sdk/python/tests/test_arvfile.py

   1 #!/usr/bin/env python
   2
   3 import bz2
   4 import gzip
   5 import io
   6 import mock
   7 import os
   8 import unittest
   9 import hashlib
  10
  11 import arvados
  12 from arvados import ArvadosFile, ArvadosFileReader, Range, import_manifest, export_manifest, KeepLocator
  13 from arvados.arvfile import SYNC_READONLY, SYNC_EXPLICIT
  14
  15 import arvados_testutil as tutil
  16 from test_stream import StreamFileReaderTestCase, StreamRetryTestMixin
  17
  18 class ArvadosFileWriterTestCase(unittest.TestCase):
  19     class MockKeep(object):
  20         def __init__(self, blocks):
  21             self.blocks = blocks
  22             self.requests = []
  23         def get(self, locator, num_retries=0, cache_only=False):
  24             self.requests.append(locator)
  25             return self.blocks.get(locator)
  26         def put(self, data):
  27             pdh = "%s+%i" % (hashlib.md5(data).hexdigest(), len(data))
  28             self.blocks[pdh] = str(data)
  29             return pdh
  30
  31     class MockApi(object):
  32         def __init__(self, b, r):
  33             self.b = b
  34             self.r = r
  35         class MockCollections(object):
  36             def __init__(self, b, r):
  37                 self.b = b
  38                 self.r = r
  39             class Execute(object):
  40                 def __init__(self, r):
  41                     self.r = r
  42                 def execute(self, num_retries=None):
  43                     return self.r
  44             def create(self, ensure_unique_name=False, body=None):
  45                 if body != self.b:
  46                     raise Exception("Body %s does not match expectation %s" % (body, self.b))
  47                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.r)
  48             def update(self, uuid=None, body=None):
  49                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.r)
  50         def collections(self):
  51             return ArvadosFileWriterTestCase.MockApi.MockCollections(self.b, self.r)
  52
  53
  54     def test_truncate(self):
  55         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
  56         api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate",
  57                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"},
  58                                                 {"uuid":"zzzzz-4zz18-mockcollection0"})
  59         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
  60                              api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
  61             writer = c.open("count.txt", "r+")
  62             self.assertEqual(writer.size(), 10)
  63             writer.seek(5)
  64             self.assertEqual("56789", writer.read(8))
  65             writer.truncate(8)
  66             writer.seek(5, os.SEEK_SET)
  67             self.assertEqual("567", writer.read(8))
  68
  69             self.assertEqual(None, c._manifest_locator)
  70             self.assertEqual(True, c.modified())
  71             c.save_as("test_truncate")
  72             self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
  73             self.assertEqual(False, c.modified())
  74
  75     def test_append(self):
  76         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
  77         api = ArvadosFileWriterTestCase.MockApi({"name":"test_append",
  78                                                  "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"},
  79                                                 {"uuid":"zzzzz-4zz18-mockcollection0"})
  80         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
  81                              api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
  82             writer = c.open("count.txt", "r+")
  83             writer.seek(5, os.SEEK_SET)
  84             self.assertEqual("56789", writer.read(8))
  85             writer.seek(10, os.SEEK_SET)
  86             writer.write("foo")
  87             self.assertEqual(writer.size(), 13)
  88             writer.seek(5, os.SEEK_SET)
  89             self.assertEqual("56789foo", writer.read(8))
  90
  91             self.assertEqual(None, c._manifest_locator)
  92             self.assertEqual(True, c.modified())
  93             self.assertEqual(None, keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
  94             c.save_as("test_append")
  95             self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
  96             self.assertEqual(False, c.modified())
  97             self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
  98
  99     def test_write0(self):
 100         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 101         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 102                              keep=keep, sync=SYNC_EXPLICIT) as c:
 103             writer = c.open("count.txt", "r+")
 104             self.assertEqual("0123456789", writer.readfrom(0, 13))
 105             writer.seek(0, os.SEEK_SET)
 106             writer.write("foo")
 107             self.assertEqual(writer.size(), 10)
 108             self.assertEqual("foo3456789", writer.readfrom(0, 13))
 109             self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", export_manifest(c))
 110
 111     def test_write1(self):
 112         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 113         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 114                              keep=keep, sync=SYNC_EXPLICIT) as c:
 115             writer = c.open("count.txt", "r+")
 116             self.assertEqual("0123456789", writer.readfrom(0, 13))
 117             writer.seek(3, os.SEEK_SET)
 118             writer.write("foo")
 119             self.assertEqual(writer.size(), 10)
 120             self.assertEqual("012foo6789", writer.readfrom(0, 13))
 121             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", export_manifest(c))
 122
 123     def test_write2(self):
 124         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 125         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 126                              keep=keep, sync=SYNC_EXPLICIT) as c:
 127             writer = c.open("count.txt", "r+")
 128             self.assertEqual("0123456789", writer.readfrom(0, 13))
 129             writer.seek(7, os.SEEK_SET)
 130             writer.write("foo")
 131             self.assertEqual(writer.size(), 10)
 132             self.assertEqual("0123456foo", writer.readfrom(0, 13))
 133             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", export_manifest(c))
 134
 135     def test_write3(self):
 136         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 137         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
 138                              keep=keep, sync=SYNC_EXPLICIT) as c:
 139             writer = c.open("count.txt", "r+")
 140             self.assertEqual("012345678901234", writer.readfrom(0, 15))
 141             writer.seek(7, os.SEEK_SET)
 142             writer.write("foobar")
 143             self.assertEqual(writer.size(), 20)
 144             self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
 145             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", export_manifest(c))
 146
 147     def test_write4(self):
 148         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 149         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
 150                              keep=keep, sync=SYNC_EXPLICIT) as c:
 151             writer = c.open("count.txt", "r+")
 152             self.assertEqual("012301230123", writer.readfrom(0, 15))
 153             writer.seek(2, os.SEEK_SET)
 154             writer.write("abcdefg")
 155             self.assertEqual(writer.size(), 12)
 156             self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
 157             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", export_manifest(c))
 158
 159     def test_write_large(self):
 160         keep = ArvadosFileWriterTestCase.MockKeep({})
 161         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 162                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"},
 163                                                 {"uuid":"zzzzz-4zz18-mockcollection0"})
 164         with import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 165                              api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
 166             writer = c.open("count.txt", "r+")
 167             text = ''.join(["0123456789" for a in xrange(0, 100)])
 168             for b in xrange(0, 100000):
 169                 writer.write(text)
 170             self.assertEqual(writer.size(), 100000000)
 171
 172             self.assertEqual(None, c._manifest_locator)
 173             self.assertEqual(True, c.modified())
 174             c.save_as("test_write_large")
 175             self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
 176             self.assertEqual(False, c.modified())
 177
 178     def test_write_rewrite0(self):
 179         keep = ArvadosFileWriterTestCase.MockKeep({})
 180         with import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 181                              keep=keep, sync=SYNC_EXPLICIT) as c:
 182             writer = c.open("count.txt", "r+")
 183             for b in xrange(0, 10):
 184                 writer.seek(0, os.SEEK_SET)
 185                 writer.write("0123456789")
 186             writer.arvadosfile._repack_writes()
 187             self.assertEqual(writer.size(), 10)
 188             self.assertEqual("0123456789", writer.readfrom(0, 20))
 189             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", export_manifest(c))
 190
 191     def test_write_rewrite1(self):
 192         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 193         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 194                              keep=keep, sync=SYNC_EXPLICIT) as c:
 195             writer = c.open("count.txt", "r+")
 196             for b in xrange(0, 10):
 197                 writer.seek(10, os.SEEK_SET)
 198                 writer.write("abcdefghij")
 199             writer.arvadosfile._repack_writes()
 200             self.assertEqual(writer.size(), 20)
 201             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 202             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", export_manifest(c))
 203
 204     def test_write_rewrite2(self):
 205         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 206         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 207                              keep=keep, sync=SYNC_EXPLICIT) as c:
 208             writer = c.open("count.txt", "r+")
 209             for b in xrange(0, 10):
 210                 writer.seek(5, os.SEEK_SET)
 211                 writer.write("abcdefghij")
 212             writer.arvadosfile._repack_writes()
 213             self.assertEqual(writer.size(), 15)
 214             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 215             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", export_manifest(c))
 216
 217     def test_write_large_rewrite0(self):
 218         keep = ArvadosFileWriterTestCase.MockKeep({})
 219         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 220                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"},
 221                                                 {"uuid":"zzzzz-4zz18-mockcollection0"})
 222         with import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 223                              api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
 224             writer = c.open("count.txt", "r+")
 225             text = ''.join(["0123456789" for a in xrange(0, 100)])
 226             for b in xrange(0, 100000):
 227                 writer.write(text)
 228             writer.seek(0, os.SEEK_SET)
 229             writer.write("foo")
 230             self.assertEqual(writer.size(), 100000000)
 231
 232             self.assertEqual(None, c._manifest_locator)
 233             self.assertEqual(True, c.modified())
 234             c.save_as("test_write_large")
 235             self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
 236             self.assertEqual(False, c.modified())
 237
 238     def test_create(self):
 239         keep = ArvadosFileWriterTestCase.MockKeep({})
 240         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 241                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 242                                                 {"uuid":"zzzzz-4zz18-mockcollection0"})
 243         with arvados.Collection(api_client=api, keep_client=keep, sync=SYNC_EXPLICIT) as c:
 244             writer = c.open("count.txt", "w+")
 245             self.assertEqual(writer.size(), 0)
 246             writer.write("01234567")
 247             self.assertEqual(writer.size(), 8)
 248
 249             self.assertEqual(None, c._manifest_locator)
 250             self.assertEqual(True, c.modified())
 251             self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 252             c.save_as("test_create")
 253             self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
 254             self.assertEqual(False, c.modified())
 255             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 256
 257
 258     def test_create_subdir(self):
 259         keep = ArvadosFileWriterTestCase.MockKeep({})
 260         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 261                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 262                                                 {"uuid":"zzzzz-4zz18-mockcollection0"})
 263         with arvados.Collection(api_client=api, keep_client=keep, sync=SYNC_EXPLICIT) as c:
 264             writer = c.open("foo/bar/count.txt", "w+")
 265             writer.write("01234567")
 266             c.save_as("test_create")
 267
 268     def test_overwrite(self):
 269         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 270         api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
 271                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 272                                                 {"uuid":"zzzzz-4zz18-mockcollection0"})
 273         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 274                              api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
 275             writer = c.open("count.txt", "w+")
 276             self.assertEqual(writer.size(), 0)
 277             writer.write("01234567")
 278             self.assertEqual(writer.size(), 8)
 279
 280             self.assertEqual(None, c._manifest_locator)
 281             self.assertEqual(True, c.modified())
 282             c.save_as("test_overwrite")
 283             self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
 284             self.assertEqual(False, c.modified())
 285
 286     def test_file_not_found(self):
 287         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 288             with self.assertRaises(IOError):
 289                 writer = c.open("nocount.txt", "r")
 290
 291     def test_cannot_open_directory(self):
 292         with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 293             with self.assertRaises(IOError):
 294                 writer = c.open(".", "r")
 295
 296     def test_create_multiple(self):
 297         keep = ArvadosFileWriterTestCase.MockKeep({})
 298         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
 299                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"},
 300                                                 {"uuid":"zzzzz-4zz18-mockcollection0"})
 301         with arvados.Collection(api_client=api, keep_client=keep, sync=SYNC_EXPLICIT) as c:
 302             w1 = c.open("count1.txt", "w")
 303             w2 = c.open("count2.txt", "w")
 304             w1.write("01234567")
 305             w2.write("abcdefgh")
 306             self.assertEqual(w1.size(), 8)
 307             self.assertEqual(w2.size(), 8)
 308
 309             self.assertEqual(None, c._manifest_locator)
 310             self.assertEqual(True, c.modified())
 311             self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 312             c.save_as("test_create_multiple")
 313             self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
 314             self.assertEqual(False, c.modified())
 315             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 316
 317
 318 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
 319     class MockParent(object):
 320         class MockBlockMgr(object):
 321             def __init__(self, blocks, nocache):
 322                 self.blocks = blocks
 323                 self.nocache = nocache
 324
 325             def block_prefetch(self, loc):
 326                 pass
 327
 328             def get_block(self, loc, num_retries=0, cache_only=False):
 329                 if self.nocache and cache_only:
 330                     return None
 331                 return self.blocks[loc]
 332
 333         def __init__(self, blocks, nocache):
 334             self.blocks = blocks
 335             self.nocache = nocache
 336
 337         def _my_block_manager(self):
 338             return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
 339
 340         def sync_mode(self):
 341             return SYNC_READONLY
 342
 343     def make_count_reader(self, nocache=False):
 344         stream = []
 345         n = 0
 346         blocks = {}
 347         for d in ['01234', '34567', '67890']:
 348             loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d))
 349             blocks[loc] = d
 350             stream.append(Range(loc, n, len(d)))
 351             n += len(d)
 352         af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
 353         return ArvadosFileReader(af, "count.txt")
 354
 355     def test_read_returns_first_block(self):
 356         # read() calls will be aligned on block boundaries - see #3663.
 357         sfile = self.make_count_reader(nocache=True)
 358         self.assertEqual('123', sfile.read(10))
 359
 360     def test_successive_reads(self):
 361         sfile = self.make_count_reader(nocache=True)
 362         for expect in ['123', '456', '789', '']:
 363             self.assertEqual(expect, sfile.read(10))
 364
 365     def test_tell_after_block_read(self):
 366         sfile = self.make_count_reader(nocache=True)
 367         sfile.read(5)
 368         self.assertEqual(3, sfile.tell())
 369
 370     def test_prefetch(self):
 371         keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
 372         with import_manifest(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep=keep) as c:
 373             r = c.open("count.txt", "r")
 374             self.assertEqual("0123", r.read(4))
 375         self.assertTrue("2e9ec317e197819358fbc43afca7d837+8" in keep.requests)
 376         self.assertTrue("e8dc4081b13434b45189a720b77b6818+8" in keep.requests)
 377
 378
 379 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
 380     def reader_for(self, coll_name, **kwargs):
 381         stream = []
 382         segments = []
 383         n = 0
 384         for d in self.manifest_for(coll_name).split():
 385             try:
 386                 k = KeepLocator(d)
 387                 segments.append(Range(n, n, k.size))
 388                 stream.append(Range(d, n, k.size))
 389                 n += k.size
 390             except ValueError:
 391                 pass
 392         col = arvados.Collection(keep_client=self.keep_client())
 393         col._my_block_manager().prefetch_enabled = False
 394         af = ArvadosFile(col,
 395                          stream=stream,
 396                          segments=segments)
 397         return ArvadosFileReader(af, "test", **kwargs)
 398
 399     def read_for_test(self, reader, byte_count, **kwargs):
 400         return reader.read(byte_count, **kwargs)
 401
 402
 403 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
 404     def read_for_test(self, reader, byte_count, **kwargs):
 405         return reader.readfrom(0, byte_count, **kwargs)
 406
 407
 408 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
 409     def read_for_test(self, reader, byte_count, **kwargs):
 410         return ''.join(reader.readall(**kwargs))
 411
 412
 413 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
 414     def read_for_test(self, reader, byte_count, **kwargs):
 415         return ''.join(reader.readall_decompressed(**kwargs))
 416
 417
 418 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
 419     def read_for_test(self, reader, byte_count, **kwargs):
 420         return ''.join(reader.readlines(**kwargs))