#
# SPDX-License-Identifier: Apache-2.0
+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
+from builtins import next
+
import functools
import json
import logging
import os
import unittest
import copy
-import StringIO
+import io
import arvados
import arvados_cwl
+import arvados_cwl.executor
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
+from .test_container import CollectionMock
if not os.getenv('ARVADOS_DEBUG'):
logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
class TestJob(unittest.TestCase):
+ def helper(self, runner, enable_reuse=True):
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1.0-dev1")
+
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
+ loadingContext = arvados_cwl.context.ArvLoadingContext(
+ {"avsc_names": avsc_names,
+ "basedir": "",
+ "make_fs_access": make_fs_access,
+ "loader": Loader({}),
+ "metadata": {"cwlVersion": "v1.1.0-dev1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"},
+ "makeTool": runner.arv_make_tool})
+ runtimeContext = arvados_cwl.context.ArvRuntimeContext(
+ {"work_api": "jobs",
+ "basedir": "",
+ "name": "test_run_job_"+str(enable_reuse),
+ "make_fs_access": make_fs_access,
+ "enable_reuse": enable_reuse,
+ "priority": 500})
+
+ return loadingContext, runtimeContext
+
# 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')
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"}
"id": "#",
"class": "CommandLineTool"
})
- 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({}),
- metadata={"cwlVersion": "v1.0"})
+
+ loadingContext, runtimeContext = self.helper(runner, enable_reuse)
+
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
- for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
- j.run(enable_reuse=enable_reuse)
+ for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
+ j.run(runtimeContext)
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
# 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)
+ bytes(b'Permission denied'))
+ j.run(runtimeContext)
else:
assert not runner.api.links().create.called
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
-
-
tool = {
"inputs": [],
"outputs": [],
"id": "#",
"class": "CommandLineTool"
}
- 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({}),
- metadata={"cwlVersion": "v1.0"})
+
+ loadingContext, runtimeContext = self.helper(runner)
+
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
- for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
- j.run(enable_reuse=True)
+ for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
+ j.run(runtimeContext)
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
runner.num_retries = 0
runner.ignore_docker_for_reuse = False
- 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
+ reader().keys.return_value = "log.txt"
+ reader().open.return_value = io.StringIO(
+ str(u"""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": []},
{"items": [{"manifest_text": "ABC"}]})
- arvjob = arvados_cwl.ArvadosJob(runner)
- arvjob.name = "testjob"
- arvjob.builder = mock.MagicMock()
+ arvjob = arvados_cwl.ArvadosJob(runner,
+ mock.MagicMock(),
+ {},
+ None,
+ [],
+ [],
+ "testjob")
arvjob.output_callback = mock.MagicMock()
arvjob.collect_outputs = mock.MagicMock()
arvjob.collect_outputs.return_value = {"out": "stuff"}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.num_retries = 0
- 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
+ reader().keys.return_value = "log.txt"
+ reader().open.return_value = io.StringIO(
+ str(u"""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 = arvados_cwl.ArvadosJob(runner,
+ mock.MagicMock(),
+ {},
+ None,
+ [],
+ [],
+ "testjob")
arvjob.output_callback = mock.MagicMock()
arvjob.collect_outputs = mock.MagicMock()
arvjob.collect_outputs.return_value = {"out": "stuff"}
class TestWorkflow(unittest.TestCase):
+ def helper(self, runner, enable_reuse=True):
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1.0-dev1")
+
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
+
+ document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=make_fs_access(""))
+ document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session)
+ document_loader.fetch_text = document_loader.fetcher.fetch_text
+ document_loader.check_exists = document_loader.fetcher.check_exists
+
+ loadingContext = arvados_cwl.context.ArvLoadingContext(
+ {"avsc_names": avsc_names,
+ "basedir": "",
+ "make_fs_access": make_fs_access,
+ "loader": document_loader,
+ "metadata": {"cwlVersion": "v1.1.0-dev1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"},
+ "construct_tool_object": runner.arv_make_tool})
+ runtimeContext = arvados_cwl.context.ArvRuntimeContext(
+ {"work_api": "jobs",
+ "basedir": "",
+ "name": "test_run_wf_"+str(enable_reuse),
+ "make_fs_access": make_fs_access,
+ "enable_reuse": enable_reuse,
+ "priority": 500})
+
+ return loadingContext, runtimeContext
+
# The test passes no builder.resources
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.collection.CollectionReader")
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
- runner = arvados_cwl.ArvCwlRunner(api)
+ runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'jobs')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
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")
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
- collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
- document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=api, fs_access=make_fs_access(""))
- document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session)
- document_loader.fetch_text = document_loader.fetcher.fetch_text
- document_loader.check_exists = document_loader.fetcher.check_exists
+ loadingContext, runtimeContext = self.helper(runner)
- tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
+ tool, metadata = loadingContext.loader.resolve_ref("tests/wf/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
- mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+ mockc = mock.MagicMock()
+ mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mockc, *args, **kwargs)
+ mockcollectionreader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "token.txt")
- 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)
+ arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
- it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access, tmp_outdir_prefix="")
- it.next().run()
- it.next().run()
+ it = arvtool.job({}, mock.MagicMock(), runtimeContext)
+
+ next(it).run(runtimeContext)
+ next(it).run(runtimeContext)
with open("tests/wf/scatter2_subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'},
'task.vwd': {
- 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
- 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+ 'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
+ 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
},
'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
'task.stdout': 'cwl.output.json'}]},
['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(
-'''{
+ mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)])
+ mockc.open().__enter__().write.assert_has_calls([mock.call(
+bytes(b'''{
"fileblub": {
"basename": "token.txt",
"class": "File",
- "location": "/keep/99999999999999999999999999999999+118/token.txt"
+ "location": "/keep/99999999999999999999999999999999+118/token.txt",
+ "size": 0
},
"sleeptime": 5
-}''')])
+}'''))])
# The test passes no builder.resources
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.collection.Collection")
@mock.patch('arvados.commands.keepdocker.list_images_in_arv')
def test_overall_resource_singlecontainer(self, list_images_in_arv, mockcollection, mockcollectionreader):
+ # TODO copy this over to test_container
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
- runner = arvados_cwl.ArvCwlRunner(api)
+ runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'jobs')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
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")
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
- collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
- document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=api, fs_access=make_fs_access(""))
- document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session)
- document_loader.fetch_text = document_loader.fetcher.fetch_text
- document_loader.check_exists = document_loader.fetcher.check_exists
-
- tool, metadata = document_loader.resolve_ref("tests/wf/echo-wf.cwl")
- metadata["cwlVersion"] = tool["cwlVersion"]
+ loadingContext, runtimeContext = self.helper(runner)
+ loadingContext.do_update = True
+ tool, metadata = loadingContext.loader.resolve_ref("tests/wf/echo-wf.cwl")
- mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+ mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mock.MagicMock(), *args, **kwargs)
- 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)
+ arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
- it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access, tmp_outdir_prefix="")
- it.next().run()
- it.next().run()
+ it = arvtool.job({}, mock.MagicMock(), runtimeContext)
+
+ next(it).run(runtimeContext)
+ next(it).run(runtimeContext)
with open("tests/wf/echo-subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'},
'task.vwd': {
- 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
- 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+ 'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
+ 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
},
'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
'task.stdout': 'cwl.output.json'}]},
api = mock.MagicMock()
api._rootDesc = copy.deepcopy(get_rootDesc())
del api._rootDesc.get('resources')['jobs']['methods']['create']
- runner = arvados_cwl.ArvCwlRunner(api)
+ runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'containers')
projects / arvados.git / blobdiff