X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f159fab8f9d6bc4254192ce43432defd5bd400aa..ac0dc6c57a2b4f736b6faf62421de56a3355db04:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 8875b7d954..5f92cee942 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -2,8 +2,14 @@ # # 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 cStringIO +import io import functools import hashlib import json @@ -12,9 +18,21 @@ import mock import sys import unittest +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 @@ -32,7 +50,7 @@ def stubs(func): @mock.patch("arvados.keep.KeepClient") @mock.patch("arvados.events.subscribe") def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs): - class Stubs: + class Stubs(object): pass stubs = Stubs() stubs.events = events @@ -46,16 +64,35 @@ def stubs(func): keep_client2.put.side_effect = putstub stubs.keep_client = keep_client2 - stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] + stubs.docker_images = { + "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")], + "debian:8": [("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, + } class CollectionExecute(object): def __init__(self, exe): @@ -64,18 +101,18 @@ def stubs(func): 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) + 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 + "manifest_text": mt.decode('utf-8') } return CollectionExecute(created_collections[uuid]) def collection_getstub(created_collections, uuid): - for v in created_collections.itervalues(): + for v in viewvalues(created_collections): if uuid in (v["uuid"], v["portable_data_hash"]): return CollectionExecute(v) @@ -85,10 +122,35 @@ def stubs(func): "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) @@ -113,7 +175,7 @@ def stubs(func): } stubs.expect_job_spec = { 'runtime_constraints': { - 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024 }, 'script_parameters': { @@ -137,7 +199,7 @@ def stubs(func): }], 'class': 'Directory' }, - 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main' + 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main' }, 'repository': 'arvados', 'script_version': 'master', @@ -151,7 +213,7 @@ def stubs(func): 'owner_uuid': None, "components": { "cwl-runner": { - 'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024}, + '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": { @@ -169,7 +231,7 @@ def stubs(func): 'size': 0 } ]}}, - 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main', + 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main', 'arv:debug': True, 'arv:enable_reuse': True, 'arv:on_error': 'continue' @@ -239,17 +301,17 @@ def stubs(func): 'state': 'Committed', 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--eval-timeout=20', '--thread-count=4', - '--enable-reuse', '--debug', '--on-error=continue', + '--eval-timeout=20', '--thread-count=1', + '--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': 'arvados/jobs:'+arvados_cwl.__version__, + 'container_image': '999999999999999999999999999999d3+99', 'output_path': '/var/spool/cwl', 'cwd': '/var/spool/cwl', 'runtime_constraints': { 'API': True, 'vcpus': 1, - 'ram': 1024*1024*1024 + 'ram': (1024+256)*1024*1024 }, 'use_existing': True, 'properties': {}, @@ -273,16 +335,21 @@ def stubs(func): class TestSubmit(unittest.TestCase): - @mock.patch("arvados_cwl.runner.arv_docker_get_image") + @mock.patch("arvados_cwl.arvdocker.arv_docker_get_image") @mock.patch("time.sleep") @stubs def test_submit(self, stubs, tm, arvdock): - capture_stdout = cStringIO.StringIO() + def get_image(api_client, dockerRequirement, pull_image, project_uuid): + if dockerRequirement["dockerPull"] == 'arvados/jobs:'+arvados_cwl.__version__: + return '999999999999999999999999999999d3+99' + elif dockerRequirement["dockerPull"] == "debian:8": + return '999999999999999999999999999999d4+99' + arvdock.side_effect = get_image + exited = arvados_cwl.main( ["--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.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.collections().create.assert_has_calls([ mock.call(body=JsonDiffMatcher({ @@ -299,32 +366,31 @@ class TestSubmit(unittest.TestCase): }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': - '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n', + ". 68089141fbf7e020ac90a9d6a575bc8f+1312 0:1312: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, {"class": "DockerRequirement", "dockerPull": "debian:8", 'http://arvados.org/cwl#dockerCollectionPDH': '999999999999999999999999999999d4+99'}, 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=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') - + self.assertEqual(exited, 0) @mock.patch("time.sleep") @stubs def test_submit_no_reuse(self, stubs, tm): - capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--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.capture_stdout, sys.stderr, api_client=stubs.api) expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False} @@ -332,8 +398,9 @@ class TestSubmit(unittest.TestCase): stubs.api.pipeline_instances().create.assert_called_with( body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') + self.assertEqual(exited, 0) @stubs def test_error_when_multiple_storage_classes_specified(self, stubs): @@ -347,49 +414,44 @@ class TestSubmit(unittest.TestCase): @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) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) 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=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') - + self.assertEqual(exited, 0) @mock.patch("time.sleep") @stubs def test_submit_runner_ram(self, stubs, tm): - capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - capture_stdout, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 0) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) 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=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') - + self.assertEqual(exited, 0) @mock.patch("time.sleep") @stubs def test_submit_invalid_runner_ram(self, stubs, tm): - capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - capture_stdout, sys.stderr, api_client=stubs.api) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 1) @mock.patch("time.sleep") @@ -397,30 +459,27 @@ class TestSubmit(unittest.TestCase): def test_submit_output_name(self, stubs, tm): output_name = "test_output_name" - capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--output-name", output_name, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - capture_stdout, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 0) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) 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(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') - + self.assertEqual(exited, 0) @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) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) @@ -428,7 +487,7 @@ class TestSubmit(unittest.TestCase): stubs.api.pipeline_instances().create.assert_called_with( body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @mock.patch("time.sleep") @@ -436,11 +495,10 @@ class TestSubmit(unittest.TestCase): def test_submit_output_tags(self, stubs, tm): output_tags = "tag0,tag1,tag2" - capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--output-tags", output_tags, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - capture_stdout, sys.stderr, api_client=stubs.api) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) @@ -448,7 +506,7 @@ class TestSubmit(unittest.TestCase): stubs.api.pipeline_instances().create.assert_called_with( body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @mock.patch("time.sleep") @@ -470,15 +528,10 @@ class TestSubmit(unittest.TestCase): @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("") + 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({ @@ -497,52 +550,47 @@ class TestSubmit(unittest.TestCase): 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(), + 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): - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse", - "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("") + 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', - '--eval-timeout=20', '--thread-count=4', - '--disable-reuse', '--debug', '--on-error=continue', + '--eval-timeout=20', '--thread-count=1', + '--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(capture_stdout.getvalue(), + 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): - 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) + 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', - '--eval-timeout=20', '--thread-count=4', - '--disable-reuse', '--debug', '--on-error=continue', + '--eval-timeout=20', '--thread-count=1', + '--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" @@ -559,90 +607,79 @@ class TestSubmit(unittest.TestCase): stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.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("") + 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', - '--eval-timeout=20', '--thread-count=4', - '--enable-reuse', '--debug', '--on-error=stop', + '--eval-timeout=20', '--thread-count=1', + '--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(capture_stdout.getvalue(), + 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" - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name, - "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("") + 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', - '--eval-timeout=20', '--thread-count=4', - '--enable-reuse', + '--eval-timeout=20', '--thread-count=1', + '--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(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + self.assertEqual(exited, 0) @stubs def test_submit_storage_classes(self, stubs): - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo", - "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("") + 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', - '--eval-timeout=20', '--thread-count=4', - '--enable-reuse', "--debug", + '--eval-timeout=20', '--thread-count=1', + '--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(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + self.assertEqual(exited, 0) @mock.patch("arvados_cwl.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") - @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None)) + @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None)) @stubs def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): def set_final_output(job_order, output_callback, runtimeContext): @@ -650,20 +687,17 @@ class TestSubmit(unittest.TestCase): return [] job.side_effect = set_final_output - try: - exited = arvados_cwl.main( - ["--debug", "--local", "--storage-classes=foo", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) - self.assertEqual(exited, 0) - except: - logging.exception("") + exited = arvados_cwl.main( + ["--debug", "--local", "--storage-classes=foo", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stdin, 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("arvados_cwl.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") - @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None)) + @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None)) @stubs def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): def set_final_output(job_order, output_callback, runtimeContext): @@ -671,141 +705,120 @@ class TestSubmit(unittest.TestCase): return [] job.side_effect = set_final_output - try: - exited = arvados_cwl.main( - ["--debug", "--local", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) - self.assertEqual(exited, 0) - except: - logging.exception("") + exited = arvados_cwl.main( + ["--debug", "--local", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stdin, 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) @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("") + 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', - '--eval-timeout=20', '--thread-count=4', - '--enable-reuse', '--debug', '--on-error=continue', + '--eval-timeout=20', '--thread-count=1', + '--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(capture_stdout.getvalue(), + 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): - 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("") + 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', - '--eval-timeout=20', '--thread-count=4', - '--enable-reuse', '--debug', '--on-error=continue', + '--eval-timeout=20', '--thread-count=1', + '--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(capture_stdout.getvalue(), + 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" - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags, - "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("") + 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', - '--eval-timeout=20', '--thread-count=4', - '--enable-reuse', + '--eval-timeout=20', '--thread-count=1', + '--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(capture_stdout.getvalue(), + 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): - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048", - "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("") + 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*1024*1024 + expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024 stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) - self.assertEqual(capture_stdout.getvalue(), + 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): - capture_stdout = cStringIO.StringIO() 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"], - capture_stdout, sys.stderr, api_client=stubs.api) + 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): - 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=containers", "--debug", "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"], - capture_stdout, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 0) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) expect_container = { 'priority': 500, @@ -831,17 +844,17 @@ class TestSubmit(unittest.TestCase): }, 'state': 'Committed', 'output_path': '/var/spool/cwl', 'name': 'expect_arvworkflow.cwl#main', - 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'container_image': '999999999999999999999999999999d3+99', 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--eval-timeout=20', '--thread-count=4', - '--enable-reuse', '--debug', '--on-error=continue', + '--eval-timeout=20', '--thread-count=1', + '--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': 1073741824 + 'ram': 1342177280 }, 'use_existing': True, 'properties': {}, @@ -850,24 +863,21 @@ class TestSubmit(unittest.TestCase): stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) - self.assertEqual(capture_stdout.getvalue(), + 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_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) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX" @@ -877,20 +887,18 @@ class TestSubmit(unittest.TestCase): expect_pipeline["name"] = "expect_arvworkflow.cwl#main" stubs.api.pipeline_instances().create.assert_called_with( body=JsonDiffMatcher(expect_pipeline)) + self.assertEqual(exited, 0) @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(), "name": "a test workflow"} exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"], - capture_stdout, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 0) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) expect_container = { 'priority': 500, @@ -930,7 +938,11 @@ class TestSubmit(unittest.TestCase): 'id': '#submit_tool.cwl/x'} ], 'requirements': [ - {'dockerPull': 'debian:8', 'class': 'DockerRequirement'} + { + 'dockerPull': 'debian:8', + 'class': 'DockerRequirement', + "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" + } ], 'id': '#submit_tool.cwl', 'outputs': [], @@ -949,17 +961,17 @@ class TestSubmit(unittest.TestCase): }, 'state': 'Committed', 'output_path': '/var/spool/cwl', 'name': 'a test workflow', - 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'container_image': "999999999999999999999999999999d3+99", 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--eval-timeout=20', '--thread-count=4', - '--enable-reuse', '--debug', '--on-error=continue', + '--eval-timeout=20', '--thread-count=1', + '--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': 1073741824 + 'ram': 1342177280 }, 'use_existing': True, 'properties': { @@ -970,211 +982,222 @@ class TestSubmit(unittest.TestCase): stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') - + self.assertEqual(exited, 0) @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("") + 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(capture_stdout.getvalue(), + 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' - 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("") + 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', - "--eval-timeout=20", "--thread-count=4", - '--enable-reuse', '--debug', '--on-error=continue', + "--eval-timeout=20", "--thread-count=1", + '--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(capture_stdout.getvalue(), + 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): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60", - "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("") + 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', - '--eval-timeout=60.0', '--thread-count=4', - '--enable-reuse', '--debug', '--on-error=continue', + '--eval-timeout=60.0', '--thread-count=1', + '--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(capture_stdout.getvalue(), + 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', + '--eval-timeout=20', '--thread-count=1', + '--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): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20", - "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("") + 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', '--eval-timeout=20', '--thread-count=20', - '--enable-reuse', '--debug', '--on-error=continue', + '--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(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') - + self.assertEqual(exited, 0) @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("") + 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"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) - stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123" + stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "999999999999999999999999999999d5+99" 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(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') + self.assertEqual(exited, 0) @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("") + 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"] = "arvados/jobs:123" + 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(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + self.assertEqual(exited, 0) @stubs def test_submit_priority(self, stubs): - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669", - "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("") + 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(capture_stdout.getvalue(), + 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): - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", - "tests/wf/submit_wf_runner_resources.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("") + 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 * 2**20 + "ram": (2000+512) * 2**20 } expect_container["name"] = "submit_wf_runner_resources.cwl" expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [ { "class": "http://arvados.org/cwl#WorkflowRunnerResources", "coresMin": 2, - "ramMin": 2000 + "ramMin": 2000, + "keep_cache": 512 } ] expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = { "arv": "http://arvados.org/cwl#", } + expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=1', + '--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(capture_stdout.getvalue(), + 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() @@ -1200,21 +1223,18 @@ class TestSubmit(unittest.TestCase): "properties": "" }], "items_available": 1, "offset": 0},) arvrunner.api.collections().create().execute.return_value = {"uuid": ""} - self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, + 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): - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", - "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"], - capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) - self.assertEqual(exited, 0) - except: - logging.exception("") - + 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": [ @@ -1224,14 +1244,15 @@ class TestSubmit(unittest.TestCase): "--no-log-timestamps", "--disable-validate", "--eval-timeout=20", - '--thread-count=4', + '--thread-count=1', "--enable-reuse", + "--collection-cache-size=256", '--debug', "--on-error=continue", "/var/lib/cwl/workflow.json#main", "/var/lib/cwl/cwl.input.json" ], - "container_image": "arvados/jobs:"+arvados_cwl.__version__, + "container_image": "999999999999999999999999999999d3+99", "cwd": "/var/spool/cwl", "mounts": { "/var/lib/cwl/cwl.input.json": { @@ -1293,7 +1314,8 @@ class TestSubmit(unittest.TestCase): "hints": [ { "class": "DockerRequirement", - "dockerPull": "debian:8" + "dockerPull": "debian:8", + "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" }, { "class": "http://commonwl.org/cwltool#Secrets", @@ -1352,7 +1374,7 @@ class TestSubmit(unittest.TestCase): "properties": {}, "runtime_constraints": { "API": True, - "ram": 1073741824, + "ram": 1342177280, "vcpus": 1 }, "secret_mounts": { @@ -1367,8 +1389,9 @@ class TestSubmit(unittest.TestCase): stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + self.assertEqual(exited, 0) @stubs def test_submit_request_uuid(self, stubs): @@ -1380,20 +1403,132 @@ class TestSubmit(unittest.TestCase): "state": "Queued" } - capture_stdout = cStringIO.StringIO() - try: - 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"], - capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) - self.assertEqual(exited, 0) - except: - logging.exception("") + 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(capture_stdout.getvalue(), + 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) + + @mock.patch("arvados.collection.CollectionReader") + @stubs + def test_submit_uuid_inputs(self, stubs, collectionReader): + 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.assertRegexpMatches( + 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.assertRegexpMatches( + capture_stderr.getvalue(), + r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found") + finally: + cwltool_logger.removeHandler(stderr_logger) class TestCreateTemplate(unittest.TestCase): @@ -1422,15 +1557,12 @@ class TestCreateTemplate(unittest.TestCase): 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.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.pipeline_instances().create.refute_called() stubs.api.jobs().create.refute_called() @@ -1447,24 +1579,21 @@ class TestCreateTemplate(unittest.TestCase): stubs.api.pipeline_templates().create.assert_called_with( body=JsonDiffMatcher(expect_template), ensure_unique_name=True) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_template_uuid + '\n') - + self.assertEqual(exited, 0) @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.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.pipeline_instances().create.refute_called() stubs.api.jobs().create.refute_called() @@ -1481,16 +1610,14 @@ class TestCreateTemplate(unittest.TestCase): stubs.api.pipeline_templates().create.assert_called_with( body=JsonDiffMatcher(expect_template), ensure_unique_name=True) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_pipeline_template_uuid + '\n') - + self.assertEqual(exited, 0) @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", @@ -1498,8 +1625,7 @@ class TestCreateTemplate(unittest.TestCase): "--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.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.pipeline_instances().create.refute_called() stubs.api.jobs().create.refute_called() @@ -1517,8 +1643,9 @@ class TestCreateTemplate(unittest.TestCase): stubs.api.pipeline_templates().update.assert_called_with( body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), self.existing_template_uuid + '\n') + self.assertEqual(exited, 0) class TestCreateWorkflow(unittest.TestCase): @@ -1530,15 +1657,12 @@ class TestCreateWorkflow(unittest.TestCase): def test_create(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/wf/submit_wf.cwl", "tests/submit_test_job.json"], - capture_stdout, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 0) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.pipeline_templates().create.refute_called() stubs.api.container_requests().create.refute_called() @@ -1554,24 +1678,21 @@ class TestCreateWorkflow(unittest.TestCase): stubs.api.workflows().create.assert_called_with( body=JsonDiffMatcher(body)) - self.assertEqual(capture_stdout.getvalue(), + 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' - 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.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.pipeline_templates().create.refute_called() stubs.api.container_requests().create.refute_called() @@ -1587,36 +1708,38 @@ class TestCreateWorkflow(unittest.TestCase): stubs.api.workflows().create.assert_called_with( body=JsonDiffMatcher(body)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') + self.assertEqual(exited, 0) @stubs def test_incompatible_api(self, stubs): - capture_stderr = cStringIO.StringIO() - logging.getLogger('arvados.cwl-runner').addHandler( - logging.StreamHandler(capture_stderr)) + capture_stderr = StringIO() + acr_logger = logging.getLogger('arvados.cwl-runner') + stderr_logger = logging.StreamHandler(capture_stderr) + acr_logger.addHandler(stderr_logger) - exited = arvados_cwl.main( - ["--update-workflow", self.existing_workflow_uuid, - "--api=jobs", - "--debug", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - sys.stderr, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 1) - self.assertRegexpMatches( - capture_stderr.getvalue(), - "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid)) + try: + exited = arvados_cwl.main( + ["--update-workflow", self.existing_workflow_uuid, + "--api=jobs", + "--debug", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stderr, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 1) + self.assertRegexpMatches( + capture_stderr.getvalue(), + "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid)) + finally: + acr_logger.removeHandler(stderr_logger) @stubs def test_update(self, stubs): - capture_stdout = cStringIO.StringIO() - exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - capture_stdout, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 0) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) body = { "workflow": { @@ -1628,20 +1751,17 @@ class TestCreateWorkflow(unittest.TestCase): stubs.api.workflows().update.assert_called_with( uuid=self.existing_workflow_uuid, body=JsonDiffMatcher(body)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), self.existing_workflow_uuid + '\n') - + self.assertEqual(exited, 0) @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) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) body = { "workflow": { @@ -1653,23 +1773,20 @@ class TestCreateWorkflow(unittest.TestCase): stubs.api.workflows().update.assert_called_with( uuid=self.existing_workflow_uuid, body=JsonDiffMatcher(body)) - self.assertEqual(capture_stdout.getvalue(), + 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' - 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) + 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()) @@ -1685,20 +1802,21 @@ class TestCreateWorkflow(unittest.TestCase): stubs.api.workflows().create.assert_called_with( body=JsonDiffMatcher(body)) - self.assertEqual(capture_stdout.getvalue(), + self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') + self.assertEqual(exited, 0) class TestTemplateInputs(unittest.TestCase): expect_template = { "components": { "inputs_test.cwl": { 'runtime_constraints': { - 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024 }, 'script_parameters': { 'cwl:tool': - '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main', + 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main', 'optionalFloatInput': None, 'fileInput': { 'type': 'File', @@ -1741,27 +1859,28 @@ class TestTemplateInputs(unittest.TestCase): exited = arvados_cwl.main( ["--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.capture_stdout, sys.stderr, api_client=stubs.api) stubs.api.pipeline_templates().create.assert_called_with( body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True) + self.assertEqual(exited, 0) + @stubs def test_inputs(self, stubs): exited = arvados_cwl.main( ["--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) + stubs.capture_stdout, sys.stderr, api_client=stubs.api) expect_template = copy.deepcopy(self.expect_template) params = expect_template[ "components"]["inputs_test.cwl"]["script_parameters"] params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt' - params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main' + params["cwl:tool"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main' 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) + self.assertEqual(exited, 0)