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._ranges import Range
  13 from arvados.keep import KeepLocator
  14 from arvados.collection import Collection, CollectionReader
  15 from arvados.arvfile import ArvadosFile, ArvadosFileReader
  16
  17 import arvados_testutil as tutil
  18 from test_stream import StreamFileReaderTestCase, StreamRetryTestMixin
  19
  20 class ArvadosFileWriterTestCase(unittest.TestCase):
  21     class MockKeep(object):
  22         def __init__(self, blocks):
  23             self.blocks = blocks
  24             self.requests = []
  25         def get(self, locator, num_retries=0):
  26             self.requests.append(locator)
  27             return self.blocks.get(locator)
  28         def get_from_cache(self, locator):
  29             self.requests.append(locator)
  30             return self.blocks.get(locator)
  31         def put(self, data, num_retries=None):
  32             pdh = "%s+%i" % (hashlib.md5(data).hexdigest(), len(data))
  33             self.blocks[pdh] = str(data)
  34             return pdh
  35
  36     class MockApi(object):
  37         def __init__(self, b, r):
  38             self.body = b
  39             self.response = r
  40         class MockCollections(object):
  41             def __init__(self, b, r):
  42                 self.body = b
  43                 self.response = r
  44             class Execute(object):
  45                 def __init__(self, r):
  46                     self.response = r
  47                 def execute(self, num_retries=None):
  48                     return self.response
  49             def create(self, ensure_unique_name=False, body=None):
  50                 if body != self.body:
  51                     raise Exception("Body %s does not match expectation %s" % (body, self.body))
  52                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  53             def update(self, uuid=None, body=None):
  54                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  55         def collections(self):
  56             return ArvadosFileWriterTestCase.MockApi.MockCollections(self.body, self.response)
  57
  58
  59     def test_truncate(self):
  60         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
  61         api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate",
  62                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"},
  63                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
  64                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"})
  65         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
  66                              api_client=api, keep_client=keep) as c:
  67             writer = c.open("count.txt", "r+")
  68             self.assertEqual(writer.size(), 10)
  69             self.assertEqual("0123456789", writer.read(12))
  70
  71             writer.truncate(8)
  72
  73             # Make sure reading off the end doesn't break
  74             self.assertEqual("", writer.read(12))
  75
  76             self.assertEqual(writer.size(), 8)
  77             writer.seek(0, os.SEEK_SET)
  78             self.assertEqual("01234567", writer.read(12))
  79
  80             self.assertEqual(None, c.manifest_locator())
  81             self.assertEqual(True, c.modified())
  82             c.save_new("test_truncate")
  83             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
  84             self.assertEqual(False, c.modified())
  85
  86     def test_write_to_end(self):
  87         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
  88         api = ArvadosFileWriterTestCase.MockApi({"name":"test_append",
  89                                                  "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"},
  90                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
  91                                                  "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"})
  92         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
  93                              api_client=api, keep_client=keep) as c:
  94             writer = c.open("count.txt", "r+")
  95             self.assertEqual(writer.size(), 10)
  96
  97             writer.seek(5, os.SEEK_SET)
  98             self.assertEqual("56789", writer.read(8))
  99
 100             writer.seek(10, os.SEEK_SET)
 101             writer.write("foo")
 102             self.assertEqual(writer.size(), 13)
 103
 104             writer.seek(5, os.SEEK_SET)
 105             self.assertEqual("56789foo", writer.read(8))
 106
 107             self.assertEqual(None, c.manifest_locator())
 108             self.assertEqual(True, c.modified())
 109             self.assertEqual(None, keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 110
 111             c.save_new("test_append")
 112             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 113             self.assertEqual(False, c.modified())
 114             self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 115
 116
 117     def test_append(self):
 118         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 119         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep)
 120         writer = c.open("count.txt", "a+")
 121         self.assertEqual(writer.read(20), "0123456789")
 122         writer.seek(0, os.SEEK_SET)
 123
 124         writer.write("hello")
 125         self.assertEqual(writer.read(20), "0123456789hello")
 126         writer.seek(0, os.SEEK_SET)
 127
 128         writer.write("world")
 129         self.assertEqual(writer.read(20), "0123456789helloworld")
 130
 131         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.manifest_text())
 132
 133     def test_write_at_beginning(self):
 134         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 135         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 136                              keep_client=keep) as c:
 137             writer = c.open("count.txt", "r+")
 138             self.assertEqual("0123456789", writer.readfrom(0, 13))
 139             writer.seek(0, os.SEEK_SET)
 140             writer.write("foo")
 141             self.assertEqual(writer.size(), 10)
 142             self.assertEqual("foo3456789", writer.readfrom(0, 13))
 143             self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", c.manifest_text())
 144
 145     def test_write_empty(self):
 146         keep = ArvadosFileWriterTestCase.MockKeep({})
 147         with Collection(keep_client=keep) as c:
 148             writer = c.open("count.txt", "w")
 149             self.assertEqual(writer.size(), 0)
 150             self.assertEqual(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n", c.manifest_text())
 151
 152     def test_get_manifest_text_commits(self):
 153         keep = ArvadosFileWriterTestCase.MockKeep({})
 154         with Collection(keep_client=keep) as c:
 155             writer = c.open("count.txt", "w")
 156             writer.write("0123456789")
 157             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text(strip=True))
 158             self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 159             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text(strip=False))
 160             self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 161
 162     def test_write_in_middle(self):
 163         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 164         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 165                              keep_client=keep) as c:
 166             writer = c.open("count.txt", "r+")
 167             self.assertEqual("0123456789", writer.readfrom(0, 13))
 168             writer.seek(3, os.SEEK_SET)
 169             writer.write("foo")
 170             self.assertEqual(writer.size(), 10)
 171             self.assertEqual("012foo6789", writer.readfrom(0, 13))
 172             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.manifest_text())
 173
 174     def test_write_at_end(self):
 175         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 176         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 177                              keep_client=keep) as c:
 178             writer = c.open("count.txt", "r+")
 179             self.assertEqual("0123456789", writer.readfrom(0, 13))
 180             writer.seek(7, os.SEEK_SET)
 181             writer.write("foo")
 182             self.assertEqual(writer.size(), 10)
 183             self.assertEqual("0123456foo", writer.readfrom(0, 13))
 184             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.manifest_text())
 185
 186     def test_write_across_segment_boundary(self):
 187         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 188         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
 189                              keep_client=keep) as c:
 190             writer = c.open("count.txt", "r+")
 191             self.assertEqual("012345678901234", writer.readfrom(0, 15))
 192             writer.seek(7, os.SEEK_SET)
 193             writer.write("foobar")
 194             self.assertEqual(writer.size(), 20)
 195             self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
 196             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.manifest_text())
 197
 198     def test_write_across_several_segments(self):
 199         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 200         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
 201                              keep_client=keep) as c:
 202             writer = c.open("count.txt", "r+")
 203             self.assertEqual("012301230123", writer.readfrom(0, 15))
 204             writer.seek(2, os.SEEK_SET)
 205             writer.write("abcdefg")
 206             self.assertEqual(writer.size(), 12)
 207             self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
 208             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.manifest_text())
 209
 210     def test_write_large(self):
 211         keep = ArvadosFileWriterTestCase.MockKeep({})
 212         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 213                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"},
 214                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 215                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"})
 216         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 217                              api_client=api, keep_client=keep) as c:
 218             writer = c.open("count.txt", "r+")
 219             text = ''.join(["0123456789" for a in xrange(0, 100)])
 220             for b in xrange(0, 100000):
 221                 writer.write(text)
 222             self.assertEqual(writer.size(), 100000000)
 223
 224             self.assertEqual(None, c.manifest_locator())
 225             self.assertEqual(True, c.modified())
 226             c.save_new("test_write_large")
 227             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 228             self.assertEqual(False, c.modified())
 229
 230     def test_rewrite_on_empty_file(self):
 231         keep = ArvadosFileWriterTestCase.MockKeep({})
 232         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 233                              keep_client=keep) as c:
 234             writer = c.open("count.txt", "r+")
 235             for b in xrange(0, 10):
 236                 writer.seek(0, os.SEEK_SET)
 237                 writer.write("0123456789")
 238
 239             self.assertEqual(writer.size(), 10)
 240             self.assertEqual("0123456789", writer.readfrom(0, 20))
 241             self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.manifest_text(strip=True))
 242             writer.flush()
 243             self.assertEqual(writer.size(), 10)
 244             self.assertEqual("0123456789", writer.readfrom(0, 20))
 245             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.manifest_text(strip=True))
 246
 247     def test_rewrite_append_existing_file(self):
 248         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 249         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 250                              keep_client=keep) as c:
 251             writer = c.open("count.txt", "r+")
 252             for b in xrange(0, 10):
 253                 writer.seek(10, os.SEEK_SET)
 254                 writer.write("abcdefghij")
 255
 256             self.assertEqual(writer.size(), 20)
 257             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 258             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.manifest_text(strip=True))
 259
 260             writer.arvadosfile.flush()
 261             self.assertEqual(writer.size(), 20)
 262             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 263             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.manifest_text(strip=True))
 264
 265     def test_rewrite_over_existing_file(self):
 266         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 267         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 268                              keep_client=keep) as c:
 269             writer = c.open("count.txt", "r+")
 270             for b in xrange(0, 10):
 271                 writer.seek(5, os.SEEK_SET)
 272                 writer.write("abcdefghij")
 273
 274             self.assertEqual(writer.size(), 15)
 275             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 276             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.manifest_text(strip=True))
 277
 278             writer.arvadosfile.flush()
 279
 280             self.assertEqual(writer.size(), 15)
 281             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 282             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.manifest_text(strip=True))
 283
 284     def test_write_large_rewrite(self):
 285         keep = ArvadosFileWriterTestCase.MockKeep({})
 286         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 287                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"},
 288                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 289                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"})
 290         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 291                              api_client=api, keep_client=keep) as c:
 292             writer = c.open("count.txt", "r+")
 293             text = ''.join(["0123456789" for a in xrange(0, 100)])
 294             for b in xrange(0, 100000):
 295                 writer.write(text)
 296             writer.seek(0, os.SEEK_SET)
 297             writer.write("foo")
 298             self.assertEqual(writer.size(), 100000000)
 299
 300             self.assertEqual(None, c.manifest_locator())
 301             self.assertEqual(True, c.modified())
 302             c.save_new("test_write_large")
 303             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 304             self.assertEqual(False, c.modified())
 305
 306     def test_create(self):
 307         keep = ArvadosFileWriterTestCase.MockKeep({})
 308         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 309                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 310                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 311                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 312         with Collection(api_client=api, keep_client=keep) as c:
 313             writer = c.open("count.txt", "w+")
 314             self.assertEqual(writer.size(), 0)
 315             writer.write("01234567")
 316             self.assertEqual(writer.size(), 8)
 317
 318             self.assertEqual(None, c.manifest_locator())
 319             self.assertEqual(True, c.modified())
 320             self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 321             c.save_new("test_create")
 322             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 323             self.assertEqual(False, c.modified())
 324             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 325
 326
 327     def test_create_subdir(self):
 328         keep = ArvadosFileWriterTestCase.MockKeep({})
 329         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 330                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 331                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 332                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 333         with Collection(api_client=api, keep_client=keep) as c:
 334             self.assertIsNone(c.api_response())
 335             writer = c.open("foo/bar/count.txt", "w+")
 336             writer.write("01234567")
 337             c.save_new("test_create")
 338             self.assertEqual(c.api_response(), api.response)
 339
 340     def test_overwrite(self):
 341         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 342         api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
 343                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 344                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 345                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 346         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 347                              api_client=api, keep_client=keep) as c:
 348             writer = c.open("count.txt", "w+")
 349             self.assertEqual(writer.size(), 0)
 350             writer.write("01234567")
 351             self.assertEqual(writer.size(), 8)
 352
 353             self.assertEqual(None, c.manifest_locator())
 354             self.assertEqual(True, c.modified())
 355             c.save_new("test_overwrite")
 356             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 357             self.assertEqual(False, c.modified())
 358
 359     def test_file_not_found(self):
 360         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 361             with self.assertRaises(IOError):
 362                 writer = c.open("nocount.txt", "r")
 363
 364     def test_cannot_open_directory(self):
 365         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 366             with self.assertRaises(IOError):
 367                 writer = c.open(".", "r")
 368
 369     def test_create_multiple(self):
 370         keep = ArvadosFileWriterTestCase.MockKeep({})
 371         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
 372                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"},
 373                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 374                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"})
 375         with Collection(api_client=api, keep_client=keep) as c:
 376             w1 = c.open("count1.txt", "w")
 377             w2 = c.open("count2.txt", "w")
 378             w1.write("01234567")
 379             w2.write("abcdefgh")
 380             self.assertEqual(w1.size(), 8)
 381             self.assertEqual(w2.size(), 8)
 382
 383             self.assertEqual(None, c.manifest_locator())
 384             self.assertEqual(True, c.modified())
 385             self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 386             c.save_new("test_create_multiple")
 387             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 388             self.assertEqual(False, c.modified())
 389             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 390
 391
 392 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
 393     class MockParent(object):
 394         class MockBlockMgr(object):
 395             def __init__(self, blocks, nocache):
 396                 self.blocks = blocks
 397                 self.nocache = nocache
 398
 399             def block_prefetch(self, loc):
 400                 pass
 401
 402             def get_block_contents(self, loc, num_retries=0, cache_only=False):
 403                 if self.nocache and cache_only:
 404                     return None
 405                 return self.blocks[loc]
 406
 407         def __init__(self, blocks, nocache):
 408             self.blocks = blocks
 409             self.nocache = nocache
 410             self.lock = arvados.arvfile.NoopLock()
 411
 412         def root_collection(self):
 413             return self
 414
 415         def _my_block_manager(self):
 416             return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
 417
 418
 419     def make_count_reader(self, nocache=False):
 420         stream = []
 421         n = 0
 422         blocks = {}
 423         for d in ['01234', '34567', '67890']:
 424             loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d))
 425             blocks[loc] = d
 426             stream.append(Range(loc, n, len(d)))
 427             n += len(d)
 428         af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
 429         return ArvadosFileReader(af, "count.txt")
 430
 431     def test_read_returns_first_block(self):
 432         # read() calls will be aligned on block boundaries - see #3663.
 433         sfile = self.make_count_reader(nocache=True)
 434         self.assertEqual('123', sfile.read(10))
 435
 436     def test_successive_reads(self):
 437         sfile = self.make_count_reader(nocache=True)
 438         for expect in ['123', '456', '789', '']:
 439             self.assertEqual(expect, sfile.read(10))
 440
 441     def test_tell_after_block_read(self):
 442         sfile = self.make_count_reader(nocache=True)
 443         sfile.read(5)
 444         self.assertEqual(3, sfile.tell())
 445
 446     def test_prefetch(self):
 447         keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
 448         with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
 449             r = c.open("count.txt", "r")
 450             self.assertEqual("0123", r.read(4))
 451         self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
 452         self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
 453
 454     def test__eq__from_manifest(self):
 455         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 456             with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
 457                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 458                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 459
 460     def test__eq__from_writes(self):
 461         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 462             with Collection() as c2:
 463                 with c2.open("count1.txt", "w") as f:
 464                     f.write("0123456789")
 465
 466                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 467                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 468
 469     def test__ne__(self):
 470         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 471             with Collection() as c2:
 472                 with c2.open("count1.txt", "w") as f:
 473                     f.write("1234567890")
 474
 475                 self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
 476                 self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
 477
 478
 479 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
 480     def reader_for(self, coll_name, **kwargs):
 481         stream = []
 482         segments = []
 483         n = 0
 484         for d in self.manifest_for(coll_name).split():
 485             try:
 486                 k = KeepLocator(d)
 487                 segments.append(Range(n, n, k.size))
 488                 stream.append(Range(d, n, k.size))
 489                 n += k.size
 490             except ValueError:
 491                 pass
 492
 493         blockmanager = arvados.arvfile._BlockManager(self.keep_client())
 494         blockmanager.prefetch_enabled = False
 495         col = Collection(keep_client=self.keep_client(), block_manager=blockmanager)
 496         af = ArvadosFile(col,
 497                          stream=stream,
 498                          segments=segments)
 499         return ArvadosFileReader(af, "test", **kwargs)
 500
 501     def read_for_test(self, reader, byte_count, **kwargs):
 502         return reader.read(byte_count, **kwargs)
 503
 504
 505 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
 506     def read_for_test(self, reader, byte_count, **kwargs):
 507         return reader.readfrom(0, byte_count, **kwargs)
 508
 509
 510 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
 511     def read_for_test(self, reader, byte_count, **kwargs):
 512         return ''.join(reader.readall(**kwargs))
 513
 514
 515 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
 516     def read_for_test(self, reader, byte_count, **kwargs):
 517         return ''.join(reader.readall_decompressed(**kwargs))
 518
 519
 520 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
 521     def read_for_test(self, reader, byte_count, **kwargs):
 522         return ''.join(reader.readlines(**kwargs))
 523
 524 class BlockManagerTest(unittest.TestCase):
 525     def test_bufferblock_append(self):
 526         keep = ArvadosFileWriterTestCase.MockKeep({})
 527         blockmanager = arvados.arvfile._BlockManager(keep)
 528         bufferblock = blockmanager.alloc_bufferblock()
 529         bufferblock.append("foo")
 530
 531         self.assertEqual(bufferblock.size(), 3)
 532         self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 533         self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 534
 535         bufferblock.append("bar")
 536
 537         self.assertEqual(bufferblock.size(), 6)
 538         self.assertEqual(bufferblock.buffer_view[0:6], "foobar")
 539         self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
 540
 541         bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 542         with self.assertRaises(arvados.errors.AssertionError):
 543             bufferblock.append("bar")
 544
 545     def test_bufferblock_dup(self):
 546         keep = ArvadosFileWriterTestCase.MockKeep({})
 547         blockmanager = arvados.arvfile._BlockManager(keep)
 548         bufferblock = blockmanager.alloc_bufferblock()
 549         bufferblock.append("foo")
 550
 551         self.assertEqual(bufferblock.size(), 3)
 552         self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 553         self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 554         bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 555
 556         bufferblock2 = blockmanager.dup_block(bufferblock, None)
 557         self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
 558
 559         bufferblock2.append("bar")
 560
 561         self.assertEqual(bufferblock2.size(), 6)
 562         self.assertEqual(bufferblock2.buffer_view[0:6], "foobar")
 563         self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
 564
 565         self.assertEqual(bufferblock.size(), 3)
 566         self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 567         self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 568
 569     def test_bufferblock_get(self):
 570         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 571         blockmanager = arvados.arvfile._BlockManager(keep)
 572         bufferblock = blockmanager.alloc_bufferblock()
 573         bufferblock.append("foo")
 574
 575         self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), "0123456789")
 576         self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), "foo")
 577
 578     def test_bufferblock_commit(self):
 579         mockkeep = mock.MagicMock()
 580         blockmanager = arvados.arvfile._BlockManager(mockkeep)
 581         bufferblock = blockmanager.alloc_bufferblock()
 582         bufferblock.owner = ArvadosFile(Collection(block_manager=blockmanager),
 583                                         [Range(bufferblock.blockid, 0, 3)], [Range(0, 0, 3)])
 584         bufferblock.owner._current_bblock = bufferblock
 585         bufferblock.append("foo")
 586         blockmanager.commit_all()
 587         self.assertTrue(mockkeep.put.called)
 588         self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 589         self.assertIsNone(bufferblock.buffer_view)
 590
 591
 592     def test_bufferblock_commit_with_error(self):
 593         mockkeep = mock.MagicMock()
 594         mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail")
 595         blockmanager = arvados.arvfile._BlockManager(mockkeep)
 596         bufferblock = blockmanager.alloc_bufferblock()
 597         bufferblock.owner = ArvadosFile(Collection(block_manager=blockmanager),
 598                                         [Range(bufferblock.blockid, 0, 3)], [Range(0, 0, 3)])
 599         bufferblock.owner._current_bblock = bufferblock
 600         bufferblock.append("foo")
 601         with self.assertRaises(arvados.errors.KeepWriteError) as err:
 602             blockmanager.commit_all()
 603         self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
 604         self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)