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
  14 from .matcher import JsonDiffMatcher
  15
  16
  17 def stubs(func):
  18     @functools.wraps(func)
  19     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  20     @mock.patch("arvados.collection.KeepClient")
  21     @mock.patch("arvados.events.subscribe")
  22     def wrapped(self, events, KeepClient, keepdocker, *args, **kwargs):
  23         class Stubs:
  24             pass
  25         stubs = Stubs()
  26         stubs.events = events
  27         stubs.KeepClient = KeepClient
  28         stubs.keepdocker = keepdocker
  29
  30         def putstub(p, **kwargs):
  31             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
  32         stubs.KeepClient().put.side_effect = putstub
  33
  34         stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  35         stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
  36
  37         stubs.api = mock.MagicMock()
  38         stubs.api.users().current().execute.return_value = {
  39             "uuid": stubs.fake_user_uuid,
  40         }
  41         stubs.api.collections().list().execute.return_value = {"items": []}
  42         stubs.api.collections().create().execute.side_effect = ({
  43             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
  44             "portable_data_hash": "99999999999999999999999999999991+99",
  45             "manifest_text": ""
  46         }, {
  47             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
  48             "portable_data_hash": "99999999999999999999999999999992+99",
  49             "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"
  50         },
  51         {
  52             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4",
  53             "portable_data_hash": "99999999999999999999999999999994+99",
  54             "manifest_text": ""
  55         },
  56         {
  57             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz5",
  58             "portable_data_hash": "99999999999999999999999999999995+99",
  59             "manifest_text": ""
  60         }        )
  61         stubs.api.collections().get().execute.return_value = {
  62             "portable_data_hash": "99999999999999999999999999999993+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"}
  63
  64         stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  65         stubs.api.jobs().create().execute.return_value = {
  66             "uuid": stubs.expect_job_uuid,
  67             "state": "Queued",
  68         }
  69
  70         stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
  71         stubs.api.container_requests().create().execute.return_value = {
  72             "uuid": stubs.expect_container_request_uuid,
  73             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
  74             "state": "Queued"
  75         }
  76
  77         stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
  78         stubs.api.pipeline_templates().create().execute.return_value = {
  79             "uuid": stubs.expect_pipeline_template_uuid,
  80         }
  81         stubs.expect_job_spec = {
  82             'runtime_constraints': {
  83                 'docker_image': 'arvados/jobs'
  84             },
  85             'script_parameters': {
  86                 'x': {
  87                     'basename': 'blorp.txt',
  88                     'location': '99999999999999999999999999999994+99/blorp.txt',
  89                     'class': 'File'
  90                 },
  91                 'cwl:tool':
  92                 '99999999999999999999999999999991+99/wf/submit_wf.cwl'
  93             },
  94             'repository': 'arvados',
  95             'script_version': 'master',
  96             'script': 'cwl-runner'
  97         }
  98
  99         stubs.expect_container_spec = {
 100             'priority': 1,
 101             'mounts': {
 102                 '/var/spool/cwl': {
 103                     'writable': True,
 104                     'kind': 'collection'
 105                 },
 106                 '/var/lib/cwl/workflow': {
 107                     'portable_data_hash': '99999999999999999999999999999991+99',
 108                     'kind': 'collection'
 109                 },
 110                 'stdout': {
 111                     'path': '/var/spool/cwl/cwl.output.json',
 112                     'kind': 'file'
 113                 },
 114                 '/var/lib/cwl/job/cwl.input.json': {
 115                     'portable_data_hash': '765fda0d9897729ff467a4609879c00a+60/cwl.input.json',
 116                     'kind': 'collection'
 117                 }
 118             },
 119             'state': 'Committed',
 120             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 121             'command': ['arvados-cwl-runner', '--local', '--api=containers', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
 122             'name': 'submit_wf.cwl',
 123             'container_image': '99999999999999999999999999999993+99',
 124             'output_path': '/var/spool/cwl',
 125             'cwd': '/var/spool/cwl',
 126             'runtime_constraints': {
 127                 'API': True,
 128                 'vcpus': 1,
 129                 'ram': 268435456
 130             }
 131         }
 132
 133         stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
 134         stubs.api.workflows().create().execute.return_value = {
 135             "uuid": stubs.expect_workflow_uuid,
 136         }
 137
 138         return func(self, stubs, *args, **kwargs)
 139     return wrapped
 140
 141
 142 class TestSubmit(unittest.TestCase):
 143     @stubs
 144     def test_submit(self, stubs):
 145         capture_stdout = cStringIO.StringIO()
 146         exited = arvados_cwl.main(
 147             ["--submit", "--no-wait",
 148              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 149             capture_stdout, sys.stderr, api_client=stubs.api)
 150         self.assertEqual(exited, 0)
 151
 152         stubs.api.collections().create.assert_has_calls([
 153             mock.call(),
 154             mock.call(body={
 155                 'manifest_text':
 156                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
 157                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
 158                 '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
 159                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 160                 'name': 'submit_wf.cwl',
 161             }, ensure_unique_name=True),
 162             mock.call().execute(),
 163             mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
 164                             '0:0:blub.txt 0:0:submit_tool.cwl\n',
 165                             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 166                             'name': 'New collection'
 167             }, ensure_unique_name=True),
 168             mock.call().execute(num_retries=4),
 169             mock.call(body={
 170                 'manifest_text':
 171                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 172                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 173                 'name': '#',
 174             }, ensure_unique_name=True),
 175             mock.call().execute()])
 176
 177         expect_job = copy.deepcopy(stubs.expect_job_spec)
 178         expect_job["owner_uuid"] = stubs.fake_user_uuid
 179         stubs.api.jobs().create.assert_called_with(
 180             body=expect_job,
 181             find_or_create=True)
 182         self.assertEqual(capture_stdout.getvalue(),
 183                          stubs.expect_job_uuid + '\n')
 184
 185     @stubs
 186     def test_submit_with_project_uuid(self, stubs):
 187         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 188
 189         exited = arvados_cwl.main(
 190             ["--submit", "--no-wait",
 191              "--project-uuid", project_uuid,
 192              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 193             sys.stdout, sys.stderr, api_client=stubs.api)
 194         self.assertEqual(exited, 0)
 195
 196         expect_body = copy.deepcopy(stubs.expect_job_spec)
 197         expect_body["owner_uuid"] = project_uuid
 198         stubs.api.jobs().create.assert_called_with(
 199             body=expect_body,
 200             find_or_create=True)
 201
 202     @stubs
 203     def test_submit_container(self, stubs):
 204         capture_stdout = cStringIO.StringIO()
 205         exited = arvados_cwl.main(
 206             ["--submit", "--no-wait", "--api=containers", "--debug",
 207              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 208             capture_stdout, sys.stderr, api_client=stubs.api)
 209         self.assertEqual(exited, 0)
 210
 211         stubs.api.collections().create.assert_has_calls([
 212             mock.call(),
 213             mock.call(body={
 214                 'manifest_text':
 215                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
 216                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
 217                 '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
 218                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 219                 'name': 'submit_wf.cwl',
 220             }, ensure_unique_name=True),
 221             mock.call().execute(),
 222             mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
 223                             '0:0:blub.txt 0:0:submit_tool.cwl\n',
 224                             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 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_container = copy.deepcopy(stubs.expect_container_spec)
 237         expect_container["owner_uuid"] = stubs.fake_user_uuid
 238         stubs.api.container_requests().create.assert_called_with(
 239             body=expect_container)
 240         self.assertEqual(capture_stdout.getvalue(),
 241                          stubs.expect_container_request_uuid + '\n')
 242
 243
 244 class TestCreateTemplate(unittest.TestCase):
 245     @stubs
 246     def test_create(self, stubs):
 247         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 248
 249         capture_stdout = cStringIO.StringIO()
 250
 251         exited = arvados_cwl.main(
 252             ["--create-template", "--debug",
 253              "--project-uuid", project_uuid,
 254              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 255             capture_stdout, sys.stderr, api_client=stubs.api)
 256         self.assertEqual(exited, 0)
 257
 258         stubs.api.pipeline_instances().create.refute_called()
 259         stubs.api.jobs().create.refute_called()
 260
 261         expect_component = copy.deepcopy(stubs.expect_job_spec)
 262         expect_component['script_parameters']['x'] = {
 263             'dataclass': 'File',
 264             'required': True,
 265             'type': 'File',
 266             'value': '99999999999999999999999999999994+99/blorp.txt',
 267         }
 268         expect_template = {
 269             "components": {
 270                 "submit_wf.cwl": expect_component,
 271             },
 272             "name": "submit_wf.cwl",
 273             "owner_uuid": project_uuid,
 274         }
 275         stubs.api.pipeline_templates().create.assert_called_with(
 276             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 277
 278         self.assertEqual(capture_stdout.getvalue(),
 279                          stubs.expect_pipeline_template_uuid + '\n')
 280
 281
 282 class TestCreateWorkflow(unittest.TestCase):
 283     @stubs
 284     def test_create(self, stubs):
 285         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 286
 287         capture_stdout = cStringIO.StringIO()
 288
 289         exited = arvados_cwl.main(
 290             ["--create-workflow", "--debug",
 291              "--project-uuid", project_uuid,
 292              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 293             capture_stdout, sys.stderr, api_client=stubs.api)
 294         self.assertEqual(exited, 0)
 295
 296         stubs.api.pipeline_templates().create.refute_called()
 297         stubs.api.container_requests().create.refute_called()
 298
 299         with open("tests/wf/expect_packed.cwl") as f:
 300             expect_workflow = f.read()
 301
 302         body = {
 303             "workflow": {
 304                 "owner_uuid": project_uuid,
 305                 "name": "submit_wf.cwl",
 306                 "description": "",
 307                 "workflow": expect_workflow
 308                 }
 309         }
 310         stubs.api.workflows().create.assert_called_with(
 311             body=JsonDiffMatcher(body))
 312
 313         self.assertEqual(capture_stdout.getvalue(),
 314                          stubs.expect_workflow_uuid + '\n')
 315
 316
 317 class TestTemplateInputs(unittest.TestCase):
 318     expect_template = {
 319         "components": {
 320             "inputs_test.cwl": {
 321                 'runtime_constraints': {
 322                     'docker_image': 'arvados/jobs',
 323                 },
 324                 'script_parameters': {
 325                     'cwl:tool':
 326                     '99999999999999999999999999999991+99/'
 327                     'wf/inputs_test.cwl',
 328                     'optionalFloatInput': None,
 329                     'fileInput': {
 330                         'type': 'File',
 331                         'dataclass': 'File',
 332                         'required': True,
 333                         'title': "It's a file; we expect to find some characters in it.",
 334                         'description': 'If there were anything further to say, it would be said here,\nor here.'
 335                     },
 336                     'floatInput': {
 337                         'type': 'float',
 338                         'dataclass': 'number',
 339                         'required': True,
 340                         'title': 'Floats like a duck',
 341                         'default': 0.1,
 342                         'value': 0.1,
 343                     },
 344                     'optionalFloatInput': {
 345                         'type': ['null', 'float'],
 346                         'dataclass': 'number',
 347                         'required': False,
 348                     },
 349                     'boolInput': {
 350                         'type': 'boolean',
 351                         'dataclass': 'boolean',
 352                         'required': True,
 353                         'title': 'True or false?',
 354                     },
 355                 },
 356                 'repository': 'arvados',
 357                 'script_version': 'master',
 358                 'script': 'cwl-runner',
 359             },
 360         },
 361         "name": "inputs_test.cwl",
 362     }
 363
 364     @stubs
 365     def test_inputs_empty(self, stubs):
 366         exited = arvados_cwl.main(
 367             ["--create-template", "--no-wait",
 368              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
 369             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
 370         self.assertEqual(exited, 0)
 371
 372         expect_template = copy.deepcopy(self.expect_template)
 373         expect_template["owner_uuid"] = stubs.fake_user_uuid
 374
 375         stubs.api.pipeline_templates().create.assert_called_with(
 376             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 377
 378     @stubs
 379     def test_inputs(self, stubs):
 380         exited = arvados_cwl.main(
 381             ["--create-template", "--no-wait",
 382              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
 383             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
 384         self.assertEqual(exited, 0)
 385
 386         self.expect_template["owner_uuid"] = stubs.fake_user_uuid
 387
 388         expect_template = copy.deepcopy(self.expect_template)
 389         expect_template["owner_uuid"] = stubs.fake_user_uuid
 390         params = expect_template[
 391             "components"]["inputs_test.cwl"]["script_parameters"]
 392         params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
 393         params["floatInput"]["value"] = 1.234
 394         params["boolInput"]["value"] = True
 395
 396         stubs.api.pipeline_templates().create.assert_called_with(
 397             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)