X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5836e576fe0b78c50383cf56e1c4fb4521daeca1..9b16a843a641159867ea390c4c2384b320183b15:/sdk/cwl/tests/test_job.py diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py index 30930dd49a..c110bc5d53 100644 --- a/sdk/cwl/tests/test_job.py +++ b/sdk/cwl/tests/test_job.py @@ -26,6 +26,28 @@ if not os.getenv('ARVADOS_DEBUG'): class TestJob(unittest.TestCase): + def helper(self, runner, enable_reuse=True): + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") + + make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, + collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) + loadingContext = arvados_cwl.context.ArvLoadingContext( + {"avsc_names": avsc_names, + "basedir": "", + "make_fs_access": make_fs_access, + "loader": Loader({}), + "metadata": {"cwlVersion": "v1.0"}, + "makeTool": runner.arv_make_tool}) + runtimeContext = arvados_cwl.context.ArvRuntimeContext( + {"work_api": "jobs", + "basedir": "", + "name": "test_run_job_"+str(enable_reuse), + "make_fs_access": make_fs_access, + "enable_reuse": enable_reuse, + "priority": 500}) + + return loadingContext, runtimeContext + # The test passes no builder.resources # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} @mock.patch('arvados.commands.keepdocker.list_images_in_arv') @@ -35,7 +57,6 @@ class TestJob(unittest.TestCase): 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_value = {"portable_data_hash": "99999999999999999999999999999993+99"} @@ -56,14 +77,13 @@ class TestJob(unittest.TestCase): "id": "#", "class": "CommandLineTool" }) - 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({}), - metadata={"cwlVersion": "v1.0"}) + + loadingContext, runtimeContext = self.helper(runner, enable_reuse) + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): - j.run(enable_reuse=enable_reuse) + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) runner.api.jobs().create.assert_called_with( body=JsonDiffMatcher({ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', @@ -105,7 +125,7 @@ class TestJob(unittest.TestCase): runner.api.links().create.side_effect = ApiError( mock.MagicMock(return_value={'status': 403}), 'Permission denied') - j.run(enable_reuse=enable_reuse) + j.run(runtimeContext) else: assert not runner.api.links().create.called @@ -122,9 +142,6 @@ class TestJob(unittest.TestCase): 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": [], @@ -148,14 +165,13 @@ class TestJob(unittest.TestCase): "id": "#", "class": "CommandLineTool" } - 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({}), - metadata={"cwlVersion": "v1.0"}) + + loadingContext, runtimeContext = self.helper(runner) + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access): - j.run(enable_reuse=True) + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) runner.api.jobs().create.assert_called_with( body=JsonDiffMatcher({ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', @@ -205,9 +221,13 @@ class TestJob(unittest.TestCase): {"items": []}, {"items": [{"manifest_text": "ABC"}]}) - arvjob = arvados_cwl.ArvadosJob(runner) - arvjob.name = "testjob" - arvjob.builder = mock.MagicMock() + arvjob = arvados_cwl.ArvadosJob(runner, + mock.MagicMock(), + {}, + None, + [], + [], + "testjob") arvjob.output_callback = mock.MagicMock() arvjob.collect_outputs = mock.MagicMock() arvjob.collect_outputs.return_value = {"out": "stuff"} @@ -275,9 +295,13 @@ class TestJob(unittest.TestCase): {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]}, ) - arvjob = arvados_cwl.ArvadosJob(runner) - arvjob.name = "testjob" - arvjob.builder = mock.MagicMock() + arvjob = arvados_cwl.ArvadosJob(runner, + mock.MagicMock(), + {}, + None, + [], + [], + "testjob") arvjob.output_callback = mock.MagicMock() arvjob.collect_outputs = mock.MagicMock() arvjob.collect_outputs.return_value = {"out": "stuff"} @@ -309,6 +333,34 @@ class TestJob(unittest.TestCase): class TestWorkflow(unittest.TestCase): + def helper(self, runner, enable_reuse=True): + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") + + make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, + collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) + + document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=make_fs_access("")) + document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session) + document_loader.fetch_text = document_loader.fetcher.fetch_text + document_loader.check_exists = document_loader.fetcher.check_exists + + loadingContext = arvados_cwl.context.ArvLoadingContext( + {"avsc_names": avsc_names, + "basedir": "", + "make_fs_access": make_fs_access, + "loader": document_loader, + "metadata": {"cwlVersion": "v1.0"}, + "construct_tool_object": runner.arv_make_tool}) + runtimeContext = arvados_cwl.context.ArvRuntimeContext( + {"work_api": "jobs", + "basedir": "", + "name": "test_run_wf_"+str(enable_reuse), + "make_fs_access": make_fs_access, + "enable_reuse": enable_reuse, + "priority": 500}) + + return loadingContext, runtimeContext + # The test passes no builder.resources # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} @mock.patch("arvados.collection.CollectionReader") @@ -330,27 +382,20 @@ class TestWorkflow(unittest.TestCase): 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") - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=api, fs_access=make_fs_access("")) - document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session) - document_loader.fetch_text = document_loader.fetcher.fetch_text - document_loader.check_exists = document_loader.fetcher.check_exists + loadingContext, runtimeContext = self.helper(runner) - tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl") + tool, metadata = loadingContext.loader.resolve_ref("tests/wf/scatter2.cwl") metadata["cwlVersion"] = tool["cwlVersion"] mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118" - 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 = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext) arvtool.formatgraph = None - it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access, tmp_outdir_prefix="") - it.next().run() - it.next().run() + it = arvtool.job({}, mock.MagicMock(), runtimeContext) + + it.next().run(runtimeContext) + it.next().run(runtimeContext) with open("tests/wf/scatter2_subwf.cwl") as f: subwf = StripYAMLComments(f.read()) @@ -416,27 +461,19 @@ class TestWorkflow(unittest.TestCase): 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") - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=api, fs_access=make_fs_access("")) - document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session) - document_loader.fetch_text = document_loader.fetcher.fetch_text - document_loader.check_exists = document_loader.fetcher.check_exists + loadingContext, runtimeContext = self.helper(runner) - tool, metadata = document_loader.resolve_ref("tests/wf/echo-wf.cwl") + tool, metadata = loadingContext.loader.resolve_ref("tests/wf/echo-wf.cwl") metadata["cwlVersion"] = tool["cwlVersion"] mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118" - 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 = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext) arvtool.formatgraph = None - it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access, tmp_outdir_prefix="") - it.next().run() - it.next().run() + it = arvtool.job({}, mock.MagicMock(), runtimeContext) + it.next().run(runtimeContext) + it.next().run(runtimeContext) with open("tests/wf/echo-subwf.cwl") as f: subwf = StripYAMLComments(f.read())