+# 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
stubs.events = events
stubs.keepdocker = keepdocker
-
def putstub(p, **kwargs):
return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
keep_client1().put.side_effect = putstub
"uuid": stubs.fake_user_uuid,
}
stubs.api.collections().list().execute.return_value = {"items": []}
- stubs.api.collections().create().execute.side_effect = ({
- "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
- "portable_data_hash": "99999999999999999999999999999991+99",
- "manifest_text": ""
- }, {
- "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
- "portable_data_hash": "99999999999999999999999999999992+99",
- "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"
- },
- {
- "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4",
- "portable_data_hash": "99999999999999999999999999999994+99",
- "manifest_text": ""
- },
- {
- "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz5",
- "portable_data_hash": "99999999999999999999999999999995+99",
- "manifest_text": ""
- },
- {
- "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz6",
- "portable_data_hash": "99999999999999999999999999999996+99",
- "manifest_text": ""
- }
- )
- stubs.api.collections().get().execute.return_value = {
- "portable_data_hash": "99999999999999999999999999999993+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"}
+
+ class CollectionExecute(object):
+ def __init__(self, exe):
+ self.exe = exe
+ def execute(self, num_retries=None):
+ return self.exe
+
+ def collection_createstub(created_collections, body, ensure_unique_name=None):
+ mt = body["manifest_text"]
+ uuid = "zzzzz-4zz18-zzzzzzzzzzzzzz%d" % len(created_collections)
+ pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
+ created_collections[uuid] = {
+ "uuid": uuid,
+ "portable_data_hash": pdh,
+ "manifest_text": mt
+ }
+ return CollectionExecute(created_collections[uuid])
+
+ def collection_getstub(created_collections, uuid):
+ for v in created_collections.itervalues():
+ if uuid in (v["uuid"], v["portable_data_hash"]):
+ return CollectionExecute(v)
+
+ created_collections = {}
+ stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
+ stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
stubs.api.jobs().create().execute.return_value = {
'script_parameters': {
'x': {
'basename': 'blorp.txt',
- 'location': 'keep:99999999999999999999999999999992+99/blorp.txt',
+ 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
'class': 'File'
},
'y': {
}],
'class': 'Directory'
},
- 'cwl:tool':
- '99999999999999999999999999999994+99/workflow.cwl#main'
+ 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main'
},
'repository': 'arvados',
'script_version': 'master',
'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:99999999999999999999999999999992+99/blorp.txt'}},
+ 'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'}},
'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
'listing': [
{'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
]}},
- 'cwl:tool': '99999999999999999999999999999994+99/workflow.cwl#main',
+ 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
'arv:enable_reuse': True,
'arv:on_error': 'continue'
},
'kind': 'json',
'content': {
'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
- 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:99999999999999999999999999999992+99/blorp.txt'},
+ 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'},
'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
{'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
]}
self.assertEqual(exited, 0)
stubs.api.collections().create.assert_has_calls([
- mock.call(),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
- 'owner_uuid': None,
+ 'replication_desired': None,
'name': 'submit_tool.cwl dependencies',
}), ensure_unique_name=True),
- mock.call().execute(),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': None,
+ 'replication_desired': None,
'name': 'submit_wf.cwl input',
}), ensure_unique_name=True),
- mock.call().execute()])
+ mock.call(body=JsonDiffMatcher({
+ 'manifest_text':
+ '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n',
+ 'replication_desired': None,
+ 'name': 'submit_wf.cwl',
+ }), ensure_unique_name=True) ])
arvdock.assert_has_calls([
mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
expect_pipeline["name"] = "hello job 123"
stubs.api.pipeline_instances().create.assert_called_with(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
logging.exception("")
stubs.api.collections().create.assert_has_calls([
- mock.call(),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
- 'owner_uuid': None,
+ 'replication_desired': None,
'name': 'submit_tool.cwl dependencies',
}), ensure_unique_name=True),
- mock.call().execute(),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': None,
+ 'replication_desired': None,
'name': 'submit_wf.cwl input',
- }), ensure_unique_name=True),
- mock.call().execute()])
+ }), ensure_unique_name=True)])
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+
+ @stubs
+ def test_submit_container_output_ttl(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=continue',
+ "--intermediate-output-ttl=3600",
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+ @stubs
+ def test_submit_container_trash_intermediate(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=continue',
+ "--trash-intermediate",
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
@stubs
def test_submit_container_output_tags(self, stubs):
output_tags = "tag0,tag1,tag2"
arvrunner.project_uuid = ""
api.return_value = mock.MagicMock()
arvrunner.api = api.return_value
- arvrunner.api.links().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0},
- {"items": [], "items_available": 0, "offset": 0},
- {"items": [], "items_available": 0, "offset": 0},
- {"items": [{"created_at": "",
- "head_uuid": "",
- "link_class": "docker_image_hash",
- "name": "123456",
- "owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
- {"items": [], "items_available": 0, "offset": 0},
- {"items": [{"created_at": "",
- "head_uuid": "",
+ arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
+ "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
"link_class": "docker_image_repo+tag",
"name": "arvados/jobs:"+arvados_cwl.__version__,
"owner_uuid": "",
"link_class": "docker_image_hash",
"name": "123456",
"owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0} ,
+ "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
)
find_one_image_hash.return_value = "123456"
- arvrunner.api.collections().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0},
- {"items": [{"uuid": "",
+ arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
"owner_uuid": "",
"manifest_text": "",
"properties": ""
- }], "items_available": 1, "offset": 0},
- {"items": [{"uuid": ""}], "items_available": 1, "offset": 0})
+ }], "items_available": 1, "offset": 0},)
arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
- self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
+ self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
+ arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
class TestCreateTemplate(unittest.TestCase):
existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
'dataclass': 'File',
'required': True,
'type': 'File',
- 'value': '99999999999999999999999999999992+99/blorp.txt',
+ 'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
}
expect_component['script_parameters']['y'] = {
'dataclass': 'Collection',
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):
self.existing_workflow_uuid + '\n')
+ @stubs
+ def test_create_collection_per_tool(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--debug",
+ "--api=containers",
+ "--project-uuid", project_uuid,
+ "tests/collection_per_tool/collection_per_tool.cwl"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
+ expect_workflow = StripYAMLComments(open(toolfile).read())
+
+ body = {
+ "workflow": {
+ "owner_uuid": project_uuid,
+ "name": "collection_per_tool.cwl",
+ "description": "",
+ "definition": expect_workflow,
+ }
+ }
+ stubs.api.workflows().create.assert_called_with(
+ body=JsonDiffMatcher(body))
+
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_workflow_uuid + '\n')
+
class TestTemplateInputs(unittest.TestCase):
expect_template = {
"components": {
},
'script_parameters': {
'cwl:tool':
- '99999999999999999999999999999992+99/workflow.cwl#main',
+ '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main',
'optionalFloatInput': None,
'fileInput': {
'type': 'File',
expect_template = copy.deepcopy(self.expect_template)
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
- params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt'
- params["cwl:tool"] = '99999999999999999999999999999994+99/workflow.cwl#main'
+ params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
+ params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main'
params["floatInput"]["value"] = 1.234
params["boolInput"]["value"] = True
projects / arvados.git / blobdiff