#
# 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
# sharing link on the job
runner.api.links().create.side_effect = ApiError(
mock.MagicMock(return_value={'status': 403}),
- 'Permission denied')
+ bytes(b'Permission denied'))
j.run(runtimeContext)
else:
assert not runner.api.links().create.called
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": []},
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"}]},
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"]]
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), runtimeContext)
- it.next().run(runtimeContext)
- it.next().run(runtimeContext)
+ next(it).run(runtimeContext)
+ next(it).run(runtimeContext)
with open("tests/wf/scatter2_subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
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",
"size": 0
},
"sleeptime": 5
-}''')])
+}'''))])
# The test passes no builder.resources
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
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"]]
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), runtimeContext)
- it.next().run(runtimeContext)
- it.next().run(runtimeContext)
+
+ next(it).run(runtimeContext)
+ next(it).run(runtimeContext)
with open("tests/wf/echo-subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
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')