sdk/python/tests/test_arvfile.py

   1 from __future__ import absolute_import
   2 from builtins import hex
   3 from builtins import str
   4 from builtins import range
   5 from builtins import object
   6 import bz2
   7 import datetime
   8 import gzip
   9 import io
  10 import mock
  11 import os
  12 import unittest
  13 import time
  14
  15 import arvados
  16 from arvados._ranges import Range
  17 from arvados.keep import KeepLocator
  18 from arvados.collection import Collection, CollectionReader
  19 from arvados.arvfile import ArvadosFile, ArvadosFileReader
  20
  21 from . import arvados_testutil as tutil
  22 from .test_stream import StreamFileReaderTestCase, StreamRetryTestMixin
  23
  24 class ArvadosFileWriterTestCase(unittest.TestCase):
  25     class MockKeep(object):
  26         def __init__(self, blocks):
  27             self.blocks = blocks
  28             self.requests = []
  29         def get(self, locator, num_retries=0):
  30             self.requests.append(locator)
  31             return self.blocks.get(locator)
  32         def get_from_cache(self, locator):
  33             self.requests.append(locator)
  34             return self.blocks.get(locator)
  35         def put(self, data, num_retries=None, copies=None):
  36             pdh = tutil.str_keep_locator(data)
  37             self.blocks[pdh] = bytes(data)
  38             return pdh
  39
  40     class MockApi(object):
  41         def __init__(self, b, r):
  42             self.body = b
  43             self.response = r
  44             self._schema = ArvadosFileWriterTestCase.MockApi.MockSchema()
  45             self._rootDesc = {}
  46         class MockSchema(object):
  47             def __init__(self):
  48                 self.schemas = {'Collection': {'properties': {'replication_desired': {'type':'integer'}}}}
  49         class MockCollections(object):
  50             def __init__(self, b, r):
  51                 self.body = b
  52                 self.response = r
  53             class Execute(object):
  54                 def __init__(self, r):
  55                     self.response = r
  56                 def execute(self, num_retries=None):
  57                     return self.response
  58             def create(self, ensure_unique_name=False, body=None):
  59                 if body != self.body:
  60                     raise Exception("Body %s does not match expectation %s" % (body, self.body))
  61                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  62             def update(self, uuid=None, body=None):
  63                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  64         def collections(self):
  65             return ArvadosFileWriterTestCase.MockApi.MockCollections(self.body, self.response)
  66
  67
  68     def test_truncate(self):
  69         keep = ArvadosFileWriterTestCase.MockKeep({
  70             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
  71         })
  72         api = ArvadosFileWriterTestCase.MockApi({
  73             "name": "test_truncate",
  74             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
  75             "replication_desired": None,
  76         }, {
  77             "uuid": "zzzzz-4zz18-mockcollection0",
  78             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
  79             "portable_data_hash":"7fcd0eaac3aad4c31a6a0e756475da92+52",
  80         })
  81         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
  82                              api_client=api, keep_client=keep) as c:
  83             writer = c.open("count.txt", "rb+")
  84             self.assertEqual(writer.size(), 10)
  85             self.assertEqual(b"0123456789", writer.read(12))
  86
  87             writer.truncate(8)
  88
  89             # Make sure reading off the end doesn't break
  90             self.assertEqual(b"", writer.read(12))
  91
  92             self.assertEqual(writer.size(), 8)
  93             writer.seek(0, os.SEEK_SET)
  94             self.assertEqual(b"01234567", writer.read(12))
  95
  96             self.assertIsNone(c.manifest_locator())
  97             self.assertTrue(c.modified())
  98             c.save_new("test_truncate")
  99             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 100             self.assertFalse(c.modified())
 101
 102
 103     def test_truncate2(self):
 104         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 105         api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate2",
 106                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n",
 107                                                  "replication_desired":None},
 108                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 109                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n",
 110                                                  "portable_data_hash":"272da898abdf86ddc71994835e3155f8+95"})
 111         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 112                              api_client=api, keep_client=keep) as c:
 113             writer = c.open("count.txt", "r+")
 114             self.assertEqual(writer.size(), 10)
 115             self.assertEqual("0123456789", writer.read(12))
 116
 117             # extend file size
 118             writer.truncate(12)
 119
 120             self.assertEqual(writer.size(), 12)
 121             writer.seek(0, os.SEEK_SET)
 122             self.assertEqual(b"0123456789\x00\x00", writer.read(12))
 123
 124             self.assertIsNone(c.manifest_locator())
 125             self.assertTrue(c.modified())
 126             c.save_new("test_truncate2")
 127             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 128             self.assertFalse(c.modified())
 129
 130     def test_truncate3(self):
 131         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789",
 132                                                    "a925576942e94b2ef57a066101b48876+10": "abcdefghij"})
 133         api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate",
 134                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
 135                                                  "replication_desired":None},
 136                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 137                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
 138                                                  "portable_data_hash":"7fcd0eaac3aad4c31a6a0e756475da92+52"})
 139         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n',
 140                              api_client=api, keep_client=keep) as c:
 141             writer = c.open("count.txt", "r+")
 142             self.assertEqual(writer.size(), 20)
 143             self.assertEqual("0123456789ab", writer.read(12))
 144             self.assertEqual(12, writer.tell())
 145
 146             writer.truncate(8)
 147
 148             # Make sure reading off the end doesn't break
 149             self.assertEqual(12, writer.tell())
 150             self.assertEqual("", writer.read(12))
 151
 152             self.assertEqual(writer.size(), 8)
 153             self.assertEqual(2, writer.seek(-10, os.SEEK_CUR))
 154             self.assertEqual("234567", writer.read(12))
 155
 156             self.assertIsNone(c.manifest_locator())
 157             self.assertTrue(c.modified())
 158             c.save_new("test_truncate")
 159             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 160             self.assertFalse(c.modified())
 161
 162
 163
 164     def test_write_to_end(self):
 165         keep = ArvadosFileWriterTestCase.MockKeep({
 166             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 167         })
 168         api = ArvadosFileWriterTestCase.MockApi({
 169             "name": "test_append",
 170             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
 171             "replication_desired": None,
 172         }, {
 173             "uuid": "zzzzz-4zz18-mockcollection0",
 174             "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
 175             "portable_data_hash": "c5c3af76565c8efb6a806546bcf073f3+88",
 176         })
 177         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 178                              api_client=api, keep_client=keep) as c:
 179             writer = c.open("count.txt", "rb+")
 180             self.assertEqual(writer.size(), 10)
 181
 182             self.assertEqual(5, writer.seek(5, os.SEEK_SET))
 183             self.assertEqual(b"56789", writer.read(8))
 184
 185             writer.seek(10, os.SEEK_SET)
 186             writer.write("foo")
 187             self.assertEqual(writer.size(), 13)
 188
 189             writer.seek(5, os.SEEK_SET)
 190             self.assertEqual(b"56789foo", writer.read(8))
 191
 192             self.assertIsNone(c.manifest_locator())
 193             self.assertTrue(c.modified())
 194             self.assertIsNone(keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 195
 196             c.save_new("test_append")
 197             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 198             self.assertFalse(c.modified())
 199             self.assertEqual(b"foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 200
 201
 202     def test_append(self):
 203         keep = ArvadosFileWriterTestCase.MockKeep({
 204             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 205         })
 206         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep)
 207         writer = c.open("count.txt", "ab+")
 208         self.assertEqual(writer.read(20), b"0123456789")
 209         writer.seek(0, os.SEEK_SET)
 210
 211         writer.write("hello")
 212         self.assertEqual(writer.read(20), b"0123456789hello")
 213         writer.seek(0, os.SEEK_SET)
 214
 215         writer.write("world")
 216         self.assertEqual(writer.read(20), b"0123456789helloworld")
 217
 218         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.portable_manifest_text())
 219
 220     def test_write_at_beginning(self):
 221         keep = ArvadosFileWriterTestCase.MockKeep({
 222             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 223         })
 224         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 225                              keep_client=keep) as c:
 226             writer = c.open("count.txt", "rb+")
 227             self.assertEqual(b"0123456789", writer.readfrom(0, 13))
 228             writer.seek(0, os.SEEK_SET)
 229             writer.write("foo")
 230             self.assertEqual(writer.size(), 10)
 231             self.assertEqual(b"foo3456789", writer.readfrom(0, 13))
 232             self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", c.portable_manifest_text())
 233
 234     def test_write_empty(self):
 235         keep = ArvadosFileWriterTestCase.MockKeep({})
 236         with Collection(keep_client=keep) as c:
 237             writer = c.open("count.txt", "wb")
 238             self.assertEqual(writer.size(), 0)
 239             self.assertEqual(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n", c.portable_manifest_text())
 240
 241     def test_save_manifest_text(self):
 242         keep = ArvadosFileWriterTestCase.MockKeep({})
 243         with Collection(keep_client=keep) as c:
 244             writer = c.open("count.txt", "wb")
 245             writer.write(b"0123456789")
 246             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
 247             self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 248
 249             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.save_new(create_collection_record=False))
 250             self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 251
 252     def test_get_manifest_text_commits(self):
 253          keep = ArvadosFileWriterTestCase.MockKeep({})
 254          with Collection(keep_client=keep) as c:
 255              writer = c.open("count.txt", "wb")
 256              writer.write("0123456789")
 257              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
 258              self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 259              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text())
 260              self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 261
 262
 263     def test_write_in_middle(self):
 264         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
 265         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 266                              keep_client=keep) as c:
 267             writer = c.open("count.txt", "rb+")
 268             self.assertEqual(b"0123456789", writer.readfrom(0, 13))
 269             writer.seek(3, os.SEEK_SET)
 270             writer.write("foo")
 271             self.assertEqual(writer.size(), 10)
 272             self.assertEqual(b"012foo6789", writer.readfrom(0, 13))
 273             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.portable_manifest_text())
 274
 275     def test_write_at_end(self):
 276         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
 277         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 278                              keep_client=keep) as c:
 279             writer = c.open("count.txt", "rb+")
 280             self.assertEqual(b"0123456789", writer.readfrom(0, 13))
 281             writer.seek(7, os.SEEK_SET)
 282             writer.write("foo")
 283             self.assertEqual(writer.size(), 10)
 284             self.assertEqual(b"0123456foo", writer.readfrom(0, 13))
 285             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text())
 286
 287     def test_write_across_segment_boundary(self):
 288         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
 289         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
 290                              keep_client=keep) as c:
 291             writer = c.open("count.txt", "rb+")
 292             self.assertEqual(b"012345678901234", writer.readfrom(0, 15))
 293             writer.seek(7, os.SEEK_SET)
 294             writer.write("foobar")
 295             self.assertEqual(writer.size(), 20)
 296             self.assertEqual(b"0123456foobar34", writer.readfrom(0, 15))
 297             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text())
 298
 299     def test_write_across_several_segments(self):
 300         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
 301         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
 302                              keep_client=keep) as c:
 303             writer = c.open("count.txt", "rb+")
 304             self.assertEqual(b"012301230123", writer.readfrom(0, 15))
 305             writer.seek(2, os.SEEK_SET)
 306             writer.write("abcdefg")
 307             self.assertEqual(writer.size(), 12)
 308             self.assertEqual(b"01abcdefg123", writer.readfrom(0, 15))
 309             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text())
 310
 311     def test_write_large(self):
 312         keep = ArvadosFileWriterTestCase.MockKeep({})
 313         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 314                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
 315                                                  "replication_desired":None},
 316                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 317                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
 318                                                  "portable_data_hash":"9132ca8e3f671c76103a38f5bc24328c+108"})
 319         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 320                              api_client=api, keep_client=keep) as c:
 321             writer = c.open("count.txt", "rb+")
 322             text = "0123456789" * 100
 323             for b in range(0, 100000):
 324                 writer.write(text)
 325             self.assertEqual(writer.size(), 100000000)
 326
 327             self.assertIsNone(c.manifest_locator())
 328             self.assertTrue(c.modified())
 329             c.save_new("test_write_large")
 330             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 331             self.assertFalse(c.modified())
 332
 333
 334     def test_large_write(self):
 335         keep = ArvadosFileWriterTestCase.MockKeep({})
 336         api = ArvadosFileWriterTestCase.MockApi({}, {})
 337         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 338                              api_client=api, keep_client=keep) as c:
 339             writer = c.open("count.txt", "rb+")
 340             self.assertEqual(writer.size(), 0)
 341
 342             text = "0123456789"
 343             writer.write(text)
 344             text = "0123456789" * 9999999
 345             writer.write(text)
 346             self.assertEqual(writer.size(), 100000000)
 347
 348             self.assertEqual(c.manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n")
 349
 350     def test_sparse_write(self):
 351         keep = ArvadosFileWriterTestCase.MockKeep({})
 352         api = ArvadosFileWriterTestCase.MockApi({}, {})
 353         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 354                              api_client=api, keep_client=keep) as c:
 355             writer = c.open("count.txt", "r+")
 356             self.assertEqual(writer.size(), 0)
 357
 358             text = "0123456789"
 359             writer.seek(2)
 360             writer.write(text)
 361             self.assertEqual(writer.size(), 12)
 362             writer.seek(0, os.SEEK_SET)
 363             self.assertEqual(writer.read(), b"\x00\x00"+text)
 364
 365             self.assertEqual(c.manifest_text(), ". 7f614da9329cd3aebf59b91aadc30bf0+67108864 781e5e245d69b566979b86e28d23f2c7+10 0:2:count.txt 67108864:10:count.txt\n")
 366
 367
 368     def test_sparse_write2(self):
 369         keep = ArvadosFileWriterTestCase.MockKeep({})
 370         api = ArvadosFileWriterTestCase.MockApi({}, {})
 371         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 372                              api_client=api, keep_client=keep) as c:
 373             writer = c.open("count.txt", "r+")
 374             self.assertEqual(writer.size(), 0)
 375
 376             text = "0123456789"
 377             writer.seek((arvados.config.KEEP_BLOCK_SIZE*2) + 2)
 378             writer.write(text)
 379             self.assertEqual(writer.size(), (arvados.config.KEEP_BLOCK_SIZE*2) + 12)
 380             writer.seek(0, os.SEEK_SET)
 381
 382             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")
 383
 384
 385     def test_sparse_write3(self):
 386         keep = ArvadosFileWriterTestCase.MockKeep({})
 387         api = ArvadosFileWriterTestCase.MockApi({}, {})
 388         for r in [[0, 1, 2, 3, 4], [4, 3, 2, 1, 0], [3, 2, 0, 4, 1]]:
 389             with Collection() as c:
 390                 writer = c.open("count.txt", "r+")
 391                 self.assertEqual(writer.size(), 0)
 392
 393                 for i in r:
 394                     w = ("%s" % i) * 10
 395                     writer.seek(i*10)
 396                     writer.write(w)
 397                 writer.seek(0)
 398                 self.assertEqual(writer.read(), "00000000001111111111222222222233333333334444444444")
 399
 400     def test_sparse_write4(self):
 401         keep = ArvadosFileWriterTestCase.MockKeep({})
 402         api = ArvadosFileWriterTestCase.MockApi({}, {})
 403         for r in [[0, 1, 2, 4], [4, 2, 1, 0], [2, 0, 4, 1]]:
 404             with Collection() as c:
 405                 writer = c.open("count.txt", "r+")
 406                 self.assertEqual(writer.size(), 0)
 407
 408                 for i in r:
 409                     w = ("%s" % i) * 10
 410                     writer.seek(i*10)
 411                     writer.write(w)
 412                 writer.seek(0)
 413                 self.assertEqual(writer.read(), b"000000000011111111112222222222\x00\x00\x00\x00\x00\x00\x00\x00\x00\x004444444444")
 414
 415
 416     def test_rewrite_on_empty_file(self):
 417         keep = ArvadosFileWriterTestCase.MockKeep({})
 418         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 419                              keep_client=keep) as c:
 420             writer = c.open("count.txt", "rb+")
 421             for b in range(0, 10):
 422                 writer.seek(0, os.SEEK_SET)
 423                 writer.write("0123456789")
 424
 425             self.assertEqual(writer.size(), 10)
 426             self.assertEqual(b"0123456789", writer.readfrom(0, 20))
 427             self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.portable_manifest_text())
 428             writer.flush()
 429             self.assertEqual(writer.size(), 10)
 430             self.assertEqual(b"0123456789", writer.readfrom(0, 20))
 431             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.portable_manifest_text())
 432
 433     def test_rewrite_append_existing_file(self):
 434         keep = ArvadosFileWriterTestCase.MockKeep({
 435             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 436         })
 437         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 438                              keep_client=keep) as c:
 439             writer = c.open("count.txt", "rb+")
 440             for b in range(0, 10):
 441                 writer.seek(10, os.SEEK_SET)
 442                 writer.write("abcdefghij")
 443
 444             self.assertEqual(writer.size(), 20)
 445             self.assertEqual(b"0123456789abcdefghij", writer.readfrom(0, 20))
 446             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 447
 448             writer.arvadosfile.flush()
 449             self.assertEqual(writer.size(), 20)
 450             self.assertEqual(b"0123456789abcdefghij", writer.readfrom(0, 20))
 451             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.portable_manifest_text())
 452
 453     def test_rewrite_over_existing_file(self):
 454         keep = ArvadosFileWriterTestCase.MockKeep({
 455             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 456         })
 457         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 458                              keep_client=keep) as c:
 459             writer = c.open("count.txt", "rb+")
 460             for b in range(0, 10):
 461                 writer.seek(5, os.SEEK_SET)
 462                 writer.write("abcdefghij")
 463
 464             self.assertEqual(writer.size(), 15)
 465             self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20))
 466             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 467
 468             writer.arvadosfile.flush()
 469
 470             self.assertEqual(writer.size(), 15)
 471             self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20))
 472             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.portable_manifest_text())
 473
 474     def test_write_large_rewrite(self):
 475         keep = ArvadosFileWriterTestCase.MockKeep({})
 476         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 477                                                  "manifest_text": ". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n",
 478                                                  "replication_desired":None},
 479                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 480                                                  "manifest_text": ". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n",
 481                                                  "portable_data_hash":"217665c6b713e1b78dfba7ebd42344db+156"})
 482         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 483                              api_client=api, keep_client=keep) as c:
 484             writer = c.open("count.txt", "rb+")
 485             text = b''.join([b"0123456789" for a in range(0, 100)])
 486             for b in range(0, 100000):
 487                 writer.write(text)
 488             writer.seek(0, os.SEEK_SET)
 489             writer.write("foo")
 490             self.assertEqual(writer.size(), 100000000)
 491
 492             self.assertIsNone(c.manifest_locator())
 493             self.assertTrue(c.modified())
 494             c.save_new("test_write_large")
 495             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 496             self.assertFalse(c.modified())
 497
 498     def test_create(self):
 499         keep = ArvadosFileWriterTestCase.MockKeep({})
 500         api = ArvadosFileWriterTestCase.MockApi({
 501             "name":"test_create",
 502             "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 503             "replication_desired":None,
 504         }, {
 505             "uuid":"zzzzz-4zz18-mockcollection0",
 506             "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 507             "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51",
 508         })
 509         with Collection(api_client=api, keep_client=keep) as c:
 510             writer = c.open("count.txt", "wb+")
 511             self.assertEqual(writer.size(), 0)
 512             writer.write("01234567")
 513             self.assertEqual(writer.size(), 8)
 514
 515             self.assertIsNone(c.manifest_locator())
 516             self.assertTrue(c.modified())
 517             self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 518             c.save_new("test_create")
 519             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 520             self.assertFalse(c.modified())
 521             self.assertEqual(b"01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 522
 523
 524     def test_create_subdir(self):
 525         keep = ArvadosFileWriterTestCase.MockKeep({})
 526         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 527                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 528                                                  "replication_desired":None},
 529                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 530                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 531                                                  "portable_data_hash":"1b02aaa62528d28a5be41651cbb9d7c7+59"})
 532         with Collection(api_client=api, keep_client=keep) as c:
 533             self.assertIsNone(c.api_response())
 534             writer = c.open("foo/bar/count.txt", "wb+")
 535             writer.write("01234567")
 536             self.assertFalse(c.committed())
 537             c.save_new("test_create")
 538             self.assertTrue(c.committed())
 539             self.assertEqual(c.api_response(), api.response)
 540
 541     def test_overwrite(self):
 542         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 543         api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
 544                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 545                                                  "replication_desired":None},
 546                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 547                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 548                                                  "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51"})
 549         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 550                              api_client=api, keep_client=keep) as c:
 551             writer = c.open("count.txt", "wb+")
 552             self.assertEqual(writer.size(), 0)
 553             writer.write("01234567")
 554             self.assertEqual(writer.size(), 8)
 555
 556             self.assertIsNone(c.manifest_locator())
 557             self.assertTrue(c.modified())
 558             c.save_new("test_overwrite")
 559             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 560             self.assertFalse(c.modified())
 561
 562     def test_file_not_found(self):
 563         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 564             with self.assertRaises(IOError):
 565                 writer = c.open("nocount.txt", "rb")
 566
 567     def test_cannot_open_directory(self):
 568         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 569             with self.assertRaises(IOError):
 570                 writer = c.open(".", "rb")
 571
 572     def test_create_multiple(self):
 573         keep = ArvadosFileWriterTestCase.MockKeep({})
 574         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
 575                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
 576                                                  "replication_desired":None},
 577                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 578                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
 579                                                  "portable_data_hash":"71e7bb6c00d31fc2b4364199fd97be08+102"})
 580         with Collection(api_client=api, keep_client=keep) as c:
 581             w1 = c.open("count1.txt", "wb")
 582             w2 = c.open("count2.txt", "wb")
 583             w1.write("01234567")
 584             w2.write("abcdefgh")
 585             self.assertEqual(w1.size(), 8)
 586             self.assertEqual(w2.size(), 8)
 587
 588             self.assertIsNone(c.manifest_locator())
 589             self.assertTrue(c.modified())
 590             self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 591             c.save_new("test_create_multiple")
 592             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 593             self.assertFalse(c.modified())
 594             self.assertEqual(b"01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 595
 596
 597 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
 598     class MockParent(object):
 599         class MockBlockMgr(object):
 600             def __init__(self, blocks, nocache):
 601                 self.blocks = blocks
 602                 self.nocache = nocache
 603
 604             def block_prefetch(self, loc):
 605                 pass
 606
 607             def get_block_contents(self, loc, num_retries=0, cache_only=False):
 608                 if self.nocache and cache_only:
 609                     return None
 610                 return self.blocks[loc]
 611
 612         def __init__(self, blocks, nocache):
 613             self.blocks = blocks
 614             self.nocache = nocache
 615             self.lock = arvados.arvfile.NoopLock()
 616
 617         def root_collection(self):
 618             return self
 619
 620         def _my_block_manager(self):
 621             return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
 622
 623
 624     def make_count_reader(self, nocache=False):
 625         stream = []
 626         n = 0
 627         blocks = {}
 628         for d in [b'01234', b'34567', b'67890']:
 629             loc = tutil.str_keep_locator(d)
 630             blocks[loc] = d
 631             stream.append(Range(loc, n, len(d)))
 632             n += len(d)
 633         af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), "count.txt", stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
 634         return ArvadosFileReader(af, mode="rb")
 635
 636     def test_read_block_crossing_behavior(self):
 637         # read() needs to return all the data requested if possible, even if it
 638         # crosses uncached blocks: https://arvados.org/issues/5856
 639         sfile = self.make_count_reader(nocache=True)
 640         self.assertEqual(b'12345678', sfile.read(8))
 641
 642     def test_successive_reads(self):
 643         # Override StreamFileReaderTestCase.test_successive_reads
 644         sfile = self.make_count_reader(nocache=True)
 645         self.assertEqual(b'1234', sfile.read(4))
 646         self.assertEqual(b'5678', sfile.read(4))
 647         self.assertEqual(b'9', sfile.read(4))
 648         self.assertEqual(b'', sfile.read(4))
 649
 650     def test_tell_after_block_read(self):
 651         # Override StreamFileReaderTestCase.test_tell_after_block_read
 652         sfile = self.make_count_reader(nocache=True)
 653         self.assertEqual(b'12345678', sfile.read(8))
 654         self.assertEqual(8, sfile.tell())
 655
 656     def test_prefetch(self):
 657         keep = ArvadosFileWriterTestCase.MockKeep({
 658             "2e9ec317e197819358fbc43afca7d837+8": b"01234567",
 659             "e8dc4081b13434b45189a720b77b6818+8": b"abcdefgh",
 660         })
 661         with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
 662             r = c.open("count.txt", "rb")
 663             self.assertEqual(b"0123", r.read(4))
 664         self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
 665         self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
 666
 667     def test__eq__from_manifest(self):
 668         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 669             with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
 670                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 671                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 672
 673     def test__eq__from_writes(self):
 674         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 675             with Collection() as c2:
 676                 f = c2.open("count1.txt", "wb")
 677                 f.write("0123456789")
 678
 679                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 680                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 681
 682     def test__ne__(self):
 683         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 684             with Collection() as c2:
 685                 f = c2.open("count1.txt", "wb")
 686                 f.write("1234567890")
 687
 688                 self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
 689                 self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
 690
 691
 692 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
 693     def reader_for(self, coll_name, **kwargs):
 694         stream = []
 695         segments = []
 696         n = 0
 697         for d in self.manifest_for(coll_name).split():
 698             try:
 699                 k = KeepLocator(d)
 700                 segments.append(Range(n, n, k.size))
 701                 stream.append(Range(d, n, k.size))
 702                 n += k.size
 703             except ValueError:
 704                 pass
 705
 706         blockmanager = arvados.arvfile._BlockManager(self.keep_client())
 707         blockmanager.prefetch_enabled = False
 708         col = Collection(keep_client=self.keep_client(), block_manager=blockmanager)
 709         af = ArvadosFile(col, "test",
 710                          stream=stream,
 711                          segments=segments)
 712         kwargs.setdefault('mode', 'rb')
 713         return ArvadosFileReader(af, **kwargs)
 714
 715     def read_for_test(self, reader, byte_count, **kwargs):
 716         return reader.read(byte_count, **kwargs)
 717
 718
 719 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
 720     def read_for_test(self, reader, byte_count, **kwargs):
 721         return reader.readfrom(0, byte_count, **kwargs)
 722
 723
 724 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
 725     def read_for_test(self, reader, byte_count, **kwargs):
 726         return b''.join(reader.readall(**kwargs))
 727
 728
 729 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
 730     def read_for_test(self, reader, byte_count, **kwargs):
 731         return b''.join(reader.readall_decompressed(**kwargs))
 732
 733
 734 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
 735     def read_for_test(self, reader, byte_count, **kwargs):
 736         return ''.join(reader.readlines(**kwargs)).encode()
 737
 738
 739 class ArvadosFileTestCase(unittest.TestCase):
 740     def datetime_to_hex(self, dt):
 741         return hex(int(time.mktime(dt.timetuple())))[2:]
 742
 743     def test_permission_expired(self):
 744         base_manifest = ". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@{} 0:10:count.txt\n"
 745         now = datetime.datetime.now()
 746         a_week_ago = now - datetime.timedelta(days=7)
 747         a_month_ago = now - datetime.timedelta(days=30)
 748         a_week_from_now = now + datetime.timedelta(days=7)
 749         with Collection(base_manifest.format(self.datetime_to_hex(a_week_from_now))) as c:
 750             self.assertFalse(c.find('count.txt').permission_expired())
 751         with Collection(base_manifest.format(self.datetime_to_hex(a_week_ago))) as c:
 752             f = c.find('count.txt')
 753             self.assertTrue(f.permission_expired())
 754             self.assertTrue(f.permission_expired(a_week_from_now))
 755             self.assertFalse(f.permission_expired(a_month_ago))
 756
 757
 758 class BlockManagerTest(unittest.TestCase):
 759     def test_bufferblock_append(self):
 760         keep = ArvadosFileWriterTestCase.MockKeep({})
 761         with arvados.arvfile._BlockManager(keep) as blockmanager:
 762             bufferblock = blockmanager.alloc_bufferblock()
 763             bufferblock.append("foo")
 764
 765             self.assertEqual(bufferblock.size(), 3)
 766             self.assertEqual(bufferblock.buffer_view[0:3], b"foo")
 767             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 768
 769             bufferblock.append("bar")
 770
 771             self.assertEqual(bufferblock.size(), 6)
 772             self.assertEqual(bufferblock.buffer_view[0:6], b"foobar")
 773             self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
 774
 775             bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 776             with self.assertRaises(arvados.errors.AssertionError):
 777                 bufferblock.append("bar")
 778
 779     def test_bufferblock_dup(self):
 780         keep = ArvadosFileWriterTestCase.MockKeep({})
 781         with arvados.arvfile._BlockManager(keep) as blockmanager:
 782             bufferblock = blockmanager.alloc_bufferblock()
 783             bufferblock.append("foo")
 784
 785             self.assertEqual(bufferblock.size(), 3)
 786             self.assertEqual(bufferblock.buffer_view[0:3], b"foo")
 787             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 788             bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 789
 790             bufferblock2 = blockmanager.dup_block(bufferblock, None)
 791             self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
 792
 793             bufferblock2.append("bar")
 794
 795             self.assertEqual(bufferblock2.size(), 6)
 796             self.assertEqual(bufferblock2.buffer_view[0:6], b"foobar")
 797             self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
 798
 799             self.assertEqual(bufferblock.size(), 3)
 800             self.assertEqual(bufferblock.buffer_view[0:3], b"foo")
 801             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 802
 803     def test_bufferblock_get(self):
 804         keep = ArvadosFileWriterTestCase.MockKeep({
 805             "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
 806         })
 807         with arvados.arvfile._BlockManager(keep) as blockmanager:
 808             bufferblock = blockmanager.alloc_bufferblock()
 809             bufferblock.append("foo")
 810
 811             self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), b"0123456789")
 812             self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), b"foo")
 813
 814     def test_bufferblock_commit(self):
 815         mockkeep = mock.MagicMock()
 816         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 817             bufferblock = blockmanager.alloc_bufferblock()
 818             bufferblock.owner = mock.MagicMock()
 819             def flush(sync=None):
 820                 blockmanager.commit_bufferblock(bufferblock, sync)
 821             bufferblock.owner.flush.side_effect = flush
 822             bufferblock.append("foo")
 823             blockmanager.commit_all()
 824             self.assertTrue(bufferblock.owner.flush.called)
 825             self.assertTrue(mockkeep.put.called)
 826             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 827             self.assertIsNone(bufferblock.buffer_view)
 828
 829     def test_bufferblock_commit_pending(self):
 830         # Test for bug #7225
 831         mockkeep = mock.MagicMock()
 832         mockkeep.put.side_effect = lambda x: time.sleep(1)
 833         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 834             bufferblock = blockmanager.alloc_bufferblock()
 835             bufferblock.append("foo")
 836
 837             blockmanager.commit_bufferblock(bufferblock, False)
 838             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)
 839
 840             blockmanager.commit_bufferblock(bufferblock, True)
 841             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 842
 843
 844     def test_bufferblock_commit_with_error(self):
 845         mockkeep = mock.MagicMock()
 846         mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail")
 847         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 848             bufferblock = blockmanager.alloc_bufferblock()
 849             bufferblock.owner = mock.MagicMock()
 850             def flush(sync=None):
 851                 blockmanager.commit_bufferblock(bufferblock, sync)
 852             bufferblock.owner.flush.side_effect = flush
 853             bufferblock.append("foo")
 854             with self.assertRaises(arvados.errors.KeepWriteError) as err:
 855                 blockmanager.commit_all()
 856             self.assertTrue(bufferblock.owner.flush.called)
 857             self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
 858             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.ERROR)