-#!/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
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
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):
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())
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())
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)
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)
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):
"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)
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"
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")
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)
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):
"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")
"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)
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({})
"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)
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):
def __init__(self, blocks, nocache):
self.blocks = blocks
self.nocache = nocache
+ self.num_get_threads = 1
def block_prefetch(self, loc):
pass
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)
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"])
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"])
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):
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):
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)
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)
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
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")
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
projects / arvados.git / blobdiff