X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/8ff3fd06e165a275f53884d1d20287b68c1b32bd..48c38895200cdafaaeca37299bf8352878389a77:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 90dab01471..397ae14225 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 @@ -11,6 +17,18 @@ import logging import mock import sys import unittest +import cwltool.process + +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 @@ -33,7 +51,7 @@ 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 @@ -60,8 +78,14 @@ def stubs(func): 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, @@ -78,18 +102,18 @@ def stubs(func): return self.exe def collection_createstub(created_collections, body, ensure_unique_name=None): - mt = body["manifest_text"] + 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) @@ -99,6 +123,11 @@ 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", @@ -285,7 +314,7 @@ def stubs(func): 'vcpus': 1, 'ram': (1024+256)*1024*1024 }, - 'use_existing': True, + 'use_existing': False, 'properties': {}, 'secret_mounts': {} } @@ -307,75 +336,9 @@ def stubs(func): class TestSubmit(unittest.TestCase): - @mock.patch("arvados_cwl.arvdocker.arv_docker_get_image") - @mock.patch("time.sleep") - @stubs - def test_submit(self, stubs, tm, arvdock): - 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 - - capture_stdout = cStringIO.StringIO() - 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.api.collections().create.assert_has_calls([ - 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), - 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': - ". 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(), - stubs.expect_pipeline_uuid + '\n') - - - @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) - - expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) - expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False} - expect_pipeline["properties"] = {"run_options": {"enable_job_reuse": False}} - stubs.api.pipeline_instances().create.assert_called_with( - body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(capture_stdout.getvalue(), - stubs.expect_pipeline_uuid + '\n') + def setUp(self): + cwltool.process._names = set() @stubs def test_error_when_multiple_storage_classes_specified(self, stubs): @@ -386,173 +349,64 @@ class TestSubmit(unittest.TestCase): sys.stdin, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 1) - @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) - - 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(), - stubs.expect_pipeline_uuid + '\n') - - - @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) - - 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(), - stubs.expect_pipeline_uuid + '\n') - - @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") - @stubs - 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) - - 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(), - stubs.expect_pipeline_uuid + '\n') - - - @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) - self.assertEqual(exited, 0) - - expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) - expect_pipeline["name"] = "hello job 123" - - stubs.api.pipeline_instances().create.assert_called_with( - body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(capture_stdout.getvalue(), - stubs.expect_pipeline_uuid + '\n') - - @mock.patch("time.sleep") - @stubs - 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) - self.assertEqual(exited, 0) - - expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) - expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags - - stubs.api.pipeline_instances().create.assert_called_with( - body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(capture_stdout.getvalue(), - stubs.expect_pipeline_uuid + '\n') - - @mock.patch("time.sleep") - @stubs - def test_submit_with_project_uuid(self, stubs, tm): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--debug", - "--project-uuid", project_uuid, - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - sys.stdout, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 0) - - expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) - expect_pipeline["owner_uuid"] = project_uuid - stubs.api.pipeline_instances().create.assert_called_with( - body=JsonDiffMatcher(expect_pipeline)) @stubs def test_submit_container(self, stubs): - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) - self.assertEqual(exited, 0) - except: - logging.exception("") + 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': - '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', + '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'replication_desired': None, - 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', + 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': - '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', + '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', 'replication_desired': None, - 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', - }), ensure_unique_name=False)]) + '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(capture_stdout.getvalue(), + 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): - 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"] = [ @@ -566,18 +420,16 @@ 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_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) @@ -602,21 +454,16 @@ 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', @@ -628,22 +475,18 @@ 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_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', @@ -656,20 +499,16 @@ 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_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', @@ -681,8 +520,9 @@ 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) @mock.patch("arvados_cwl.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") @@ -694,16 +534,13 @@ 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") @@ -715,28 +552,20 @@ 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', @@ -749,20 +578,17 @@ 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_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', @@ -775,22 +601,18 @@ 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_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', @@ -802,56 +624,48 @@ 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_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+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, @@ -889,54 +703,27 @@ class TestSubmit(unittest.TestCase): 'vcpus': 1, 'ram': 1342177280 }, - 'use_existing': True, + 'use_existing': False, 'properties': {}, 'secret_mounts': {} } 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') - - - @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) - expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) - expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX" - del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"] - del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"] - expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main" - expect_pipeline["name"] = "expect_arvworkflow.cwl#main" - stubs.api.pipeline_instances().create.assert_called_with( - body=JsonDiffMatcher(expect_pipeline)) - @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, @@ -1011,7 +798,7 @@ class TestSubmit(unittest.TestCase): 'vcpus': 1, 'ram': 1342177280 }, - 'use_existing': True, + 'use_existing': False, 'properties': { "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37" }, @@ -1020,60 +807,47 @@ 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): - capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 0) - capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job_missing.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, 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 @@ -1087,21 +861,16 @@ 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_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', @@ -1113,21 +882,16 @@ 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_collection_cache(self, stubs): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500", - "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", "--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', @@ -1140,22 +904,16 @@ 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_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', @@ -1167,82 +925,48 @@ 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_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("") - - 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(), - 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"] = "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"] = { @@ -1270,8 +994,9 @@ 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) def tearDown(self): arvados_cwl.arvdocker.arv_docker_clear_cache() @@ -1315,16 +1040,10 @@ class TestSubmit(unittest.TestCase): @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": [ @@ -1474,16 +1193,18 @@ class TestSubmit(unittest.TestCase): } }, "state": "Committed", - "use_existing": True + "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_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 = { @@ -1492,176 +1213,132 @@ 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), cluster_id="zzzzz") - self.assertEqual(capture_stdout.getvalue(), + 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): - capture_stdout = cStringIO.StringIO() stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123" - try: - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb", - "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-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(capture_stdout.getvalue(), + 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): - capture_stdout = cStringIO.StringIO() 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"], - 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, 1) - -class TestCreateTemplate(unittest.TestCase): - existing_template_uuid = "zzzzz-d1hrv-validworkfloyml" - - def _adjust_script_params(self, expect_component): - expect_component['script_parameters']['x'] = { - 'dataclass': 'File', - 'required': True, - 'type': 'File', - 'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', - } - expect_component['script_parameters']['y'] = { - 'dataclass': 'Collection', - 'required': True, - 'type': 'Directory', - 'value': '99999999999999999999999999999998+99', - } - expect_component['script_parameters']['z'] = { - 'dataclass': 'Collection', - 'required': True, - 'type': 'Directory', - } - + @mock.patch("arvados.collection.CollectionReader") @stubs - def test_create(self, stubs): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - - capture_stdout = cStringIO.StringIO() + 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( - ["--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.api.pipeline_instances().create.refute_called() - stubs.api.jobs().create.refute_called() - - expect_component = copy.deepcopy(stubs.expect_job_spec) - self._adjust_script_params(expect_component) - expect_template = { - "components": { - "submit_wf.cwl": expect_component, - }, - "name": "submit_wf.cwl", - "owner_uuid": project_uuid, - } - stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(expect_template), ensure_unique_name=True) - - self.assertEqual(capture_stdout.getvalue(), - stubs.expect_pipeline_template_uuid + '\n') - - - @stubs - def test_create_name(self, stubs): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - - capture_stdout = cStringIO.StringIO() + ["--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) - 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) + 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.api.pipeline_instances().create.refute_called() - stubs.api.jobs().create.refute_called() - - expect_component = copy.deepcopy(stubs.expect_job_spec) - self._adjust_script_params(expect_component) - expect_template = { - "components": { - "testing 123": expect_component, - }, - "name": "testing 123", - "owner_uuid": project_uuid, - } - stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(expect_template), ensure_unique_name=True) - - self.assertEqual(capture_stdout.getvalue(), - stubs.expect_pipeline_template_uuid + '\n') - + @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_update_name(self, stubs): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + def test_submit_unknown_uuid_inputs(self, stubs, collectionReader): + collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt") + capture_stderr = StringIO() - capture_stdout = cStringIO.StringIO() + cwltool_logger = logging.getLogger('cwltool') + stderr_logger = logging.StreamHandler(capture_stderr) + cwltool_logger.addHandler(stderr_logger) exited = arvados_cwl.main( - ["--update-workflow", self.existing_template_uuid, - "--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.api.pipeline_instances().create.refute_called() - stubs.api.jobs().create.refute_called() - - expect_component = copy.deepcopy(stubs.expect_job_spec) - self._adjust_script_params(expect_component) - expect_template = { - "components": { - "testing 123": expect_component, - }, - "name": "testing 123", - "owner_uuid": project_uuid, - } - stubs.api.pipeline_templates().create.refute_called() - stubs.api.pipeline_templates().update.assert_called_with( - body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid) + ["--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) - self.assertEqual(capture_stdout.getvalue(), - self.existing_template_uuid + '\n') + 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 TestCreateWorkflow(unittest.TestCase): @@ -1673,15 +1350,12 @@ 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() @@ -1697,24 +1371,21 @@ 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() @@ -1730,36 +1401,18 @@ 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)) - - 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)) @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": { @@ -1771,20 +1424,17 @@ 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": { @@ -1796,23 +1446,20 @@ 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()) @@ -1828,83 +1475,42 @@ 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') - -class TestTemplateInputs(unittest.TestCase): - expect_template = { - "components": { - "inputs_test.cwl": { - 'runtime_constraints': { - 'docker_image': '999999999999999999999999999999d3+99', - 'min_ram_mb_per_node': 1024 - }, - 'script_parameters': { - 'cwl:tool': - 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main', - 'optionalFloatInput': None, - 'fileInput': { - 'type': 'File', - 'dataclass': 'File', - 'required': True, - 'title': "It's a file; we expect to find some characters in it.", - 'description': 'If there were anything further to say, it would be said here,\nor here.' - }, - 'floatInput': { - 'type': 'float', - 'dataclass': 'number', - 'required': True, - 'title': 'Floats like a duck', - 'default': 0.1, - 'value': 0.1, - }, - 'optionalFloatInput': { - 'type': ['null', 'float'], - 'dataclass': 'number', - 'required': False, - }, - 'boolInput': { - 'type': 'boolean', - 'dataclass': 'boolean', - 'required': True, - 'title': 'True or false?', - }, - }, - 'repository': 'arvados', - 'script_version': 'master', - 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', - 'script': 'cwl-runner', - }, - }, - "name": "inputs_test.cwl", - } + self.assertEqual(exited, 0) @stubs - def test_inputs_empty(self, stubs): + def test_create_with_imports(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + 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) + ["--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.assert_called_with( - body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True) + 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_inputs(self, stubs): + def test_create_with_no_input(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + 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) + ["--create-workflow", "--debug", + "--api=containers", + "--project-uuid", project_uuid, + "tests/wf/revsort/revsort.cwl"], + 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"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main' - params["floatInput"]["value"] = 1.234 - params["boolInput"]["value"] = True + stubs.api.pipeline_templates().create.refute_called() + stubs.api.container_requests().create.refute_called() - stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(expect_template), ensure_unique_name=True) + self.assertEqual(stubs.capture_stdout.getvalue(), + stubs.expect_workflow_uuid + '\n') + self.assertEqual(exited, 0)