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=4',
 277                         '--enable-reuse', '--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*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=4',
 562             '--disable-reuse', '--debug', '--on-error=continue',
 563             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 564         expect_container["use_existing"] = False
 565
 566         stubs.api.container_requests().create.assert_called_with(
 567             body=JsonDiffMatcher(expect_container))
 568         self.assertEqual(capture_stdout.getvalue(),
 569                          stubs.expect_container_request_uuid + '\n')
 570
 571
 572     @stubs
 573     def test_submit_container_reuse_disabled_by_workflow(self, stubs):
 574         capture_stdout = cStringIO.StringIO()
 575
 576         exited = arvados_cwl.main(
 577             ["--submit", "--no-wait", "--api=containers", "--debug",
 578              "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
 579             capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 580         self.assertEqual(exited, 0)
 581
 582         expect_container = copy.deepcopy(stubs.expect_container_spec)
 583         expect_container["command"] = [
 584             'arvados-cwl-runner', '--local', '--api=containers',
 585             '--no-log-timestamps', '--disable-validate',
 586             '--eval-timeout=20', '--thread-count=4',
 587             '--disable-reuse', '--debug', '--on-error=continue',
 588             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 589         expect_container["use_existing"] = False
 590         expect_container["name"] = "submit_wf_no_reuse.cwl"
 591         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
 592             {
 593                 "class": "http://arvados.org/cwl#ReuseRequirement",
 594                 "enableReuse": False,
 595             },
 596         ]
 597         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
 598             "arv": "http://arvados.org/cwl#",
 599             "cwltool": "http://commonwl.org/cwltool#"
 600         }
 601
 602         stubs.api.container_requests().create.assert_called_with(
 603             body=JsonDiffMatcher(expect_container))
 604         self.assertEqual(capture_stdout.getvalue(),
 605                          stubs.expect_container_request_uuid + '\n')
 606
 607
 608     @stubs
 609     def test_submit_container_on_error(self, stubs):
 610         capture_stdout = cStringIO.StringIO()
 611         try:
 612             exited = arvados_cwl.main(
 613                 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
 614                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 615                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 616             self.assertEqual(exited, 0)
 617         except:
 618             logging.exception("")
 619
 620         expect_container = copy.deepcopy(stubs.expect_container_spec)
 621         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 622                                        '--no-log-timestamps', '--disable-validate',
 623                                        '--eval-timeout=20', '--thread-count=4',
 624                                        '--enable-reuse', '--debug', '--on-error=stop',
 625                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 626
 627         stubs.api.container_requests().create.assert_called_with(
 628             body=JsonDiffMatcher(expect_container))
 629         self.assertEqual(capture_stdout.getvalue(),
 630                          stubs.expect_container_request_uuid + '\n')
 631
 632     @stubs
 633     def test_submit_container_output_name(self, stubs):
 634         output_name = "test_output_name"
 635
 636         capture_stdout = cStringIO.StringIO()
 637         try:
 638             exited = arvados_cwl.main(
 639                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
 640                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 641                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 642             self.assertEqual(exited, 0)
 643         except:
 644             logging.exception("")
 645
 646         expect_container = copy.deepcopy(stubs.expect_container_spec)
 647         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 648                                        '--no-log-timestamps', '--disable-validate',
 649                                        '--eval-timeout=20', '--thread-count=4',
 650                                        '--enable-reuse',
 651                                        "--output-name="+output_name, '--debug', '--on-error=continue',
 652                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 653         expect_container["output_name"] = output_name
 654
 655         stubs.api.container_requests().create.assert_called_with(
 656             body=JsonDiffMatcher(expect_container))
 657         self.assertEqual(capture_stdout.getvalue(),
 658                          stubs.expect_container_request_uuid + '\n')
 659
 660     @stubs
 661     def test_submit_storage_classes(self, stubs):
 662         capture_stdout = cStringIO.StringIO()
 663         try:
 664             exited = arvados_cwl.main(
 665                 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
 666                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 667                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 668             self.assertEqual(exited, 0)
 669         except:
 670             logging.exception("")
 671
 672         expect_container = copy.deepcopy(stubs.expect_container_spec)
 673         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 674                                        '--no-log-timestamps', '--disable-validate',
 675                                        '--eval-timeout=20', '--thread-count=4',
 676                                        '--enable-reuse', "--debug",
 677                                        "--storage-classes=foo", '--on-error=continue',
 678                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 679
 680         stubs.api.container_requests().create.assert_called_with(
 681             body=JsonDiffMatcher(expect_container))
 682         self.assertEqual(capture_stdout.getvalue(),
 683                          stubs.expect_container_request_uuid + '\n')
 684
 685     @mock.patch("arvados_cwl.task_queue.TaskQueue")
 686     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
 687     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
 688     @stubs
 689     def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
 690         def set_final_output(job_order, output_callback, runtimeContext):
 691             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
 692             return []
 693         job.side_effect = set_final_output
 694
 695         try:
 696             exited = arvados_cwl.main(
 697                 ["--debug", "--local", "--storage-classes=foo",
 698                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 699                 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 700             self.assertEqual(exited, 0)
 701         except:
 702             logging.exception("")
 703
 704         make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
 705
 706     @mock.patch("arvados_cwl.task_queue.TaskQueue")
 707     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
 708     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
 709     @stubs
 710     def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
 711         def set_final_output(job_order, output_callback, runtimeContext):
 712             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
 713             return []
 714         job.side_effect = set_final_output
 715
 716         try:
 717             exited = arvados_cwl.main(
 718                 ["--debug", "--local",
 719                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 720                 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 721             self.assertEqual(exited, 0)
 722         except:
 723             logging.exception("")
 724
 725         make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
 726
 727     @stubs
 728     def test_submit_container_output_ttl(self, stubs):
 729         capture_stdout = cStringIO.StringIO()
 730         try:
 731             exited = arvados_cwl.main(
 732                 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
 733                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 734                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 735             self.assertEqual(exited, 0)
 736         except:
 737             logging.exception("")
 738
 739         expect_container = copy.deepcopy(stubs.expect_container_spec)
 740         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 741                                        '--no-log-timestamps', '--disable-validate',
 742                                        '--eval-timeout=20', '--thread-count=4',
 743                                        '--enable-reuse', '--debug', '--on-error=continue',
 744                                        "--intermediate-output-ttl=3600",
 745                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 746
 747         stubs.api.container_requests().create.assert_called_with(
 748             body=JsonDiffMatcher(expect_container))
 749         self.assertEqual(capture_stdout.getvalue(),
 750                          stubs.expect_container_request_uuid + '\n')
 751
 752     @stubs
 753     def test_submit_container_trash_intermediate(self, stubs):
 754         capture_stdout = cStringIO.StringIO()
 755         try:
 756             exited = arvados_cwl.main(
 757                 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
 758                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 759                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 760             self.assertEqual(exited, 0)
 761         except:
 762             logging.exception("")
 763
 764         expect_container = copy.deepcopy(stubs.expect_container_spec)
 765         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 766                                        '--no-log-timestamps', '--disable-validate',
 767                                        '--eval-timeout=20', '--thread-count=4',
 768                                        '--enable-reuse', '--debug', '--on-error=continue',
 769                                        "--trash-intermediate",
 770                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 771
 772         stubs.api.container_requests().create.assert_called_with(
 773             body=JsonDiffMatcher(expect_container))
 774         self.assertEqual(capture_stdout.getvalue(),
 775                          stubs.expect_container_request_uuid + '\n')
 776
 777     @stubs
 778     def test_submit_container_output_tags(self, stubs):
 779         output_tags = "tag0,tag1,tag2"
 780
 781         capture_stdout = cStringIO.StringIO()
 782         try:
 783             exited = arvados_cwl.main(
 784                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
 785                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 786                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 787             self.assertEqual(exited, 0)
 788         except:
 789             logging.exception("")
 790
 791         expect_container = copy.deepcopy(stubs.expect_container_spec)
 792         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 793                                        '--no-log-timestamps', '--disable-validate',
 794                                        '--eval-timeout=20', '--thread-count=4',
 795                                        '--enable-reuse',
 796                                        "--output-tags="+output_tags, '--debug', '--on-error=continue',
 797                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 798
 799         stubs.api.container_requests().create.assert_called_with(
 800             body=JsonDiffMatcher(expect_container))
 801         self.assertEqual(capture_stdout.getvalue(),
 802                          stubs.expect_container_request_uuid + '\n')
 803
 804     @stubs
 805     def test_submit_container_runner_ram(self, stubs):
 806         capture_stdout = cStringIO.StringIO()
 807         try:
 808             exited = arvados_cwl.main(
 809                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
 810                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 811                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 812             self.assertEqual(exited, 0)
 813         except:
 814             logging.exception("")
 815
 816         expect_container = copy.deepcopy(stubs.expect_container_spec)
 817         expect_container["runtime_constraints"]["ram"] = 2048*1024*1024
 818
 819         stubs.api.container_requests().create.assert_called_with(
 820             body=JsonDiffMatcher(expect_container))
 821         self.assertEqual(capture_stdout.getvalue(),
 822                          stubs.expect_container_request_uuid + '\n')
 823
 824     @mock.patch("arvados.collection.CollectionReader")
 825     @mock.patch("time.sleep")
 826     @stubs
 827     def test_submit_file_keepref(self, stubs, tm, collectionReader):
 828         capture_stdout = cStringIO.StringIO()
 829         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
 830         exited = arvados_cwl.main(
 831             ["--submit", "--no-wait", "--api=containers", "--debug",
 832              "tests/wf/submit_keepref_wf.cwl"],
 833             capture_stdout, sys.stderr, api_client=stubs.api)
 834         self.assertEqual(exited, 0)
 835
 836
 837     @mock.patch("arvados.collection.CollectionReader")
 838     @mock.patch("time.sleep")
 839     @stubs
 840     def test_submit_keepref(self, stubs, tm, reader):
 841         capture_stdout = cStringIO.StringIO()
 842
 843         with open("tests/wf/expect_arvworkflow.cwl") as f:
 844             reader().open().__enter__().read.return_value = f.read()
 845
 846         exited = arvados_cwl.main(
 847             ["--submit", "--no-wait", "--api=containers", "--debug",
 848              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 849             capture_stdout, sys.stderr, api_client=stubs.api)
 850         self.assertEqual(exited, 0)
 851
 852         expect_container = {
 853             'priority': 500,
 854             'mounts': {
 855                 '/var/spool/cwl': {
 856                     'writable': True,
 857                     'kind': 'collection'
 858                 },
 859                 'stdout': {
 860                     'path': '/var/spool/cwl/cwl.output.json',
 861                     'kind': 'file'
 862                 },
 863                 '/var/lib/cwl/workflow': {
 864                     'portable_data_hash': '99999999999999999999999999999994+99',
 865                     'kind': 'collection'
 866                 },
 867                 '/var/lib/cwl/cwl.input.json': {
 868                     'content': {
 869                         'x': 'XxX'
 870                     },
 871                     'kind': 'json'
 872                 }
 873             }, 'state': 'Committed',
 874             'output_path': '/var/spool/cwl',
 875             'name': 'expect_arvworkflow.cwl#main',
 876             'container_image': '999999999999999999999999999999d3+99',
 877             'command': ['arvados-cwl-runner', '--local', '--api=containers',
 878                         '--no-log-timestamps', '--disable-validate',
 879                         '--eval-timeout=20', '--thread-count=4',
 880                         '--enable-reuse', '--debug', '--on-error=continue',
 881                         '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
 882             'cwd': '/var/spool/cwl',
 883             'runtime_constraints': {
 884                 'API': True,
 885                 'vcpus': 1,
 886                 'ram': 1073741824
 887             },
 888             'use_existing': True,
 889             'properties': {},
 890             'secret_mounts': {}
 891         }
 892
 893         stubs.api.container_requests().create.assert_called_with(
 894             body=JsonDiffMatcher(expect_container))
 895         self.assertEqual(capture_stdout.getvalue(),
 896                          stubs.expect_container_request_uuid + '\n')
 897
 898
 899     @mock.patch("arvados.collection.CollectionReader")
 900     @mock.patch("time.sleep")
 901     @stubs
 902     def test_submit_jobs_keepref(self, stubs, tm, reader):
 903         capture_stdout = cStringIO.StringIO()
 904
 905         with open("tests/wf/expect_arvworkflow.cwl") as f:
 906             reader().open().__enter__().read.return_value = f.read()
 907
 908         exited = arvados_cwl.main(
 909             ["--submit", "--no-wait", "--api=jobs", "--debug",
 910              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 911             capture_stdout, sys.stderr, api_client=stubs.api)
 912         self.assertEqual(exited, 0)
 913
 914         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 915         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
 916         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
 917         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
 918         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
 919         expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
 920         stubs.api.pipeline_instances().create.assert_called_with(
 921             body=JsonDiffMatcher(expect_pipeline))
 922
 923     @mock.patch("time.sleep")
 924     @stubs
 925     def test_submit_arvworkflow(self, stubs, tm):
 926         capture_stdout = cStringIO.StringIO()
 927
 928         with open("tests/wf/expect_arvworkflow.cwl") as f:
 929             stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
 930
 931         exited = arvados_cwl.main(
 932             ["--submit", "--no-wait", "--api=containers", "--debug",
 933              "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
 934             capture_stdout, sys.stderr, api_client=stubs.api)
 935         self.assertEqual(exited, 0)
 936
 937         expect_container = {
 938             'priority': 500,
 939             'mounts': {
 940                 '/var/spool/cwl': {
 941                     'writable': True,
 942                     'kind': 'collection'
 943                 },
 944                 'stdout': {
 945                     'path': '/var/spool/cwl/cwl.output.json',
 946                     'kind': 'file'
 947                 },
 948                 '/var/lib/cwl/workflow.json': {
 949                     'kind': 'json',
 950                     'content': {
 951                         'cwlVersion': 'v1.0',
 952                         '$graph': [
 953                             {
 954                                 'id': '#main',
 955                                 'inputs': [
 956                                     {'type': 'string', 'id': '#main/x'}
 957                                 ],
 958                                 'steps': [
 959                                     {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
 960                                      'run': '#submit_tool.cwl',
 961                                      'id': '#main/step1',
 962                                      'out': []}
 963                                 ],
 964                                 'class': 'Workflow',
 965                                 'outputs': []
 966                             },
 967                             {
 968                                 'inputs': [
 969                                     {
 970                                         'inputBinding': {'position': 1},
 971                                         'type': 'string',
 972                                         'id': '#submit_tool.cwl/x'}
 973                                 ],
 974                                 'requirements': [
 975                                     {
 976                                         'dockerPull': 'debian:8',
 977                                         'class': 'DockerRequirement',
 978                                         "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
 979                                     }
 980                                 ],
 981                                 'id': '#submit_tool.cwl',
 982                                 'outputs': [],
 983                                 'baseCommand': 'cat',
 984                                 'class': 'CommandLineTool'
 985                             }
 986                         ]
 987                     }
 988                 },
 989                 '/var/lib/cwl/cwl.input.json': {
 990                     'content': {
 991                         'x': 'XxX'
 992                     },
 993                     'kind': 'json'
 994                 }
 995             }, 'state': 'Committed',
 996             'output_path': '/var/spool/cwl',
 997             'name': 'a test workflow',
 998             'container_image': "999999999999999999999999999999d3+99",
 999             'command': ['arvados-cwl-runner', '--local', '--api=containers',
1000                         '--no-log-timestamps', '--disable-validate',
1001                         '--eval-timeout=20', '--thread-count=4',
1002                         '--enable-reuse', '--debug', '--on-error=continue',
1003                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
1004             'cwd': '/var/spool/cwl',
1005             'runtime_constraints': {
1006                 'API': True,
1007                 'vcpus': 1,
1008                 'ram': 1073741824
1009             },
1010             'use_existing': True,
1011             'properties': {
1012                 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
1013             },
1014             'secret_mounts': {}
1015         }
1016
1017         stubs.api.container_requests().create.assert_called_with(
1018             body=JsonDiffMatcher(expect_container))
1019         self.assertEqual(capture_stdout.getvalue(),
1020                          stubs.expect_container_request_uuid + '\n')
1021
1022
1023     @stubs
1024     def test_submit_container_name(self, stubs):
1025         capture_stdout = cStringIO.StringIO()
1026         try:
1027             exited = arvados_cwl.main(
1028                 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
1029                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1030                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1031             self.assertEqual(exited, 0)
1032         except:
1033             logging.exception("")
1034
1035         expect_container = copy.deepcopy(stubs.expect_container_spec)
1036         expect_container["name"] = "hello container 123"
1037
1038         stubs.api.container_requests().create.assert_called_with(
1039             body=JsonDiffMatcher(expect_container))
1040         self.assertEqual(capture_stdout.getvalue(),
1041                          stubs.expect_container_request_uuid + '\n')
1042
1043
1044     @stubs
1045     def test_submit_container_project(self, stubs):
1046         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1047         capture_stdout = cStringIO.StringIO()
1048         try:
1049             exited = arvados_cwl.main(
1050                 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
1051                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1052                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1053             self.assertEqual(exited, 0)
1054         except:
1055             logging.exception("")
1056
1057         expect_container = copy.deepcopy(stubs.expect_container_spec)
1058         expect_container["owner_uuid"] = project_uuid
1059         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1060                                        '--no-log-timestamps', '--disable-validate',
1061                                        "--eval-timeout=20", "--thread-count=4",
1062                                        '--enable-reuse', '--debug', '--on-error=continue',
1063                                        '--project-uuid='+project_uuid,
1064                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1065
1066         stubs.api.container_requests().create.assert_called_with(
1067             body=JsonDiffMatcher(expect_container))
1068         self.assertEqual(capture_stdout.getvalue(),
1069                          stubs.expect_container_request_uuid + '\n')
1070
1071     @stubs
1072     def test_submit_container_eval_timeout(self, stubs):
1073         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1074         capture_stdout = cStringIO.StringIO()
1075         try:
1076             exited = arvados_cwl.main(
1077                 ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
1078                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1079                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1080             self.assertEqual(exited, 0)
1081         except:
1082             logging.exception("")
1083
1084         expect_container = copy.deepcopy(stubs.expect_container_spec)
1085         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1086                                        '--no-log-timestamps', '--disable-validate',
1087                                        '--eval-timeout=60.0', '--thread-count=4',
1088                                        '--enable-reuse', '--debug', '--on-error=continue',
1089                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1090
1091         stubs.api.container_requests().create.assert_called_with(
1092             body=JsonDiffMatcher(expect_container))
1093         self.assertEqual(capture_stdout.getvalue(),
1094                          stubs.expect_container_request_uuid + '\n')
1095
1096
1097     @stubs
1098     def test_submit_container_thread_count(self, stubs):
1099         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1100         capture_stdout = cStringIO.StringIO()
1101         try:
1102             exited = arvados_cwl.main(
1103                 ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
1104                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1105                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1106             self.assertEqual(exited, 0)
1107         except:
1108             logging.exception("")
1109
1110         expect_container = copy.deepcopy(stubs.expect_container_spec)
1111         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1112                                        '--no-log-timestamps', '--disable-validate',
1113                                        '--eval-timeout=20', '--thread-count=20',
1114                                        '--enable-reuse', '--debug', '--on-error=continue',
1115                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1116
1117         stubs.api.container_requests().create.assert_called_with(
1118             body=JsonDiffMatcher(expect_container))
1119         self.assertEqual(capture_stdout.getvalue(),
1120                          stubs.expect_container_request_uuid + '\n')
1121
1122
1123     @stubs
1124     def test_submit_job_runner_image(self, stubs):
1125         capture_stdout = cStringIO.StringIO()
1126         try:
1127             exited = arvados_cwl.main(
1128                 ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
1129                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1130                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1131             self.assertEqual(exited, 0)
1132         except:
1133             logging.exception("")
1134
1135         stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "999999999999999999999999999999d5+99"
1136
1137         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
1138         stubs.api.pipeline_instances().create.assert_called_with(
1139             body=JsonDiffMatcher(expect_pipeline))
1140         self.assertEqual(capture_stdout.getvalue(),
1141                          stubs.expect_pipeline_uuid + '\n')
1142
1143     @stubs
1144     def test_submit_container_runner_image(self, stubs):
1145         capture_stdout = cStringIO.StringIO()
1146         try:
1147             exited = arvados_cwl.main(
1148                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
1149                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1150                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1151             self.assertEqual(exited, 0)
1152         except:
1153             logging.exception("")
1154
1155         stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
1156
1157         expect_container = copy.deepcopy(stubs.expect_container_spec)
1158         stubs.api.container_requests().create.assert_called_with(
1159             body=JsonDiffMatcher(expect_container))
1160         self.assertEqual(capture_stdout.getvalue(),
1161                          stubs.expect_container_request_uuid + '\n')
1162
1163     @stubs
1164     def test_submit_priority(self, stubs):
1165         capture_stdout = cStringIO.StringIO()
1166         try:
1167             exited = arvados_cwl.main(
1168                 ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
1169                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1170                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1171             self.assertEqual(exited, 0)
1172         except:
1173             logging.exception("")
1174
1175         stubs.expect_container_spec["priority"] = 669
1176
1177         expect_container = copy.deepcopy(stubs.expect_container_spec)
1178         stubs.api.container_requests().create.assert_called_with(
1179             body=JsonDiffMatcher(expect_container))
1180         self.assertEqual(capture_stdout.getvalue(),
1181                          stubs.expect_container_request_uuid + '\n')
1182
1183
1184     @stubs
1185     def test_submit_wf_runner_resources(self, stubs):
1186         capture_stdout = cStringIO.StringIO()
1187         try:
1188             exited = arvados_cwl.main(
1189                 ["--submit", "--no-wait", "--api=containers", "--debug",
1190                  "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
1191                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1192             self.assertEqual(exited, 0)
1193         except:
1194             logging.exception("")
1195
1196         expect_container = copy.deepcopy(stubs.expect_container_spec)
1197         expect_container["runtime_constraints"] = {
1198             "API": True,
1199             "vcpus": 2,
1200             "ram": 2000 * 2**20
1201         }
1202         expect_container["name"] = "submit_wf_runner_resources.cwl"
1203         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1204             {
1205                 "class": "http://arvados.org/cwl#WorkflowRunnerResources",
1206                 "coresMin": 2,
1207                 "ramMin": 2000
1208             }
1209         ]
1210         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
1211             "arv": "http://arvados.org/cwl#",
1212         }
1213
1214         stubs.api.container_requests().create.assert_called_with(
1215             body=JsonDiffMatcher(expect_container))
1216         self.assertEqual(capture_stdout.getvalue(),
1217                          stubs.expect_container_request_uuid + '\n')
1218
1219     def tearDown(self):
1220         arvados_cwl.arvdocker.arv_docker_clear_cache()
1221
1222     @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
1223     @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
1224     @mock.patch("arvados.api")
1225     def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
1226         arvados_cwl.arvdocker.arv_docker_clear_cache()
1227
1228         arvrunner = mock.MagicMock()
1229         arvrunner.project_uuid = ""
1230         api.return_value = mock.MagicMock()
1231         arvrunner.api = api.return_value
1232         arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
1233                                                                         "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1234                                                                         "link_class": "docker_image_repo+tag",
1235                                                                         "name": "arvados/jobs:"+arvados_cwl.__version__,
1236                                                                         "owner_uuid": "",
1237                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1238                                                             {"items": [{"created_at": "",
1239                                                                         "head_uuid": "",
1240                                                                         "link_class": "docker_image_hash",
1241                                                                         "name": "123456",
1242                                                                         "owner_uuid": "",
1243                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
1244         )
1245         find_one_image_hash.return_value = "123456"
1246
1247         arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1248                                                                               "owner_uuid": "",
1249                                                                               "manifest_text": "",
1250                                                                               "properties": ""
1251                                                                           }], "items_available": 1, "offset": 0},)
1252         arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
1253         arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1254                                                                   "portable_data_hash": "9999999999999999999999999999999b+99"}
1255         self.assertEqual("9999999999999999999999999999999b+99",
1256                          arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
1257
1258
1259     @stubs
1260     def test_submit_secrets(self, stubs):
1261         capture_stdout = cStringIO.StringIO()
1262         try:
1263             exited = arvados_cwl.main(
1264                 ["--submit", "--no-wait", "--api=containers", "--debug",
1265                  "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
1266                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1267             self.assertEqual(exited, 0)
1268         except:
1269             logging.exception("")
1270
1271
1272         expect_container = {
1273             "command": [
1274                 "arvados-cwl-runner",
1275                 "--local",
1276                 "--api=containers",
1277                 "--no-log-timestamps",
1278                 "--disable-validate",
1279                 "--eval-timeout=20",
1280                 '--thread-count=4',
1281                 "--enable-reuse",
1282                 '--debug',
1283                 "--on-error=continue",
1284                 "/var/lib/cwl/workflow.json#main",
1285                 "/var/lib/cwl/cwl.input.json"
1286             ],
1287             "container_image": "999999999999999999999999999999d3+99",
1288             "cwd": "/var/spool/cwl",
1289             "mounts": {
1290                 "/var/lib/cwl/cwl.input.json": {
1291                     "content": {
1292                         "pw": {
1293                             "$include": "/secrets/s0"
1294                         }
1295                     },
1296                     "kind": "json"
1297                 },
1298                 "/var/lib/cwl/workflow.json": {
1299                     "content": {
1300                         "$graph": [
1301                             {
1302                                 "$namespaces": {
1303                                     "cwltool": "http://commonwl.org/cwltool#"
1304                                 },
1305                                 "arguments": [
1306                                     "md5sum",
1307                                     "example.conf"
1308                                 ],
1309                                 "class": "CommandLineTool",
1310                                 "hints": [
1311                                     {
1312                                         "class": "http://commonwl.org/cwltool#Secrets",
1313                                         "secrets": [
1314                                             "#secret_job.cwl/pw"
1315                                         ]
1316                                     }
1317                                 ],
1318                                 "id": "#secret_job.cwl",
1319                                 "inputs": [
1320                                     {
1321                                         "id": "#secret_job.cwl/pw",
1322                                         "type": "string"
1323                                     }
1324                                 ],
1325                                 "outputs": [
1326                                     {
1327                                         "id": "#secret_job.cwl/out",
1328                                         "type": "stdout"
1329                                     }
1330                                 ],
1331                                 "stdout": "hashed_example.txt",
1332                                 "requirements": [
1333                                     {
1334                                         "class": "InitialWorkDirRequirement",
1335                                         "listing": [
1336                                             {
1337                                                 "entry": "username: user\npassword: $(inputs.pw)\n",
1338                                                 "entryname": "example.conf"
1339                                             }
1340                                         ]
1341                                     }
1342                                 ]
1343                             },
1344                             {
1345                                 "class": "Workflow",
1346                                 "hints": [
1347                                     {
1348                                         "class": "DockerRequirement",
1349                                         "dockerPull": "debian:8",
1350                                         "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
1351                                     },
1352                                     {
1353                                         "class": "http://commonwl.org/cwltool#Secrets",
1354                                         "secrets": [
1355                                             "#main/pw"
1356                                         ]
1357                                     }
1358                                 ],
1359                                 "id": "#main",
1360                                 "inputs": [
1361                                     {
1362                                         "id": "#main/pw",
1363                                         "type": "string"
1364                                     }
1365                                 ],
1366                                 "outputs": [
1367                                     {
1368                                         "id": "#main/out",
1369                                         "outputSource": "#main/step1/out",
1370                                         "type": "File"
1371                                     }
1372                                 ],
1373                                 "steps": [
1374                                     {
1375                                         "id": "#main/step1",
1376                                         "in": [
1377                                             {
1378                                                 "id": "#main/step1/pw",
1379                                                 "source": "#main/pw"
1380                                             }
1381                                         ],
1382                                         "out": [
1383                                             "#main/step1/out"
1384                                         ],
1385                                         "run": "#secret_job.cwl"
1386                                     }
1387                                 ]
1388                             }
1389                         ],
1390                         "cwlVersion": "v1.0"
1391                     },
1392                     "kind": "json"
1393                 },
1394                 "/var/spool/cwl": {
1395                     "kind": "collection",
1396                     "writable": True
1397                 },
1398                 "stdout": {
1399                     "kind": "file",
1400                     "path": "/var/spool/cwl/cwl.output.json"
1401                 }
1402             },
1403             "name": "secret_wf.cwl",
1404             "output_path": "/var/spool/cwl",
1405             "priority": 500,
1406             "properties": {},
1407             "runtime_constraints": {
1408                 "API": True,
1409                 "ram": 1073741824,
1410                 "vcpus": 1
1411             },
1412             "secret_mounts": {
1413                 "/secrets/s0": {
1414                     "content": "blorp",
1415                     "kind": "text"
1416                 }
1417             },
1418             "state": "Committed",
1419             "use_existing": True
1420         }
1421
1422         stubs.api.container_requests().create.assert_called_with(
1423             body=JsonDiffMatcher(expect_container))
1424         self.assertEqual(capture_stdout.getvalue(),
1425                          stubs.expect_container_request_uuid + '\n')
1426
1427     @stubs
1428     def test_submit_request_uuid(self, stubs):
1429         stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
1430
1431         stubs.api.container_requests().update().execute.return_value = {
1432             "uuid": stubs.expect_container_request_uuid,
1433             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
1434             "state": "Queued"
1435         }
1436
1437         capture_stdout = cStringIO.StringIO()
1438         try:
1439             exited = arvados_cwl.main(
1440                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
1441                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1442                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1443             self.assertEqual(exited, 0)
1444         except:
1445             logging.exception("")
1446
1447         stubs.api.container_requests().update.assert_called_with(
1448             uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec), cluster_id="zzzzz")
1449         self.assertEqual(capture_stdout.getvalue(),
1450                          stubs.expect_container_request_uuid + '\n')
1451
1452     @stubs
1453     def test_submit_container_cluster_id(self, stubs):
1454         capture_stdout = cStringIO.StringIO()
1455         try:
1456             exited = arvados_cwl.main(
1457                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb",
1458                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1459                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1460             self.assertEqual(exited, 0)
1461         except:
1462             logging.exception("")
1463
1464         expect_container = copy.deepcopy(stubs.expect_container_spec)
1465
1466         stubs.api.container_requests().create.assert_called_with(
1467             body=JsonDiffMatcher(expect_container), cluster_id="zbbbb")
1468         self.assertEqual(capture_stdout.getvalue(),
1469                          stubs.expect_container_request_uuid + '\n')
1470
1471
1472 class TestCreateTemplate(unittest.TestCase):
1473     existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
1474
1475     def _adjust_script_params(self, expect_component):
1476         expect_component['script_parameters']['x'] = {
1477             'dataclass': 'File',
1478             'required': True,
1479             'type': 'File',
1480             'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
1481         }
1482         expect_component['script_parameters']['y'] = {
1483             'dataclass': 'Collection',
1484             'required': True,
1485             'type': 'Directory',
1486             'value': '99999999999999999999999999999998+99',
1487         }
1488         expect_component['script_parameters']['z'] = {
1489             'dataclass': 'Collection',
1490             'required': True,
1491             'type': 'Directory',
1492         }
1493
1494     @stubs
1495     def test_create(self, stubs):
1496         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1497
1498         capture_stdout = cStringIO.StringIO()
1499
1500         exited = arvados_cwl.main(
1501             ["--create-workflow", "--debug",
1502              "--api=jobs",
1503              "--project-uuid", project_uuid,
1504              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1505             capture_stdout, sys.stderr, api_client=stubs.api)
1506         self.assertEqual(exited, 0)
1507
1508         stubs.api.pipeline_instances().create.refute_called()
1509         stubs.api.jobs().create.refute_called()
1510
1511         expect_component = copy.deepcopy(stubs.expect_job_spec)
1512         self._adjust_script_params(expect_component)
1513         expect_template = {
1514             "components": {
1515                 "submit_wf.cwl": expect_component,
1516             },
1517             "name": "submit_wf.cwl",
1518             "owner_uuid": project_uuid,
1519         }
1520         stubs.api.pipeline_templates().create.assert_called_with(
1521             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1522
1523         self.assertEqual(capture_stdout.getvalue(),
1524                          stubs.expect_pipeline_template_uuid + '\n')
1525
1526
1527     @stubs
1528     def test_create_name(self, stubs):
1529         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1530
1531         capture_stdout = cStringIO.StringIO()
1532
1533         exited = arvados_cwl.main(
1534             ["--create-workflow", "--debug",
1535              "--project-uuid", project_uuid,
1536              "--api=jobs",
1537              "--name", "testing 123",
1538              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1539             capture_stdout, sys.stderr, api_client=stubs.api)
1540         self.assertEqual(exited, 0)
1541
1542         stubs.api.pipeline_instances().create.refute_called()
1543         stubs.api.jobs().create.refute_called()
1544
1545         expect_component = copy.deepcopy(stubs.expect_job_spec)
1546         self._adjust_script_params(expect_component)
1547         expect_template = {
1548             "components": {
1549                 "testing 123": expect_component,
1550             },
1551             "name": "testing 123",
1552             "owner_uuid": project_uuid,
1553         }
1554         stubs.api.pipeline_templates().create.assert_called_with(
1555             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1556
1557         self.assertEqual(capture_stdout.getvalue(),
1558                          stubs.expect_pipeline_template_uuid + '\n')
1559
1560
1561     @stubs
1562     def test_update_name(self, stubs):
1563         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1564
1565         capture_stdout = cStringIO.StringIO()
1566
1567         exited = arvados_cwl.main(
1568             ["--update-workflow", self.existing_template_uuid,
1569              "--debug",
1570              "--project-uuid", project_uuid,
1571              "--api=jobs",
1572              "--name", "testing 123",
1573              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1574             capture_stdout, sys.stderr, api_client=stubs.api)
1575         self.assertEqual(exited, 0)
1576
1577         stubs.api.pipeline_instances().create.refute_called()
1578         stubs.api.jobs().create.refute_called()
1579
1580         expect_component = copy.deepcopy(stubs.expect_job_spec)
1581         self._adjust_script_params(expect_component)
1582         expect_template = {
1583             "components": {
1584                 "testing 123": expect_component,
1585             },
1586             "name": "testing 123",
1587             "owner_uuid": project_uuid,
1588         }
1589         stubs.api.pipeline_templates().create.refute_called()
1590         stubs.api.pipeline_templates().update.assert_called_with(
1591             body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
1592
1593         self.assertEqual(capture_stdout.getvalue(),
1594                          self.existing_template_uuid + '\n')
1595
1596
1597 class TestCreateWorkflow(unittest.TestCase):
1598     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1599     expect_workflow = StripYAMLComments(
1600         open("tests/wf/expect_packed.cwl").read())
1601
1602     @stubs
1603     def test_create(self, stubs):
1604         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1605
1606         capture_stdout = cStringIO.StringIO()
1607
1608         exited = arvados_cwl.main(
1609             ["--create-workflow", "--debug",
1610              "--api=containers",
1611              "--project-uuid", project_uuid,
1612              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1613             capture_stdout, sys.stderr, api_client=stubs.api)
1614         self.assertEqual(exited, 0)
1615
1616         stubs.api.pipeline_templates().create.refute_called()
1617         stubs.api.container_requests().create.refute_called()
1618
1619         body = {
1620             "workflow": {
1621                 "owner_uuid": project_uuid,
1622                 "name": "submit_wf.cwl",
1623                 "description": "",
1624                 "definition": self.expect_workflow,
1625             }
1626         }
1627         stubs.api.workflows().create.assert_called_with(
1628             body=JsonDiffMatcher(body))
1629
1630         self.assertEqual(capture_stdout.getvalue(),
1631                          stubs.expect_workflow_uuid + '\n')
1632
1633
1634     @stubs
1635     def test_create_name(self, stubs):
1636         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1637
1638         capture_stdout = cStringIO.StringIO()
1639
1640         exited = arvados_cwl.main(
1641             ["--create-workflow", "--debug",
1642              "--api=containers",
1643              "--project-uuid", project_uuid,
1644              "--name", "testing 123",
1645              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1646             capture_stdout, sys.stderr, api_client=stubs.api)
1647         self.assertEqual(exited, 0)
1648
1649         stubs.api.pipeline_templates().create.refute_called()
1650         stubs.api.container_requests().create.refute_called()
1651
1652         body = {
1653             "workflow": {
1654                 "owner_uuid": project_uuid,
1655                 "name": "testing 123",
1656                 "description": "",
1657                 "definition": self.expect_workflow,
1658             }
1659         }
1660         stubs.api.workflows().create.assert_called_with(
1661             body=JsonDiffMatcher(body))
1662
1663         self.assertEqual(capture_stdout.getvalue(),
1664                          stubs.expect_workflow_uuid + '\n')
1665
1666     @stubs
1667     def test_incompatible_api(self, stubs):
1668         capture_stderr = cStringIO.StringIO()
1669         logging.getLogger('arvados.cwl-runner').addHandler(
1670             logging.StreamHandler(capture_stderr))
1671
1672         exited = arvados_cwl.main(
1673             ["--update-workflow", self.existing_workflow_uuid,
1674              "--api=jobs",
1675              "--debug",
1676              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1677             sys.stderr, sys.stderr, api_client=stubs.api)
1678         self.assertEqual(exited, 1)
1679         self.assertRegexpMatches(
1680             capture_stderr.getvalue(),
1681             "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
1682
1683     @stubs
1684     def test_update(self, stubs):
1685         capture_stdout = cStringIO.StringIO()
1686
1687         exited = arvados_cwl.main(
1688             ["--update-workflow", self.existing_workflow_uuid,
1689              "--debug",
1690              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1691             capture_stdout, sys.stderr, api_client=stubs.api)
1692         self.assertEqual(exited, 0)
1693
1694         body = {
1695             "workflow": {
1696                 "name": "submit_wf.cwl",
1697                 "description": "",
1698                 "definition": self.expect_workflow,
1699             }
1700         }
1701         stubs.api.workflows().update.assert_called_with(
1702             uuid=self.existing_workflow_uuid,
1703             body=JsonDiffMatcher(body))
1704         self.assertEqual(capture_stdout.getvalue(),
1705                          self.existing_workflow_uuid + '\n')
1706
1707
1708     @stubs
1709     def test_update_name(self, stubs):
1710         capture_stdout = cStringIO.StringIO()
1711
1712         exited = arvados_cwl.main(
1713             ["--update-workflow", self.existing_workflow_uuid,
1714              "--debug", "--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         body = {
1720             "workflow": {
1721                 "name": "testing 123",
1722                 "description": "",
1723                 "definition": self.expect_workflow,
1724             }
1725         }
1726         stubs.api.workflows().update.assert_called_with(
1727             uuid=self.existing_workflow_uuid,
1728             body=JsonDiffMatcher(body))
1729         self.assertEqual(capture_stdout.getvalue(),
1730                          self.existing_workflow_uuid + '\n')
1731
1732
1733     @stubs
1734     def test_create_collection_per_tool(self, stubs):
1735         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1736
1737         capture_stdout = cStringIO.StringIO()
1738
1739         exited = arvados_cwl.main(
1740             ["--create-workflow", "--debug",
1741              "--api=containers",
1742              "--project-uuid", project_uuid,
1743              "tests/collection_per_tool/collection_per_tool.cwl"],
1744             capture_stdout, sys.stderr, api_client=stubs.api)
1745         self.assertEqual(exited, 0)
1746
1747         toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1748         expect_workflow = StripYAMLComments(open(toolfile).read())
1749
1750         body = {
1751             "workflow": {
1752                 "owner_uuid": project_uuid,
1753                 "name": "collection_per_tool.cwl",
1754                 "description": "",
1755                 "definition": expect_workflow,
1756             }
1757         }
1758         stubs.api.workflows().create.assert_called_with(
1759             body=JsonDiffMatcher(body))
1760
1761         self.assertEqual(capture_stdout.getvalue(),
1762                          stubs.expect_workflow_uuid + '\n')
1763
1764 class TestTemplateInputs(unittest.TestCase):
1765     expect_template = {
1766         "components": {
1767             "inputs_test.cwl": {
1768                 'runtime_constraints': {
1769                     'docker_image': '999999999999999999999999999999d3+99',
1770                     'min_ram_mb_per_node': 1024
1771                 },
1772                 'script_parameters': {
1773                     'cwl:tool':
1774                     'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main',
1775                     'optionalFloatInput': None,
1776                     'fileInput': {
1777                         'type': 'File',
1778                         'dataclass': 'File',
1779                         'required': True,
1780                         'title': "It's a file; we expect to find some characters in it.",
1781                         'description': 'If there were anything further to say, it would be said here,\nor here.'
1782                     },
1783                     'floatInput': {
1784                         'type': 'float',
1785                         'dataclass': 'number',
1786                         'required': True,
1787                         'title': 'Floats like a duck',
1788                         'default': 0.1,
1789                         'value': 0.1,
1790                     },
1791                     'optionalFloatInput': {
1792                         'type': ['null', 'float'],
1793                         'dataclass': 'number',
1794                         'required': False,
1795                     },
1796                     'boolInput': {
1797                         'type': 'boolean',
1798                         'dataclass': 'boolean',
1799                         'required': True,
1800                         'title': 'True or false?',
1801                     },
1802                 },
1803                 'repository': 'arvados',
1804                 'script_version': 'master',
1805                 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
1806                 'script': 'cwl-runner',
1807             },
1808         },
1809         "name": "inputs_test.cwl",
1810     }
1811
1812     @stubs
1813     def test_inputs_empty(self, stubs):
1814         exited = arvados_cwl.main(
1815             ["--create-template",
1816              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
1817             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1818         self.assertEqual(exited, 0)
1819
1820         stubs.api.pipeline_templates().create.assert_called_with(
1821             body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
1822
1823     @stubs
1824     def test_inputs(self, stubs):
1825         exited = arvados_cwl.main(
1826             ["--create-template",
1827              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
1828             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1829         self.assertEqual(exited, 0)
1830
1831         expect_template = copy.deepcopy(self.expect_template)
1832         params = expect_template[
1833             "components"]["inputs_test.cwl"]["script_parameters"]
1834         params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
1835         params["cwl:tool"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main'
1836         params["floatInput"]["value"] = 1.234
1837         params["boolInput"]["value"] = True
1838
1839         stubs.api.pipeline_templates().create.assert_called_with(
1840             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)