X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/08cc91f0493dd8dfe27046faf02c2c907e50443e..a894a61cc9004e184bc63f9f0a785f555d6c6829:/sdk/cwl/tests/test_job.py diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py index dba65b0f8a..8d12aab7e2 100644 --- a/sdk/cwl/tests/test_job.py +++ b/sdk/cwl/tests/test_job.py @@ -1,9 +1,13 @@ -import arvados_cwl 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) @@ -18,16 +22,20 @@ class TestJob(unittest.TestCase): 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") + runner.num_retries = 0 + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") tool = { "inputs": [], "outputs": [], - "baseCommand": "ls" + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}] } - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, avsc_names=avsc_names, basedir="") + make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api) + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, + basedir="", make_fs_access=make_fs_access, loader=Loader({})) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir=""): + for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): j.run() runner.api.jobs().create.assert_called_with( body={ @@ -35,8 +43,8 @@ class TestJob(unittest.TestCase): 'runtime_constraints': {}, 'script_parameters': { 'tasks': [{ - 'task.env': {'TMPDIR': '$(task.tmpdir)'}, - 'command': ['ls'] + 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'}, + 'command': ['ls', '$(task.outdir)'] }], }, 'script_version': 'master', @@ -63,7 +71,11 @@ class TestJob(unittest.TestCase): runner = mock.MagicMock() runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3") + runner.num_retries = 0 + arvados_cwl.add_arv_hints() + + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") + tool = { "inputs": [], @@ -73,12 +85,20 @@ class TestJob(unittest.TestCase): "coresMin": 3, "ramMin": 3000, "tmpdirMin": 4000 + }, { + "class": "http://arvados.org/cwl#RuntimeConstraints", + "keep_cache": 512, + "outputDirType": "keep_output_dir" + }, { + "class": "http://arvados.org/cwl#APIRequirement", }], "baseCommand": "ls" } - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, avsc_names=avsc_names) + make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api) + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, + make_fs_access=make_fs_access, loader=Loader({})) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir=""): + for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): j.run() runner.api.jobs().create.assert_called_with( body={ @@ -86,7 +106,8 @@ class TestJob(unittest.TestCase): 'runtime_constraints': {}, 'script_parameters': { 'tasks': [{ - 'task.env': {'TMPDIR': '$(task.tmpdir)'}, + 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'}, + 'task.keepTmpOutput': True, 'command': ['ls'] }] }, @@ -98,7 +119,8 @@ class TestJob(unittest.TestCase): 'docker_image': 'arvados/jobs', 'min_cores_per_node': 3, 'min_ram_mb_per_node': 3000, - 'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize + 'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize + 'keep_cache_mb_per_task': 512 } }, find_or_create=True, @@ -107,8 +129,8 @@ class TestJob(unittest.TestCase): ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'], ['docker_image_locator', 'in docker', 'arvados/jobs']]) - @mock.patch("arvados.collection.Collection") - def test_done(self, col): + @mock.patch("arvados.collection.CollectionReader") + def test_done(self, reader): api = mock.MagicMock() runner = mock.MagicMock() @@ -117,7 +139,7 @@ class TestJob(unittest.TestCase): runner.num_retries = 0 runner.ignore_docker_for_reuse = False - col().open.return_value = [] + reader().open.return_value = [] api.collections().list().execute.side_effect = ({"items": []}, {"items": [{"manifest_text": "XYZ"}]}) @@ -151,8 +173,8 @@ class TestJob(unittest.TestCase): 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'name': 'Output 9999999 of testjob'}) - @mock.patch("arvados.collection.Collection") - def test_done_use_existing_collection(self, col): + @mock.patch("arvados.collection.CollectionReader") + def test_done_use_existing_collection(self, reader): api = mock.MagicMock() runner = mock.MagicMock() @@ -160,7 +182,7 @@ class TestJob(unittest.TestCase): runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.num_retries = 0 - col().open.return_value = [] + reader().open.return_value = [] api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},) arvjob = arvados_cwl.ArvadosJob(runner) @@ -184,3 +206,69 @@ class TestJob(unittest.TestCase): 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("")