X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/75953fd324f2629f282f6b98e96dc1cef8bc2da4..093ec98e4a065acfc537ea22c08c337c115fe273:/sdk/python/tests/test_collections.py diff --git a/sdk/python/tests/test_collections.py b/sdk/python/tests/test_collections.py index a315044912..5cf4993b2f 100644 --- a/sdk/python/tests/test_collections.py +++ b/sdk/python/tests/test_collections.py @@ -1,3 +1,7 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + from __future__ import absolute_import from builtins import object @@ -5,10 +9,12 @@ import arvados import copy import mock import os -import pprint +import random import re import sys -import tempfile +import datetime +import ciso8601 +import time import unittest from . import run_test_server @@ -30,7 +36,8 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, @classmethod def setUpClass(cls): super(ArvadosCollectionsTest, cls).setUpClass() - run_test_server.authorize_with('active') + # need admin privileges to make collections with unsigned blocks + run_test_server.authorize_with('admin') cls.api_client = arvados.api('v1') cls.keep_client = arvados.KeepClient(api_client=cls.api_client, local_store=cls.local_store) @@ -52,7 +59,7 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" + "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n", "wrong manifest: got {}".format(cw.manifest_text())) - cw.finish() + cw.save_new() return cw.portable_data_hash() def test_pdh_is_native_str(self): @@ -91,6 +98,8 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, self.assertEqual(stream0.readfrom(2**26, 0), b'', 'reading zero bytes should have returned empty string') + self.assertEqual(3, len(cr)) + self.assertTrue(cr) def _test_subset(self, collection, expected): cr = arvados.CollectionReader(collection, self.api_client) @@ -311,7 +320,7 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, def __init__(self, content, num_retries=0): self.content = content - def get(self, locator, num_retries=0): + def get(self, locator, num_retries=0, prefetch=False): return self.content[locator] def test_stream_reader(self): @@ -497,15 +506,6 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, self.assertRaises(arvados.errors.AssertionError, cwriter.write, "badtext") - def test_read_arbitrary_data_with_collection_reader(self): - # arv-get relies on this to do "arv-get {keep-locator} -". - self.write_foo_bar_baz() - self.assertEqual( - 'foobar', - arvados.CollectionReader( - '3858f62230ac3c915f300c664312c63f+6' - ).manifest_text()) - class CollectionTestMixin(tutil.ApiClientMock): API_COLLECTIONS = run_test_server.fixture('collections') @@ -561,34 +561,13 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): api_client=client) self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text()) - def test_locator_init_fallback_to_keep(self): - # crunch-job needs this to read manifests that have only ever - # been written to Keep. - client = self.api_client_mock(200) - self.mock_get_collection(client, 404, None) - with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200): - reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH, - api_client=client) - self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text()) - - def test_uuid_init_no_fallback_to_keep(self): - # Do not look up a collection UUID in Keep. - client = self.api_client_mock(404) - with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200): - with self.assertRaises(arvados.errors.ApiError): - reader = arvados.CollectionReader(self.DEFAULT_UUID, - api_client=client) - - def test_try_keep_first_if_permission_hint(self): - # To verify that CollectionReader tries Keep first here, we - # mock API server to return the wrong data. - client = self.api_client_mock(200) - with tutil.mock_keep_responses(self.ALT_MANIFEST, 200): - self.assertEqual( - self.ALT_MANIFEST, - arvados.CollectionReader( - self.ALT_DATA_HASH + '+Affffffffffffffffffffffffffffffffffffffff@fedcba98', - api_client=client).manifest_text()) + def test_init_no_fallback_to_keep(self): + # Do not look up a collection UUID or PDH in Keep. + for key in [self.DEFAULT_UUID, self.DEFAULT_DATA_HASH]: + client = self.api_client_mock(404) + with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200): + with self.assertRaises(arvados.errors.ApiError): + reader = arvados.CollectionReader(key, api_client=client) def test_init_num_retries_propagated(self): # More of an integration test... @@ -626,21 +605,14 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): reader = arvados.CollectionReader('d41d8cd98f00b204e9800998ecf8427e+0', api_client=client) self.assertEqual('', reader.manifest_text()) + self.assertEqual(0, len(reader)) + self.assertFalse(reader) def test_api_response(self): client = self.api_client_mock() reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) self.assertEqual(self.DEFAULT_COLLECTION, reader.api_response()) - def test_api_response_with_collection_from_keep(self): - client = self.api_client_mock() - self.mock_get_collection(client, 404, 'foo') - with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200): - reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH, - api_client=client) - api_response = reader.api_response() - self.assertIsNone(api_response) - def check_open_file(self, coll_file, stream_name, file_name, file_size): self.assertFalse(coll_file.closed, "returned file is not open") self.assertEqual(stream_name, coll_file.stream_name()) @@ -830,6 +802,18 @@ class CollectionMethods(run_test_server.TestCaseWithServers): self.assertEqual(fn0, c.items()[0][0]) self.assertEqual(fn1, c.items()[1][0]) + def test_get_properties(self): + c = Collection() + self.assertEqual(c.get_properties(), {}) + c.save_new(properties={"foo":"bar"}) + self.assertEqual(c.get_properties(), {"foo":"bar"}) + + def test_get_trash_at(self): + c = Collection() + self.assertEqual(c.get_trash_at(), None) + c.save_new(trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111)) + self.assertEqual(c.get_trash_at(), ciso8601.parse_datetime('2111-01-01T11:11:11.111111000Z')) + class CollectionOpenModes(run_test_server.TestCaseWithServers): @@ -850,17 +834,58 @@ class CollectionOpenModes(run_test_server.TestCaseWithServers): with c.open('foo', 'wb') as f: f.write('foo') for mode in ['r', 'rt', 'r+', 'rt+', 'w', 'wt', 'a', 'at']: - if sys.version_info >= (3, 0): - with self.assertRaises(NotImplementedError): - c.open('foo', mode) - else: - with c.open('foo', mode) as f: - if mode[0] == 'r' and '+' not in mode: - self.assertEqual('foo', f.read(3)) - else: - f.write('bar') - f.seek(-3, os.SEEK_CUR) - self.assertEqual('bar', f.read(3)) + with c.open('foo', mode) as f: + if mode[0] == 'r' and '+' not in mode: + self.assertEqual('foo', f.read(3)) + else: + f.write('bar') + f.seek(0, os.SEEK_SET) + self.assertEqual('bar', f.read(3)) + + +class TextModes(run_test_server.TestCaseWithServers): + + def setUp(self): + arvados.config.KEEP_BLOCK_SIZE = 4 + if sys.version_info < (3, 0): + import unicodedata + self.sailboat = unicodedata.lookup('SAILBOAT') + self.snowman = unicodedata.lookup('SNOWMAN') + else: + self.sailboat = '\N{SAILBOAT}' + self.snowman = '\N{SNOWMAN}' + + def tearDown(self): + arvados.config.KEEP_BLOCK_SIZE = 2 ** 26 + + def test_read_sailboat_across_block_boundary(self): + c = Collection() + f = c.open('sailboats', 'wb') + data = self.sailboat.encode('utf-8') + f.write(data) + f.write(data[:1]) + f.write(data[1:]) + f.write(b'\n') + f.close() + self.assertRegex(c.portable_manifest_text(), r'\+4 .*\+3 ') + + f = c.open('sailboats', 'r') + string = f.readline() + self.assertEqual(string, self.sailboat+self.sailboat+'\n') + f.close() + + def test_write_snowman_across_block_boundary(self): + c = Collection() + f = c.open('snowmany', 'w') + data = self.snowman + f.write(data+data+'\n'+data+'\n') + f.close() + self.assertRegex(c.portable_manifest_text(), r'\+4 .*\+4 .*\+3 ') + + f = c.open('snowmany', 'r') + self.assertEqual(f.readline(), self.snowman+self.snowman+'\n') + self.assertEqual(f.readline(), self.snowman+'\n') + f.close() class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): @@ -883,6 +908,37 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): self.assertEqual(c1.manifest_text, c2.manifest_text) self.assertNotEqual(c1.replication_desired, c2.replication_desired) + def test_storage_classes_desired_kept_on_load(self): + m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n' + c1 = Collection(m, storage_classes_desired=['archival']) + c1.save_new() + loc = c1.manifest_locator() + c2 = Collection(loc) + self.assertEqual(c1.manifest_text, c2.manifest_text) + self.assertEqual(c1.storage_classes_desired(), c2.storage_classes_desired()) + + def test_storage_classes_change_after_save(self): + m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n' + c1 = Collection(m, storage_classes_desired=['archival']) + c1.save_new() + loc = c1.manifest_locator() + c2 = Collection(loc) + self.assertEqual(['archival'], c2.storage_classes_desired()) + c2.save(storage_classes=['highIO']) + self.assertEqual(['highIO'], c2.storage_classes_desired()) + c3 = Collection(loc) + self.assertEqual(c1.manifest_text, c3.manifest_text) + self.assertEqual(['highIO'], c3.storage_classes_desired()) + + def test_storage_classes_desired_not_loaded_if_provided(self): + m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n' + c1 = Collection(m, storage_classes_desired=['archival']) + c1.save_new() + loc = c1.manifest_locator() + c2 = Collection(loc, storage_classes_desired=['default']) + self.assertEqual(c1.manifest_text, c2.manifest_text) + self.assertNotEqual(c1.storage_classes_desired(), c2.storage_classes_desired()) + def test_init_manifest(self): m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt @@ -925,10 +981,49 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): self.assertIs(c.find("./nonexistant.txt"), None) self.assertIs(c.find("./nonexistantsubdir/nonexistant.txt"), None) + def test_escaped_paths_dont_get_unescaped_on_manifest(self): + # Dir & file names are literally '\056' (escaped form: \134056) + manifest = './\\134056\\040Test d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\134056\n' + c = Collection(manifest) + self.assertEqual(c.portable_manifest_text(), manifest) + + def test_other_special_chars_on_file_token(self): + cases = [ + ('\\000', '\0'), + ('\\011', '\t'), + ('\\012', '\n'), + ('\\072', ':'), + ('\\134400', '\\400'), + ] + for encoded, decoded in cases: + manifest = '. d41d8cd98f00b204e9800998ecf8427e+0 0:0:some%sfile.txt\n' % encoded + c = Collection(manifest) + self.assertEqual(c.portable_manifest_text(), manifest) + self.assertIn('some%sfile.txt' % decoded, c.keys()) + + def test_escaped_paths_do_get_unescaped_on_listing(self): + # Dir & file names are literally '\056' (escaped form: \134056) + manifest = './\\134056\\040Test d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\134056\n' + c = Collection(manifest) + self.assertIn('\\056 Test', c.keys()) + self.assertIn('\\056', c['\\056 Test'].keys()) + + def test_make_empty_dir_with_escaped_chars(self): + c = Collection() + c.mkdirs('./Empty\\056Dir') + self.assertEqual(c.portable_manifest_text(), + './Empty\\134056Dir d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\056\n') + + def test_make_empty_dir_with_spaces(self): + c = Collection() + c.mkdirs('./foo bar/baz waz') + self.assertEqual(c.portable_manifest_text(), + './foo\\040bar/baz\\040waz d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\056\n') + def test_remove_in_subdir(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n') c.remove("foo/count2.txt") - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text()) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\056\n", c.portable_manifest_text()) def test_remove_empty_subdir(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n') @@ -1173,7 +1268,117 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): self.assertEqual(c1["count1.txt"].size(), 0) +class NewCollectionTestCaseWithServersAndTokens(run_test_server.TestCaseWithServers): + MAIN_SERVER = {} + KEEP_SERVER = {} + local_locator_re = r"[0-9a-f]{32}\+\d+\+A[a-f0-9]{40}@[a-f0-9]{8}" + remote_locator_re = r"[0-9a-f]{32}\+\d+\+R[a-z]{5}-[a-f0-9]{40}@[a-f0-9]{8}" + + def setUp(self): + self.keep_put = getattr(arvados.keep.KeepClient, 'put') + + @mock.patch('arvados.keep.KeepClient.put', autospec=True) + def test_storage_classes_desired(self, put_mock): + put_mock.side_effect = self.keep_put + c = Collection(storage_classes_desired=['default']) + with c.open("file.txt", 'wb') as f: + f.write('content') + c.save_new() + _, kwargs = put_mock.call_args + self.assertEqual(['default'], kwargs['classes']) + + @mock.patch('arvados.keep.KeepClient.put', autospec=True) + def test_repacked_block_submission_get_permission_token(self, mocked_put): + ''' + Make sure that those blocks that are committed after repacking small ones, + get their permission tokens assigned on the collection manifest. + ''' + def wrapped_keep_put(*args, **kwargs): + # Simulate slow put operations + time.sleep(1) + return self.keep_put(*args, **kwargs) + + mocked_put.side_effect = wrapped_keep_put + c = Collection() + # Write 70 files ~1MiB each so we force to produce 1 big block by repacking + # small ones before finishing the upload. + for i in range(70): + f = c.open("file_{}.txt".format(i), 'wb') + f.write(random.choice('abcdefghijklmnopqrstuvwxyz') * (2**20+i)) + f.close(flush=False) + # We should get 2 blocks with their tokens + self.assertEqual(len(re.findall(self.local_locator_re, c.manifest_text())), 2) + + @mock.patch('arvados.keep.KeepClient.refresh_signature') + def test_copy_remote_blocks_on_save_new(self, rs_mock): + remote_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+Remote-" + "a" * 40 + "@abcdef01" + local_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+A" + "b" * 40 + "@abcdef01" + rs_mock.return_value = local_block_loc + c = Collection(". " + remote_block_loc + " 0:3:foofile.txt\n") + self.assertEqual( + len(re.findall(self.remote_locator_re, c.manifest_text())), 1) + self.assertEqual( + len(re.findall(self.local_locator_re, c.manifest_text())), 0) + c.save_new() + rs_mock.assert_called() + self.assertEqual( + len(re.findall(self.remote_locator_re, c.manifest_text())), 0) + self.assertEqual( + len(re.findall(self.local_locator_re, c.manifest_text())), 1) + + @mock.patch('arvados.keep.KeepClient.refresh_signature') + def test_copy_remote_blocks_on_save(self, rs_mock): + remote_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+Remote-" + "a" * 40 + "@abcdef01" + local_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+A" + "b" * 40 + "@abcdef01" + rs_mock.return_value = local_block_loc + # Remote collection + remote_c = Collection(". " + remote_block_loc + " 0:3:foofile.txt\n") + self.assertEqual( + len(re.findall(self.remote_locator_re, remote_c.manifest_text())), 1) + # Local collection + local_c = Collection() + with local_c.open('barfile.txt', 'wb') as f: + f.write('bar') + local_c.save_new() + self.assertEqual( + len(re.findall(self.local_locator_re, local_c.manifest_text())), 1) + self.assertEqual( + len(re.findall(self.remote_locator_re, local_c.manifest_text())), 0) + # Copy remote file to local collection + local_c.copy('./foofile.txt', './copied/foofile.txt', remote_c) + self.assertEqual( + len(re.findall(self.local_locator_re, local_c.manifest_text())), 1) + self.assertEqual( + len(re.findall(self.remote_locator_re, local_c.manifest_text())), 1) + # Save local collection: remote block should be copied + local_c.save() + rs_mock.assert_called() + self.assertEqual( + len(re.findall(self.local_locator_re, local_c.manifest_text())), 2) + self.assertEqual( + len(re.findall(self.remote_locator_re, local_c.manifest_text())), 0) + + class NewCollectionTestCaseWithServers(run_test_server.TestCaseWithServers): + def test_preserve_version_on_save(self): + c = Collection() + c.save_new(preserve_version=True) + coll_record = arvados.api().collections().get(uuid=c.manifest_locator()).execute() + self.assertEqual(coll_record['version'], 1) + self.assertEqual(coll_record['preserve_version'], True) + with c.open("foo.txt", "wb") as foo: + foo.write(b"foo") + c.save(preserve_version=True) + coll_record = arvados.api().collections().get(uuid=c.manifest_locator()).execute() + self.assertEqual(coll_record['version'], 2) + self.assertEqual(coll_record['preserve_version'], True) + with c.open("bar.txt", "wb") as foo: + foo.write(b"bar") + c.save(preserve_version=False) + coll_record = arvados.api().collections().get(uuid=c.manifest_locator()).execute() + self.assertEqual(coll_record['version'], 3) + self.assertEqual(coll_record['preserve_version'], False) + def test_get_manifest_text_only_committed(self): c = Collection() with c.open("count.txt", "wb") as f: @@ -1269,9 +1474,9 @@ class NewCollectionTestCaseWithServers(run_test_server.TestCaseWithServers): c["b1"].writeto(0, b"1b", 0) - self.assertEquals(c.manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1 2:2:b2\n") - self.assertEquals(c["b1"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1\n") - self.assertEquals(c["b2"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 2:2:b2\n") + self.assertEqual(c.manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1 2:2:b2\n") + self.assertEqual(c["b1"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1\n") + self.assertEqual(c["b2"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 2:2:b2\n") class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers): @@ -1296,17 +1501,43 @@ class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers): def test_create_and_save(self): c = self.create_count_txt() - c.save() + c.save(properties={'type' : 'Intermediate'}, + storage_classes=['archive'], + trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111)) + self.assertRegex( c.manifest_text(), r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",) + self.assertEqual(c.api_response()["storage_classes_desired"], ['archive']) + self.assertEqual(c.api_response()["properties"], {'type' : 'Intermediate'}) + self.assertEqual(c.api_response()["trash_at"], '2111-01-01T11:11:11.111111000Z') + def test_create_and_save_new(self): c = self.create_count_txt() - c.save_new() + c.save_new(properties={'type' : 'Intermediate'}, + storage_classes=['archive'], + trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111)) + self.assertRegex( c.manifest_text(), r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",) + self.assertEqual(c.api_response()["storage_classes_desired"], ['archive']) + self.assertEqual(c.api_response()["properties"], {'type' : 'Intermediate'}) + self.assertEqual(c.api_response()["trash_at"], '2111-01-01T11:11:11.111111000Z') + + def test_create_and_save_after_commiting(self): + c = self.create_count_txt() + c.save(properties={'type' : 'Intermediate'}, + storage_classes=['hot'], + trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111)) + c.save(properties={'type' : 'Output'}, + storage_classes=['cold'], + trash_at=datetime.datetime(2222, 2, 2, 22, 22, 22, 222222)) + + self.assertEqual(c.api_response()["storage_classes_desired"], ['cold']) + self.assertEqual(c.api_response()["properties"], {'type' : 'Output'}) + self.assertEqual(c.api_response()["trash_at"], '2222-02-02T22:22:22.222222000Z') def test_create_diff_apply(self): c1 = self.create_count_txt()