-import unittest
-import mock
import arvados_cwl
+import logging
+import mock
+import unittest
+import os
+import functools
+import cwltool.process
+
+if not os.getenv('ARVADOS_DEBUG'):
+ logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
+ logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
+
class TestJob(unittest.TestCase):
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
def test_run(self):
runner = mock.MagicMock()
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
+
tool = {
"inputs": [],
"outputs": [],
- "baseCommand": "ls"
+ "baseCommand": "ls",
+ "arguments": [{"valueFrom": "$(runtime.outdir)"}]
}
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool)
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="", make_fs_access=make_fs_access)
arvtool.formatgraph = None
- for j in arvtool.job({}, "", mock.MagicMock()):
+ for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
j.run()
- runner.api.jobs().create.assert_called_with(body={
- 'runtime_constraints': {},
- 'script_parameters': {
- 'tasks': [{
- 'task.env': {'TMPDIR': '$(task.tmpdir)'},
- 'command': ['ls']
- }],
- 'crunchrunner': '83db29f08544e1c319572a6bd971088a+140/crunchrunner'
- },
- 'script_version': 'master',
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
- 'repository': 'arvados',
- 'script': 'crunchrunner',
- 'runtime_constraints': {
- 'min_cores_per_node': 1,
- 'min_ram_mb_per_node': 1024,
- 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
- }
- }, find_or_create=True)
+ runner.api.jobs().create.assert_called_with(
+ body={
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'runtime_constraints': {},
+ 'script_parameters': {
+ 'tasks': [{
+ 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+ 'command': ['ls', '$(task.outdir)']
+ }],
+ },
+ 'script_version': 'master',
+ 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'repository': 'arvados',
+ 'script': 'crunchrunner',
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs',
+ 'min_cores_per_node': 1,
+ 'min_ram_mb_per_node': 1024,
+ 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
+ }
+ },
+ find_or_create=True,
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']]
+ )
# The test passes some fields in builder.resources
# For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
def test_resource_requirements(self):
runner = mock.MagicMock()
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
+
tool = {
"inputs": [],
"outputs": [],
}],
"baseCommand": "ls"
}
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool)
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, make_fs_access=make_fs_access)
arvtool.formatgraph = None
- for j in arvtool.job({}, "", mock.MagicMock()):
+ for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
j.run()
- runner.api.jobs().create.assert_called_with(body={
- 'runtime_constraints': {},
- 'script_parameters': {
- 'tasks': [{
- 'task.env': {'TMPDIR': '$(task.tmpdir)'},
- 'command': ['ls']
- }],
- 'crunchrunner': '83db29f08544e1c319572a6bd971088a+140/crunchrunner'
+ runner.api.jobs().create.assert_called_with(
+ body={
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'runtime_constraints': {},
+ 'script_parameters': {
+ 'tasks': [{
+ 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+ 'command': ['ls']
+ }]
},
'script_version': 'master',
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
- 'repository': 'arvados',
- 'script': 'crunchrunner',
- 'runtime_constraints': {
- 'min_cores_per_node': 3,
- 'min_ram_mb_per_node': 3000,
- 'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
- }
- }, find_or_create=True)
+ 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'repository': 'arvados',
+ 'script': 'crunchrunner',
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs',
+ 'min_cores_per_node': 3,
+ 'min_ram_mb_per_node': 3000,
+ 'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
+ }
+ },
+ find_or_create=True,
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']])
+
+ @mock.patch("arvados.collection.Collection")
+ def test_done(self, col):
+ api = mock.MagicMock()
+
+ runner = mock.MagicMock()
+ runner.api = api
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.num_retries = 0
+ runner.ignore_docker_for_reuse = False
+
+ col().open.return_value = []
+ api.collections().list().execute.side_effect = ({"items": []},
+ {"items": [{"manifest_text": "XYZ"}]})
+
+ arvjob = arvados_cwl.ArvadosJob(runner)
+ arvjob.name = "testjob"
+ arvjob.builder = mock.MagicMock()
+ arvjob.output_callback = mock.MagicMock()
+ arvjob.collect_outputs = mock.MagicMock()
+
+ arvjob.done({
+ "state": "Complete",
+ "output": "99999999999999999999999999999993+99",
+ "log": "99999999999999999999999999999994+99",
+ "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ })
+
+ api.collections().list.assert_has_calls([
+ mock.call(),
+ mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
+ ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
+ ['name', '=', 'Output 9999999 of testjob']]),
+ mock.call().execute(num_retries=0),
+ mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
+ select=['manifest_text']),
+ mock.call().execute(num_retries=0)])
+
+ api.collections().create.assert_called_with(
+ ensure_unique_name=True,
+ body={'portable_data_hash': '99999999999999999999999999999993+99',
+ 'manifest_text': 'XYZ',
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'name': 'Output 9999999 of testjob'})
+
+ @mock.patch("arvados.collection.Collection")
+ def test_done_use_existing_collection(self, col):
+ api = mock.MagicMock()
+
+ runner = mock.MagicMock()
+ runner.api = api
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.num_retries = 0
+
+ col().open.return_value = []
+ api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
+
+ arvjob = arvados_cwl.ArvadosJob(runner)
+ arvjob.name = "testjob"
+ arvjob.builder = mock.MagicMock()
+ arvjob.output_callback = mock.MagicMock()
+ arvjob.collect_outputs = mock.MagicMock()
+
+ arvjob.done({
+ "state": "Complete",
+ "output": "99999999999999999999999999999993+99",
+ "log": "99999999999999999999999999999994+99",
+ "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ })
+
+ api.collections().list.assert_has_calls([
+ mock.call(),
+ mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
+ ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
+ ['name', '=', 'Output 9999999 of testjob']]),
+ mock.call().execute(num_retries=0)])
+
+ self.assertFalse(api.collections().create.called)
projects / arvados.git / blobdiff