sdk/cwl/tests/test_submit.py

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