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