+# 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
+
_rootDesc = None
def stubs(func):
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:99999999999999999999999999999994+99/blorp.txt',
+ 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
'class': 'File'
},
'y': {
}],
'class': 'Directory'
},
- 'cwl:tool':
- '99999999999999999999999999999991+99/wf/submit_wf.cwl'
+ 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main'
},
'repository': 'arvados',
- 'script_version': arvados_cwl.__version__,
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
'script': 'cwl-runner'
}
stubs.pipeline_component = stubs.expect_job_spec.copy()
'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:99999999999999999999999999999994+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': '99999999999999999999999999999991+99/wf/submit_wf.cwl',
- 'arv:enable_reuse': True
+ 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
+ 'arv:enable_reuse': True,
+ 'arv:on_error': 'continue'
},
'repository': 'arvados',
- 'script_version': arvados_cwl.__version__,
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
'script': 'cwl-runner',
'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
}
stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
+ with open("tests/wf/submit_wf_packed.cwl") as f:
+ expect_packed_workflow = yaml.round_trip_load(f)
+
stubs.expect_container_spec = {
'priority': 1,
'mounts': {
'writable': True,
'kind': 'collection'
},
- '/var/lib/cwl/workflow': {
- 'portable_data_hash': '99999999999999999999999999999991+99',
- 'kind': 'collection'
+ '/var/lib/cwl/workflow.json': {
+ 'content': expect_packed_workflow,
+ 'kind': 'json'
},
'stdout': {
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json',
- 'kind': 'collection'
+ '/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'},
+ 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
+ {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+ ]}
+ },
+ 'kind': 'json'
}
},
'state': 'Committed',
'owner_uuid': None,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'name': 'submit_wf.cwl',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'output_path': '/var/spool/cwl',
'API': True,
'vcpus': 1,
'ram': 1024*1024*1024
- }
+ },
+ "properties": {}
}
stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
class TestSubmit(unittest.TestCase):
+ @mock.patch("arvados_cwl.runner.arv_docker_get_image")
@mock.patch("time.sleep")
@stubs
- def test_submit(self, stubs, tm):
+ def test_submit(self, stubs, tm, arvdock):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug",
+ ["--submit", "--no-wait", "--api=jobs", "--debug",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.collections().create.assert_has_calls([
- mock.call(),
- mock.call(body={
+ mock.call(body=JsonDiffMatcher({
'manifest_text':
- './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
- '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
- 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
- 'owner_uuid': None,
- 'name': 'submit_wf.cwl',
- }, ensure_unique_name=True),
- mock.call().execute(),
- mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
- '0:0:blub.txt 0:0:submit_tool.cwl\n',
- 'replication_desired': None,
- 'name': 'New collection'
- }, ensure_unique_name=True),
- mock.call().execute(num_retries=4),
- mock.call(body={
+ '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
+ 'replication_desired': None,
+ 'name': 'submit_tool.cwl dependencies',
+ }), ensure_unique_name=True),
+ mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': None,
- 'name': '#',
- }, ensure_unique_name=True),
- mock.call().execute()])
+ 'replication_desired': None,
+ 'name': 'submit_wf.cwl input',
+ }), ensure_unique_name=True),
+ 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),
+ mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
+ ])
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
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')
def test_submit_no_reuse(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--disable-reuse",
+ ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
+ expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
+
+ stubs.api.pipeline_instances().create.assert_called_with(
+ body=JsonDiffMatcher(expect_pipeline))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_pipeline_uuid + '\n')
+
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_on_error(self, stubs, tm):
+ capture_stdout = cStringIO.StringIO()
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
+
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')
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
-
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
+
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')
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
+ expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
+
+ stubs.api.pipeline_instances().create.assert_called_with(
+ body=JsonDiffMatcher(expect_pipeline))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_pipeline_uuid + '\n')
+
+
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_pipeline_name(self, stubs, tm):
+ capture_stdout = cStringIO.StringIO()
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--debug", "--name=hello job 123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ 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')
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
-
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
+
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')
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["owner_uuid"] = project_uuid
stubs.api.pipeline_instances().create.assert_called_with(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
@stubs
def test_submit_container(self, stubs):
logging.exception("")
stubs.api.collections().create.assert_has_calls([
- mock.call(),
- mock.call(body={
+ mock.call(body=JsonDiffMatcher({
'manifest_text':
- './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
- '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
- 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
- 'owner_uuid': None,
- 'name': 'submit_wf.cwl',
- }, ensure_unique_name=True),
- mock.call().execute(),
- mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
- '0:0:blub.txt 0:0:submit_tool.cwl\n',
- 'name': 'New collection',
- 'replication_desired': None,
- }, ensure_unique_name=True),
- mock.call().execute(num_retries=4),
- mock.call(body={
+ '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
+ 'replication_desired': None,
+ 'name': 'submit_tool.cwl dependencies',
+ }), ensure_unique_name=True),
+ mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': None,
- 'name': '#',
- }, ensure_unique_name=True),
- mock.call().execute()])
+ 'replication_desired': None,
+ 'name': 'submit_wf.cwl input',
+ }), ensure_unique_name=True)])
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--disable-reuse', '--on-error=continue',
+ '/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_on_error(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
+ "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=stop',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ "--output-name="+output_name, '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ expect_container["output_name"] = output_name
+
+ 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_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=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
-
expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
except:
logging.exception("")
- stubs.expect_container_spec["runtime_constraints"]["ram"] = 2048*1024*1024
-
expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["runtime_constraints"]["ram"] = 2048*1024*1024
+
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
'portable_data_hash': '99999999999999999999999999999994+99',
'kind': 'collection'
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'e5454f8ca7d5b181e21ecd45841e3373+58/cwl.input.json',
- 'kind': 'collection'}
+ '/var/lib/cwl/cwl.input.json': {
+ 'content': {
+ 'x': 'XxX'
+ },
+ 'kind': 'json'
+ }
}, 'state': 'Committed',
'owner_uuid': None,
'output_path': '/var/spool/cwl',
'name': 'expect_arvworkflow.cwl#main',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
'vcpus': 1,
'ram': 1073741824
- }
+ },
+ "properties": {}
}
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ @mock.patch("arvados.collection.CollectionReader")
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_jobs_keepref(self, stubs, tm, reader):
+ capture_stdout = cStringIO.StringIO()
+
+ with open("tests/wf/expect_arvworkflow.cwl") as f:
+ reader().open().__enter__().read.return_value = f.read()
+
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=jobs", "--debug",
+ "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
+ del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
+ del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
+ expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
+ stubs.api.pipeline_instances().create.assert_called_with(
+ body=JsonDiffMatcher(expect_pipeline))
+
@mock.patch("time.sleep")
@stubs
def test_submit_arvworkflow(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
with open("tests/wf/expect_arvworkflow.cwl") as f:
- stubs.api.workflows().get().execute.return_value = {"definition": f.read()}
+ stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
},
'/var/lib/cwl/workflow.json': {
'kind': 'json',
- 'json': {
+ 'content': {
'cwlVersion': 'v1.0',
'$graph': [
+ {
+ 'id': '#main',
+ 'inputs': [
+ {'type': 'string', 'id': '#main/x'}
+ ],
+ 'steps': [
+ {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
+ 'run': '#submit_tool.cwl',
+ 'id': '#main/step1',
+ 'out': []}
+ ],
+ 'class': 'Workflow',
+ 'outputs': []
+ },
{
'inputs': [
{
'outputs': [],
'baseCommand': 'cat',
'class': 'CommandLineTool'
- }, {
- 'id': '#main',
- 'inputs': [
- {'type': 'string', 'id': '#main/x'}
- ],
- 'steps': [
- {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
- 'run': '#submit_tool.cwl',
- 'id': '#main/step1',
- 'out': []}
- ],
- 'class': 'Workflow',
- 'outputs': []
}
]
}
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'e5454f8ca7d5b181e21ecd45841e3373+58/cwl.input.json',
- 'kind': 'collection'}
+ '/var/lib/cwl/cwl.input.json': {
+ 'content': {
+ 'x': 'XxX'
+ },
+ 'kind': 'json'
+ }
}, 'state': 'Committed',
'owner_uuid': None,
'output_path': '/var/spool/cwl',
- 'name': 'arvwf:962eh-7fd4e-gkbzl62qqtfig37#main',
+ 'name': 'a test workflow',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
'vcpus': 1,
'ram': 1073741824
+ },
+ "properties": {
+ "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
}
}
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+
+ @stubs
+ def test_submit_container_name(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
+ "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["name"] = "hello container 123"
+
+ 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_job_runner_image(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
+ "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("")
+
+ stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
+
+ expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ stubs.api.pipeline_instances().create.assert_called_with(
+ body=JsonDiffMatcher(expect_pipeline))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_pipeline_uuid + '\n')
+
+ @stubs
+ def test_submit_container_runner_image(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
+ "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("")
+
+ stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
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))
+ self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
+ arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
class TestCreateTemplate(unittest.TestCase):
- @stubs
- def test_create(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
- capture_stdout = cStringIO.StringIO()
-
- exited = arvados_cwl.main(
- ["--create-workflow", "--debug",
- "--project-uuid", project_uuid,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
- stubs.api.pipeline_instances().create.refute_called()
- stubs.api.jobs().create.refute_called()
-
- expect_component = copy.deepcopy(stubs.expect_job_spec)
+ def _adjust_script_params(self, expect_component):
expect_component['script_parameters']['x'] = {
'dataclass': 'File',
'required': True,
'type': 'File',
- 'value': '99999999999999999999999999999994+99/blorp.txt',
+ 'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
}
expect_component['script_parameters']['y'] = {
'dataclass': 'Collection',
'required': True,
'type': 'Directory',
}
+
+ @stubs
+ def test_create(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--debug",
+ "--api=jobs",
+ "--project-uuid", project_uuid,
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ stubs.api.pipeline_instances().create.refute_called()
+ stubs.api.jobs().create.refute_called()
+
+ expect_component = copy.deepcopy(stubs.expect_job_spec)
+ self._adjust_script_params(expect_component)
expect_template = {
"components": {
"submit_wf.cwl": expect_component,
stubs.expect_pipeline_template_uuid + '\n')
+ @stubs
+ def test_create_name(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--debug",
+ "--project-uuid", project_uuid,
+ "--api=jobs",
+ "--name", "testing 123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ stubs.api.pipeline_instances().create.refute_called()
+ stubs.api.jobs().create.refute_called()
+
+ expect_component = copy.deepcopy(stubs.expect_job_spec)
+ self._adjust_script_params(expect_component)
+ expect_template = {
+ "components": {
+ "testing 123": expect_component,
+ },
+ "name": "testing 123",
+ "owner_uuid": project_uuid,
+ }
+ stubs.api.pipeline_templates().create.assert_called_with(
+ body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_pipeline_template_uuid + '\n')
+
+
+ @stubs
+ def test_update_name(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--update-workflow", self.existing_template_uuid,
+ "--debug",
+ "--project-uuid", project_uuid,
+ "--api=jobs",
+ "--name", "testing 123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ stubs.api.pipeline_instances().create.refute_called()
+ stubs.api.jobs().create.refute_called()
+
+ expect_component = copy.deepcopy(stubs.expect_job_spec)
+ self._adjust_script_params(expect_component)
+ expect_template = {
+ "components": {
+ "testing 123": expect_component,
+ },
+ "name": "testing 123",
+ "owner_uuid": project_uuid,
+ }
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.pipeline_templates().update.assert_called_with(
+ body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
+
+ self.assertEqual(capture_stdout.getvalue(),
+ self.existing_template_uuid + '\n')
+
+
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.assertEqual(capture_stdout.getvalue(),
stubs.expect_workflow_uuid + '\n')
+
+ @stubs
+ def test_create_name(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--debug",
+ "--api=containers",
+ "--project-uuid", project_uuid,
+ "--name", "testing 123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
+
+ body = {
+ "workflow": {
+ "owner_uuid": project_uuid,
+ "name": "testing 123",
+ "description": "",
+ "definition": self.expect_workflow,
+ }
+ }
+ stubs.api.workflows().create.assert_called_with(
+ body=JsonDiffMatcher(body))
+
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_workflow_uuid + '\n')
+
@stubs
def test_incompatible_api(self, stubs):
capture_stderr = cStringIO.StringIO()
self.existing_workflow_uuid + '\n')
+ @stubs
+ def test_update_name(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--update-workflow", self.existing_workflow_uuid,
+ "--debug", "--name", "testing 123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ body = {
+ "workflow": {
+ "name": "testing 123",
+ "description": "",
+ "definition": self.expect_workflow,
+ }
+ }
+ stubs.api.workflows().update.assert_called_with(
+ uuid=self.existing_workflow_uuid,
+ body=JsonDiffMatcher(body))
+ self.assertEqual(capture_stdout.getvalue(),
+ 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':
- '99999999999999999999999999999991+99/'
- 'wf/inputs_test.cwl',
+ '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main',
'optionalFloatInput': None,
'fileInput': {
'type': 'File',
},
},
'repository': 'arvados',
- 'script_version': arvados_cwl.__version__,
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
'script': 'cwl-runner',
},
},
@stubs
def test_inputs_empty(self, stubs):
exited = arvados_cwl.main(
- ["--create-template", "--no-wait",
+ ["--create-template",
"tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
@stubs
def test_inputs(self, stubs):
exited = arvados_cwl.main(
- ["--create-template", "--no-wait",
+ ["--create-template",
"tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_template = copy.deepcopy(self.expect_template)
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
- params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
+ 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