X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/21bf21abe900918a7882f7e43c102418e04159be..bfe31b5db42a7c66b49ebcd519e90d590cafe825:/sdk/cwl/tests/test_job.py diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py index 4473b88ca0..9cac68aa6c 100644 --- a/sdk/cwl/tests/test_job.py +++ b/sdk/cwl/tests/test_job.py @@ -2,6 +2,11 @@ # # SPDX-License-Identifier: Apache-2.0 +from future import standard_library +standard_library.install_aliases() +from builtins import str +from builtins import next + import functools import json import logging @@ -9,16 +14,18 @@ import mock import os import unittest import copy -import StringIO +import io import arvados import arvados_cwl +import arvados_cwl.executor import cwltool.process from arvados.errors import ApiError from schema_salad.ref_resolver import Loader from schema_salad.sourceline import cmap from .mock_discovery import get_rootDesc from .matcher import JsonDiffMatcher, StripYAMLComments +from .test_container import CollectionMock if not os.getenv('ARVADOS_DEBUG'): logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN) @@ -27,7 +34,7 @@ if not os.getenv('ARVADOS_DEBUG'): class TestJob(unittest.TestCase): def helper(self, runner, enable_reuse=True): - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1.0-dev1") make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) @@ -36,7 +43,7 @@ class TestJob(unittest.TestCase): "basedir": "", "make_fs_access": make_fs_access, "loader": Loader({}), - "metadata": {"cwlVersion": "v1.0"}, + "metadata": {"cwlVersion": "v1.1.0-dev1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}, "makeTool": runner.arv_make_tool}) runtimeContext = arvados_cwl.context.ArvRuntimeContext( {"work_api": "jobs", @@ -124,7 +131,7 @@ class TestJob(unittest.TestCase): # sharing link on the job runner.api.links().create.side_effect = ApiError( mock.MagicMock(return_value={'status': 403}), - 'Permission denied') + bytes(b'Permission denied')) j.run(runtimeContext) else: assert not runner.api.links().create.called @@ -211,11 +218,12 @@ class TestJob(unittest.TestCase): runner.num_retries = 0 runner.ignore_docker_for_reuse = False - reader().open.return_value = StringIO.StringIO( - """2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir + reader().keys.return_value = "log.txt" + reader().open.return_value = io.StringIO( + str(u"""2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.outdir)=/tmp/crunch-job-task-work/compute3.1/outdir 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep - """) + """)) api.collections().list().execute.side_effect = ({"items": []}, {"items": [{"manifest_text": "XYZ"}]}, {"items": []}, @@ -284,11 +292,12 @@ class TestJob(unittest.TestCase): runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.num_retries = 0 - reader().open.return_value = StringIO.StringIO( - """2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir + reader().keys.return_value = "log.txt" + reader().open.return_value = io.StringIO( + str(u"""2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.outdir)=/tmp/crunch-job-task-work/compute3.1/outdir 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep - """) + """)) api.collections().list().execute.side_effect = ( {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]}, @@ -334,7 +343,7 @@ class TestJob(unittest.TestCase): class TestWorkflow(unittest.TestCase): def helper(self, runner, enable_reuse=True): - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1.0-dev1") make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) @@ -349,7 +358,7 @@ class TestWorkflow(unittest.TestCase): "basedir": "", "make_fs_access": make_fs_access, "loader": document_loader, - "metadata": {"cwlVersion": "v1.0"}, + "metadata": {"cwlVersion": "v1.1.0-dev1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}, "construct_tool_object": runner.arv_make_tool}) runtimeContext = arvados_cwl.context.ArvRuntimeContext( {"work_api": "jobs", @@ -372,7 +381,7 @@ class TestWorkflow(unittest.TestCase): api = mock.MagicMock() api._rootDesc = get_rootDesc() - runner = arvados_cwl.ArvCwlRunner(api) + runner = arvados_cwl.executor.ArvCwlExecutor(api) self.assertEqual(runner.work_api, 'jobs') list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] @@ -388,15 +397,16 @@ class TestWorkflow(unittest.TestCase): tool, metadata = loadingContext.loader.resolve_ref("tests/wf/scatter2.cwl") metadata["cwlVersion"] = tool["cwlVersion"] - mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118" + mockc = mock.MagicMock() + mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mockc, *args, **kwargs) mockcollectionreader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "token.txt") arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext) arvtool.formatgraph = None it = arvtool.job({}, mock.MagicMock(), runtimeContext) - it.next().run(runtimeContext) - it.next().run(runtimeContext) + next(it).run(runtimeContext) + next(it).run(runtimeContext) with open("tests/wf/scatter2_subwf.cwl") as f: subwf = StripYAMLComments(f.read()) @@ -412,8 +422,8 @@ class TestWorkflow(unittest.TestCase): 'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'}, 'task.vwd': { - 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl', - 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml' + 'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl', + 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml' }, 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'], 'task.stdout': 'cwl.output.json'}]}, @@ -430,9 +440,9 @@ class TestWorkflow(unittest.TestCase): ['docker_image_locator', 'in docker', 'arvados/jobs']], find_or_create=True) - mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)]) - mockcollection().open().__enter__().write.assert_has_calls([mock.call( -'''{ + mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)]) + mockc.open().__enter__().write.assert_has_calls([mock.call( +bytes(b'''{ "fileblub": { "basename": "token.txt", "class": "File", @@ -440,7 +450,7 @@ class TestWorkflow(unittest.TestCase): "size": 0 }, "sleeptime": 5 -}''')]) +}'''))]) # The test passes no builder.resources # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} @@ -448,12 +458,13 @@ class TestWorkflow(unittest.TestCase): @mock.patch("arvados.collection.Collection") @mock.patch('arvados.commands.keepdocker.list_images_in_arv') def test_overall_resource_singlecontainer(self, list_images_in_arv, mockcollection, mockcollectionreader): + # TODO copy this over to test_container arvados_cwl.add_arv_hints() api = mock.MagicMock() api._rootDesc = get_rootDesc() - runner = arvados_cwl.ArvCwlRunner(api) + runner = arvados_cwl.executor.ArvCwlExecutor(api) self.assertEqual(runner.work_api, 'jobs') list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] @@ -465,17 +476,17 @@ class TestWorkflow(unittest.TestCase): runner.num_retries = 0 loadingContext, runtimeContext = self.helper(runner) - + loadingContext.do_update = True tool, metadata = loadingContext.loader.resolve_ref("tests/wf/echo-wf.cwl") - metadata["cwlVersion"] = tool["cwlVersion"] - mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118" + mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mock.MagicMock(), *args, **kwargs) arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext) arvtool.formatgraph = None it = arvtool.job({}, mock.MagicMock(), runtimeContext) - it.next().run(runtimeContext) - it.next().run(runtimeContext) + + next(it).run(runtimeContext) + next(it).run(runtimeContext) with open("tests/wf/echo-subwf.cwl") as f: subwf = StripYAMLComments(f.read()) @@ -491,8 +502,8 @@ class TestWorkflow(unittest.TestCase): 'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'}, 'task.vwd': { - 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl', - 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml' + 'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl', + 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml' }, 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'], 'task.stdout': 'cwl.output.json'}]}, @@ -515,5 +526,5 @@ class TestWorkflow(unittest.TestCase): api = mock.MagicMock() api._rootDesc = copy.deepcopy(get_rootDesc()) del api._rootDesc.get('resources')['jobs']['methods']['create'] - runner = arvados_cwl.ArvCwlRunner(api) + runner = arvados_cwl.executor.ArvCwlExecutor(api) self.assertEqual(runner.work_api, 'containers')