sdk/python/tests/test_arvfile.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 from __future__ import absolute_import
   6 from builtins import hex
   7 from builtins import str
   8 from builtins import range
   9 from builtins import object
  10 import datetime
  11 import mock
  12 import os
  13 import unittest
  14 import time
  15
  16 import arvados
  17 from arvados._ranges import Range
  18 from arvados.keep import KeepLocator
  19 from arvados.collection import Collection
  20 from arvados.arvfile import ArvadosFile, ArvadosFileReader
  21
  22 from . import arvados_testutil as tutil
  23 from .test_stream import StreamFileReaderTestCase, StreamRetryTestMixin
  24
  25 class ArvadosFileWriterTestCase(unittest.TestCase):
  26     class MockKeep(object):
  27         def __init__(self, blocks):
  28             self.blocks = blocks
  29             self.requests = []
  30         def get(self, locator, num_retries=0, prefetch=False):
  31             self.requests.append(locator)
  32             return self.blocks.get(locator)
  33         def get_from_cache(self, locator):
  34             self.requests.append(locator)
  35             return self.blocks.get(locator)
  36         def put(self, data, num_retries=None, copies=None, classes=[]):
  37             pdh = tutil.str_keep_locator(data)
  38             self.blocks[pdh] = bytes(data)
  39             return pdh
  40
  41     class MockApi(object):
  42         def __init__(self, b, r):
  43             self.body = b
  44             self.response = r
  45             self._schema = ArvadosFileWriterTestCase.MockApi.MockSchema()
  46             self._rootDesc = {}
  47         class MockSchema(object):
  48             def __init__(self):
  49                 self.schemas = {'Collection': {'properties': {'replication_desired': {'type':'integer'}}}}
  50         class MockCollections(object):
  51             def __init__(self, b, r):
  52                 self.body = b
  53                 self.response = r
  54             class Execute(object):
  55                 def __init__(self, r):
  56                     self.response = r
  57                 def execute(self, num_retries=None):
  58                     return self.response
  59             def create(self, ensure_unique_name=False, body=None):
  60                 if body != self.body:
  61                     raise Exception("Body %s does not match expectation %s" % (body, self.body))
  62                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  63             def update(self, uuid=None, body=None):
  64                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  65         def collections(self):
  66             return ArvadosFileWriterTestCase.MockApi.MockCollections(self.body, self.response)
  67
  68
  69     def test_truncate(self):
  70         keep = ArvadosFileWriterTestCase.MockKeep({
  71             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
  72         })
  73         api = ArvadosFileWriterTestCase.MockApi({
  74             "name": "test_truncate",
  75             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
  76             "replication_desired": None,
  77         }, {
  78             "uuid": "zzzzz-4zz18-mockcollection0",
  79             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
  80             "portable_data_hash":"7fcd0eaac3aad4c31a6a0e756475da92+52",
  81         })
  82         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
  83                         api_client=api, keep_client=keep) as c:
  84             writer = c.open("count.txt", "rb+")
  85             self.assertEqual(writer.size(), 10)
  86             self.assertEqual(b"0123456789", writer.read(12))
  87
  88             writer.truncate(8)
  89
  90             # Make sure reading off the end doesn't break
  91             self.assertEqual(b"", writer.read(12))
  92
  93             self.assertEqual(writer.size(), 8)
  94             writer.seek(0, os.SEEK_SET)
  95             self.assertEqual(b"01234567", writer.read(12))
  96
  97             self.assertIsNone(c.manifest_locator())
  98             self.assertTrue(c.modified())
  99             c.save_new("test_truncate")
 100             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 101             self.assertFalse(c.modified())
 102
 103
 104     def test_truncate2(self):
 105         keep = ArvadosFileWriterTestCase.MockKeep({
 106             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 107         })
 108         api = ArvadosFileWriterTestCase.MockApi({
 109             "name": "test_truncate2",
 110             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n",
 111             "replication_desired": None,
 112         }, {
 113             "uuid": "zzzzz-4zz18-mockcollection0",
 114             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n",
 115             "portable_data_hash": "272da898abdf86ddc71994835e3155f8+95",
 116         })
 117         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 118                         api_client=api, keep_client=keep) as c:
 119             writer = c.open("count.txt", "rb+")
 120             self.assertEqual(writer.size(), 10)
 121             self.assertEqual(b"0123456789", writer.read(12))
 122
 123             # extend file size
 124             writer.truncate(12)
 125
 126             self.assertEqual(writer.size(), 12)
 127             writer.seek(0, os.SEEK_SET)
 128             self.assertEqual(b"0123456789\x00\x00", writer.read(12))
 129
 130             self.assertIsNone(c.manifest_locator())
 131             self.assertTrue(c.modified())
 132             c.save_new("test_truncate2")
 133             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 134             self.assertFalse(c.modified())
 135
 136     def test_truncate3(self):
 137         keep = ArvadosFileWriterTestCase.MockKeep({
 138             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 139             "a925576942e94b2ef57a066101b48876+10": b"abcdefghij",
 140         })
 141         api = ArvadosFileWriterTestCase.MockApi({
 142             "name": "test_truncate",
 143             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
 144             "replication_desired": None,
 145         }, {
 146             "uuid": "zzzzz-4zz18-mockcollection0",
 147             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
 148             "portable_data_hash": "7fcd0eaac3aad4c31a6a0e756475da92+52",
 149         })
 150         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n',
 151                         api_client=api, keep_client=keep) as c:
 152             writer = c.open("count.txt", "rb+")
 153             self.assertEqual(writer.size(), 20)
 154             self.assertEqual(b"0123456789ab", writer.read(12))
 155             self.assertEqual(12, writer.tell())
 156
 157             writer.truncate(8)
 158
 159             # Make sure reading off the end doesn't break
 160             self.assertEqual(12, writer.tell())
 161             self.assertEqual(b"", writer.read(12))
 162
 163             self.assertEqual(writer.size(), 8)
 164             self.assertEqual(2, writer.seek(-10, os.SEEK_CUR))
 165             self.assertEqual(b"234567", writer.read(12))
 166
 167             self.assertIsNone(c.manifest_locator())
 168             self.assertTrue(c.modified())
 169             c.save_new("test_truncate")
 170             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 171             self.assertFalse(c.modified())
 172
 173     def test_write_to_end(self):
 174         keep = ArvadosFileWriterTestCase.MockKeep({
 175             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 176         })
 177         api = ArvadosFileWriterTestCase.MockApi({
 178             "name": "test_append",
 179             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
 180             "replication_desired": None,
 181         }, {
 182             "uuid": "zzzzz-4zz18-mockcollection0",
 183             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
 184             "portable_data_hash": "c5c3af76565c8efb6a806546bcf073f3+88",
 185         })
 186         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 187                              api_client=api, keep_client=keep) as c:
 188             writer = c.open("count.txt", "rb+")
 189             self.assertEqual(writer.size(), 10)
 190
 191             self.assertEqual(5, writer.seek(5, os.SEEK_SET))
 192             self.assertEqual(b"56789", writer.read(8))
 193
 194             writer.seek(10, os.SEEK_SET)
 195             writer.write("foo")
 196             self.assertEqual(writer.size(), 13)
 197
 198             writer.seek(5, os.SEEK_SET)
 199             self.assertEqual(b"56789foo", writer.read(8))
 200
 201             self.assertIsNone(c.manifest_locator())
 202             self.assertTrue(c.modified())
 203             self.assertIsNone(keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 204
 205             c.save_new("test_append")
 206             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 207             self.assertFalse(c.modified())
 208             self.assertEqual(b"foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 209
 210
 211     def test_append(self):
 212         keep = ArvadosFileWriterTestCase.MockKeep({
 213             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 214         })
 215         for (mode, convert) in (
 216                 ('a+', lambda data: data.decode(encoding='utf-8')),
 217                 ('at+', lambda data: data.decode(encoding='utf-8')),
 218                 ('ab+', lambda data: data)):
 219             c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep)
 220             writer = c.open("count.txt", mode)
 221             self.assertEqual(writer.read(20), convert(b"0123456789"))
 222
 223             writer.seek(0, os.SEEK_SET)
 224             writer.write(convert(b"hello"))
 225             self.assertEqual(writer.read(), convert(b""))
 226             if 'b' in mode:
 227                 writer.seek(-5, os.SEEK_CUR)
 228                 self.assertEqual(writer.read(3), convert(b"hel"))
 229                 self.assertEqual(writer.read(), convert(b"lo"))
 230             else:
 231                 with self.assertRaises(IOError):
 232                     writer.seek(-5, os.SEEK_CUR)
 233                 with self.assertRaises(IOError):
 234                     writer.seek(-3, os.SEEK_END)
 235             writer.seek(0, os.SEEK_SET)
 236             writer.read(7)
 237             self.assertEqual(7, writer.tell())
 238             self.assertEqual(7, writer.seek(7, os.SEEK_SET))
 239
 240             writer.seek(0, os.SEEK_SET)
 241             self.assertEqual(writer.read(), convert(b"0123456789hello"))
 242
 243             writer.seek(0)
 244             writer.write(convert(b"world"))
 245             self.assertEqual(writer.read(), convert(b""))
 246             writer.seek(0)
 247             self.assertEqual(writer.read(), convert(b"0123456789helloworld"))
 248
 249             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.portable_manifest_text())
 250
 251     def test_write_at_beginning(self):
 252         keep = ArvadosFileWriterTestCase.MockKeep({
 253             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 254         })
 255         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 256                              keep_client=keep) as c:
 257             writer = c.open("count.txt", "rb+")
 258             self.assertEqual(b"0123456789", writer.readfrom(0, 13))
 259             writer.seek(0, os.SEEK_SET)
 260             writer.write("foo")
 261             self.assertEqual(writer.size(), 10)
 262             self.assertEqual(b"foo3456789", writer.readfrom(0, 13))
 263             self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", c.portable_manifest_text())
 264
 265     def test_write_empty(self):
 266         keep = ArvadosFileWriterTestCase.MockKeep({})
 267         with Collection(keep_client=keep) as c:
 268             writer = c.open("count.txt", "wb")
 269             self.assertEqual(writer.size(), 0)
 270             self.assertEqual(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n", c.portable_manifest_text())
 271
 272     def test_save_manifest_text(self):
 273         keep = ArvadosFileWriterTestCase.MockKeep({})
 274         with Collection(keep_client=keep) as c:
 275             writer = c.open("count.txt", "wb")
 276             writer.write(b"0123456789")
 277             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
 278             self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 279
 280             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.save_new(create_collection_record=False))
 281             self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 282
 283     def test_get_manifest_text_commits(self):
 284          keep = ArvadosFileWriterTestCase.MockKeep({})
 285          with Collection(keep_client=keep) as c:
 286              writer = c.open("count.txt", "wb")
 287              writer.write("0123456789")
 288              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
 289              self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 290              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text())
 291              self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 292
 293
 294     def test_write_in_middle(self):
 295         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
 296         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 297                              keep_client=keep) as c:
 298             writer = c.open("count.txt", "rb+")
 299             self.assertEqual(b"0123456789", writer.readfrom(0, 13))
 300             writer.seek(3, os.SEEK_SET)
 301             writer.write("foo")
 302             self.assertEqual(writer.size(), 10)
 303             self.assertEqual(b"012foo6789", writer.readfrom(0, 13))
 304             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.portable_manifest_text())
 305
 306     def test_write_at_end(self):
 307         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
 308         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 309                              keep_client=keep) as c:
 310             writer = c.open("count.txt", "rb+")
 311             self.assertEqual(b"0123456789", writer.readfrom(0, 13))
 312             writer.seek(7, os.SEEK_SET)
 313             writer.write("foo")
 314             self.assertEqual(writer.size(), 10)
 315             self.assertEqual(b"0123456foo", writer.readfrom(0, 13))
 316             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text())
 317
 318     def test_write_across_segment_boundary(self):
 319         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
 320         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
 321                              keep_client=keep) as c:
 322             writer = c.open("count.txt", "rb+")
 323             self.assertEqual(b"012345678901234", writer.readfrom(0, 15))
 324             writer.seek(7, os.SEEK_SET)
 325             writer.write("foobar")
 326             self.assertEqual(writer.size(), 20)
 327             self.assertEqual(b"0123456foobar34", writer.readfrom(0, 15))
 328             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text())
 329
 330     def test_write_across_several_segments(self):
 331         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
 332         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
 333                              keep_client=keep) as c:
 334             writer = c.open("count.txt", "rb+")
 335             self.assertEqual(b"012301230123", writer.readfrom(0, 15))
 336             writer.seek(2, os.SEEK_SET)
 337             writer.write("abcdefg")
 338             self.assertEqual(writer.size(), 12)
 339             self.assertEqual(b"01abcdefg123", writer.readfrom(0, 15))
 340             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text())
 341
 342     def test_write_large(self):
 343         keep = ArvadosFileWriterTestCase.MockKeep({})
 344         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 345                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
 346                                                  "replication_desired":None},
 347                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 348                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
 349                                                  "portable_data_hash":"9132ca8e3f671c76103a38f5bc24328c+108"})
 350         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 351                              api_client=api, keep_client=keep) as c:
 352             writer = c.open("count.txt", "rb+")
 353             text = "0123456789" * 100
 354             for b in range(0, 100000):
 355                 writer.write(text)
 356             self.assertEqual(writer.size(), 100000000)
 357
 358             self.assertIsNone(c.manifest_locator())
 359             self.assertTrue(c.modified())
 360             c.save_new("test_write_large")
 361             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 362             self.assertFalse(c.modified())
 363
 364     def test_large_write(self):
 365         keep = ArvadosFileWriterTestCase.MockKeep({})
 366         api = ArvadosFileWriterTestCase.MockApi({}, {})
 367         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 368                              api_client=api, keep_client=keep) as c:
 369             writer = c.open("count.txt", "rb+")
 370             self.assertEqual(writer.size(), 0)
 371
 372             text = "0123456789"
 373             writer.write(text)
 374             text = "0123456789" * 9999999
 375             writer.write(text)
 376             self.assertEqual(writer.size(), 100000000)
 377
 378             self.assertEqual(c.manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n")
 379
 380     def test_sparse_write(self):
 381         keep = ArvadosFileWriterTestCase.MockKeep({})
 382         api = ArvadosFileWriterTestCase.MockApi({}, {})
 383         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 384                              api_client=api, keep_client=keep) as c:
 385             writer = c.open("count.txt", "rb+")
 386             self.assertEqual(writer.size(), 0)
 387
 388             text = b"0123456789"
 389             writer.seek(2)
 390             writer.write(text)
 391             self.assertEqual(writer.size(), 12)
 392             writer.seek(0, os.SEEK_SET)
 393             self.assertEqual(writer.read(), b"\x00\x00"+text)
 394
 395             self.assertEqual(c.manifest_text(), ". 7f614da9329cd3aebf59b91aadc30bf0+67108864 781e5e245d69b566979b86e28d23f2c7+10 0:2:count.txt 67108864:10:count.txt\n")
 396
 397     def test_sparse_write2(self):
 398         keep = ArvadosFileWriterTestCase.MockKeep({})
 399         api = ArvadosFileWriterTestCase.MockApi({}, {})
 400         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 401                              api_client=api, keep_client=keep) as c:
 402             writer = c.open("count.txt", "rb+")
 403             self.assertEqual(writer.size(), 0)
 404
 405             text = "0123456789"
 406             writer.seek((arvados.config.KEEP_BLOCK_SIZE*2) + 2)
 407             writer.write(text)
 408             self.assertEqual(writer.size(), (arvados.config.KEEP_BLOCK_SIZE*2) + 12)
 409             writer.seek(0, os.SEEK_SET)
 410
 411             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")
 412
 413     def test_sparse_write3(self):
 414         keep = ArvadosFileWriterTestCase.MockKeep({})
 415         api = ArvadosFileWriterTestCase.MockApi({}, {})
 416         for r in [[0, 1, 2, 3, 4], [4, 3, 2, 1, 0], [3, 2, 0, 4, 1]]:
 417             with Collection() as c:
 418                 writer = c.open("count.txt", "rb+")
 419                 self.assertEqual(writer.size(), 0)
 420
 421                 for i in r:
 422                     w = ("%s" % i) * 10
 423                     writer.seek(i*10)
 424                     writer.write(w.encode())
 425                 writer.seek(0)
 426                 self.assertEqual(writer.read(), b"00000000001111111111222222222233333333334444444444")
 427
 428     def test_sparse_write4(self):
 429         keep = ArvadosFileWriterTestCase.MockKeep({})
 430         api = ArvadosFileWriterTestCase.MockApi({}, {})
 431         for r in [[0, 1, 2, 4], [4, 2, 1, 0], [2, 0, 4, 1]]:
 432             with Collection() as c:
 433                 writer = c.open("count.txt", "rb+")
 434                 self.assertEqual(writer.size(), 0)
 435
 436                 for i in r:
 437                     w = ("%s" % i) * 10
 438                     writer.seek(i*10)
 439                     writer.write(w.encode())
 440                 writer.seek(0)
 441                 self.assertEqual(writer.read(), b"000000000011111111112222222222\x00\x00\x00\x00\x00\x00\x00\x00\x00\x004444444444")
 442
 443     def test_rewrite_on_empty_file(self):
 444         keep = ArvadosFileWriterTestCase.MockKeep({})
 445         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 446                              keep_client=keep) as c:
 447             writer = c.open("count.txt", "rb+")
 448             for b in range(0, 10):
 449                 writer.seek(0, os.SEEK_SET)
 450                 writer.write("0123456789")
 451
 452             self.assertEqual(writer.size(), 10)
 453             self.assertEqual(b"0123456789", writer.readfrom(0, 20))
 454             self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.portable_manifest_text())
 455             writer.flush()
 456             self.assertEqual(writer.size(), 10)
 457             self.assertEqual(b"0123456789", writer.readfrom(0, 20))
 458             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.portable_manifest_text())
 459
 460     def test_rewrite_append_existing_file(self):
 461         keep = ArvadosFileWriterTestCase.MockKeep({
 462             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 463         })
 464         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 465                              keep_client=keep) as c:
 466             writer = c.open("count.txt", "rb+")
 467             for b in range(0, 10):
 468                 writer.seek(10, os.SEEK_SET)
 469                 writer.write("abcdefghij")
 470
 471             self.assertEqual(writer.size(), 20)
 472             self.assertEqual(b"0123456789abcdefghij", writer.readfrom(0, 20))
 473             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 474
 475             writer.arvadosfile.flush()
 476             self.assertEqual(writer.size(), 20)
 477             self.assertEqual(b"0123456789abcdefghij", writer.readfrom(0, 20))
 478             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.portable_manifest_text())
 479
 480     def test_rewrite_over_existing_file(self):
 481         keep = ArvadosFileWriterTestCase.MockKeep({
 482             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 483         })
 484         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 485                              keep_client=keep) as c:
 486             writer = c.open("count.txt", "rb+")
 487             for b in range(0, 10):
 488                 writer.seek(5, os.SEEK_SET)
 489                 writer.write("abcdefghij")
 490
 491             self.assertEqual(writer.size(), 15)
 492             self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20))
 493             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 494
 495             writer.arvadosfile.flush()
 496
 497             self.assertEqual(writer.size(), 15)
 498             self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20))
 499             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.portable_manifest_text())
 500
 501     def test_write_large_rewrite(self):
 502         keep = ArvadosFileWriterTestCase.MockKeep({})
 503         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 504                                                  "manifest_text": ". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n",
 505                                                  "replication_desired":None},
 506                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 507                                                  "manifest_text": ". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n",
 508                                                  "portable_data_hash":"217665c6b713e1b78dfba7ebd42344db+156"})
 509         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 510                              api_client=api, keep_client=keep) as c:
 511             writer = c.open("count.txt", "rb+")
 512             text = b''.join([b"0123456789" for a in range(0, 100)])
 513             for b in range(0, 100000):
 514                 writer.write(text)
 515             writer.seek(0, os.SEEK_SET)
 516             writer.write("foo")
 517             self.assertEqual(writer.size(), 100000000)
 518
 519             self.assertIsNone(c.manifest_locator())
 520             self.assertTrue(c.modified())
 521             c.save_new("test_write_large")
 522             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 523             self.assertFalse(c.modified())
 524
 525     def test_create(self):
 526         keep = ArvadosFileWriterTestCase.MockKeep({})
 527         api = ArvadosFileWriterTestCase.MockApi({
 528             "name":"test_create",
 529             "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 530             "replication_desired":None,
 531         }, {
 532             "uuid":"zzzzz-4zz18-mockcollection0",
 533             "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 534             "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51",
 535         })
 536         with Collection(api_client=api, keep_client=keep) as c:
 537             writer = c.open("count.txt", "wb+")
 538             self.assertEqual(writer.size(), 0)
 539             writer.write("01234567")
 540             self.assertEqual(writer.size(), 8)
 541
 542             self.assertIsNone(c.manifest_locator())
 543             self.assertTrue(c.modified())
 544             self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 545             c.save_new("test_create")
 546             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 547             self.assertFalse(c.modified())
 548             self.assertEqual(b"01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 549
 550
 551     def test_create_subdir(self):
 552         keep = ArvadosFileWriterTestCase.MockKeep({})
 553         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 554                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 555                                                  "replication_desired":None},
 556                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 557                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 558                                                  "portable_data_hash":"1b02aaa62528d28a5be41651cbb9d7c7+59"})
 559         with Collection(api_client=api, keep_client=keep) as c:
 560             self.assertIsNone(c.api_response())
 561             writer = c.open("foo/bar/count.txt", "wb+")
 562             writer.write("01234567")
 563             self.assertFalse(c.committed())
 564             c.save_new("test_create")
 565             self.assertTrue(c.committed())
 566             self.assertEqual(c.api_response(), api.response)
 567
 568     def test_overwrite(self):
 569         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 570         api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
 571                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 572                                                  "replication_desired":None},
 573                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 574                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 575                                                  "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51"})
 576         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 577                              api_client=api, keep_client=keep) as c:
 578             writer = c.open("count.txt", "wb+")
 579             self.assertEqual(writer.size(), 0)
 580             writer.write("01234567")
 581             self.assertEqual(writer.size(), 8)
 582
 583             self.assertIsNone(c.manifest_locator())
 584             self.assertTrue(c.modified())
 585             c.save_new("test_overwrite")
 586             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 587             self.assertFalse(c.modified())
 588
 589     def test_file_not_found(self):
 590         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 591             with self.assertRaises(IOError):
 592                 writer = c.open("nocount.txt", "rb")
 593
 594     def test_cannot_open_directory(self):
 595         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 596             with self.assertRaises(IOError):
 597                 writer = c.open(".", "rb")
 598
 599     def test_create_multiple(self):
 600         keep = ArvadosFileWriterTestCase.MockKeep({})
 601         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
 602                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
 603                                                  "replication_desired":None},
 604                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 605                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
 606                                                  "portable_data_hash":"71e7bb6c00d31fc2b4364199fd97be08+102"})
 607         with Collection(api_client=api, keep_client=keep) as c:
 608             w1 = c.open("count1.txt", "wb")
 609             w2 = c.open("count2.txt", "wb")
 610             w1.write("01234567")
 611             w2.write("abcdefgh")
 612             self.assertEqual(w1.size(), 8)
 613             self.assertEqual(w2.size(), 8)
 614
 615             self.assertIsNone(c.manifest_locator())
 616             self.assertTrue(c.modified())
 617             self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 618             c.save_new("test_create_multiple")
 619             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 620             self.assertFalse(c.modified())
 621             self.assertEqual(b"01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 622
 623
 624 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
 625     class MockParent(object):
 626         class MockBlockMgr(object):
 627             def __init__(self, blocks, nocache):
 628                 self.blocks = blocks
 629                 self.nocache = nocache
 630                 self.num_get_threads = 1
 631
 632             def block_prefetch(self, loc):
 633                 pass
 634
 635             def get_block_contents(self, loc, num_retries=0, cache_only=False):
 636                 if self.nocache and cache_only:
 637                     return None
 638                 return self.blocks[loc]
 639
 640         def __init__(self, blocks, nocache):
 641             self.blocks = blocks
 642             self.nocache = nocache
 643             self.lock = arvados.arvfile.NoopLock()
 644
 645         def root_collection(self):
 646             return self
 647
 648         def _my_block_manager(self):
 649             return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
 650
 651
 652     def make_count_reader(self, nocache=False):
 653         stream = []
 654         n = 0
 655         blocks = {}
 656         for d in [b'01234', b'34567', b'67890']:
 657             loc = tutil.str_keep_locator(d)
 658             blocks[loc] = d
 659             stream.append(Range(loc, n, len(d)))
 660             n += len(d)
 661         af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), "count.txt", stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
 662         return ArvadosFileReader(af, mode="rb")
 663
 664     def test_read_block_crossing_behavior(self):
 665         # read() needs to return all the data requested if possible, even if it
 666         # crosses uncached blocks: https://arvados.org/issues/5856
 667         sfile = self.make_count_reader(nocache=True)
 668         self.assertEqual(b'12345678', sfile.read(8))
 669
 670     def test_successive_reads(self):
 671         # Override StreamFileReaderTestCase.test_successive_reads
 672         sfile = self.make_count_reader(nocache=True)
 673         self.assertEqual(b'1234', sfile.read(4))
 674         self.assertEqual(b'5678', sfile.read(4))
 675         self.assertEqual(b'9', sfile.read(4))
 676         self.assertEqual(b'', sfile.read(4))
 677
 678     def test_tell_after_block_read(self):
 679         # Override StreamFileReaderTestCase.test_tell_after_block_read
 680         sfile = self.make_count_reader(nocache=True)
 681         self.assertEqual(b'12345678', sfile.read(8))
 682         self.assertEqual(8, sfile.tell())
 683
 684     def test_prefetch(self):
 685         keep = ArvadosFileWriterTestCase.MockKeep({
 686             "2e9ec317e197819358fbc43afca7d837+8": b"01234567",
 687             "e8dc4081b13434b45189a720b77b6818+8": b"abcdefgh",
 688         })
 689         with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
 690             r = c.open("count.txt", "rb")
 691             self.assertEqual(b"0123", r.read(4))
 692         self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
 693         self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
 694
 695     def test__eq__from_manifest(self):
 696         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 697             with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
 698                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 699                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 700
 701     def test__eq__from_writes(self):
 702         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 703             with Collection() as c2:
 704                 f = c2.open("count1.txt", "wb")
 705                 f.write("0123456789")
 706
 707                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 708                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 709
 710     def test__ne__(self):
 711         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 712             with Collection() as c2:
 713                 f = c2.open("count1.txt", "wb")
 714                 f.write("1234567890")
 715
 716                 self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
 717                 self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
 718
 719
 720 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
 721     def reader_for(self, coll_name, **kwargs):
 722         stream = []
 723         segments = []
 724         n = 0
 725         for d in self.manifest_for(coll_name).split():
 726             try:
 727                 k = KeepLocator(d)
 728                 segments.append(Range(n, n, k.size))
 729                 stream.append(Range(d, n, k.size))
 730                 n += k.size
 731             except ValueError:
 732                 pass
 733
 734         blockmanager = arvados.arvfile._BlockManager(self.keep_client())
 735         blockmanager.prefetch_enabled = False
 736         col = Collection(keep_client=self.keep_client(), block_manager=blockmanager)
 737         af = ArvadosFile(col, "test",
 738                          stream=stream,
 739                          segments=segments)
 740         kwargs.setdefault('mode', 'rb')
 741         return ArvadosFileReader(af, **kwargs)
 742
 743     def read_for_test(self, reader, byte_count, **kwargs):
 744         return reader.read(byte_count, **kwargs)
 745
 746
 747 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
 748     def read_for_test(self, reader, byte_count, **kwargs):
 749         return reader.readfrom(0, byte_count, **kwargs)
 750
 751
 752 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
 753     def read_for_test(self, reader, byte_count, **kwargs):
 754         return b''.join(reader.readall(**kwargs))
 755
 756
 757 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
 758     def read_for_test(self, reader, byte_count, **kwargs):
 759         return b''.join(reader.readall_decompressed(**kwargs))
 760
 761
 762 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
 763     def read_for_test(self, reader, byte_count, **kwargs):
 764         return ''.join(reader.readlines(**kwargs)).encode()
 765
 766
 767 class ArvadosFileTestCase(unittest.TestCase):
 768     def datetime_to_hex(self, dt):
 769         return hex(int(time.mktime(dt.timetuple())))[2:]
 770
 771     def test_permission_expired(self):
 772         base_manifest = ". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@{} 0:10:count.txt\n"
 773         now = datetime.datetime.now()
 774         a_week_ago = now - datetime.timedelta(days=7)
 775         a_month_ago = now - datetime.timedelta(days=30)
 776         a_week_from_now = now + datetime.timedelta(days=7)
 777         with Collection(base_manifest.format(self.datetime_to_hex(a_week_from_now))) as c:
 778             self.assertFalse(c.find('count.txt').permission_expired())
 779         with Collection(base_manifest.format(self.datetime_to_hex(a_week_ago))) as c:
 780             f = c.find('count.txt')
 781             self.assertTrue(f.permission_expired())
 782             self.assertTrue(f.permission_expired(a_week_from_now))
 783             self.assertFalse(f.permission_expired(a_month_ago))
 784
 785
 786 class BlockManagerTest(unittest.TestCase):
 787     def test_bufferblock_append(self):
 788         keep = ArvadosFileWriterTestCase.MockKeep({})
 789         with arvados.arvfile._BlockManager(keep) as blockmanager:
 790             bufferblock = blockmanager.alloc_bufferblock()
 791             bufferblock.append("foo")
 792
 793             self.assertEqual(bufferblock.size(), 3)
 794             self.assertEqual(bufferblock.buffer_view[0:3], b"foo")
 795             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 796
 797             bufferblock.append("bar")
 798
 799             self.assertEqual(bufferblock.size(), 6)
 800             self.assertEqual(bufferblock.buffer_view[0:6], b"foobar")
 801             self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
 802
 803             bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 804             with self.assertRaises(arvados.errors.AssertionError):
 805                 bufferblock.append("bar")
 806
 807     def test_bufferblock_dup(self):
 808         keep = ArvadosFileWriterTestCase.MockKeep({})
 809         with arvados.arvfile._BlockManager(keep) as blockmanager:
 810             bufferblock = blockmanager.alloc_bufferblock()
 811             bufferblock.append("foo")
 812
 813             self.assertEqual(bufferblock.size(), 3)
 814             self.assertEqual(bufferblock.buffer_view[0:3], b"foo")
 815             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 816             bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 817
 818             bufferblock2 = blockmanager.dup_block(bufferblock, None)
 819             self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
 820
 821             bufferblock2.append("bar")
 822
 823             self.assertEqual(bufferblock2.size(), 6)
 824             self.assertEqual(bufferblock2.buffer_view[0:6], b"foobar")
 825             self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
 826
 827             self.assertEqual(bufferblock.size(), 3)
 828             self.assertEqual(bufferblock.buffer_view[0:3], b"foo")
 829             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 830
 831     def test_bufferblock_get(self):
 832         keep = ArvadosFileWriterTestCase.MockKeep({
 833             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 834         })
 835         with arvados.arvfile._BlockManager(keep) as blockmanager:
 836             bufferblock = blockmanager.alloc_bufferblock()
 837             bufferblock.append("foo")
 838
 839             self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), b"0123456789")
 840             self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), b"foo")
 841
 842     def test_bufferblock_commit(self):
 843         mockkeep = mock.MagicMock()
 844         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 845             bufferblock = blockmanager.alloc_bufferblock()
 846             bufferblock.owner = mock.MagicMock(spec=arvados.arvfile.ArvadosFile)
 847             def flush(sync=None):
 848                 blockmanager.commit_bufferblock(bufferblock, sync)
 849             bufferblock.owner.flush.side_effect = flush
 850             bufferblock.append("foo")
 851             blockmanager.commit_all()
 852             self.assertTrue(bufferblock.owner.flush.called)
 853             self.assertTrue(mockkeep.put.called)
 854             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 855             self.assertIsNone(bufferblock.buffer_view)
 856
 857     def test_bufferblock_commit_pending(self):
 858         # Test for bug #7225
 859         mockkeep = mock.MagicMock()
 860         mockkeep.put.side_effect = lambda *args, **kwargs: time.sleep(1)
 861         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 862             bufferblock = blockmanager.alloc_bufferblock()
 863             bufferblock.append("foo")
 864
 865             blockmanager.commit_bufferblock(bufferblock, False)
 866             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)
 867
 868             blockmanager.commit_bufferblock(bufferblock, True)
 869             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 870
 871     def test_bufferblock_commit_with_error(self):
 872         mockkeep = mock.MagicMock()
 873         mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail")
 874         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 875             bufferblock = blockmanager.alloc_bufferblock()
 876             bufferblock.owner = mock.MagicMock(spec=arvados.arvfile.ArvadosFile)
 877             def flush(sync=None):
 878                 blockmanager.commit_bufferblock(bufferblock, sync)
 879             bufferblock.owner.flush.side_effect = flush
 880             bufferblock.append("foo")
 881             with self.assertRaises(arvados.errors.KeepWriteError) as err:
 882                 blockmanager.commit_all()
 883             self.assertTrue(bufferblock.owner.flush.called)
 884             self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
 885             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.ERROR)