# Copyright (C) The Arvados Authors. All rights reserved. # # SPDX-License-Identifier: Apache-2.0 from future import standard_library standard_library.install_aliases() from builtins import object from builtins import str from future.utils import viewvalues import copy import io import functools import hashlib import json import logging import mock import sys import unittest import cwltool.process import re from io import BytesIO # StringIO.StringIO and io.StringIO have different behavior write() is # called with both python2 (byte) strings and unicode strings # (specifically there's some logging in cwltool that causes trouble). # This isn't a problem on python3 because all string are unicode. if sys.version_info[0] < 3: from StringIO import StringIO else: from io import StringIO import arvados import arvados.collection import arvados_cwl import arvados_cwl.executor import arvados_cwl.runner import arvados.keep from .matcher import JsonDiffMatcher, StripYAMLComments from .mock_discovery import get_rootDesc import ruamel.yaml as yaml _rootDesc = None def stubs(func): @functools.wraps(func) @mock.patch("arvados.commands.keepdocker.list_images_in_arv") @mock.patch("arvados.collection.KeepClient") @mock.patch("arvados.keep.KeepClient") @mock.patch("arvados.events.subscribe") def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs): class Stubs(object): pass stubs = Stubs() 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 keep_client1.put.side_effect = putstub keep_client2().put.side_effect = putstub keep_client2.put.side_effect = putstub stubs.keep_client = keep_client2 stubs.docker_images = { "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")], "debian:buster-slim": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")], "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")], "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")], } def kd(a, b, image_name=None, image_tag=None): return stubs.docker_images.get("%s:%s" % (image_name, image_tag), []) stubs.keepdocker.side_effect = kd stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz" stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz" if sys.version_info[0] < 3: stubs.capture_stdout = BytesIO() else: stubs.capture_stdout = StringIO() stubs.api = mock.MagicMock() stubs.api._rootDesc = get_rootDesc() stubs.api._rootDesc["uuidPrefix"] = "zzzzz" stubs.api.users().current().execute.return_value = { "uuid": stubs.fake_user_uuid, } stubs.api.collections().list().execute.return_value = {"items": []} stubs.api.containers().current().execute.return_value = { "uuid": stubs.fake_container_uuid, } stubs.api.config()["StorageClasses"].items.return_value = { "default": { "Default": True } }.items() 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"].encode('utf-8') uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%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.decode('utf-8') } return CollectionExecute(created_collections[uuid]) def collection_getstub(created_collections, uuid): for v in viewvalues(created_collections): if uuid in (v["uuid"], v["portable_data_hash"]): return CollectionExecute(v) created_collections = { "99999999999999999999999999999998+99": { "uuid": "", "portable_data_hash": "99999999999999999999999999999998+99", "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt" }, "99999999999999999999999999999997+99": { "uuid": "", "portable_data_hash": "99999999999999999999999999999997+99", "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt" }, "99999999999999999999999999999994+99": { "uuid": "", "portable_data_hash": "99999999999999999999999999999994+99", "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl" }, "zzzzz-4zz18-zzzzzzzzzzzzzd3": { "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd3", "portable_data_hash": "999999999999999999999999999999d3+99", "manifest_text": "" }, "zzzzz-4zz18-zzzzzzzzzzzzzd4": { "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd4", "portable_data_hash": "999999999999999999999999999999d4+99", "manifest_text": "" }, "zzzzz-4zz18-zzzzzzzzzzzzzd5": { "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd5", "portable_data_hash": "999999999999999999999999999999d5+99", "manifest_text": "" }, "zzzzz-4zz18-zzzzzzzzzzzzzd6": { "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd6", "portable_data_hash": "999999999999999999999999999999d6+99", "manifest_text": "" } } 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 = { "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': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024 }, 'script_parameters': { 'x': { 'basename': 'blorp.txt', 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/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", "size": 0 }], 'class': 'Directory' }, 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main' }, 'repository': 'arvados', 'script_version': 'master', 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner' } stubs.pipeline_component = stubs.expect_job_spec.copy() stubs.expect_pipeline_instance = { 'name': 'submit_wf.cwl', 'state': 'RunningOnServer', 'owner_uuid': None, "components": { "cwl-runner": { 'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', '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', "size": 16 }}, 'z': {"value": {'basename': 'anonymous', 'class': 'Directory', 'listing': [ { 'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt', 'size': 0 } ]}}, 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main', 'arv:debug': True, 'arv:enable_reuse': True, 'arv:on_error': 'continue' }, 'repository': 'arvados', 'script_version': 'master', 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner', 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'} } } } 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 with open("tests/wf/submit_wf_packed.cwl") as f: expect_packed_workflow = yaml.round_trip_load(f) stubs.expect_container_spec = { 'priority': 500, 'mounts': { '/var/spool/cwl': { 'writable': True, '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/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', "size": 16 }, 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [ {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt', 'size': 0 } ]} }, 'kind': 'json' } }, 'secret_mounts': {}, 'state': 'Committed', 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], 'name': 'submit_wf.cwl', 'container_image': '999999999999999999999999999999d3+99', 'output_path': '/var/spool/cwl', 'cwd': '/var/spool/cwl', 'runtime_constraints': { 'API': True, 'vcpus': 1, 'ram': (1024+256)*1024*1024 }, 'use_existing': False, 'properties': {}, 'secret_mounts': {} } stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz" stubs.api.workflows().create().execute.return_value = { "uuid": stubs.expect_workflow_uuid, } def update_mock(**kwargs): stubs.updated_uuid = kwargs.get('uuid') return mock.DEFAULT stubs.api.workflows().update.side_effect = update_mock stubs.api.workflows().update().execute.side_effect = lambda **kwargs: { "uuid": stubs.updated_uuid, } return func(self, stubs, *args, **kwargs) return wrapped class TestSubmit(unittest.TestCase): def setUp(self): cwltool.process._names = set() arvados_cwl.arvdocker.arv_docker_clear_cache() @mock.patch("time.sleep") @stubs def test_submit_invalid_runner_ram(self, stubs, tm): exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 1) @stubs def test_submit_container(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) stubs.api.collections().create.assert_has_calls([ mock.call(body=JsonDiffMatcher({ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'replication_desired': None, 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', 'replication_desired': None, 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', }), ensure_unique_name=False), ]) expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_tool(self, stubs): # test for issue #16139 exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_no_reuse(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = [ 'arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--disable-reuse', "--collection-cache-size=256", '--debug', '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_reuse_disabled_by_workflow(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"], stubs.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-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--disable-reuse', "--collection-cache-size=256", '--debug', '--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"]["$graph"][1]["hints"] = [ { "class": "http://arvados.org/cwl#ReuseRequirement", "enableReuse": False, }, ] expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = { "arv": "http://arvados.org/cwl#", "cwltool": "http://commonwl.org/cwltool#" } stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @stubs def test_submit_container_on_error(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=stop', '/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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_output_name(self, stubs): output_name = "test_output_name" exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", "--output-name="+output_name, '--debug', '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_storage_classes(self, stubs): exited = arvados_cwl.main( ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", "--debug", "--storage-classes=foo", '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_multiple_storage_classes(self, stubs): exited = arvados_cwl.main( ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", "--debug", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @mock.patch("cwltool.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection") @stubs def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): final_output_c = arvados.collection.Collection() make_output.return_value = ({},final_output_c) def set_final_output(job_order, output_callback, runtimeContext): output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") return [] job.side_effect = set_final_output exited = arvados_cwl.main( ["--debug", "--local", "--storage-classes=foo", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') self.assertEqual(exited, 0) @mock.patch("cwltool.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection") @stubs def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): final_output_c = arvados.collection.Collection() make_output.return_value = ({},final_output_c) def set_final_output(job_order, output_callback, runtimeContext): output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") return [] job.side_effect = set_final_output exited = arvados_cwl.main( ["--debug", "--local", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') self.assertEqual(exited, 0) @mock.patch("cwltool.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection") @stubs def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq): final_output_c = arvados.collection.Collection() make_output.return_value = ({},final_output_c) def set_final_output(job_order, output_callback, runtimeContext): output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") return [] job.side_effect = set_final_output exited = arvados_cwl.main( ["--debug", "--local", "tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') self.assertEqual(exited, 0) @stubs def test_submit_container_output_ttl(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_trash_intermediate(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_output_tags(self, stubs): output_tags = "tag0,tag1,tag2" exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", "--output-tags="+output_tags, '--debug', '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_runner_ram(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024 stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @mock.patch("arvados.collection.CollectionReader") @mock.patch("time.sleep") @stubs def test_submit_file_keepref(self, stubs, tm, collectionReader): collectionReader().exists.return_value = True collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt") exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_keepref_wf.cwl"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) @mock.patch("arvados.collection.CollectionReader") @mock.patch("time.sleep") @stubs def test_submit_keepref(self, stubs, tm, reader): 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=containers", "--debug", "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) expect_container = { 'priority': 500, 'mounts': { '/var/spool/cwl': { 'writable': True, 'kind': 'collection' }, 'stdout': { 'path': '/var/spool/cwl/cwl.output.json', 'kind': 'file' }, '/var/lib/cwl/workflow': { 'portable_data_hash': '99999999999999999999999999999994+99', 'kind': 'collection' }, '/var/lib/cwl/cwl.input.json': { 'content': { 'x': 'XxX' }, 'kind': 'json' } }, 'state': 'Committed', 'output_path': '/var/spool/cwl', 'name': 'expect_arvworkflow.cwl#main', 'container_image': '999999999999999999999999999999d3+99', 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--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': 1342177280 }, 'use_existing': False, 'properties': {}, 'secret_mounts': {} } stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @mock.patch("time.sleep") @stubs def test_submit_arvworkflow(self, stubs, tm): with open("tests/wf/expect_arvworkflow.cwl") as f: stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"} exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) expect_container = { 'priority': 500, 'mounts': { '/var/spool/cwl': { 'writable': True, 'kind': 'collection' }, 'stdout': { 'path': '/var/spool/cwl/cwl.output.json', 'kind': 'file' }, '/var/lib/cwl/workflow.json': { 'kind': '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': [ { 'inputBinding': {'position': 1}, 'type': 'string', 'id': '#submit_tool.cwl/x'} ], 'requirements': [ { 'dockerPull': 'debian:buster-slim', 'class': 'DockerRequirement', "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" } ], 'id': '#submit_tool.cwl', 'outputs': [], 'baseCommand': 'cat', 'class': 'CommandLineTool' } ] } }, '/var/lib/cwl/cwl.input.json': { 'content': { 'x': 'XxX' }, 'kind': 'json' } }, 'state': 'Committed', 'output_path': '/var/spool/cwl', 'name': 'a test workflow', 'container_image': "999999999999999999999999999999d3+99", 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--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': 1342177280 }, 'use_existing': False, 'properties': { "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37" }, 'secret_mounts': {} } stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_name(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) 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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_missing_input(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 0) exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job_missing.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) @stubs def test_submit_container_project(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) 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', '--disable-validate', '--disable-color', "--eval-timeout=20", "--thread-count=0", '--enable-reuse', "--collection-cache-size=256", '--debug', '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_eval_timeout(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=60.0', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_collection_cache(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=500", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024 stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_thread_count(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=20', '--enable-reuse', "--collection-cache-size=256", '--debug', '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_runner_image(self, stubs): 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"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99" expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_priority(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) stubs.expect_container_spec["priority"] = 669 expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_wf_runner_resources(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["runtime_constraints"] = { "API": True, "vcpus": 2, "ram": (2000+512) * 2**20 } expect_container["name"] = "submit_wf_runner_resources.cwl" expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [ { "class": "http://arvados.org/cwl#WorkflowRunnerResources", "coresMin": 2, "ramMin": 2000, "keep_cache": 512 } ] expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = { "arv": "http://arvados.org/cwl#", } expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=512", '--debug', '--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(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) def tearDown(self): arvados_cwl.arvdocker.arv_docker_clear_cache() @mock.patch("arvados.commands.keepdocker.find_one_image_hash") @mock.patch("cwltool.docker.DockerCommandLineJob.get_image") @mock.patch("arvados.api") def test_arvados_jobs_image(self, api, get_image, find_one_image_hash): arvados_cwl.arvdocker.arv_docker_clear_cache() arvrunner = mock.MagicMock() arvrunner.project_uuid = "" api.return_value = mock.MagicMock() arvrunner.api = api.return_value 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": "", "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}, {"items": [{"created_at": "", "head_uuid": "", "link_class": "docker_image_hash", "name": "123456", "owner_uuid": "", "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0} ) find_one_image_hash.return_value = "123456" arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", "owner_uuid": "", "manifest_text": "", "properties": "" }], "items_available": 1, "offset": 0},) arvrunner.api.collections().create().execute.return_value = {"uuid": ""} arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", "portable_data_hash": "9999999999999999999999999999999b+99"} self.assertEqual("9999999999999999999999999999999b+99", arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__)) @stubs def test_submit_secrets(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = { "command": [ "arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps", "--disable-validate", "--disable-color", "--eval-timeout=20", '--thread-count=0', "--enable-reuse", "--collection-cache-size=256", '--debug', "--on-error=continue", "/var/lib/cwl/workflow.json#main", "/var/lib/cwl/cwl.input.json" ], "container_image": "999999999999999999999999999999d3+99", "cwd": "/var/spool/cwl", "mounts": { "/var/lib/cwl/cwl.input.json": { "content": { "pw": { "$include": "/secrets/s0" } }, "kind": "json" }, "/var/lib/cwl/workflow.json": { "content": { "$graph": [ { "$namespaces": { "cwltool": "http://commonwl.org/cwltool#" }, "arguments": [ "md5sum", "example.conf" ], "class": "CommandLineTool", "hints": [ { "class": "http://commonwl.org/cwltool#Secrets", "secrets": [ "#secret_job.cwl/pw" ] } ], "id": "#secret_job.cwl", "inputs": [ { "id": "#secret_job.cwl/pw", "type": "string" } ], "outputs": [ { "id": "#secret_job.cwl/out", "type": "File", "outputBinding": { "glob": "hashed_example.txt" } } ], "stdout": "hashed_example.txt", "requirements": [ { "class": "InitialWorkDirRequirement", "listing": [ { "entry": "username: user\npassword: $(inputs.pw)\n", "entryname": "example.conf" } ] } ] }, { "class": "Workflow", "hints": [ { "class": "DockerRequirement", "dockerPull": "debian:buster-slim", "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" }, { "class": "http://commonwl.org/cwltool#Secrets", "secrets": [ "#main/pw" ] } ], "id": "#main", "inputs": [ { "id": "#main/pw", "type": "string" } ], "outputs": [ { "id": "#main/out", "outputSource": "#main/step1/out", "type": "File" } ], "steps": [ { "id": "#main/step1", "in": [ { "id": "#main/step1/pw", "source": "#main/pw" } ], "out": [ "#main/step1/out" ], "run": "#secret_job.cwl" } ] } ], "cwlVersion": "v1.0" }, "kind": "json" }, "/var/spool/cwl": { "kind": "collection", "writable": True }, "stdout": { "kind": "file", "path": "/var/spool/cwl/cwl.output.json" } }, "name": "secret_wf.cwl", "output_path": "/var/spool/cwl", "priority": 500, "properties": {}, "runtime_constraints": { "API": True, "ram": 1342177280, "vcpus": 1 }, "secret_mounts": { "/secrets/s0": { "content": "blorp", "kind": "text" } }, "state": "Committed", "use_existing": False } stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_request_uuid(self, stubs): stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123" stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy" stubs.api.container_requests().update().execute.return_value = { "uuid": stubs.expect_container_request_uuid, "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz", "state": "Queued" } exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) stubs.api.container_requests().update.assert_called_with( uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_container_cluster_id(self, stubs): stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123" exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container), cluster_id="zbbbb") self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_validate_cluster_id(self, stubs): stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123" exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zcccc", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) @stubs def test_submit_validate_project_uuid(self, stubs): # Fails with bad cluster prefix exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzb-j7d0g-zzzzzzzzzzzzzzz", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) # Project lookup fails stubs.api.groups().get().execute.side_effect = Exception("Bad project") exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-j7d0g-zzzzzzzzzzzzzzx", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) # It should work this time because it is looking up a user (and only group is stubbed out to fail) exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-tpzed-zzzzzzzzzzzzzzx", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 0) @mock.patch("arvados.collection.CollectionReader") @stubs def test_submit_uuid_inputs(self, stubs, collectionReader): collectionReader().exists.return_value = True collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt") def list_side_effect(**kwargs): m = mock.MagicMock() if "count" in kwargs: m.execute.return_value = {"items": [ {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999998+99"} ]} else: m.execute.return_value = {"items": []} return m stubs.api.collections().list.side_effect = list_side_effect exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz' expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz' expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz' stubs.api.collections().list.assert_has_calls([ mock.call(count='none', filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz']]], select=['uuid', 'portable_data_hash'])]) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_submit_mismatched_uuid_inputs(self, stubs): def list_side_effect(**kwargs): m = mock.MagicMock() if "count" in kwargs: m.execute.return_value = {"items": [ {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999997+99"} ]} else: m.execute.return_value = {"items": []} return m stubs.api.collections().list.side_effect = list_side_effect for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"): capture_stderr = StringIO() cwltool_logger = logging.getLogger('cwltool') stderr_logger = logging.StreamHandler(capture_stderr) cwltool_logger.addHandler(stderr_logger) try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", infile], stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) self.assertRegex( re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()), r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99") finally: cwltool_logger.removeHandler(stderr_logger) @mock.patch("arvados.collection.CollectionReader") @stubs def test_submit_unknown_uuid_inputs(self, stubs, collectionReader): collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt") capture_stderr = StringIO() cwltool_logger = logging.getLogger('cwltool') stderr_logger = logging.StreamHandler(capture_stderr) cwltool_logger.addHandler(stderr_logger) exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"], stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client) try: self.assertEqual(exited, 1) self.assertRegex( capture_stderr.getvalue(), r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found") finally: cwltool_logger.removeHandler(stderr_logger) class TestCreateWorkflow(unittest.TestCase): existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml" expect_workflow = StripYAMLComments( open("tests/wf/expect_upload_packed.cwl").read().rstrip()) def setUp(self): cwltool.process._names = set() arvados_cwl.arvdocker.arv_docker_clear_cache() @stubs def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} exited = arvados_cwl.main( ["--create-workflow", "--debug", "--api=containers", "--project-uuid", project_uuid, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.pipeline_templates().create.refute_called() stubs.api.container_requests().create.refute_called() body = { "workflow": { "owner_uuid": project_uuid, "name": "submit_wf.cwl", "description": "", "definition": self.expect_workflow, } } stubs.api.workflows().create.assert_called_with( body=JsonDiffMatcher(body)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_create_name(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} 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"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) 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(stubs.capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_update(self, stubs): exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) body = { "workflow": { "name": "submit_wf.cwl", "description": "", "definition": self.expect_workflow, } } stubs.api.workflows().update.assert_called_with( uuid=self.existing_workflow_uuid, body=JsonDiffMatcher(body)) self.assertEqual(stubs.capture_stdout.getvalue(), self.existing_workflow_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_update_name(self, stubs): exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, "--debug", "--name", "testing 123", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) 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(stubs.capture_stdout.getvalue(), self.existing_workflow_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_create_collection_per_tool(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} exited = arvados_cwl.main( ["--create-workflow", "--debug", "--api=containers", "--project-uuid", project_uuid, "tests/collection_per_tool/collection_per_tool.cwl"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl" expect_workflow = StripYAMLComments(open(toolfile).read().rstrip()) 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(stubs.capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_create_with_imports(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} exited = arvados_cwl.main( ["--create-workflow", "--debug", "--api=containers", "--project-uuid", project_uuid, "tests/wf/feddemo/feddemo.cwl"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.pipeline_templates().create.refute_called() stubs.api.container_requests().create.refute_called() self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) @stubs def test_create_with_no_input(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} exited = arvados_cwl.main( ["--create-workflow", "--debug", "--api=containers", "--project-uuid", project_uuid, "tests/wf/revsort/revsort.cwl"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.pipeline_templates().create.refute_called() stubs.api.container_requests().create.refute_called() self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0)