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