+# 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"
+ },
+ "99999999999999999999999999999994+99": {
+ "uuid": "",
+ "portable_data_hash": "99999999999999999999999999999994+99",
+ "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
+ }
+ }
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',
+ "size": 16
+ }},
'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'
+ }
]}},
'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',
+ "size": 16
+ },
'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'
+ }
]}
},
'kind': 'json'
'vcpus': 1,
'ram': 1024*1024*1024
},
- "properties": {}
+ 'use_existing': True,
+ 'properties': {}
}
stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
+ expect_pipeline["properties"] = {"run_options": {"enable_job_reuse": False}}
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
logging.exception("")
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']
+ 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']
+ expect_container["use_existing"] = False
+
+ 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_reuse_disabled_by_workflow(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+
+ 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']
+ expect_container["use_existing"] = False
+ expect_container["name"] = "submit_wf_no_reuse.cwl"
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+ {
+ "class": "http://arvados.org/cwl#ReuseRequirement",
+ "enableReuse": False,
+ },
+ ]
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=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"
'vcpus': 1,
'ram': 1073741824
},
- "properties": {}
+ 'use_existing': True,
+ 'properties': {}
}
stubs.api.container_requests().create.assert_called_with(
'vcpus': 1,
'ram': 1073741824
},
- "properties": {
+ 'use_existing': True,
+ 'properties': {
"template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
}
}
stubs.expect_container_request_uuid + '\n')
+ @stubs
+ def test_submit_container_project(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
+ "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["owner_uuid"] = project_uuid
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=continue', '--project-uuid='+project_uuid,
+ '/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_job_runner_image(self, stubs):
capture_stdout = cStringIO.StringIO()
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": {
projects / arvados.git / blobdiff