sdk/cwl/tests/test_job.py

   1 import unittest
   2 import mock
   3 import arvados_cwl
   4
   5 class TestJob(unittest.TestCase):
   6
   7     # The test passes no builder.resources
   8     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
   9     def test_run(self):
  10         runner = mock.MagicMock()
  11         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  12         tool = {
  13             "inputs": [],
  14             "outputs": [],
  15             "baseCommand": "ls"
  16         }
  17         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool)
  18         arvtool.formatgraph = None
  19         for j in arvtool.job({}, "", mock.MagicMock()):
  20             j.run()
  21         runner.api.jobs().create.assert_called_with(body={
  22             'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  23             'runtime_constraints': {},
  24             'script_parameters': {
  25                 'tasks': [{
  26                     'task.env': {'TMPDIR': '$(task.tmpdir)'},
  27                     'command': ['ls']
  28                 }],
  29                 'crunchrunner': arvados_cwl.crunchrunner_pdh + '/crunchrunner'
  30             },
  31             'script_version': 'master',
  32             'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  33             'repository': 'arvados',
  34             'script': 'crunchrunner',
  35             'runtime_constraints': {
  36                 'min_cores_per_node': 1,
  37                 'min_ram_mb_per_node': 1024,
  38                 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
  39             }
  40         }, find_or_create=True)
  41
  42     # The test passes some fields in builder.resources
  43     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  44     def test_resource_requirements(self):
  45         runner = mock.MagicMock()
  46         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  47         tool = {
  48             "inputs": [],
  49             "outputs": [],
  50             "hints": [{
  51                 "class": "ResourceRequirement",
  52                 "coresMin": 3,
  53                 "ramMin": 3000,
  54                 "tmpdirMin": 4000
  55             }],
  56             "baseCommand": "ls"
  57         }
  58         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool)
  59         arvtool.formatgraph = None
  60         for j in arvtool.job({}, "", mock.MagicMock()):
  61             j.run()
  62         runner.api.jobs().create.assert_called_with(body={
  63             'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  64             'runtime_constraints': {},
  65             'script_parameters': {
  66                 'tasks': [{
  67                     'task.env': {'TMPDIR': '$(task.tmpdir)'},
  68                     'command': ['ls']
  69                 }],
  70                 'crunchrunner': arvados_cwl.crunchrunner_pdh + '/crunchrunner'
  71             },
  72             'script_version': 'master',
  73             'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  74             'repository': 'arvados',
  75             'script': 'crunchrunner',
  76             'runtime_constraints': {
  77                 'min_cores_per_node': 3,
  78                 'min_ram_mb_per_node': 3000,
  79                 'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
  80             }
  81         }, find_or_create=True)
  82
  83     @mock.patch("arvados.collection.Collection")
  84     def test_done(self, col):
  85         api = mock.MagicMock()
  86
  87         runner = mock.MagicMock()
  88         runner.api = api
  89         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  90         runner.num_retries = 0
  91
  92         col().open.return_value = []
  93         api.collections().list().execute.side_effect = ({"items": []},
  94                                                         {"items": [{"manifest_text": "XYZ"}]})
  95
  96         arvjob = arvados_cwl.ArvadosJob(runner)
  97         arvjob.name = "testjob"
  98         arvjob.builder = mock.MagicMock()
  99         arvjob.output_callback = mock.MagicMock()
 100         arvjob.collect_outputs = mock.MagicMock()
 101
 102         arvjob.done({
 103             "state": "Complete",
 104             "output": "99999999999999999999999999999993+99",
 105             "log": "99999999999999999999999999999994+99",
 106             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 107         })
 108
 109         api.collections().list.assert_has_calls([
 110             mock.call(),
 111             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 112                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 113                           ['name', '=', 'Output 9999999 of testjob']]),
 114             mock.call().execute(num_retries=0),
 115             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 116                  select=['manifest_text']),
 117             mock.call().execute(num_retries=0)])
 118
 119         api.collections().create.assert_called_with(
 120             ensure_unique_name=True,
 121             body={'portable_data_hash': '99999999999999999999999999999993+99',
 122                   'manifest_text': 'XYZ',
 123                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 124                   'name': 'Output 9999999 of testjob'})
 125
 126     @mock.patch("arvados.collection.Collection")
 127     def test_done_use_existing_collection(self, col):
 128         api = mock.MagicMock()
 129
 130         runner = mock.MagicMock()
 131         runner.api = api
 132         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 133         runner.num_retries = 0
 134
 135         col().open.return_value = []
 136         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 137
 138         arvjob = arvados_cwl.ArvadosJob(runner)
 139         arvjob.name = "testjob"
 140         arvjob.builder = mock.MagicMock()
 141         arvjob.output_callback = mock.MagicMock()
 142         arvjob.collect_outputs = mock.MagicMock()
 143
 144         arvjob.done({
 145             "state": "Complete",
 146             "output": "99999999999999999999999999999993+99",
 147             "log": "99999999999999999999999999999994+99",
 148             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 149         })
 150
 151         api.collections().list.assert_has_calls([
 152             mock.call(),
 153             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 154                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 155                                ['name', '=', 'Output 9999999 of testjob']]),
 156             mock.call().execute(num_retries=0)])
 157
 158         self.assertFalse(api.collections().create.called)