-from __future__ import absolute_import
-from builtins import hex
-from builtins import str
-from builtins import range
-from builtins import object
-import bz2
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import datetime
-import gzip
-import io
-import mock
import os
-import unittest
import time
+import unittest
+
+from unittest import mock
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):
+ self.num_prefetch_threads = 1
+ 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] = bytes(data)
return pdh
+ def block_prefetch(self, loc):
+ self.requests.append(loc)
class MockApi(object):
def __init__(self, b, r):
"portable_data_hash":"7fcd0eaac3aad4c31a6a0e756475da92+52",
})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
- api_client=api, keep_client=keep) as c:
+ 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))
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())
+ c.save_new("test_truncate")
+ self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
+ self.assertFalse(c.modified())
+
def test_write_to_end(self):
keep = ArvadosFileWriterTestCase.MockKeep({
"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
writer = c.open("count.txt", "rb+")
self.assertEqual(writer.size(), 10)
- writer.seek(5, os.SEEK_SET)
+ self.assertEqual(5, writer.seek(5, os.SEEK_SET))
self.assertEqual(b"56789", writer.read(8))
writer.seek(10, os.SEEK_SET)
keep = ArvadosFileWriterTestCase.MockKeep({
"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
})
- c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep)
- writer = c.open("count.txt", "ab+")
- self.assertEqual(writer.read(20), b"0123456789")
- writer.seek(0, os.SEEK_SET)
+ 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), b"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), b"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({
self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
self.assertFalse(c.modified())
-
def test_large_write(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi({}, {})
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(api_client=api, keep_client=keep) 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(api_client=api, keep_client=keep) 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',
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:
def __init__(self, blocks, nocache):
self.blocks = blocks
self.nocache = nocache
+ self._keep = ArvadosFileWriterTestCase.MockKeep({})
+ self.prefetch_lookahead = 0
def block_prefetch(self, loc):
pass
with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
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)
+ self.assertEqual(["2e9ec317e197819358fbc43afca7d837+8",
+ "e8dc4081b13434b45189a720b77b6818+8"], keep.requests)
+
+ def test_prefetch_disabled(self):
+ keep = ArvadosFileWriterTestCase.MockKeep({
+ "2e9ec317e197819358fbc43afca7d837+8": b"01234567",
+ "e8dc4081b13434b45189a720b77b6818+8": b"abcdefgh",
+ })
+ keep.num_prefetch_threads = 0
+ with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
+ r = c.open("count.txt", "rb")
+ self.assertEqual(b"0123", r.read(4))
+
+ self.assertEqual(["2e9ec317e197819358fbc43afca7d837+8"], keep.requests)
+
+ def test_prefetch_first_read_only(self):
+ # test behavior that prefetch only happens every 128 reads
+ # check that it doesn't make a prefetch request on the second read
+ 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", "rb")
+ self.assertEqual(b"0123", r.read(4))
+ self.assertEqual(b"45", r.read(2))
+ self.assertEqual(["2e9ec317e197819358fbc43afca7d837+8",
+ "e8dc4081b13434b45189a720b77b6818+8",
+ "2e9ec317e197819358fbc43afca7d837+8"], keep.requests)
+ self.assertEqual(3, len(keep.requests))
+
+ def test_prefetch_again(self):
+ # test behavior that prefetch only happens every 128 reads
+ # check that it does make another prefetch request after 128 reads
+ 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", "rb")
+ for i in range(0, 129):
+ r.seek(0)
+ self.assertEqual(b"0123", r.read(4))
+ self.assertEqual(["2e9ec317e197819358fbc43afca7d837+8",
+ "e8dc4081b13434b45189a720b77b6818+8",
+ "2e9ec317e197819358fbc43afca7d837+8",
+ "2e9ec317e197819358fbc43afca7d837+8"], keep.requests[0:4])
+ self.assertEqual(["2e9ec317e197819358fbc43afca7d837+8",
+ "2e9ec317e197819358fbc43afca7d837+8",
+ "2e9ec317e197819358fbc43afca7d837+8",
+ "e8dc4081b13434b45189a720b77b6818+8"], keep.requests[127:131])
+ # gets the 1st block 129 times from keep (cache),
+ # and the 2nd block twice to get 131 requests
+ self.assertEqual(131, len(keep.requests))
def test__eq__from_manifest(self):
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
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