# Copyright (C) The Arvados Authors. All rights reserved. # # SPDX-License-Identifier: Apache-2.0 import functools import json import logging import mock import os import unittest import copy 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, StripYAMLComments if not os.getenv('ARVADOS_DEBUG'): logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN) logging.getLogger('arvados.arv-run').setLevel(logging.WARN) 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') def test_run(self, list_images_in_arv): for enable_reuse in (True, False): runner = mock.MagicMock() runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.num_retries = 0 list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] runner.api.collections().get().execute.return_value = {"portable_data_hash": "99999999999999999999999999999993+99"} # Simulate reused job from another project so that we can check is a can_read # link is added. runner.api.jobs().create().execute.return_value = { 'state': 'Complete' if enable_reuse else 'Queued', 'owner_uuid': 'zzzzz-tpzed-yyyyyyyyyyyyyyy' if enable_reuse else 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'uuid': 'zzzzz-819sb-yyyyyyyyyyyyyyy', 'output': None, } tool = cmap({ "inputs": [], "outputs": [], "baseCommand": "ls", "arguments": [{"valueFrom": "$(runtime.outdir)"}], "id": "#", "class": "CommandLineTool" }) loadingContext, runtimeContext = self.helper(runner, enable_reuse) arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None for j in arvtool.job({}, mock.MagicMock(), runtimeContext): j.run(runtimeContext) runner.api.jobs().create.assert_called_with( body=JsonDiffMatcher({ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'runtime_constraints': {}, 'script_parameters': { 'tasks': [{ 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'}, 'command': ['ls', '$(task.outdir)'] }], }, 'script_version': 'master', 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d', 'repository': 'arvados', 'script': 'crunchrunner', 'runtime_constraints': { 'docker_image': 'arvados/jobs', 'min_cores_per_node': 1, 'min_ram_mb_per_node': 1024, 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize } }), find_or_create=enable_reuse, filters=[['repository', '=', 'arvados'], ['script', '=', 'crunchrunner'], ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'], ['docker_image_locator', 'in docker', 'arvados/jobs']] ) if enable_reuse: runner.api.links().create.assert_called_with( body=JsonDiffMatcher({ 'link_class': 'permission', 'name': 'can_read', "tail_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", "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 # The test passes some fields in builder.resources # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} @mock.patch('arvados.commands.keepdocker.list_images_in_arv') def test_resource_requirements(self, list_images_in_arv): runner = mock.MagicMock() runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.num_retries = 0 arvados_cwl.add_arv_hints() list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"} tool = { "inputs": [], "outputs": [], "hints": [{ "class": "ResourceRequirement", "coresMin": 3, "ramMin": 3000, "tmpdirMin": 4000 }, { "class": "http://arvados.org/cwl#RuntimeConstraints", "keep_cache": 512, "outputDirType": "keep_output_dir" }, { "class": "http://arvados.org/cwl#APIRequirement", }, { "class": "http://arvados.org/cwl#ReuseRequirement", "enableReuse": False }], "baseCommand": "ls", "id": "#", "class": "CommandLineTool" } loadingContext, runtimeContext = self.helper(runner) arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None 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', 'runtime_constraints': {}, 'script_parameters': { 'tasks': [{ 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'}, 'task.keepTmpOutput': True, 'command': ['ls'] }] }, 'script_version': 'master', 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d', 'repository': 'arvados', 'script': 'crunchrunner', 'runtime_constraints': { 'docker_image': 'arvados/jobs', 'min_cores_per_node': 3, 'min_ram_mb_per_node': 3512, # ramMin + keep_cache 'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize 'keep_cache_mb_per_task': 512 } }), find_or_create=False, filters=[['repository', '=', 'arvados'], ['script', '=', 'crunchrunner'], ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'], ['docker_image_locator', 'in docker', 'arvados/jobs']]) @mock.patch("arvados.collection.CollectionReader") def test_done(self, reader): api = mock.MagicMock() runner = mock.MagicMock() runner.api = api runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" 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 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": []}, {"items": [{"manifest_text": "ABC"}]}) 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"} arvjob.done({ "state": "Complete", "output": "99999999999999999999999999999993+99", "log": "99999999999999999999999999999994+99", "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz" }) api.collections().list.assert_has_calls([ mock.call(), # Output collection check mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'], ['portable_data_hash', '=', '99999999999999999999999999999993+99'], ['name', '=', 'Output 9999999 of testjob']]), mock.call().execute(num_retries=0), mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']], select=['manifest_text']), mock.call().execute(num_retries=0), # Log collection's turn mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'], ['portable_data_hash', '=', '99999999999999999999999999999994+99'], ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]), mock.call().execute(num_retries=0), mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999994+99']], select=['manifest_text']), mock.call().execute(num_retries=0)]) api.collections().create.assert_has_calls([ mock.call(ensure_unique_name=True, body={'portable_data_hash': '99999999999999999999999999999993+99', 'manifest_text': 'XYZ', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'name': 'Output 9999999 of testjob'}), mock.call().execute(num_retries=0), mock.call(ensure_unique_name=True, body={'portable_data_hash': '99999999999999999999999999999994+99', 'manifest_text': 'ABC', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'name': 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz'}), mock.call().execute(num_retries=0), ]) arvjob.output_callback.assert_called_with({"out": "stuff"}, "success") @mock.patch("arvados.collection.CollectionReader") def test_done_use_existing_collection(self, reader): api = mock.MagicMock() runner = mock.MagicMock() runner.api = api 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 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"}]}, {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]}, ) 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"} arvjob.done({ "state": "Complete", "output": "99999999999999999999999999999993+99", "log": "99999999999999999999999999999994+99", "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz" }) api.collections().list.assert_has_calls([ mock.call(), # Output collection mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'], ['portable_data_hash', '=', '99999999999999999999999999999993+99'], ['name', '=', 'Output 9999999 of testjob']]), mock.call().execute(num_retries=0), # Log collection mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'], ['portable_data_hash', '=', '99999999999999999999999999999994+99'], ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]), mock.call().execute(num_retries=0) ]) self.assertFalse(api.collections().create.called) arvjob.output_callback.assert_called_with({"out": "stuff"}, "success") 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, 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/scatter2.cwl") metadata["cwlVersion"] = tool["cwlVersion"] mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118" 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/scatter2_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)/99999999999999999999999999999999+118/workflow.cwl', 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/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': 2048, 'min_cores_per_node': 1, '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) mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)]) mockcollection().open().__enter__().write.assert_has_calls([mock.call( '''{ "fileblub": { "basename": "token.txt", "class": "File", "location": "/keep/99999999999999999999999999999999+118/token.txt" }, "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().portable_data_hash.return_value = "99999999999999999999999999999999+118" 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)/99999999999999999999999999999999+118/workflow.cwl', 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/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() api = mock.MagicMock() api._rootDesc = copy.deepcopy(get_rootDesc()) del api._rootDesc.get('resources')['jobs']['methods']['create'] runner = arvados_cwl.ArvCwlRunner(api) self.assertEqual(runner.work_api, 'containers')