X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/47e42f1129363c2565e69c36ff26ce9c42731fb8..060d38d627bd1e51dd2b3c6e7de9af6aa7d7b6f3:/sdk/cwl/tests/test_job.py diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py index 8d12aab7e2..5d140ba6b9 100644 --- a/sdk/cwl/tests/test_job.py +++ b/sdk/cwl/tests/test_job.py @@ -1,79 +1,125 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + +import functools +import json import logging import mock -import unittest import os -import functools -import json +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): # The test passes no builder.resources # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} - def test_run(self): - runner = mock.MagicMock() - 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") + @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 + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") - tool = { - "inputs": [], - "outputs": [], - "baseCommand": "ls", - "arguments": [{"valueFrom": "$(runtime.outdir)"}] - } - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, - basedir="", make_fs_access=make_fs_access, loader=Loader({})) - arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): - j.run() - runner.api.jobs().create.assert_called_with( - body={ - 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', - 'runtime_constraints': {}, - 'script_parameters': { - 'tasks': [{ - 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'}, - 'command': ['ls', '$(task.outdir)'] - }], - }, - 'script_version': 'master', - 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6', - '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=True, - filters=[['repository', '=', 'arvados'], - ['script', '=', 'crunchrunner'], - ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'], - ['docker_image_locator', 'in docker', 'arvados/jobs']] - ) + 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": "$(runtime.outdir)"}] + }) + make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, + collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, + basedir="", make_fs_access=make_fs_access, loader=Loader({})) + arvtool.formatgraph = None + for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): + j.run(enable_reuse=enable_reuse) + runner.api.jobs().create.assert_called_with( + body=JsonDiffMatcher({ + 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', + 'runtime_constraints': {}, + 'script_parameters': { + 'tasks': [{ + 'task.env': {'HOME': '$(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(enable_reuse=enable_reuse) + j.output_callback.assert_called_with({}, 'success') + 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} - def test_resource_requirements(self): + @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"} + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") @@ -91,17 +137,22 @@ class TestJob(unittest.TestCase): "outputDirType": "keep_output_dir" }, { "class": "http://arvados.org/cwl#APIRequirement", + }, + { + "class": "http://arvados.org/cwl#ReuseRequirement", + "enableReuse": False }], "baseCommand": "ls" } - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api) + 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({})) arvtool.formatgraph = None for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): - j.run() + j.run(enable_reuse=True) runner.api.jobs().create.assert_called_with( - body={ + body=JsonDiffMatcher({ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'runtime_constraints': {}, 'script_parameters': { @@ -112,21 +163,21 @@ class TestJob(unittest.TestCase): }] }, 'script_version': 'master', - 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6', + 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d', 'repository': 'arvados', 'script': 'crunchrunner', 'runtime_constraints': { 'docker_image': 'arvados/jobs', 'min_cores_per_node': 3, - 'min_ram_mb_per_node': 3000, + '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=True, + }), + find_or_create=False, filters=[['repository', '=', 'arvados'], ['script', '=', 'crunchrunner'], - ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'], + ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'], ['docker_image_locator', 'in docker', 'arvados/jobs']]) @mock.patch("arvados.collection.CollectionReader") @@ -139,15 +190,22 @@ class TestJob(unittest.TestCase): runner.num_retries = 0 runner.ignore_docker_for_reuse = False - reader().open.return_value = [] + 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": [{"manifest_text": "XYZ"}]}, + {"items": []}, + {"items": [{"manifest_text": "ABC"}]}) arvjob = arvados_cwl.ArvadosJob(runner) arvjob.name = "testjob" arvjob.builder = mock.MagicMock() arvjob.output_callback = mock.MagicMock() arvjob.collect_outputs = mock.MagicMock() + arvjob.collect_outputs.return_value = {"out": "stuff"} arvjob.done({ "state": "Complete", @@ -158,20 +216,39 @@ class TestJob(unittest.TestCase): 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_called_with( - ensure_unique_name=True, - body={'portable_data_hash': '99999999999999999999999999999993+99', - 'manifest_text': 'XYZ', - 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', - 'name': 'Output 9999999 of testjob'}) + 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): @@ -182,14 +259,23 @@ class TestJob(unittest.TestCase): runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.num_retries = 0 - reader().open.return_value = [] - api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},) + 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) arvjob.name = "testjob" arvjob.builder = mock.MagicMock() arvjob.output_callback = mock.MagicMock() arvjob.collect_outputs = mock.MagicMock() + arvjob.collect_outputs.return_value = {"out": "stuff"} arvjob.done({ "state": "Complete", @@ -200,75 +286,103 @@ class TestJob(unittest.TestCase): 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)]) + 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): # The test passes no builder.resources # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} @mock.patch("arvados.collection.Collection") - def test_run(self, mockcollection): - try: - arvados_cwl.add_arv_hints() + @mock.patch('arvados.commands.keepdocker.list_images_in_arv') + def test_run(self, list_images_in_arv, mockcollection): + arvados_cwl.add_arv_hints() - runner = arvados_cwl.ArvCwlRunner(mock.MagicMock()) - 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") + api = mock.MagicMock() + api._rootDesc = get_rootDesc() - tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl") - metadata["cwlVersion"] = tool["cwlVersion"] + runner = arvados_cwl.ArvCwlRunner(api) + self.assertEqual(runner.work_api, 'jobs') - mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118" + list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] + runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"} - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api) - 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.formatgraph = None - it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access) - it.next().run() - it.next().run() - - with open("tests/wf/scatter2_subwf.cwl") as f: - subwf = f.read() - - mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)]) - mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')]) - - runner.api.jobs().create.assert_called_with( - body={ - 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6', - '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', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'], - ['docker_image_locator', 'in docker', 'arvados/jobs']], - find_or_create=True) - except: - logging.exception("") + 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") + metadata["cwlVersion"] = tool["cwlVersion"] + + mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118" + + 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.formatgraph = None + it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access) + it.next().run() + it.next().run() + + 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( +'''{ + "sleeptime": 5 +}''')]) + + 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')