+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import copy
import cStringIO
import functools
import arvados_cwl.runner
import arvados.keep
-from .matcher import JsonDiffMatcher
+from .matcher import JsonDiffMatcher, StripYAMLComments
from .mock_discovery import get_rootDesc
import ruamel.yaml as yaml
if uuid in (v["uuid"], v["portable_data_hash"]):
return CollectionExecute(v)
- created_collections = {}
+ created_collections = {
+ "99999999999999999999999999999998+99": {
+ "uuid": "",
+ "portable_data_hash": "99999999999999999999999999999998+99",
+ "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
+ }}
stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
'script_parameters': {
'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
- 'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'}},
+ 'x': {"value": {
+ 'basename': 'blorp.txt',
+ 'class': 'File',
+ 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+ "nameext": ".txt",
+ "nameroot": "blorp"
+ }},
'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
'listing': [
- {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+ {
+ 'basename': 'renamed.txt',
+ 'class': 'File', 'location':
+ 'keep:99999999999999999999999999999998+99/file1.txt',
+ "nameext": ".txt",
+ "nameroot": "renamed"
+ }
]}},
'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
'arv:enable_reuse': True,
'/var/lib/cwl/cwl.input.json': {
'kind': 'json',
'content': {
- 'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
- 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'},
+ 'y': {
+ 'basename': '99999999999999999999999999999998+99',
+ 'location': 'keep:99999999999999999999999999999998+99',
+ 'class': 'Directory'},
+ 'x': {
+ 'basename': u'blorp.txt',
+ 'class': 'File',
+ 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+ "nameext": ".txt",
+ "nameroot": "blorp"
+ },
'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
- {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+ {'basename': 'renamed.txt',
+ 'class': 'File',
+ 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
+ "nameext": ".txt",
+ "nameroot": "renamed"
+ }
]}
},
'kind': 'json'
class TestCreateWorkflow(unittest.TestCase):
existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
- expect_workflow = open("tests/wf/expect_packed.cwl").read()
+ expect_workflow = StripYAMLComments(
+ open("tests/wf/expect_packed.cwl").read())
@stubs
def test_create(self, stubs):
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- expect_workflow = open("tests/collection_per_tool/collection_per_tool_packed.cwl").read()
+ toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
+ expect_workflow = StripYAMLComments(open(toolfile).read())
body = {
"workflow": {