X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5e66fb80a5053b1c51b58191f042dbc40839ba9d..ac0dc6c57a2b4f736b6faf62421de56a3355db04:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 7f1688c756..5f92cee942 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -6,6 +6,7 @@ from future import standard_library standard_library.install_aliases() from builtins import object from builtins import str +from future.utils import viewvalues import copy import io @@ -17,7 +18,16 @@ import mock import sys import unittest -from io import BytesIO, StringIO +from io import BytesIO + +# StringIO.StringIO and io.StringIO have different behavior write() is +# called with both python2 (byte) strings and unicode strings +# (specifically there's some logging in cwltool that causes trouble). +# This isn't a problem on python3 because all string are unicode. +if sys.version_info[0] < 3: + from StringIO import StringIO +else: + from io import StringIO import arvados import arvados.collection @@ -74,6 +84,7 @@ def stubs(func): stubs.api = mock.MagicMock() stubs.api._rootDesc = get_rootDesc() + stubs.api._rootDesc["uuidPrefix"] = "zzzzz" stubs.api.users().current().execute.return_value = { "uuid": stubs.fake_user_uuid, @@ -101,7 +112,7 @@ def stubs(func): return CollectionExecute(created_collections[uuid]) def collection_getstub(created_collections, uuid): - for v in created_collections.values(): + for v in viewvalues(created_collections): if uuid in (v["uuid"], v["portable_data_hash"]): return CollectionExecute(v) @@ -111,6 +122,11 @@ def stubs(func): "portable_data_hash": "99999999999999999999999999999998+99", "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt" }, + "99999999999999999999999999999997+99": { + "uuid": "", + "portable_data_hash": "99999999999999999999999999999997+99", + "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt" + }, "99999999999999999999999999999994+99": { "uuid": "", "portable_data_hash": "99999999999999999999999999999994+99", @@ -511,7 +527,7 @@ class TestSubmit(unittest.TestCase): body=JsonDiffMatcher(expect_pipeline)) @stubs - def test_submit_container(self, stubs): + def test_submit_container(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -558,7 +574,7 @@ class TestSubmit(unittest.TestCase): stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(stubs.capture_stdout.getvalue(), - stubs.expect_container_request_uuid + '\n') + stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @stubs @@ -601,7 +617,7 @@ class TestSubmit(unittest.TestCase): ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) - + expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', @@ -619,7 +635,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_output_name(self, stubs): output_name = "test_output_name" - + exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -641,7 +657,7 @@ class TestSubmit(unittest.TestCase): self.assertEqual(exited, 0) @stubs - def test_submit_storage_classes(self, stubs): + def test_submit_storage_classes(self, stubs): exited = arvados_cwl.main( ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -725,7 +741,7 @@ class TestSubmit(unittest.TestCase): ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) - + expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', @@ -1393,7 +1409,7 @@ class TestSubmit(unittest.TestCase): stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) stubs.api.container_requests().update.assert_called_with( - uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec), cluster_id="zzzzz") + uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec)) self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) @@ -1424,6 +1440,96 @@ class TestSubmit(unittest.TestCase): stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) + @mock.patch("arvados.collection.CollectionReader") + @stubs + def test_submit_uuid_inputs(self, stubs, collectionReader): + collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt") + def list_side_effect(**kwargs): + m = mock.MagicMock() + if "count" in kwargs: + m.execute.return_value = {"items": [ + {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999998+99"} + ]} + else: + m.execute.return_value = {"items": []} + return m + stubs.api.collections().list.side_effect = list_side_effect + + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", + "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + + expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz' + expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz' + expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz' + + stubs.api.collections().list.assert_has_calls([ + mock.call(count='none', + filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz']]], + select=['uuid', 'portable_data_hash'])]) + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container)) + self.assertEqual(stubs.capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + self.assertEqual(exited, 0) + + @stubs + def test_submit_mismatched_uuid_inputs(self, stubs): + def list_side_effect(**kwargs): + m = mock.MagicMock() + if "count" in kwargs: + m.execute.return_value = {"items": [ + {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999997+99"} + ]} + else: + m.execute.return_value = {"items": []} + return m + stubs.api.collections().list.side_effect = list_side_effect + + for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"): + capture_stderr = StringIO() + cwltool_logger = logging.getLogger('cwltool') + stderr_logger = logging.StreamHandler(capture_stderr) + cwltool_logger.addHandler(stderr_logger) + + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", + "tests/wf/submit_wf.cwl", infile], + stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client) + + self.assertEqual(exited, 1) + self.assertRegexpMatches( + capture_stderr.getvalue(), + r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99") + finally: + cwltool_logger.removeHandler(stderr_logger) + + @mock.patch("arvados.collection.CollectionReader") + @stubs + def test_submit_unknown_uuid_inputs(self, stubs, collectionReader): + collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt") + capture_stderr = StringIO() + + cwltool_logger = logging.getLogger('cwltool') + stderr_logger = logging.StreamHandler(capture_stderr) + cwltool_logger.addHandler(stderr_logger) + + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", + "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"], + stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client) + + try: + self.assertEqual(exited, 1) + self.assertRegexpMatches( + capture_stderr.getvalue(), + r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found") + finally: + cwltool_logger.removeHandler(stderr_logger) + class TestCreateTemplate(unittest.TestCase): existing_template_uuid = "zzzzz-d1hrv-validworkfloyml" @@ -1540,7 +1646,7 @@ class TestCreateTemplate(unittest.TestCase): self.assertEqual(stubs.capture_stdout.getvalue(), self.existing_template_uuid + '\n') self.assertEqual(exited, 0) - + class TestCreateWorkflow(unittest.TestCase): existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml" @@ -1608,20 +1714,24 @@ class TestCreateWorkflow(unittest.TestCase): @stubs def test_incompatible_api(self, stubs): - capture_stderr = io.StringIO() - logging.getLogger('arvados.cwl-runner').addHandler( - logging.StreamHandler(capture_stderr)) - - exited = arvados_cwl.main( - ["--update-workflow", self.existing_workflow_uuid, - "--api=jobs", - "--debug", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - sys.stderr, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 1) - self.assertRegexpMatches( - capture_stderr.getvalue(), - "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid)) + capture_stderr = StringIO() + acr_logger = logging.getLogger('arvados.cwl-runner') + stderr_logger = logging.StreamHandler(capture_stderr) + acr_logger.addHandler(stderr_logger) + + try: + exited = arvados_cwl.main( + ["--update-workflow", self.existing_workflow_uuid, + "--api=jobs", + "--debug", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stderr, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 1) + self.assertRegexpMatches( + capture_stderr.getvalue(), + "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid)) + finally: + acr_logger.removeHandler(stderr_logger) @stubs def test_update(self, stubs):