X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/04f9ccc7ca627d41175f44f515e4581b6937f43b..95e5ccacf6c1193b313fa90a6d39baafa2ba67d8:/sdk/cwl/tests/test_job.py diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py index fa043baa42..20efe15139 100644 --- a/sdk/cwl/tests/test_job.py +++ b/sdk/cwl/tests/test_job.py @@ -1,3 +1,7 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + import functools import json import logging @@ -10,10 +14,12 @@ import StringIO import arvados import arvados_cwl 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 +from .matcher import JsonDiffMatcher, StripYAMLComments +from .test_container import CollectionMock if not os.getenv('ARVADOS_DEBUG'): logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN) @@ -21,6 +27,28 @@ 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") + + make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, + collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) + loadingContext = arvados_cwl.context.ArvLoadingContext( + {"avsc_names": avsc_names, + "basedir": "", + "make_fs_access": make_fs_access, + "loader": Loader({}), + "metadata": {"cwlVersion": "v1.0"}, + "makeTool": runner.arv_make_tool}) + runtimeContext = arvados_cwl.context.ArvRuntimeContext( + {"work_api": "jobs", + "basedir": "", + "name": "test_run_job_"+str(enable_reuse), + "make_fs_access": make_fs_access, + "enable_reuse": enable_reuse, + "priority": 500}) + + return loadingContext, runtimeContext + # The test passes no builder.resources # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} @mock.patch('arvados.commands.keepdocker.list_images_in_arv') @@ -30,7 +58,6 @@ class TestJob(unittest.TestCase): runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.num_retries = 0 - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] runner.api.collections().get().execute.return_value = {"portable_data_hash": "99999999999999999999999999999993+99"} @@ -47,15 +74,17 @@ class TestJob(unittest.TestCase): "inputs": [], "outputs": [], "baseCommand": "ls", - "arguments": [{"valueFrom": "$(runtime.outdir)"}] + "arguments": [{"valueFrom": "$(runtime.outdir)"}], + "id": "#", + "class": "CommandLineTool" }) - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, - basedir="", make_fs_access=make_fs_access, loader=Loader({})) + + loadingContext, runtimeContext = self.helper(runner, enable_reuse) + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): - j.run(enable_reuse=enable_reuse) + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) runner.api.jobs().create.assert_called_with( body=JsonDiffMatcher({ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', @@ -92,6 +121,12 @@ class TestJob(unittest.TestCase): "head_uuid": "zzzzz-819sb-yyyyyyyyyyyyyyy", }) ) + # Simulate an API excepction when trying to create a + # sharing link on the job + runner.api.links().create.side_effect = ApiError( + mock.MagicMock(return_value={'status': 403}), + 'Permission denied') + j.run(runtimeContext) else: assert not runner.api.links().create.called @@ -108,9 +143,6 @@ class TestJob(unittest.TestCase): list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"} - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") - - tool = { "inputs": [], "outputs": [], @@ -125,16 +157,22 @@ class TestJob(unittest.TestCase): "outputDirType": "keep_output_dir" }, { "class": "http://arvados.org/cwl#APIRequirement", + }, + { + "class": "http://arvados.org/cwl#ReuseRequirement", + "enableReuse": False }], - "baseCommand": "ls" + "baseCommand": "ls", + "id": "#", + "class": "CommandLineTool" } - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, - make_fs_access=make_fs_access, loader=Loader({})) + + loadingContext, runtimeContext = self.helper(runner) + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): - j.run() + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) runner.api.jobs().create.assert_called_with( body=JsonDiffMatcher({ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', @@ -158,7 +196,7 @@ class TestJob(unittest.TestCase): 'keep_cache_mb_per_task': 512 } }), - find_or_create=True, + find_or_create=False, filters=[['repository', '=', 'arvados'], ['script', '=', 'crunchrunner'], ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'], @@ -184,9 +222,13 @@ class TestJob(unittest.TestCase): {"items": []}, {"items": [{"manifest_text": "ABC"}]}) - arvjob = arvados_cwl.ArvadosJob(runner) - arvjob.name = "testjob" - arvjob.builder = mock.MagicMock() + arvjob = arvados_cwl.ArvadosJob(runner, + mock.MagicMock(), + {}, + None, + [], + [], + "testjob") arvjob.output_callback = mock.MagicMock() arvjob.collect_outputs = mock.MagicMock() arvjob.collect_outputs.return_value = {"out": "stuff"} @@ -254,9 +296,13 @@ class TestJob(unittest.TestCase): {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]}, ) - arvjob = arvados_cwl.ArvadosJob(runner) - arvjob.name = "testjob" - arvjob.builder = mock.MagicMock() + arvjob = arvados_cwl.ArvadosJob(runner, + mock.MagicMock(), + {}, + None, + [], + [], + "testjob") arvjob.output_callback = mock.MagicMock() arvjob.collect_outputs = mock.MagicMock() arvjob.collect_outputs.return_value = {"out": "stuff"} @@ -288,11 +334,40 @@ 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") + + make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, + collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) + + document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=make_fs_access("")) + document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session) + document_loader.fetch_text = document_loader.fetcher.fetch_text + document_loader.check_exists = document_loader.fetcher.check_exists + + loadingContext = arvados_cwl.context.ArvLoadingContext( + {"avsc_names": avsc_names, + "basedir": "", + "make_fs_access": make_fs_access, + "loader": document_loader, + "metadata": {"cwlVersion": "v1.0"}, + "construct_tool_object": runner.arv_make_tool}) + runtimeContext = arvados_cwl.context.ArvRuntimeContext( + {"work_api": "jobs", + "basedir": "", + "name": "test_run_wf_"+str(enable_reuse), + "make_fs_access": make_fs_access, + "enable_reuse": enable_reuse, + "priority": 500}) + + return loadingContext, runtimeContext + # The test passes no builder.resources # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} + @mock.patch("arvados.collection.CollectionReader") @mock.patch("arvados.collection.Collection") @mock.patch('arvados.commands.keepdocker.list_images_in_arv') - def test_run(self, list_images_in_arv, mockcollection): + def test_run(self, list_images_in_arv, mockcollection, mockcollectionreader): arvados_cwl.add_arv_hints() api = mock.MagicMock() @@ -303,29 +378,30 @@ class TestWorkflow(unittest.TestCase): list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"} + runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]} runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.num_retries = 0 - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") - tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl") + loadingContext, runtimeContext = self.helper(runner) + + 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") - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names, - basedir="", make_fs_access=make_fs_access, loader=document_loader, - makeTool=runner.arv_make_tool, metadata=metadata) + arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext) arvtool.formatgraph = None - it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access) - it.next().run() - it.next().run() + it = arvtool.job({}, mock.MagicMock(), runtimeContext) + + it.next().run(runtimeContext) + it.next().run(runtimeContext) with open("tests/wf/scatter2_subwf.cwl") as f: - subwf = f.read() + subwf = StripYAMLComments(f.read()) runner.api.jobs().create.assert_called_with( body=JsonDiffMatcher({ @@ -338,8 +414,8 @@ 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'}]}, @@ -356,12 +432,85 @@ 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( '''{ + "fileblub": { + "basename": "token.txt", + "class": "File", + "location": "/keep/99999999999999999999999999999999+118/token.txt", + "size": 0 + }, "sleeptime": 5 }''')]) + # The test passes no builder.resources + # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} + @mock.patch("arvados.collection.CollectionReader") + @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): + arvados_cwl.add_arv_hints() + + api = mock.MagicMock() + api._rootDesc = get_rootDesc() + + runner = arvados_cwl.ArvCwlRunner(api) + self.assertEqual(runner.work_api, 'jobs') + + list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] + runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"} + runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]} + + runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + runner.ignore_docker_for_reuse = False + runner.num_retries = 0 + + loadingContext, runtimeContext = self.helper(runner) + + tool, metadata = loadingContext.loader.resolve_ref("tests/wf/echo-wf.cwl") + metadata["cwlVersion"] = tool["cwlVersion"] + + 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) + + with open("tests/wf/echo-subwf.cwl") as f: + subwf = StripYAMLComments(f.read()) + + runner.api.jobs().create.assert_called_with( + body=JsonDiffMatcher({ + 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d', + 'repository': 'arvados', + 'script_version': 'master', + 'script': 'crunchrunner', + 'script_parameters': { + 'tasks': [{'task.env': { + 'HOME': '$(task.outdir)', + 'TMPDIR': '$(task.tmpdir)'}, + 'task.vwd': { + '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'}]}, + 'runtime_constraints': { + 'min_scratch_mb_per_node': 4096, + 'min_cores_per_node': 3, + 'docker_image': 'arvados/jobs', + 'min_ram_mb_per_node': 1024 + }, + 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}), + filters=[['repository', '=', 'arvados'], + ['script', '=', 'crunchrunner'], + ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'], + ['docker_image_locator', 'in docker', 'arvados/jobs']], + find_or_create=True) + def test_default_work_api(self): arvados_cwl.add_arv_hints()