X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/efd0065027f09031c28d1da41cf5fc4e226ce098..98457f6fdb93116d31bec47057094041e9c47bde:/sdk/cwl/tests/test_job.py diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py index f552cd82f4..e95589cf65 100644 --- a/sdk/cwl/tests/test_job.py +++ b/sdk/cwl/tests/test_job.py @@ -1,6 +1,19 @@ -import unittest + +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): @@ -9,40 +22,57 @@ class TestJob(unittest.TestCase): def test_run(self): runner = mock.MagicMock() runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + runner.ignore_docker_for_reuse = False + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3") + tool = { "inputs": [], "outputs": [], - "baseCommand": "ls" + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}] } - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool) + make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api) + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, + basedir="", make_fs_access=make_fs_access, loader=Loader({})) arvtool.formatgraph = None - for j in arvtool.job({}, "", mock.MagicMock()): + for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): j.run() - runner.api.jobs().create.assert_called_with(body={ - 'runtime_constraints': {}, - 'script_parameters': { - 'tasks': [{ - 'task.env': {'TMPDIR': '$(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 - } - }, find_or_create=True) + 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', '$(task.outdir)'] + }], + }, + 'script_version': 'master', + 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6', + 'repository': 'arvados', + 'script': 'crunchrunner', + 'runtime_constraints': { + 'docker_image': 'arvados/jobs', + 'min_cores_per_node': 1, + 'min_ram_mb_per_node': 1024, + 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize + } + }, + find_or_create=True, + filters=[['repository', '=', 'arvados'], + ['script', '=', 'crunchrunner'], + ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'], + ['docker_image_locator', 'in docker', 'arvados/jobs']] + ) # The test passes some fields in builder.resources # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} def test_resource_requirements(self): runner = mock.MagicMock() runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + runner.ignore_docker_for_reuse = False + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3") + tool = { "inputs": [], "outputs": [], @@ -54,26 +84,166 @@ class TestJob(unittest.TestCase): }], "baseCommand": "ls" } - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool) + make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api) + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, + make_fs_access=make_fs_access, loader=Loader({})) arvtool.formatgraph = None - for j in arvtool.job({}, "", mock.MagicMock()): + for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): j.run() - runner.api.jobs().create.assert_called_with(body={ - 'runtime_constraints': {}, - 'script_parameters': { - 'tasks': [{ - 'task.env': {'TMPDIR': '$(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)'}, + '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', + 'min_cores_per_node': 3, + 'min_ram_mb_per_node': 3000, + 'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize + } + }, + 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.Collection") + def test_done(self, col): + 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 + + col().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.Collection") + def test_done_use_existing_collection(self, col): + api = mock.MagicMock() + + runner = mock.MagicMock() + runner.api = api + runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + runner.num_retries = 0 + + col().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} + def test_run(self): + arvados_cwl.add_arv_hints() + + runner = arvados_cwl.ArvCwlRunner(mock.MagicMock()) + runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + runner.ignore_docker_for_reuse = False + 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"] + + 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() + + 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.json': '$(task.keep)/f101400a398097d4398cdb3eb5d1a7ca+118/workflow.json', + 'cwl.input.json': '$(task.keep)/f101400a398097d4398cdb3eb5d1a7ca+118/cwl.input.json' + }, + 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'workflow.json', u'cwl.input.json'], + '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)