import logging import mock import unittest import os import functools import json import arvados_cwl import cwltool.process from schema_salad.ref_resolver import Loader 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") 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']] ) # 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): runner = mock.MagicMock() runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.num_retries = 0 arvados_cwl.add_arv_hints() document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") 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", }], "baseCommand": "ls" } 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(), 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)'}, 'task.keepTmpOutput': True, 'command': ['ls'] }] }, 'script_version': 'master', 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6', 'repository': 'arvados', 'script': 'crunchrunner', 'runtime_constraints': { 'docker_image': 'arvados/jobs', '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']]) @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") def test_run(self, mockcollection): try: 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") 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() 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("")