X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/18b51f2620505d4efbc9de322e24d5218a5ca19b..d6cccb3ea4e5f076a436d9935e3835d4b620b859:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index f718a86b36..5d2d0d0111 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -1,9 +1,12 @@ +from future import standard_library +standard_library.install_aliases() +from builtins import object # Copyright (C) The Arvados Authors. All rights reserved. # # SPDX-License-Identifier: Apache-2.0 import copy -import cStringIO +import io import functools import hashlib import json @@ -15,6 +18,7 @@ import unittest import arvados import arvados.collection import arvados_cwl +import arvados_cwl.executor import arvados_cwl.runner import arvados.keep @@ -32,7 +36,7 @@ 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 @@ -46,7 +50,16 @@ 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" @@ -69,7 +82,7 @@ def stubs(func): def collection_createstub(created_collections, body, ensure_unique_name=None): mt = body["manifest_text"] - uuid = "zzzzz-4zz18-zzzzzzzzzzzzzz%d" % len(created_collections) + uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections) pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt)) created_collections[uuid] = { "uuid": uuid, @@ -79,7 +92,7 @@ def stubs(func): return CollectionExecute(created_collections[uuid]) def collection_getstub(created_collections, uuid): - for v in created_collections.itervalues(): + for v in created_collections.values(): if uuid in (v["uuid"], v["portable_data_hash"]): return CollectionExecute(v) @@ -93,6 +106,26 @@ def stubs(func): "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) @@ -117,7 +150,7 @@ 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': { @@ -141,7 +174,7 @@ def stubs(func): }], 'class': 'Directory' }, - 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main' + 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main' }, 'repository': 'arvados', 'script_version': 'master', @@ -155,7 +188,7 @@ 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": { @@ -173,7 +206,7 @@ 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' @@ -243,17 +276,17 @@ 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': {}, @@ -277,11 +310,18 @@ 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 + + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=jobs", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -303,13 +343,14 @@ 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) ]) @@ -323,7 +364,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_no_reuse(self, stubs, tm): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -351,7 +392,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_on_error(self, stubs, tm): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -370,7 +411,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_runner_ram(self, stubs, tm): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -389,7 +430,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_invalid_runner_ram(self, stubs, tm): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -401,7 +442,7 @@ class TestSubmit(unittest.TestCase): def test_submit_output_name(self, stubs, tm): output_name = "test_output_name" - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--output-name", output_name, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -420,7 +461,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_pipeline_name(self, stubs, tm): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--name=hello job 123", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -440,7 +481,7 @@ class TestSubmit(unittest.TestCase): def test_submit_output_tags(self, stubs, tm): output_tags = "tag0,tag1,tag2" - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--output-tags", output_tags, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -474,7 +515,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -506,7 +547,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_no_reuse(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse", @@ -520,8 +561,9 @@ class TestSubmit(unittest.TestCase): 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 @@ -533,7 +575,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_reuse_disabled_by_workflow(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -545,8 +587,8 @@ class TestSubmit(unittest.TestCase): 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" @@ -569,7 +611,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_on_error(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop", @@ -582,8 +624,9 @@ class TestSubmit(unittest.TestCase): 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( @@ -595,7 +638,7 @@ class TestSubmit(unittest.TestCase): def test_submit_container_output_name(self, stubs): output_name = "test_output_name" - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name, @@ -608,8 +651,8 @@ class TestSubmit(unittest.TestCase): 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 @@ -621,7 +664,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_storage_classes(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo", @@ -634,8 +677,8 @@ class TestSubmit(unittest.TestCase): 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'] @@ -646,7 +689,7 @@ class TestSubmit(unittest.TestCase): @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): @@ -667,7 +710,7 @@ class TestSubmit(unittest.TestCase): @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): @@ -688,7 +731,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_output_ttl(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600", @@ -701,8 +744,9 @@ class TestSubmit(unittest.TestCase): 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'] @@ -713,7 +757,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_trash_intermediate(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate", @@ -726,8 +770,9 @@ class TestSubmit(unittest.TestCase): 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'] @@ -740,7 +785,7 @@ class TestSubmit(unittest.TestCase): def test_submit_container_output_tags(self, stubs): output_tags = "tag0,tag1,tag2" - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags, @@ -753,8 +798,8 @@ class TestSubmit(unittest.TestCase): 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'] @@ -765,7 +810,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_runner_ram(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048", @@ -776,7 +821,7 @@ class TestSubmit(unittest.TestCase): logging.exception("") 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)) @@ -787,7 +832,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_file_keepref(self, stubs, tm, collectionReader): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt") exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -800,7 +845,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_keepref(self, stubs, tm, reader): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() with open("tests/wf/expect_arvworkflow.cwl") as f: reader().open().__enter__().read.return_value = f.read() @@ -835,17 +880,17 @@ 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': {}, @@ -862,7 +907,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_jobs_keepref(self, stubs, tm, reader): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() with open("tests/wf/expect_arvworkflow.cwl") as f: reader().open().__enter__().read.return_value = f.read() @@ -885,7 +930,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_arvworkflow(self, stubs, tm): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() with open("tests/wf/expect_arvworkflow.cwl") as f: stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"} @@ -934,7 +979,11 @@ 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': [], @@ -953,17 +1002,17 @@ 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': { @@ -980,7 +1029,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_name(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123", @@ -999,10 +1048,27 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') + @stubs + def test_submit_missing_input(self, stubs): + capture_stdout = io.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) + self.assertEqual(exited, 0) + + capture_stdout = io.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) + self.assertEqual(exited, 1) + + @stubs def test_submit_container_project(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid, @@ -1016,8 +1082,9 @@ class TestSubmit(unittest.TestCase): 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'] @@ -1029,7 +1096,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_eval_timeout(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60", @@ -1042,9 +1109,37 @@ class TestSubmit(unittest.TestCase): 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(), + stubs.expect_container_request_uuid + '\n') + + @stubs + def test_submit_container_collection_cache(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + capture_stdout = io.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("") + + 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)) @@ -1055,7 +1150,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_thread_count(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20", @@ -1069,7 +1164,8 @@ class TestSubmit(unittest.TestCase): 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( @@ -1080,7 +1176,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_job_runner_image(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123", @@ -1090,7 +1186,7 @@ class TestSubmit(unittest.TestCase): except: logging.exception("") - 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( @@ -1100,7 +1196,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_runner_image(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123", @@ -1110,7 +1206,7 @@ class TestSubmit(unittest.TestCase): except: logging.exception("") - 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( @@ -1120,7 +1216,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_priority(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669", @@ -1141,7 +1237,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_wf_runner_resources(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -1155,30 +1251,40 @@ class TestSubmit(unittest.TestCase): 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(), stubs.expect_container_request_uuid + '\n') + 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() @@ -1204,12 +1310,15 @@ 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() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -1228,14 +1337,15 @@ 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": { @@ -1297,7 +1407,8 @@ 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", @@ -1356,7 +1467,7 @@ class TestSubmit(unittest.TestCase): "properties": {}, "runtime_constraints": { "API": True, - "ram": 1073741824, + "ram": 1342177280, "vcpus": 1 }, "secret_mounts": { @@ -1384,7 +1495,7 @@ class TestSubmit(unittest.TestCase): "state": "Queued" } - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy", @@ -1395,10 +1506,41 @@ class TestSubmit(unittest.TestCase): logging.exception("") stubs.api.container_requests().update.assert_called_with( - uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec)) + uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec), cluster_id="zzzzz") self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + @stubs + def test_submit_container_cluster_id(self, stubs): + capture_stdout = io.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("") + + 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(), + stubs.expect_container_request_uuid + '\n') + + + @stubs + def test_submit_validate_cluster_id(self, stubs): + capture_stdout = io.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) + self.assertEqual(exited, 1) + class TestCreateTemplate(unittest.TestCase): existing_template_uuid = "zzzzz-d1hrv-validworkfloyml" @@ -1426,7 +1568,7 @@ class TestCreateTemplate(unittest.TestCase): def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--create-workflow", "--debug", @@ -1459,7 +1601,7 @@ class TestCreateTemplate(unittest.TestCase): def test_create_name(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--create-workflow", "--debug", @@ -1493,7 +1635,7 @@ class TestCreateTemplate(unittest.TestCase): def test_update_name(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--update-workflow", self.existing_template_uuid, @@ -1534,7 +1676,7 @@ class TestCreateWorkflow(unittest.TestCase): def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--create-workflow", "--debug", @@ -1566,7 +1708,7 @@ class TestCreateWorkflow(unittest.TestCase): def test_create_name(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--create-workflow", "--debug", @@ -1596,7 +1738,7 @@ class TestCreateWorkflow(unittest.TestCase): @stubs def test_incompatible_api(self, stubs): - capture_stderr = cStringIO.StringIO() + capture_stderr = io.StringIO() logging.getLogger('arvados.cwl-runner').addHandler( logging.StreamHandler(capture_stderr)) @@ -1613,7 +1755,7 @@ class TestCreateWorkflow(unittest.TestCase): @stubs def test_update(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, @@ -1638,7 +1780,7 @@ class TestCreateWorkflow(unittest.TestCase): @stubs def test_update_name(self, stubs): - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, @@ -1665,7 +1807,7 @@ class TestCreateWorkflow(unittest.TestCase): def test_create_collection_per_tool(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - capture_stdout = cStringIO.StringIO() + capture_stdout = io.StringIO() exited = arvados_cwl.main( ["--create-workflow", "--debug", @@ -1697,12 +1839,12 @@ class TestTemplateInputs(unittest.TestCase): "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', @@ -1745,7 +1887,7 @@ 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) + io.StringIO(), sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.api.pipeline_templates().create.assert_called_with( @@ -1756,14 +1898,14 @@ class TestTemplateInputs(unittest.TestCase): 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) + io.StringIO(), sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) 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