+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import functools
import json
import logging
import mock
import os
import unittest
+import copy
+import StringIO
import arvados
import arvados_cwl
import cwltool.process
+from arvados.errors import ApiError
from schema_salad.ref_resolver import Loader
+from schema_salad.sourceline import cmap
+from .mock_discovery import get_rootDesc
+from .matcher import JsonDiffMatcher, StripYAMLComments
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):
# The test passes no builder.resources
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch('arvados.commands.keepdocker.list_images_in_arv')
def test_run(self, list_images_in_arv):
- runner = mock.MagicMock()
- runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
- runner.ignore_docker_for_reuse = False
- runner.num_retries = 0
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
-
- list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
- runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
-
- tool = {
- "inputs": [],
- "outputs": [],
- "baseCommand": "ls",
- "arguments": [{"valueFrom": "$(runtime.outdir)"}]
- }
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
- basedir="", make_fs_access=make_fs_access, loader=Loader({}))
- arvtool.formatgraph = None
- for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
- j.run()
- runner.api.jobs().create.assert_called_with(
- body={
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
- 'runtime_constraints': {},
- 'script_parameters': {
- 'tasks': [{
- 'task.env': {'HOME': '$(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:'+arvados_cwl.__version__,
- '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:'+arvados_cwl.__version__]]
- )
+ for enable_reuse in (True, False):
+ runner = mock.MagicMock()
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ runner.num_retries = 0
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+
+ list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
+ runner.api.collections().get().execute.return_value = {"portable_data_hash": "99999999999999999999999999999993+99"}
+ # Simulate reused job from another project so that we can check is a can_read
+ # link is added.
+ runner.api.jobs().create().execute.return_value = {
+ 'state': 'Complete' if enable_reuse else 'Queued',
+ 'owner_uuid': 'zzzzz-tpzed-yyyyyyyyyyyyyyy' if enable_reuse else 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'uuid': 'zzzzz-819sb-yyyyyyyyyyyyyyy',
+ 'output': None,
+ }
+
+ tool = cmap({
+ "inputs": [],
+ "outputs": [],
+ "baseCommand": "ls",
+ "arguments": [{"valueFrom": "$(runtime.outdir)"}]
+ })
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
+ basedir="", make_fs_access=make_fs_access, loader=Loader({}))
+ arvtool.formatgraph = None
+ for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
+ j.run(enable_reuse=enable_reuse)
+ runner.api.jobs().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'runtime_constraints': {},
+ 'script_parameters': {
+ 'tasks': [{
+ 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+ 'command': ['ls', '$(task.outdir)']
+ }],
+ },
+ 'script_version': 'master',
+ 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
+ '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=enable_reuse,
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']]
+ )
+ if enable_reuse:
+ runner.api.links().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'link_class': 'permission',
+ 'name': 'can_read',
+ "tail_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
+ "head_uuid": "zzzzz-819sb-yyyyyyyyyyyyyyy",
+ })
+ )
+ # Simulate an API excepction when trying to create a
+ # sharing link on the job
+ runner.api.links().create.side_effect = ApiError(
+ mock.MagicMock(return_value={'status': 403}),
+ 'Permission denied')
+ j.run(enable_reuse=enable_reuse)
+ j.output_callback.assert_called_with({}, 'success')
+ else:
+ assert not runner.api.links().create.called
# The test passes some fields in builder.resources
# For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
"outputDirType": "keep_output_dir"
}, {
"class": "http://arvados.org/cwl#APIRequirement",
+ },
+ {
+ "class": "http://arvados.org/cwl#ReuseRequirement",
+ "enableReuse": False
}],
"baseCommand": "ls"
}
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
make_fs_access=make_fs_access, loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
- j.run()
+ j.run(enable_reuse=True)
runner.api.jobs().create.assert_called_with(
- body={
+ body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'runtime_constraints': {},
'script_parameters': {
}]
},
'script_version': 'master',
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
- 'min_ram_mb_per_node': 3000,
+ 'min_ram_mb_per_node': 3512, # ramMin + keep_cache
'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
'keep_cache_mb_per_task': 512
}
- },
- find_or_create=True,
+ }),
+ find_or_create=False,
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
- ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
- ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]])
+ ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']])
@mock.patch("arvados.collection.CollectionReader")
def test_done(self, reader):
runner.num_retries = 0
runner.ignore_docker_for_reuse = False
- reader().open.return_value = []
+ reader().open.return_value = StringIO.StringIO(
+ """2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir
+2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.outdir)=/tmp/crunch-job-task-work/compute3.1/outdir
+2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
+ """)
api.collections().list().execute.side_effect = ({"items": []},
- {"items": [{"manifest_text": "XYZ"}]})
+ {"items": [{"manifest_text": "XYZ"}]},
+ {"items": []},
+ {"items": [{"manifest_text": "ABC"}]})
arvjob = arvados_cwl.ArvadosJob(runner)
arvjob.name = "testjob"
arvjob.builder = mock.MagicMock()
arvjob.output_callback = mock.MagicMock()
arvjob.collect_outputs = mock.MagicMock()
+ arvjob.collect_outputs.return_value = {"out": "stuff"}
arvjob.done({
"state": "Complete",
api.collections().list.assert_has_calls([
mock.call(),
+ # Output collection check
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),
+ # Log collection's turn
+ mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
+ ['portable_data_hash', '=', '99999999999999999999999999999994+99'],
+ ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]),
+ mock.call().execute(num_retries=0),
+ mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999994+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'})
+ api.collections().create.assert_has_calls([
+ mock.call(ensure_unique_name=True,
+ body={'portable_data_hash': '99999999999999999999999999999993+99',
+ 'manifest_text': 'XYZ',
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'name': 'Output 9999999 of testjob'}),
+ mock.call().execute(num_retries=0),
+ mock.call(ensure_unique_name=True,
+ body={'portable_data_hash': '99999999999999999999999999999994+99',
+ 'manifest_text': 'ABC',
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'name': 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
+ mock.call().execute(num_retries=0),
+ ])
+
+ arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
@mock.patch("arvados.collection.CollectionReader")
def test_done_use_existing_collection(self, reader):
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.num_retries = 0
- reader().open.return_value = []
- api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
+ reader().open.return_value = StringIO.StringIO(
+ """2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir
+2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.outdir)=/tmp/crunch-job-task-work/compute3.1/outdir
+2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
+ """)
+
+ api.collections().list().execute.side_effect = (
+ {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
+ {"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.collect_outputs.return_value = {"out": "stuff"}
arvjob.done({
"state": "Complete",
api.collections().list.assert_has_calls([
mock.call(),
+ # Output collection
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().execute(num_retries=0),
+ # Log collection
+ mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
+ ['portable_data_hash', '=', '99999999999999999999999999999994+99'],
+ ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]),
+ mock.call().execute(num_retries=0)
+ ])
self.assertFalse(api.collections().create.called)
+ arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
+
class TestWorkflow(unittest.TestCase):
# The test passes no builder.resources
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
- api._rootDesc = arvados.api('v1')._rootDesc
+ api._rootDesc = get_rootDesc()
+
runner = arvados_cwl.ArvCwlRunner(api)
self.assertEqual(runner.work_api, 'jobs')
mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
basedir="", make_fs_access=make_fs_access, loader=document_loader,
makeTool=runner.arv_make_tool, metadata=metadata)
it.next().run()
with open("tests/wf/scatter2_subwf.cwl") as f:
- subwf = f.read()
+ subwf = StripYAMLComments(f.read())
runner.api.jobs().create.assert_called_with(
- body={
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ body=JsonDiffMatcher({
+ 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script_version': 'master',
'script': 'crunchrunner',
'runtime_constraints': {
'min_scratch_mb_per_node': 2048,
'min_cores_per_node': 1,
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
- ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
- ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]],
+ ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']],
find_or_create=True)
mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
- mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
+ mockcollection().open().__enter__().write.assert_has_calls([mock.call(
+'''{
+ "sleeptime": 5
+}''')])
def test_default_work_api(self):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
- api._rootDesc = arvados.api('v1')._rootDesc
+ api._rootDesc = copy.deepcopy(get_rootDesc())
del api._rootDesc.get('resources')['jobs']['methods']['create']
runner = arvados_cwl.ArvCwlRunner(api)
self.assertEqual(runner.work_api, 'containers')
projects / arvados.git / blobdiff