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
  13 from .matcher import JsonDiffMatcher
  14
  15
  16 def stubs(func):
  17     @functools.wraps(func)
  18     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  19     @mock.patch("arvados.collection.KeepClient")
  20     @mock.patch("arvados.events.subscribe")
  21     def wrapped(self, events, KeepClient, keepdocker, *args, **kwargs):
  22         class Stubs:
  23             pass
  24         stubs = Stubs()
  25         stubs.events = events
  26         stubs.KeepClient = KeepClient
  27         stubs.keepdocker = keepdocker
  28
  29         def putstub(p, **kwargs):
  30             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
  31         stubs.KeepClient().put.side_effect = putstub
  32
  33         stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  34         stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
  35
  36         stubs.api = mock.MagicMock()
  37         stubs.api.users().current().execute.return_value = {
  38             "uuid": stubs.fake_user_uuid,
  39         }
  40         stubs.api.collections().list().execute.return_value = {"items": []}
  41         stubs.api.collections().create().execute.side_effect = ({
  42             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
  43             "portable_data_hash": "99999999999999999999999999999991+99",
  44             "manifest_text": ""
  45         }, {
  46             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
  47             "portable_data_hash": "99999999999999999999999999999992+99",
  48             "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"
  49         },
  50         {
  51             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4",
  52             "portable_data_hash": "99999999999999999999999999999994+99",
  53             "manifest_text": ""
  54         },
  55         {
  56             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz5",
  57             "portable_data_hash": "99999999999999999999999999999995+99",
  58             "manifest_text": ""
  59         }        )
  60         stubs.api.collections().get().execute.return_value = {
  61             "portable_data_hash": "99999999999999999999999999999993+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"}
  62
  63         stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  64         stubs.api.jobs().create().execute.return_value = {
  65             "uuid": stubs.expect_job_uuid,
  66             "state": "Queued",
  67         }
  68
  69         stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
  70         stubs.api.container_requests().create().execute.return_value = {
  71             "uuid": stubs.expect_container_request_uuid,
  72             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
  73             "state": "Queued"
  74         }
  75
  76         stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
  77         stubs.api.pipeline_templates().create().execute.return_value = {
  78             "uuid": stubs.expect_pipeline_template_uuid,
  79         }
  80         stubs.expect_job_spec = {
  81             'runtime_constraints': {
  82                 'docker_image': 'arvados/jobs'
  83             },
  84             'script_parameters': {
  85                 'x': {
  86                     'basename': 'blorp.txt',
  87                     'location': '99999999999999999999999999999994+99/blorp.txt',
  88                     'class': 'File'
  89                 },
  90                 'cwl:tool':
  91                 '99999999999999999999999999999991+99/wf/submit_wf.cwl'
  92             },
  93             'repository': 'arvados',
  94             'script_version': 'master',
  95             'script': 'cwl-runner'
  96         }
  97
  98         stubs.expect_container_spec = {
  99             'priority': 1,
 100             'mounts': {
 101                 '/var/spool/cwl': {
 102                     'writable': True,
 103                     'kind': 'collection'
 104                 },
 105                 '/var/lib/cwl/workflow': {
 106                     'portable_data_hash': '99999999999999999999999999999991+99',
 107                     'kind': 'collection'
 108                 },
 109                 'stdout': {
 110                     'path': '/var/spool/cwl/cwl.output.json',
 111                     'kind': 'file'
 112                 },
 113                 '/var/lib/cwl/job/cwl.input.json': {
 114                     'portable_data_hash': '765fda0d9897729ff467a4609879c00a+60/cwl.input.json',
 115                     'kind': 'collection'
 116                 }
 117             },
 118             'state': 'Committed',
 119             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 120             'command': ['arvados-cwl-runner', '--local', '--api=containers', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
 121             'name': 'submit_wf.cwl',
 122             'container_image': '99999999999999999999999999999993+99',
 123             'output_path': '/var/spool/cwl',
 124             'cwd': '/var/spool/cwl',
 125             'runtime_constraints': {
 126                 'API': True,
 127                 'vcpus': 1,
 128                 'ram': 268435456
 129             }
 130         }
 131         return func(self, stubs, *args, **kwargs)
 132     return wrapped
 133
 134
 135 class TestSubmit(unittest.TestCase):
 136     @stubs
 137     def test_submit(self, stubs):
 138         capture_stdout = cStringIO.StringIO()
 139         exited = arvados_cwl.main(
 140             ["--submit", "--no-wait",
 141              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 142             capture_stdout, sys.stderr, api_client=stubs.api)
 143         self.assertEqual(exited, 0)
 144
 145         stubs.api.collections().create.assert_has_calls([
 146             mock.call(),
 147             mock.call(body={
 148                 'manifest_text':
 149                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
 150                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
 151                 '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
 152                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 153                 'name': 'submit_wf.cwl',
 154             }, ensure_unique_name=True),
 155             mock.call().execute(),
 156             mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
 157                             '0:0:blub.txt 0:0:submit_tool.cwl\n',
 158                             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 159                             'name': 'New collection'},
 160                       ensure_unique_name=True),
 161             mock.call().execute(num_retries=4),
 162             mock.call(body={
 163                 'manifest_text':
 164                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 165                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 166                 'name': '#',
 167             }, ensure_unique_name=True),
 168             mock.call().execute()])
 169
 170         expect_job = copy.deepcopy(stubs.expect_job_spec)
 171         expect_job["owner_uuid"] = stubs.fake_user_uuid
 172         stubs.api.jobs().create.assert_called_with(
 173             body=expect_job,
 174             find_or_create=True)
 175         self.assertEqual(capture_stdout.getvalue(),
 176                          stubs.expect_job_uuid + '\n')
 177
 178     @stubs
 179     def test_submit_with_project_uuid(self, stubs):
 180         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 181
 182         exited = arvados_cwl.main(
 183             ["--submit", "--no-wait",
 184              "--project-uuid", project_uuid,
 185              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 186             sys.stdout, sys.stderr, api_client=stubs.api)
 187         self.assertEqual(exited, 0)
 188
 189         expect_body = copy.deepcopy(stubs.expect_job_spec)
 190         expect_body["owner_uuid"] = project_uuid
 191         stubs.api.jobs().create.assert_called_with(
 192             body=expect_body,
 193             find_or_create=True)
 194
 195     @stubs
 196     def test_submit_container(self, stubs):
 197         capture_stdout = cStringIO.StringIO()
 198         exited = arvados_cwl.main(
 199             ["--submit", "--no-wait", "--api=containers", "--debug",
 200              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 201             capture_stdout, sys.stderr, api_client=stubs.api)
 202         self.assertEqual(exited, 0)
 203
 204         stubs.api.collections().create.assert_has_calls([
 205             mock.call(),
 206             mock.call(body={
 207                 'manifest_text':
 208                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
 209                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
 210                 '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
 211                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 212                 'name': 'submit_wf.cwl',
 213             }, ensure_unique_name=True),
 214             mock.call().execute(),
 215             mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
 216                             '0:0:blub.txt 0:0:submit_tool.cwl\n',
 217                             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 218                             'name': 'New collection'},
 219                       ensure_unique_name=True),
 220             mock.call().execute(num_retries=4),
 221             mock.call(body={
 222                 'manifest_text':
 223                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 224                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 225                 'name': '#',
 226             }, ensure_unique_name=True),
 227             mock.call().execute()])
 228
 229         expect_container = copy.deepcopy(stubs.expect_container_spec)
 230         expect_container["owner_uuid"] = stubs.fake_user_uuid
 231         stubs.api.container_requests().create.assert_called_with(
 232             body=expect_container)
 233         self.assertEqual(capture_stdout.getvalue(),
 234                          stubs.expect_container_request_uuid + '\n')
 235
 236
 237 class TestCreateTemplate(unittest.TestCase):
 238     @stubs
 239     def test_create(self, stubs):
 240         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 241
 242         capture_stdout = cStringIO.StringIO()
 243
 244         exited = arvados_cwl.main(
 245             ["--create-template", "--no-wait", "--debug",
 246              "--project-uuid", project_uuid,
 247              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 248             capture_stdout, sys.stderr, api_client=stubs.api)
 249         self.assertEqual(exited, 0)
 250
 251         stubs.api.pipeline_instances().create.refute_called()
 252         stubs.api.jobs().create.refute_called()
 253
 254         expect_component = copy.deepcopy(stubs.expect_job_spec)
 255         expect_component['script_parameters']['x'] = {
 256             'dataclass': 'File',
 257             'required': True,
 258             'type': 'File',
 259             'value': '99999999999999999999999999999994+99/blorp.txt',
 260         }
 261         expect_template = {
 262             "components": {
 263                 "submit_wf.cwl": expect_component,
 264             },
 265             "name": "submit_wf.cwl",
 266             "owner_uuid": project_uuid,
 267         }
 268         stubs.api.pipeline_templates().create.assert_called_with(
 269             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 270
 271         self.assertEqual(capture_stdout.getvalue(),
 272                          stubs.expect_pipeline_template_uuid + '\n')
 273
 274
 275 class TestTemplateInputs(unittest.TestCase):
 276     expect_template = {
 277         "components": {
 278             "inputs_test.cwl": {
 279                 'runtime_constraints': {
 280                     'docker_image': 'arvados/jobs',
 281                 },
 282                 'script_parameters': {
 283                     'cwl:tool':
 284                     '99999999999999999999999999999991+99/'
 285                     'wf/inputs_test.cwl',
 286                     'optionalFloatInput': None,
 287                     'fileInput': {
 288                         'type': 'File',
 289                         'dataclass': 'File',
 290                         'required': True,
 291                         'title': "It's a file; we expect to find some characters in it.",
 292                         'description': 'If there were anything further to say, it would be said here,\nor here.'
 293                     },
 294                     'floatInput': {
 295                         'type': 'float',
 296                         'dataclass': 'number',
 297                         'required': True,
 298                         'title': 'Floats like a duck',
 299                         'default': 0.1,
 300                         'value': 0.1,
 301                     },
 302                     'optionalFloatInput': {
 303                         'type': ['null', 'float'],
 304                         'dataclass': 'number',
 305                         'required': False,
 306                     },
 307                     'boolInput': {
 308                         'type': 'boolean',
 309                         'dataclass': 'boolean',
 310                         'required': True,
 311                         'title': 'True or false?',
 312                     },
 313                 },
 314                 'repository': 'arvados',
 315                 'script_version': 'master',
 316                 'script': 'cwl-runner',
 317             },
 318         },
 319         "name": "inputs_test.cwl",
 320     }
 321
 322     @stubs
 323     def test_inputs_empty(self, stubs):
 324         exited = arvados_cwl.main(
 325             ["--create-template", "--no-wait",
 326              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
 327             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
 328         self.assertEqual(exited, 0)
 329
 330         expect_template = copy.deepcopy(self.expect_template)
 331         expect_template["owner_uuid"] = stubs.fake_user_uuid
 332
 333         stubs.api.pipeline_templates().create.assert_called_with(
 334             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 335
 336     @stubs
 337     def test_inputs(self, stubs):
 338         exited = arvados_cwl.main(
 339             ["--create-template", "--no-wait",
 340              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
 341             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
 342         self.assertEqual(exited, 0)
 343
 344         self.expect_template["owner_uuid"] = stubs.fake_user_uuid
 345
 346         expect_template = copy.deepcopy(self.expect_template)
 347         expect_template["owner_uuid"] = stubs.fake_user_uuid
 348         params = expect_template[
 349             "components"]["inputs_test.cwl"]["script_parameters"]
 350         params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
 351         params["floatInput"]["value"] = 1.234
 352         params["boolInput"]["value"] = True
 353
 354         stubs.api.pipeline_templates().create.assert_called_with(
 355             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)