X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f04cfcce18c6e4bd1faf3140ccbc835328580024..c2af1e524e87fa76f51bed62d4821d4fe1b7fcc0:/sdk/cwl/tests/test_job.py?ds=sidebyside diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py index 56f311026e..f1c6ba01b1 100644 --- a/sdk/cwl/tests/test_job.py +++ b/sdk/cwl/tests/test_job.py @@ -1,49 +1,93 @@ -import unittest +import functools +import json +import logging import mock +import os +import unittest +import copy + +import arvados import arvados_cwl +import cwltool.process +from schema_salad.ref_resolver import Loader +from .mock_discovery import get_rootDesc + +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" - tool = { - "inputs": [], - "outputs": [], - "baseCommand": "ls" - } - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool) - arvtool.formatgraph = None - for j in arvtool.job({}, "", mock.MagicMock()): - j.run() - runner.api.jobs().create.assert_called_with(body={ - 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', - 'runtime_constraints': {}, - 'script_parameters': { - 'tasks': [{ - 'task.env': {'TMPDIR': '$(task.tmpdir)'}, - 'command': ['ls'] - }], - 'crunchrunner': '83db29f08544e1c319572a6bd971088a+140/crunchrunner' - }, - 'script_version': 'master', - 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6', - 'repository': 'arvados', - 'script': 'crunchrunner', - 'runtime_constraints': { - 'min_cores_per_node': 1, - 'min_ram_mb_per_node': 1024, - 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize + @mock.patch('arvados.commands.keepdocker.list_images_in_arv') + def test_run(self, list_images_in_arv): + for enable_reuse in (True, False): + runner = mock.MagicMock() + runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + runner.ignore_docker_for_reuse = False + runner.num_retries = 0 + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") + + list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]] + runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"} + + tool = { + "inputs": [], + "outputs": [], + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}] } - }, find_or_create=True) + 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(enable_reuse=enable_reuse) + 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:'+arvados_cwl.__version__, + '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', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'], + ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]] + ) # 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") + + tool = { "inputs": [], "outputs": [], @@ -52,30 +96,205 @@ class TestJob(unittest.TestCase): "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", }], "baseCommand": "ls" } - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool) + 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, + make_fs_access=make_fs_access, loader=Loader({})) arvtool.formatgraph = None - for j in arvtool.job({}, "", mock.MagicMock()): + 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': {'TMPDIR': '$(task.tmpdir)'}, - 'command': ['ls'] - }], - 'crunchrunner': '83db29f08544e1c319572a6bd971088a+140/crunchrunner' + 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)'}, + 'task.keepTmpOutput': True, + 'command': ['ls'] + }] }, 'script_version': 'master', - 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6', - 'repository': 'arvados', - 'script': 'crunchrunner', - 'runtime_constraints': { - 'min_cores_per_node': 3, - 'min_ram_mb_per_node': 3000, - 'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize - } - }, find_or_create=True) + 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6', + 'repository': 'arvados', + 'script': 'crunchrunner', + 'runtime_constraints': { + 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'min_cores_per_node': 3, + 'min_ram_mb_per_node': 3000, + 'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize + 'keep_cache_mb_per_task': 512 + } + }, + find_or_create=True, + filters=[['repository', '=', 'arvados'], + ['script', '=', 'crunchrunner'], + ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'], + ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]]) + + @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 = [] + api.collections().list().execute.side_effect = ({"items": []}, + {"items": [{"manifest_text": "XYZ"}]}) + + arvjob = arvados_cwl.ArvadosJob(runner) + arvjob.name = "testjob" + arvjob.builder = mock.MagicMock() + arvjob.output_callback = mock.MagicMock() + arvjob.collect_outputs = mock.MagicMock() + + arvjob.done({ + "state": "Complete", + "output": "99999999999999999999999999999993+99", + "log": "99999999999999999999999999999994+99", + "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + }) + + api.collections().list.assert_has_calls([ + mock.call(), + 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)]) + + 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'}) + + @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 = [] + api.collections().list().execute.side_effect = ({"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.done({ + "state": "Complete", + "output": "99999999999999999999999999999993+99", + "log": "99999999999999999999999999999994+99", + "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + }) + + api.collections().list.assert_has_calls([ + mock.call(), + mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'], + ['portable_data_hash', '=', '99999999999999999999999999999993+99'], + ['name', '=', 'Output 9999999 of testjob']]), + mock.call().execute(num_retries=0)]) + + self.assertFalse(api.collections().create.called) + + +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") + @mock.patch('arvados.commands.keepdocker.list_images_in_arv') + def test_run(self, list_images_in_arv, mockcollection): + 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.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, 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() + + 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:'+arvados_cwl.__version__, + '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:'+arvados_cwl.__version__]], + 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')