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         }, {
  45             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
  46             "portable_data_hash": "99999999999999999999999999999992+99",
  47         },
  48         {
  49             "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4",
  50             "portable_data_hash": "99999999999999999999999999999994+99",
  51             "manifest_text": ""
  52         })
  53         stubs.api.collections().get().execute.return_value = {
  54             "portable_data_hash": "99999999999999999999999999999993+99"}
  55
  56         stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  57         stubs.api.jobs().create().execute.return_value = {
  58             "uuid": stubs.expect_job_uuid,
  59             "state": "Queued",
  60         }
  61
  62         stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
  63         stubs.api.container_requests().create().execute.return_value = {
  64             "uuid": stubs.expect_container_request_uuid,
  65             "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
  66             "state": "Queued"
  67         }
  68
  69         stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
  70         stubs.api.pipeline_templates().create().execute.return_value = {
  71             "uuid": stubs.expect_pipeline_template_uuid,
  72         }
  73         stubs.expect_job_spec = {
  74             'runtime_constraints': {
  75                 'docker_image': 'arvados/jobs'
  76             },
  77             'script_parameters': {
  78                 'x': {
  79                     'path': '99999999999999999999999999999992+99/blorp.txt',
  80                     'class': 'File'
  81                 },
  82                 'cwl:tool':
  83                 '99999999999999999999999999999991+99/wf/submit_wf.cwl'
  84             },
  85             'repository': 'arvados',
  86             'script_version': 'master',
  87             'script': 'cwl-runner'
  88         }
  89
  90         stubs.expect_container_spec = {
  91             'priority': 1,
  92             'mounts': {
  93                 'stdout': {
  94                     'path': '/var/spool/cwl/cwl.output.json',
  95                     'kind': 'file'
  96                 },
  97                 '/var/lib/cwl/workflow/submit_wf.cwl': {
  98                     'portable_data_hash': '999999999999999999999999991+99',
  99                     'kind': 'collection'
 100                 },
 101                 '/var/lib/cwl/job/cwl.input.json': {
 102                     'portable_data_hash': '102435082199e5229f99b01165b67096+60/cwl.input.json',
 103                     'kind': 'collection'
 104                 }
 105             },
 106             'state': 'Committed',
 107             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 108             'command': ['arvados-cwl-runner', '--local', '--crunch2', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
 109             'name': 'submit_wf.cwl',
 110             'container_image': '99999999999999999999999999999993+99',
 111             'output_path': '/var/spool/cwl',
 112             'cwd': '/var/spool/cwl',
 113             'runtime_constraints': {
 114                 'vcpus': 1,
 115                 'ram': 268435456
 116             }
 117         }
 118         return func(self, stubs, *args, **kwargs)
 119     return wrapped
 120
 121
 122 class TestSubmit(unittest.TestCase):
 123     @stubs
 124     def test_submit(self, stubs):
 125         capture_stdout = cStringIO.StringIO()
 126         exited = arvados_cwl.main(
 127             ["--submit", "--no-wait",
 128              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 129             capture_stdout, sys.stderr, api_client=stubs.api)
 130         self.assertEqual(exited, 0)
 131
 132         stubs.api.collections().create.assert_has_calls([
 133             mock.call(),
 134             mock.call(body={
 135                 'manifest_text':
 136                 './tool a3954c369b8924d40547ec8cf5f6a7f4+449 '
 137                 '0:16:blub.txt 16:433:submit_tool.cwl\n./wf '
 138                 'e046cace0b1a0a6ee645f6ea8688f7e2+364 0:364:submit_wf.cwl\n',
 139                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 140                 'name': 'submit_wf.cwl',
 141             }, ensure_unique_name=True),
 142             mock.call().execute(),
 143             mock.call(body={
 144                 'manifest_text':
 145                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 146                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 147                 'name': '#',
 148             }, ensure_unique_name=True),
 149             mock.call().execute()])
 150
 151         expect_job = copy.deepcopy(stubs.expect_job_spec)
 152         expect_job["owner_uuid"] = stubs.fake_user_uuid
 153         stubs.api.jobs().create.assert_called_with(
 154             body=expect_job,
 155             find_or_create=True)
 156         self.assertEqual(capture_stdout.getvalue(),
 157                          stubs.expect_job_uuid + '\n')
 158
 159     @stubs
 160     def test_submit_with_project_uuid(self, stubs):
 161         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 162
 163         exited = arvados_cwl.main(
 164             ["--submit", "--no-wait",
 165              "--project-uuid", project_uuid,
 166              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 167             sys.stdout, sys.stderr, api_client=stubs.api)
 168         self.assertEqual(exited, 0)
 169
 170         expect_body = copy.deepcopy(stubs.expect_job_spec)
 171         expect_body["owner_uuid"] = project_uuid
 172         stubs.api.jobs().create.assert_called_with(
 173             body=expect_body,
 174             find_or_create=True)
 175
 176     @stubs
 177     def test_submit_container(self, stubs):
 178         capture_stdout = cStringIO.StringIO()
 179         exited = arvados_cwl.main(
 180             ["--submit", "--no-wait", "--crunch2", "--debug",
 181              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 182             capture_stdout, sys.stderr, api_client=stubs.api)
 183         self.assertEqual(exited, 0)
 184
 185         stubs.api.collections().create.assert_has_calls([
 186             mock.call(),
 187             mock.call(body={
 188                 'manifest_text':
 189                 './tool a3954c369b8924d40547ec8cf5f6a7f4+449 '
 190                 '0:16:blub.txt 16:433:submit_tool.cwl\n./wf '
 191                 'e046cace0b1a0a6ee645f6ea8688f7e2+364 0:364:submit_wf.cwl\n',
 192                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 193                 'name': 'submit_wf.cwl',
 194             }, ensure_unique_name=True),
 195             mock.call().execute(),
 196             mock.call(body={
 197                 'manifest_text':
 198                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
 199                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
 200                 'name': '#',
 201             }, ensure_unique_name=True),
 202             mock.call().execute()])
 203
 204         expect_container = copy.deepcopy(stubs.expect_container_spec)
 205         expect_container["owner_uuid"] = stubs.fake_user_uuid
 206         stubs.api.container_requests().create.assert_called_with(
 207             body=expect_container)
 208         self.assertEqual(capture_stdout.getvalue(),
 209                          stubs.expect_container_request_uuid + '\n')
 210
 211
 212 class TestCreateTemplate(unittest.TestCase):
 213     @stubs
 214     def test_create(self, stubs):
 215         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 216
 217         capture_stdout = cStringIO.StringIO()
 218
 219         exited = arvados_cwl.main(
 220             ["--create-template", "--no-wait",
 221              "--project-uuid", project_uuid,
 222              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
 223             capture_stdout, sys.stderr, api_client=stubs.api)
 224         self.assertEqual(exited, 0)
 225
 226         stubs.api.pipeline_instances().create.refute_called()
 227         stubs.api.jobs().create.refute_called()
 228
 229         expect_component = copy.deepcopy(stubs.expect_job_spec)
 230         expect_component['script_parameters']['x'] = {
 231             'dataclass': 'File',
 232             'required': True,
 233             'type': 'File',
 234             'value': '99999999999999999999999999999992+99/blorp.txt',
 235         }
 236         expect_template = {
 237             "components": {
 238                 "submit_wf.cwl": expect_component,
 239             },
 240             "name": "submit_wf.cwl",
 241             "owner_uuid": project_uuid,
 242         }
 243         stubs.api.pipeline_templates().create.assert_called_with(
 244             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 245
 246         self.assertEqual(capture_stdout.getvalue(),
 247                          stubs.expect_pipeline_template_uuid + '\n')
 248
 249
 250 class TestTemplateInputs(unittest.TestCase):
 251     expect_template = {
 252         "components": {
 253             "inputs_test.cwl": {
 254                 'runtime_constraints': {
 255                     'docker_image': 'arvados/jobs',
 256                 },
 257                 'script_parameters': {
 258                     'cwl:tool':
 259                     '99999999999999999999999999999991+99/'
 260                     'wf/inputs_test.cwl',
 261                     'optionalFloatInput': None,
 262                     'fileInput': {
 263                         'type': 'File',
 264                         'dataclass': 'File',
 265                         'required': True,
 266                         'title': "It's a file; we expect to find some characters in it.",
 267                         'description': 'If there were anything further to say, it would be said here,\nor here.'
 268                     },
 269                     'floatInput': {
 270                         'type': 'float',
 271                         'dataclass': 'number',
 272                         'required': True,
 273                         'title': 'Floats like a duck',
 274                         'default': 0.1,
 275                         'value': 0.1,
 276                     },
 277                     'optionalFloatInput': {
 278                         'type': ['null', 'float'],
 279                         'dataclass': 'number',
 280                         'required': False,
 281                     },
 282                     'boolInput': {
 283                         'type': 'boolean',
 284                         'dataclass': 'boolean',
 285                         'required': True,
 286                         'title': 'True or false?',
 287                     },
 288                 },
 289                 'repository': 'arvados',
 290                 'script_version': 'master',
 291                 'script': 'cwl-runner',
 292             },
 293         },
 294         "name": "inputs_test.cwl",
 295     }
 296
 297     @stubs
 298     def test_inputs_empty(self, stubs):
 299         exited = arvados_cwl.main(
 300             ["--create-template", "--no-wait",
 301              "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
 302             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
 303         self.assertEqual(exited, 0)
 304
 305         expect_template = copy.deepcopy(self.expect_template)
 306         expect_template["owner_uuid"] = stubs.fake_user_uuid
 307
 308         stubs.api.pipeline_templates().create.assert_called_with(
 309             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
 310
 311     @stubs
 312     def test_inputs(self, stubs):
 313         exited = arvados_cwl.main(
 314             ["--create-template", "--no-wait",
 315              "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
 316             cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
 317         self.assertEqual(exited, 0)
 318
 319         self.expect_template["owner_uuid"] = stubs.fake_user_uuid
 320
 321         expect_template = copy.deepcopy(self.expect_template)
 322         expect_template["owner_uuid"] = stubs.fake_user_uuid
 323         params = expect_template[
 324             "components"]["inputs_test.cwl"]["script_parameters"]
 325         params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt'
 326         params["floatInput"]["value"] = 1.234
 327         params["boolInput"]["value"] = True
 328
 329         stubs.api.pipeline_templates().create.assert_called_with(
 330             body=JsonDiffMatcher(expect_template), ensure_unique_name=True)