-import arvados
-import arvados.keep
-import arvados.collection
-import arvados_cwl
import copy
import cStringIO
import functools
import hashlib
+import json
+import logging
import mock
import sys
import unittest
-import json
+
+import arvados
+import arvados.collection
+import arvados_cwl
+import arvados.keep
from .matcher import JsonDiffMatcher
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
@mock.patch("arvados.collection.KeepClient")
@mock.patch("arvados.events.subscribe")
- def wrapped(self, events, KeepClient, keepdocker, *args, **kwargs):
+ def wrapped(self, events, keep_client, keepdocker, *args, **kwargs):
class Stubs:
pass
stubs = Stubs()
stubs.events = events
- stubs.KeepClient = KeepClient
stubs.keepdocker = keepdocker
+ stubs.keep_client = keep_client
def putstub(p, **kwargs):
return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
- stubs.KeepClient().put.side_effect = putstub
+ stubs.keep_client().put.side_effect = putstub
+ stubs.keep_client.put.side_effect = putstub
stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
+
stubs.api = mock.MagicMock()
+ stubs.api._rootDesc = arvados.api('v1')._rootDesc
stubs.api.users().current().execute.return_value = {
"uuid": stubs.fake_user_uuid,
}
"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"}
'script_parameters': {
'x': {
'basename': 'blorp.txt',
- 'location': '99999999999999999999999999999994+99/blorp.txt',
+ 'location': 'keep:99999999999999999999999999999994+99/blorp.txt',
'class': 'File'
},
+ 'y': {
+ 'basename': '99999999999999999999999999999998+99',
+ 'location': 'keep:99999999999999999999999999999998+99',
+ 'class': 'Directory'
+ },
+ 'z': {
+ 'basename': 'anonymous',
+ "listing": [{
+ "basename": "renamed.txt",
+ "class": "File",
+ "location": "keep:99999999999999999999999999999998+99/file1.txt"
+ }],
+ 'class': 'Directory'
+ },
'cwl:tool':
'99999999999999999999999999999991+99/wf/submit_wf.cwl'
},
'script_version': 'master',
'script': 'cwl-runner'
}
+ stubs.pipeline_component = stubs.expect_job_spec.copy()
+ stubs.expect_pipeline_instance = {
+ 'name': 'submit_wf.cwl',
+ 'state': 'RunningOnServer',
+ "components": {
+ "cwl-runner": {
+ 'runtime_constraints': {'docker_image': 'arvados/jobs'},
+ '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'}},
+ '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'
+ },
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'cwl-runner'
+ }
+ }
+ }
+ stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
+ stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
+ stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
+ stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
+ stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
+ "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
+ "state": "Queued"
+ }
+ stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
+ stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
stubs.expect_container_spec = {
'priority': 1,
'kind': 'file'
},
'/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': '765fda0d9897729ff467a4609879c00a+60/cwl.input.json',
+ 'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json',
'kind': 'collection'
}
},
class TestSubmit(unittest.TestCase):
+ @mock.patch("time.sleep")
@stubs
- def test_submit(self, stubs):
+ def test_submit(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--submit", "--no-wait",
+ ["--submit", "--no-wait", "--debug",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
'manifest_text':
'./tool d51232d96b6116d964a69bfb7e0c73bf+450 '
'0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
- '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
+ 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
'name': 'submit_wf.cwl',
}, ensure_unique_name=True),
mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
'0:0:blub.txt 0:0:submit_tool.cwl\n',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'replication_desired': None,
'name': 'New collection'
}, ensure_unique_name=True),
mock.call().execute(num_retries=4),
}, ensure_unique_name=True),
mock.call().execute()])
- expect_job = copy.deepcopy(stubs.expect_job_spec)
- expect_job["owner_uuid"] = stubs.fake_user_uuid
- stubs.api.jobs().create.assert_called_with(
- body=expect_job,
- find_or_create=True)
+ expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["owner_uuid"] = stubs.fake_user_uuid
+ stubs.api.pipeline_instances().create.assert_called_with(
+ body=expect_pipeline)
self.assertEqual(capture_stdout.getvalue(),
- stubs.expect_job_uuid + '\n')
+ stubs.expect_pipeline_uuid + '\n')
+ @mock.patch("time.sleep")
@stubs
- def test_submit_with_project_uuid(self, stubs):
+ def test_submit_with_project_uuid(self, stubs, tm):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
exited = arvados_cwl.main(
sys.stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- expect_body = copy.deepcopy(stubs.expect_job_spec)
- expect_body["owner_uuid"] = project_uuid
- stubs.api.jobs().create.assert_called_with(
- body=expect_body,
- find_or_create=True)
+ 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)
@stubs
def test_submit_container(self, stubs):
capture_stdout = cStringIO.StringIO()
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "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.api.collections().create.assert_has_calls([
mock.call(),
'manifest_text':
'./tool d51232d96b6116d964a69bfb7e0c73bf+450 '
'0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
- '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
+ 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
'name': 'submit_wf.cwl',
}, ensure_unique_name=True),
'0:0:blub.txt 0:0:submit_tool.cwl\n',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
'name': 'New collection',
+ 'replication_desired': None,
}, ensure_unique_name=True),
mock.call().execute(num_retries=4),
mock.call(body={
'type': 'File',
'value': '99999999999999999999999999999994+99/blorp.txt',
}
+ expect_component['script_parameters']['y'] = {
+ 'dataclass': 'Collection',
+ 'required': True,
+ 'type': 'Directory',
+ 'value': '99999999999999999999999999999998+99',
+ }
+ expect_component['script_parameters']['z'] = {
+ 'dataclass': 'Collection',
+ 'required': True,
+ 'type': 'Directory',
+ }
expect_template = {
"components": {
"submit_wf.cwl": expect_component,
"owner_uuid": project_uuid,
"name": "submit_wf.cwl",
"description": "",
- "workflow": expect_workflow
+ "definition": expect_workflow
}
}
stubs.api.workflows().create.assert_called_with(
projects / arvados.git / blobdiff