X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/56ad30382d7d4e11cb0160c5f2e30077e1f41c8b..e5db78600aa8e617ca250c4b15f09e4d05b866cc:/sdk/python/tests/test_collections.py diff --git a/sdk/python/tests/test_collections.py b/sdk/python/tests/test_collections.py index d47d318b11..24e0f41d99 100644 --- a/sdk/python/tests/test_collections.py +++ b/sdk/python/tests/test_collections.py @@ -1,19 +1,26 @@ -# usage example: +# Copyright (C) The Arvados Authors. All rights reserved. # -# ARVADOS_API_TOKEN=abc ARVADOS_API_HOST=arvados.local python -m unittest discover +# SPDX-License-Identifier: Apache-2.0 +from __future__ import absolute_import + +from builtins import object import arvados import copy -import hashlib import mock import os -import pprint +import random import re -import tempfile +import sys +import datetime +import ciso8601 +import time import unittest -import run_test_server -import arvados_testutil as tutil +from . import run_test_server +from arvados._ranges import Range, LocatorAndRange +from arvados.collection import Collection, CollectionReader +from . import arvados_testutil as tutil class TestResumableWriter(arvados.ResumableCollectionWriter): KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K. @@ -29,7 +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) @@ -39,24 +47,28 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, self.assertEqual(cw.current_stream_name(), '.', 'current_stream_name() should be "." now') cw.set_current_file_name('foo.txt') - cw.write('foo') + cw.write(b'foo') self.assertEqual(cw.current_file_name(), 'foo.txt', 'current_file_name() should be foo.txt now') cw.start_new_file('bar.txt') - cw.write('bar') + cw.write(b'bar') cw.start_new_stream('baz') - cw.write('baz') + cw.write(b'baz') cw.set_current_file_name('baz.txt') self.assertEqual(cw.manifest_text(), ". 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): + pdh = self.write_foo_bar_baz() + self.assertEqual(type(''), type(pdh)) + def test_keep_local_store(self): - self.assertEqual(self.keep_client.put('foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put') - self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), 'foo', 'wrong data from Keep.get') + 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(), @@ -71,21 +83,23 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, for s in cr.all_streams(): for f in s.all_files(): got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]] - expected = [[3, '.', 'foo.txt', 'foo'], - [3, '.', 'bar.txt', 'bar'], - [3, './baz', 'baz.txt', 'baz']] + expected = [[3, '.', 'foo.txt', b'foo'], + [3, '.', 'bar.txt', b'bar'], + [3, './baz', 'baz.txt', b'baz']] self.assertEqual(got, expected) stream0 = cr.all_streams()[0] self.assertEqual(stream0.readfrom(0, 0), - '', + b'', 'reading zero bytes should have returned empty string') self.assertEqual(stream0.readfrom(0, 2**26), - 'foobar', + b'foobar', 'reading entire stream failed') 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) @@ -101,50 +115,50 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, def test_collection_manifest_subset(self): foobarbaz = self.write_foo_bar_baz() self._test_subset(foobarbaz, - [[3, '.', 'bar.txt', 'bar'], - [3, '.', 'foo.txt', 'foo'], - [3, './baz', 'baz.txt', 'baz']]) + [[3, '.', 'bar.txt', b'bar'], + [3, '.', 'foo.txt', b'foo'], + [3, './baz', 'baz.txt', b'baz']]) self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" % - (self.keep_client.put("foo"), - self.keep_client.put("bar"))), - [[3, '.', 'bar.txt', 'bar'], - [3, '.', 'foo.txt', 'foo']]) + (self.keep_client.put(b"foo"), + self.keep_client.put(b"bar"))), + [[3, '.', 'bar.txt', b'bar'], + [3, '.', 'foo.txt', b'foo']]) self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" % - (self.keep_client.put("foo"), - self.keep_client.put("bar"))), - [[2, '.', 'fo.txt', 'fo'], - [4, '.', 'obar.txt', 'obar']]) + (self.keep_client.put(b"foo"), + self.keep_client.put(b"bar"))), + [[2, '.', 'fo.txt', b'fo'], + [4, '.', 'obar.txt', b'obar']]) self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" % - (self.keep_client.put("foo"), - self.keep_client.put("bar"))), - [[2, '.', 'ar.txt', 'ar'], - [2, '.', 'fo.txt', 'fo'], - [2, '.', 'ob.txt', 'ob'], - [0, '.', 'zero.txt', '']]) + (self.keep_client.put(b"foo"), + self.keep_client.put(b"bar"))), + [[2, '.', 'ar.txt', b'ar'], + [2, '.', 'fo.txt', b'fo'], + [2, '.', 'ob.txt', b'ob'], + [0, '.', 'zero.txt', b'']]) def test_collection_empty_file(self): cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('zero.txt') - cw.write('') + cw.write(b'') self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n") self.check_manifest_file_sizes(cw.manifest_text(), [0]) cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('zero.txt') - cw.write('') + cw.write(b'') cw.start_new_file('one.txt') - cw.write('1') + cw.write(b'1') cw.start_new_stream('foo') cw.start_new_file('zero.txt') - cw.write('') + cw.write(b'') self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0]) def test_no_implicit_normalize(self): cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('b') - cw.write('b') + cw.write(b'b') cw.start_new_file('a') - cw.write('') + cw.write(b'') self.check_manifest_file_sizes(cw.manifest_text(), [1,0]) self.check_manifest_file_sizes( arvados.CollectionReader( @@ -210,114 +224,116 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8) def test_locators_and_ranges(self): - blocks2 = [['a', 10, 0], - ['b', 10, 10], - ['c', 10, 20], - ['d', 10, 30], - ['e', 10, 40], - ['f', 10, 50]] - - self.assertEqual(arvados.locators_and_ranges(blocks2, 2, 2), [['a', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [['b', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [['c', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [['d', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [['e', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [['f', 10, 2, 2]]) + 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(arvados.locators_and_ranges(blocks2, 2, 2), [LocatorAndRange('a', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [LocatorAndRange('b', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [LocatorAndRange('c', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [LocatorAndRange('d', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [LocatorAndRange('e', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [LocatorAndRange('f', 10, 2, 2)]) self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), []) self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), []) - self.assertEqual(arvados.locators_and_ranges(blocks2, 0, 2), [['a', 10, 0, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [['b', 10, 0, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [['c', 10, 0, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [['d', 10, 0, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [['e', 10, 0, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [['f', 10, 0, 2]]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 0, 2), [LocatorAndRange('a', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [LocatorAndRange('b', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [LocatorAndRange('c', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [LocatorAndRange('d', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [LocatorAndRange('e', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [LocatorAndRange('f', 10, 0, 2)]) self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), []) self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), []) - self.assertEqual(arvados.locators_and_ranges(blocks2, 9, 2), [['a', 10, 9, 1], ['b', 10, 0, 1]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [['b', 10, 9, 1], ['c', 10, 0, 1]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [['c', 10, 9, 1], ['d', 10, 0, 1]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [['d', 10, 9, 1], ['e', 10, 0, 1]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [['e', 10, 9, 1], ['f', 10, 0, 1]]) - self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [['f', 10, 9, 1]]) - - - blocks3 = [['a', 10, 0], - ['b', 10, 10], - ['c', 10, 20], - ['d', 10, 30], - ['e', 10, 40], - ['f', 10, 50], - ['g', 10, 60]] - - self.assertEqual(arvados.locators_and_ranges(blocks3, 2, 2), [['a', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [['b', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [['c', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [['d', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [['e', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [['f', 10, 2, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [['g', 10, 2, 2]]) - - - blocks = [['a', 10, 0], - ['b', 15, 10], - ['c', 5, 25]] + self.assertEqual(arvados.locators_and_ranges(blocks2, 9, 2), [LocatorAndRange('a', 10, 9, 1), LocatorAndRange('b', 10, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [LocatorAndRange('b', 10, 9, 1), LocatorAndRange('c', 10, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [LocatorAndRange('c', 10, 9, 1), LocatorAndRange('d', 10, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [LocatorAndRange('d', 10, 9, 1), LocatorAndRange('e', 10, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [LocatorAndRange('e', 10, 9, 1), LocatorAndRange('f', 10, 0, 1)]) + self.assertEqual(arvados.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(arvados.locators_and_ranges(blocks3, 2, 2), [LocatorAndRange('a', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [LocatorAndRange('b', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [LocatorAndRange('c', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [LocatorAndRange('d', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [LocatorAndRange('e', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [LocatorAndRange('f', 10, 2, 2)]) + self.assertEqual(arvados.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(arvados.locators_and_ranges(blocks, 1, 0), []) - self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [['a', 10, 0, 5]]) - self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [['a', 10, 3, 5]]) - self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [['a', 10, 0, 10]]) - - self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [['a', 10, 0, 10], - ['b', 15, 0, 1]]) - self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [['a', 10, 1, 9], - ['b', 15, 0, 2]]) - self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [['a', 10, 0, 10], - ['b', 15, 0, 15]]) - - self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [['a', 10, 0, 10], - ['b', 15, 0, 15], - ['c', 5, 0, 5]]) - self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [['a', 10, 1, 9], - ['b', 15, 0, 15], - ['c', 5, 0, 5]]) - self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [['a', 10, 0, 10], - ['b', 15, 0, 15], - ['c', 5, 0, 5]]) - - self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [['b', 15, 5, 5]]) - - self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [['a', 10, 8, 2], - ['b', 15, 0, 15]]) - - self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [['a', 10, 8, 2], - ['b', 15, 0, 15], - ['c', 5, 0, 3]]) - - self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [['c', 5, 1, 2]]) - - self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [['a', 10, 9, 1], - ['b', 15, 0, 14]]) - self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [['b', 15, 0, 15]]) - self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [['b', 15, 1, 14], - ['c', 5, 0, 1]]) + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [LocatorAndRange('a', 10, 0, 5)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [LocatorAndRange('a', 10, 3, 5)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [LocatorAndRange('a', 10, 0, 10)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [LocatorAndRange('a', 10, 0, 10), + LocatorAndRange('b', 15, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [LocatorAndRange('a', 10, 1, 9), + LocatorAndRange('b', 15, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [LocatorAndRange('a', 10, 0, 10), + LocatorAndRange('b', 15, 0, 15)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [LocatorAndRange('a', 10, 0, 10), + LocatorAndRange('b', 15, 0, 15), + LocatorAndRange('c', 5, 0, 5)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [LocatorAndRange('a', 10, 1, 9), + LocatorAndRange('b', 15, 0, 15), + LocatorAndRange('c', 5, 0, 5)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [LocatorAndRange('a', 10, 0, 10), + LocatorAndRange('b', 15, 0, 15), + LocatorAndRange('c', 5, 0, 5)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [LocatorAndRange('b', 15, 5, 5)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [LocatorAndRange('a', 10, 8, 2), + LocatorAndRange('b', 15, 0, 15)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [LocatorAndRange('a', 10, 8, 2), + LocatorAndRange('b', 15, 0, 15), + LocatorAndRange('c', 5, 0, 3)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [LocatorAndRange('c', 5, 1, 2)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [LocatorAndRange('a', 10, 9, 1), + LocatorAndRange('b', 15, 0, 14)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [LocatorAndRange('b', 15, 0, 15)]) + self.assertEqual(arvados.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 - 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): - keepblocks = {'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': 'abcdefghij', - 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': 'klmnopqrstuvwxy', - 'cccccccccccccccccccccccccccccccc+5': 'z0123'} + keepblocks = { + 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': b'abcdefghij', + 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': b'klmnopqrstuvwxy', + 'cccccccccccccccccccccccccccccccc+5': b'z0123', + } mk = self.MockKeep(keepblocks) sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk) - content = 'abcdefghijklmnopqrstuvwxyz0123456789' + content = b'abcdefghijklmnopqrstuvwxyz0123456789' self.assertEqual(sr.readfrom(0, 30), content[0:30]) self.assertEqual(sr.readfrom(2, 30), content[2:30]) @@ -331,7 +347,7 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, self.assertEqual(sr.readfrom(15, 5), content[15:20]) self.assertEqual(sr.readfrom(20, 5), content[20:25]) self.assertEqual(sr.readfrom(25, 5), content[25:30]) - self.assertEqual(sr.readfrom(30, 5), '') + self.assertEqual(sr.readfrom(30, 5), b'') def test_extract_file(self): m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt @@ -393,7 +409,7 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, def test_write_directory_tree_with_zero_recursion(self): cwriter = arvados.CollectionWriter(self.api_client) content = 'd1/d2/f3d1/f2f1' - blockhash = hashlib.md5(content).hexdigest() + '+' + str(len(content)) + blockhash = tutil.str_keep_locator(content) cwriter.write_directory_tree( self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']), max_manifest_depth=0) @@ -420,7 +436,7 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, def test_write_multiple_files(self): cwriter = arvados.CollectionWriter(self.api_client) for letter in 'ABC': - with self.make_test_file(letter) as testfile: + with self.make_test_file(letter.encode()) as testfile: cwriter.write_file(testfile.name, letter) self.assertEqual( cwriter.manifest_text(), @@ -431,7 +447,7 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, with self.make_test_file() as testfile: cwriter.write_file(testfile.name, 'test') resumed = TestResumableWriter.from_state(cwriter.current_state()) - self.assertEquals(cwriter.manifest_text(), resumed.manifest_text(), + self.assertEqual(cwriter.manifest_text(), resumed.manifest_text(), "resumed CollectionWriter had different manifest") def test_resume_fails_when_missing_dependency(self): @@ -463,7 +479,7 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, with self.make_test_file() as testfile: cwriter.write_file(testfile.name, 'test') orig_mtime = os.fstat(testfile.fileno()).st_mtime - testfile.write('extra') + testfile.write(b'extra') testfile.flush() os.utime(testfile.name, (orig_mtime, orig_mtime)) self.assertRaises(arvados.errors.StaleWriterStateError, @@ -490,27 +506,8 @@ 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(object): - PROXY_RESPONSE = { - 'items_available': 1, - 'items': [{ - 'uuid': 'zzzzz-bi6l4-mockproxy012345', - 'owner_uuid': 'zzzzz-tpzed-mockowner012345', - 'service_host': tutil.TEST_HOST, - 'service_port': 65535, - 'service_ssl_flag': True, - 'service_type': 'proxy', - }]} + +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'] @@ -520,45 +517,21 @@ class CollectionTestMixin(object): ALT_DATA_HASH = ALT_COLLECTION['portable_data_hash'] ALT_MANIFEST = ALT_COLLECTION['manifest_text'] - def _mock_api_call(self, mock_method, code, body): - mock_method = mock_method().execute - if code == 200: - mock_method.return_value = body - else: - mock_method.side_effect = arvados.errors.ApiError( - tutil.fake_httplib2_response(code), "{}") - - def mock_keep_services(self, api_mock, code, body): - self._mock_api_call(api_mock.keep_services().accessible, code, body) - - def api_client_mock(self, code=200): - client = mock.MagicMock(name='api_client') - self.mock_keep_services(client, code, self.PROXY_RESPONSE) + 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 - def disk_services_available(self, number_of_disks): - return { - 'items_available': number_of_disks, - 'items': [{ - 'uuid': 'zzzzz-bi6l4-mockdisk%07d' % i, - 'owner_uuid': 'zzzzz-tpzed-000000000000000', - 'service_host': tutil.TEST_HOST, - 'service_port': 65535-i, - 'service_ssl_flag': True, - 'service_type': 'disk', - } for i in range(0, number_of_disks)] - } - @tutil.skip_sleep class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): - def mock_get_collection(self, api_mock, code, body): - body = self.API_COLLECTIONS.get(body) + 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, code=200): - client = super(CollectionReaderTestCase, self).api_client_mock(code) - self.mock_get_collection(client, code, 'foo_file') + 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_no_default_retries(self): @@ -577,56 +550,33 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): def test_uuid_init_failure_raises_api_error(self): client = self.api_client_mock(500) - reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) with self.assertRaises(arvados.errors.ApiError): - reader.manifest_text() + 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_get_responses(None, 404): - reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH, - 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_get_responses(self.DEFAULT_MANIFEST, 200): + 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_uuid_init_no_fallback_to_keep(self): - # Do not look up a collection UUID in Keep. - client = self.api_client_mock(404) - reader = arvados.CollectionReader(self.DEFAULT_UUID, - api_client=client) - with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200): - with self.assertRaises(arvados.errors.ApiError): - reader.manifest_text() - - 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_get_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... client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client, num_retries=3) - with tutil.mock_get_responses('foo', 500, 500, 200): - self.assertEqual('foo', - ''.join(f.read(9) for f in reader.all_files())) + with tutil.mock_keep_responses('foo', 500, 500, 200): + self.assertEqual(b'foo', + b''.join(f.read(9) for f in reader.all_files())) def test_read_nonnormalized_manifest_with_collection_reader(self): # client should be able to use CollectionReader on a manifest without normalizing it @@ -655,37 +605,24 @@ 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_get_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()) - self.assertEqual(file_name, coll_file.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') - self.check_open_file(cfile, '.', 'foo', 3) - - def test_open_collection_file_two_arguments(self): - client = self.api_client_mock(200) - reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) - cfile = reader.open('.', 'foo') + cfile = reader.open('./foo', 'rb') self.check_open_file(cfile, '.', 'foo', 3) def test_open_deep_file(self): @@ -694,32 +631,32 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): 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') + 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(ValueError, reader.open, './nonexistent', 'foo') + 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(ValueError, reader.open, '.', 'nonexistent') + self.assertRaises(IOError, reader.open, 'nonexistent') @tutil.skip_sleep class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): def mock_keep(self, body, *codes, **headers): headers.setdefault('x-keep-replicas-stored', 2) - return tutil.mock_put_responses(body, *codes, **headers) + return tutil.mock_keep_responses(body, *codes, **headers) def foo_writer(self, **kwargs): kwargs.setdefault('api_client', self.api_client_mock()) writer = arvados.CollectionWriter(**kwargs) writer.start_new_file('foo') - writer.write('foo') + writer.write(b'foo') return writer def test_write_whole_collection(self): @@ -735,29 +672,29 @@ class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): def test_write_insufficient_replicas_via_proxy(self): writer = self.foo_writer(replication=3) - with self.mock_keep(None, 200, headers={'x-keep-replicas-stored': 2}): + with self.mock_keep(None, 200, **{'x-keep-replicas-stored': 2}): with self.assertRaises(arvados.errors.KeepWriteError): writer.manifest_text() def test_write_insufficient_replicas_via_disks(self): client = mock.MagicMock(name='api_client') - self.mock_keep_services(client, 200, self.disk_services_available(2)) - writer = self.foo_writer(api_client=client, replication=3) with self.mock_keep( None, 200, 200, **{'x-keep-replicas-stored': 1}) as keepmock: + self.mock_keep_services(client, status=200, service_type='disk', count=2) + writer = self.foo_writer(api_client=client, replication=3) with self.assertRaises(arvados.errors.KeepWriteError): writer.manifest_text() def test_write_three_replicas(self): client = mock.MagicMock(name='api_client') - self.mock_keep_services(client, 200, self.disk_services_available(6)) - writer = self.foo_writer(api_client=client, replication=3) with self.mock_keep( - None, 200, 500, 200, 500, 200, 200, + "", 500, 500, 500, 200, 200, 200, **{'x-keep-replicas-stored': 1}) as keepmock: + self.mock_keep_services(client, status=200, service_type='disk', count=6) + writer = self.foo_writer(api_client=client, replication=3) writer.manifest_text() - self.assertEqual(5, keepmock.call_count) + self.assertEqual(6, keepmock.call_count) def test_write_whole_collection_through_retries(self): writer = self.foo_writer(num_retries=2) @@ -778,8 +715,8 @@ class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): with writer.open('out') as out_file: self.assertEqual('.', writer.current_stream_name()) self.assertEqual('out', writer.current_file_name()) - out_file.write('test data') - data_loc = hashlib.md5('test data').hexdigest() + '+9' + out_file.write(b'test data') + data_loc = tutil.str_keep_locator('test data') self.assertTrue(out_file.closed, "writer file not closed after context") self.assertRaises(ValueError, out_file.write, 'extra text') with self.mock_keep(data_loc, 200) as keep_mock: @@ -791,22 +728,21 @@ class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): writer = arvados.CollectionWriter(client) with writer.open('six') as out_file: out_file.writelines(['12', '34', '56']) - data_loc = hashlib.md5('123456').hexdigest() + '+6' + data_loc = tutil.str_keep_locator('123456') with self.mock_keep(data_loc, 200) as keep_mock: self.assertEqual(". {} 0:6:six\n".format(data_loc), writer.manifest_text()) def test_open_flush(self): client = self.api_client_mock() - writer = arvados.CollectionWriter(client) - with writer.open('flush_test') as out_file: - out_file.write('flush1') - data_loc1 = hashlib.md5('flush1').hexdigest() + '+6' - with self.mock_keep(data_loc1, 200) as keep_mock: + data_loc1 = tutil.str_keep_locator('flush1') + data_loc2 = tutil.str_keep_locator('flush2') + with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock: + writer = arvados.CollectionWriter(client) + with writer.open('flush_test') as out_file: + out_file.write(b'flush1') out_file.flush() - out_file.write('flush2') - data_loc2 = hashlib.md5('flush2').hexdigest() + '+6' - with self.mock_keep(data_loc2, 200) as keep_mock: + out_file.write(b'flush2') self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1, data_loc2), writer.manifest_text()) @@ -815,25 +751,24 @@ class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): client = self.api_client_mock() writer = arvados.CollectionWriter(client) with writer.open('.', '1') as out_file: - out_file.write('1st') + out_file.write(b'1st') with writer.open('.', '2') as out_file: - out_file.write('2nd') - data_loc = hashlib.md5('1st2nd').hexdigest() + '+6' + out_file.write(b'2nd') + data_loc = tutil.str_keep_locator('1st2nd') with self.mock_keep(data_loc, 200) as keep_mock: self.assertEqual(". {} 0:3:1 3:3:2\n".format(data_loc), writer.manifest_text()) def test_two_opens_two_streams(self): client = self.api_client_mock() - writer = arvados.CollectionWriter(client) - with writer.open('file') as out_file: - out_file.write('file') - data_loc1 = hashlib.md5('file').hexdigest() + '+4' - with self.mock_keep(data_loc1, 200) as keep_mock: + data_loc1 = tutil.str_keep_locator('file') + data_loc2 = tutil.str_keep_locator('indir') + with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock: + writer = arvados.CollectionWriter(client) + with writer.open('file') as out_file: + out_file.write(b'file') with writer.open('./dir', 'indir') as out_file: - out_file.write('indir') - data_loc2 = hashlib.md5('indir').hexdigest() + '+5' - with self.mock_keep(data_loc2, 200) as keep_mock: + out_file.write(b'indir') expected = ". {} 0:4:file\n./dir {} 0:5:indir\n".format( data_loc1, data_loc2) self.assertEqual(expected, writer.manifest_text()) @@ -845,5 +780,845 @@ class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): self.assertRaises(arvados.errors.AssertionError, writer.open, 'two') +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())) + if sys.version_info < (3, 0): + # keys() supports indexing only for python2 callers. + fn0 = c.keys()[0] + fn1 = c.keys()[1] + else: + 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 + 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): + + 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()