X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/16f704326f44fd1e5e5e60b936c9b5895d6a6ff8..b670c0c80785770774e28a80d883dc258510bdb0:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 39117d86e3..d2c4d9c2ea 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -18,7 +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 @@ -75,6 +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, @@ -112,6 +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", @@ -339,15 +354,15 @@ class TestSubmit(unittest.TestCase): stubs.api.collections().create.assert_has_calls([ mock.call(body=JsonDiffMatcher({ 'manifest_text': - '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', + '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'replication_desired': None, - 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', + 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': - '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', + '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', 'replication_desired': None, - 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', + 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': @@ -418,6 +433,7 @@ class TestSubmit(unittest.TestCase): def test_submit_runner_ram(self, stubs, tm): exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048", + "--api=jobs", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) @@ -446,6 +462,7 @@ class TestSubmit(unittest.TestCase): exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--output-name", output_name, + "--api=jobs", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) @@ -463,6 +480,7 @@ class TestSubmit(unittest.TestCase): def test_submit_pipeline_name(self, stubs, tm): exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--name=hello job 123", + "--api=jobs", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) @@ -482,6 +500,7 @@ class TestSubmit(unittest.TestCase): exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--output-tags", output_tags, + "--api=jobs", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) @@ -502,6 +521,7 @@ class TestSubmit(unittest.TestCase): exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--project-uuid", project_uuid, + "--api=jobs", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], sys.stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) @@ -521,16 +541,17 @@ class TestSubmit(unittest.TestCase): stubs.api.collections().create.assert_has_calls([ mock.call(body=JsonDiffMatcher({ 'manifest_text': - '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', + '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'replication_desired': None, - 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', + 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': - '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', + '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', 'replication_desired': None, - 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', - }), ensure_unique_name=False)]) + 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', + }), ensure_unique_name=False), + ]) expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( @@ -1380,6 +1401,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_request_uuid(self, stubs): + stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123" stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy" stubs.api.container_requests().update().execute.return_value = { @@ -1425,9 +1447,99 @@ 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" + existing_template_uuid = "zzzzz-p5p6p-validworkfloyml" def _adjust_script_params(self, expect_component): expect_component['script_parameters']['x'] = { @@ -1609,22 +1721,24 @@ class TestCreateWorkflow(unittest.TestCase): @stubs def test_incompatible_api(self, stubs): - capture_stderr = io.StringIO() + capture_stderr = StringIO() acr_logger = logging.getLogger('arvados.cwl-runner') stderr_logger = logging.StreamHandler(capture_stderr) acr_logger.addHandler(stderr_logger) - 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)) - acr_logger.removeHandler(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): @@ -1750,7 +1864,7 @@ class TestTemplateInputs(unittest.TestCase): @stubs def test_inputs_empty(self, stubs): exited = arvados_cwl.main( - ["--create-template", + ["--debug", "--api=jobs", "--create-template", "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) @@ -1762,7 +1876,7 @@ class TestTemplateInputs(unittest.TestCase): @stubs def test_inputs(self, stubs): exited = arvados_cwl.main( - ["--create-template", + ["--api=jobs", "--create-template", "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api)