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_save_manifest_text(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())
 158             self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 159
 160             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.save_new(create_collection_record=False))
 161             self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 162
 163     def test_write_in_middle(self):
 164         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 165         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 166                              keep_client=keep) as c:
 167             writer = c.open("count.txt", "r+")
 168             self.assertEqual("0123456789", writer.readfrom(0, 13))
 169             writer.seek(3, os.SEEK_SET)
 170             writer.write("foo")
 171             self.assertEqual(writer.size(), 10)
 172             self.assertEqual("012foo6789", writer.readfrom(0, 13))
 173             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.manifest_text())
 174
 175     def test_write_at_end(self):
 176         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 177         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 178                              keep_client=keep) as c:
 179             writer = c.open("count.txt", "r+")
 180             self.assertEqual("0123456789", writer.readfrom(0, 13))
 181             writer.seek(7, os.SEEK_SET)
 182             writer.write("foo")
 183             self.assertEqual(writer.size(), 10)
 184             self.assertEqual("0123456foo", writer.readfrom(0, 13))
 185             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.manifest_text())
 186
 187     def test_write_across_segment_boundary(self):
 188         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 189         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
 190                              keep_client=keep) as c:
 191             writer = c.open("count.txt", "r+")
 192             self.assertEqual("012345678901234", writer.readfrom(0, 15))
 193             writer.seek(7, os.SEEK_SET)
 194             writer.write("foobar")
 195             self.assertEqual(writer.size(), 20)
 196             self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
 197             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.manifest_text())
 198
 199     def test_write_across_several_segments(self):
 200         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 201         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
 202                              keep_client=keep) as c:
 203             writer = c.open("count.txt", "r+")
 204             self.assertEqual("012301230123", writer.readfrom(0, 15))
 205             writer.seek(2, os.SEEK_SET)
 206             writer.write("abcdefg")
 207             self.assertEqual(writer.size(), 12)
 208             self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
 209             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.manifest_text())
 210
 211     def test_write_large(self):
 212         keep = ArvadosFileWriterTestCase.MockKeep({})
 213         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 214                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"},
 215                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 216                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"})
 217         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 218                              api_client=api, keep_client=keep) as c:
 219             writer = c.open("count.txt", "r+")
 220             text = ''.join(["0123456789" for a in xrange(0, 100)])
 221             for b in xrange(0, 100000):
 222                 writer.write(text)
 223             self.assertEqual(writer.size(), 100000000)
 224
 225             self.assertEqual(None, c.manifest_locator())
 226             self.assertEqual(True, c.modified())
 227             c.save_new("test_write_large")
 228             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 229             self.assertEqual(False, c.modified())
 230
 231     def test_rewrite_on_empty_file(self):
 232         keep = ArvadosFileWriterTestCase.MockKeep({})
 233         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 234                              keep_client=keep) as c:
 235             writer = c.open("count.txt", "r+")
 236             for b in xrange(0, 10):
 237                 writer.seek(0, os.SEEK_SET)
 238                 writer.write("0123456789")
 239
 240             self.assertEqual(writer.size(), 10)
 241             self.assertEqual("0123456789", writer.readfrom(0, 20))
 242             self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.manifest_text(strip=True))
 243             writer.flush()
 244             self.assertEqual(writer.size(), 10)
 245             self.assertEqual("0123456789", writer.readfrom(0, 20))
 246             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.manifest_text(strip=True))
 247
 248     def test_rewrite_append_existing_file(self):
 249         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 250         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 251                              keep_client=keep) as c:
 252             writer = c.open("count.txt", "r+")
 253             for b in xrange(0, 10):
 254                 writer.seek(10, os.SEEK_SET)
 255                 writer.write("abcdefghij")
 256
 257             self.assertEqual(writer.size(), 20)
 258             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 259             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.manifest_text(strip=True))
 260
 261             writer.arvadosfile.flush()
 262             self.assertEqual(writer.size(), 20)
 263             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 264             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.manifest_text(strip=True))
 265
 266     def test_rewrite_over_existing_file(self):
 267         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 268         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 269                              keep_client=keep) as c:
 270             writer = c.open("count.txt", "r+")
 271             for b in xrange(0, 10):
 272                 writer.seek(5, os.SEEK_SET)
 273                 writer.write("abcdefghij")
 274
 275             self.assertEqual(writer.size(), 15)
 276             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 277             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.manifest_text(strip=True))
 278
 279             writer.arvadosfile.flush()
 280
 281             self.assertEqual(writer.size(), 15)
 282             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 283             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.manifest_text(strip=True))
 284
 285     def test_write_large_rewrite(self):
 286         keep = ArvadosFileWriterTestCase.MockKeep({})
 287         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 288                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"},
 289                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 290                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"})
 291         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 292                              api_client=api, keep_client=keep) as c:
 293             writer = c.open("count.txt", "r+")
 294             text = ''.join(["0123456789" for a in xrange(0, 100)])
 295             for b in xrange(0, 100000):
 296                 writer.write(text)
 297             writer.seek(0, os.SEEK_SET)
 298             writer.write("foo")
 299             self.assertEqual(writer.size(), 100000000)
 300
 301             self.assertEqual(None, c.manifest_locator())
 302             self.assertEqual(True, c.modified())
 303             c.save_new("test_write_large")
 304             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 305             self.assertEqual(False, c.modified())
 306
 307     def test_create(self):
 308         keep = ArvadosFileWriterTestCase.MockKeep({})
 309         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 310                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 311                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 312                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 313         with Collection(api_client=api, keep_client=keep) as c:
 314             writer = c.open("count.txt", "w+")
 315             self.assertEqual(writer.size(), 0)
 316             writer.write("01234567")
 317             self.assertEqual(writer.size(), 8)
 318
 319             self.assertEqual(None, c.manifest_locator())
 320             self.assertEqual(True, c.modified())
 321             self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 322             c.save_new("test_create")
 323             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 324             self.assertEqual(False, c.modified())
 325             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 326
 327
 328     def test_create_subdir(self):
 329         keep = ArvadosFileWriterTestCase.MockKeep({})
 330         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 331                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 332                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 333                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 334         with Collection(api_client=api, keep_client=keep) as c:
 335             self.assertIsNone(c.api_response())
 336             writer = c.open("foo/bar/count.txt", "w+")
 337             writer.write("01234567")
 338             c.save_new("test_create")
 339             self.assertEqual(c.api_response(), api.response)
 340
 341     def test_overwrite(self):
 342         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 343         api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
 344                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 345                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 346                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 347         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 348                              api_client=api, keep_client=keep) as c:
 349             writer = c.open("count.txt", "w+")
 350             self.assertEqual(writer.size(), 0)
 351             writer.write("01234567")
 352             self.assertEqual(writer.size(), 8)
 353
 354             self.assertEqual(None, c.manifest_locator())
 355             self.assertEqual(True, c.modified())
 356             c.save_new("test_overwrite")
 357             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 358             self.assertEqual(False, c.modified())
 359
 360     def test_file_not_found(self):
 361         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 362             with self.assertRaises(IOError):
 363                 writer = c.open("nocount.txt", "r")
 364
 365     def test_cannot_open_directory(self):
 366         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 367             with self.assertRaises(IOError):
 368                 writer = c.open(".", "r")
 369
 370     def test_create_multiple(self):
 371         keep = ArvadosFileWriterTestCase.MockKeep({})
 372         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
 373                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"},
 374                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 375                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"})
 376         with Collection(api_client=api, keep_client=keep) as c:
 377             w1 = c.open("count1.txt", "w")
 378             w2 = c.open("count2.txt", "w")
 379             w1.write("01234567")
 380             w2.write("abcdefgh")
 381             self.assertEqual(w1.size(), 8)
 382             self.assertEqual(w2.size(), 8)
 383
 384             self.assertEqual(None, c.manifest_locator())
 385             self.assertEqual(True, c.modified())
 386             self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 387             c.save_new("test_create_multiple")
 388             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 389             self.assertEqual(False, c.modified())
 390             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 391
 392
 393 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
 394     class MockParent(object):
 395         class MockBlockMgr(object):
 396             def __init__(self, blocks, nocache):
 397                 self.blocks = blocks
 398                 self.nocache = nocache
 399
 400             def block_prefetch(self, loc):
 401                 pass
 402
 403             def get_block_contents(self, loc, num_retries=0, cache_only=False):
 404                 if self.nocache and cache_only:
 405                     return None
 406                 return self.blocks[loc]
 407
 408         def __init__(self, blocks, nocache):
 409             self.blocks = blocks
 410             self.nocache = nocache
 411             self.lock = arvados.arvfile.NoopLock()
 412
 413         def root_collection(self):
 414             return self
 415
 416         def _my_block_manager(self):
 417             return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
 418
 419
 420     def make_count_reader(self, nocache=False):
 421         stream = []
 422         n = 0
 423         blocks = {}
 424         for d in ['01234', '34567', '67890']:
 425             loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d))
 426             blocks[loc] = d
 427             stream.append(Range(loc, n, len(d)))
 428             n += len(d)
 429         af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
 430         return ArvadosFileReader(af, "count.txt")
 431
 432     def test_read_returns_first_block(self):
 433         # read() calls will be aligned on block boundaries - see #3663.
 434         sfile = self.make_count_reader(nocache=True)
 435         self.assertEqual('123', sfile.read(10))
 436
 437     def test_successive_reads(self):
 438         sfile = self.make_count_reader(nocache=True)
 439         for expect in ['123', '456', '789', '']:
 440             self.assertEqual(expect, sfile.read(10))
 441
 442     def test_tell_after_block_read(self):
 443         sfile = self.make_count_reader(nocache=True)
 444         sfile.read(5)
 445         self.assertEqual(3, sfile.tell())
 446
 447     def test_prefetch(self):
 448         keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
 449         with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
 450             r = c.open("count.txt", "r")
 451             self.assertEqual("0123", r.read(4))
 452         self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
 453         self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
 454
 455     def test__eq__from_manifest(self):
 456         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 457             with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
 458                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 459                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 460
 461     def test__eq__from_writes(self):
 462         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 463             with Collection() as c2:
 464                 with c2.open("count1.txt", "w") as f:
 465                     f.write("0123456789")
 466
 467                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 468                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 469
 470     def test__ne__(self):
 471         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 472             with Collection() as c2:
 473                 with c2.open("count1.txt", "w") as f:
 474                     f.write("1234567890")
 475
 476                 self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
 477                 self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
 478
 479
 480 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
 481     def reader_for(self, coll_name, **kwargs):
 482         stream = []
 483         segments = []
 484         n = 0
 485         for d in self.manifest_for(coll_name).split():
 486             try:
 487                 k = KeepLocator(d)
 488                 segments.append(Range(n, n, k.size))
 489                 stream.append(Range(d, n, k.size))
 490                 n += k.size
 491             except ValueError:
 492                 pass
 493
 494         blockmanager = arvados.arvfile._BlockManager(self.keep_client())
 495         blockmanager.prefetch_enabled = False
 496         col = Collection(keep_client=self.keep_client(), block_manager=blockmanager)
 497         af = ArvadosFile(col,
 498                          stream=stream,
 499                          segments=segments)
 500         return ArvadosFileReader(af, "test", **kwargs)
 501
 502     def read_for_test(self, reader, byte_count, **kwargs):
 503         return reader.read(byte_count, **kwargs)
 504
 505
 506 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
 507     def read_for_test(self, reader, byte_count, **kwargs):
 508         return reader.readfrom(0, byte_count, **kwargs)
 509
 510
 511 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
 512     def read_for_test(self, reader, byte_count, **kwargs):
 513         return ''.join(reader.readall(**kwargs))
 514
 515
 516 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
 517     def read_for_test(self, reader, byte_count, **kwargs):
 518         return ''.join(reader.readall_decompressed(**kwargs))
 519
 520
 521 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
 522     def read_for_test(self, reader, byte_count, **kwargs):
 523         return ''.join(reader.readlines(**kwargs))
 524
 525 class BlockManagerTest(unittest.TestCase):
 526     def test_bufferblock_append(self):
 527         keep = ArvadosFileWriterTestCase.MockKeep({})
 528         blockmanager = arvados.arvfile._BlockManager(keep)
 529         bufferblock = blockmanager.alloc_bufferblock()
 530         bufferblock.append("foo")
 531
 532         self.assertEqual(bufferblock.size(), 3)
 533         self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 534         self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 535
 536         bufferblock.append("bar")
 537
 538         self.assertEqual(bufferblock.size(), 6)
 539         self.assertEqual(bufferblock.buffer_view[0:6], "foobar")
 540         self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
 541
 542         bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 543         with self.assertRaises(arvados.errors.AssertionError):
 544             bufferblock.append("bar")
 545
 546     def test_bufferblock_dup(self):
 547         keep = ArvadosFileWriterTestCase.MockKeep({})
 548         blockmanager = arvados.arvfile._BlockManager(keep)
 549         bufferblock = blockmanager.alloc_bufferblock()
 550         bufferblock.append("foo")
 551
 552         self.assertEqual(bufferblock.size(), 3)
 553         self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 554         self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 555         bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 556
 557         bufferblock2 = blockmanager.dup_block(bufferblock, None)
 558         self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
 559
 560         bufferblock2.append("bar")
 561
 562         self.assertEqual(bufferblock2.size(), 6)
 563         self.assertEqual(bufferblock2.buffer_view[0:6], "foobar")
 564         self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
 565
 566         self.assertEqual(bufferblock.size(), 3)
 567         self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 568         self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 569
 570     def test_bufferblock_get(self):
 571         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 572         blockmanager = arvados.arvfile._BlockManager(keep)
 573         bufferblock = blockmanager.alloc_bufferblock()
 574         bufferblock.append("foo")
 575
 576         self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), "0123456789")
 577         self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), "foo")
 578
 579     def test_bufferblock_commit(self):
 580         mockkeep = mock.MagicMock()
 581         blockmanager = arvados.arvfile._BlockManager(mockkeep)
 582         bufferblock = blockmanager.alloc_bufferblock()
 583         bufferblock.owner = ArvadosFile(Collection(block_manager=blockmanager),
 584                                         [Range(bufferblock.blockid, 0, 3)], [Range(0, 0, 3)])
 585         bufferblock.owner._current_bblock = bufferblock
 586         bufferblock.append("foo")
 587         blockmanager.commit_all()
 588         self.assertTrue(mockkeep.put.called)
 589         self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 590         self.assertIsNone(bufferblock.buffer_view)
 591
 592
 593     def test_bufferblock_commit_with_error(self):
 594         mockkeep = mock.MagicMock()
 595         mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail")
 596         blockmanager = arvados.arvfile._BlockManager(mockkeep)
 597         bufferblock = blockmanager.alloc_bufferblock()
 598         bufferblock.owner = ArvadosFile(Collection(block_manager=blockmanager),
 599                                         [Range(bufferblock.blockid, 0, 3)], [Range(0, 0, 3)])
 600         bufferblock.owner._current_bblock = bufferblock
 601         bufferblock.append("foo")
 602         with self.assertRaises(arvados.errors.KeepWriteError) as err:
 603             blockmanager.commit_all()
 604         self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
 605         self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)