X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/7e54f217895d2f401563c54704c73a196e2d236d..3fa6aa4043286ad61e5f29c136d3cc2942e8750d:/sdk/cwl/tests/test_make_output.py diff --git a/sdk/cwl/tests/test_make_output.py b/sdk/cwl/tests/test_make_output.py index cd66eb1506..dd1da0b524 100644 --- a/sdk/cwl/tests/test_make_output.py +++ b/sdk/cwl/tests/test_make_output.py @@ -1,24 +1,40 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + +from future import standard_library +standard_library.install_aliases() + import functools import json import logging import mock import os -import StringIO +import io import unittest import arvados import arvados_cwl +import arvados_cwl.executor +from .mock_discovery import get_rootDesc class TestMakeOutput(unittest.TestCase): def setUp(self): self.api = mock.MagicMock() - self.api._rootDesc = arvados.api('v1')._rootDesc + self.api._rootDesc = get_rootDesc() + + def tearDown(self): + root_logger = logging.getLogger('') + + # Remove existing RuntimeStatusLoggingHandlers if they exist + handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)] + root_logger.handlers = handlers @mock.patch("arvados.collection.Collection") @mock.patch("arvados.collection.CollectionReader") def test_make_output_collection(self, reader, col): keep_client = mock.MagicMock() - runner = arvados_cwl.ArvCwlRunner(self.api, keep_client=keep_client) + runner = arvados_cwl.executor.ArvCwlExecutor(self.api, keep_client=keep_client) runner.project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' final = mock.MagicMock() @@ -26,12 +42,15 @@ class TestMakeOutput(unittest.TestCase): readermock = mock.MagicMock() reader.return_value = readermock - cwlout = StringIO.StringIO() + final_uuid = final.manifest_locator() + num_retries = runner.num_retries + + cwlout = io.StringIO() openmock = mock.MagicMock() final.open.return_value = openmock openmock.__enter__.return_value = cwlout - runner.make_output_collection("Test output", { + _, runner.final_output_collection = runner.make_output_collection("Test output", ["foo"], "tag0,tag1,tag2", {}, { "foo": { "class": "File", "location": "keep:99999999999999999999999999999991+99/foo.txt", @@ -41,22 +60,122 @@ class TestMakeOutput(unittest.TestCase): "bar": { "class": "File", "location": "keep:99999999999999999999999999999992+99/bar.txt", - "basename": "baz.txt" + "basename": "baz.txt", + "size": 4 } }) final.copy.assert_has_calls([mock.call('bar.txt', 'baz.txt', overwrite=False, source_collection=readermock)]) final.copy.assert_has_calls([mock.call('foo.txt', 'foo.txt', overwrite=False, source_collection=readermock)]) - final.save_new.assert_has_calls([mock.call(ensure_unique_name=True, name='Test output', owner_uuid='zzzzz-j7d0g-zzzzzzzzzzzzzzz')]) + final.save_new.assert_has_calls([mock.call(ensure_unique_name=True, name='Test output', owner_uuid='zzzzz-j7d0g-zzzzzzzzzzzzzzz', properties={}, storage_classes=['foo'])]) self.assertEqual("""{ "bar": { + "basename": "baz.txt", "class": "File", - "location": "baz.txt" + "location": "baz.txt", + "size": 4 }, "foo": { + "basename": "foo.txt", "class": "File", - "location": "foo.txt" + "location": "foo.txt", + "size": 3 } }""", cwlout.getvalue()) self.assertIs(final, runner.final_output_collection) + self.assertIs(final_uuid, runner.final_output_collection.manifest_locator()) + self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag0"}), mock.call().execute(num_retries=num_retries)]) + self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag1"}), mock.call().execute(num_retries=num_retries)]) + self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag2"}), mock.call().execute(num_retries=num_retries)]) + + @mock.patch("arvados.collection.Collection") + @mock.patch("arvados.collection.CollectionReader") + def test_make_output_for_multiple_file_targets(self, reader, col): + keep_client = mock.MagicMock() + runner = arvados_cwl.executor.ArvCwlExecutor(self.api, keep_client=keep_client) + runner.project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + + final = mock.MagicMock() + col.return_value = final + readermock = mock.MagicMock() + reader.return_value = readermock + + # This output describes a single file listed in 2 different directories + _, runner.final_output_collection = runner.make_output_collection("Test output", ["foo"], "", {}, { 'out': [ + { + 'basename': 'testdir1', + 'listing': [ + { + 'basename': 'test.txt', + 'nameroot': 'test', + 'nameext': '.txt', + 'location': 'keep:99999999999999999999999999999991+99/test.txt', + 'class': 'File', + 'size': 16 + } + ], + 'location': '_:99999999999999999999999999999992+99', + 'class': 'Directory' + }, + { + 'basename': 'testdir2', + 'listing': [ + { + 'basename': 'test.txt', + 'nameroot': 'test', + 'nameext': '.txt', + 'location': 'keep:99999999999999999999999999999991+99/test.txt', + 'class': + 'File', + 'size': 16 + } + ], + 'location': '_:99999999999999999999999999999993+99', + 'class': 'Directory' + }]}) + + # Check that copy is called on the collection for both locations + final.copy.assert_any_call("test.txt", "testdir1/test.txt", source_collection=mock.ANY, overwrite=mock.ANY) + final.copy.assert_any_call("test.txt", "testdir2/test.txt", source_collection=mock.ANY, overwrite=mock.ANY) + + @mock.patch("arvados.collection.Collection") + @mock.patch("arvados.collection.CollectionReader") + def test_make_output_for_literal_name_conflicts(self, reader, col): + keep_client = mock.MagicMock() + runner = arvados_cwl.executor.ArvCwlExecutor(self.api, keep_client=keep_client) + runner.project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + + final = mock.MagicMock() + col.return_value = final + readermock = mock.MagicMock() + reader.return_value = readermock + + # This output describes two literals with the same basename + _, runner.final_output_collection = runner.make_output_collection("Test output", ["foo"], "", {}, [ + { + 'lit': + { + 'basename': 'a_file', + 'nameext': '', + 'nameroot': 'a_file', + 'location': '_:f168fc0c-4291-40aa-a04e-366d57390560', + 'class': 'File', + 'contents': 'Hello file literal.' + } + }, + { + 'lit': + { + 'basename': 'a_file', + 'nameext': '', + 'nameroot': 'a_file', + 'location': '_:1728da8f-c64e-4a3e-b2e2-1ee356be7bc8', + 'class': 'File', + 'contents': 'Hello file literal.' + } + }]) + + # Check that the file name conflict is resolved and open is called for both + final.open.assert_any_call("a_file", "wb") + final.open.assert_any_call("a_file_2", "wb")