sdk/cwl/tests/test_submit.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 import copy
   6 import cStringIO
   7 import functools
   8 import hashlib
   9 import json
  10 import logging
  11 import mock
  12 import sys
  13 import unittest
  14
  15 import arvados
  16 import arvados.collection
  17 import arvados_cwl
  18 import arvados_cwl.runner
  19 import arvados.keep
  20
  21 from .matcher import JsonDiffMatcher, StripYAMLComments
  22 from .mock_discovery import get_rootDesc
  23
  24 import ruamel.yaml as yaml
  25
  26 _rootDesc = None
  27
  28 def stubs(func):
  29     @functools.wraps(func)
  30     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  31     @mock.patch("arvados.collection.KeepClient")
  32     @mock.patch("arvados.keep.KeepClient")
  33     @mock.patch("arvados.events.subscribe")
  34     def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs):
  35         class Stubs:
  36             pass
  37         stubs = Stubs()
  38         stubs.events = events
  39         stubs.keepdocker = keepdocker
  40
  41         def putstub(p, **kwargs):
  42             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
  43         keep_client1().put.side_effect = putstub
  44         keep_client1.put.side_effect = putstub
  45         keep_client2().put.side_effect = putstub
  46         keep_client2.put.side_effect = putstub
  47
  48         stubs.keep_client = keep_client2
  49         stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  50         stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
  51
  52         stubs.api = mock.MagicMock()
  53         stubs.api._rootDesc = get_rootDesc()
  54
  55         stubs.api.users().current().execute.return_value = {
  56             "uuid": stubs.fake_user_uuid,
  57         }
  58         stubs.api.collections().list().execute.return_value = {"items": []}
  59
  60         class CollectionExecute(object):
  61             def __init__(self, exe):
  62                 self.exe = exe
  63             def execute(self, num_retries=None):
  64                 return self.exe
  65
  66         def collection_createstub(created_collections, body, ensure_unique_name=None):
  67             mt = body["manifest_text"]
  68             uuid = "zzzzz-4zz18-zzzzzzzzzzzzzz%d" % len(created_collections)
  69             pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
  70             created_collections[uuid] = {
  71                 "uuid": uuid,
  72                 "portable_data_hash": pdh,
  73                 "manifest_text": mt
  74             }
  75             return CollectionExecute(created_collections[uuid])
  76
  77         def collection_getstub(created_collections, uuid):
  78             for v in created_collections.itervalues():
  79                 if uuid in (v["uuid"], v["portable_data_hash"]):
  80                     return CollectionExecute(v)
  81
  82         created_collections = {
  83             "99999999999999999999999999999998+99": {
  84                 "uuid": "",
  85                 "portable_data_hash": "99999999999999999999999999999998+99",
  86                 "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
  87             },
  88             "99999999999999999999999999999994+99": {
  89                 "uuid": "",
  90                 "portable_data_hash": "99999999999999999999999999999994+99",
  91                 "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
  92             }
  93         }
  94         stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
  95         stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
  96
  97         stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  98         stubs.api.jobs().create().execute.return_value = {
  99             "uuid": stubs.expect_job_uuid,
 100             "state": "Queued",
 101         }
 102
 103         stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
 104         stubs.api.container_requests().create().execute.return_value = {
 105             "uuid": stubs.expect_container_request_uuid,
 106             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
 107             "state": "Queued"
 108         }
 109
 110         stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
 111         stubs.api.pipeline_templates().create().execute.return_value = {
 112             "uuid": stubs.expect_pipeline_template_uuid,
 113         }
 114         stubs.expect_job_spec = {
 115             'runtime_constraints': {
 116                 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
 117                 'min_ram_mb_per_node': 1024
 118             },
 119             'script_parameters': {
 120                 'x': {
 121                     'basename': 'blorp.txt',
 122                     'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 123                     'class': 'File'
 124                 },
 125                 'y': {
 126                     'basename': '99999999999999999999999999999998+99',
 127                     'location': 'keep:99999999999999999999999999999998+99',
 128                     'class': 'Directory'
 129                 },
 130                 'z': {
 131                     'basename': 'anonymous',
 132                     "listing": [{
 133                         "basename": "renamed.txt",
 134                         "class": "File",
 135                         "location": "keep:99999999999999999999999999999998+99/file1.txt",
 136                         "size": 0
 137                     }],
 138                     'class': 'Directory'
 139                 },
 140                 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main'
 141             },
 142             'repository': 'arvados',
 143             'script_version': 'master',
 144             'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
 145             'script': 'cwl-runner'
 146         }
 147         stubs.pipeline_component = stubs.expect_job_spec.copy()
 148         stubs.expect_pipeline_instance = {
 149             'name': 'submit_wf.cwl',
 150             'state': 'RunningOnServer',
 151             'owner_uuid': None,
 152             "components": {
 153                 "cwl-runner": {
 154                     'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
 155                     'script_parameters': {
 156                         'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
 157                         'x': {"value": {
 158                             'basename': 'blorp.txt',
 159                             'class': 'File',
 160                             'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 161                             "size": 16
 162                         }},
 163                         'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
 164                               'listing': [
 165                                   {
 166                                       'basename': 'renamed.txt',
 167                                       'class': 'File', 'location':
 168                                       'keep:99999999999999999999999999999998+99/file1.txt',
 169                                       'size': 0
 170                                   }
 171                               ]}},
 172                         'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
 173                         'arv:debug': True,
 174                         'arv:enable_reuse': True,
 175                         'arv:on_error': 'continue'
 176                     },
 177                     'repository': 'arvados',
 178                     'script_version': 'master',
 179                     'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
 180                     'script': 'cwl-runner',
 181                     'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
 182                 }
 183             }
 184         }
 185         stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
 186         stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
 187         stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
 188         stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
 189         stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
 190             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 191             "state": "Queued"
 192         }
 193         stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
 194         stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
 195
 196         with open("tests/wf/submit_wf_packed.cwl") as f:
 197             expect_packed_workflow = yaml.round_trip_load(f)
 198
 199         stubs.expect_container_spec = {
 200             'priority': 500,
 201             'mounts': {
 202                 '/var/spool/cwl': {
 203                     'writable': True,
 204                     'kind': 'collection'
 205                 },
 206                 '/var/lib/cwl/workflow.json': {
 207                     'content': expect_packed_workflow,
 208                     'kind': 'json'
 209                 },
 210                 'stdout': {
 211                     'path': '/var/spool/cwl/cwl.output.json',
 212                     'kind': 'file'
 213                 },
 214                 '/var/lib/cwl/cwl.input.json': {
 215                     'kind': 'json',
 216                     'content': {
 217                         'y': {
 218                             'basename': '99999999999999999999999999999998+99',
 219                             'location': 'keep:99999999999999999999999999999998+99',
 220                             'class': 'Directory'},
 221                         'x': {
 222                             'basename': u'blorp.txt',
 223                             'class': 'File',
 224                             'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
 225                             "size": 16
 226                         },
 227                         'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
 228                             {'basename': 'renamed.txt',
 229                              'class': 'File',
 230                              'location': 'keep:99999999999999999999999999999998+99/file1.txt',
 231                              'size': 0
 232                             }
 233                         ]}
 234                     },
 235                     'kind': 'json'
 236                 }
 237             },
 238             'secret_mounts': {},
 239             'state': 'Committed',
 240             'command': ['arvados-cwl-runner', '--local', '--api=containers',
 241                         '--no-log-timestamps', '--disable-validate',
 242                         '--eval-timeout=20', '--thread-count=4',
 243                         '--enable-reuse', '--debug', '--on-error=continue',
 244                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
 245             'name': 'submit_wf.cwl',
 246             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
 247             'output_path': '/var/spool/cwl',
 248             'cwd': '/var/spool/cwl',
 249             'runtime_constraints': {
 250                 'API': True,
 251                 'vcpus': 1,
 252                 'ram': 1024*1024*1024
 253             },
 254             'use_existing': True,
 255             'properties': {},
 256             'secret_mounts': {}
 257         }
 258
 259         stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
 260         stubs.api.workflows().create().execute.return_value = {
 261             "uuid": stubs.expect_workflow_uuid,
 262         }
 263         def update_mock(**kwargs):
 264             stubs.updated_uuid = kwargs.get('uuid')
 265             return mock.DEFAULT
 266         stubs.api.workflows().update.side_effect = update_mock
 267         stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
 268             "uuid": stubs.updated_uuid,
 269         }
 270
 271         return func(self, stubs, *args, **kwargs)
 272     return wrapped
 273
 274
 275 class TestSubmit(unittest.TestCase):
 276     @mock.patch("arvados_cwl.runner.arv_docker_get_image")
 277     @mock.patch("time.sleep")
 278     @stubs
 279     def test_submit(self, stubs, tm, arvdock):
 280         capture_stdout = cStringIO.StringIO()
 281         exited = arvados_cwl.main(
 282             ["--submit", "--no-wait", "--api=jobs", "--debug",
 283              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 284             capture_stdout, sys.stderr, api_client=stubs.api)
 285         self.assertEqual(exited, 0)
 286
 287         stubs.api.collections().create.assert_has_calls([
 288             mock.call(body=JsonDiffMatcher({
 289                 'manifest_text':
 290                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
 291                 'replication_desired': None,
 292                 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
 293             }), ensure_unique_name=False),
 294             mock.call(body=JsonDiffMatcher({
 295                 'manifest_text':
 296                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 297                 'replication_desired': None,
 298                 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
 299             }), ensure_unique_name=False),
 300             mock.call(body=JsonDiffMatcher({
 301                 'manifest_text':
 302                 '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n',
 303                 'replication_desired': None,
 304                 'name': 'submit_wf.cwl',
 305             }), ensure_unique_name=True)        ])
 306
 307         arvdock.assert_has_calls([
 308             mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
 309             mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
 310         ])
 311
 312         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 313         stubs.api.pipeline_instances().create.assert_called_with(
 314             body=JsonDiffMatcher(expect_pipeline))
 315         self.assertEqual(capture_stdout.getvalue(),
 316                          stubs.expect_pipeline_uuid + '\n')
 317
 318
 319     @mock.patch("time.sleep")
 320     @stubs
 321     def test_submit_no_reuse(self, stubs, tm):
 322         capture_stdout = cStringIO.StringIO()
 323         exited = arvados_cwl.main(
 324             ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
 325              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 326             capture_stdout, sys.stderr, api_client=stubs.api)
 327         self.assertEqual(exited, 0)
 328
 329         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 330         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
 331         expect_pipeline["properties"] = {"run_options": {"enable_job_reuse": False}}
 332
 333         stubs.api.pipeline_instances().create.assert_called_with(
 334             body=JsonDiffMatcher(expect_pipeline))
 335         self.assertEqual(capture_stdout.getvalue(),
 336                          stubs.expect_pipeline_uuid + '\n')
 337
 338     @stubs
 339     def test_error_when_multiple_storage_classes_specified(self, stubs):
 340         storage_classes = "foo,bar"
 341         exited = arvados_cwl.main(
 342                 ["--debug", "--storage-classes", storage_classes,
 343                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 344                 sys.stdin, sys.stderr, api_client=stubs.api)
 345         self.assertEqual(exited, 1)
 346
 347     @mock.patch("time.sleep")
 348     @stubs
 349     def test_submit_on_error(self, stubs, tm):
 350         capture_stdout = cStringIO.StringIO()
 351         exited = arvados_cwl.main(
 352             ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
 353              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 354             capture_stdout, sys.stderr, api_client=stubs.api)
 355         self.assertEqual(exited, 0)
 356
 357         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 358         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
 359
 360         stubs.api.pipeline_instances().create.assert_called_with(
 361             body=JsonDiffMatcher(expect_pipeline))
 362         self.assertEqual(capture_stdout.getvalue(),
 363                          stubs.expect_pipeline_uuid + '\n')
 364
 365
 366     @mock.patch("time.sleep")
 367     @stubs
 368     def test_submit_runner_ram(self, stubs, tm):
 369         capture_stdout = cStringIO.StringIO()
 370         exited = arvados_cwl.main(
 371             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
 372              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 373             capture_stdout, sys.stderr, api_client=stubs.api)
 374         self.assertEqual(exited, 0)
 375
 376         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 377         expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
 378
 379         stubs.api.pipeline_instances().create.assert_called_with(
 380             body=JsonDiffMatcher(expect_pipeline))
 381         self.assertEqual(capture_stdout.getvalue(),
 382                          stubs.expect_pipeline_uuid + '\n')
 383
 384
 385     @mock.patch("time.sleep")
 386     @stubs
 387     def test_submit_invalid_runner_ram(self, stubs, tm):
 388         capture_stdout = cStringIO.StringIO()
 389         exited = arvados_cwl.main(
 390             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
 391              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 392             capture_stdout, sys.stderr, api_client=stubs.api)
 393         self.assertEqual(exited, 1)
 394
 395     @mock.patch("time.sleep")
 396     @stubs
 397     def test_submit_output_name(self, stubs, tm):
 398         output_name = "test_output_name"
 399
 400         capture_stdout = cStringIO.StringIO()
 401         exited = arvados_cwl.main(
 402             ["--submit", "--no-wait", "--debug", "--output-name", output_name,
 403              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 404             capture_stdout, sys.stderr, api_client=stubs.api)
 405         self.assertEqual(exited, 0)
 406
 407         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 408         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
 409
 410         stubs.api.pipeline_instances().create.assert_called_with(
 411             body=JsonDiffMatcher(expect_pipeline))
 412         self.assertEqual(capture_stdout.getvalue(),
 413                          stubs.expect_pipeline_uuid + '\n')
 414
 415
 416     @mock.patch("time.sleep")
 417     @stubs
 418     def test_submit_pipeline_name(self, stubs, tm):
 419         capture_stdout = cStringIO.StringIO()
 420         exited = arvados_cwl.main(
 421             ["--submit", "--no-wait", "--debug", "--name=hello job 123",
 422              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 423             capture_stdout, sys.stderr, api_client=stubs.api)
 424         self.assertEqual(exited, 0)
 425
 426         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 427         expect_pipeline["name"] = "hello job 123"
 428
 429         stubs.api.pipeline_instances().create.assert_called_with(
 430             body=JsonDiffMatcher(expect_pipeline))
 431         self.assertEqual(capture_stdout.getvalue(),
 432                          stubs.expect_pipeline_uuid + '\n')
 433
 434     @mock.patch("time.sleep")
 435     @stubs
 436     def test_submit_output_tags(self, stubs, tm):
 437         output_tags = "tag0,tag1,tag2"
 438
 439         capture_stdout = cStringIO.StringIO()
 440         exited = arvados_cwl.main(
 441             ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
 442              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 443             capture_stdout, sys.stderr, api_client=stubs.api)
 444         self.assertEqual(exited, 0)
 445
 446         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 447         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
 448
 449         stubs.api.pipeline_instances().create.assert_called_with(
 450             body=JsonDiffMatcher(expect_pipeline))
 451         self.assertEqual(capture_stdout.getvalue(),
 452                          stubs.expect_pipeline_uuid + '\n')
 453
 454     @mock.patch("time.sleep")
 455     @stubs
 456     def test_submit_with_project_uuid(self, stubs, tm):
 457         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 458
 459         exited = arvados_cwl.main(
 460             ["--submit", "--no-wait", "--debug",
 461              "--project-uuid", project_uuid,
 462              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 463             sys.stdout, sys.stderr, api_client=stubs.api)
 464         self.assertEqual(exited, 0)
 465
 466         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 467         expect_pipeline["owner_uuid"] = project_uuid
 468         stubs.api.pipeline_instances().create.assert_called_with(
 469             body=JsonDiffMatcher(expect_pipeline))
 470
 471     @stubs
 472     def test_submit_container(self, stubs):
 473         capture_stdout = cStringIO.StringIO()
 474         try:
 475             exited = arvados_cwl.main(
 476                 ["--submit", "--no-wait", "--api=containers", "--debug",
 477                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 478                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 479             self.assertEqual(exited, 0)
 480         except:
 481             logging.exception("")
 482
 483         stubs.api.collections().create.assert_has_calls([
 484             mock.call(body=JsonDiffMatcher({
 485                 'manifest_text':
 486                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
 487                 'replication_desired': None,
 488                 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
 489             }), ensure_unique_name=False),
 490             mock.call(body=JsonDiffMatcher({
 491                 'manifest_text':
 492                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 493                 'replication_desired': None,
 494                 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
 495             }), ensure_unique_name=False)])
 496
 497         expect_container = copy.deepcopy(stubs.expect_container_spec)
 498         stubs.api.container_requests().create.assert_called_with(
 499             body=JsonDiffMatcher(expect_container))
 500         self.assertEqual(capture_stdout.getvalue(),
 501                          stubs.expect_container_request_uuid + '\n')
 502
 503     @stubs
 504     def test_submit_container_no_reuse(self, stubs):
 505         capture_stdout = cStringIO.StringIO()
 506         try:
 507             exited = arvados_cwl.main(
 508                 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
 509                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 510                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 511             self.assertEqual(exited, 0)
 512         except:
 513             logging.exception("")
 514
 515         expect_container = copy.deepcopy(stubs.expect_container_spec)
 516         expect_container["command"] = [
 517             'arvados-cwl-runner', '--local', '--api=containers',
 518             '--no-log-timestamps', '--disable-validate',
 519             '--eval-timeout=20', '--thread-count=4',
 520             '--disable-reuse', '--debug', '--on-error=continue',
 521             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 522         expect_container["use_existing"] = False
 523
 524         stubs.api.container_requests().create.assert_called_with(
 525             body=JsonDiffMatcher(expect_container))
 526         self.assertEqual(capture_stdout.getvalue(),
 527                          stubs.expect_container_request_uuid + '\n')
 528
 529
 530     @stubs
 531     def test_submit_container_reuse_disabled_by_workflow(self, stubs):
 532         capture_stdout = cStringIO.StringIO()
 533
 534         exited = arvados_cwl.main(
 535             ["--submit", "--no-wait", "--api=containers", "--debug",
 536              "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
 537             capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 538         self.assertEqual(exited, 0)
 539
 540         expect_container = copy.deepcopy(stubs.expect_container_spec)
 541         expect_container["command"] = [
 542             'arvados-cwl-runner', '--local', '--api=containers',
 543             '--no-log-timestamps', '--disable-validate',
 544             '--eval-timeout=20', '--thread-count=4',
 545             '--disable-reuse', '--debug', '--on-error=continue',
 546             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 547         expect_container["use_existing"] = False
 548         expect_container["name"] = "submit_wf_no_reuse.cwl"
 549         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
 550             {
 551                 "class": "http://arvados.org/cwl#ReuseRequirement",
 552                 "enableReuse": False,
 553             },
 554         ]
 555         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
 556             "arv": "http://arvados.org/cwl#",
 557             "cwltool": "http://commonwl.org/cwltool#"
 558         }
 559
 560         stubs.api.container_requests().create.assert_called_with(
 561             body=JsonDiffMatcher(expect_container))
 562         self.assertEqual(capture_stdout.getvalue(),
 563                          stubs.expect_container_request_uuid + '\n')
 564
 565
 566     @stubs
 567     def test_submit_container_on_error(self, stubs):
 568         capture_stdout = cStringIO.StringIO()
 569         try:
 570             exited = arvados_cwl.main(
 571                 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
 572                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 573                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 574             self.assertEqual(exited, 0)
 575         except:
 576             logging.exception("")
 577
 578         expect_container = copy.deepcopy(stubs.expect_container_spec)
 579         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 580                                        '--no-log-timestamps', '--disable-validate',
 581                                        '--eval-timeout=20', '--thread-count=4',
 582                                        '--enable-reuse', '--debug', '--on-error=stop',
 583                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 584
 585         stubs.api.container_requests().create.assert_called_with(
 586             body=JsonDiffMatcher(expect_container))
 587         self.assertEqual(capture_stdout.getvalue(),
 588                          stubs.expect_container_request_uuid + '\n')
 589
 590     @stubs
 591     def test_submit_container_output_name(self, stubs):
 592         output_name = "test_output_name"
 593
 594         capture_stdout = cStringIO.StringIO()
 595         try:
 596             exited = arvados_cwl.main(
 597                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
 598                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 599                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 600             self.assertEqual(exited, 0)
 601         except:
 602             logging.exception("")
 603
 604         expect_container = copy.deepcopy(stubs.expect_container_spec)
 605         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 606                                        '--no-log-timestamps', '--disable-validate',
 607                                        '--eval-timeout=20', '--thread-count=4',
 608                                        '--enable-reuse',
 609                                        "--output-name="+output_name, '--debug', '--on-error=continue',
 610                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 611         expect_container["output_name"] = output_name
 612
 613         stubs.api.container_requests().create.assert_called_with(
 614             body=JsonDiffMatcher(expect_container))
 615         self.assertEqual(capture_stdout.getvalue(),
 616                          stubs.expect_container_request_uuid + '\n')
 617
 618     @stubs
 619     def test_submit_storage_classes(self, stubs):
 620         capture_stdout = cStringIO.StringIO()
 621         try:
 622             exited = arvados_cwl.main(
 623                 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
 624                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 625                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 626             self.assertEqual(exited, 0)
 627         except:
 628             logging.exception("")
 629
 630         expect_container = copy.deepcopy(stubs.expect_container_spec)
 631         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 632                                        '--no-log-timestamps', '--disable-validate',
 633                                        '--eval-timeout=20', '--thread-count=4',
 634                                        '--enable-reuse', "--debug",
 635                                        "--storage-classes=foo", '--on-error=continue',
 636                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 637
 638         stubs.api.container_requests().create.assert_called_with(
 639             body=JsonDiffMatcher(expect_container))
 640         self.assertEqual(capture_stdout.getvalue(),
 641                          stubs.expect_container_request_uuid + '\n')
 642
 643     @mock.patch("arvados_cwl.task_queue.TaskQueue")
 644     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
 645     @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None))
 646     @stubs
 647     def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
 648         def set_final_output(job_order, output_callback, runtimeContext):
 649             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
 650             return []
 651         job.side_effect = set_final_output
 652
 653         try:
 654             exited = arvados_cwl.main(
 655                 ["--debug", "--local", "--storage-classes=foo",
 656                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 657                 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 658             self.assertEqual(exited, 0)
 659         except:
 660             logging.exception("")
 661
 662         make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
 663
 664     @mock.patch("arvados_cwl.task_queue.TaskQueue")
 665     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
 666     @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None))
 667     @stubs
 668     def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
 669         def set_final_output(job_order, output_callback, runtimeContext):
 670             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
 671             return []
 672         job.side_effect = set_final_output
 673
 674         try:
 675             exited = arvados_cwl.main(
 676                 ["--debug", "--local",
 677                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 678                 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 679             self.assertEqual(exited, 0)
 680         except:
 681             logging.exception("")
 682
 683         make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
 684
 685     @stubs
 686     def test_submit_container_output_ttl(self, stubs):
 687         capture_stdout = cStringIO.StringIO()
 688         try:
 689             exited = arvados_cwl.main(
 690                 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
 691                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 692                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 693             self.assertEqual(exited, 0)
 694         except:
 695             logging.exception("")
 696
 697         expect_container = copy.deepcopy(stubs.expect_container_spec)
 698         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 699                                        '--no-log-timestamps', '--disable-validate',
 700                                        '--eval-timeout=20', '--thread-count=4',
 701                                        '--enable-reuse', '--debug', '--on-error=continue',
 702                                        "--intermediate-output-ttl=3600",
 703                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 704
 705         stubs.api.container_requests().create.assert_called_with(
 706             body=JsonDiffMatcher(expect_container))
 707         self.assertEqual(capture_stdout.getvalue(),
 708                          stubs.expect_container_request_uuid + '\n')
 709
 710     @stubs
 711     def test_submit_container_trash_intermediate(self, stubs):
 712         capture_stdout = cStringIO.StringIO()
 713         try:
 714             exited = arvados_cwl.main(
 715                 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
 716                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 717                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 718             self.assertEqual(exited, 0)
 719         except:
 720             logging.exception("")
 721
 722         expect_container = copy.deepcopy(stubs.expect_container_spec)
 723         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 724                                        '--no-log-timestamps', '--disable-validate',
 725                                        '--eval-timeout=20', '--thread-count=4',
 726                                        '--enable-reuse', '--debug', '--on-error=continue',
 727                                        "--trash-intermediate",
 728                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 729
 730         stubs.api.container_requests().create.assert_called_with(
 731             body=JsonDiffMatcher(expect_container))
 732         self.assertEqual(capture_stdout.getvalue(),
 733                          stubs.expect_container_request_uuid + '\n')
 734
 735     @stubs
 736     def test_submit_container_output_tags(self, stubs):
 737         output_tags = "tag0,tag1,tag2"
 738
 739         capture_stdout = cStringIO.StringIO()
 740         try:
 741             exited = arvados_cwl.main(
 742                 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
 743                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 744                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 745             self.assertEqual(exited, 0)
 746         except:
 747             logging.exception("")
 748
 749         expect_container = copy.deepcopy(stubs.expect_container_spec)
 750         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
 751                                        '--no-log-timestamps', '--disable-validate',
 752                                        '--eval-timeout=20', '--thread-count=4',
 753                                        '--enable-reuse',
 754                                        "--output-tags="+output_tags, '--debug', '--on-error=continue',
 755                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 756
 757         stubs.api.container_requests().create.assert_called_with(
 758             body=JsonDiffMatcher(expect_container))
 759         self.assertEqual(capture_stdout.getvalue(),
 760                          stubs.expect_container_request_uuid + '\n')
 761
 762     @stubs
 763     def test_submit_container_runner_ram(self, stubs):
 764         capture_stdout = cStringIO.StringIO()
 765         try:
 766             exited = arvados_cwl.main(
 767                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
 768                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 769                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 770             self.assertEqual(exited, 0)
 771         except:
 772             logging.exception("")
 773
 774         expect_container = copy.deepcopy(stubs.expect_container_spec)
 775         expect_container["runtime_constraints"]["ram"] = 2048*1024*1024
 776
 777         stubs.api.container_requests().create.assert_called_with(
 778             body=JsonDiffMatcher(expect_container))
 779         self.assertEqual(capture_stdout.getvalue(),
 780                          stubs.expect_container_request_uuid + '\n')
 781
 782     @mock.patch("arvados.collection.CollectionReader")
 783     @mock.patch("time.sleep")
 784     @stubs
 785     def test_submit_file_keepref(self, stubs, tm, collectionReader):
 786         capture_stdout = cStringIO.StringIO()
 787         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
 788         exited = arvados_cwl.main(
 789             ["--submit", "--no-wait", "--api=containers", "--debug",
 790              "tests/wf/submit_keepref_wf.cwl"],
 791             capture_stdout, sys.stderr, api_client=stubs.api)
 792         self.assertEqual(exited, 0)
 793
 794
 795     @mock.patch("arvados.collection.CollectionReader")
 796     @mock.patch("time.sleep")
 797     @stubs
 798     def test_submit_keepref(self, stubs, tm, reader):
 799         capture_stdout = cStringIO.StringIO()
 800
 801         with open("tests/wf/expect_arvworkflow.cwl") as f:
 802             reader().open().__enter__().read.return_value = f.read()
 803
 804         exited = arvados_cwl.main(
 805             ["--submit", "--no-wait", "--api=containers", "--debug",
 806              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 807             capture_stdout, sys.stderr, api_client=stubs.api)
 808         self.assertEqual(exited, 0)
 809
 810         expect_container = {
 811             'priority': 500,
 812             'mounts': {
 813                 '/var/spool/cwl': {
 814                     'writable': True,
 815                     'kind': 'collection'
 816                 },
 817                 'stdout': {
 818                     'path': '/var/spool/cwl/cwl.output.json',
 819                     'kind': 'file'
 820                 },
 821                 '/var/lib/cwl/workflow': {
 822                     'portable_data_hash': '99999999999999999999999999999994+99',
 823                     'kind': 'collection'
 824                 },
 825                 '/var/lib/cwl/cwl.input.json': {
 826                     'content': {
 827                         'x': 'XxX'
 828                     },
 829                     'kind': 'json'
 830                 }
 831             }, 'state': 'Committed',
 832             'output_path': '/var/spool/cwl',
 833             'name': 'expect_arvworkflow.cwl#main',
 834             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
 835             'command': ['arvados-cwl-runner', '--local', '--api=containers',
 836                         '--no-log-timestamps', '--disable-validate',
 837                         '--eval-timeout=20', '--thread-count=4',
 838                         '--enable-reuse', '--debug', '--on-error=continue',
 839                         '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
 840             'cwd': '/var/spool/cwl',
 841             'runtime_constraints': {
 842                 'API': True,
 843                 'vcpus': 1,
 844                 'ram': 1073741824
 845             },
 846             'use_existing': True,
 847             'properties': {},
 848             'secret_mounts': {}
 849         }
 850
 851         stubs.api.container_requests().create.assert_called_with(
 852             body=JsonDiffMatcher(expect_container))
 853         self.assertEqual(capture_stdout.getvalue(),
 854                          stubs.expect_container_request_uuid + '\n')
 855
 856
 857     @mock.patch("arvados.collection.CollectionReader")
 858     @mock.patch("time.sleep")
 859     @stubs
 860     def test_submit_jobs_keepref(self, stubs, tm, reader):
 861         capture_stdout = cStringIO.StringIO()
 862
 863         with open("tests/wf/expect_arvworkflow.cwl") as f:
 864             reader().open().__enter__().read.return_value = f.read()
 865
 866         exited = arvados_cwl.main(
 867             ["--submit", "--no-wait", "--api=jobs", "--debug",
 868              "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
 869             capture_stdout, sys.stderr, api_client=stubs.api)
 870         self.assertEqual(exited, 0)
 871
 872         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 873         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
 874         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
 875         del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
 876         expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
 877         expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
 878         stubs.api.pipeline_instances().create.assert_called_with(
 879             body=JsonDiffMatcher(expect_pipeline))
 880
 881     @mock.patch("time.sleep")
 882     @stubs
 883     def test_submit_arvworkflow(self, stubs, tm):
 884         capture_stdout = cStringIO.StringIO()
 885
 886         with open("tests/wf/expect_arvworkflow.cwl") as f:
 887             stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
 888
 889         exited = arvados_cwl.main(
 890             ["--submit", "--no-wait", "--api=containers", "--debug",
 891              "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
 892             capture_stdout, sys.stderr, api_client=stubs.api)
 893         self.assertEqual(exited, 0)
 894
 895         expect_container = {
 896             'priority': 500,
 897             'mounts': {
 898                 '/var/spool/cwl': {
 899                     'writable': True,
 900                     'kind': 'collection'
 901                 },
 902                 'stdout': {
 903                     'path': '/var/spool/cwl/cwl.output.json',
 904                     'kind': 'file'
 905                 },
 906                 '/var/lib/cwl/workflow.json': {
 907                     'kind': 'json',
 908                     'content': {
 909                         'cwlVersion': 'v1.0',
 910                         '$graph': [
 911                             {
 912                                 'id': '#main',
 913                                 'inputs': [
 914                                     {'type': 'string', 'id': '#main/x'}
 915                                 ],
 916                                 'steps': [
 917                                     {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
 918                                      'run': '#submit_tool.cwl',
 919                                      'id': '#main/step1',
 920                                      'out': []}
 921                                 ],
 922                                 'class': 'Workflow',
 923                                 'outputs': []
 924                             },
 925                             {
 926                                 'inputs': [
 927                                     {
 928                                         'inputBinding': {'position': 1},
 929                                         'type': 'string',
 930                                         'id': '#submit_tool.cwl/x'}
 931                                 ],
 932                                 'requirements': [
 933                                     {'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
 934                                 ],
 935                                 'id': '#submit_tool.cwl',
 936                                 'outputs': [],
 937                                 'baseCommand': 'cat',
 938                                 'class': 'CommandLineTool'
 939                             }
 940                         ]
 941                     }
 942                 },
 943                 '/var/lib/cwl/cwl.input.json': {
 944                     'content': {
 945                         'x': 'XxX'
 946                     },
 947                     'kind': 'json'
 948                 }
 949             }, 'state': 'Committed',
 950             'output_path': '/var/spool/cwl',
 951             'name': 'a test workflow',
 952             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
 953             'command': ['arvados-cwl-runner', '--local', '--api=containers',
 954                         '--no-log-timestamps', '--disable-validate',
 955                         '--eval-timeout=20', '--thread-count=4',
 956                         '--enable-reuse', '--debug', '--on-error=continue',
 957                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
 958             'cwd': '/var/spool/cwl',
 959             'runtime_constraints': {
 960                 'API': True,
 961                 'vcpus': 1,
 962                 'ram': 1073741824
 963             },
 964             'use_existing': True,
 965             'properties': {
 966                 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
 967             },
 968             'secret_mounts': {}
 969         }
 970
 971         stubs.api.container_requests().create.assert_called_with(
 972             body=JsonDiffMatcher(expect_container))
 973         self.assertEqual(capture_stdout.getvalue(),
 974                          stubs.expect_container_request_uuid + '\n')
 975
 976
 977     @stubs
 978     def test_submit_container_name(self, stubs):
 979         capture_stdout = cStringIO.StringIO()
 980         try:
 981             exited = arvados_cwl.main(
 982                 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
 983                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 984                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 985             self.assertEqual(exited, 0)
 986         except:
 987             logging.exception("")
 988
 989         expect_container = copy.deepcopy(stubs.expect_container_spec)
 990         expect_container["name"] = "hello container 123"
 991
 992         stubs.api.container_requests().create.assert_called_with(
 993             body=JsonDiffMatcher(expect_container))
 994         self.assertEqual(capture_stdout.getvalue(),
 995                          stubs.expect_container_request_uuid + '\n')
 996
 997
 998     @stubs
 999     def test_submit_container_project(self, stubs):
1000         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1001         capture_stdout = cStringIO.StringIO()
1002         try:
1003             exited = arvados_cwl.main(
1004                 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
1005                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1006                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1007             self.assertEqual(exited, 0)
1008         except:
1009             logging.exception("")
1010
1011         expect_container = copy.deepcopy(stubs.expect_container_spec)
1012         expect_container["owner_uuid"] = project_uuid
1013         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1014                                        '--no-log-timestamps', '--disable-validate',
1015                                        "--eval-timeout=20", "--thread-count=4",
1016                                        '--enable-reuse', '--debug', '--on-error=continue',
1017                                        '--project-uuid='+project_uuid,
1018                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1019
1020         stubs.api.container_requests().create.assert_called_with(
1021             body=JsonDiffMatcher(expect_container))
1022         self.assertEqual(capture_stdout.getvalue(),
1023                          stubs.expect_container_request_uuid + '\n')
1024
1025     @stubs
1026     def test_submit_container_eval_timeout(self, stubs):
1027         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1028         capture_stdout = cStringIO.StringIO()
1029         try:
1030             exited = arvados_cwl.main(
1031                 ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
1032                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1033                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1034             self.assertEqual(exited, 0)
1035         except:
1036             logging.exception("")
1037
1038         expect_container = copy.deepcopy(stubs.expect_container_spec)
1039         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1040                                        '--no-log-timestamps', '--disable-validate',
1041                                        '--eval-timeout=60.0', '--thread-count=4',
1042                                        '--enable-reuse', '--debug', '--on-error=continue',
1043                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1044
1045         stubs.api.container_requests().create.assert_called_with(
1046             body=JsonDiffMatcher(expect_container))
1047         self.assertEqual(capture_stdout.getvalue(),
1048                          stubs.expect_container_request_uuid + '\n')
1049
1050
1051     @stubs
1052     def test_submit_container_thread_count(self, stubs):
1053         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1054         capture_stdout = cStringIO.StringIO()
1055         try:
1056             exited = arvados_cwl.main(
1057                 ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
1058                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1059                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1060             self.assertEqual(exited, 0)
1061         except:
1062             logging.exception("")
1063
1064         expect_container = copy.deepcopy(stubs.expect_container_spec)
1065         expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1066                                        '--no-log-timestamps', '--disable-validate',
1067                                        '--eval-timeout=20', '--thread-count=20',
1068                                        '--enable-reuse', '--debug', '--on-error=continue',
1069                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1070
1071         stubs.api.container_requests().create.assert_called_with(
1072             body=JsonDiffMatcher(expect_container))
1073         self.assertEqual(capture_stdout.getvalue(),
1074                          stubs.expect_container_request_uuid + '\n')
1075
1076
1077     @stubs
1078     def test_submit_job_runner_image(self, stubs):
1079         capture_stdout = cStringIO.StringIO()
1080         try:
1081             exited = arvados_cwl.main(
1082                 ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
1083                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1084                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1085             self.assertEqual(exited, 0)
1086         except:
1087             logging.exception("")
1088
1089         stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
1090
1091         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
1092         stubs.api.pipeline_instances().create.assert_called_with(
1093             body=JsonDiffMatcher(expect_pipeline))
1094         self.assertEqual(capture_stdout.getvalue(),
1095                          stubs.expect_pipeline_uuid + '\n')
1096
1097     @stubs
1098     def test_submit_container_runner_image(self, stubs):
1099         capture_stdout = cStringIO.StringIO()
1100         try:
1101             exited = arvados_cwl.main(
1102                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
1103                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1104                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1105             self.assertEqual(exited, 0)
1106         except:
1107             logging.exception("")
1108
1109         stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
1110
1111         expect_container = copy.deepcopy(stubs.expect_container_spec)
1112         stubs.api.container_requests().create.assert_called_with(
1113             body=JsonDiffMatcher(expect_container))
1114         self.assertEqual(capture_stdout.getvalue(),
1115                          stubs.expect_container_request_uuid + '\n')
1116
1117     @stubs
1118     def test_submit_priority(self, stubs):
1119         capture_stdout = cStringIO.StringIO()
1120         try:
1121             exited = arvados_cwl.main(
1122                 ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
1123                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1124                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1125             self.assertEqual(exited, 0)
1126         except:
1127             logging.exception("")
1128
1129         stubs.expect_container_spec["priority"] = 669
1130
1131         expect_container = copy.deepcopy(stubs.expect_container_spec)
1132         stubs.api.container_requests().create.assert_called_with(
1133             body=JsonDiffMatcher(expect_container))
1134         self.assertEqual(capture_stdout.getvalue(),
1135                          stubs.expect_container_request_uuid + '\n')
1136
1137
1138     @stubs
1139     def test_submit_wf_runner_resources(self, stubs):
1140         capture_stdout = cStringIO.StringIO()
1141         try:
1142             exited = arvados_cwl.main(
1143                 ["--submit", "--no-wait", "--api=containers", "--debug",
1144                  "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
1145                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1146             self.assertEqual(exited, 0)
1147         except:
1148             logging.exception("")
1149
1150         expect_container = copy.deepcopy(stubs.expect_container_spec)
1151         expect_container["runtime_constraints"] = {
1152             "API": True,
1153             "vcpus": 2,
1154             "ram": 2000 * 2**20
1155         }
1156         expect_container["name"] = "submit_wf_runner_resources.cwl"
1157         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1158             {
1159                 "class": "http://arvados.org/cwl#WorkflowRunnerResources",
1160                 "coresMin": 2,
1161                 "ramMin": 2000
1162             }
1163         ]
1164         expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
1165             "arv": "http://arvados.org/cwl#",
1166         }
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     @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
1175     @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
1176     @mock.patch("arvados.api")
1177     def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
1178         arvrunner = mock.MagicMock()
1179         arvrunner.project_uuid = ""
1180         api.return_value = mock.MagicMock()
1181         arvrunner.api = api.return_value
1182         arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
1183                                                                         "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1184                                                                         "link_class": "docker_image_repo+tag",
1185                                                                         "name": "arvados/jobs:"+arvados_cwl.__version__,
1186                                                                         "owner_uuid": "",
1187                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1188                                                             {"items": [{"created_at": "",
1189                                                                         "head_uuid": "",
1190                                                                         "link_class": "docker_image_hash",
1191                                                                         "name": "123456",
1192                                                                         "owner_uuid": "",
1193                                                                         "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
1194         )
1195         find_one_image_hash.return_value = "123456"
1196
1197         arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1198                                                                               "owner_uuid": "",
1199                                                                               "manifest_text": "",
1200                                                                               "properties": ""
1201                                                                           }], "items_available": 1, "offset": 0},)
1202         arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
1203         self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
1204                          arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
1205
1206     @stubs
1207     def test_submit_secrets(self, stubs):
1208         capture_stdout = cStringIO.StringIO()
1209         try:
1210             exited = arvados_cwl.main(
1211                 ["--submit", "--no-wait", "--api=containers", "--debug",
1212                  "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
1213                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1214             self.assertEqual(exited, 0)
1215         except:
1216             logging.exception("")
1217
1218
1219         expect_container = {
1220             "command": [
1221                 "arvados-cwl-runner",
1222                 "--local",
1223                 "--api=containers",
1224                 "--no-log-timestamps",
1225                 "--disable-validate",
1226                 "--eval-timeout=20",
1227                 '--thread-count=4',
1228                 "--enable-reuse",
1229                 '--debug',
1230                 "--on-error=continue",
1231                 "/var/lib/cwl/workflow.json#main",
1232                 "/var/lib/cwl/cwl.input.json"
1233             ],
1234             "container_image": "arvados/jobs:"+arvados_cwl.__version__,
1235             "cwd": "/var/spool/cwl",
1236             "mounts": {
1237                 "/var/lib/cwl/cwl.input.json": {
1238                     "content": {
1239                         "pw": {
1240                             "$include": "/secrets/s0"
1241                         }
1242                     },
1243                     "kind": "json"
1244                 },
1245                 "/var/lib/cwl/workflow.json": {
1246                     "content": {
1247                         "$graph": [
1248                             {
1249                                 "$namespaces": {
1250                                     "cwltool": "http://commonwl.org/cwltool#"
1251                                 },
1252                                 "arguments": [
1253                                     "md5sum",
1254                                     "example.conf"
1255                                 ],
1256                                 "class": "CommandLineTool",
1257                                 "hints": [
1258                                     {
1259                                         "class": "http://commonwl.org/cwltool#Secrets",
1260                                         "secrets": [
1261                                             "#secret_job.cwl/pw"
1262                                         ]
1263                                     }
1264                                 ],
1265                                 "id": "#secret_job.cwl",
1266                                 "inputs": [
1267                                     {
1268                                         "id": "#secret_job.cwl/pw",
1269                                         "type": "string"
1270                                     }
1271                                 ],
1272                                 "outputs": [
1273                                     {
1274                                         "id": "#secret_job.cwl/out",
1275                                         "type": "stdout"
1276                                     }
1277                                 ],
1278                                 "stdout": "hashed_example.txt",
1279                                 "requirements": [
1280                                     {
1281                                         "class": "InitialWorkDirRequirement",
1282                                         "listing": [
1283                                             {
1284                                                 "entry": "username: user\npassword: $(inputs.pw)\n",
1285                                                 "entryname": "example.conf"
1286                                             }
1287                                         ]
1288                                     }
1289                                 ]
1290                             },
1291                             {
1292                                 "class": "Workflow",
1293                                 "hints": [
1294                                     {
1295                                         "class": "DockerRequirement",
1296                                         "dockerPull": "debian:8"
1297                                     },
1298                                     {
1299                                         "class": "http://commonwl.org/cwltool#Secrets",
1300                                         "secrets": [
1301                                             "#main/pw"
1302                                         ]
1303                                     }
1304                                 ],
1305                                 "id": "#main",
1306                                 "inputs": [
1307                                     {
1308                                         "id": "#main/pw",
1309                                         "type": "string"
1310                                     }
1311                                 ],
1312                                 "outputs": [
1313                                     {
1314                                         "id": "#main/out",
1315                                         "outputSource": "#main/step1/out",
1316                                         "type": "File"
1317                                     }
1318                                 ],
1319                                 "steps": [
1320                                     {
1321                                         "id": "#main/step1",
1322                                         "in": [
1323                                             {
1324                                                 "id": "#main/step1/pw",
1325                                                 "source": "#main/pw"
1326                                             }
1327                                         ],
1328                                         "out": [
1329                                             "#main/step1/out"
1330                                         ],
1331                                         "run": "#secret_job.cwl"
1332                                     }
1333                                 ]
1334                             }
1335                         ],
1336                         "cwlVersion": "v1.0"
1337                     },
1338                     "kind": "json"
1339                 },
1340                 "/var/spool/cwl": {
1341                     "kind": "collection",
1342                     "writable": True
1343                 },
1344                 "stdout": {
1345                     "kind": "file",
1346                     "path": "/var/spool/cwl/cwl.output.json"
1347                 }
1348             },
1349             "name": "secret_wf.cwl",
1350             "output_path": "/var/spool/cwl",
1351             "priority": 500,
1352             "properties": {},
1353             "runtime_constraints": {
1354                 "API": True,
1355                 "ram": 1073741824,
1356                 "vcpus": 1
1357             },
1358             "secret_mounts": {
1359                 "/secrets/s0": {
1360                     "content": "blorp",
1361                     "kind": "text"
1362                 }
1363             },
1364             "state": "Committed",
1365             "use_existing": True
1366         }
1367
1368         stubs.api.container_requests().create.assert_called_with(
1369             body=JsonDiffMatcher(expect_container))
1370         self.assertEqual(capture_stdout.getvalue(),
1371                          stubs.expect_container_request_uuid + '\n')
1372
1373     @stubs
1374     def test_submit_request_uuid(self, stubs):
1375         stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
1376
1377         stubs.api.container_requests().update().execute.return_value = {
1378             "uuid": stubs.expect_container_request_uuid,
1379             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
1380             "state": "Queued"
1381         }
1382
1383         capture_stdout = cStringIO.StringIO()
1384         try:
1385             exited = arvados_cwl.main(
1386                 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
1387                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1388                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1389             self.assertEqual(exited, 0)
1390         except:
1391             logging.exception("")
1392
1393         stubs.api.container_requests().update.assert_called_with(
1394             uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
1395         self.assertEqual(capture_stdout.getvalue(),
1396                          stubs.expect_container_request_uuid + '\n')
1397
1398
1399 class TestCreateTemplate(unittest.TestCase):
1400     existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
1401
1402     def _adjust_script_params(self, expect_component):
1403         expect_component['script_parameters']['x'] = {
1404             'dataclass': 'File',
1405             'required': True,
1406             'type': 'File',
1407             'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
1408         }
1409         expect_component['script_parameters']['y'] = {
1410             'dataclass': 'Collection',
1411             'required': True,
1412             'type': 'Directory',
1413             'value': '99999999999999999999999999999998+99',
1414         }
1415         expect_component['script_parameters']['z'] = {
1416             'dataclass': 'Collection',
1417             'required': True,
1418             'type': 'Directory',
1419         }
1420
1421     @stubs
1422     def test_create(self, stubs):
1423         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1424
1425         capture_stdout = cStringIO.StringIO()
1426
1427         exited = arvados_cwl.main(
1428             ["--create-workflow", "--debug",
1429              "--api=jobs",
1430              "--project-uuid", project_uuid,
1431              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1432             capture_stdout, sys.stderr, api_client=stubs.api)
1433         self.assertEqual(exited, 0)
1434
1435         stubs.api.pipeline_instances().create.refute_called()
1436         stubs.api.jobs().create.refute_called()
1437
1438         expect_component = copy.deepcopy(stubs.expect_job_spec)
1439         self._adjust_script_params(expect_component)
1440         expect_template = {
1441             "components": {
1442                 "submit_wf.cwl": expect_component,
1443             },
1444             "name": "submit_wf.cwl",
1445             "owner_uuid": project_uuid,
1446         }
1447         stubs.api.pipeline_templates().create.assert_called_with(
1448             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1449
1450         self.assertEqual(capture_stdout.getvalue(),
1451                          stubs.expect_pipeline_template_uuid + '\n')
1452
1453
1454     @stubs
1455     def test_create_name(self, stubs):
1456         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1457
1458         capture_stdout = cStringIO.StringIO()
1459
1460         exited = arvados_cwl.main(
1461             ["--create-workflow", "--debug",
1462              "--project-uuid", project_uuid,
1463              "--api=jobs",
1464              "--name", "testing 123",
1465              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1466             capture_stdout, sys.stderr, api_client=stubs.api)
1467         self.assertEqual(exited, 0)
1468
1469         stubs.api.pipeline_instances().create.refute_called()
1470         stubs.api.jobs().create.refute_called()
1471
1472         expect_component = copy.deepcopy(stubs.expect_job_spec)
1473         self._adjust_script_params(expect_component)
1474         expect_template = {
1475             "components": {
1476                 "testing 123": expect_component,
1477             },
1478             "name": "testing 123",
1479             "owner_uuid": project_uuid,
1480         }
1481         stubs.api.pipeline_templates().create.assert_called_with(
1482             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1483
1484         self.assertEqual(capture_stdout.getvalue(),
1485                          stubs.expect_pipeline_template_uuid + '\n')
1486
1487
1488     @stubs
1489     def test_update_name(self, stubs):
1490         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1491
1492         capture_stdout = cStringIO.StringIO()
1493
1494         exited = arvados_cwl.main(
1495             ["--update-workflow", self.existing_template_uuid,
1496              "--debug",
1497              "--project-uuid", project_uuid,
1498              "--api=jobs",
1499              "--name", "testing 123",
1500              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1501             capture_stdout, sys.stderr, api_client=stubs.api)
1502         self.assertEqual(exited, 0)
1503
1504         stubs.api.pipeline_instances().create.refute_called()
1505         stubs.api.jobs().create.refute_called()
1506
1507         expect_component = copy.deepcopy(stubs.expect_job_spec)
1508         self._adjust_script_params(expect_component)
1509         expect_template = {
1510             "components": {
1511                 "testing 123": expect_component,
1512             },
1513             "name": "testing 123",
1514             "owner_uuid": project_uuid,
1515         }
1516         stubs.api.pipeline_templates().create.refute_called()
1517         stubs.api.pipeline_templates().update.assert_called_with(
1518             body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
1519
1520         self.assertEqual(capture_stdout.getvalue(),
1521                          self.existing_template_uuid + '\n')
1522
1523
1524 class TestCreateWorkflow(unittest.TestCase):
1525     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1526     expect_workflow = StripYAMLComments(
1527         open("tests/wf/expect_packed.cwl").read())
1528
1529     @stubs
1530     def test_create(self, stubs):
1531         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1532
1533         capture_stdout = cStringIO.StringIO()
1534
1535         exited = arvados_cwl.main(
1536             ["--create-workflow", "--debug",
1537              "--api=containers",
1538              "--project-uuid", project_uuid,
1539              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1540             capture_stdout, sys.stderr, api_client=stubs.api)
1541         self.assertEqual(exited, 0)
1542
1543         stubs.api.pipeline_templates().create.refute_called()
1544         stubs.api.container_requests().create.refute_called()
1545
1546         body = {
1547             "workflow": {
1548                 "owner_uuid": project_uuid,
1549                 "name": "submit_wf.cwl",
1550                 "description": "",
1551                 "definition": self.expect_workflow,
1552             }
1553         }
1554         stubs.api.workflows().create.assert_called_with(
1555             body=JsonDiffMatcher(body))
1556
1557         self.assertEqual(capture_stdout.getvalue(),
1558                          stubs.expect_workflow_uuid + '\n')
1559
1560
1561     @stubs
1562     def test_create_name(self, stubs):
1563         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1564
1565         capture_stdout = cStringIO.StringIO()
1566
1567         exited = arvados_cwl.main(
1568             ["--create-workflow", "--debug",
1569              "--api=containers",
1570              "--project-uuid", project_uuid,
1571              "--name", "testing 123",
1572              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1573             capture_stdout, sys.stderr, api_client=stubs.api)
1574         self.assertEqual(exited, 0)
1575
1576         stubs.api.pipeline_templates().create.refute_called()
1577         stubs.api.container_requests().create.refute_called()
1578
1579         body = {
1580             "workflow": {
1581                 "owner_uuid": project_uuid,
1582                 "name": "testing 123",
1583                 "description": "",
1584                 "definition": self.expect_workflow,
1585             }
1586         }
1587         stubs.api.workflows().create.assert_called_with(
1588             body=JsonDiffMatcher(body))
1589
1590         self.assertEqual(capture_stdout.getvalue(),
1591                          stubs.expect_workflow_uuid + '\n')
1592
1593     @stubs
1594     def test_incompatible_api(self, stubs):
1595         capture_stderr = cStringIO.StringIO()
1596         logging.getLogger('arvados.cwl-runner').addHandler(
1597             logging.StreamHandler(capture_stderr))
1598
1599         exited = arvados_cwl.main(
1600             ["--update-workflow", self.existing_workflow_uuid,
1601              "--api=jobs",
1602              "--debug",
1603              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1604             sys.stderr, sys.stderr, api_client=stubs.api)
1605         self.assertEqual(exited, 1)
1606         self.assertRegexpMatches(
1607             capture_stderr.getvalue(),
1608             "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
1609
1610     @stubs
1611     def test_update(self, stubs):
1612         capture_stdout = cStringIO.StringIO()
1613
1614         exited = arvados_cwl.main(
1615             ["--update-workflow", self.existing_workflow_uuid,
1616              "--debug",
1617              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1618             capture_stdout, sys.stderr, api_client=stubs.api)
1619         self.assertEqual(exited, 0)
1620
1621         body = {
1622             "workflow": {
1623                 "name": "submit_wf.cwl",
1624                 "description": "",
1625                 "definition": self.expect_workflow,
1626             }
1627         }
1628         stubs.api.workflows().update.assert_called_with(
1629             uuid=self.existing_workflow_uuid,
1630             body=JsonDiffMatcher(body))
1631         self.assertEqual(capture_stdout.getvalue(),
1632                          self.existing_workflow_uuid + '\n')
1633
1634
1635     @stubs
1636     def test_update_name(self, stubs):
1637         capture_stdout = cStringIO.StringIO()
1638
1639         exited = arvados_cwl.main(
1640             ["--update-workflow", self.existing_workflow_uuid,
1641              "--debug", "--name", "testing 123",
1642              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1643             capture_stdout, sys.stderr, api_client=stubs.api)
1644         self.assertEqual(exited, 0)
1645
1646         body = {
1647             "workflow": {
1648                 "name": "testing 123",
1649                 "description": "",
1650                 "definition": self.expect_workflow,
1651             }
1652         }
1653         stubs.api.workflows().update.assert_called_with(
1654             uuid=self.existing_workflow_uuid,
1655             body=JsonDiffMatcher(body))
1656         self.assertEqual(capture_stdout.getvalue(),
1657                          self.existing_workflow_uuid + '\n')
1658
1659
1660     @stubs
1661     def test_create_collection_per_tool(self, stubs):
1662         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1663
1664         capture_stdout = cStringIO.StringIO()
1665
1666         exited = arvados_cwl.main(
1667             ["--create-workflow", "--debug",
1668              "--api=containers",
1669              "--project-uuid", project_uuid,
1670              "tests/collection_per_tool/collection_per_tool.cwl"],
1671             capture_stdout, sys.stderr, api_client=stubs.api)
1672         self.assertEqual(exited, 0)
1673
1674         toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1675         expect_workflow = StripYAMLComments(open(toolfile).read())
1676
1677         body = {
1678             "workflow": {
1679                 "owner_uuid": project_uuid,
1680                 "name": "collection_per_tool.cwl",
1681                 "description": "",
1682                 "definition": expect_workflow,
1683             }
1684         }
1685         stubs.api.workflows().create.assert_called_with(
1686             body=JsonDiffMatcher(body))
1687
1688         self.assertEqual(capture_stdout.getvalue(),
1689                          stubs.expect_workflow_uuid + '\n')
1690
1691 class TestTemplateInputs(unittest.TestCase):
1692     expect_template = {
1693         "components": {
1694             "inputs_test.cwl": {
1695                 'runtime_constraints': {
1696                     'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
1697                     'min_ram_mb_per_node': 1024
1698                 },
1699                 'script_parameters': {
1700                     'cwl:tool':
1701                     '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main',
1702                     'optionalFloatInput': None,
1703                     'fileInput': {
1704                         'type': 'File',
1705                         'dataclass': 'File',
1706                         'required': True,
1707                         'title': "It's a file; we expect to find some characters in it.",
1708                         'description': 'If there were anything further to say, it would be said here,\nor here.'
1709                     },
1710                     'floatInput': {
1711                         'type': 'float',
1712                         'dataclass': 'number',
1713                         'required': True,
1714                         'title': 'Floats like a duck',
1715                         'default': 0.1,
1716                         'value': 0.1,
1717                     },
1718                     'optionalFloatInput': {
1719                         'type': ['null', 'float'],
1720                         'dataclass': 'number',
1721                         'required': False,
1722                     },
1723                     'boolInput': {
1724                         'type': 'boolean',
1725                         'dataclass': 'boolean',
1726                         'required': True,
1727                         'title': 'True or false?',
1728                     },
1729                 },
1730                 'repository': 'arvados',
1731                 'script_version': 'master',
1732                 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
1733                 'script': 'cwl-runner',
1734             },
1735         },
1736         "name": "inputs_test.cwl",
1737     }
1738
1739     @stubs
1740     def test_inputs_empty(self, stubs):
1741         exited = arvados_cwl.main(
1742             ["--create-template",
1743              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
1744             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1745         self.assertEqual(exited, 0)
1746
1747         stubs.api.pipeline_templates().create.assert_called_with(
1748             body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
1749
1750     @stubs
1751     def test_inputs(self, stubs):
1752         exited = arvados_cwl.main(
1753             ["--create-template",
1754              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
1755             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1756         self.assertEqual(exited, 0)
1757
1758         expect_template = copy.deepcopy(self.expect_template)
1759         params = expect_template[
1760             "components"]["inputs_test.cwl"]["script_parameters"]
1761         params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
1762         params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main'
1763         params["floatInput"]["value"] = 1.234
1764         params["boolInput"]["value"] = True
1765
1766         stubs.api.pipeline_templates().create.assert_called_with(
1767             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)