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             "99999999999999999999999999999994+99": {
  89                 "uuid": "",
  90                 "portable_data_hash": "99999999999999999999999999999994+99",
  91                 "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
  92             }
  93         }
  94         stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
  95         stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
  96
  97         stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  98         stubs.api.jobs().create().execute.return_value = {
  99             "uuid": stubs.expect_job_uuid,
 100             "state": "Queued",
 101         }
 102
 103         stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
 104         stubs.api.container_requests().create().execute.return_value = {
 105             "uuid": stubs.expect_container_request_uuid,
 106             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
 107             "state": "Queued"
 108         }
 109
 110         stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
 111         stubs.api.pipeline_templates().create().execute.return_value = {
 112             "uuid": stubs.expect_pipeline_template_uuid,
 113         }
 114         stubs.expect_job_spec = {
 115             'runtime_constraints': {
 116                 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
 117                 'min_ram_mb_per_node': 1024
 118             },
 119             'script_parameters': {
 120                 'x': {
 121                     'basename': 'blorp.txt',
 122                     'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 123                     'class': 'File'
 124                 },
 125                 'y': {
 126                     'basename': '99999999999999999999999999999998+99',
 127                     'location': 'keep:99999999999999999999999999999998+99',
 128                     'class': 'Directory'
 129                 },
 130                 'z': {
 131                     'basename': 'anonymous',
 132                     "listing": [{
 133                         "basename": "renamed.txt",
 134                         "class": "File",
 135                         "location": "keep:99999999999999999999999999999998+99/file1.txt"
 136                     }],
 137                     'class': 'Directory'
 138                 },
 139                 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main'
 140             },
 141             'repository': 'arvados',
 142             'script_version': 'master',
 143             'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
 144             'script': 'cwl-runner'
 145         }
 146         stubs.pipeline_component = stubs.expect_job_spec.copy()
 147         stubs.expect_pipeline_instance = {
 148             'name': 'submit_wf.cwl',
 149             'state': 'RunningOnServer',
 150             'owner_uuid': None,
 151             "components": {
 152                 "cwl-runner": {
 153                     'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
 154                     'script_parameters': {
 155                         'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
 156                         'x': {"value": {
 157                             'basename': 'blorp.txt',
 158                             'class': 'File',
 159                             'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 160                             "size": 16
 161                         }},
 162                         'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
 163                               'listing': [
 164                                   {
 165                                       'basename': 'renamed.txt',
 166                                       'class': 'File', 'location':
 167                                       'keep:99999999999999999999999999999998+99/file1.txt'
 168                                   }
 169                               ]}},
 170                         'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
 171                         'arv:debug': True,
 172                         'arv:enable_reuse': True,
 173                         'arv:on_error': 'continue'
 174                     },
 175                     'repository': 'arvados',
 176                     'script_version': 'master',
 177                     'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
 178                     'script': 'cwl-runner',
 179                     'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
 180                 }
 181             }
 182         }
 183         stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
 184         stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
 185         stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
 186         stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
 187         stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
 188             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 189             "state": "Queued"
 190         }
 191         stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
 192         stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
 193
 194         with open("tests/wf/submit_wf_packed.cwl") as f:
 195             expect_packed_workflow = yaml.round_trip_load(f)
 196
 197         stubs.expect_container_spec = {
 198             'priority': 500,
 199             'mounts': {
 200                 '/var/spool/cwl': {
 201                     'writable': True,
 202                     'kind': 'collection'
 203                 },
 204                 '/var/lib/cwl/workflow.json': {
 205                     'content': expect_packed_workflow,
 206                     'kind': 'json'
 207                 },
 208                 'stdout': {
 209                     'path': '/var/spool/cwl/cwl.output.json',
 210                     'kind': 'file'
 211                 },
 212                 '/var/lib/cwl/cwl.input.json': {
 213                     'kind': 'json',
 214                     'content': {
 215                         'y': {
 216                             'basename': '99999999999999999999999999999998+99',
 217                             'location': 'keep:99999999999999999999999999999998+99',
 218                             'class': 'Directory'},
 219                         'x': {
 220                             'basename': u'blorp.txt',
 221                             'class': 'File',
 222                             'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 223                             "size": 16
 224                         },
 225                         'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
 226                             {'basename': 'renamed.txt',
 227                              'class': 'File',
 228                              'location': 'keep:99999999999999999999999999999998+99/file1.txt'
 229                             }
 230                         ]}
 231                     },
 232                     'kind': 'json'
 233                 }
 234             },
 235             'secret_mounts': {},
 236             'state': 'Committed',
 237             'command': ['arvados-cwl-runner', '--local', '--api=containers',
 238                         '--no-log-timestamps', '--disable-validate',
 239                         '--eval-timeout=20', '--thread-count=4',
 240                         '--enable-reuse', '--debug', '--on-error=continue',
 241                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
 242             'name': 'submit_wf.cwl',
 243             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
 244             'output_path': '/var/spool/cwl',
 245             'cwd': '/var/spool/cwl',
 246             'runtime_constraints': {
 247                 'API': True,
 248                 'vcpus': 1,
 249                 'ram': 1024*1024*1024
 250             },
 251             'use_existing': True,
 252             'properties': {},
 253             'secret_mounts': {}
 254         }
 255
 256         stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
 257         stubs.api.workflows().create().execute.return_value = {
 258             "uuid": stubs.expect_workflow_uuid,
 259         }
 260         def update_mock(**kwargs):
 261             stubs.updated_uuid = kwargs.get('uuid')
 262             return mock.DEFAULT
 263         stubs.api.workflows().update.side_effect = update_mock
 264         stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
 265             "uuid": stubs.updated_uuid,
 266         }
 267
 268         return func(self, stubs, *args, **kwargs)
 269     return wrapped
 270
 271
 272 class TestSubmit(unittest.TestCase):
 273     @mock.patch("arvados_cwl.runner.arv_docker_get_image")
 274     @mock.patch("time.sleep")
 275     @stubs
 276     def test_submit(self, stubs, tm, arvdock):
 277         capture_stdout = cStringIO.StringIO()
 278         exited = arvados_cwl.main(
 279             ["--submit", "--no-wait", "--api=jobs", "--debug",
 280              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 281             capture_stdout, sys.stderr, api_client=stubs.api)
 282         self.assertEqual(exited, 0)
 283
 284         stubs.api.collections().create.assert_has_calls([
 285             mock.call(body=JsonDiffMatcher({
 286                 'manifest_text':
 287                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
 288                 'replication_desired': None,
 289                 'name': 'submit_tool.cwl dependencies',
 290             }), ensure_unique_name=True),
 291             mock.call(body=JsonDiffMatcher({
 292                 'manifest_text':
 293                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 294                 'replication_desired': None,
 295                 'name': 'submit_wf.cwl input',
 296             }), ensure_unique_name=True),
 297             mock.call(body=JsonDiffMatcher({
 298                 'manifest_text':
 299                 '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n',
 300                 'replication_desired': None,
 301                 'name': 'submit_wf.cwl',
 302             }), ensure_unique_name=True)        ])
 303
 304         arvdock.assert_has_calls([
 305             mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
 306             mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
 307         ])
 308
 309         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 310         stubs.api.pipeline_instances().create.assert_called_with(
 311             body=JsonDiffMatcher(expect_pipeline))
 312         self.assertEqual(capture_stdout.getvalue(),
 313                          stubs.expect_pipeline_uuid + '\n')
 314
 315
 316     @mock.patch("time.sleep")
 317     @stubs
 318     def test_submit_no_reuse(self, stubs, tm):
 319         capture_stdout = cStringIO.StringIO()
 320         exited = arvados_cwl.main(
 321             ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
 322              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 323             capture_stdout, sys.stderr, api_client=stubs.api)
 324         self.assertEqual(exited, 0)
 325
 326         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 327         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
 328         expect_pipeline["properties"] = {"run_options": {"enable_job_reuse": False}}
 329
 330         stubs.api.pipeline_instances().create.assert_called_with(
 331             body=JsonDiffMatcher(expect_pipeline))
 332         self.assertEqual(capture_stdout.getvalue(),
 333                          stubs.expect_pipeline_uuid + '\n')
 334
 335     @stubs
 336     def test_error_when_multiple_storage_classes_specified(self, stubs):
 337         storage_classes = "foo,bar"
 338         exited = arvados_cwl.main(
 339                 ["--debug", "--storage-classes", storage_classes,
 340                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 341                 sys.stdin, sys.stderr, api_client=stubs.api)
 342         self.assertEqual(exited, 1)
 343
 344     @mock.patch("time.sleep")
 345     @stubs
 346     def test_submit_on_error(self, stubs, tm):
 347         capture_stdout = cStringIO.StringIO()
 348         exited = arvados_cwl.main(
 349             ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
 350              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 351             capture_stdout, sys.stderr, api_client=stubs.api)
 352         self.assertEqual(exited, 0)
 353
 354         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 355         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
 356
 357         stubs.api.pipeline_instances().create.assert_called_with(
 358             body=JsonDiffMatcher(expect_pipeline))
 359         self.assertEqual(capture_stdout.getvalue(),
 360                          stubs.expect_pipeline_uuid + '\n')
 361
 362
 363     @mock.patch("time.sleep")
 364     @stubs
 365     def test_submit_runner_ram(self, stubs, tm):
 366         capture_stdout = cStringIO.StringIO()
 367         exited = arvados_cwl.main(
 368             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
 369              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 370             capture_stdout, sys.stderr, api_client=stubs.api)
 371         self.assertEqual(exited, 0)
 372
 373         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 374         expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
 375
 376         stubs.api.pipeline_instances().create.assert_called_with(
 377             body=JsonDiffMatcher(expect_pipeline))
 378         self.assertEqual(capture_stdout.getvalue(),
 379                          stubs.expect_pipeline_uuid + '\n')
 380
 381
 382     @mock.patch("time.sleep")
 383     @stubs
 384     def test_submit_invalid_runner_ram(self, stubs, tm):
 385         capture_stdout = cStringIO.StringIO()
 386         exited = arvados_cwl.main(
 387             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
 388              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 389             capture_stdout, sys.stderr, api_client=stubs.api)
 390         self.assertEqual(exited, 1)
 391
 392     @mock.patch("time.sleep")
 393     @stubs
 394     def test_submit_output_name(self, stubs, tm):
 395         output_name = "test_output_name"
 396
 397         capture_stdout = cStringIO.StringIO()
 398         exited = arvados_cwl.main(
 399             ["--submit", "--no-wait", "--debug", "--output-name", output_name,
 400              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 401             capture_stdout, sys.stderr, api_client=stubs.api)
 402         self.assertEqual(exited, 0)
 403
 404         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 405         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
 406
 407         stubs.api.pipeline_instances().create.assert_called_with(
 408             body=JsonDiffMatcher(expect_pipeline))
 409         self.assertEqual(capture_stdout.getvalue(),
 410                          stubs.expect_pipeline_uuid + '\n')
 411
 412
 413     @mock.patch("time.sleep")
 414     @stubs
 415     def test_submit_pipeline_name(self, stubs, tm):
 416         capture_stdout = cStringIO.StringIO()
 417         exited = arvados_cwl.main(
 418             ["--submit", "--no-wait", "--debug", "--name=hello job 123",
 419              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 420             capture_stdout, sys.stderr, api_client=stubs.api)
 421         self.assertEqual(exited, 0)
 422
 423         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 424         expect_pipeline["name"] = "hello job 123"
 425
 426         stubs.api.pipeline_instances().create.assert_called_with(
 427             body=JsonDiffMatcher(expect_pipeline))
 428         self.assertEqual(capture_stdout.getvalue(),
 429                          stubs.expect_pipeline_uuid + '\n')
 430
 431     @mock.patch("time.sleep")
 432     @stubs
 433     def test_submit_output_tags(self, stubs, tm):
 434         output_tags = "tag0,tag1,tag2"
 435
 436         capture_stdout = cStringIO.StringIO()
 437         exited = arvados_cwl.main(
 438             ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
 439              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 440             capture_stdout, sys.stderr, api_client=stubs.api)
 441         self.assertEqual(exited, 0)
 442
 443         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 444         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
 445
 446         stubs.api.pipeline_instances().create.assert_called_with(
 447             body=JsonDiffMatcher(expect_pipeline))
 448         self.assertEqual(capture_stdout.getvalue(),
 449                          stubs.expect_pipeline_uuid + '\n')
 450
 451     @mock.patch("time.sleep")
 452     @stubs
 453     def test_submit_with_project_uuid(self, stubs, tm):
 454         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 455
 456         exited = arvados_cwl.main(
 457             ["--submit", "--no-wait", "--debug",
 458              "--project-uuid", project_uuid,
 459              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 460             sys.stdout, sys.stderr, api_client=stubs.api)
 461         self.assertEqual(exited, 0)
 462
 463         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 464         expect_pipeline["owner_uuid"] = project_uuid
 465         stubs.api.pipeline_instances().create.assert_called_with(
 466             body=JsonDiffMatcher(expect_pipeline))
 467
 468     @stubs
 469     def test_submit_container(self, stubs):
 470         capture_stdout = cStringIO.StringIO()
 471         try:
 472             exited = arvados_cwl.main(
 473                 ["--submit", "--no-wait", "--api=containers", "--debug",
 474                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 475                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 476             self.assertEqual(exited, 0)
 477         except:
 478             logging.exception("")
 479
 480         stubs.api.collections().create.assert_has_calls([
 481             mock.call(body=JsonDiffMatcher({
 482                 'manifest_text':
 483                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
 484                 'replication_desired': None,
 485                 'name': 'submit_tool.cwl dependencies',
 486             }), ensure_unique_name=True),
 487             mock.call(body=JsonDiffMatcher({
 488                 'manifest_text':
 489                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 490                 'replication_desired': None,
 491                 'name': 'submit_wf.cwl input',
 492             }), ensure_unique_name=True)])
 493
 494         expect_container = copy.deepcopy(stubs.expect_container_spec)
 495         stubs.api.container_requests().create.assert_called_with(
 496             body=JsonDiffMatcher(expect_container))
 497         self.assertEqual(capture_stdout.getvalue(),
 498                          stubs.expect_container_request_uuid + '\n')
 499
 500     @stubs
 501     def test_submit_container_no_reuse(self, stubs):
 502         capture_stdout = cStringIO.StringIO()
 503         try:
 504             exited = arvados_cwl.main(
 505                 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
 506                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 507                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 508             self.assertEqual(exited, 0)
 509         except:
 510             logging.exception("")
 511
 512         expect_container = copy.deepcopy(stubs.expect_container_spec)
 513         expect_container["command"] = [
 514             'arvados-cwl-runner', '--local', '--api=containers',
 515             '--no-log-timestamps', '--disable-validate',
 516             '--eval-timeout=20', '--thread-count=4',
 517             '--disable-reuse', '--debug', '--on-error=continue',
 518             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 519         expect_container["use_existing"] = False
 520
 521         stubs.api.container_requests().create.assert_called_with(
 522             body=JsonDiffMatcher(expect_container))
 523         self.assertEqual(capture_stdout.getvalue(),
 524                          stubs.expect_container_request_uuid + '\n')
 525
 526
 527     @stubs
 528     def test_submit_container_reuse_disabled_by_workflow(self, stubs):
 529         capture_stdout = cStringIO.StringIO()
 530
 531         exited = arvados_cwl.main(
 532             ["--submit", "--no-wait", "--api=containers", "--debug",
 533              "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
 534             capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 535         self.assertEqual(exited, 0)
 536
 537         expect_container = copy.deepcopy(stubs.expect_container_spec)
 538         expect_container["command"] = [
 539             'arvados-cwl-runner', '--local', '--api=containers',
 540             '--no-log-timestamps', '--disable-validate',
 541             '--eval-timeout=20', '--thread-count=4',
 542             '--disable-reuse', '--debug', '--on-error=continue',
 543             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 544         expect_container["use_existing"] = False
 545         expect_container["name"] = "submit_wf_no_reuse.cwl"
 546         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
 547             {
 548                 "class": "http://arvados.org/cwl#ReuseRequirement",
 549                 "enableReuse": False,
 550             },
 551         ]
 552         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
 553             "arv": "http://arvados.org/cwl#",
 554             "cwltool": "http://commonwl.org/cwltool#"
 555         }
 556
 557         stubs.api.container_requests().create.assert_called_with(
 558             body=JsonDiffMatcher(expect_container))
 559         self.assertEqual(capture_stdout.getvalue(),
 560                          stubs.expect_container_request_uuid + '\n')
 561
 562
 563     @stubs
 564     def test_submit_container_on_error(self, stubs):
 565         capture_stdout = cStringIO.StringIO()
 566         try:
 567             exited = arvados_cwl.main(
 568                 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
 569                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 570                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 571             self.assertEqual(exited, 0)
 572         except:
 573             logging.exception("")
 574
 575         expect_container = copy.deepcopy(stubs.expect_container_spec)
 576         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 577                                        '--no-log-timestamps', '--disable-validate',
 578                                        '--eval-timeout=20', '--thread-count=4',
 579                                        '--enable-reuse', '--debug', '--on-error=stop',
 580                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 581
 582         stubs.api.container_requests().create.assert_called_with(
 583             body=JsonDiffMatcher(expect_container))
 584         self.assertEqual(capture_stdout.getvalue(),
 585                          stubs.expect_container_request_uuid + '\n')
 586
 587     @stubs
 588     def test_submit_container_output_name(self, stubs):
 589         output_name = "test_output_name"
 590
 591         capture_stdout = cStringIO.StringIO()
 592         try:
 593             exited = arvados_cwl.main(
 594                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
 595                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 596                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 597             self.assertEqual(exited, 0)
 598         except:
 599             logging.exception("")
 600
 601         expect_container = copy.deepcopy(stubs.expect_container_spec)
 602         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 603                                        '--no-log-timestamps', '--disable-validate',
 604                                        '--eval-timeout=20', '--thread-count=4',
 605                                        '--enable-reuse',
 606                                        "--output-name="+output_name, '--debug', '--on-error=continue',
 607                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 608         expect_container["output_name"] = output_name
 609
 610         stubs.api.container_requests().create.assert_called_with(
 611             body=JsonDiffMatcher(expect_container))
 612         self.assertEqual(capture_stdout.getvalue(),
 613                          stubs.expect_container_request_uuid + '\n')
 614
 615     @stubs
 616     def test_submit_storage_classes(self, stubs):
 617         capture_stdout = cStringIO.StringIO()
 618         try:
 619             exited = arvados_cwl.main(
 620                 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
 621                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 622                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 623             self.assertEqual(exited, 0)
 624         except:
 625             logging.exception("")
 626
 627         expect_container = copy.deepcopy(stubs.expect_container_spec)
 628         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 629                                        '--no-log-timestamps', '--disable-validate',
 630                                        '--eval-timeout=20', '--thread-count=4',
 631                                        '--enable-reuse', "--debug",
 632                                        "--storage-classes=foo", '--on-error=continue',
 633                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 634
 635         stubs.api.container_requests().create.assert_called_with(
 636             body=JsonDiffMatcher(expect_container))
 637         self.assertEqual(capture_stdout.getvalue(),
 638                          stubs.expect_container_request_uuid + '\n')
 639
 640     @mock.patch("arvados_cwl.task_queue.TaskQueue")
 641     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
 642     @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None))
 643     @stubs
 644     def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
 645         def set_final_output(job_order, output_callback, runtimeContext):
 646             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
 647             return []
 648         job.side_effect = set_final_output
 649
 650         try:
 651             exited = arvados_cwl.main(
 652                 ["--debug", "--local", "--storage-classes=foo",
 653                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 654                 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 655             self.assertEqual(exited, 0)
 656         except:
 657             logging.exception("")
 658
 659         make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
 660
 661     @mock.patch("arvados_cwl.task_queue.TaskQueue")
 662     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
 663     @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None))
 664     @stubs
 665     def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
 666         def set_final_output(job_order, output_callback, runtimeContext):
 667             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
 668             return []
 669         job.side_effect = set_final_output
 670
 671         try:
 672             exited = arvados_cwl.main(
 673                 ["--debug", "--local",
 674                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 675                 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 676             self.assertEqual(exited, 0)
 677         except:
 678             logging.exception("")
 679
 680         make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
 681
 682     @stubs
 683     def test_submit_container_output_ttl(self, stubs):
 684         capture_stdout = cStringIO.StringIO()
 685         try:
 686             exited = arvados_cwl.main(
 687                 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
 688                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 689                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 690             self.assertEqual(exited, 0)
 691         except:
 692             logging.exception("")
 693
 694         expect_container = copy.deepcopy(stubs.expect_container_spec)
 695         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 696                                        '--no-log-timestamps', '--disable-validate',
 697                                        '--eval-timeout=20', '--thread-count=4',
 698                                        '--enable-reuse', '--debug', '--on-error=continue',
 699                                        "--intermediate-output-ttl=3600",
 700                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 701
 702         stubs.api.container_requests().create.assert_called_with(
 703             body=JsonDiffMatcher(expect_container))
 704         self.assertEqual(capture_stdout.getvalue(),
 705                          stubs.expect_container_request_uuid + '\n')
 706
 707     @stubs
 708     def test_submit_container_trash_intermediate(self, stubs):
 709         capture_stdout = cStringIO.StringIO()
 710         try:
 711             exited = arvados_cwl.main(
 712                 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
 713                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 714                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 715             self.assertEqual(exited, 0)
 716         except:
 717             logging.exception("")
 718
 719         expect_container = copy.deepcopy(stubs.expect_container_spec)
 720         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 721                                        '--no-log-timestamps', '--disable-validate',
 722                                        '--eval-timeout=20', '--thread-count=4',
 723                                        '--enable-reuse', '--debug', '--on-error=continue',
 724                                        "--trash-intermediate",
 725                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 726
 727         stubs.api.container_requests().create.assert_called_with(
 728             body=JsonDiffMatcher(expect_container))
 729         self.assertEqual(capture_stdout.getvalue(),
 730                          stubs.expect_container_request_uuid + '\n')
 731
 732     @stubs
 733     def test_submit_container_output_tags(self, stubs):
 734         output_tags = "tag0,tag1,tag2"
 735
 736         capture_stdout = cStringIO.StringIO()
 737         try:
 738             exited = arvados_cwl.main(
 739                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
 740                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 741                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 742             self.assertEqual(exited, 0)
 743         except:
 744             logging.exception("")
 745
 746         expect_container = copy.deepcopy(stubs.expect_container_spec)
 747         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 748                                        '--no-log-timestamps', '--disable-validate',
 749                                        '--eval-timeout=20', '--thread-count=4',
 750                                        '--enable-reuse',
 751                                        "--output-tags="+output_tags, '--debug', '--on-error=continue',
 752                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 753
 754         stubs.api.container_requests().create.assert_called_with(
 755             body=JsonDiffMatcher(expect_container))
 756         self.assertEqual(capture_stdout.getvalue(),
 757                          stubs.expect_container_request_uuid + '\n')
 758
 759     @stubs
 760     def test_submit_container_runner_ram(self, stubs):
 761         capture_stdout = cStringIO.StringIO()
 762         try:
 763             exited = arvados_cwl.main(
 764                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
 765                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 766                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 767             self.assertEqual(exited, 0)
 768         except:
 769             logging.exception("")
 770
 771         expect_container = copy.deepcopy(stubs.expect_container_spec)
 772         expect_container["runtime_constraints"]["ram"] = 2048*1024*1024
 773
 774         stubs.api.container_requests().create.assert_called_with(
 775             body=JsonDiffMatcher(expect_container))
 776         self.assertEqual(capture_stdout.getvalue(),
 777                          stubs.expect_container_request_uuid + '\n')
 778
 779     @mock.patch("arvados.collection.CollectionReader")
 780     @mock.patch("time.sleep")
 781     @stubs
 782     def test_submit_file_keepref(self, stubs, tm, collectionReader):
 783         capture_stdout = cStringIO.StringIO()
 784         exited = arvados_cwl.main(
 785             ["--submit", "--no-wait", "--api=containers", "--debug",
 786              "tests/wf/submit_keepref_wf.cwl"],
 787             capture_stdout, sys.stderr, api_client=stubs.api)
 788         self.assertEqual(exited, 0)
 789
 790
 791     @mock.patch("arvados.collection.CollectionReader")
 792     @mock.patch("time.sleep")
 793     @stubs
 794     def test_submit_keepref(self, stubs, tm, reader):
 795         capture_stdout = cStringIO.StringIO()
 796
 797         with open("tests/wf/expect_arvworkflow.cwl") as f:
 798             reader().open().__enter__().read.return_value = f.read()
 799
 800         exited = arvados_cwl.main(
 801             ["--submit", "--no-wait", "--api=containers", "--debug",
 802              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 803             capture_stdout, sys.stderr, api_client=stubs.api)
 804         self.assertEqual(exited, 0)
 805
 806         expect_container = {
 807             'priority': 500,
 808             'mounts': {
 809                 '/var/spool/cwl': {
 810                     'writable': True,
 811                     'kind': 'collection'
 812                 },
 813                 'stdout': {
 814                     'path': '/var/spool/cwl/cwl.output.json',
 815                     'kind': 'file'
 816                 },
 817                 '/var/lib/cwl/workflow': {
 818                     'portable_data_hash': '99999999999999999999999999999994+99',
 819                     'kind': 'collection'
 820                 },
 821                 '/var/lib/cwl/cwl.input.json': {
 822                     'content': {
 823                         'x': 'XxX'
 824                     },
 825                     'kind': 'json'
 826                 }
 827             }, 'state': 'Committed',
 828             'output_path': '/var/spool/cwl',
 829             'name': 'expect_arvworkflow.cwl#main',
 830             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
 831             'command': ['arvados-cwl-runner', '--local', '--api=containers',
 832                         '--no-log-timestamps', '--disable-validate',
 833                         '--eval-timeout=20', '--thread-count=4',
 834                         '--enable-reuse', '--debug', '--on-error=continue',
 835                         '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
 836             'cwd': '/var/spool/cwl',
 837             'runtime_constraints': {
 838                 'API': True,
 839                 'vcpus': 1,
 840                 'ram': 1073741824
 841             },
 842             'use_existing': True,
 843             'properties': {},
 844             'secret_mounts': {}
 845         }
 846
 847         stubs.api.container_requests().create.assert_called_with(
 848             body=JsonDiffMatcher(expect_container))
 849         self.assertEqual(capture_stdout.getvalue(),
 850                          stubs.expect_container_request_uuid + '\n')
 851
 852
 853     @mock.patch("arvados.collection.CollectionReader")
 854     @mock.patch("time.sleep")
 855     @stubs
 856     def test_submit_jobs_keepref(self, stubs, tm, reader):
 857         capture_stdout = cStringIO.StringIO()
 858
 859         with open("tests/wf/expect_arvworkflow.cwl") as f:
 860             reader().open().__enter__().read.return_value = f.read()
 861
 862         exited = arvados_cwl.main(
 863             ["--submit", "--no-wait", "--api=jobs", "--debug",
 864              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 865             capture_stdout, sys.stderr, api_client=stubs.api)
 866         self.assertEqual(exited, 0)
 867
 868         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 869         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
 870         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
 871         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
 872         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
 873         expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
 874         stubs.api.pipeline_instances().create.assert_called_with(
 875             body=JsonDiffMatcher(expect_pipeline))
 876
 877     @mock.patch("time.sleep")
 878     @stubs
 879     def test_submit_arvworkflow(self, stubs, tm):
 880         capture_stdout = cStringIO.StringIO()
 881
 882         with open("tests/wf/expect_arvworkflow.cwl") as f:
 883             stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
 884
 885         exited = arvados_cwl.main(
 886             ["--submit", "--no-wait", "--api=containers", "--debug",
 887              "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
 888             capture_stdout, sys.stderr, api_client=stubs.api)
 889         self.assertEqual(exited, 0)
 890
 891         expect_container = {
 892             'priority': 500,
 893             'mounts': {
 894                 '/var/spool/cwl': {
 895                     'writable': True,
 896                     'kind': 'collection'
 897                 },
 898                 'stdout': {
 899                     'path': '/var/spool/cwl/cwl.output.json',
 900                     'kind': 'file'
 901                 },
 902                 '/var/lib/cwl/workflow.json': {
 903                     'kind': 'json',
 904                     'content': {
 905                         'cwlVersion': 'v1.0',
 906                         '$graph': [
 907                             {
 908                                 'id': '#main',
 909                                 'inputs': [
 910                                     {'type': 'string', 'id': '#main/x'}
 911                                 ],
 912                                 'steps': [
 913                                     {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
 914                                      'run': '#submit_tool.cwl',
 915                                      'id': '#main/step1',
 916                                      'out': []}
 917                                 ],
 918                                 'class': 'Workflow',
 919                                 'outputs': []
 920                             },
 921                             {
 922                                 'inputs': [
 923                                     {
 924                                         'inputBinding': {'position': 1},
 925                                         'type': 'string',
 926                                         'id': '#submit_tool.cwl/x'}
 927                                 ],
 928                                 'requirements': [
 929                                     {'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
 930                                 ],
 931                                 'id': '#submit_tool.cwl',
 932                                 'outputs': [],
 933                                 'baseCommand': 'cat',
 934                                 'class': 'CommandLineTool'
 935                             }
 936                         ]
 937                     }
 938                 },
 939                 '/var/lib/cwl/cwl.input.json': {
 940                     'content': {
 941                         'x': 'XxX'
 942                     },
 943                     'kind': 'json'
 944                 }
 945             }, 'state': 'Committed',
 946             'output_path': '/var/spool/cwl',
 947             'name': 'a test workflow',
 948             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
 949             'command': ['arvados-cwl-runner', '--local', '--api=containers',
 950                         '--no-log-timestamps', '--disable-validate',
 951                         '--eval-timeout=20', '--thread-count=4',
 952                         '--enable-reuse', '--debug', '--on-error=continue',
 953                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
 954             'cwd': '/var/spool/cwl',
 955             'runtime_constraints': {
 956                 'API': True,
 957                 'vcpus': 1,
 958                 'ram': 1073741824
 959             },
 960             'use_existing': True,
 961             'properties': {
 962                 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
 963             },
 964             'secret_mounts': {}
 965         }
 966
 967         stubs.api.container_requests().create.assert_called_with(
 968             body=JsonDiffMatcher(expect_container))
 969         self.assertEqual(capture_stdout.getvalue(),
 970                          stubs.expect_container_request_uuid + '\n')
 971
 972
 973     @stubs
 974     def test_submit_container_name(self, stubs):
 975         capture_stdout = cStringIO.StringIO()
 976         try:
 977             exited = arvados_cwl.main(
 978                 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
 979                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 980                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 981             self.assertEqual(exited, 0)
 982         except:
 983             logging.exception("")
 984
 985         expect_container = copy.deepcopy(stubs.expect_container_spec)
 986         expect_container["name"] = "hello container 123"
 987
 988         stubs.api.container_requests().create.assert_called_with(
 989             body=JsonDiffMatcher(expect_container))
 990         self.assertEqual(capture_stdout.getvalue(),
 991                          stubs.expect_container_request_uuid + '\n')
 992
 993
 994     @stubs
 995     def test_submit_container_project(self, stubs):
 996         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 997         capture_stdout = cStringIO.StringIO()
 998         try:
 999             exited = arvados_cwl.main(
1000                 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
1001                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1002                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1003             self.assertEqual(exited, 0)
1004         except:
1005             logging.exception("")
1006
1007         expect_container = copy.deepcopy(stubs.expect_container_spec)
1008         expect_container["owner_uuid"] = project_uuid
1009         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1010                                        '--no-log-timestamps', '--disable-validate',
1011                                        "--eval-timeout=20", "--thread-count=4",
1012                                        '--enable-reuse', '--debug', '--on-error=continue',
1013                                        '--project-uuid='+project_uuid,
1014                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1015
1016         stubs.api.container_requests().create.assert_called_with(
1017             body=JsonDiffMatcher(expect_container))
1018         self.assertEqual(capture_stdout.getvalue(),
1019                          stubs.expect_container_request_uuid + '\n')
1020
1021     @stubs
1022     def test_submit_container_eval_timeout(self, stubs):
1023         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1024         capture_stdout = cStringIO.StringIO()
1025         try:
1026             exited = arvados_cwl.main(
1027                 ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
1028                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1029                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1030             self.assertEqual(exited, 0)
1031         except:
1032             logging.exception("")
1033
1034         expect_container = copy.deepcopy(stubs.expect_container_spec)
1035         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1036                                        '--no-log-timestamps', '--disable-validate',
1037                                        '--eval-timeout=60.0', '--thread-count=4',
1038                                        '--enable-reuse', '--debug', '--on-error=continue',
1039                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1040
1041         stubs.api.container_requests().create.assert_called_with(
1042             body=JsonDiffMatcher(expect_container))
1043         self.assertEqual(capture_stdout.getvalue(),
1044                          stubs.expect_container_request_uuid + '\n')
1045
1046
1047     @stubs
1048     def test_submit_container_thread_count(self, stubs):
1049         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1050         capture_stdout = cStringIO.StringIO()
1051         try:
1052             exited = arvados_cwl.main(
1053                 ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
1054                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1055                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1056             self.assertEqual(exited, 0)
1057         except:
1058             logging.exception("")
1059
1060         expect_container = copy.deepcopy(stubs.expect_container_spec)
1061         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1062                                        '--no-log-timestamps', '--disable-validate',
1063                                        '--eval-timeout=20', '--thread-count=20',
1064                                        '--enable-reuse', '--debug', '--on-error=continue',
1065                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1066
1067         stubs.api.container_requests().create.assert_called_with(
1068             body=JsonDiffMatcher(expect_container))
1069         self.assertEqual(capture_stdout.getvalue(),
1070                          stubs.expect_container_request_uuid + '\n')
1071
1072
1073     @stubs
1074     def test_submit_job_runner_image(self, stubs):
1075         capture_stdout = cStringIO.StringIO()
1076         try:
1077             exited = arvados_cwl.main(
1078                 ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
1079                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1080                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1081             self.assertEqual(exited, 0)
1082         except:
1083             logging.exception("")
1084
1085         stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
1086
1087         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
1088         stubs.api.pipeline_instances().create.assert_called_with(
1089             body=JsonDiffMatcher(expect_pipeline))
1090         self.assertEqual(capture_stdout.getvalue(),
1091                          stubs.expect_pipeline_uuid + '\n')
1092
1093     @stubs
1094     def test_submit_container_runner_image(self, stubs):
1095         capture_stdout = cStringIO.StringIO()
1096         try:
1097             exited = arvados_cwl.main(
1098                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
1099                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1100                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1101             self.assertEqual(exited, 0)
1102         except:
1103             logging.exception("")
1104
1105         stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
1106
1107         expect_container = copy.deepcopy(stubs.expect_container_spec)
1108         stubs.api.container_requests().create.assert_called_with(
1109             body=JsonDiffMatcher(expect_container))
1110         self.assertEqual(capture_stdout.getvalue(),
1111                          stubs.expect_container_request_uuid + '\n')
1112
1113     @stubs
1114     def test_submit_priority(self, stubs):
1115         capture_stdout = cStringIO.StringIO()
1116         try:
1117             exited = arvados_cwl.main(
1118                 ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
1119                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1120                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1121             self.assertEqual(exited, 0)
1122         except:
1123             logging.exception("")
1124
1125         stubs.expect_container_spec["priority"] = 669
1126
1127         expect_container = copy.deepcopy(stubs.expect_container_spec)
1128         stubs.api.container_requests().create.assert_called_with(
1129             body=JsonDiffMatcher(expect_container))
1130         self.assertEqual(capture_stdout.getvalue(),
1131                          stubs.expect_container_request_uuid + '\n')
1132
1133
1134     @stubs
1135     def test_submit_wf_runner_resources(self, stubs):
1136         capture_stdout = cStringIO.StringIO()
1137         try:
1138             exited = arvados_cwl.main(
1139                 ["--submit", "--no-wait", "--api=containers", "--debug",
1140                  "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
1141                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1142             self.assertEqual(exited, 0)
1143         except:
1144             logging.exception("")
1145
1146         expect_container = copy.deepcopy(stubs.expect_container_spec)
1147         expect_container["runtime_constraints"] = {
1148             "API": True,
1149             "vcpus": 2,
1150             "ram": 2000 * 2**20
1151         }
1152         expect_container["name"] = "submit_wf_runner_resources.cwl"
1153         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1154             {
1155                 "class": "http://arvados.org/cwl#WorkflowRunnerResources",
1156                 "coresMin": 2,
1157                 "ramMin": 2000
1158             }
1159         ]
1160         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
1161             "arv": "http://arvados.org/cwl#",
1162         }
1163
1164         stubs.api.container_requests().create.assert_called_with(
1165             body=JsonDiffMatcher(expect_container))
1166         self.assertEqual(capture_stdout.getvalue(),
1167                          stubs.expect_container_request_uuid + '\n')
1168
1169
1170     @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
1171     @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
1172     @mock.patch("arvados.api")
1173     def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
1174         arvrunner = mock.MagicMock()
1175         arvrunner.project_uuid = ""
1176         api.return_value = mock.MagicMock()
1177         arvrunner.api = api.return_value
1178         arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
1179                                                                         "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1180                                                                         "link_class": "docker_image_repo+tag",
1181                                                                         "name": "arvados/jobs:"+arvados_cwl.__version__,
1182                                                                         "owner_uuid": "",
1183                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1184                                                             {"items": [{"created_at": "",
1185                                                                         "head_uuid": "",
1186                                                                         "link_class": "docker_image_hash",
1187                                                                         "name": "123456",
1188                                                                         "owner_uuid": "",
1189                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
1190         )
1191         find_one_image_hash.return_value = "123456"
1192
1193         arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1194                                                                               "owner_uuid": "",
1195                                                                               "manifest_text": "",
1196                                                                               "properties": ""
1197                                                                           }], "items_available": 1, "offset": 0},)
1198         arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
1199         self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
1200                          arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
1201
1202     @stubs
1203     def test_submit_secrets(self, stubs):
1204         capture_stdout = cStringIO.StringIO()
1205         try:
1206             exited = arvados_cwl.main(
1207                 ["--submit", "--no-wait", "--api=containers", "--debug",
1208                  "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
1209                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1210             self.assertEqual(exited, 0)
1211         except:
1212             logging.exception("")
1213
1214
1215         expect_container = {
1216             "command": [
1217                 "arvados-cwl-runner",
1218                 "--local",
1219                 "--api=containers",
1220                 "--no-log-timestamps",
1221                 "--disable-validate",
1222                 "--eval-timeout=20",
1223                 '--thread-count=4',
1224                 "--enable-reuse",
1225                 '--debug',
1226                 "--on-error=continue",
1227                 "/var/lib/cwl/workflow.json#main",
1228                 "/var/lib/cwl/cwl.input.json"
1229             ],
1230             "container_image": "arvados/jobs:"+arvados_cwl.__version__,
1231             "cwd": "/var/spool/cwl",
1232             "mounts": {
1233                 "/var/lib/cwl/cwl.input.json": {
1234                     "content": {
1235                         "pw": {
1236                             "$include": "/secrets/s0"
1237                         }
1238                     },
1239                     "kind": "json"
1240                 },
1241                 "/var/lib/cwl/workflow.json": {
1242                     "content": {
1243                         "$graph": [
1244                             {
1245                                 "$namespaces": {
1246                                     "cwltool": "http://commonwl.org/cwltool#"
1247                                 },
1248                                 "arguments": [
1249                                     "md5sum",
1250                                     "example.conf"
1251                                 ],
1252                                 "class": "CommandLineTool",
1253                                 "hints": [
1254                                     {
1255                                         "class": "http://commonwl.org/cwltool#Secrets",
1256                                         "secrets": [
1257                                             "#secret_job.cwl/pw"
1258                                         ]
1259                                     }
1260                                 ],
1261                                 "id": "#secret_job.cwl",
1262                                 "inputs": [
1263                                     {
1264                                         "id": "#secret_job.cwl/pw",
1265                                         "type": "string"
1266                                     }
1267                                 ],
1268                                 "outputs": [
1269                                     {
1270                                         "id": "#secret_job.cwl/out",
1271                                         "type": "stdout"
1272                                     }
1273                                 ],
1274                                 "stdout": "hashed_example.txt",
1275                                 "requirements": [
1276                                     {
1277                                         "class": "InitialWorkDirRequirement",
1278                                         "listing": [
1279                                             {
1280                                                 "entry": "username: user\npassword: $(inputs.pw)\n",
1281                                                 "entryname": "example.conf"
1282                                             }
1283                                         ]
1284                                     }
1285                                 ]
1286                             },
1287                             {
1288                                 "class": "Workflow",
1289                                 "hints": [
1290                                     {
1291                                         "class": "DockerRequirement",
1292                                         "dockerPull": "debian:8"
1293                                     },
1294                                     {
1295                                         "class": "http://commonwl.org/cwltool#Secrets",
1296                                         "secrets": [
1297                                             "#main/pw"
1298                                         ]
1299                                     }
1300                                 ],
1301                                 "id": "#main",
1302                                 "inputs": [
1303                                     {
1304                                         "id": "#main/pw",
1305                                         "type": "string"
1306                                     }
1307                                 ],
1308                                 "outputs": [
1309                                     {
1310                                         "id": "#main/out",
1311                                         "outputSource": "#main/step1/out",
1312                                         "type": "File"
1313                                     }
1314                                 ],
1315                                 "steps": [
1316                                     {
1317                                         "id": "#main/step1",
1318                                         "in": [
1319                                             {
1320                                                 "id": "#main/step1/pw",
1321                                                 "source": "#main/pw"
1322                                             }
1323                                         ],
1324                                         "out": [
1325                                             "#main/step1/out"
1326                                         ],
1327                                         "run": "#secret_job.cwl"
1328                                     }
1329                                 ]
1330                             }
1331                         ],
1332                         "cwlVersion": "v1.0"
1333                     },
1334                     "kind": "json"
1335                 },
1336                 "/var/spool/cwl": {
1337                     "kind": "collection",
1338                     "writable": True
1339                 },
1340                 "stdout": {
1341                     "kind": "file",
1342                     "path": "/var/spool/cwl/cwl.output.json"
1343                 }
1344             },
1345             "name": "secret_wf.cwl",
1346             "output_path": "/var/spool/cwl",
1347             "priority": 500,
1348             "properties": {},
1349             "runtime_constraints": {
1350                 "API": True,
1351                 "ram": 1073741824,
1352                 "vcpus": 1
1353             },
1354             "secret_mounts": {
1355                 "/secrets/s0": {
1356                     "content": "blorp",
1357                     "kind": "text"
1358                 }
1359             },
1360             "state": "Committed",
1361             "use_existing": True
1362         }
1363
1364         stubs.api.container_requests().create.assert_called_with(
1365             body=JsonDiffMatcher(expect_container))
1366         self.assertEqual(capture_stdout.getvalue(),
1367                          stubs.expect_container_request_uuid + '\n')
1368
1369     @stubs
1370     def test_submit_request_uuid(self, stubs):
1371         stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
1372
1373         stubs.api.container_requests().update().execute.return_value = {
1374             "uuid": stubs.expect_container_request_uuid,
1375             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
1376             "state": "Queued"
1377         }
1378
1379         capture_stdout = cStringIO.StringIO()
1380         try:
1381             exited = arvados_cwl.main(
1382                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
1383                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1384                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1385             self.assertEqual(exited, 0)
1386         except:
1387             logging.exception("")
1388
1389         stubs.api.container_requests().update.assert_called_with(
1390             uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
1391         self.assertEqual(capture_stdout.getvalue(),
1392                          stubs.expect_container_request_uuid + '\n')
1393
1394
1395 class TestCreateTemplate(unittest.TestCase):
1396     existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
1397
1398     def _adjust_script_params(self, expect_component):
1399         expect_component['script_parameters']['x'] = {
1400             'dataclass': 'File',
1401             'required': True,
1402             'type': 'File',
1403             'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
1404         }
1405         expect_component['script_parameters']['y'] = {
1406             'dataclass': 'Collection',
1407             'required': True,
1408             'type': 'Directory',
1409             'value': '99999999999999999999999999999998+99',
1410         }
1411         expect_component['script_parameters']['z'] = {
1412             'dataclass': 'Collection',
1413             'required': True,
1414             'type': 'Directory',
1415         }
1416
1417     @stubs
1418     def test_create(self, stubs):
1419         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1420
1421         capture_stdout = cStringIO.StringIO()
1422
1423         exited = arvados_cwl.main(
1424             ["--create-workflow", "--debug",
1425              "--api=jobs",
1426              "--project-uuid", project_uuid,
1427              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1428             capture_stdout, sys.stderr, api_client=stubs.api)
1429         self.assertEqual(exited, 0)
1430
1431         stubs.api.pipeline_instances().create.refute_called()
1432         stubs.api.jobs().create.refute_called()
1433
1434         expect_component = copy.deepcopy(stubs.expect_job_spec)
1435         self._adjust_script_params(expect_component)
1436         expect_template = {
1437             "components": {
1438                 "submit_wf.cwl": expect_component,
1439             },
1440             "name": "submit_wf.cwl",
1441             "owner_uuid": project_uuid,
1442         }
1443         stubs.api.pipeline_templates().create.assert_called_with(
1444             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1445
1446         self.assertEqual(capture_stdout.getvalue(),
1447                          stubs.expect_pipeline_template_uuid + '\n')
1448
1449
1450     @stubs
1451     def test_create_name(self, stubs):
1452         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1453
1454         capture_stdout = cStringIO.StringIO()
1455
1456         exited = arvados_cwl.main(
1457             ["--create-workflow", "--debug",
1458              "--project-uuid", project_uuid,
1459              "--api=jobs",
1460              "--name", "testing 123",
1461              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1462             capture_stdout, sys.stderr, api_client=stubs.api)
1463         self.assertEqual(exited, 0)
1464
1465         stubs.api.pipeline_instances().create.refute_called()
1466         stubs.api.jobs().create.refute_called()
1467
1468         expect_component = copy.deepcopy(stubs.expect_job_spec)
1469         self._adjust_script_params(expect_component)
1470         expect_template = {
1471             "components": {
1472                 "testing 123": expect_component,
1473             },
1474             "name": "testing 123",
1475             "owner_uuid": project_uuid,
1476         }
1477         stubs.api.pipeline_templates().create.assert_called_with(
1478             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1479
1480         self.assertEqual(capture_stdout.getvalue(),
1481                          stubs.expect_pipeline_template_uuid + '\n')
1482
1483
1484     @stubs
1485     def test_update_name(self, stubs):
1486         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1487
1488         capture_stdout = cStringIO.StringIO()
1489
1490         exited = arvados_cwl.main(
1491             ["--update-workflow", self.existing_template_uuid,
1492              "--debug",
1493              "--project-uuid", project_uuid,
1494              "--api=jobs",
1495              "--name", "testing 123",
1496              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1497             capture_stdout, sys.stderr, api_client=stubs.api)
1498         self.assertEqual(exited, 0)
1499
1500         stubs.api.pipeline_instances().create.refute_called()
1501         stubs.api.jobs().create.refute_called()
1502
1503         expect_component = copy.deepcopy(stubs.expect_job_spec)
1504         self._adjust_script_params(expect_component)
1505         expect_template = {
1506             "components": {
1507                 "testing 123": expect_component,
1508             },
1509             "name": "testing 123",
1510             "owner_uuid": project_uuid,
1511         }
1512         stubs.api.pipeline_templates().create.refute_called()
1513         stubs.api.pipeline_templates().update.assert_called_with(
1514             body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
1515
1516         self.assertEqual(capture_stdout.getvalue(),
1517                          self.existing_template_uuid + '\n')
1518
1519
1520 class TestCreateWorkflow(unittest.TestCase):
1521     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1522     expect_workflow = StripYAMLComments(
1523         open("tests/wf/expect_packed.cwl").read())
1524
1525     @stubs
1526     def test_create(self, stubs):
1527         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1528
1529         capture_stdout = cStringIO.StringIO()
1530
1531         exited = arvados_cwl.main(
1532             ["--create-workflow", "--debug",
1533              "--api=containers",
1534              "--project-uuid", project_uuid,
1535              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1536             capture_stdout, sys.stderr, api_client=stubs.api)
1537         self.assertEqual(exited, 0)
1538
1539         stubs.api.pipeline_templates().create.refute_called()
1540         stubs.api.container_requests().create.refute_called()
1541
1542         body = {
1543             "workflow": {
1544                 "owner_uuid": project_uuid,
1545                 "name": "submit_wf.cwl",
1546                 "description": "",
1547                 "definition": self.expect_workflow,
1548             }
1549         }
1550         stubs.api.workflows().create.assert_called_with(
1551             body=JsonDiffMatcher(body))
1552
1553         self.assertEqual(capture_stdout.getvalue(),
1554                          stubs.expect_workflow_uuid + '\n')
1555
1556
1557     @stubs
1558     def test_create_name(self, stubs):
1559         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1560
1561         capture_stdout = cStringIO.StringIO()
1562
1563         exited = arvados_cwl.main(
1564             ["--create-workflow", "--debug",
1565              "--api=containers",
1566              "--project-uuid", project_uuid,
1567              "--name", "testing 123",
1568              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1569             capture_stdout, sys.stderr, api_client=stubs.api)
1570         self.assertEqual(exited, 0)
1571
1572         stubs.api.pipeline_templates().create.refute_called()
1573         stubs.api.container_requests().create.refute_called()
1574
1575         body = {
1576             "workflow": {
1577                 "owner_uuid": project_uuid,
1578                 "name": "testing 123",
1579                 "description": "",
1580                 "definition": self.expect_workflow,
1581             }
1582         }
1583         stubs.api.workflows().create.assert_called_with(
1584             body=JsonDiffMatcher(body))
1585
1586         self.assertEqual(capture_stdout.getvalue(),
1587                          stubs.expect_workflow_uuid + '\n')
1588
1589     @stubs
1590     def test_incompatible_api(self, stubs):
1591         capture_stderr = cStringIO.StringIO()
1592         logging.getLogger('arvados.cwl-runner').addHandler(
1593             logging.StreamHandler(capture_stderr))
1594
1595         exited = arvados_cwl.main(
1596             ["--update-workflow", self.existing_workflow_uuid,
1597              "--api=jobs",
1598              "--debug",
1599              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1600             sys.stderr, sys.stderr, api_client=stubs.api)
1601         self.assertEqual(exited, 1)
1602         self.assertRegexpMatches(
1603             capture_stderr.getvalue(),
1604             "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
1605
1606     @stubs
1607     def test_update(self, stubs):
1608         capture_stdout = cStringIO.StringIO()
1609
1610         exited = arvados_cwl.main(
1611             ["--update-workflow", self.existing_workflow_uuid,
1612              "--debug",
1613              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1614             capture_stdout, sys.stderr, api_client=stubs.api)
1615         self.assertEqual(exited, 0)
1616
1617         body = {
1618             "workflow": {
1619                 "name": "submit_wf.cwl",
1620                 "description": "",
1621                 "definition": self.expect_workflow,
1622             }
1623         }
1624         stubs.api.workflows().update.assert_called_with(
1625             uuid=self.existing_workflow_uuid,
1626             body=JsonDiffMatcher(body))
1627         self.assertEqual(capture_stdout.getvalue(),
1628                          self.existing_workflow_uuid + '\n')
1629
1630
1631     @stubs
1632     def test_update_name(self, stubs):
1633         capture_stdout = cStringIO.StringIO()
1634
1635         exited = arvados_cwl.main(
1636             ["--update-workflow", self.existing_workflow_uuid,
1637              "--debug", "--name", "testing 123",
1638              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1639             capture_stdout, sys.stderr, api_client=stubs.api)
1640         self.assertEqual(exited, 0)
1641
1642         body = {
1643             "workflow": {
1644                 "name": "testing 123",
1645                 "description": "",
1646                 "definition": self.expect_workflow,
1647             }
1648         }
1649         stubs.api.workflows().update.assert_called_with(
1650             uuid=self.existing_workflow_uuid,
1651             body=JsonDiffMatcher(body))
1652         self.assertEqual(capture_stdout.getvalue(),
1653                          self.existing_workflow_uuid + '\n')
1654
1655
1656     @stubs
1657     def test_create_collection_per_tool(self, stubs):
1658         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1659
1660         capture_stdout = cStringIO.StringIO()
1661
1662         exited = arvados_cwl.main(
1663             ["--create-workflow", "--debug",
1664              "--api=containers",
1665              "--project-uuid", project_uuid,
1666              "tests/collection_per_tool/collection_per_tool.cwl"],
1667             capture_stdout, sys.stderr, api_client=stubs.api)
1668         self.assertEqual(exited, 0)
1669
1670         toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1671         expect_workflow = StripYAMLComments(open(toolfile).read())
1672
1673         body = {
1674             "workflow": {
1675                 "owner_uuid": project_uuid,
1676                 "name": "collection_per_tool.cwl",
1677                 "description": "",
1678                 "definition": expect_workflow,
1679             }
1680         }
1681         stubs.api.workflows().create.assert_called_with(
1682             body=JsonDiffMatcher(body))
1683
1684         self.assertEqual(capture_stdout.getvalue(),
1685                          stubs.expect_workflow_uuid + '\n')
1686
1687 class TestTemplateInputs(unittest.TestCase):
1688     expect_template = {
1689         "components": {
1690             "inputs_test.cwl": {
1691                 'runtime_constraints': {
1692                     'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
1693                     'min_ram_mb_per_node': 1024
1694                 },
1695                 'script_parameters': {
1696                     'cwl:tool':
1697                     '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main',
1698                     'optionalFloatInput': None,
1699                     'fileInput': {
1700                         'type': 'File',
1701                         'dataclass': 'File',
1702                         'required': True,
1703                         'title': "It's a file; we expect to find some characters in it.",
1704                         'description': 'If there were anything further to say, it would be said here,\nor here.'
1705                     },
1706                     'floatInput': {
1707                         'type': 'float',
1708                         'dataclass': 'number',
1709                         'required': True,
1710                         'title': 'Floats like a duck',
1711                         'default': 0.1,
1712                         'value': 0.1,
1713                     },
1714                     'optionalFloatInput': {
1715                         'type': ['null', 'float'],
1716                         'dataclass': 'number',
1717                         'required': False,
1718                     },
1719                     'boolInput': {
1720                         'type': 'boolean',
1721                         'dataclass': 'boolean',
1722                         'required': True,
1723                         'title': 'True or false?',
1724                     },
1725                 },
1726                 'repository': 'arvados',
1727                 'script_version': 'master',
1728                 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
1729                 'script': 'cwl-runner',
1730             },
1731         },
1732         "name": "inputs_test.cwl",
1733     }
1734
1735     @stubs
1736     def test_inputs_empty(self, stubs):
1737         exited = arvados_cwl.main(
1738             ["--create-template",
1739              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
1740             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1741         self.assertEqual(exited, 0)
1742
1743         stubs.api.pipeline_templates().create.assert_called_with(
1744             body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
1745
1746     @stubs
1747     def test_inputs(self, stubs):
1748         exited = arvados_cwl.main(
1749             ["--create-template",
1750              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
1751             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1752         self.assertEqual(exited, 0)
1753
1754         expect_template = copy.deepcopy(self.expect_template)
1755         params = expect_template[
1756             "components"]["inputs_test.cwl"]["script_parameters"]
1757         params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
1758         params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main'
1759         params["floatInput"]["value"] = 1.234
1760         params["boolInput"]["value"] = True
1761
1762         stubs.api.pipeline_templates().create.assert_called_with(
1763             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)