+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import functools
import json
import logging
from schema_salad.ref_resolver import Loader
from schema_salad.sourceline import cmap
from .mock_discovery import get_rootDesc
-from .matcher import JsonDiffMatcher
+from .matcher import JsonDiffMatcher, StripYAMLComments
if not os.getenv('ARVADOS_DEBUG'):
logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
class TestWorkflow(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.collection.CollectionReader")
@mock.patch("arvados.collection.Collection")
@mock.patch('arvados.commands.keepdocker.list_images_in_arv')
- def test_run(self, list_images_in_arv, mockcollection):
+ def test_run(self, list_images_in_arv, mockcollection, mockcollectionreader):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
+ runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]}
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/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
- 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=JsonDiffMatcher({
mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
mockcollection().open().__enter__().write.assert_has_calls([mock.call(
'''{
+ "fileblub": {
+ "basename": "token.txt",
+ "class": "File",
+ "location": "/keep/99999999999999999999999999999999+118/token.txt"
+ },
"sleeptime": 5
}''')])