X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f69e114cf6dbe51525e98ca30a52ef3dd4341167..093ec98e4a065acfc537ea22c08c337c115fe273:/sdk/python/tests/test_arvfile.py diff --git a/sdk/python/tests/test_arvfile.py b/sdk/python/tests/test_arvfile.py index 6c4976ee0d..b45a592ecd 100644 --- a/sdk/python/tests/test_arvfile.py +++ b/sdk/python/tests/test_arvfile.py @@ -1,10 +1,13 @@ -#!/usr/bin/env python +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 from __future__ import absolute_import -import bz2 +from builtins import hex +from builtins import str +from builtins import range +from builtins import object import datetime -import gzip -import io import mock import os import unittest @@ -13,7 +16,7 @@ import time import arvados from arvados._ranges import Range from arvados.keep import KeepLocator -from arvados.collection import Collection, CollectionReader +from arvados.collection import Collection from arvados.arvfile import ArvadosFile, ArvadosFileReader from . import arvados_testutil as tutil @@ -24,15 +27,15 @@ class ArvadosFileWriterTestCase(unittest.TestCase): def __init__(self, blocks): self.blocks = blocks self.requests = [] - def get(self, locator, num_retries=0): + def get(self, locator, num_retries=0, prefetch=False): self.requests.append(locator) return self.blocks.get(locator) def get_from_cache(self, locator): self.requests.append(locator) return self.blocks.get(locator) - def put(self, data, num_retries=None, copies=None): + def put(self, data, num_retries=None, copies=None, classes=[]): pdh = tutil.str_keep_locator(data) - self.blocks[pdh] = str(data) + self.blocks[pdh] = bytes(data) return pdh class MockApi(object): @@ -64,27 +67,102 @@ class ArvadosFileWriterTestCase(unittest.TestCase): def test_truncate(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate", - "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n", - "replication_desired":None}, - {"uuid":"zzzzz-4zz18-mockcollection0", - "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n", - "portable_data_hash":"7fcd0eaac3aad4c31a6a0e756475da92+52"}) + keep = ArvadosFileWriterTestCase.MockKeep({ + "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789", + }) + api = ArvadosFileWriterTestCase.MockApi({ + "name": "test_truncate", + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n", + "replication_desired": None, + }, { + "uuid": "zzzzz-4zz18-mockcollection0", + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n", + "portable_data_hash":"7fcd0eaac3aad4c31a6a0e756475da92+52", + }) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - api_client=api, keep_client=keep) as c: - writer = c.open("count.txt", "r+") + api_client=api, keep_client=keep) as c: + writer = c.open("count.txt", "rb+") self.assertEqual(writer.size(), 10) - self.assertEqual("0123456789", writer.read(12)) + self.assertEqual(b"0123456789", writer.read(12)) writer.truncate(8) # Make sure reading off the end doesn't break - self.assertEqual("", writer.read(12)) + self.assertEqual(b"", writer.read(12)) self.assertEqual(writer.size(), 8) writer.seek(0, os.SEEK_SET) - self.assertEqual("01234567", writer.read(12)) + self.assertEqual(b"01234567", writer.read(12)) + + self.assertIsNone(c.manifest_locator()) + self.assertTrue(c.modified()) + c.save_new("test_truncate") + self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) + self.assertFalse(c.modified()) + + + def test_truncate2(self): + keep = ArvadosFileWriterTestCase.MockKeep({ + "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789", + }) + api = ArvadosFileWriterTestCase.MockApi({ + "name": "test_truncate2", + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n", + "replication_desired": None, + }, { + "uuid": "zzzzz-4zz18-mockcollection0", + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n", + "portable_data_hash": "272da898abdf86ddc71994835e3155f8+95", + }) + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', + api_client=api, keep_client=keep) as c: + writer = c.open("count.txt", "rb+") + self.assertEqual(writer.size(), 10) + self.assertEqual(b"0123456789", writer.read(12)) + + # extend file size + writer.truncate(12) + + self.assertEqual(writer.size(), 12) + writer.seek(0, os.SEEK_SET) + self.assertEqual(b"0123456789\x00\x00", writer.read(12)) + + self.assertIsNone(c.manifest_locator()) + self.assertTrue(c.modified()) + c.save_new("test_truncate2") + self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) + self.assertFalse(c.modified()) + + def test_truncate3(self): + keep = ArvadosFileWriterTestCase.MockKeep({ + "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789", + "a925576942e94b2ef57a066101b48876+10": b"abcdefghij", + }) + api = ArvadosFileWriterTestCase.MockApi({ + "name": "test_truncate", + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n", + "replication_desired": None, + }, { + "uuid": "zzzzz-4zz18-mockcollection0", + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n", + "portable_data_hash": "7fcd0eaac3aad4c31a6a0e756475da92+52", + }) + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n', + api_client=api, keep_client=keep) as c: + writer = c.open("count.txt", "rb+") + self.assertEqual(writer.size(), 20) + self.assertEqual(b"0123456789ab", writer.read(12)) + self.assertEqual(12, writer.tell()) + + writer.truncate(8) + + # Make sure reading off the end doesn't break + self.assertEqual(12, writer.tell()) + self.assertEqual(b"", writer.read(12)) + + self.assertEqual(writer.size(), 8) + self.assertEqual(2, writer.seek(-10, os.SEEK_CUR)) + self.assertEqual(b"234567", writer.read(12)) self.assertIsNone(c.manifest_locator()) self.assertTrue(c.modified()) @@ -93,27 +171,32 @@ class ArvadosFileWriterTestCase(unittest.TestCase): self.assertFalse(c.modified()) def test_write_to_end(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - api = ArvadosFileWriterTestCase.MockApi({"name":"test_append", - "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n", - "replication_desired":None}, - {"uuid":"zzzzz-4zz18-mockcollection0", - "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n", - "portable_data_hash":"c5c3af76565c8efb6a806546bcf073f3+88"}) + keep = ArvadosFileWriterTestCase.MockKeep({ + "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789", + }) + api = ArvadosFileWriterTestCase.MockApi({ + "name": "test_append", + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n", + "replication_desired": None, + }, { + "uuid": "zzzzz-4zz18-mockcollection0", + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n", + "portable_data_hash": "c5c3af76565c8efb6a806546bcf073f3+88", + }) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', api_client=api, keep_client=keep) as c: - writer = c.open("count.txt", "r+") + writer = c.open("count.txt", "rb+") self.assertEqual(writer.size(), 10) - writer.seek(5, os.SEEK_SET) - self.assertEqual("56789", writer.read(8)) + self.assertEqual(5, writer.seek(5, os.SEEK_SET)) + self.assertEqual(b"56789", writer.read(8)) writer.seek(10, os.SEEK_SET) writer.write("foo") self.assertEqual(writer.size(), 13) writer.seek(5, os.SEEK_SET) - self.assertEqual("56789foo", writer.read(8)) + self.assertEqual(b"56789foo", writer.read(8)) self.assertIsNone(c.manifest_locator()) self.assertTrue(c.modified()) @@ -122,49 +205,75 @@ class ArvadosFileWriterTestCase(unittest.TestCase): c.save_new("test_append") self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) self.assertFalse(c.modified()) - self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3")) + self.assertEqual(b"foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3")) def test_append(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep) - writer = c.open("count.txt", "a+") - self.assertEqual(writer.read(20), "0123456789") - writer.seek(0, os.SEEK_SET) + keep = ArvadosFileWriterTestCase.MockKeep({ + "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789", + }) + for (mode, convert) in ( + ('a+', lambda data: data.decode(encoding='utf-8')), + ('at+', lambda data: data.decode(encoding='utf-8')), + ('ab+', lambda data: data)): + c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep) + writer = c.open("count.txt", mode) + self.assertEqual(writer.read(20), convert(b"0123456789")) + + writer.seek(0, os.SEEK_SET) + writer.write(convert(b"hello")) + self.assertEqual(writer.read(), convert(b"")) + if 'b' in mode: + writer.seek(-5, os.SEEK_CUR) + self.assertEqual(writer.read(3), convert(b"hel")) + self.assertEqual(writer.read(), convert(b"lo")) + else: + with self.assertRaises(IOError): + writer.seek(-5, os.SEEK_CUR) + with self.assertRaises(IOError): + writer.seek(-3, os.SEEK_END) + writer.seek(0, os.SEEK_SET) + writer.read(7) + self.assertEqual(7, writer.tell()) + self.assertEqual(7, writer.seek(7, os.SEEK_SET)) - writer.write("hello") - self.assertEqual(writer.read(20), "0123456789hello") - writer.seek(0, os.SEEK_SET) + writer.seek(0, os.SEEK_SET) + self.assertEqual(writer.read(), convert(b"0123456789hello")) - writer.write("world") - self.assertEqual(writer.read(20), "0123456789helloworld") + writer.seek(0) + writer.write(convert(b"world")) + self.assertEqual(writer.read(), convert(b"")) + writer.seek(0) + self.assertEqual(writer.read(), convert(b"0123456789helloworld")) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.portable_manifest_text()) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.portable_manifest_text()) def test_write_at_beginning(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + keep = ArvadosFileWriterTestCase.MockKeep({ + "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789", + }) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep) as c: - writer = c.open("count.txt", "r+") - self.assertEqual("0123456789", writer.readfrom(0, 13)) + writer = c.open("count.txt", "rb+") + self.assertEqual(b"0123456789", writer.readfrom(0, 13)) writer.seek(0, os.SEEK_SET) writer.write("foo") self.assertEqual(writer.size(), 10) - self.assertEqual("foo3456789", writer.readfrom(0, 13)) + self.assertEqual(b"foo3456789", writer.readfrom(0, 13)) self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", c.portable_manifest_text()) def test_write_empty(self): keep = ArvadosFileWriterTestCase.MockKeep({}) with Collection(keep_client=keep) as c: - writer = c.open("count.txt", "w") + writer = c.open("count.txt", "wb") self.assertEqual(writer.size(), 0) self.assertEqual(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n", c.portable_manifest_text()) def test_save_manifest_text(self): keep = ArvadosFileWriterTestCase.MockKeep({}) with Collection(keep_client=keep) as c: - writer = c.open("count.txt", "w") - writer.write("0123456789") + writer = c.open("count.txt", "wb") + writer.write(b"0123456789") self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text()) self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks) @@ -174,7 +283,7 @@ class ArvadosFileWriterTestCase(unittest.TestCase): def test_get_manifest_text_commits(self): keep = ArvadosFileWriterTestCase.MockKeep({}) with Collection(keep_client=keep) as c: - writer = c.open("count.txt", "w") + writer = c.open("count.txt", "wb") writer.write("0123456789") self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text()) self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks) @@ -183,51 +292,51 @@ class ArvadosFileWriterTestCase(unittest.TestCase): def test_write_in_middle(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"}) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep) as c: - writer = c.open("count.txt", "r+") - self.assertEqual("0123456789", writer.readfrom(0, 13)) + writer = c.open("count.txt", "rb+") + self.assertEqual(b"0123456789", writer.readfrom(0, 13)) writer.seek(3, os.SEEK_SET) writer.write("foo") self.assertEqual(writer.size(), 10) - self.assertEqual("012foo6789", writer.readfrom(0, 13)) + self.assertEqual(b"012foo6789", writer.readfrom(0, 13)) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.portable_manifest_text()) def test_write_at_end(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"}) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep) as c: - writer = c.open("count.txt", "r+") - self.assertEqual("0123456789", writer.readfrom(0, 13)) + writer = c.open("count.txt", "rb+") + self.assertEqual(b"0123456789", writer.readfrom(0, 13)) writer.seek(7, os.SEEK_SET) writer.write("foo") self.assertEqual(writer.size(), 10) - self.assertEqual("0123456foo", writer.readfrom(0, 13)) + self.assertEqual(b"0123456foo", writer.readfrom(0, 13)) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text()) def test_write_across_segment_boundary(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"}) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n', keep_client=keep) as c: - writer = c.open("count.txt", "r+") - self.assertEqual("012345678901234", writer.readfrom(0, 15)) + writer = c.open("count.txt", "rb+") + self.assertEqual(b"012345678901234", writer.readfrom(0, 15)) writer.seek(7, os.SEEK_SET) writer.write("foobar") self.assertEqual(writer.size(), 20) - self.assertEqual("0123456foobar34", writer.readfrom(0, 15)) + self.assertEqual(b"0123456foobar34", writer.readfrom(0, 15)) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text()) def test_write_across_several_segments(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"}) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt', keep_client=keep) as c: - writer = c.open("count.txt", "r+") - self.assertEqual("012301230123", writer.readfrom(0, 15)) + writer = c.open("count.txt", "rb+") + self.assertEqual(b"012301230123", writer.readfrom(0, 15)) writer.seek(2, os.SEEK_SET) writer.write("abcdefg") self.assertEqual(writer.size(), 12) - self.assertEqual("01abcdefg123", writer.readfrom(0, 15)) + self.assertEqual(b"01abcdefg123", writer.readfrom(0, 15)) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text()) def test_write_large(self): @@ -240,9 +349,9 @@ class ArvadosFileWriterTestCase(unittest.TestCase): "portable_data_hash":"9132ca8e3f671c76103a38f5bc24328c+108"}) with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', api_client=api, keep_client=keep) as c: - writer = c.open("count.txt", "r+") + writer = c.open("count.txt", "rb+") text = "0123456789" * 100 - for b in xrange(0, 100000): + for b in range(0, 100000): writer.write(text) self.assertEqual(writer.size(), 100000000) @@ -252,13 +361,12 @@ class ArvadosFileWriterTestCase(unittest.TestCase): self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) self.assertFalse(c.modified()) - def test_large_write(self): keep = ArvadosFileWriterTestCase.MockKeep({}) api = ArvadosFileWriterTestCase.MockApi({}, {}) with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', api_client=api, keep_client=keep) as c: - writer = c.open("count.txt", "r+") + writer = c.open("count.txt", "rb+") self.assertEqual(writer.size(), 0) text = "0123456789" @@ -269,73 +377,140 @@ class ArvadosFileWriterTestCase(unittest.TestCase): self.assertEqual(c.manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n") + def test_sparse_write(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + api = ArvadosFileWriterTestCase.MockApi({}, {}) + with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', + api_client=api, keep_client=keep) as c: + writer = c.open("count.txt", "rb+") + self.assertEqual(writer.size(), 0) + + text = b"0123456789" + writer.seek(2) + writer.write(text) + self.assertEqual(writer.size(), 12) + writer.seek(0, os.SEEK_SET) + self.assertEqual(writer.read(), b"\x00\x00"+text) + + self.assertEqual(c.manifest_text(), ". 7f614da9329cd3aebf59b91aadc30bf0+67108864 781e5e245d69b566979b86e28d23f2c7+10 0:2:count.txt 67108864:10:count.txt\n") + + def test_sparse_write2(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + api = ArvadosFileWriterTestCase.MockApi({}, {}) + with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', + api_client=api, keep_client=keep) as c: + writer = c.open("count.txt", "rb+") + self.assertEqual(writer.size(), 0) + + text = "0123456789" + writer.seek((arvados.config.KEEP_BLOCK_SIZE*2) + 2) + writer.write(text) + self.assertEqual(writer.size(), (arvados.config.KEEP_BLOCK_SIZE*2) + 12) + writer.seek(0, os.SEEK_SET) + + self.assertEqual(c.manifest_text(), ". 7f614da9329cd3aebf59b91aadc30bf0+67108864 781e5e245d69b566979b86e28d23f2c7+10 0:67108864:count.txt 0:67108864:count.txt 0:2:count.txt 67108864:10:count.txt\n") + + def test_sparse_write3(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + api = ArvadosFileWriterTestCase.MockApi({}, {}) + for r in [[0, 1, 2, 3, 4], [4, 3, 2, 1, 0], [3, 2, 0, 4, 1]]: + with Collection() as c: + writer = c.open("count.txt", "rb+") + self.assertEqual(writer.size(), 0) + + for i in r: + w = ("%s" % i) * 10 + writer.seek(i*10) + writer.write(w.encode()) + writer.seek(0) + self.assertEqual(writer.read(), b"00000000001111111111222222222233333333334444444444") + + def test_sparse_write4(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + api = ArvadosFileWriterTestCase.MockApi({}, {}) + for r in [[0, 1, 2, 4], [4, 2, 1, 0], [2, 0, 4, 1]]: + with Collection() as c: + writer = c.open("count.txt", "rb+") + self.assertEqual(writer.size(), 0) + + for i in r: + w = ("%s" % i) * 10 + writer.seek(i*10) + writer.write(w.encode()) + writer.seek(0) + self.assertEqual(writer.read(), b"000000000011111111112222222222\x00\x00\x00\x00\x00\x00\x00\x00\x00\x004444444444") + def test_rewrite_on_empty_file(self): keep = ArvadosFileWriterTestCase.MockKeep({}) with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', keep_client=keep) as c: - writer = c.open("count.txt", "r+") - for b in xrange(0, 10): + writer = c.open("count.txt", "rb+") + for b in range(0, 10): writer.seek(0, os.SEEK_SET) writer.write("0123456789") self.assertEqual(writer.size(), 10) - self.assertEqual("0123456789", writer.readfrom(0, 20)) + self.assertEqual(b"0123456789", writer.readfrom(0, 20)) self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.portable_manifest_text()) writer.flush() self.assertEqual(writer.size(), 10) - self.assertEqual("0123456789", writer.readfrom(0, 20)) + self.assertEqual(b"0123456789", writer.readfrom(0, 20)) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.portable_manifest_text()) def test_rewrite_append_existing_file(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + keep = ArvadosFileWriterTestCase.MockKeep({ + "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789", + }) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt', keep_client=keep) as c: - writer = c.open("count.txt", "r+") - for b in xrange(0, 10): + writer = c.open("count.txt", "rb+") + for b in range(0, 10): writer.seek(10, os.SEEK_SET) writer.write("abcdefghij") self.assertEqual(writer.size(), 20) - self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20)) + self.assertEqual(b"0123456789abcdefghij", writer.readfrom(0, 20)) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.portable_manifest_text()) writer.arvadosfile.flush() self.assertEqual(writer.size(), 20) - self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20)) + self.assertEqual(b"0123456789abcdefghij", writer.readfrom(0, 20)) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.portable_manifest_text()) def test_rewrite_over_existing_file(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + keep = ArvadosFileWriterTestCase.MockKeep({ + "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789", + }) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt', keep_client=keep) as c: - writer = c.open("count.txt", "r+") - for b in xrange(0, 10): + writer = c.open("count.txt", "rb+") + for b in range(0, 10): writer.seek(5, os.SEEK_SET) writer.write("abcdefghij") self.assertEqual(writer.size(), 15) - self.assertEqual("01234abcdefghij", writer.readfrom(0, 20)) + self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20)) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.portable_manifest_text()) writer.arvadosfile.flush() self.assertEqual(writer.size(), 15) - self.assertEqual("01234abcdefghij", writer.readfrom(0, 20)) + self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20)) self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.portable_manifest_text()) def test_write_large_rewrite(self): keep = ArvadosFileWriterTestCase.MockKeep({}) api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large", - "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n", + "manifest_text": ". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n", "replication_desired":None}, {"uuid":"zzzzz-4zz18-mockcollection0", - "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n", + "manifest_text": ". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n", "portable_data_hash":"217665c6b713e1b78dfba7ebd42344db+156"}) with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', api_client=api, keep_client=keep) as c: - writer = c.open("count.txt", "r+") - text = ''.join(["0123456789" for a in xrange(0, 100)]) - for b in xrange(0, 100000): + writer = c.open("count.txt", "rb+") + text = b''.join([b"0123456789" for a in range(0, 100)]) + for b in range(0, 100000): writer.write(text) writer.seek(0, os.SEEK_SET) writer.write("foo") @@ -349,14 +524,17 @@ class ArvadosFileWriterTestCase(unittest.TestCase): def test_create(self): keep = ArvadosFileWriterTestCase.MockKeep({}) - api = ArvadosFileWriterTestCase.MockApi({"name":"test_create", - "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n", - "replication_desired":None}, - {"uuid":"zzzzz-4zz18-mockcollection0", - "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n", - "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51"}) + api = ArvadosFileWriterTestCase.MockApi({ + "name":"test_create", + "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n", + "replication_desired":None, + }, { + "uuid":"zzzzz-4zz18-mockcollection0", + "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n", + "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51", + }) with Collection(api_client=api, keep_client=keep) as c: - writer = c.open("count.txt", "w+") + writer = c.open("count.txt", "wb+") self.assertEqual(writer.size(), 0) writer.write("01234567") self.assertEqual(writer.size(), 8) @@ -367,7 +545,7 @@ class ArvadosFileWriterTestCase(unittest.TestCase): c.save_new("test_create") self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) self.assertFalse(c.modified()) - self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8")) + self.assertEqual(b"01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8")) def test_create_subdir(self): @@ -380,7 +558,7 @@ class ArvadosFileWriterTestCase(unittest.TestCase): "portable_data_hash":"1b02aaa62528d28a5be41651cbb9d7c7+59"}) with Collection(api_client=api, keep_client=keep) as c: self.assertIsNone(c.api_response()) - writer = c.open("foo/bar/count.txt", "w+") + writer = c.open("foo/bar/count.txt", "wb+") writer.write("01234567") self.assertFalse(c.committed()) c.save_new("test_create") @@ -397,7 +575,7 @@ class ArvadosFileWriterTestCase(unittest.TestCase): "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51"}) with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', api_client=api, keep_client=keep) as c: - writer = c.open("count.txt", "w+") + writer = c.open("count.txt", "wb+") self.assertEqual(writer.size(), 0) writer.write("01234567") self.assertEqual(writer.size(), 8) @@ -411,12 +589,12 @@ class ArvadosFileWriterTestCase(unittest.TestCase): def test_file_not_found(self): with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c: with self.assertRaises(IOError): - writer = c.open("nocount.txt", "r") + writer = c.open("nocount.txt", "rb") def test_cannot_open_directory(self): with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c: with self.assertRaises(IOError): - writer = c.open(".", "r") + writer = c.open(".", "rb") def test_create_multiple(self): keep = ArvadosFileWriterTestCase.MockKeep({}) @@ -427,8 +605,8 @@ class ArvadosFileWriterTestCase(unittest.TestCase): "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n", "portable_data_hash":"71e7bb6c00d31fc2b4364199fd97be08+102"}) with Collection(api_client=api, keep_client=keep) as c: - w1 = c.open("count1.txt", "w") - w2 = c.open("count2.txt", "w") + w1 = c.open("count1.txt", "wb") + w2 = c.open("count2.txt", "wb") w1.write("01234567") w2.write("abcdefgh") self.assertEqual(w1.size(), 8) @@ -440,7 +618,7 @@ class ArvadosFileWriterTestCase(unittest.TestCase): c.save_new("test_create_multiple") self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) self.assertFalse(c.modified()) - self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8")) + self.assertEqual(b"01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8")) class ArvadosFileReaderTestCase(StreamFileReaderTestCase): @@ -449,6 +627,7 @@ class ArvadosFileReaderTestCase(StreamFileReaderTestCase): def __init__(self, blocks, nocache): self.blocks = blocks self.nocache = nocache + self.num_get_threads = 1 def block_prefetch(self, loc): pass @@ -474,39 +653,42 @@ class ArvadosFileReaderTestCase(StreamFileReaderTestCase): stream = [] n = 0 blocks = {} - for d in ['01234', '34567', '67890']: + for d in [b'01234', b'34567', b'67890']: loc = tutil.str_keep_locator(d) blocks[loc] = d stream.append(Range(loc, n, len(d))) n += len(d) af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), "count.txt", stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)]) - return ArvadosFileReader(af) + return ArvadosFileReader(af, mode="rb") def test_read_block_crossing_behavior(self): # read() needs to return all the data requested if possible, even if it # crosses uncached blocks: https://arvados.org/issues/5856 sfile = self.make_count_reader(nocache=True) - self.assertEqual('12345678', sfile.read(8)) + self.assertEqual(b'12345678', sfile.read(8)) def test_successive_reads(self): # Override StreamFileReaderTestCase.test_successive_reads sfile = self.make_count_reader(nocache=True) - self.assertEqual('1234', sfile.read(4)) - self.assertEqual('5678', sfile.read(4)) - self.assertEqual('9', sfile.read(4)) - self.assertEqual('', sfile.read(4)) + self.assertEqual(b'1234', sfile.read(4)) + self.assertEqual(b'5678', sfile.read(4)) + self.assertEqual(b'9', sfile.read(4)) + self.assertEqual(b'', sfile.read(4)) def test_tell_after_block_read(self): # Override StreamFileReaderTestCase.test_tell_after_block_read sfile = self.make_count_reader(nocache=True) - self.assertEqual('12345678', sfile.read(8)) + self.assertEqual(b'12345678', sfile.read(8)) self.assertEqual(8, sfile.tell()) def test_prefetch(self): - keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"}) + keep = ArvadosFileWriterTestCase.MockKeep({ + "2e9ec317e197819358fbc43afca7d837+8": b"01234567", + "e8dc4081b13434b45189a720b77b6818+8": b"abcdefgh", + }) with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c: - r = c.open("count.txt", "r") - self.assertEqual("0123", r.read(4)) + r = c.open("count.txt", "rb") + self.assertEqual(b"0123", r.read(4)) self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests) self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests) @@ -519,7 +701,7 @@ class ArvadosFileReaderTestCase(StreamFileReaderTestCase): def test__eq__from_writes(self): with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1: with Collection() as c2: - f = c2.open("count1.txt", "w") + f = c2.open("count1.txt", "wb") f.write("0123456789") self.assertTrue(c1["count1.txt"] == c2["count1.txt"]) @@ -528,7 +710,7 @@ class ArvadosFileReaderTestCase(StreamFileReaderTestCase): def test__ne__(self): with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1: with Collection() as c2: - f = c2.open("count1.txt", "w") + f = c2.open("count1.txt", "wb") f.write("1234567890") self.assertTrue(c1["count1.txt"] != c2["count1.txt"]) @@ -555,6 +737,7 @@ class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin): af = ArvadosFile(col, "test", stream=stream, segments=segments) + kwargs.setdefault('mode', 'rb') return ArvadosFileReader(af, **kwargs) def read_for_test(self, reader, byte_count, **kwargs): @@ -568,17 +751,17 @@ class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase): class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase): def read_for_test(self, reader, byte_count, **kwargs): - return ''.join(reader.readall(**kwargs)) + return b''.join(reader.readall(**kwargs)) class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase): def read_for_test(self, reader, byte_count, **kwargs): - return ''.join(reader.readall_decompressed(**kwargs)) + return b''.join(reader.readall_decompressed(**kwargs)) class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase): def read_for_test(self, reader, byte_count, **kwargs): - return ''.join(reader.readlines(**kwargs)) + return ''.join(reader.readlines(**kwargs)).encode() class ArvadosFileTestCase(unittest.TestCase): @@ -608,13 +791,13 @@ class BlockManagerTest(unittest.TestCase): bufferblock.append("foo") self.assertEqual(bufferblock.size(), 3) - self.assertEqual(bufferblock.buffer_view[0:3], "foo") + self.assertEqual(bufferblock.buffer_view[0:3], b"foo") self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3") bufferblock.append("bar") self.assertEqual(bufferblock.size(), 6) - self.assertEqual(bufferblock.buffer_view[0:6], "foobar") + self.assertEqual(bufferblock.buffer_view[0:6], b"foobar") self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6") bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING) @@ -628,7 +811,7 @@ class BlockManagerTest(unittest.TestCase): bufferblock.append("foo") self.assertEqual(bufferblock.size(), 3) - self.assertEqual(bufferblock.buffer_view[0:3], "foo") + self.assertEqual(bufferblock.buffer_view[0:3], b"foo") self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3") bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING) @@ -638,27 +821,29 @@ class BlockManagerTest(unittest.TestCase): bufferblock2.append("bar") self.assertEqual(bufferblock2.size(), 6) - self.assertEqual(bufferblock2.buffer_view[0:6], "foobar") + self.assertEqual(bufferblock2.buffer_view[0:6], b"foobar") self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6") self.assertEqual(bufferblock.size(), 3) - self.assertEqual(bufferblock.buffer_view[0:3], "foo") + self.assertEqual(bufferblock.buffer_view[0:3], b"foo") self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3") def test_bufferblock_get(self): - keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + keep = ArvadosFileWriterTestCase.MockKeep({ + "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789", + }) with arvados.arvfile._BlockManager(keep) as blockmanager: bufferblock = blockmanager.alloc_bufferblock() bufferblock.append("foo") - self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), "0123456789") - self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), "foo") + self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), b"0123456789") + self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), b"foo") def test_bufferblock_commit(self): mockkeep = mock.MagicMock() with arvados.arvfile._BlockManager(mockkeep) as blockmanager: bufferblock = blockmanager.alloc_bufferblock() - bufferblock.owner = mock.MagicMock() + bufferblock.owner = mock.MagicMock(spec=arvados.arvfile.ArvadosFile) def flush(sync=None): blockmanager.commit_bufferblock(bufferblock, sync) bufferblock.owner.flush.side_effect = flush @@ -672,7 +857,7 @@ class BlockManagerTest(unittest.TestCase): def test_bufferblock_commit_pending(self): # Test for bug #7225 mockkeep = mock.MagicMock() - mockkeep.put.side_effect = lambda x: time.sleep(1) + mockkeep.put.side_effect = lambda *args, **kwargs: time.sleep(1) with arvados.arvfile._BlockManager(mockkeep) as blockmanager: bufferblock = blockmanager.alloc_bufferblock() bufferblock.append("foo") @@ -683,13 +868,12 @@ class BlockManagerTest(unittest.TestCase): blockmanager.commit_bufferblock(bufferblock, True) self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED) - def test_bufferblock_commit_with_error(self): mockkeep = mock.MagicMock() mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail") with arvados.arvfile._BlockManager(mockkeep) as blockmanager: bufferblock = blockmanager.alloc_bufferblock() - bufferblock.owner = mock.MagicMock() + bufferblock.owner = mock.MagicMock(spec=arvados.arvfile.ArvadosFile) def flush(sync=None): blockmanager.commit_bufferblock(bufferblock, sync) bufferblock.owner.flush.side_effect = flush