-import unittest
+import copy
+import cStringIO
+import functools
+import hashlib
+import json
+import logging
import mock
-import arvados_cwl
import sys
+import unittest
+
import arvados
-import arvados.keep
import arvados.collection
-import hashlib
+import arvados_cwl
+import arvados.keep
-class TestSubmit(unittest.TestCase):
+from .matcher import JsonDiffMatcher
+
+
+def stubs(func):
+ @functools.wraps(func)
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
@mock.patch("arvados.collection.KeepClient")
@mock.patch("arvados.events.subscribe")
- def test_submit(self, events, keep, keepdocker):
- api = mock.MagicMock()
+ def wrapped(self, events, keep_client, keepdocker, *args, **kwargs):
+ class Stubs:
+ pass
+ stubs = Stubs()
+ stubs.events = events
+ stubs.keepdocker = keepdocker
+ stubs.keep_client = keep_client
+
def putstub(p, **kwargs):
return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
- keep().put.side_effect = putstub
- keepdocker.return_value = True
- api.users().current().execute.return_value = {"uuid": "zzzzz-tpzed-zzzzzzzzzzzzzzz"}
- api.collections().list().execute.return_value = {"items": []}
- api.collections().create().execute.side_effect = ({"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
- "portable_data_hash": "99999999999999999999999999999991+99"},
- {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
- "portable_data_hash": "99999999999999999999999999999992+99"})
- api.jobs().create().execute.return_value = {"uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", "state": "Queued"}
-
- arvados_cwl.main(["--debug", "--submit", "--no-wait", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdout, sys.stderr, api_client=api)
-
- api.collections().create.assert_has_calls([
+ 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,
+ }
+ 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"}
+
+ stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ stubs.api.jobs().create().execute.return_value = {
+ "uuid": stubs.expect_job_uuid,
+ "state": "Queued",
+ }
+
+ stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+ stubs.api.container_requests().create().execute.return_value = {
+ "uuid": stubs.expect_container_request_uuid,
+ "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
+ "state": "Queued"
+ }
+
+ stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
+ stubs.api.pipeline_templates().create().execute.return_value = {
+ "uuid": stubs.expect_pipeline_template_uuid,
+ }
+ stubs.expect_job_spec = {
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs'
+ },
+ 'script_parameters': {
+ 'x': {
+ 'basename': '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'
+ },
+ 'repository': 'arvados',
+ '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,
+ 'mounts': {
+ '/var/spool/cwl': {
+ 'writable': True,
+ 'kind': 'collection'
+ },
+ '/var/lib/cwl/workflow': {
+ 'portable_data_hash': '99999999999999999999999999999991+99',
+ 'kind': 'collection'
+ },
+ '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'
+ }
+ },
+ 'state': 'Committed',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
+ 'name': 'submit_wf.cwl',
+ 'container_image': '99999999999999999999999999999993+99',
+ 'output_path': '/var/spool/cwl',
+ 'cwd': '/var/spool/cwl',
+ 'runtime_constraints': {
+ 'API': True,
+ 'vcpus': 1,
+ 'ram': 268435456
+ }
+ }
+
+ stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
+ stubs.api.workflows().create().execute.return_value = {
+ "uuid": stubs.expect_workflow_uuid,
+ }
+
+ return func(self, stubs, *args, **kwargs)
+ return wrapped
+
+
+class TestSubmit(unittest.TestCase):
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit(self, stubs, tm):
+ capture_stdout = cStringIO.StringIO()
+ exited = arvados_cwl.main(
+ ["--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)
+
+ stubs.api.collections().create.assert_has_calls([
mock.call(),
- mock.call(body={'manifest_text': './tool b0fa9cffda3d37ba401bc338bb0b54a6+257 0:16:blub.txt 16:241:submit_tool.cwl\n./wf 888e237b758adf86ca66c36f7bd88a24+175 0:175:submit_wf.cwl\n',
+ mock.call(body={
+ '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': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ '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',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
- 'name': 'submit_wf.cwl'
- }, ensure_unique_name=True),
+ 'replication_desired': None,
+ 'name': 'New collection'
+ }, ensure_unique_name=True),
+ mock.call().execute(num_retries=4),
+ mock.call(body={
+ 'manifest_text':
+ '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': '#',
+ }, ensure_unique_name=True),
+ mock.call().execute()])
+
+ 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_pipeline_uuid + '\n')
+
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_with_project_uuid(self, stubs, tm):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait",
+ "--project-uuid", project_uuid,
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ 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()
+ 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(),
+ mock.call(body={
+ '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': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': 'submit_wf.cwl',
+ }, ensure_unique_name=True),
mock.call().execute(),
- mock.call(body={'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
+ mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
+ '0:0:blub.txt 0:0:submit_tool.cwl\n',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
- 'name': '#'
- }, ensure_unique_name=True),
+ 'name': 'New collection',
+ 'replication_desired': None,
+ }, ensure_unique_name=True),
+ mock.call().execute(num_retries=4),
+ mock.call(body={
+ 'manifest_text':
+ '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': '#',
+ }, ensure_unique_name=True),
mock.call().execute()])
- api.jobs().create.assert_called_with(
- body={
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["owner_uuid"] = stubs.fake_user_uuid
+ stubs.api.container_requests().create.assert_called_with(
+ body=expect_container)
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+
+class TestCreateTemplate(unittest.TestCase):
+ @stubs
+ def test_create(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-template", "--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)
+
+ stubs.api.pipeline_instances().create.refute_called()
+ stubs.api.jobs().create.refute_called()
+
+ expect_component = copy.deepcopy(stubs.expect_job_spec)
+ expect_component['script_parameters']['x'] = {
+ 'dataclass': 'File',
+ 'required': True,
+ '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,
+ },
+ "name": "submit_wf.cwl",
+ "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')
+
+
+class TestCreateWorkflow(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)
+
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
+
+ with open("tests/wf/expect_packed.cwl") as f:
+ expect_workflow = f.read()
+
+ body = {
+ "workflow": {
+ "owner_uuid": project_uuid,
+ "name": "submit_wf.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": {
+ "inputs_test.cwl": {
'runtime_constraints': {
- 'docker_image': 'arvados/jobs'
+ 'docker_image': 'arvados/jobs',
},
- 'script_parameters': {
- 'x': {
- 'path': '99999999999999999999999999999992+99/blorp.txt',
- 'class': 'File'
+ 'script_parameters': {
+ 'cwl:tool':
+ '99999999999999999999999999999991+99/'
+ 'wf/inputs_test.cwl',
+ 'optionalFloatInput': None,
+ 'fileInput': {
+ 'type': 'File',
+ 'dataclass': 'File',
+ 'required': True,
+ 'title': "It's a file; we expect to find some characters in it.",
+ 'description': 'If there were anything further to say, it would be said here,\nor here.'
+ },
+ 'floatInput': {
+ 'type': 'float',
+ 'dataclass': 'number',
+ 'required': True,
+ 'title': 'Floats like a duck',
+ 'default': 0.1,
+ 'value': 0.1,
+ },
+ 'optionalFloatInput': {
+ 'type': ['null', 'float'],
+ 'dataclass': 'number',
+ 'required': False,
+ },
+ 'boolInput': {
+ 'type': 'boolean',
+ 'dataclass': 'boolean',
+ 'required': True,
+ 'title': 'True or false?',
+ },
},
- 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl'
- },
- 'repository': 'arvados',
+ 'repository': 'arvados',
'script_version': 'master',
- 'script': 'cwl-runner'
+ 'script': 'cwl-runner',
},
- find_or_create=True)
+ },
+ "name": "inputs_test.cwl",
+ }
+
+ @stubs
+ def test_inputs_empty(self, stubs):
+ exited = arvados_cwl.main(
+ ["--create-template", "--no-wait",
+ "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
+ cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ expect_template = copy.deepcopy(self.expect_template)
+ expect_template["owner_uuid"] = stubs.fake_user_uuid
+
+ stubs.api.pipeline_templates().create.assert_called_with(
+ body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+
+ @stubs
+ def test_inputs(self, stubs):
+ exited = arvados_cwl.main(
+ ["--create-template", "--no-wait",
+ "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
+ cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ self.expect_template["owner_uuid"] = stubs.fake_user_uuid
+
+ expect_template = copy.deepcopy(self.expect_template)
+ expect_template["owner_uuid"] = stubs.fake_user_uuid
+ params = expect_template[
+ "components"]["inputs_test.cwl"]["script_parameters"]
+ params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
+ params["floatInput"]["value"] = 1.234
+ params["boolInput"]["value"] = True
+
+ stubs.api.pipeline_templates().create.assert_called_with(
+ body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
projects / arvados.git / blobdiff