X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/46a6199f3a40a24ee145adc390500190b17a6395..607fe087f6167061714a524dd53cbbc21b974973:/sdk/python/tests/test_collections.py diff --git a/sdk/python/tests/test_collections.py b/sdk/python/tests/test_collections.py index 13fc88def3..24f305ac73 100644 --- a/sdk/python/tests/test_collections.py +++ b/sdk/python/tests/test_collections.py @@ -1,21 +1,20 @@ -# usage example: -# -# ARVADOS_API_TOKEN=abc ARVADOS_API_HOST=arvados.local python -m unittest discover +from __future__ import absolute_import +from builtins import object import arvados import copy -import hashlib import mock import os import pprint import re +import sys import tempfile import unittest -import run_test_server +from . import run_test_server from arvados._ranges import Range, LocatorAndRange from arvados.collection import Collection, CollectionReader -import arvados_testutil as tutil +from . import arvados_testutil as tutil class TestResumableWriter(arvados.ResumableCollectionWriter): KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K. @@ -41,13 +40,13 @@ 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" + @@ -57,8 +56,8 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, return cw.portable_data_hash() 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(), @@ -73,20 +72,20 @@ 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') def _test_subset(self, collection, expected): @@ -103,50 +102,50 @@ 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( @@ -312,14 +311,16 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, 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]) @@ -333,7 +334,7 @@ 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 @@ -395,7 +396,7 @@ 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) @@ -422,7 +423,7 @@ 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(), @@ -465,7 +466,7 @@ 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, @@ -520,8 +521,8 @@ class CollectionTestMixin(tutil.ApiClientMock): @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, status=200): @@ -591,8 +592,8 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client, num_retries=3) with tutil.mock_keep_responses('foo', 500, 500, 200): - self.assertEqual('foo', - ''.join(f.read(9) for f in reader.all_files())) + 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 @@ -645,7 +646,7 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): 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') + cfile = reader.open('./foo', 'rb') self.check_open_file(cfile, '.', 'foo', 3) def test_open_deep_file(self): @@ -654,7 +655,7 @@ 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) @@ -679,7 +680,7 @@ class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): 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): @@ -738,8 +739,8 @@ 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: @@ -751,21 +752,21 @@ 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() - data_loc1 = hashlib.md5('flush1').hexdigest() + '+6' - data_loc2 = hashlib.md5('flush2').hexdigest() + '+6' + 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('flush1') + out_file.write(b'flush1') out_file.flush() - out_file.write('flush2') + out_file.write(b'flush2') self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1, data_loc2), writer.manifest_text()) @@ -774,24 +775,24 @@ 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() - data_loc1 = hashlib.md5('file').hexdigest() + '+4' - data_loc2 = hashlib.md5('indir').hexdigest() + '+5' + 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('file') + out_file.write(b'file') with writer.open('./dir', 'indir') as out_file: - out_file.write('indir') + 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()) @@ -803,8 +804,58 @@ class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): self.assertRaises(arvados.errors.AssertionError, writer.open, 'two') +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', 'wb') 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']: + if sys.version_info >= (3, 0): + with self.assertRaises(NotImplementedError): + c.open('foo', mode) + else: + with c.open('foo', mode) as f: + if mode[0] == 'r' and '+' not in mode: + self.assertEqual('foo', f.read(3)) + else: + f.write('bar') + f.seek(-3, os.SEEK_CUR) + self.assertEqual('bar', f.read(3)) + + 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, c2.manifest_text) + 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, c2.manifest_text) + self.assertNotEqual(c1.replication_desired, c2.replication_desired) + def test_init_manifest(self): m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt @@ -844,6 +895,8 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): 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_remove_in_subdir(self): c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n') @@ -910,11 +963,15 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n') d = c2.diff(c1) - self.assertEqual(d, [('del', './count2.txt', c2["count2.txt"]), - ('add', './count1.txt', c1["count1.txt"])]) + self.assertEqual(sorted(d), [ + ('add', './count1.txt', c1["count1.txt"]), + ('del', './count2.txt', c2["count2.txt"]), + ]) d = c1.diff(c2) - self.assertEqual(d, [('del', './count1.txt', c1["count1.txt"]), - ('add', './count2.txt', c2["count2.txt"])]) + 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()) @@ -923,9 +980,9 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): 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, []) + self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])]) d = c1.diff(c2) - self.assertEqual(d, []) + 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) @@ -947,9 +1004,15 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): 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(d, [('del', './count2.txt', c2["count2.txt"])]) + 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(d, [('add', './count2.txt', c2["count2.txt"])]) + 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) @@ -959,10 +1022,15 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): 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(d, [('del', './foo', c2["foo"])]) + self.assertEqual(sorted(d), [ + ('del', './foo', c2["foo"]), + ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]), + ]) d = c1.diff(c2) - self.assertEqual(d, [('add', './foo', c2["foo"])]) - + 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()) @@ -970,13 +1038,18 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): 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(d, [('del', './foo/count3.txt', c2.find("foo/count3.txt")), - ('add', './foo/count2.txt', c1.find("foo/count2.txt"))]) + 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(d, [('del', './foo/count2.txt', c1.find("foo/count2.txt")), - ('add', './foo/count3.txt', c2.find("foo/count3.txt"))]) + 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) @@ -986,9 +1059,15 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): 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(d, [('mod', './foo', c2["foo"], c1["foo"])]) + 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(d, [('mod', './foo', c1["foo"], c2["foo"])]) + 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) @@ -998,10 +1077,12 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n') c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n') d = c1.diff(c2) - self.assertEqual(d, [('del', './count1.txt', c1["count1.txt"]), - ('add', './count2.txt', c2["count2.txt"])]) - f = c1.open("count1.txt", "w") - f.write("zzzzz") + 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) @@ -1012,25 +1093,31 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): 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", "w") - f.write("zzzzz") + 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.assertRegexpMatches(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~$") + self.assertRegex( + c1.portable_manifest_text(), + r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$") 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(d, [('del', './count2.txt', c1["count2.txt"]), - ('add', './count1.txt', c2["count1.txt"])]) - f = c1.open("count1.txt", "w") - f.write("zzzzz") + 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.assertRegexpMatches(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~$") + self.assertRegex( + c1.portable_manifest_text(), + r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$") def test_conflict_del(self): c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') @@ -1041,22 +1128,125 @@ class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): # c1 deleted, so c2 mod will go to a conflict file c1.apply(d) - self.assertRegexpMatches(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~$") + self.assertRegex( + c1.portable_manifest_text(), + r"\. 5348b82a029fd9e971a811ce1f71360b\+43 0:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$") 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", "w") + 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", "w").close() + c1.open("count1.txt", "wb").close() self.assertEqual(c1["count1.txt"].size(), 0) +class NewCollectionTestCaseWithServers(run_test_server.TestCaseWithServers): + 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", "w") + f.write("0123456789") + f.close(flush=False) + foo = c.open("foo.txt", "w") + foo.write("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", "r+") + 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", "w") + f.write("0123456789") + f.close(flush=False) + foo = c.open("foo.txt", "w") + foo.write("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", "r+") + f.write("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", "w").close() + c["b1"].writeto(0, "b1", 0) + + c.open("b2", "w").close() + c["b2"].writeto(0, "b2", 0) + + c["b1"].writeto(0, "1b", 0) + + self.assertEquals(c.manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1 2:2:b2\n") + self.assertEquals(c["b1"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1\n") + self.assertEquals(c["b2"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 2:2:b2\n") + + class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers): MAIN_SERVER = {} KEEP_SERVER = {} @@ -1070,8 +1260,8 @@ class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers): self.assertEqual(c.portable_data_hash(), "d41d8cd98f00b204e9800998ecf8427e+0") self.assertEqual(c.api_response()["portable_data_hash"], "d41d8cd98f00b204e9800998ecf8427e+0" ) - with c.open("count.txt", "w") as f: - f.write("0123456789") + 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") @@ -1080,20 +1270,24 @@ class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers): def test_create_and_save(self): c = self.create_count_txt() c.save() - self.assertRegexpMatches(c.manifest_text(), r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",) + self.assertRegex( + c.manifest_text(), + r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",) def test_create_and_save_new(self): c = self.create_count_txt() c.save_new() - self.assertRegexpMatches(c.manifest_text(), r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",) + self.assertRegex( + c.manifest_text(), + r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",) def test_create_diff_apply(self): c1 = self.create_count_txt() c1.save() c2 = Collection(c1.manifest_locator()) - with c2.open("count.txt", "w") as f: - f.write("abcdefg") + with c2.open("count.txt", "wb") as f: + f.write(b"abcdefg") diff = c1.diff(c2) @@ -1120,8 +1314,8 @@ class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers): c1.save() c2 = arvados.collection.Collection(c1.manifest_locator()) - with c2.open("count.txt", "w") as f: - f.write("abcdefg") + with c2.open("count.txt", "wb") as f: + f.write(b"abcdefg") c2.save() @@ -1134,17 +1328,19 @@ class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers): c1 = self.create_count_txt() c1.save() - with c1.open("count.txt", "w") as f: - f.write("XYZ") + with c1.open("count.txt", "wb") as f: + f.write(b"XYZ") c2 = arvados.collection.Collection(c1.manifest_locator()) - with c2.open("count.txt", "w") as f: - f.write("abcdefg") + with c2.open("count.txt", "wb") as f: + f.write(b"abcdefg") c2.save() c1.update() - self.assertRegexpMatches(c1.manifest_text(), r"\. e65075d550f9b5bf9992fa1d71a131be\+3 7ac66c0f148de9519b8bd264312c4d64\+7\+A[a-f0-9]{40}@[a-f0-9]{8} 0:3:count\.txt 3:7:count\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$") + self.assertRegex( + c1.manifest_text(), + r"\. e65075d550f9b5bf9992fa1d71a131be\+3\S* 7ac66c0f148de9519b8bd264312c4d64\+7\S* 0:3:count\.txt 3:7:count\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$") if __name__ == '__main__':