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.executor
  19 import arvados_cwl.runner
  20 import arvados.keep
  21
  22 from .matcher import JsonDiffMatcher, StripYAMLComments
  23 from .mock_discovery import get_rootDesc
  24
  25 import ruamel.yaml as yaml
  26
  27 _rootDesc = None
  28
  29 def stubs(func):
  30     @functools.wraps(func)
  31     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  32     @mock.patch("arvados.collection.KeepClient")
  33     @mock.patch("arvados.keep.KeepClient")
  34     @mock.patch("arvados.events.subscribe")
  35     def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs):
  36         class Stubs:
  37             pass
  38         stubs = Stubs()
  39         stubs.events = events
  40         stubs.keepdocker = keepdocker
  41
  42         def putstub(p, **kwargs):
  43             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
  44         keep_client1().put.side_effect = putstub
  45         keep_client1.put.side_effect = putstub
  46         keep_client2().put.side_effect = putstub
  47         keep_client2.put.side_effect = putstub
  48
  49         stubs.keep_client = keep_client2
  50         stubs.docker_images = {
  51             "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")],
  52             "debian:8": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")],
  53             "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")],
  54             "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")],
  55         }
  56         def kd(a, b, image_name=None, image_tag=None):
  57             return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
  58         stubs.keepdocker.side_effect = kd
  59
  60         stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
  61         stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz"
  62
  63         stubs.api = mock.MagicMock()
  64         stubs.api._rootDesc = get_rootDesc()
  65
  66         stubs.api.users().current().execute.return_value = {
  67             "uuid": stubs.fake_user_uuid,
  68         }
  69         stubs.api.collections().list().execute.return_value = {"items": []}
  70         stubs.api.containers().current().execute.return_value = {
  71             "uuid": stubs.fake_container_uuid,
  72         }
  73
  74         class CollectionExecute(object):
  75             def __init__(self, exe):
  76                 self.exe = exe
  77             def execute(self, num_retries=None):
  78                 return self.exe
  79
  80         def collection_createstub(created_collections, body, ensure_unique_name=None):
  81             mt = body["manifest_text"]
  82             uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections)
  83             pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
  84             created_collections[uuid] = {
  85                 "uuid": uuid,
  86                 "portable_data_hash": pdh,
  87                 "manifest_text": mt
  88             }
  89             return CollectionExecute(created_collections[uuid])
  90
  91         def collection_getstub(created_collections, uuid):
  92             for v in created_collections.itervalues():
  93                 if uuid in (v["uuid"], v["portable_data_hash"]):
  94                     return CollectionExecute(v)
  95
  96         created_collections = {
  97             "99999999999999999999999999999998+99": {
  98                 "uuid": "",
  99                 "portable_data_hash": "99999999999999999999999999999998+99",
 100                 "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
 101             },
 102             "99999999999999999999999999999994+99": {
 103                 "uuid": "",
 104                 "portable_data_hash": "99999999999999999999999999999994+99",
 105                 "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
 106             },
 107             "zzzzz-4zz18-zzzzzzzzzzzzzd3": {
 108                 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd3",
 109                 "portable_data_hash": "999999999999999999999999999999d3+99",
 110                 "manifest_text": ""
 111             },
 112             "zzzzz-4zz18-zzzzzzzzzzzzzd4": {
 113                 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd4",
 114                 "portable_data_hash": "999999999999999999999999999999d4+99",
 115                 "manifest_text": ""
 116             },
 117             "zzzzz-4zz18-zzzzzzzzzzzzzd5": {
 118                 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd5",
 119                 "portable_data_hash": "999999999999999999999999999999d5+99",
 120                 "manifest_text": ""
 121             },
 122             "zzzzz-4zz18-zzzzzzzzzzzzzd6": {
 123                 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd6",
 124                 "portable_data_hash": "999999999999999999999999999999d6+99",
 125                 "manifest_text": ""
 126             }
 127         }
 128         stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
 129         stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
 130
 131         stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 132         stubs.api.jobs().create().execute.return_value = {
 133             "uuid": stubs.expect_job_uuid,
 134             "state": "Queued",
 135         }
 136
 137         stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
 138         stubs.api.container_requests().create().execute.return_value = {
 139             "uuid": stubs.expect_container_request_uuid,
 140             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
 141             "state": "Queued"
 142         }
 143
 144         stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
 145         stubs.api.pipeline_templates().create().execute.return_value = {
 146             "uuid": stubs.expect_pipeline_template_uuid,
 147         }
 148         stubs.expect_job_spec = {
 149             'runtime_constraints': {
 150                 'docker_image': '999999999999999999999999999999d3+99',
 151                 'min_ram_mb_per_node': 1024
 152             },
 153             'script_parameters': {
 154                 'x': {
 155                     'basename': 'blorp.txt',
 156                     'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 157                     'class': 'File'
 158                 },
 159                 'y': {
 160                     'basename': '99999999999999999999999999999998+99',
 161                     'location': 'keep:99999999999999999999999999999998+99',
 162                     'class': 'Directory'
 163                 },
 164                 'z': {
 165                     'basename': 'anonymous',
 166                     "listing": [{
 167                         "basename": "renamed.txt",
 168                         "class": "File",
 169                         "location": "keep:99999999999999999999999999999998+99/file1.txt",
 170                         "size": 0
 171                     }],
 172                     'class': 'Directory'
 173                 },
 174                 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
 175             },
 176             'repository': 'arvados',
 177             'script_version': 'master',
 178             'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
 179             'script': 'cwl-runner'
 180         }
 181         stubs.pipeline_component = stubs.expect_job_spec.copy()
 182         stubs.expect_pipeline_instance = {
 183             'name': 'submit_wf.cwl',
 184             'state': 'RunningOnServer',
 185             'owner_uuid': None,
 186             "components": {
 187                 "cwl-runner": {
 188                     'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024},
 189                     'script_parameters': {
 190                         'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
 191                         'x': {"value": {
 192                             'basename': 'blorp.txt',
 193                             'class': 'File',
 194                             'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 195                             "size": 16
 196                         }},
 197                         'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
 198                               'listing': [
 199                                   {
 200                                       'basename': 'renamed.txt',
 201                                       'class': 'File', 'location':
 202                                       'keep:99999999999999999999999999999998+99/file1.txt',
 203                                       'size': 0
 204                                   }
 205                               ]}},
 206                         'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
 207                         'arv:debug': True,
 208                         'arv:enable_reuse': True,
 209                         'arv:on_error': 'continue'
 210                     },
 211                     'repository': 'arvados',
 212                     'script_version': 'master',
 213                     'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
 214                     'script': 'cwl-runner',
 215                     'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
 216                 }
 217             }
 218         }
 219         stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
 220         stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
 221         stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
 222         stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
 223         stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
 224             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 225             "state": "Queued"
 226         }
 227         stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
 228         stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
 229
 230         with open("tests/wf/submit_wf_packed.cwl") as f:
 231             expect_packed_workflow = yaml.round_trip_load(f)
 232
 233         stubs.expect_container_spec = {
 234             'priority': 500,
 235             'mounts': {
 236                 '/var/spool/cwl': {
 237                     'writable': True,
 238                     'kind': 'collection'
 239                 },
 240                 '/var/lib/cwl/workflow.json': {
 241                     'content': expect_packed_workflow,
 242                     'kind': 'json'
 243                 },
 244                 'stdout': {
 245                     'path': '/var/spool/cwl/cwl.output.json',
 246                     'kind': 'file'
 247                 },
 248                 '/var/lib/cwl/cwl.input.json': {
 249                     'kind': 'json',
 250                     'content': {
 251                         'y': {
 252                             'basename': '99999999999999999999999999999998+99',
 253                             'location': 'keep:99999999999999999999999999999998+99',
 254                             'class': 'Directory'},
 255                         'x': {
 256                             'basename': u'blorp.txt',
 257                             'class': 'File',
 258                             'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 259                             "size": 16
 260                         },
 261                         'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
 262                             {'basename': 'renamed.txt',
 263                              'class': 'File',
 264                              'location': 'keep:99999999999999999999999999999998+99/file1.txt',
 265                              'size': 0
 266                             }
 267                         ]}
 268                     },
 269                     'kind': 'json'
 270                 }
 271             },
 272             'secret_mounts': {},
 273             'state': 'Committed',
 274             'command': ['arvados-cwl-runner', '--local', '--api=containers',
 275                         '--no-log-timestamps', '--disable-validate',
 276                         '--eval-timeout=20', '--thread-count=1',
 277                         '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
 278                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
 279             'name': 'submit_wf.cwl',
 280             'container_image': '999999999999999999999999999999d3+99',
 281             'output_path': '/var/spool/cwl',
 282             'cwd': '/var/spool/cwl',
 283             'runtime_constraints': {
 284                 'API': True,
 285                 'vcpus': 1,
 286                 'ram': (1024+256)*1024*1024
 287             },
 288             'use_existing': True,
 289             'properties': {},
 290             'secret_mounts': {}
 291         }
 292
 293         stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
 294         stubs.api.workflows().create().execute.return_value = {
 295             "uuid": stubs.expect_workflow_uuid,
 296         }
 297         def update_mock(**kwargs):
 298             stubs.updated_uuid = kwargs.get('uuid')
 299             return mock.DEFAULT
 300         stubs.api.workflows().update.side_effect = update_mock
 301         stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
 302             "uuid": stubs.updated_uuid,
 303         }
 304
 305         return func(self, stubs, *args, **kwargs)
 306     return wrapped
 307
 308
 309 class TestSubmit(unittest.TestCase):
 310     @mock.patch("arvados_cwl.arvdocker.arv_docker_get_image")
 311     @mock.patch("time.sleep")
 312     @stubs
 313     def test_submit(self, stubs, tm, arvdock):
 314         def get_image(api_client, dockerRequirement, pull_image, project_uuid):
 315             if dockerRequirement["dockerPull"] == 'arvados/jobs:'+arvados_cwl.__version__:
 316                 return '999999999999999999999999999999d3+99'
 317             elif dockerRequirement["dockerPull"] == "debian:8":
 318                 return '999999999999999999999999999999d4+99'
 319         arvdock.side_effect = get_image
 320
 321         capture_stdout = cStringIO.StringIO()
 322         exited = arvados_cwl.main(
 323             ["--submit", "--no-wait", "--api=jobs", "--debug",
 324              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 325             capture_stdout, sys.stderr, api_client=stubs.api)
 326         self.assertEqual(exited, 0)
 327
 328         stubs.api.collections().create.assert_has_calls([
 329             mock.call(body=JsonDiffMatcher({
 330                 'manifest_text':
 331                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
 332                 'replication_desired': None,
 333                 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
 334             }), ensure_unique_name=False),
 335             mock.call(body=JsonDiffMatcher({
 336                 'manifest_text':
 337                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 338                 'replication_desired': None,
 339                 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
 340             }), ensure_unique_name=False),
 341             mock.call(body=JsonDiffMatcher({
 342                 'manifest_text':
 343                 ". 68089141fbf7e020ac90a9d6a575bc8f+1312 0:1312:workflow.cwl\n",
 344                 'replication_desired': None,
 345                 'name': 'submit_wf.cwl',
 346             }), ensure_unique_name=True)        ])
 347
 348         arvdock.assert_has_calls([
 349             mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
 350             mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8", 'http://arvados.org/cwl#dockerCollectionPDH': '999999999999999999999999999999d4+99'}, True, None),
 351             mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
 352         ])
 353
 354         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 355         stubs.api.pipeline_instances().create.assert_called_with(
 356             body=JsonDiffMatcher(expect_pipeline))
 357         self.assertEqual(capture_stdout.getvalue(),
 358                          stubs.expect_pipeline_uuid + '\n')
 359
 360
 361     @mock.patch("time.sleep")
 362     @stubs
 363     def test_submit_no_reuse(self, stubs, tm):
 364         capture_stdout = cStringIO.StringIO()
 365         exited = arvados_cwl.main(
 366             ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
 367              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 368             capture_stdout, sys.stderr, api_client=stubs.api)
 369         self.assertEqual(exited, 0)
 370
 371         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 372         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
 373         expect_pipeline["properties"] = {"run_options": {"enable_job_reuse": False}}
 374
 375         stubs.api.pipeline_instances().create.assert_called_with(
 376             body=JsonDiffMatcher(expect_pipeline))
 377         self.assertEqual(capture_stdout.getvalue(),
 378                          stubs.expect_pipeline_uuid + '\n')
 379
 380     @stubs
 381     def test_error_when_multiple_storage_classes_specified(self, stubs):
 382         storage_classes = "foo,bar"
 383         exited = arvados_cwl.main(
 384                 ["--debug", "--storage-classes", storage_classes,
 385                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 386                 sys.stdin, sys.stderr, api_client=stubs.api)
 387         self.assertEqual(exited, 1)
 388
 389     @mock.patch("time.sleep")
 390     @stubs
 391     def test_submit_on_error(self, stubs, tm):
 392         capture_stdout = cStringIO.StringIO()
 393         exited = arvados_cwl.main(
 394             ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
 395              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 396             capture_stdout, sys.stderr, api_client=stubs.api)
 397         self.assertEqual(exited, 0)
 398
 399         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 400         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
 401
 402         stubs.api.pipeline_instances().create.assert_called_with(
 403             body=JsonDiffMatcher(expect_pipeline))
 404         self.assertEqual(capture_stdout.getvalue(),
 405                          stubs.expect_pipeline_uuid + '\n')
 406
 407
 408     @mock.patch("time.sleep")
 409     @stubs
 410     def test_submit_runner_ram(self, stubs, tm):
 411         capture_stdout = cStringIO.StringIO()
 412         exited = arvados_cwl.main(
 413             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
 414              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 415             capture_stdout, sys.stderr, api_client=stubs.api)
 416         self.assertEqual(exited, 0)
 417
 418         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 419         expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
 420
 421         stubs.api.pipeline_instances().create.assert_called_with(
 422             body=JsonDiffMatcher(expect_pipeline))
 423         self.assertEqual(capture_stdout.getvalue(),
 424                          stubs.expect_pipeline_uuid + '\n')
 425
 426
 427     @mock.patch("time.sleep")
 428     @stubs
 429     def test_submit_invalid_runner_ram(self, stubs, tm):
 430         capture_stdout = cStringIO.StringIO()
 431         exited = arvados_cwl.main(
 432             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
 433              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 434             capture_stdout, sys.stderr, api_client=stubs.api)
 435         self.assertEqual(exited, 1)
 436
 437     @mock.patch("time.sleep")
 438     @stubs
 439     def test_submit_output_name(self, stubs, tm):
 440         output_name = "test_output_name"
 441
 442         capture_stdout = cStringIO.StringIO()
 443         exited = arvados_cwl.main(
 444             ["--submit", "--no-wait", "--debug", "--output-name", output_name,
 445              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 446             capture_stdout, sys.stderr, api_client=stubs.api)
 447         self.assertEqual(exited, 0)
 448
 449         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 450         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
 451
 452         stubs.api.pipeline_instances().create.assert_called_with(
 453             body=JsonDiffMatcher(expect_pipeline))
 454         self.assertEqual(capture_stdout.getvalue(),
 455                          stubs.expect_pipeline_uuid + '\n')
 456
 457
 458     @mock.patch("time.sleep")
 459     @stubs
 460     def test_submit_pipeline_name(self, stubs, tm):
 461         capture_stdout = cStringIO.StringIO()
 462         exited = arvados_cwl.main(
 463             ["--submit", "--no-wait", "--debug", "--name=hello job 123",
 464              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 465             capture_stdout, sys.stderr, api_client=stubs.api)
 466         self.assertEqual(exited, 0)
 467
 468         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 469         expect_pipeline["name"] = "hello job 123"
 470
 471         stubs.api.pipeline_instances().create.assert_called_with(
 472             body=JsonDiffMatcher(expect_pipeline))
 473         self.assertEqual(capture_stdout.getvalue(),
 474                          stubs.expect_pipeline_uuid + '\n')
 475
 476     @mock.patch("time.sleep")
 477     @stubs
 478     def test_submit_output_tags(self, stubs, tm):
 479         output_tags = "tag0,tag1,tag2"
 480
 481         capture_stdout = cStringIO.StringIO()
 482         exited = arvados_cwl.main(
 483             ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
 484              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 485             capture_stdout, sys.stderr, api_client=stubs.api)
 486         self.assertEqual(exited, 0)
 487
 488         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 489         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
 490
 491         stubs.api.pipeline_instances().create.assert_called_with(
 492             body=JsonDiffMatcher(expect_pipeline))
 493         self.assertEqual(capture_stdout.getvalue(),
 494                          stubs.expect_pipeline_uuid + '\n')
 495
 496     @mock.patch("time.sleep")
 497     @stubs
 498     def test_submit_with_project_uuid(self, stubs, tm):
 499         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 500
 501         exited = arvados_cwl.main(
 502             ["--submit", "--no-wait", "--debug",
 503              "--project-uuid", project_uuid,
 504              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 505             sys.stdout, sys.stderr, api_client=stubs.api)
 506         self.assertEqual(exited, 0)
 507
 508         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 509         expect_pipeline["owner_uuid"] = project_uuid
 510         stubs.api.pipeline_instances().create.assert_called_with(
 511             body=JsonDiffMatcher(expect_pipeline))
 512
 513     @stubs
 514     def test_submit_container(self, stubs):
 515         capture_stdout = cStringIO.StringIO()
 516         try:
 517             exited = arvados_cwl.main(
 518                 ["--submit", "--no-wait", "--api=containers", "--debug",
 519                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 520                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 521             self.assertEqual(exited, 0)
 522         except:
 523             logging.exception("")
 524
 525         stubs.api.collections().create.assert_has_calls([
 526             mock.call(body=JsonDiffMatcher({
 527                 'manifest_text':
 528                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
 529                 'replication_desired': None,
 530                 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
 531             }), ensure_unique_name=False),
 532             mock.call(body=JsonDiffMatcher({
 533                 'manifest_text':
 534                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 535                 'replication_desired': None,
 536                 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
 537             }), ensure_unique_name=False)])
 538
 539         expect_container = copy.deepcopy(stubs.expect_container_spec)
 540         stubs.api.container_requests().create.assert_called_with(
 541             body=JsonDiffMatcher(expect_container))
 542         self.assertEqual(capture_stdout.getvalue(),
 543                          stubs.expect_container_request_uuid + '\n')
 544
 545     @stubs
 546     def test_submit_container_no_reuse(self, stubs):
 547         capture_stdout = cStringIO.StringIO()
 548         try:
 549             exited = arvados_cwl.main(
 550                 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
 551                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 552                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 553             self.assertEqual(exited, 0)
 554         except:
 555             logging.exception("")
 556
 557         expect_container = copy.deepcopy(stubs.expect_container_spec)
 558         expect_container["command"] = [
 559             'arvados-cwl-runner', '--local', '--api=containers',
 560             '--no-log-timestamps', '--disable-validate',
 561             '--eval-timeout=20', '--thread-count=1',
 562             '--disable-reuse', "--collection-cache-size=256",
 563             '--debug', '--on-error=continue',
 564             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 565         expect_container["use_existing"] = False
 566
 567         stubs.api.container_requests().create.assert_called_with(
 568             body=JsonDiffMatcher(expect_container))
 569         self.assertEqual(capture_stdout.getvalue(),
 570                          stubs.expect_container_request_uuid + '\n')
 571
 572
 573     @stubs
 574     def test_submit_container_reuse_disabled_by_workflow(self, stubs):
 575         capture_stdout = cStringIO.StringIO()
 576
 577         exited = arvados_cwl.main(
 578             ["--submit", "--no-wait", "--api=containers", "--debug",
 579              "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
 580             capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 581         self.assertEqual(exited, 0)
 582
 583         expect_container = copy.deepcopy(stubs.expect_container_spec)
 584         expect_container["command"] = [
 585             'arvados-cwl-runner', '--local', '--api=containers',
 586             '--no-log-timestamps', '--disable-validate',
 587             '--eval-timeout=20', '--thread-count=1',
 588             '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
 589             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 590         expect_container["use_existing"] = False
 591         expect_container["name"] = "submit_wf_no_reuse.cwl"
 592         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
 593             {
 594                 "class": "http://arvados.org/cwl#ReuseRequirement",
 595                 "enableReuse": False,
 596             },
 597         ]
 598         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
 599             "arv": "http://arvados.org/cwl#",
 600             "cwltool": "http://commonwl.org/cwltool#"
 601         }
 602
 603         stubs.api.container_requests().create.assert_called_with(
 604             body=JsonDiffMatcher(expect_container))
 605         self.assertEqual(capture_stdout.getvalue(),
 606                          stubs.expect_container_request_uuid + '\n')
 607
 608
 609     @stubs
 610     def test_submit_container_on_error(self, stubs):
 611         capture_stdout = cStringIO.StringIO()
 612         try:
 613             exited = arvados_cwl.main(
 614                 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
 615                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 616                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 617             self.assertEqual(exited, 0)
 618         except:
 619             logging.exception("")
 620
 621         expect_container = copy.deepcopy(stubs.expect_container_spec)
 622         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 623                                        '--no-log-timestamps', '--disable-validate',
 624                                        '--eval-timeout=20', '--thread-count=1',
 625                                        '--enable-reuse', "--collection-cache-size=256",
 626                                        '--debug', '--on-error=stop',
 627                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 628
 629         stubs.api.container_requests().create.assert_called_with(
 630             body=JsonDiffMatcher(expect_container))
 631         self.assertEqual(capture_stdout.getvalue(),
 632                          stubs.expect_container_request_uuid + '\n')
 633
 634     @stubs
 635     def test_submit_container_output_name(self, stubs):
 636         output_name = "test_output_name"
 637
 638         capture_stdout = cStringIO.StringIO()
 639         try:
 640             exited = arvados_cwl.main(
 641                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
 642                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 643                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 644             self.assertEqual(exited, 0)
 645         except:
 646             logging.exception("")
 647
 648         expect_container = copy.deepcopy(stubs.expect_container_spec)
 649         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 650                                        '--no-log-timestamps', '--disable-validate',
 651                                        '--eval-timeout=20', '--thread-count=1',
 652                                        '--enable-reuse', "--collection-cache-size=256",
 653                                        "--output-name="+output_name, '--debug', '--on-error=continue',
 654                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 655         expect_container["output_name"] = output_name
 656
 657         stubs.api.container_requests().create.assert_called_with(
 658             body=JsonDiffMatcher(expect_container))
 659         self.assertEqual(capture_stdout.getvalue(),
 660                          stubs.expect_container_request_uuid + '\n')
 661
 662     @stubs
 663     def test_submit_storage_classes(self, stubs):
 664         capture_stdout = cStringIO.StringIO()
 665         try:
 666             exited = arvados_cwl.main(
 667                 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
 668                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 669                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 670             self.assertEqual(exited, 0)
 671         except:
 672             logging.exception("")
 673
 674         expect_container = copy.deepcopy(stubs.expect_container_spec)
 675         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 676                                        '--no-log-timestamps', '--disable-validate',
 677                                        '--eval-timeout=20', '--thread-count=1',
 678                                        '--enable-reuse', "--collection-cache-size=256", "--debug",
 679                                        "--storage-classes=foo", '--on-error=continue',
 680                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 681
 682         stubs.api.container_requests().create.assert_called_with(
 683             body=JsonDiffMatcher(expect_container))
 684         self.assertEqual(capture_stdout.getvalue(),
 685                          stubs.expect_container_request_uuid + '\n')
 686
 687     @mock.patch("arvados_cwl.task_queue.TaskQueue")
 688     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
 689     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
 690     @stubs
 691     def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
 692         def set_final_output(job_order, output_callback, runtimeContext):
 693             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
 694             return []
 695         job.side_effect = set_final_output
 696
 697         try:
 698             exited = arvados_cwl.main(
 699                 ["--debug", "--local", "--storage-classes=foo",
 700                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 701                 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 702             self.assertEqual(exited, 0)
 703         except:
 704             logging.exception("")
 705
 706         make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
 707
 708     @mock.patch("arvados_cwl.task_queue.TaskQueue")
 709     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
 710     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
 711     @stubs
 712     def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
 713         def set_final_output(job_order, output_callback, runtimeContext):
 714             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
 715             return []
 716         job.side_effect = set_final_output
 717
 718         try:
 719             exited = arvados_cwl.main(
 720                 ["--debug", "--local",
 721                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 722                 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 723             self.assertEqual(exited, 0)
 724         except:
 725             logging.exception("")
 726
 727         make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
 728
 729     @stubs
 730     def test_submit_container_output_ttl(self, stubs):
 731         capture_stdout = cStringIO.StringIO()
 732         try:
 733             exited = arvados_cwl.main(
 734                 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
 735                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 736                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 737             self.assertEqual(exited, 0)
 738         except:
 739             logging.exception("")
 740
 741         expect_container = copy.deepcopy(stubs.expect_container_spec)
 742         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 743                                        '--no-log-timestamps', '--disable-validate',
 744                                        '--eval-timeout=20', '--thread-count=1',
 745                                        '--enable-reuse', "--collection-cache-size=256", '--debug',
 746                                        '--on-error=continue',
 747                                        "--intermediate-output-ttl=3600",
 748                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 749
 750         stubs.api.container_requests().create.assert_called_with(
 751             body=JsonDiffMatcher(expect_container))
 752         self.assertEqual(capture_stdout.getvalue(),
 753                          stubs.expect_container_request_uuid + '\n')
 754
 755     @stubs
 756     def test_submit_container_trash_intermediate(self, stubs):
 757         capture_stdout = cStringIO.StringIO()
 758         try:
 759             exited = arvados_cwl.main(
 760                 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
 761                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 762                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 763             self.assertEqual(exited, 0)
 764         except:
 765             logging.exception("")
 766
 767         expect_container = copy.deepcopy(stubs.expect_container_spec)
 768         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 769                                        '--no-log-timestamps', '--disable-validate',
 770                                        '--eval-timeout=20', '--thread-count=1',
 771                                        '--enable-reuse', "--collection-cache-size=256",
 772                                        '--debug', '--on-error=continue',
 773                                        "--trash-intermediate",
 774                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 775
 776         stubs.api.container_requests().create.assert_called_with(
 777             body=JsonDiffMatcher(expect_container))
 778         self.assertEqual(capture_stdout.getvalue(),
 779                          stubs.expect_container_request_uuid + '\n')
 780
 781     @stubs
 782     def test_submit_container_output_tags(self, stubs):
 783         output_tags = "tag0,tag1,tag2"
 784
 785         capture_stdout = cStringIO.StringIO()
 786         try:
 787             exited = arvados_cwl.main(
 788                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
 789                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 790                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 791             self.assertEqual(exited, 0)
 792         except:
 793             logging.exception("")
 794
 795         expect_container = copy.deepcopy(stubs.expect_container_spec)
 796         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 797                                        '--no-log-timestamps', '--disable-validate',
 798                                        '--eval-timeout=20', '--thread-count=1',
 799                                        '--enable-reuse', "--collection-cache-size=256",
 800                                        "--output-tags="+output_tags, '--debug', '--on-error=continue',
 801                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 802
 803         stubs.api.container_requests().create.assert_called_with(
 804             body=JsonDiffMatcher(expect_container))
 805         self.assertEqual(capture_stdout.getvalue(),
 806                          stubs.expect_container_request_uuid + '\n')
 807
 808     @stubs
 809     def test_submit_container_runner_ram(self, stubs):
 810         capture_stdout = cStringIO.StringIO()
 811         try:
 812             exited = arvados_cwl.main(
 813                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
 814                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 815                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 816             self.assertEqual(exited, 0)
 817         except:
 818             logging.exception("")
 819
 820         expect_container = copy.deepcopy(stubs.expect_container_spec)
 821         expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024
 822
 823         stubs.api.container_requests().create.assert_called_with(
 824             body=JsonDiffMatcher(expect_container))
 825         self.assertEqual(capture_stdout.getvalue(),
 826                          stubs.expect_container_request_uuid + '\n')
 827
 828     @mock.patch("arvados.collection.CollectionReader")
 829     @mock.patch("time.sleep")
 830     @stubs
 831     def test_submit_file_keepref(self, stubs, tm, collectionReader):
 832         capture_stdout = cStringIO.StringIO()
 833         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
 834         exited = arvados_cwl.main(
 835             ["--submit", "--no-wait", "--api=containers", "--debug",
 836              "tests/wf/submit_keepref_wf.cwl"],
 837             capture_stdout, sys.stderr, api_client=stubs.api)
 838         self.assertEqual(exited, 0)
 839
 840
 841     @mock.patch("arvados.collection.CollectionReader")
 842     @mock.patch("time.sleep")
 843     @stubs
 844     def test_submit_keepref(self, stubs, tm, reader):
 845         capture_stdout = cStringIO.StringIO()
 846
 847         with open("tests/wf/expect_arvworkflow.cwl") as f:
 848             reader().open().__enter__().read.return_value = f.read()
 849
 850         exited = arvados_cwl.main(
 851             ["--submit", "--no-wait", "--api=containers", "--debug",
 852              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 853             capture_stdout, sys.stderr, api_client=stubs.api)
 854         self.assertEqual(exited, 0)
 855
 856         expect_container = {
 857             'priority': 500,
 858             'mounts': {
 859                 '/var/spool/cwl': {
 860                     'writable': True,
 861                     'kind': 'collection'
 862                 },
 863                 'stdout': {
 864                     'path': '/var/spool/cwl/cwl.output.json',
 865                     'kind': 'file'
 866                 },
 867                 '/var/lib/cwl/workflow': {
 868                     'portable_data_hash': '99999999999999999999999999999994+99',
 869                     'kind': 'collection'
 870                 },
 871                 '/var/lib/cwl/cwl.input.json': {
 872                     'content': {
 873                         'x': 'XxX'
 874                     },
 875                     'kind': 'json'
 876                 }
 877             }, 'state': 'Committed',
 878             'output_path': '/var/spool/cwl',
 879             'name': 'expect_arvworkflow.cwl#main',
 880             'container_image': '999999999999999999999999999999d3+99',
 881             'command': ['arvados-cwl-runner', '--local', '--api=containers',
 882                         '--no-log-timestamps', '--disable-validate',
 883                         '--eval-timeout=20', '--thread-count=1',
 884                         '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
 885                         '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
 886             'cwd': '/var/spool/cwl',
 887             'runtime_constraints': {
 888                 'API': True,
 889                 'vcpus': 1,
 890                 'ram': 1342177280
 891             },
 892             'use_existing': True,
 893             'properties': {},
 894             'secret_mounts': {}
 895         }
 896
 897         stubs.api.container_requests().create.assert_called_with(
 898             body=JsonDiffMatcher(expect_container))
 899         self.assertEqual(capture_stdout.getvalue(),
 900                          stubs.expect_container_request_uuid + '\n')
 901
 902
 903     @mock.patch("arvados.collection.CollectionReader")
 904     @mock.patch("time.sleep")
 905     @stubs
 906     def test_submit_jobs_keepref(self, stubs, tm, reader):
 907         capture_stdout = cStringIO.StringIO()
 908
 909         with open("tests/wf/expect_arvworkflow.cwl") as f:
 910             reader().open().__enter__().read.return_value = f.read()
 911
 912         exited = arvados_cwl.main(
 913             ["--submit", "--no-wait", "--api=jobs", "--debug",
 914              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 915             capture_stdout, sys.stderr, api_client=stubs.api)
 916         self.assertEqual(exited, 0)
 917
 918         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 919         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
 920         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
 921         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
 922         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
 923         expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
 924         stubs.api.pipeline_instances().create.assert_called_with(
 925             body=JsonDiffMatcher(expect_pipeline))
 926
 927     @mock.patch("time.sleep")
 928     @stubs
 929     def test_submit_arvworkflow(self, stubs, tm):
 930         capture_stdout = cStringIO.StringIO()
 931
 932         with open("tests/wf/expect_arvworkflow.cwl") as f:
 933             stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
 934
 935         exited = arvados_cwl.main(
 936             ["--submit", "--no-wait", "--api=containers", "--debug",
 937              "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
 938             capture_stdout, sys.stderr, api_client=stubs.api)
 939         self.assertEqual(exited, 0)
 940
 941         expect_container = {
 942             'priority': 500,
 943             'mounts': {
 944                 '/var/spool/cwl': {
 945                     'writable': True,
 946                     'kind': 'collection'
 947                 },
 948                 'stdout': {
 949                     'path': '/var/spool/cwl/cwl.output.json',
 950                     'kind': 'file'
 951                 },
 952                 '/var/lib/cwl/workflow.json': {
 953                     'kind': 'json',
 954                     'content': {
 955                         'cwlVersion': 'v1.0',
 956                         '$graph': [
 957                             {
 958                                 'id': '#main',
 959                                 'inputs': [
 960                                     {'type': 'string', 'id': '#main/x'}
 961                                 ],
 962                                 'steps': [
 963                                     {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
 964                                      'run': '#submit_tool.cwl',
 965                                      'id': '#main/step1',
 966                                      'out': []}
 967                                 ],
 968                                 'class': 'Workflow',
 969                                 'outputs': []
 970                             },
 971                             {
 972                                 'inputs': [
 973                                     {
 974                                         'inputBinding': {'position': 1},
 975                                         'type': 'string',
 976                                         'id': '#submit_tool.cwl/x'}
 977                                 ],
 978                                 'requirements': [
 979                                     {
 980                                         'dockerPull': 'debian:8',
 981                                         'class': 'DockerRequirement',
 982                                         "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
 983                                     }
 984                                 ],
 985                                 'id': '#submit_tool.cwl',
 986                                 'outputs': [],
 987                                 'baseCommand': 'cat',
 988                                 'class': 'CommandLineTool'
 989                             }
 990                         ]
 991                     }
 992                 },
 993                 '/var/lib/cwl/cwl.input.json': {
 994                     'content': {
 995                         'x': 'XxX'
 996                     },
 997                     'kind': 'json'
 998                 }
 999             }, 'state': 'Committed',
1000             'output_path': '/var/spool/cwl',
1001             'name': 'a test workflow',
1002             'container_image': "999999999999999999999999999999d3+99",
1003             'command': ['arvados-cwl-runner', '--local', '--api=containers',
1004                         '--no-log-timestamps', '--disable-validate',
1005                         '--eval-timeout=20', '--thread-count=1',
1006                         '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
1007                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
1008             'cwd': '/var/spool/cwl',
1009             'runtime_constraints': {
1010                 'API': True,
1011                 'vcpus': 1,
1012                 'ram': 1342177280
1013             },
1014             'use_existing': True,
1015             'properties': {
1016                 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
1017             },
1018             'secret_mounts': {}
1019         }
1020
1021         stubs.api.container_requests().create.assert_called_with(
1022             body=JsonDiffMatcher(expect_container))
1023         self.assertEqual(capture_stdout.getvalue(),
1024                          stubs.expect_container_request_uuid + '\n')
1025
1026
1027     @stubs
1028     def test_submit_container_name(self, stubs):
1029         capture_stdout = cStringIO.StringIO()
1030         try:
1031             exited = arvados_cwl.main(
1032                 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
1033                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1034                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1035             self.assertEqual(exited, 0)
1036         except:
1037             logging.exception("")
1038
1039         expect_container = copy.deepcopy(stubs.expect_container_spec)
1040         expect_container["name"] = "hello container 123"
1041
1042         stubs.api.container_requests().create.assert_called_with(
1043             body=JsonDiffMatcher(expect_container))
1044         self.assertEqual(capture_stdout.getvalue(),
1045                          stubs.expect_container_request_uuid + '\n')
1046
1047
1048     @stubs
1049     def test_submit_missing_input(self, stubs):
1050         capture_stdout = cStringIO.StringIO()
1051         exited = arvados_cwl.main(
1052             ["--submit", "--no-wait", "--api=containers", "--debug",
1053              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1054             capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1055         self.assertEqual(exited, 0)
1056
1057         capture_stdout = cStringIO.StringIO()
1058         exited = arvados_cwl.main(
1059             ["--submit", "--no-wait", "--api=containers", "--debug",
1060              "tests/wf/submit_wf.cwl", "tests/submit_test_job_missing.json"],
1061             capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1062         self.assertEqual(exited, 1)
1063
1064
1065     @stubs
1066     def test_submit_container_project(self, stubs):
1067         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1068         capture_stdout = cStringIO.StringIO()
1069         try:
1070             exited = arvados_cwl.main(
1071                 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
1072                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1073                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1074             self.assertEqual(exited, 0)
1075         except:
1076             logging.exception("")
1077
1078         expect_container = copy.deepcopy(stubs.expect_container_spec)
1079         expect_container["owner_uuid"] = project_uuid
1080         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1081                                        '--no-log-timestamps', '--disable-validate',
1082                                        "--eval-timeout=20", "--thread-count=1",
1083                                        '--enable-reuse', "--collection-cache-size=256", '--debug',
1084                                        '--on-error=continue',
1085                                        '--project-uuid='+project_uuid,
1086                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1087
1088         stubs.api.container_requests().create.assert_called_with(
1089             body=JsonDiffMatcher(expect_container))
1090         self.assertEqual(capture_stdout.getvalue(),
1091                          stubs.expect_container_request_uuid + '\n')
1092
1093     @stubs
1094     def test_submit_container_eval_timeout(self, stubs):
1095         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1096         capture_stdout = cStringIO.StringIO()
1097         try:
1098             exited = arvados_cwl.main(
1099                 ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
1100                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1101                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1102             self.assertEqual(exited, 0)
1103         except:
1104             logging.exception("")
1105
1106         expect_container = copy.deepcopy(stubs.expect_container_spec)
1107         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1108                                        '--no-log-timestamps', '--disable-validate',
1109                                        '--eval-timeout=60.0', '--thread-count=1',
1110                                        '--enable-reuse', "--collection-cache-size=256",
1111                                        '--debug', '--on-error=continue',
1112                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1113
1114         stubs.api.container_requests().create.assert_called_with(
1115             body=JsonDiffMatcher(expect_container))
1116         self.assertEqual(capture_stdout.getvalue(),
1117                          stubs.expect_container_request_uuid + '\n')
1118
1119     @stubs
1120     def test_submit_container_collection_cache(self, stubs):
1121         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1122         capture_stdout = cStringIO.StringIO()
1123         try:
1124             exited = arvados_cwl.main(
1125                 ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
1126                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1127                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1128             self.assertEqual(exited, 0)
1129         except:
1130             logging.exception("")
1131
1132         expect_container = copy.deepcopy(stubs.expect_container_spec)
1133         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1134                                        '--no-log-timestamps', '--disable-validate',
1135                                        '--eval-timeout=20', '--thread-count=1',
1136                                        '--enable-reuse', "--collection-cache-size=500",
1137                                        '--debug', '--on-error=continue',
1138                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1139         expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024
1140
1141         stubs.api.container_requests().create.assert_called_with(
1142             body=JsonDiffMatcher(expect_container))
1143         self.assertEqual(capture_stdout.getvalue(),
1144                          stubs.expect_container_request_uuid + '\n')
1145
1146
1147     @stubs
1148     def test_submit_container_thread_count(self, stubs):
1149         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1150         capture_stdout = cStringIO.StringIO()
1151         try:
1152             exited = arvados_cwl.main(
1153                 ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
1154                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1155                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1156             self.assertEqual(exited, 0)
1157         except:
1158             logging.exception("")
1159
1160         expect_container = copy.deepcopy(stubs.expect_container_spec)
1161         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1162                                        '--no-log-timestamps', '--disable-validate',
1163                                        '--eval-timeout=20', '--thread-count=20',
1164                                        '--enable-reuse', "--collection-cache-size=256",
1165                                        '--debug', '--on-error=continue',
1166                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1167
1168         stubs.api.container_requests().create.assert_called_with(
1169             body=JsonDiffMatcher(expect_container))
1170         self.assertEqual(capture_stdout.getvalue(),
1171                          stubs.expect_container_request_uuid + '\n')
1172
1173
1174     @stubs
1175     def test_submit_job_runner_image(self, stubs):
1176         capture_stdout = cStringIO.StringIO()
1177         try:
1178             exited = arvados_cwl.main(
1179                 ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
1180                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1181                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1182             self.assertEqual(exited, 0)
1183         except:
1184             logging.exception("")
1185
1186         stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "999999999999999999999999999999d5+99"
1187
1188         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
1189         stubs.api.pipeline_instances().create.assert_called_with(
1190             body=JsonDiffMatcher(expect_pipeline))
1191         self.assertEqual(capture_stdout.getvalue(),
1192                          stubs.expect_pipeline_uuid + '\n')
1193
1194     @stubs
1195     def test_submit_container_runner_image(self, stubs):
1196         capture_stdout = cStringIO.StringIO()
1197         try:
1198             exited = arvados_cwl.main(
1199                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
1200                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1201                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1202             self.assertEqual(exited, 0)
1203         except:
1204             logging.exception("")
1205
1206         stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
1207
1208         expect_container = copy.deepcopy(stubs.expect_container_spec)
1209         stubs.api.container_requests().create.assert_called_with(
1210             body=JsonDiffMatcher(expect_container))
1211         self.assertEqual(capture_stdout.getvalue(),
1212                          stubs.expect_container_request_uuid + '\n')
1213
1214     @stubs
1215     def test_submit_priority(self, stubs):
1216         capture_stdout = cStringIO.StringIO()
1217         try:
1218             exited = arvados_cwl.main(
1219                 ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
1220                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1221                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1222             self.assertEqual(exited, 0)
1223         except:
1224             logging.exception("")
1225
1226         stubs.expect_container_spec["priority"] = 669
1227
1228         expect_container = copy.deepcopy(stubs.expect_container_spec)
1229         stubs.api.container_requests().create.assert_called_with(
1230             body=JsonDiffMatcher(expect_container))
1231         self.assertEqual(capture_stdout.getvalue(),
1232                          stubs.expect_container_request_uuid + '\n')
1233
1234
1235     @stubs
1236     def test_submit_wf_runner_resources(self, stubs):
1237         capture_stdout = cStringIO.StringIO()
1238         try:
1239             exited = arvados_cwl.main(
1240                 ["--submit", "--no-wait", "--api=containers", "--debug",
1241                  "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
1242                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1243             self.assertEqual(exited, 0)
1244         except:
1245             logging.exception("")
1246
1247         expect_container = copy.deepcopy(stubs.expect_container_spec)
1248         expect_container["runtime_constraints"] = {
1249             "API": True,
1250             "vcpus": 2,
1251             "ram": (2000+512) * 2**20
1252         }
1253         expect_container["name"] = "submit_wf_runner_resources.cwl"
1254         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1255             {
1256                 "class": "http://arvados.org/cwl#WorkflowRunnerResources",
1257                 "coresMin": 2,
1258                 "ramMin": 2000,
1259                 "keep_cache": 512
1260             }
1261         ]
1262         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
1263             "arv": "http://arvados.org/cwl#",
1264         }
1265         expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
1266                         '--no-log-timestamps', '--disable-validate',
1267                         '--eval-timeout=20', '--thread-count=1',
1268                         '--enable-reuse', "--collection-cache-size=512", '--debug', '--on-error=continue',
1269                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1270
1271         stubs.api.container_requests().create.assert_called_with(
1272             body=JsonDiffMatcher(expect_container))
1273         self.assertEqual(capture_stdout.getvalue(),
1274                          stubs.expect_container_request_uuid + '\n')
1275
1276     def tearDown(self):
1277         arvados_cwl.arvdocker.arv_docker_clear_cache()
1278
1279     @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
1280     @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
1281     @mock.patch("arvados.api")
1282     def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
1283         arvados_cwl.arvdocker.arv_docker_clear_cache()
1284
1285         arvrunner = mock.MagicMock()
1286         arvrunner.project_uuid = ""
1287         api.return_value = mock.MagicMock()
1288         arvrunner.api = api.return_value
1289         arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
1290                                                                         "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1291                                                                         "link_class": "docker_image_repo+tag",
1292                                                                         "name": "arvados/jobs:"+arvados_cwl.__version__,
1293                                                                         "owner_uuid": "",
1294                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1295                                                             {"items": [{"created_at": "",
1296                                                                         "head_uuid": "",
1297                                                                         "link_class": "docker_image_hash",
1298                                                                         "name": "123456",
1299                                                                         "owner_uuid": "",
1300                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
1301         )
1302         find_one_image_hash.return_value = "123456"
1303
1304         arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1305                                                                               "owner_uuid": "",
1306                                                                               "manifest_text": "",
1307                                                                               "properties": ""
1308                                                                           }], "items_available": 1, "offset": 0},)
1309         arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
1310         arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1311                                                                   "portable_data_hash": "9999999999999999999999999999999b+99"}
1312         self.assertEqual("9999999999999999999999999999999b+99",
1313                          arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
1314
1315
1316     @stubs
1317     def test_submit_secrets(self, stubs):
1318         capture_stdout = cStringIO.StringIO()
1319         try:
1320             exited = arvados_cwl.main(
1321                 ["--submit", "--no-wait", "--api=containers", "--debug",
1322                  "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
1323                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1324             self.assertEqual(exited, 0)
1325         except:
1326             logging.exception("")
1327
1328
1329         expect_container = {
1330             "command": [
1331                 "arvados-cwl-runner",
1332                 "--local",
1333                 "--api=containers",
1334                 "--no-log-timestamps",
1335                 "--disable-validate",
1336                 "--eval-timeout=20",
1337                 '--thread-count=1',
1338                 "--enable-reuse",
1339                 "--collection-cache-size=256",
1340                 '--debug',
1341                 "--on-error=continue",
1342                 "/var/lib/cwl/workflow.json#main",
1343                 "/var/lib/cwl/cwl.input.json"
1344             ],
1345             "container_image": "999999999999999999999999999999d3+99",
1346             "cwd": "/var/spool/cwl",
1347             "mounts": {
1348                 "/var/lib/cwl/cwl.input.json": {
1349                     "content": {
1350                         "pw": {
1351                             "$include": "/secrets/s0"
1352                         }
1353                     },
1354                     "kind": "json"
1355                 },
1356                 "/var/lib/cwl/workflow.json": {
1357                     "content": {
1358                         "$graph": [
1359                             {
1360                                 "$namespaces": {
1361                                     "cwltool": "http://commonwl.org/cwltool#"
1362                                 },
1363                                 "arguments": [
1364                                     "md5sum",
1365                                     "example.conf"
1366                                 ],
1367                                 "class": "CommandLineTool",
1368                                 "hints": [
1369                                     {
1370                                         "class": "http://commonwl.org/cwltool#Secrets",
1371                                         "secrets": [
1372                                             "#secret_job.cwl/pw"
1373                                         ]
1374                                     }
1375                                 ],
1376                                 "id": "#secret_job.cwl",
1377                                 "inputs": [
1378                                     {
1379                                         "id": "#secret_job.cwl/pw",
1380                                         "type": "string"
1381                                     }
1382                                 ],
1383                                 "outputs": [
1384                                     {
1385                                         "id": "#secret_job.cwl/out",
1386                                         "type": "stdout"
1387                                     }
1388                                 ],
1389                                 "stdout": "hashed_example.txt",
1390                                 "requirements": [
1391                                     {
1392                                         "class": "InitialWorkDirRequirement",
1393                                         "listing": [
1394                                             {
1395                                                 "entry": "username: user\npassword: $(inputs.pw)\n",
1396                                                 "entryname": "example.conf"
1397                                             }
1398                                         ]
1399                                     }
1400                                 ]
1401                             },
1402                             {
1403                                 "class": "Workflow",
1404                                 "hints": [
1405                                     {
1406                                         "class": "DockerRequirement",
1407                                         "dockerPull": "debian:8",
1408                                         "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
1409                                     },
1410                                     {
1411                                         "class": "http://commonwl.org/cwltool#Secrets",
1412                                         "secrets": [
1413                                             "#main/pw"
1414                                         ]
1415                                     }
1416                                 ],
1417                                 "id": "#main",
1418                                 "inputs": [
1419                                     {
1420                                         "id": "#main/pw",
1421                                         "type": "string"
1422                                     }
1423                                 ],
1424                                 "outputs": [
1425                                     {
1426                                         "id": "#main/out",
1427                                         "outputSource": "#main/step1/out",
1428                                         "type": "File"
1429                                     }
1430                                 ],
1431                                 "steps": [
1432                                     {
1433                                         "id": "#main/step1",
1434                                         "in": [
1435                                             {
1436                                                 "id": "#main/step1/pw",
1437                                                 "source": "#main/pw"
1438                                             }
1439                                         ],
1440                                         "out": [
1441                                             "#main/step1/out"
1442                                         ],
1443                                         "run": "#secret_job.cwl"
1444                                     }
1445                                 ]
1446                             }
1447                         ],
1448                         "cwlVersion": "v1.0"
1449                     },
1450                     "kind": "json"
1451                 },
1452                 "/var/spool/cwl": {
1453                     "kind": "collection",
1454                     "writable": True
1455                 },
1456                 "stdout": {
1457                     "kind": "file",
1458                     "path": "/var/spool/cwl/cwl.output.json"
1459                 }
1460             },
1461             "name": "secret_wf.cwl",
1462             "output_path": "/var/spool/cwl",
1463             "priority": 500,
1464             "properties": {},
1465             "runtime_constraints": {
1466                 "API": True,
1467                 "ram": 1342177280,
1468                 "vcpus": 1
1469             },
1470             "secret_mounts": {
1471                 "/secrets/s0": {
1472                     "content": "blorp",
1473                     "kind": "text"
1474                 }
1475             },
1476             "state": "Committed",
1477             "use_existing": True
1478         }
1479
1480         stubs.api.container_requests().create.assert_called_with(
1481             body=JsonDiffMatcher(expect_container))
1482         self.assertEqual(capture_stdout.getvalue(),
1483                          stubs.expect_container_request_uuid + '\n')
1484
1485     @stubs
1486     def test_submit_request_uuid(self, stubs):
1487         stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
1488
1489         stubs.api.container_requests().update().execute.return_value = {
1490             "uuid": stubs.expect_container_request_uuid,
1491             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
1492             "state": "Queued"
1493         }
1494
1495         capture_stdout = cStringIO.StringIO()
1496         try:
1497             exited = arvados_cwl.main(
1498                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
1499                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1500                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1501             self.assertEqual(exited, 0)
1502         except:
1503             logging.exception("")
1504
1505         stubs.api.container_requests().update.assert_called_with(
1506             uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec), cluster_id="zzzzz")
1507         self.assertEqual(capture_stdout.getvalue(),
1508                          stubs.expect_container_request_uuid + '\n')
1509
1510     @stubs
1511     def test_submit_container_cluster_id(self, stubs):
1512         capture_stdout = cStringIO.StringIO()
1513         stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1514         try:
1515             exited = arvados_cwl.main(
1516                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb",
1517                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1518                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1519             self.assertEqual(exited, 0)
1520         except:
1521             logging.exception("")
1522
1523         expect_container = copy.deepcopy(stubs.expect_container_spec)
1524
1525         stubs.api.container_requests().create.assert_called_with(
1526             body=JsonDiffMatcher(expect_container), cluster_id="zbbbb")
1527         self.assertEqual(capture_stdout.getvalue(),
1528                          stubs.expect_container_request_uuid + '\n')
1529
1530
1531     @stubs
1532     def test_submit_validate_cluster_id(self, stubs):
1533         capture_stdout = cStringIO.StringIO()
1534         stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1535         exited = arvados_cwl.main(
1536             ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zcccc",
1537              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1538             capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1539         self.assertEqual(exited, 1)
1540
1541
1542 class TestCreateTemplate(unittest.TestCase):
1543     existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
1544
1545     def _adjust_script_params(self, expect_component):
1546         expect_component['script_parameters']['x'] = {
1547             'dataclass': 'File',
1548             'required': True,
1549             'type': 'File',
1550             'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
1551         }
1552         expect_component['script_parameters']['y'] = {
1553             'dataclass': 'Collection',
1554             'required': True,
1555             'type': 'Directory',
1556             'value': '99999999999999999999999999999998+99',
1557         }
1558         expect_component['script_parameters']['z'] = {
1559             'dataclass': 'Collection',
1560             'required': True,
1561             'type': 'Directory',
1562         }
1563
1564     @stubs
1565     def test_create(self, stubs):
1566         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1567
1568         capture_stdout = cStringIO.StringIO()
1569
1570         exited = arvados_cwl.main(
1571             ["--create-workflow", "--debug",
1572              "--api=jobs",
1573              "--project-uuid", project_uuid,
1574              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1575             capture_stdout, sys.stderr, api_client=stubs.api)
1576         self.assertEqual(exited, 0)
1577
1578         stubs.api.pipeline_instances().create.refute_called()
1579         stubs.api.jobs().create.refute_called()
1580
1581         expect_component = copy.deepcopy(stubs.expect_job_spec)
1582         self._adjust_script_params(expect_component)
1583         expect_template = {
1584             "components": {
1585                 "submit_wf.cwl": expect_component,
1586             },
1587             "name": "submit_wf.cwl",
1588             "owner_uuid": project_uuid,
1589         }
1590         stubs.api.pipeline_templates().create.assert_called_with(
1591             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1592
1593         self.assertEqual(capture_stdout.getvalue(),
1594                          stubs.expect_pipeline_template_uuid + '\n')
1595
1596
1597     @stubs
1598     def test_create_name(self, stubs):
1599         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1600
1601         capture_stdout = cStringIO.StringIO()
1602
1603         exited = arvados_cwl.main(
1604             ["--create-workflow", "--debug",
1605              "--project-uuid", project_uuid,
1606              "--api=jobs",
1607              "--name", "testing 123",
1608              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1609             capture_stdout, sys.stderr, api_client=stubs.api)
1610         self.assertEqual(exited, 0)
1611
1612         stubs.api.pipeline_instances().create.refute_called()
1613         stubs.api.jobs().create.refute_called()
1614
1615         expect_component = copy.deepcopy(stubs.expect_job_spec)
1616         self._adjust_script_params(expect_component)
1617         expect_template = {
1618             "components": {
1619                 "testing 123": expect_component,
1620             },
1621             "name": "testing 123",
1622             "owner_uuid": project_uuid,
1623         }
1624         stubs.api.pipeline_templates().create.assert_called_with(
1625             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1626
1627         self.assertEqual(capture_stdout.getvalue(),
1628                          stubs.expect_pipeline_template_uuid + '\n')
1629
1630
1631     @stubs
1632     def test_update_name(self, stubs):
1633         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1634
1635         capture_stdout = cStringIO.StringIO()
1636
1637         exited = arvados_cwl.main(
1638             ["--update-workflow", self.existing_template_uuid,
1639              "--debug",
1640              "--project-uuid", project_uuid,
1641              "--api=jobs",
1642              "--name", "testing 123",
1643              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1644             capture_stdout, sys.stderr, api_client=stubs.api)
1645         self.assertEqual(exited, 0)
1646
1647         stubs.api.pipeline_instances().create.refute_called()
1648         stubs.api.jobs().create.refute_called()
1649
1650         expect_component = copy.deepcopy(stubs.expect_job_spec)
1651         self._adjust_script_params(expect_component)
1652         expect_template = {
1653             "components": {
1654                 "testing 123": expect_component,
1655             },
1656             "name": "testing 123",
1657             "owner_uuid": project_uuid,
1658         }
1659         stubs.api.pipeline_templates().create.refute_called()
1660         stubs.api.pipeline_templates().update.assert_called_with(
1661             body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
1662
1663         self.assertEqual(capture_stdout.getvalue(),
1664                          self.existing_template_uuid + '\n')
1665
1666
1667 class TestCreateWorkflow(unittest.TestCase):
1668     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1669     expect_workflow = StripYAMLComments(
1670         open("tests/wf/expect_packed.cwl").read())
1671
1672     @stubs
1673     def test_create(self, stubs):
1674         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1675
1676         capture_stdout = cStringIO.StringIO()
1677
1678         exited = arvados_cwl.main(
1679             ["--create-workflow", "--debug",
1680              "--api=containers",
1681              "--project-uuid", project_uuid,
1682              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1683             capture_stdout, sys.stderr, api_client=stubs.api)
1684         self.assertEqual(exited, 0)
1685
1686         stubs.api.pipeline_templates().create.refute_called()
1687         stubs.api.container_requests().create.refute_called()
1688
1689         body = {
1690             "workflow": {
1691                 "owner_uuid": project_uuid,
1692                 "name": "submit_wf.cwl",
1693                 "description": "",
1694                 "definition": self.expect_workflow,
1695             }
1696         }
1697         stubs.api.workflows().create.assert_called_with(
1698             body=JsonDiffMatcher(body))
1699
1700         self.assertEqual(capture_stdout.getvalue(),
1701                          stubs.expect_workflow_uuid + '\n')
1702
1703
1704     @stubs
1705     def test_create_name(self, stubs):
1706         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1707
1708         capture_stdout = cStringIO.StringIO()
1709
1710         exited = arvados_cwl.main(
1711             ["--create-workflow", "--debug",
1712              "--api=containers",
1713              "--project-uuid", project_uuid,
1714              "--name", "testing 123",
1715              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1716             capture_stdout, sys.stderr, api_client=stubs.api)
1717         self.assertEqual(exited, 0)
1718
1719         stubs.api.pipeline_templates().create.refute_called()
1720         stubs.api.container_requests().create.refute_called()
1721
1722         body = {
1723             "workflow": {
1724                 "owner_uuid": project_uuid,
1725                 "name": "testing 123",
1726                 "description": "",
1727                 "definition": self.expect_workflow,
1728             }
1729         }
1730         stubs.api.workflows().create.assert_called_with(
1731             body=JsonDiffMatcher(body))
1732
1733         self.assertEqual(capture_stdout.getvalue(),
1734                          stubs.expect_workflow_uuid + '\n')
1735
1736     @stubs
1737     def test_incompatible_api(self, stubs):
1738         capture_stderr = cStringIO.StringIO()
1739         logging.getLogger('arvados.cwl-runner').addHandler(
1740             logging.StreamHandler(capture_stderr))
1741
1742         exited = arvados_cwl.main(
1743             ["--update-workflow", self.existing_workflow_uuid,
1744              "--api=jobs",
1745              "--debug",
1746              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1747             sys.stderr, sys.stderr, api_client=stubs.api)
1748         self.assertEqual(exited, 1)
1749         self.assertRegexpMatches(
1750             capture_stderr.getvalue(),
1751             "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
1752
1753     @stubs
1754     def test_update(self, stubs):
1755         capture_stdout = cStringIO.StringIO()
1756
1757         exited = arvados_cwl.main(
1758             ["--update-workflow", self.existing_workflow_uuid,
1759              "--debug",
1760              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1761             capture_stdout, sys.stderr, api_client=stubs.api)
1762         self.assertEqual(exited, 0)
1763
1764         body = {
1765             "workflow": {
1766                 "name": "submit_wf.cwl",
1767                 "description": "",
1768                 "definition": self.expect_workflow,
1769             }
1770         }
1771         stubs.api.workflows().update.assert_called_with(
1772             uuid=self.existing_workflow_uuid,
1773             body=JsonDiffMatcher(body))
1774         self.assertEqual(capture_stdout.getvalue(),
1775                          self.existing_workflow_uuid + '\n')
1776
1777
1778     @stubs
1779     def test_update_name(self, stubs):
1780         capture_stdout = cStringIO.StringIO()
1781
1782         exited = arvados_cwl.main(
1783             ["--update-workflow", self.existing_workflow_uuid,
1784              "--debug", "--name", "testing 123",
1785              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1786             capture_stdout, sys.stderr, api_client=stubs.api)
1787         self.assertEqual(exited, 0)
1788
1789         body = {
1790             "workflow": {
1791                 "name": "testing 123",
1792                 "description": "",
1793                 "definition": self.expect_workflow,
1794             }
1795         }
1796         stubs.api.workflows().update.assert_called_with(
1797             uuid=self.existing_workflow_uuid,
1798             body=JsonDiffMatcher(body))
1799         self.assertEqual(capture_stdout.getvalue(),
1800                          self.existing_workflow_uuid + '\n')
1801
1802
1803     @stubs
1804     def test_create_collection_per_tool(self, stubs):
1805         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1806
1807         capture_stdout = cStringIO.StringIO()
1808
1809         exited = arvados_cwl.main(
1810             ["--create-workflow", "--debug",
1811              "--api=containers",
1812              "--project-uuid", project_uuid,
1813              "tests/collection_per_tool/collection_per_tool.cwl"],
1814             capture_stdout, sys.stderr, api_client=stubs.api)
1815         self.assertEqual(exited, 0)
1816
1817         toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1818         expect_workflow = StripYAMLComments(open(toolfile).read())
1819
1820         body = {
1821             "workflow": {
1822                 "owner_uuid": project_uuid,
1823                 "name": "collection_per_tool.cwl",
1824                 "description": "",
1825                 "definition": expect_workflow,
1826             }
1827         }
1828         stubs.api.workflows().create.assert_called_with(
1829             body=JsonDiffMatcher(body))
1830
1831         self.assertEqual(capture_stdout.getvalue(),
1832                          stubs.expect_workflow_uuid + '\n')
1833
1834 class TestTemplateInputs(unittest.TestCase):
1835     expect_template = {
1836         "components": {
1837             "inputs_test.cwl": {
1838                 'runtime_constraints': {
1839                     'docker_image': '999999999999999999999999999999d3+99',
1840                     'min_ram_mb_per_node': 1024
1841                 },
1842                 'script_parameters': {
1843                     'cwl:tool':
1844                     'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main',
1845                     'optionalFloatInput': None,
1846                     'fileInput': {
1847                         'type': 'File',
1848                         'dataclass': 'File',
1849                         'required': True,
1850                         'title': "It's a file; we expect to find some characters in it.",
1851                         'description': 'If there were anything further to say, it would be said here,\nor here.'
1852                     },
1853                     'floatInput': {
1854                         'type': 'float',
1855                         'dataclass': 'number',
1856                         'required': True,
1857                         'title': 'Floats like a duck',
1858                         'default': 0.1,
1859                         'value': 0.1,
1860                     },
1861                     'optionalFloatInput': {
1862                         'type': ['null', 'float'],
1863                         'dataclass': 'number',
1864                         'required': False,
1865                     },
1866                     'boolInput': {
1867                         'type': 'boolean',
1868                         'dataclass': 'boolean',
1869                         'required': True,
1870                         'title': 'True or false?',
1871                     },
1872                 },
1873                 'repository': 'arvados',
1874                 'script_version': 'master',
1875                 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
1876                 'script': 'cwl-runner',
1877             },
1878         },
1879         "name": "inputs_test.cwl",
1880     }
1881
1882     @stubs
1883     def test_inputs_empty(self, stubs):
1884         exited = arvados_cwl.main(
1885             ["--create-template",
1886              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
1887             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1888         self.assertEqual(exited, 0)
1889
1890         stubs.api.pipeline_templates().create.assert_called_with(
1891             body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
1892
1893     @stubs
1894     def test_inputs(self, stubs):
1895         exited = arvados_cwl.main(
1896             ["--create-template",
1897              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
1898             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1899         self.assertEqual(exited, 0)
1900
1901         expect_template = copy.deepcopy(self.expect_template)
1902         params = expect_template[
1903             "components"]["inputs_test.cwl"]["script_parameters"]
1904         params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
1905         params["cwl:tool"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main'
1906         params["floatInput"]["value"] = 1.234
1907         params["boolInput"]["value"] = True
1908
1909         stubs.api.pipeline_templates().create.assert_called_with(
1910             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)