# Copyright (C) The Arvados Authors. All rights reserved. # # SPDX-License-Identifier: Apache-2.0 import ciso8601 import copy import datetime import os import random import re import shutil import sys import tempfile import time import unittest import arvados import arvados.keep import parameterized from arvados._internal.streams import Range, LocatorAndRange, locators_and_ranges from arvados.collection import Collection, CollectionReader from . import arvados_testutil as tutil from . import run_test_server from unittest import mock @parameterized.parameterized_class([{"disk_cache": True}, {"disk_cache": False}]) class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, tutil.ArvadosBaseTestCase): disk_cache = False MAIN_SERVER = {} @classmethod def setUpClass(cls): super(ArvadosCollectionsTest, cls).setUpClass() # need admin privileges to make collections with unsigned blocks run_test_server.authorize_with('admin') if cls.disk_cache: cls._disk_cache_dir = tempfile.mkdtemp(prefix='CollectionsTest-') else: cls._disk_cache_dir = None block_cache = arvados.keep.KeepBlockCache( disk_cache=cls.disk_cache, disk_cache_dir=cls._disk_cache_dir, ) cls.api_client = arvados.api('v1') cls.keep_client = arvados.KeepClient(api_client=cls.api_client, local_store=cls.local_store, block_cache=block_cache) @classmethod def tearDownClass(cls): if cls._disk_cache_dir: shutil.rmtree(cls._disk_cache_dir) def write_foo_bar_baz(self): with arvados.collection.Collection(api_client=self.api_client).open('zzz', 'wb') as f: f.write(b'foobar') f.flush() f.write(b'baz') cw = arvados.collection.Collection( api_client=self.api_client, manifest_locator_or_text= ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" + "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n") cw.save_new() return cw.portable_data_hash() def test_pdh_is_native_str(self): pdh = self.write_foo_bar_baz() self.assertEqual(type(''), type(pdh)) def test_keep_local_store(self): self.assertEqual(self.keep_client.put(b'foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put') self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), b'foo', 'wrong data from Keep.get') def test_local_collection_writer(self): self.assertEqual(self.write_foo_bar_baz(), '23ca013983d6239e98931cc779e68426+114', 'wrong locator hash: ' + self.write_foo_bar_baz()) def test_collection_empty_file(self): cw = arvados.collection.Collection(api_client=self.api_client) with cw.open('zero.txt', 'wb') as f: pass self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n") self.check_manifest_file_sizes(cw.manifest_text(), [0]) cw = arvados.collection.Collection(api_client=self.api_client) with cw.open('zero.txt', 'wb') as f: pass with cw.open('one.txt', 'wb') as f: f.write(b'1') with cw.open('foo/zero.txt', 'wb') as f: pass # sorted, that's: [./one.txt, ./zero.txt, foo/zero.txt] self.check_manifest_file_sizes(cw.manifest_text(), [1,0,0]) def check_manifest_file_sizes(self, manifest_text, expect_sizes): got_sizes = [] def walk(subdir): for fnm in subdir: if isinstance(subdir[fnm], arvados.arvfile.ArvadosFile): got_sizes.append(subdir[fnm].size()) else: walk(subdir[fnm]) cr = arvados.CollectionReader(manifest_text, self.api_client) walk(cr) self.assertEqual(got_sizes, expect_sizes, "got wrong file sizes %s, expected %s" % (got_sizes, expect_sizes)) def test_normalized_collection(self): m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt """ self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True), """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt """) m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2 """ self.assertEqual(arvados.CollectionReader(m2, self.api_client).manifest_text(normalize=True), m2) m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt """ self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(normalize=True), """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt """) m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz ./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar """ self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(normalize=True), """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz """) m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz ./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar """ self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(normalize=True), """./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz """) with self.data_file('1000G_ref_manifest') as f6: m6 = f6.read() self.assertEqual(arvados.CollectionReader(m6, self.api_client).manifest_text(normalize=True), m6) with self.data_file('jlake_manifest') as f7: m7 = f7.read() self.assertEqual(arvados.CollectionReader(m7, self.api_client).manifest_text(normalize=True), m7) m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt """ self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8) def test_locators_and_ranges(self): blocks2 = [Range('a', 0, 10), Range('b', 10, 10), Range('c', 20, 10), Range('d', 30, 10), Range('e', 40, 10), Range('f', 50, 10)] self.assertEqual(locators_and_ranges(blocks2, 2, 2), [LocatorAndRange('a', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks2, 12, 2), [LocatorAndRange('b', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks2, 22, 2), [LocatorAndRange('c', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks2, 32, 2), [LocatorAndRange('d', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks2, 42, 2), [LocatorAndRange('e', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks2, 52, 2), [LocatorAndRange('f', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks2, 62, 2), []) self.assertEqual(locators_and_ranges(blocks2, -2, 2), []) self.assertEqual(locators_and_ranges(blocks2, 0, 2), [LocatorAndRange('a', 10, 0, 2)]) self.assertEqual(locators_and_ranges(blocks2, 10, 2), [LocatorAndRange('b', 10, 0, 2)]) self.assertEqual(locators_and_ranges(blocks2, 20, 2), [LocatorAndRange('c', 10, 0, 2)]) self.assertEqual(locators_and_ranges(blocks2, 30, 2), [LocatorAndRange('d', 10, 0, 2)]) self.assertEqual(locators_and_ranges(blocks2, 40, 2), [LocatorAndRange('e', 10, 0, 2)]) self.assertEqual(locators_and_ranges(blocks2, 50, 2), [LocatorAndRange('f', 10, 0, 2)]) self.assertEqual(locators_and_ranges(blocks2, 60, 2), []) self.assertEqual(locators_and_ranges(blocks2, -2, 2), []) self.assertEqual(locators_and_ranges(blocks2, 9, 2), [LocatorAndRange('a', 10, 9, 1), LocatorAndRange('b', 10, 0, 1)]) self.assertEqual(locators_and_ranges(blocks2, 19, 2), [LocatorAndRange('b', 10, 9, 1), LocatorAndRange('c', 10, 0, 1)]) self.assertEqual(locators_and_ranges(blocks2, 29, 2), [LocatorAndRange('c', 10, 9, 1), LocatorAndRange('d', 10, 0, 1)]) self.assertEqual(locators_and_ranges(blocks2, 39, 2), [LocatorAndRange('d', 10, 9, 1), LocatorAndRange('e', 10, 0, 1)]) self.assertEqual(locators_and_ranges(blocks2, 49, 2), [LocatorAndRange('e', 10, 9, 1), LocatorAndRange('f', 10, 0, 1)]) self.assertEqual(locators_and_ranges(blocks2, 59, 2), [LocatorAndRange('f', 10, 9, 1)]) blocks3 = [Range('a', 0, 10), Range('b', 10, 10), Range('c', 20, 10), Range('d', 30, 10), Range('e', 40, 10), Range('f', 50, 10), Range('g', 60, 10)] self.assertEqual(locators_and_ranges(blocks3, 2, 2), [LocatorAndRange('a', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks3, 12, 2), [LocatorAndRange('b', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks3, 22, 2), [LocatorAndRange('c', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks3, 32, 2), [LocatorAndRange('d', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks3, 42, 2), [LocatorAndRange('e', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks3, 52, 2), [LocatorAndRange('f', 10, 2, 2)]) self.assertEqual(locators_and_ranges(blocks3, 62, 2), [LocatorAndRange('g', 10, 2, 2)]) blocks = [Range('a', 0, 10), Range('b', 10, 15), Range('c', 25, 5)] self.assertEqual(locators_and_ranges(blocks, 1, 0), []) self.assertEqual(locators_and_ranges(blocks, 0, 5), [LocatorAndRange('a', 10, 0, 5)]) self.assertEqual(locators_and_ranges(blocks, 3, 5), [LocatorAndRange('a', 10, 3, 5)]) self.assertEqual(locators_and_ranges(blocks, 0, 10), [LocatorAndRange('a', 10, 0, 10)]) self.assertEqual(locators_and_ranges(blocks, 0, 11), [LocatorAndRange('a', 10, 0, 10), LocatorAndRange('b', 15, 0, 1)]) self.assertEqual(locators_and_ranges(blocks, 1, 11), [LocatorAndRange('a', 10, 1, 9), LocatorAndRange('b', 15, 0, 2)]) self.assertEqual(locators_and_ranges(blocks, 0, 25), [LocatorAndRange('a', 10, 0, 10), LocatorAndRange('b', 15, 0, 15)]) self.assertEqual(locators_and_ranges(blocks, 0, 30), [LocatorAndRange('a', 10, 0, 10), LocatorAndRange('b', 15, 0, 15), LocatorAndRange('c', 5, 0, 5)]) self.assertEqual(locators_and_ranges(blocks, 1, 30), [LocatorAndRange('a', 10, 1, 9), LocatorAndRange('b', 15, 0, 15), LocatorAndRange('c', 5, 0, 5)]) self.assertEqual(locators_and_ranges(blocks, 0, 31), [LocatorAndRange('a', 10, 0, 10), LocatorAndRange('b', 15, 0, 15), LocatorAndRange('c', 5, 0, 5)]) self.assertEqual(locators_and_ranges(blocks, 15, 5), [LocatorAndRange('b', 15, 5, 5)]) self.assertEqual(locators_and_ranges(blocks, 8, 17), [LocatorAndRange('a', 10, 8, 2), LocatorAndRange('b', 15, 0, 15)]) self.assertEqual(locators_and_ranges(blocks, 8, 20), [LocatorAndRange('a', 10, 8, 2), LocatorAndRange('b', 15, 0, 15), LocatorAndRange('c', 5, 0, 3)]) self.assertEqual(locators_and_ranges(blocks, 26, 2), [LocatorAndRange('c', 5, 1, 2)]) self.assertEqual(locators_and_ranges(blocks, 9, 15), [LocatorAndRange('a', 10, 9, 1), LocatorAndRange('b', 15, 0, 14)]) self.assertEqual(locators_and_ranges(blocks, 10, 15), [LocatorAndRange('b', 15, 0, 15)]) self.assertEqual(locators_and_ranges(blocks, 11, 15), [LocatorAndRange('b', 15, 1, 14), LocatorAndRange('c', 5, 0, 1)]) class MockKeep(object): def __init__(self, content, num_retries=0): self.content = content self.num_prefetch_threads = 1 def get(self, locator, num_retries=0, prefetch=False): return self.content[locator] def test_extract_file(self): m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt . 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt """ coll = arvados.CollectionReader(m1, self.api_client) m2 = coll.manifest_text(normalize=True) self.assertEqual(m2, ". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt 43:41:md6sum.txt 84:43:md7sum.txt 6:37:md8sum.txt 84:43:md8sum.txt 83:1:md9sum.txt 0:43:md9sum.txt 84:36:md9sum.txt\n") self.assertEqual(coll['md5sum.txt'].manifest_text(), ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n") self.assertEqual(coll['md6sum.txt'].manifest_text(), ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n") self.assertEqual(coll['md7sum.txt'].manifest_text(), ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n") self.assertEqual(coll['md9sum.txt'].manifest_text(), ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n") class CollectionTestMixin(tutil.ApiClientMock): API_COLLECTIONS = run_test_server.fixture('collections') DEFAULT_COLLECTION = API_COLLECTIONS['foo_file'] DEFAULT_DATA_HASH = DEFAULT_COLLECTION['portable_data_hash'] DEFAULT_MANIFEST = DEFAULT_COLLECTION['manifest_text'] DEFAULT_UUID = DEFAULT_COLLECTION['uuid'] ALT_COLLECTION = API_COLLECTIONS['bar_file'] ALT_DATA_HASH = ALT_COLLECTION['portable_data_hash'] ALT_MANIFEST = ALT_COLLECTION['manifest_text'] def api_client_mock(self, status=200): client = super(CollectionTestMixin, self).api_client_mock() self.mock_keep_services(client, status=status, service_type='proxy', count=1) return client @tutil.skip_sleep class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): def mock_get_collection(self, api_mock, code, fixturename): body = self.API_COLLECTIONS.get(fixturename) self._mock_api_call(api_mock.collections().get, code, body) def api_client_mock(self, status=200): client = super(CollectionReaderTestCase, self).api_client_mock() self.mock_get_collection(client, status, 'foo_file') return client def test_init_default_retries(self): client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) reader.manifest_text() client.collections().get().execute.assert_called_with(num_retries=10) def test_uuid_init_success(self): client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client, num_retries=3) self.assertEqual(self.DEFAULT_COLLECTION['manifest_text'], reader.manifest_text()) client.collections().get().execute.assert_called_with(num_retries=3) def test_uuid_init_failure_raises_api_error(self): client = self.api_client_mock(500) with self.assertRaises(arvados.errors.ApiError): reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) def test_locator_init(self): client = self.api_client_mock(200) # Ensure Keep will not return anything if asked. with tutil.mock_keep_responses(None, 404): reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH, api_client=client) self.assertEqual(self.DEFAULT_MANIFEST, reader.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... client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client, num_retries=3) with tutil.mock_keep_responses('foo', 500, 500, 200): self.assertEqual('foo', reader.open('foo', 'r').read()) def test_read_nonnormalized_manifest_with_collection_reader(self): # client should be able to use CollectionReader on a manifest without normalizing it client = self.api_client_mock(500) nonnormal = ". acbd18db4cc2f85cedef654fccc4a4d8+3+Aabadbadbee@abeebdee 0:3:foo.txt 1:0:bar.txt 0:3:foo.txt\n" reader = arvados.CollectionReader( nonnormal, api_client=client, num_retries=0) # Ensure stripped_manifest() doesn't mangle our manifest in # any way other than stripping hints. self.assertEqual( re.sub(r'\+[^\d\s\+]+', '', nonnormal), reader.stripped_manifest()) # Ensure stripped_manifest() didn't mutate our reader. self.assertEqual(nonnormal, reader.manifest_text()) def test_read_empty_collection(self): client = self.api_client_mock(200) self.mock_get_collection(client, 200, 'empty') 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 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()) self.assertEqual(file_name, coll_file.name) self.assertEqual(file_size, coll_file.size()) def test_open_collection_file_one_argument(self): client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) cfile = reader.open('./foo', 'rb') self.check_open_file(cfile, '.', 'foo', 3) def test_open_deep_file(self): coll_name = 'collection_with_files_in_subdir' client = self.api_client_mock(200) self.mock_get_collection(client, 200, coll_name) reader = arvados.CollectionReader( self.API_COLLECTIONS[coll_name]['uuid'], api_client=client) cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt', 'rb') self.check_open_file(cfile, './subdir2/subdir3', 'file2_in_subdir3.txt', 32) def test_open_nonexistent_stream(self): client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) self.assertRaises(IOError, reader.open, './nonexistent/foo') def test_open_nonexistent_file(self): client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) self.assertRaises(IOError, reader.open, 'nonexistent') class CollectionMethods(run_test_server.TestCaseWithServers): def test_keys_values_items_support_indexing(self): c = Collection() with c.open('foo', 'wb') as f: f.write(b'foo') with c.open('bar', 'wb') as f: f.write(b'bar') self.assertEqual(2, len(c.keys())) fn0, fn1 = c.keys() self.assertEqual(2, len(c.values())) f0 = c.values()[0] f1 = c.values()[1] self.assertEqual(2, len(c.items())) 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): def test_open_binary_modes(self): c = Collection() for mode in ['wb', 'wb+', 'ab', 'ab+']: with c.open('foo', mode) as f: f.write(b'foo') def test_open_invalid_modes(self): c = Collection() for mode in ['+r', 'aa', '++', 'r+b', 'beer', '', None]: with self.assertRaises(Exception): c.open('foo', mode) def test_open_text_modes(self): c = Collection() with c.open('foo', 'wb') as f: f.write('foo') for mode in ['r', 'rt', 'r+', 'rt+', 'w', 'wt', 'a', 'at']: 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 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): def test_replication_desired_kept_on_load(self): m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n' c1 = Collection(m, replication_desired=1) c1.save_new() loc = c1.manifest_locator() c2 = Collection(loc) self.assertEqual(c1.manifest_text(strip=True), c2.manifest_text(strip=True)) self.assertEqual(c1.replication_desired, c2.replication_desired) def test_replication_desired_not_loaded_if_provided(self): m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n' c1 = Collection(m, replication_desired=1) c1.save_new() loc = c1.manifest_locator() c2 = Collection(loc, replication_desired=2) self.assertEqual(c1.manifest_text(strip=True), c2.manifest_text(strip=True)) 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(strip=True), c2.manifest_text(strip=True)) 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(strip=True), c3.manifest_text(strip=True)) 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(strip=True), c2.manifest_text(strip=True)) 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 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt """ self.assertEqual(m1, CollectionReader(m1).manifest_text(normalize=False)) self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", CollectionReader(m1).manifest_text(normalize=True)) def test_init_manifest_with_collision(self): m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt ./md5sum.txt 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt """ with self.assertRaises(arvados.errors.ArgumentError): self.assertEqual(m1, CollectionReader(m1)) def test_init_manifest_with_error(self): m1 = """. 0:43:md5sum.txt""" with self.assertRaises(arvados.errors.ArgumentError): self.assertEqual(m1, CollectionReader(m1)) def test_remove(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n') self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text()) self.assertIn("count1.txt", c) c.remove("count1.txt") self.assertNotIn("count1.txt", c) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text()) with self.assertRaises(arvados.errors.ArgumentError): c.remove("") def test_remove_recursive(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:a/b/c/d/efg.txt 0:10:xyz.txt\n') self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:xyz.txt\n./a/b/c/d 781e5e245d69b566979b86e28d23f2c7+10 0:10:efg.txt\n", c.portable_manifest_text()) self.assertIn("a", c) self.assertEqual(1, len(c["a"].keys())) # cannot remove non-empty directory with default recursive=False with self.assertRaises(OSError): c.remove("a/b") with self.assertRaises(OSError): c.remove("a/b/c/d") c.remove("a/b", recursive=True) self.assertEqual(0, len(c["a"].keys())) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:xyz.txt\n./a d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\056\n", c.portable_manifest_text()) def test_find(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n') self.assertIs(c.find("."), c) self.assertIs(c.find("./count1.txt"), c["count1.txt"]) self.assertIs(c.find("count1.txt"), c["count1.txt"]) with self.assertRaises(IOError): c.find("/.") with self.assertRaises(arvados.errors.ArgumentError): c.find("") 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./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') c.remove("foo/count2.txt") c.remove("foo") self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text()) def test_remove_nonempty_subdir(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n') with self.assertRaises(IOError): c.remove("foo") c.remove("foo", recursive=True) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text()) def test_copy_to_file_in_dir(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c.copy("count1.txt", "foo/count2.txt") self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text()) def test_copy_file(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c.copy("count1.txt", "count2.txt") self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text()) def test_copy_to_existing_dir(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n') c.copy("count1.txt", "foo") self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text()) def test_copy_to_new_dir(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c.copy("count1.txt", "foo/") self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text()) def test_rename_file(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c.rename("count1.txt", "count2.txt") self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text()) def test_move_file_to_dir(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c.mkdirs("foo") c.rename("count1.txt", "foo/count2.txt") self.assertEqual("./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text()) def test_move_file_to_other(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c2 = Collection() c2.rename("count1.txt", "count2.txt", source_collection=c1) self.assertEqual("", c1.manifest_text()) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c2.manifest_text()) def test_clone(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n') cl = c.clone() self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", cl.portable_manifest_text()) def test_diff_del_add(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n') d = c2.diff(c1) self.assertEqual(sorted(d), [ ('add', './count1.txt', c1["count1.txt"]), ('del', './count2.txt', c2["count2.txt"]), ]) d = c1.diff(c2) self.assertEqual(sorted(d), [ ('add', './count2.txt', c2["count2.txt"]), ('del', './count1.txt', c1["count1.txt"]), ]) self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) c1.apply(d) self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) def test_diff_same(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') d = c2.diff(c1) self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])]) d = c1.diff(c2) self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])]) self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) c1.apply(d) self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) def test_diff_mod(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n') d = c2.diff(c1) self.assertEqual(d, [('mod', './count1.txt', c2["count1.txt"], c1["count1.txt"])]) d = c1.diff(c2) self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])]) self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) c1.apply(d) self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) def test_diff_add(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt 10:20:count2.txt\n') d = c2.diff(c1) self.assertEqual(sorted(d), [ ('del', './count2.txt', c2["count2.txt"]), ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]), ]) d = c1.diff(c2) self.assertEqual(sorted(d), [ ('add', './count2.txt', c2["count2.txt"]), ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]), ]) self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) c1.apply(d) self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) def test_diff_add_in_subcollection(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n') d = c2.diff(c1) self.assertEqual(sorted(d), [ ('del', './foo', c2["foo"]), ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]), ]) d = c1.diff(c2) self.assertEqual(sorted(d), [ ('add', './foo', c2["foo"]), ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]), ]) self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) c1.apply(d) self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) def test_diff_del_add_in_subcollection(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n') c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:3:count3.txt\n') d = c2.diff(c1) self.assertEqual(sorted(d), [ ('add', './foo/count2.txt', c1.find("foo/count2.txt")), ('del', './foo/count3.txt', c2.find("foo/count3.txt")), ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]), ]) d = c1.diff(c2) self.assertEqual(sorted(d), [ ('add', './foo/count3.txt', c2.find("foo/count3.txt")), ('del', './foo/count2.txt', c1.find("foo/count2.txt")), ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]), ]) self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) c1.apply(d) self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) def test_diff_mod_in_subcollection(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n') c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:3:foo\n') d = c2.diff(c1) self.assertEqual(sorted(d), [ ('mod', './foo', c2["foo"], c1["foo"]), ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]), ]) d = c1.diff(c2) self.assertEqual(sorted(d), [ ('mod', './foo', c1["foo"], c2["foo"]), ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]), ]) self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) c1.apply(d) self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text()) def test_conflict_keep_local_change(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n') d = c1.diff(c2) self.assertEqual(sorted(d), [ ('add', './count2.txt', c2["count2.txt"]), ('del', './count1.txt', c1["count1.txt"]), ]) f = c1.open("count1.txt", "wb") f.write(b"zzzzz") # c1 changed, so it should not be deleted. c1.apply(d) self.assertEqual(c1.portable_manifest_text(), ". 95ebc3c7b3b9f1d2c40fec14415d3cb8+5 5348b82a029fd9e971a811ce1f71360b+43 0:5:count1.txt 5:10:count2.txt\n") def test_conflict_mod(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt') d = c1.diff(c2) self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])]) f = c1.open("count1.txt", "wb") f.write(b"zzzzz") # c1 changed, so c2 mod will go to a conflict file c1.apply(d) self.assertRegex( c1.portable_manifest_text(), r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$") def test_conflict_add(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n') c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n') d = c1.diff(c2) self.assertEqual(sorted(d), [ ('add', './count1.txt', c2["count1.txt"]), ('del', './count2.txt', c1["count2.txt"]), ]) f = c1.open("count1.txt", "wb") f.write(b"zzzzz") # c1 added count1.txt, so c2 add will go to a conflict file c1.apply(d) self.assertRegex( c1.portable_manifest_text(), r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$") def test_conflict_del(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt') d = c1.diff(c2) self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])]) c1.remove("count1.txt") # c1 deleted, so c2 mod will go to a conflict file c1.apply(d) self.assertRegex( c1.portable_manifest_text(), r"\. 5348b82a029fd9e971a811ce1f71360b\+43 0:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$") def test_notify(self): c1 = Collection() events = [] c1.subscribe(lambda event, collection, name, item: events.append((event, collection, name, item))) f = c1.open("foo.txt", "wb") self.assertEqual(events[0], (arvados.collection.ADD, c1, "foo.txt", f.arvadosfile)) def test_open_w(self): c1 = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n") self.assertEqual(c1["count1.txt"].size(), 10) c1.open("count1.txt", "wb").close() 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: # One file committed with c.open("foo.txt", "wb") as foo: foo.write(b"foo") foo.flush() # Force block commit f.write(b"0123456789") # Other file not committed. Block not written to keep yet. self.assertEqual( c._get_manifest_text(".", strip=False, normalize=False, only_committed=True), '. acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:count.txt 0:3:foo.txt\n') # And now with the file closed... f.flush() # Force block commit self.assertEqual( c._get_manifest_text(".", strip=False, normalize=False, only_committed=True), ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:10:count.txt 10:3:foo.txt\n") def test_only_small_blocks_are_packed_together(self): c = Collection() # Write a couple of small files, f = c.open("count.txt", "wb") f.write(b"0123456789") f.close(flush=False) foo = c.open("foo.txt", "wb") foo.write(b"foo") foo.close(flush=False) # Then, write a big file, it shouldn't be packed with the ones above big = c.open("bigfile.txt", "wb") big.write(b"x" * 1024 * 1024 * 33) # 33 MB > KEEP_BLOCK_SIZE/2 big.close(flush=False) self.assertEqual( c.manifest_text("."), '. 2d303c138c118af809f39319e5d507e9+34603008 a8430a058b8fbf408e1931b794dbd6fb+13 0:34603008:bigfile.txt 34603008:10:count.txt 34603018:3:foo.txt\n') def test_flush_after_small_block_packing(self): c = Collection() # Write a couple of small files, f = c.open("count.txt", "wb") f.write(b"0123456789") f.close(flush=False) foo = c.open("foo.txt", "wb") foo.write(b"foo") foo.close(flush=False) self.assertEqual( c.manifest_text(), '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n') f = c.open("count.txt", "rb+") f.close(flush=True) self.assertEqual( c.manifest_text(), '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n') def test_write_after_small_block_packing2(self): c = Collection() # Write a couple of small files, f = c.open("count.txt", "wb") f.write(b"0123456789") f.close(flush=False) foo = c.open("foo.txt", "wb") foo.write(b"foo") foo.close(flush=False) self.assertEqual( c.manifest_text(), '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n') f = c.open("count.txt", "rb+") f.write(b"abc") f.close(flush=False) self.assertEqual( c.manifest_text(), '. 900150983cd24fb0d6963f7d28e17f72+3 a8430a058b8fbf408e1931b794dbd6fb+13 0:3:count.txt 6:7:count.txt 13:3:foo.txt\n') def test_small_block_packing_with_overwrite(self): c = Collection() c.open("b1", "wb").close() c["b1"].writeto(0, b"b1", 0) c.open("b2", "wb").close() c["b2"].writeto(0, b"b2", 0) c["b1"].writeto(0, b"1b", 0) 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): MAIN_SERVER = {} KEEP_SERVER = {} def create_count_txt(self): # Create an empty collection, save it to the API server, then write a # file, but don't save it. c = Collection() c.save_new("CollectionCreateUpdateTest", ensure_unique_name=True) self.assertEqual(c.portable_data_hash(), "d41d8cd98f00b204e9800998ecf8427e+0") self.assertEqual(c.api_response()["portable_data_hash"], "d41d8cd98f00b204e9800998ecf8427e+0" ) with c.open("count.txt", "wb") as f: f.write(b"0123456789") self.assertEqual(c.portable_manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n") return c def test_create_and_save(self): c = self.create_count_txt() 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(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() c1.save() c2 = Collection(c1.manifest_locator()) with c2.open("count.txt", "wb") as f: f.write(b"abcdefg") diff = c1.diff(c2) self.assertEqual(diff[0], (arvados.collection.MOD, u'./count.txt', c1["count.txt"], c2["count.txt"])) c1.apply(diff) self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash()) def test_diff_apply_with_token(self): baseline = CollectionReader(". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:10:count.txt\n") c = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n") other = CollectionReader(". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n") diff = baseline.diff(other) self.assertEqual(diff, [('mod', u'./count.txt', c["count.txt"], other["count.txt"])]) c.apply(diff) self.assertEqual(c.manifest_text(), ". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n") def test_create_and_update(self): c1 = self.create_count_txt() c1.save() c2 = arvados.collection.Collection(c1.manifest_locator()) with c2.open("count.txt", "wb") as f: f.write(b"abcdefg") c2.save() self.assertNotEqual(c1.portable_data_hash(), c2.portable_data_hash()) c1.update() self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash()) def test_create_and_update_with_conflict(self): c1 = self.create_count_txt() c1.save() with c1.open("count.txt", "wb") as f: f.write(b"XYZ") c2 = arvados.collection.Collection(c1.manifest_locator()) with c2.open("count.txt", "wb") as f: f.write(b"abcdefg") c2.save() c1.update() self.assertRegex( c1.manifest_text(), r"\. e65075d550f9b5bf9992fa1d71a131be\+3\S* 7ac66c0f148de9519b8bd264312c4d64\+7\S* 0:3:count\.txt 3:7:count\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$") def test_pdh_is_native_str(self): c1 = self.create_count_txt() pdh = c1.portable_data_hash() self.assertEqual(type(''), type(pdh)) if __name__ == '__main__': unittest.main()