 333         exited = arvados_cwl.main(
 334             ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
 335              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 336             capture_stdout, sys.stderr, api_client=stubs.api)
 337         self.assertEqual(exited, 0)
 338
 339         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 340         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
 341
 342         stubs.api.pipeline_instances().create.assert_called_with(
 343             body=JsonDiffMatcher(expect_pipeline))
 344         self.assertEqual(capture_stdout.getvalue(),
 345                          stubs.expect_pipeline_uuid + '\n')
 346
 347
 348     @mock.patch("time.sleep")
 349     @stubs
 350     def test_submit_runner_ram(self, stubs, tm):
 351         capture_stdout = cStringIO.StringIO()
 352         exited = arvados_cwl.main(
 353             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
 354              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 355             capture_stdout, sys.stderr, api_client=stubs.api)
 356         self.assertEqual(exited, 0)
 357
 358         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 359         expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
 360
 361         stubs.api.pipeline_instances().create.assert_called_with(
 362             body=JsonDiffMatcher(expect_pipeline))
 363         self.assertEqual(capture_stdout.getvalue(),
 364                          stubs.expect_pipeline_uuid + '\n')
 365
 366
 367     @mock.patch("time.sleep")
 368     @stubs
 369     def test_submit_invalid_runner_ram(self, stubs, tm):
 370         capture_stdout = cStringIO.StringIO()
 371         exited = arvados_cwl.main(
 372             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
 373              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 374             capture_stdout, sys.stderr, api_client=stubs.api)
 375         self.assertEqual(exited, 1)
 376
 377     @mock.patch("time.sleep")
 378     @stubs
 379     def test_submit_output_name(self, stubs, tm):
 380         output_name = "test_output_name"
 381
 382         capture_stdout = cStringIO.StringIO()
 383         exited = arvados_cwl.main(
 384             ["--submit", "--no-wait", "--debug", "--output-name", output_name,
 385              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 386             capture_stdout, sys.stderr, api_client=stubs.api)
 387         self.assertEqual(exited, 0)
 388
 389         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 390         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
 391
 392         stubs.api.pipeline_instances().create.assert_called_with(
 393             body=JsonDiffMatcher(expect_pipeline))
 394         self.assertEqual(capture_stdout.getvalue(),
 395                          stubs.expect_pipeline_uuid + '\n')
 396
 397
 398     @mock.patch("time.sleep")
 399     @stubs
 400     def test_submit_pipeline_name(self, stubs, tm):
 401         capture_stdout = cStringIO.StringIO()
 402         exited = arvados_cwl.main(
 403             ["--submit", "--no-wait", "--debug", "--name=hello job 123",
 404              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 405             capture_stdout, sys.stderr, api_client=stubs.api)
 406         self.assertEqual(exited, 0)
 407
 408         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 409         expect_pipeline["name"] = "hello job 123"
 410
 411         stubs.api.pipeline_instances().create.assert_called_with(
 412             body=JsonDiffMatcher(expect_pipeline))
 413         self.assertEqual(capture_stdout.getvalue(),
 414                          stubs.expect_pipeline_uuid + '\n')
 415
 416     @mock.patch("time.sleep")
 417     @stubs
 418     def test_submit_output_tags(self, stubs, tm):
 419         output_tags = "tag0,tag1,tag2"
 420
 421         capture_stdout = cStringIO.StringIO()
 422         exited = arvados_cwl.main(
 423             ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
 424              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 425             capture_stdout, sys.stderr, api_client=stubs.api)
 426         self.assertEqual(exited, 0)
 427
 428         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 429         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
 430
 431         stubs.api.pipeline_instances().create.assert_called_with(
 432             body=JsonDiffMatcher(expect_pipeline))
 433         self.assertEqual(capture_stdout.getvalue(),
 434                          stubs.expect_pipeline_uuid + '\n')
 435
 436     @mock.patch("time.sleep")
 437     @stubs
 438     def test_submit_with_project_uuid(self, stubs, tm):
 439         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 440
 441         exited = arvados_cwl.main(
 442             ["--submit", "--no-wait",
 443              "--project-uuid", project_uuid,
 444              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 445             sys.stdout, sys.stderr, api_client=stubs.api)
 446         self.assertEqual(exited, 0)
 447
 448         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 449         expect_pipeline["owner_uuid"] = project_uuid
 450         stubs.api.pipeline_instances().create.assert_called_with(
 451             body=JsonDiffMatcher(expect_pipeline))
 452
 453     @stubs
 454     def test_submit_container(self, stubs):
 455         capture_stdout = cStringIO.StringIO()
 456         try:
 457             exited = arvados_cwl.main(
 458                 ["--submit", "--no-wait", "--api=containers", "--debug",
 459                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 460                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 461             self.assertEqual(exited, 0)
 462         except:
 463             logging.exception("")
 464
 465         stubs.api.collections().create.assert_has_calls([
 466             mock.call(body=JsonDiffMatcher({
 467                 'manifest_text':
 468                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
 469                 'replication_desired': None,
 470                 'name': 'submit_tool.cwl dependencies',
 471             }), ensure_unique_name=True),
 472             mock.call(body=JsonDiffMatcher({
 473                 'manifest_text':
 474                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 475                 'replication_desired': None,
 476                 'name': 'submit_wf.cwl input',
 477             }), ensure_unique_name=True)])
 478
 479         expect_container = copy.deepcopy(stubs.expect_container_spec)
 480         stubs.api.container_requests().create.assert_called_with(
 481             body=JsonDiffMatcher(expect_container))
 482         self.assertEqual(capture_stdout.getvalue(),
 483                          stubs.expect_container_request_uuid + '\n')
 484
 485     @stubs
 486     def test_submit_container_no_reuse(self, stubs):
 487         capture_stdout = cStringIO.StringIO()
 488         try:
 489             exited = arvados_cwl.main(
 490                 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
 491                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 492                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 493             self.assertEqual(exited, 0)
 494         except:
 495             logging.exception("")
 496
 497         expect_container = copy.deepcopy(stubs.expect_container_spec)
 498         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
 499                                                   '--disable-reuse', '--on-error=continue',
 500                                                   '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 501
 502         stubs.api.container_requests().create.assert_called_with(
 503             body=JsonDiffMatcher(expect_container))
 504         self.assertEqual(capture_stdout.getvalue(),
 505                          stubs.expect_container_request_uuid + '\n')
 506
 507
 508     @stubs
 509     def test_submit_container_on_error(self, stubs):
 510         capture_stdout = cStringIO.StringIO()
 511         try:
 512             exited = arvados_cwl.main(
 513                 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
 514                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 515                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 516             self.assertEqual(exited, 0)
 517         except:
 518             logging.exception("")
 519
 520         expect_container = copy.deepcopy(stubs.expect_container_spec)
 521         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
 522                                                   '--enable-reuse', '--on-error=stop',
 523                                                   '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 524
 525         stubs.api.container_requests().create.assert_called_with(
 526             body=JsonDiffMatcher(expect_container))
 527         self.assertEqual(capture_stdout.getvalue(),
 528                          stubs.expect_container_request_uuid + '\n')
 529
 530     @stubs
 531     def test_submit_container_output_name(self, stubs):
 532         output_name = "test_output_name"
 533
 534         capture_stdout = cStringIO.StringIO()
 535         try:
 536             exited = arvados_cwl.main(
 537                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
 538                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 539                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 540             self.assertEqual(exited, 0)
 541         except:
 542             logging.exception("")
 543
 544         expect_container = copy.deepcopy(stubs.expect_container_spec)
 545         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
 546                                                   "--output-name="+output_name, '--enable-reuse', '--on-error=continue',
 547                                                   '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 548         expect_container["output_name"] = output_name
 549
 550         stubs.api.container_requests().create.assert_called_with(
 551             body=JsonDiffMatcher(expect_container))
 552         self.assertEqual(capture_stdout.getvalue(),
 553                          stubs.expect_container_request_uuid + '\n')
 554
 555
 556     @stubs
 557     def test_submit_container_output_ttl(self, stubs):
 558         capture_stdout = cStringIO.StringIO()
 559         try:
 560             exited = arvados_cwl.main(
 561                 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
 562                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 563                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 564             self.assertEqual(exited, 0)
 565         except:
 566             logging.exception("")
 567
 568         expect_container = copy.deepcopy(stubs.expect_container_spec)
 569         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
 570                                        '--enable-reuse', '--on-error=continue',
 571                                        "--intermediate-output-ttl=3600",
 572                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 573
 574         stubs.api.container_requests().create.assert_called_with(
 575             body=JsonDiffMatcher(expect_container))
 576         self.assertEqual(capture_stdout.getvalue(),
 577                          stubs.expect_container_request_uuid + '\n')
 578
 579     @stubs
 580     def test_submit_container_trash_intermediate(self, stubs):
 581         capture_stdout = cStringIO.StringIO()
 582         try:
 583             exited = arvados_cwl.main(
 584                 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
 585                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 586                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 587             self.assertEqual(exited, 0)
 588         except:
 589             logging.exception("")
 590
 591         expect_container = copy.deepcopy(stubs.expect_container_spec)
 592         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
 593                                        '--enable-reuse', '--on-error=continue',
 594                                        "--trash-intermediate",
 595                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 596
 597         stubs.api.container_requests().create.assert_called_with(
 598             body=JsonDiffMatcher(expect_container))
 599         self.assertEqual(capture_stdout.getvalue(),
 600                          stubs.expect_container_request_uuid + '\n')
 601
 602     @stubs
 603     def test_submit_container_output_tags(self, stubs):
 604         output_tags = "tag0,tag1,tag2"
 605
 606         capture_stdout = cStringIO.StringIO()
 607         try:
 608             exited = arvados_cwl.main(
 609                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
 610                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 611                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 612             self.assertEqual(exited, 0)
 613         except:
 614             logging.exception("")
 615
 616         expect_container = copy.deepcopy(stubs.expect_container_spec)
 617         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
 618                                                   "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue',
 619                                                   '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 620
 621         stubs.api.container_requests().create.assert_called_with(
 622             body=JsonDiffMatcher(expect_container))
 623         self.assertEqual(capture_stdout.getvalue(),
 624                          stubs.expect_container_request_uuid + '\n')
 625
 626     @stubs
 627     def test_submit_container_runner_ram(self, stubs):
 628         capture_stdout = cStringIO.StringIO()
 629         try:
 630             exited = arvados_cwl.main(
 631                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
 632                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 633                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 634             self.assertEqual(exited, 0)
 635         except:
 636             logging.exception("")
 637
 638         expect_container = copy.deepcopy(stubs.expect_container_spec)
 639         expect_container["runtime_constraints"]["ram"] = 2048*1024*1024
 640
 641         stubs.api.container_requests().create.assert_called_with(
 642             body=JsonDiffMatcher(expect_container))
 643         self.assertEqual(capture_stdout.getvalue(),
 644                          stubs.expect_container_request_uuid + '\n')
 645
 646     @mock.patch("arvados.collection.CollectionReader")
 647     @mock.patch("time.sleep")
 648     @stubs
 649     def test_submit_file_keepref(self, stubs, tm, collectionReader):
 650         capture_stdout = cStringIO.StringIO()
 651         exited = arvados_cwl.main(
 652             ["--submit", "--no-wait", "--api=containers", "--debug",
 653              "tests/wf/submit_keepref_wf.cwl"],
 654             capture_stdout, sys.stderr, api_client=stubs.api)
 655         self.assertEqual(exited, 0)
 656
 657
 658     @mock.patch("arvados.collection.CollectionReader")
 659     @mock.patch("time.sleep")
 660     @stubs
 661     def test_submit_keepref(self, stubs, tm, reader):
 662         capture_stdout = cStringIO.StringIO()
 663
 664         with open("tests/wf/expect_arvworkflow.cwl") as f:
 665             reader().open().__enter__().read.return_value = f.read()
 666
 667         exited = arvados_cwl.main(
 668             ["--submit", "--no-wait", "--api=containers", "--debug",
 669              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 670             capture_stdout, sys.stderr, api_client=stubs.api)
 671         self.assertEqual(exited, 0)
 672
 673         expect_container = {
 674             'priority': 1,
 675             'mounts': {
 676                 '/var/spool/cwl': {
 677                     'writable': True,
 678                     'kind': 'collection'
 679                 },
 680                 'stdout': {
 681                     'path': '/var/spool/cwl/cwl.output.json',
 682                     'kind': 'file'
 683                 },
 684                 '/var/lib/cwl/workflow': {
 685                     'portable_data_hash': '99999999999999999999999999999994+99',
 686                     'kind': 'collection'
 687                 },
 688                 '/var/lib/cwl/cwl.input.json': {
 689                     'content': {
 690                         'x': 'XxX'
 691                     },
 692                     'kind': 'json'
 693                 }
 694             }, 'state': 'Committed',
 695             'owner_uuid': None,
 696             'output_path': '/var/spool/cwl',
 697             'name': 'expect_arvworkflow.cwl#main',
 698             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
 699             'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
 700                         '--enable-reuse', '--on-error=continue',
 701                         '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
 702             'cwd': '/var/spool/cwl',
 703             'runtime_constraints': {
 704                 'API': True,
 705                 'vcpus': 1,
 706                 'ram': 1073741824
 707             },
 708             "properties": {}
 709         }
 710
 711         stubs.api.container_requests().create.assert_called_with(
 712             body=JsonDiffMatcher(expect_container))
 713         self.assertEqual(capture_stdout.getvalue(),
 714                          stubs.expect_container_request_uuid + '\n')
 715
 716
 717     @mock.patch("arvados.collection.CollectionReader")
 718     @mock.patch("time.sleep")
 719     @stubs
 720     def test_submit_jobs_keepref(self, stubs, tm, reader):
 721         capture_stdout = cStringIO.StringIO()
 722
 723         with open("tests/wf/expect_arvworkflow.cwl") as f:
 724             reader().open().__enter__().read.return_value = f.read()
 725
 726         exited = arvados_cwl.main(
 727             ["--submit", "--no-wait", "--api=jobs", "--debug",
 728              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 729             capture_stdout, sys.stderr, api_client=stubs.api)
 730         self.assertEqual(exited, 0)
 731
 732         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 733         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
 734         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
 735         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
 736         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
 737         expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
 738         stubs.api.pipeline_instances().create.assert_called_with(
 739             body=JsonDiffMatcher(expect_pipeline))
 740
 741     @mock.patch("time.sleep")
 742     @stubs
 743     def test_submit_arvworkflow(self, stubs, tm):
 744         capture_stdout = cStringIO.StringIO()
 745
 746         with open("tests/wf/expect_arvworkflow.cwl") as f:
 747             stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
 748
 749         exited = arvados_cwl.main(
 750             ["--submit", "--no-wait", "--api=containers", "--debug",
 751              "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
 752             capture_stdout, sys.stderr, api_client=stubs.api)
 753         self.assertEqual(exited, 0)
 754
 755         expect_container = {
 756             'priority': 1,
 757             'mounts': {
 758                 '/var/spool/cwl': {
 759                     'writable': True,
 760                     'kind': 'collection'
 761                 },
 762                 'stdout': {
 763                     'path': '/var/spool/cwl/cwl.output.json',
 764                     'kind': 'file'
 765                 },
 766                 '/var/lib/cwl/workflow.json': {
 767                     'kind': 'json',
 768                     'content': {
 769                         'cwlVersion': 'v1.0',
 770                         '$graph': [
 771                             {
 772                                 'id': '#main',
 773                                 'inputs': [
 774                                     {'type': 'string', 'id': '#main/x'}
 775                                 ],
 776                                 'steps': [
 777                                     {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
 778                                      'run': '#submit_tool.cwl',
 779                                      'id': '#main/step1',
 780                                      'out': []}
 781                                 ],
 782                                 'class': 'Workflow',
 783                                 'outputs': []
 784                             },
 785                             {
 786                                 'inputs': [
 787                                     {
 788                                         'inputBinding': {'position': 1},
 789                                         'type': 'string',
 790                                         'id': '#submit_tool.cwl/x'}
 791                                 ],
 792                                 'requirements': [
 793                                     {'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
 794                                 ],
 795                                 'id': '#submit_tool.cwl',
 796                                 'outputs': [],
 797                                 'baseCommand': 'cat',
 798                                 'class': 'CommandLineTool'
 799                             }
 800                         ]
 801                     }
 802                 },
 803                 '/var/lib/cwl/cwl.input.json': {
 804                     'content': {
 805                         'x': 'XxX'
 806                     },
 807                     'kind': 'json'
 808                 }
 809             }, 'state': 'Committed',
 810             'owner_uuid': None,
 811             'output_path': '/var/spool/cwl',
 812             'name': 'a test workflow',
 813             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
 814             'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
 815                         '--enable-reuse', '--on-error=continue',
 816                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
 817             'cwd': '/var/spool/cwl',
 818             'runtime_constraints': {
 819                 'API': True,
 820                 'vcpus': 1,
 821                 'ram': 1073741824
 822             },
 823             "properties": {
 824                 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
 825             }
 826         }
 827
 828         stubs.api.container_requests().create.assert_called_with(
 829             body=JsonDiffMatcher(expect_container))
 830         self.assertEqual(capture_stdout.getvalue(),
 831                          stubs.expect_container_request_uuid + '\n')
 832
 833
 834     @stubs
 835     def test_submit_container_name(self, stubs):
 836         capture_stdout = cStringIO.StringIO()
 837         try:
 838             exited = arvados_cwl.main(
 839                 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
 840                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 841                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 842             self.assertEqual(exited, 0)
 843         except:
 844             logging.exception("")
 845
 846         expect_container = copy.deepcopy(stubs.expect_container_spec)
 847         expect_container["name"] = "hello container 123"
 848
 849         stubs.api.container_requests().create.assert_called_with(
 850             body=JsonDiffMatcher(expect_container))
 851         self.assertEqual(capture_stdout.getvalue(),
 852                          stubs.expect_container_request_uuid + '\n')
 853
 854
 855     @stubs
 856     def test_submit_job_runner_image(self, stubs):
 857         capture_stdout = cStringIO.StringIO()
 858         try:
 859             exited = arvados_cwl.main(
 860                 ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
 861                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 862                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 863             self.assertEqual(exited, 0)
 864         except:
 865             logging.exception("")
 866
 867         stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
 868
 869         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 870         stubs.api.pipeline_instances().create.assert_called_with(
 871             body=JsonDiffMatcher(expect_pipeline))
 872         self.assertEqual(capture_stdout.getvalue(),
 873                          stubs.expect_pipeline_uuid + '\n')
 874
 875     @stubs
 876     def test_submit_container_runner_image(self, stubs):
 877         capture_stdout = cStringIO.StringIO()
 878         try:
 879             exited = arvados_cwl.main(
 880                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
 881                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 882                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 883             self.assertEqual(exited, 0)
 884         except:
 885             logging.exception("")
 886
 887         stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
 888
 889         expect_container = copy.deepcopy(stubs.expect_container_spec)
 890         stubs.api.container_requests().create.assert_called_with(
 891             body=JsonDiffMatcher(expect_container))
 892         self.assertEqual(capture_stdout.getvalue(),
 893                          stubs.expect_container_request_uuid + '\n')
 894
 895
 896     @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
 897     @mock.patch("cwltool.docker.get_image")
 898     @mock.patch("arvados.api")
 899     def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
 900         arvrunner = mock.MagicMock()
 901         arvrunner.project_uuid = ""
 902         api.return_value = mock.MagicMock()
 903         arvrunner.api = api.return_value
 904         arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
 905                                                                         "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
 906                                                                         "link_class": "docker_image_repo+tag",
 907                                                                         "name": "arvados/jobs:"+arvados_cwl.__version__,
 908                                                                         "owner_uuid": "",
 909                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
 910                                                             {"items": [{"created_at": "",
 911                                                                         "head_uuid": "",
 912                                                                         "link_class": "docker_image_hash",
 913                                                                         "name": "123456",
 914                                                                         "owner_uuid": "",
 915                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
 916         )
 917         find_one_image_hash.return_value = "123456"
 918
 919         arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
 920                                                                               "owner_uuid": "",
 921                                                                               "manifest_text": "",
 922                                                                               "properties": ""
 923                                                                           }], "items_available": 1, "offset": 0},)
 924         arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
 925         self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
 926                          arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
 927
 928 class TestCreateTemplate(unittest.TestCase):
 929     existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
 930
 931     def _adjust_script_params(self, expect_component):
 932         expect_component['script_parameters']['x'] = {
 933             'dataclass': 'File',
 934             'required': True,
 935             'type': 'File',
 936             'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 937         }
 938         expect_component['script_parameters']['y'] = {
 939             'dataclass': 'Collection',
 940             'required': True,
 941             'type': 'Directory',
 942             'value': '99999999999999999999999999999998+99',
 943         }
 944         expect_component['script_parameters']['z'] = {
 945             'dataclass': 'Collection',
 946             'required': True,
 947             'type': 'Directory',
 948         }
 949
 950     @stubs
 951     def test_create(self, stubs):
 952         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 953
 954         capture_stdout = cStringIO.StringIO()
 955
 956         exited = arvados_cwl.main(
 957             ["--create-workflow", "--debug",
 958              "--api=jobs",
 959              "--project-uuid", project_uuid,
 960              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 961             capture_stdout, sys.stderr, api_client=stubs.api)
 962         self.assertEqual(exited, 0)
 963
 964         stubs.api.pipeline_instances().create.refute_called()
 965         stubs.api.jobs().create.refute_called()
 966
 967         expect_component = copy.deepcopy(stubs.expect_job_spec)
 968         self._adjust_script_params(expect_component)
 969         expect_template = {
 970             "components": {
 971                 "submit_wf.cwl": expect_component,
 972             },
 973             "name": "submit_wf.cwl",
 974             "owner_uuid": project_uuid,
 975         }
 976         stubs.api.pipeline_templates().create.assert_called_with(
 977             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 978
 979         self.assertEqual(capture_stdout.getvalue(),
 980                          stubs.expect_pipeline_template_uuid + '\n')
 981
 982
 983     @stubs
 984     def test_create_name(self, stubs):
 985         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 986
 987         capture_stdout = cStringIO.StringIO()
 988
 989         exited = arvados_cwl.main(
 990             ["--create-workflow", "--debug",
 991              "--project-uuid", project_uuid,
 992              "--api=jobs",
 993              "--name", "testing 123",
 994              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 995             capture_stdout, sys.stderr, api_client=stubs.api)
 996         self.assertEqual(exited, 0)
 997
 998         stubs.api.pipeline_instances().create.refute_called()
 999         stubs.api.jobs().create.refute_called()
1000
1001         expect_component = copy.deepcopy(stubs.expect_job_spec)
1002         self._adjust_script_params(expect_component)
1003         expect_template = {
1004             "components": {
1005                 "testing 123": expect_component,
1006             },
1007             "name": "testing 123",
1008             "owner_uuid": project_uuid,
1009         }
1010         stubs.api.pipeline_templates().create.assert_called_with(
1011             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1012
1013         self.assertEqual(capture_stdout.getvalue(),
1014                          stubs.expect_pipeline_template_uuid + '\n')
1015
1016
1017     @stubs
1018     def test_update_name(self, stubs):
1019         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1020
1021         capture_stdout = cStringIO.StringIO()
1022
1023         exited = arvados_cwl.main(
1024             ["--update-workflow", self.existing_template_uuid,
1025              "--debug",
1026              "--project-uuid", project_uuid,
1027              "--api=jobs",
1028              "--name", "testing 123",
1029              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1030             capture_stdout, sys.stderr, api_client=stubs.api)
1031         self.assertEqual(exited, 0)
1032
1033         stubs.api.pipeline_instances().create.refute_called()
1034         stubs.api.jobs().create.refute_called()
1035
1036         expect_component = copy.deepcopy(stubs.expect_job_spec)
1037         self._adjust_script_params(expect_component)
1038         expect_template = {
1039             "components": {
1040                 "testing 123": expect_component,
1041             },
1042             "name": "testing 123",
1043             "owner_uuid": project_uuid,
1044         }
1045         stubs.api.pipeline_templates().create.refute_called()
1046         stubs.api.pipeline_templates().update.assert_called_with(
1047             body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
1048
1049         self.assertEqual(capture_stdout.getvalue(),
1050                          self.existing_template_uuid + '\n')
1051
1052
1053 class TestCreateWorkflow(unittest.TestCase):
1054     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1055     expect_workflow = StripYAMLComments(
1056         open("tests/wf/expect_packed.cwl").read())
1057
1058     @stubs
1059     def test_create(self, stubs):
1060         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1061
1062         capture_stdout = cStringIO.StringIO()
1063
1064         exited = arvados_cwl.main(
1065             ["--create-workflow", "--debug",
1066              "--api=containers",
1067              "--project-uuid", project_uuid,
1068              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1069             capture_stdout, sys.stderr, api_client=stubs.api)
1070         self.assertEqual(exited, 0)
1071
1072         stubs.api.pipeline_templates().create.refute_called()
1073         stubs.api.container_requests().create.refute_called()
1074
1075         body = {
1076             "workflow": {
1077                 "owner_uuid": project_uuid,
1078                 "name": "submit_wf.cwl",
1079                 "description": "",
1080                 "definition": self.expect_workflow,
1081             }
1082         }
1083         stubs.api.workflows().create.assert_called_with(
1084             body=JsonDiffMatcher(body))
1085
1086         self.assertEqual(capture_stdout.getvalue(),
1087                          stubs.expect_workflow_uuid + '\n')
1088
1089
1090     @stubs
1091     def test_create_name(self, stubs):
1092         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1093
1094         capture_stdout = cStringIO.StringIO()
1095
1096         exited = arvados_cwl.main(
1097             ["--create-workflow", "--debug",
1098              "--api=containers",
1099              "--project-uuid", project_uuid,
1100              "--name", "testing 123",
1101              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1102             capture_stdout, sys.stderr, api_client=stubs.api)
1103         self.assertEqual(exited, 0)
1104
1105         stubs.api.pipeline_templates().create.refute_called()
1106         stubs.api.container_requests().create.refute_called()
1107
1108         body = {
1109             "workflow": {
1110                 "owner_uuid": project_uuid,
1111                 "name": "testing 123",
1112                 "description": "",
1113                 "definition": self.expect_workflow,
1114             }
1115         }
1116         stubs.api.workflows().create.assert_called_with(
1117             body=JsonDiffMatcher(body))
1118
1119         self.assertEqual(capture_stdout.getvalue(),
1120                          stubs.expect_workflow_uuid + '\n')
1121
1122     @stubs
1123     def test_incompatible_api(self, stubs):
1124         capture_stderr = cStringIO.StringIO()
1125         logging.getLogger('arvados.cwl-runner').addHandler(
1126             logging.StreamHandler(capture_stderr))
1127
1128         exited = arvados_cwl.main(
1129             ["--update-workflow", self.existing_workflow_uuid,
1130              "--api=jobs",
1131              "--debug",
1132              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1133             sys.stderr, sys.stderr, api_client=stubs.api)
1134         self.assertEqual(exited, 1)
1135         self.assertRegexpMatches(
1136             capture_stderr.getvalue(),
1137             "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
1138
1139     @stubs
1140     def test_update(self, stubs):
1141         capture_stdout = cStringIO.StringIO()
1142
1143         exited = arvados_cwl.main(
1144             ["--update-workflow", self.existing_workflow_uuid,
1145              "--debug",
1146              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1147             capture_stdout, sys.stderr, api_client=stubs.api)
1148         self.assertEqual(exited, 0)
1149
1150         body = {
1151             "workflow": {
1152                 "name": "submit_wf.cwl",
1153                 "description": "",
1154                 "definition": self.expect_workflow,
1155             }
1156         }
1157         stubs.api.workflows().update.assert_called_with(
1158             uuid=self.existing_workflow_uuid,
1159             body=JsonDiffMatcher(body))
1160         self.assertEqual(capture_stdout.getvalue(),
1161                          self.existing_workflow_uuid + '\n')
1162
1163
1164     @stubs
1165     def test_update_name(self, stubs):
1166         capture_stdout = cStringIO.StringIO()
1167
1168         exited = arvados_cwl.main(
1169             ["--update-workflow", self.existing_workflow_uuid,
1170              "--debug", "--name", "testing 123",
1171              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1172             capture_stdout, sys.stderr, api_client=stubs.api)
1173         self.assertEqual(exited, 0)
1174
1175         body = {
1176             "workflow": {
1177                 "name": "testing 123",
1178                 "description": "",
1179                 "definition": self.expect_workflow,
1180             }
1181         }
1182         stubs.api.workflows().update.assert_called_with(
1183             uuid=self.existing_workflow_uuid,
1184             body=JsonDiffMatcher(body))
1185         self.assertEqual(capture_stdout.getvalue(),
1186                          self.existing_workflow_uuid + '\n')
1187
1188
1189     @stubs
1190     def test_create_collection_per_tool(self, stubs):
1191         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1192
1193         capture_stdout = cStringIO.StringIO()
1194
1195         exited = arvados_cwl.main(
1196             ["--create-workflow", "--debug",
1197              "--api=containers",
1198              "--project-uuid", project_uuid,
1199              "tests/collection_per_tool/collection_per_tool.cwl"],
1200             capture_stdout, sys.stderr, api_client=stubs.api)
1201         self.assertEqual(exited, 0)
1202
1203         toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1204         expect_workflow = StripYAMLComments(open(toolfile).read())
1205
1206         body = {
1207             "workflow": {
1208                 "owner_uuid": project_uuid,
1209                 "name": "collection_per_tool.cwl",
1210                 "description": "",
1211                 "definition": expect_workflow,
1212             }
1213         }
1214         stubs.api.workflows().create.assert_called_with(
1215             body=JsonDiffMatcher(body))
1216
1217         self.assertEqual(capture_stdout.getvalue(),
1218                          stubs.expect_workflow_uuid + '\n')
1219
1220 class TestTemplateInputs(unittest.TestCase):
1221     expect_template = {
1222         "components": {
1223             "inputs_test.cwl": {
1224                 'runtime_constraints': {
1225                     'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
1226                     'min_ram_mb_per_node': 1024
1227                 },
1228                 'script_parameters': {
1229                     'cwl:tool':
1230                     '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main',
1231                     'optionalFloatInput': None,
1232                     'fileInput': {
1233                         'type': 'File',
1234                         'dataclass': 'File',
1235                         'required': True,
1236                         'title': "It's a file; we expect to find some characters in it.",
1237                         'description': 'If there were anything further to say, it would be said here,\nor here.'
1238                     },
1239                     'floatInput': {
1240                         'type': 'float',
1241                         'dataclass': 'number',
1242                         'required': True,
1243                         'title': 'Floats like a duck',
1244                         'default': 0.1,
1245                         'value': 0.1,
1246                     },
1247                     'optionalFloatInput': {
1248                         'type': ['null', 'float'],
1249                         'dataclass': 'number',
1250                         'required': False,
1251                     },
1252                     'boolInput': {
1253                         'type': 'boolean',
1254                         'dataclass': 'boolean',
1255                         'required': True,
1256                         'title': 'True or false?',
1257                     },
1258                 },
1259                 'repository': 'arvados',
1260                 'script_version': 'master',
1261                 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
1262                 'script': 'cwl-runner',
1263             },
1264         },
1265         "name": "inputs_test.cwl",
1266     }
1267
1268     @stubs
1269     def test_inputs_empty(self, stubs):
1270         exited = arvados_cwl.main(
1271             ["--create-template",
1272              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
1273             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1274         self.assertEqual(exited, 0)
1275
1276         stubs.api.pipeline_templates().create.assert_called_with(
1277             body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
1278
1279     @stubs
1280     def test_inputs(self, stubs):
1281         exited = arvados_cwl.main(
1282             ["--create-template",
1283              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
1284             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1285         self.assertEqual(exited, 0)
1286
1287         expect_template = copy.deepcopy(self.expect_template)
1288         params = expect_template[
1289             "components"]["inputs_test.cwl"]["script_parameters"]
1290         params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
1291         params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main'
1292         params["floatInput"]["value"] = 1.234
1293         params["boolInput"]["value"] = True
1294
1295         stubs.api.pipeline_templates().create.assert_called_with(
1296             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)