sdk/cwl/tests/test_submit.py

   1 import copy
   2 import cStringIO
   3 import functools
   4 import hashlib
   5 import json
   6 import logging
   7 import mock
   8 import sys
   9 import unittest
  10
  11 import arvados
  12 import arvados.collection
  13 import arvados_cwl
  14 import arvados.keep
  15
  16 from .matcher import JsonDiffMatcher
  17
  18
  19 def stubs(func):
  20     @functools.wraps(func)
  21     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  22     @mock.patch("arvados.collection.KeepClient")
  23     @mock.patch("arvados.events.subscribe")
  24     def wrapped(self, events, keep_client, keepdocker, *args, **kwargs):
  25         class Stubs:
  26             pass
  27         stubs = Stubs()
  28         stubs.events = events
  29         stubs.keepdocker = keepdocker
  30         stubs.keep_client = keep_client
  31
  32         def putstub(p, **kwargs):
  33             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
  34         stubs.keep_client().put.side_effect = putstub
  35         stubs.keep_client.put.side_effect = putstub
  36
  37         stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  38         stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
  39
  40
  41         stubs.api = mock.MagicMock()
  42         stubs.api._rootDesc = arvados.api('v1')._rootDesc
  43         stubs.api.users().current().execute.return_value = {
  44             "uuid": stubs.fake_user_uuid,
  45         }
  46         stubs.api.collections().list().execute.return_value = {"items": []}
  47         stubs.api.collections().create().execute.side_effect = ({
  48             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
  49             "portable_data_hash": "99999999999999999999999999999991+99",
  50             "manifest_text": ""
  51         }, {
  52             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
  53             "portable_data_hash": "99999999999999999999999999999992+99",
  54             "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"
  55         },
  56         {
  57             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4",
  58             "portable_data_hash": "99999999999999999999999999999994+99",
  59             "manifest_text": ""
  60         },
  61         {
  62             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz5",
  63             "portable_data_hash": "99999999999999999999999999999995+99",
  64             "manifest_text": ""
  65         },
  66         {
  67             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz6",
  68             "portable_data_hash": "99999999999999999999999999999996+99",
  69             "manifest_text": ""
  70         }
  71         )
  72         stubs.api.collections().get().execute.return_value = {
  73             "portable_data_hash": "99999999999999999999999999999993+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"}
  74
  75         stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  76         stubs.api.jobs().create().execute.return_value = {
  77             "uuid": stubs.expect_job_uuid,
  78             "state": "Queued",
  79         }
  80
  81         stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
  82         stubs.api.container_requests().create().execute.return_value = {
  83             "uuid": stubs.expect_container_request_uuid,
  84             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
  85             "state": "Queued"
  86         }
  87
  88         stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
  89         stubs.api.pipeline_templates().create().execute.return_value = {
  90             "uuid": stubs.expect_pipeline_template_uuid,
  91         }
  92         stubs.expect_job_spec = {
  93             'runtime_constraints': {
  94                 'docker_image': 'arvados/jobs'
  95             },
  96             'script_parameters': {
  97                 'x': {
  98                     'basename': 'blorp.txt',
  99                     'location': 'keep:99999999999999999999999999999994+99/blorp.txt',
 100                     'class': 'File'
 101                 },
 102                 'y': {
 103                     'basename': '99999999999999999999999999999998+99',
 104                     'location': 'keep:99999999999999999999999999999998+99',
 105                     'class': 'Directory'
 106                 },
 107                 'z': {
 108                     'basename': 'anonymous',
 109                     "listing": [{
 110                         "basename": "renamed.txt",
 111                         "class": "File",
 112                         "location": "keep:99999999999999999999999999999998+99/file1.txt"
 113                     }],
 114                     'class': 'Directory'
 115                 },
 116                 'cwl:tool':
 117                 '99999999999999999999999999999991+99/wf/submit_wf.cwl'
 118             },
 119             'repository': 'arvados',
 120             'script_version': 'master',
 121             'script': 'cwl-runner'
 122         }
 123         stubs.pipeline_component = stubs.expect_job_spec.copy()
 124         stubs.expect_pipeline_instance = {
 125             'name': 'submit_wf.cwl',
 126             'state': 'RunningOnServer',
 127             "components": {
 128                 "cwl-runner": {
 129                     'runtime_constraints': {'docker_image': 'arvados/jobs'},
 130                     'script_parameters': {
 131                         'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
 132                         'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt'}},
 133                         'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
 134                               'listing': [
 135                                   {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
 136                               ]}},
 137                         'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl'
 138                     },
 139                     'repository': 'arvados',
 140                     'script_version': 'master',
 141                     'script': 'cwl-runner'
 142                 }
 143             }
 144         }
 145         stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
 146         stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
 147         stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
 148         stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
 149         stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
 150             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 151             "state": "Queued"
 152         }
 153         stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
 154         stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
 155
 156         stubs.expect_container_spec = {
 157             'priority': 1,
 158             'mounts': {
 159                 '/var/spool/cwl': {
 160                     'writable': True,
 161                     'kind': 'collection'
 162                 },
 163                 '/var/lib/cwl/workflow': {
 164                     'portable_data_hash': '99999999999999999999999999999991+99',
 165                     'kind': 'collection'
 166                 },
 167                 'stdout': {
 168                     'path': '/var/spool/cwl/cwl.output.json',
 169                     'kind': 'file'
 170                 },
 171                 '/var/lib/cwl/job/cwl.input.json': {
 172                     'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json',
 173                     'kind': 'collection'
 174                 }
 175             },
 176             'state': 'Committed',
 177             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 178             'command': ['arvados-cwl-runner', '--local', '--api=containers', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
 179             'name': 'submit_wf.cwl',
 180             'container_image': '99999999999999999999999999999993+99',
 181             'output_path': '/var/spool/cwl',
 182             'cwd': '/var/spool/cwl',
 183             'runtime_constraints': {
 184                 'API': True,
 185                 'vcpus': 1,
 186                 'ram': 268435456
 187             }
 188         }
 189
 190         stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
 191         stubs.api.workflows().create().execute.return_value = {
 192             "uuid": stubs.expect_workflow_uuid,
 193         }
 194
 195         return func(self, stubs, *args, **kwargs)
 196     return wrapped
 197
 198
 199 class TestSubmit(unittest.TestCase):
 200     @mock.patch("time.sleep")
 201     @stubs
 202     def test_submit(self, stubs, tm):
 203         capture_stdout = cStringIO.StringIO()
 204         exited = arvados_cwl.main(
 205             ["--submit", "--no-wait", "--debug",
 206              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 207             capture_stdout, sys.stderr, api_client=stubs.api)
 208         self.assertEqual(exited, 0)
 209
 210         stubs.api.collections().create.assert_has_calls([
 211             mock.call(),
 212             mock.call(body={
 213                 'manifest_text':
 214                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
 215                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
 216                 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
 217                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 218                 'name': 'submit_wf.cwl',
 219             }, ensure_unique_name=True),
 220             mock.call().execute(),
 221             mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
 222                             '0:0:blub.txt 0:0:submit_tool.cwl\n',
 223                             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 224                             'replication_desired': None,
 225                             'name': 'New collection'
 226             }, ensure_unique_name=True),
 227             mock.call().execute(num_retries=4),
 228             mock.call(body={
 229                 'manifest_text':
 230                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 231                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 232                 'name': '#',
 233             }, ensure_unique_name=True),
 234             mock.call().execute()])
 235
 236         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 237         expect_pipeline["owner_uuid"] = stubs.fake_user_uuid
 238         stubs.api.pipeline_instances().create.assert_called_with(
 239             body=expect_pipeline)
 240         self.assertEqual(capture_stdout.getvalue(),
 241                          stubs.expect_pipeline_uuid + '\n')
 242
 243     @mock.patch("time.sleep")
 244     @stubs
 245     def test_submit_with_project_uuid(self, stubs, tm):
 246         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 247
 248         exited = arvados_cwl.main(
 249             ["--submit", "--no-wait",
 250              "--project-uuid", project_uuid,
 251              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 252             sys.stdout, sys.stderr, api_client=stubs.api)
 253         self.assertEqual(exited, 0)
 254
 255         expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
 256         expect_pipeline["owner_uuid"] = project_uuid
 257         stubs.api.pipeline_instances().create.assert_called_with(
 258             body=expect_pipeline)
 259
 260     @stubs
 261     def test_submit_container(self, stubs):
 262         capture_stdout = cStringIO.StringIO()
 263         try:
 264             exited = arvados_cwl.main(
 265                 ["--submit", "--no-wait", "--api=containers", "--debug",
 266                  "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 267                 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 268             self.assertEqual(exited, 0)
 269         except:
 270             logging.exception("")
 271
 272         stubs.api.collections().create.assert_has_calls([
 273             mock.call(),
 274             mock.call(body={
 275                 'manifest_text':
 276                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
 277                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
 278                 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
 279                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 280                 'name': 'submit_wf.cwl',
 281             }, ensure_unique_name=True),
 282             mock.call().execute(),
 283             mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
 284                             '0:0:blub.txt 0:0:submit_tool.cwl\n',
 285                             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 286                             'name': 'New collection',
 287                             'replication_desired': None,
 288             }, ensure_unique_name=True),
 289             mock.call().execute(num_retries=4),
 290             mock.call(body={
 291                 'manifest_text':
 292                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 293                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 294                 'name': '#',
 295             }, ensure_unique_name=True),
 296             mock.call().execute()])
 297
 298         expect_container = copy.deepcopy(stubs.expect_container_spec)
 299         expect_container["owner_uuid"] = stubs.fake_user_uuid
 300         stubs.api.container_requests().create.assert_called_with(
 301             body=expect_container)
 302         self.assertEqual(capture_stdout.getvalue(),
 303                          stubs.expect_container_request_uuid + '\n')
 304
 305
 306 class TestCreateTemplate(unittest.TestCase):
 307     @stubs
 308     def test_create(self, stubs):
 309         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 310
 311         capture_stdout = cStringIO.StringIO()
 312
 313         exited = arvados_cwl.main(
 314             ["--create-template", "--debug",
 315              "--project-uuid", project_uuid,
 316              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 317             capture_stdout, sys.stderr, api_client=stubs.api)
 318         self.assertEqual(exited, 0)
 319
 320         stubs.api.pipeline_instances().create.refute_called()
 321         stubs.api.jobs().create.refute_called()
 322
 323         expect_component = copy.deepcopy(stubs.expect_job_spec)
 324         expect_component['script_parameters']['x'] = {
 325             'dataclass': 'File',
 326             'required': True,
 327             'type': 'File',
 328             'value': '99999999999999999999999999999994+99/blorp.txt',
 329         }
 330         expect_component['script_parameters']['y'] = {
 331             'dataclass': 'Collection',
 332             'required': True,
 333             'type': 'Directory',
 334             'value': '99999999999999999999999999999998+99',
 335         }
 336         expect_component['script_parameters']['z'] = {
 337             'dataclass': 'Collection',
 338             'required': True,
 339             'type': 'Directory',
 340         }
 341         expect_template = {
 342             "components": {
 343                 "submit_wf.cwl": expect_component,
 344             },
 345             "name": "submit_wf.cwl",
 346             "owner_uuid": project_uuid,
 347         }
 348         stubs.api.pipeline_templates().create.assert_called_with(
 349             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 350
 351         self.assertEqual(capture_stdout.getvalue(),
 352                          stubs.expect_pipeline_template_uuid + '\n')
 353
 354
 355 class TestCreateWorkflow(unittest.TestCase):
 356     @stubs
 357     def test_create(self, stubs):
 358         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 359
 360         capture_stdout = cStringIO.StringIO()
 361
 362         exited = arvados_cwl.main(
 363             ["--create-workflow", "--debug",
 364              "--project-uuid", project_uuid,
 365              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 366             capture_stdout, sys.stderr, api_client=stubs.api)
 367         self.assertEqual(exited, 0)
 368
 369         stubs.api.pipeline_templates().create.refute_called()
 370         stubs.api.container_requests().create.refute_called()
 371
 372         with open("tests/wf/expect_packed.cwl") as f:
 373             expect_workflow = f.read()
 374
 375         body = {
 376             "workflow": {
 377                 "owner_uuid": project_uuid,
 378                 "name": "submit_wf.cwl",
 379                 "description": "",
 380                 "definition": expect_workflow
 381                 }
 382         }
 383         stubs.api.workflows().create.assert_called_with(
 384             body=JsonDiffMatcher(body))
 385
 386         self.assertEqual(capture_stdout.getvalue(),
 387                          stubs.expect_workflow_uuid + '\n')
 388
 389
 390 class TestTemplateInputs(unittest.TestCase):
 391     expect_template = {
 392         "components": {
 393             "inputs_test.cwl": {
 394                 'runtime_constraints': {
 395                     'docker_image': 'arvados/jobs',
 396                 },
 397                 'script_parameters': {
 398                     'cwl:tool':
 399                     '99999999999999999999999999999991+99/'
 400                     'wf/inputs_test.cwl',
 401                     'optionalFloatInput': None,
 402                     'fileInput': {
 403                         'type': 'File',
 404                         'dataclass': 'File',
 405                         'required': True,
 406                         'title': "It's a file; we expect to find some characters in it.",
 407                         'description': 'If there were anything further to say, it would be said here,\nor here.'
 408                     },
 409                     'floatInput': {
 410                         'type': 'float',
 411                         'dataclass': 'number',
 412                         'required': True,
 413                         'title': 'Floats like a duck',
 414                         'default': 0.1,
 415                         'value': 0.1,
 416                     },
 417                     'optionalFloatInput': {
 418                         'type': ['null', 'float'],
 419                         'dataclass': 'number',
 420                         'required': False,
 421                     },
 422                     'boolInput': {
 423                         'type': 'boolean',
 424                         'dataclass': 'boolean',
 425                         'required': True,
 426                         'title': 'True or false?',
 427                     },
 428                 },
 429                 'repository': 'arvados',
 430                 'script_version': 'master',
 431                 'script': 'cwl-runner',
 432             },
 433         },
 434         "name": "inputs_test.cwl",
 435     }
 436
 437     @stubs
 438     def test_inputs_empty(self, stubs):
 439         exited = arvados_cwl.main(
 440             ["--create-template", "--no-wait",
 441              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
 442             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
 443         self.assertEqual(exited, 0)
 444
 445         expect_template = copy.deepcopy(self.expect_template)
 446         expect_template["owner_uuid"] = stubs.fake_user_uuid
 447
 448         stubs.api.pipeline_templates().create.assert_called_with(
 449             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 450
 451     @stubs
 452     def test_inputs(self, stubs):
 453         exited = arvados_cwl.main(
 454             ["--create-template", "--no-wait",
 455              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
 456             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
 457         self.assertEqual(exited, 0)
 458
 459         self.expect_template["owner_uuid"] = stubs.fake_user_uuid
 460
 461         expect_template = copy.deepcopy(self.expect_template)
 462         expect_template["owner_uuid"] = stubs.fake_user_uuid
 463         params = expect_template[
 464             "components"]["inputs_test.cwl"]["script_parameters"]
 465         params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
 466         params["floatInput"]["value"] = 1.234
 467         params["boolInput"]["value"] = True
 468
 469         stubs.api.pipeline_templates().create.assert_called_with(
 470             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)