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 import time
  11
  12 import arvados
  13 from arvados._ranges import Range
  14 from arvados.keep import KeepLocator
  15 from arvados.collection import Collection, CollectionReader
  16 from arvados.arvfile import ArvadosFile, ArvadosFileReader
  17
  18 import arvados_testutil as tutil
  19 from test_stream import StreamFileReaderTestCase, StreamRetryTestMixin
  20
  21 class ArvadosFileWriterTestCase(unittest.TestCase):
  22     class MockKeep(object):
  23         def __init__(self, blocks):
  24             self.blocks = blocks
  25             self.requests = []
  26         def get(self, locator, num_retries=0):
  27             self.requests.append(locator)
  28             return self.blocks.get(locator)
  29         def get_from_cache(self, locator):
  30             self.requests.append(locator)
  31             return self.blocks.get(locator)
  32         def put(self, data, num_retries=None):
  33             pdh = "%s+%i" % (hashlib.md5(data).hexdigest(), len(data))
  34             self.blocks[pdh] = str(data)
  35             return pdh
  36
  37     class MockApi(object):
  38         def __init__(self, b, r):
  39             self.body = b
  40             self.response = r
  41         class MockCollections(object):
  42             def __init__(self, b, r):
  43                 self.body = b
  44                 self.response = r
  45             class Execute(object):
  46                 def __init__(self, r):
  47                     self.response = r
  48                 def execute(self, num_retries=None):
  49                     return self.response
  50             def create(self, ensure_unique_name=False, body=None):
  51                 if body != self.body:
  52                     raise Exception("Body %s does not match expectation %s" % (body, self.body))
  53                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  54             def update(self, uuid=None, body=None):
  55                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  56         def collections(self):
  57             return ArvadosFileWriterTestCase.MockApi.MockCollections(self.body, self.response)
  58
  59
  60     def test_truncate(self):
  61         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
  62         api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate",
  63                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"},
  64                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
  65                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"})
  66         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
  67                              api_client=api, keep_client=keep) as c:
  68             writer = c.open("count.txt", "r+")
  69             self.assertEqual(writer.size(), 10)
  70             self.assertEqual("0123456789", writer.read(12))
  71
  72             writer.truncate(8)
  73
  74             # Make sure reading off the end doesn't break
  75             self.assertEqual("", writer.read(12))
  76
  77             self.assertEqual(writer.size(), 8)
  78             writer.seek(0, os.SEEK_SET)
  79             self.assertEqual("01234567", writer.read(12))
  80
  81             self.assertIsNone(c.manifest_locator())
  82             self.assertTrue(c.modified())
  83             c.save_new("test_truncate")
  84             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
  85             self.assertFalse(c.modified())
  86
  87     def test_write_to_end(self):
  88         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
  89         api = ArvadosFileWriterTestCase.MockApi({"name":"test_append",
  90                                                  "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"},
  91                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
  92                                                  "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"})
  93         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
  94                              api_client=api, keep_client=keep) as c:
  95             writer = c.open("count.txt", "r+")
  96             self.assertEqual(writer.size(), 10)
  97
  98             writer.seek(5, os.SEEK_SET)
  99             self.assertEqual("56789", writer.read(8))
 100
 101             writer.seek(10, os.SEEK_SET)
 102             writer.write("foo")
 103             self.assertEqual(writer.size(), 13)
 104
 105             writer.seek(5, os.SEEK_SET)
 106             self.assertEqual("56789foo", writer.read(8))
 107
 108             self.assertIsNone(c.manifest_locator())
 109             self.assertTrue(c.modified())
 110             self.assertIsNone(keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 111
 112             c.save_new("test_append")
 113             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 114             self.assertFalse(c.modified())
 115             self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 116
 117
 118     def test_append(self):
 119         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 120         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep)
 121         writer = c.open("count.txt", "a+")
 122         self.assertEqual(writer.read(20), "0123456789")
 123         writer.seek(0, os.SEEK_SET)
 124
 125         writer.write("hello")
 126         self.assertEqual(writer.read(20), "0123456789hello")
 127         writer.seek(0, os.SEEK_SET)
 128
 129         writer.write("world")
 130         self.assertEqual(writer.read(20), "0123456789helloworld")
 131
 132         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.portable_manifest_text())
 133
 134     def test_write_at_beginning(self):
 135         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 136         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 137                              keep_client=keep) as c:
 138             writer = c.open("count.txt", "r+")
 139             self.assertEqual("0123456789", writer.readfrom(0, 13))
 140             writer.seek(0, os.SEEK_SET)
 141             writer.write("foo")
 142             self.assertEqual(writer.size(), 10)
 143             self.assertEqual("foo3456789", writer.readfrom(0, 13))
 144             self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", c.portable_manifest_text())
 145
 146     def test_write_empty(self):
 147         keep = ArvadosFileWriterTestCase.MockKeep({})
 148         with Collection(keep_client=keep) as c:
 149             writer = c.open("count.txt", "w")
 150             self.assertEqual(writer.size(), 0)
 151             self.assertEqual(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n", c.portable_manifest_text())
 152
 153     def test_save_manifest_text(self):
 154         keep = ArvadosFileWriterTestCase.MockKeep({})
 155         with Collection(keep_client=keep) as c:
 156             writer = c.open("count.txt", "w")
 157             writer.write("0123456789")
 158             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
 159             self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 160
 161             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.save_new(create_collection_record=False))
 162             self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 163
 164     def test_get_manifest_text_commits(self):
 165          keep = ArvadosFileWriterTestCase.MockKeep({})
 166          with Collection(keep_client=keep) as c:
 167              writer = c.open("count.txt", "w")
 168              writer.write("0123456789")
 169              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
 170              self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 171              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text())
 172              self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 173
 174
 175     def test_write_in_middle(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(3, os.SEEK_SET)
 182             writer.write("foo")
 183             self.assertEqual(writer.size(), 10)
 184             self.assertEqual("012foo6789", writer.readfrom(0, 13))
 185             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.portable_manifest_text())
 186
 187     def test_write_at_end(self):
 188         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 189         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 190                              keep_client=keep) as c:
 191             writer = c.open("count.txt", "r+")
 192             self.assertEqual("0123456789", writer.readfrom(0, 13))
 193             writer.seek(7, os.SEEK_SET)
 194             writer.write("foo")
 195             self.assertEqual(writer.size(), 10)
 196             self.assertEqual("0123456foo", writer.readfrom(0, 13))
 197             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text())
 198
 199     def test_write_across_segment_boundary(self):
 200         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 201         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
 202                              keep_client=keep) as c:
 203             writer = c.open("count.txt", "r+")
 204             self.assertEqual("012345678901234", writer.readfrom(0, 15))
 205             writer.seek(7, os.SEEK_SET)
 206             writer.write("foobar")
 207             self.assertEqual(writer.size(), 20)
 208             self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
 209             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text())
 210
 211     def test_write_across_several_segments(self):
 212         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 213         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
 214                              keep_client=keep) as c:
 215             writer = c.open("count.txt", "r+")
 216             self.assertEqual("012301230123", writer.readfrom(0, 15))
 217             writer.seek(2, os.SEEK_SET)
 218             writer.write("abcdefg")
 219             self.assertEqual(writer.size(), 12)
 220             self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
 221             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text())
 222
 223     def test_write_large(self):
 224         keep = ArvadosFileWriterTestCase.MockKeep({})
 225         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 226                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"},
 227                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 228                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"})
 229         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 230                              api_client=api, keep_client=keep) as c:
 231             writer = c.open("count.txt", "r+")
 232             text = "0123456789" * 100
 233             for b in xrange(0, 100000):
 234                 writer.write(text)
 235             self.assertEqual(writer.size(), 100000000)
 236
 237             self.assertIsNone(c.manifest_locator())
 238             self.assertTrue(c.modified())
 239             c.save_new("test_write_large")
 240             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 241             self.assertFalse(c.modified())
 242
 243
 244     def test_large_write(self):
 245         keep = ArvadosFileWriterTestCase.MockKeep({})
 246         api = ArvadosFileWriterTestCase.MockApi({}, {})
 247         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 248                              api_client=api, keep_client=keep) as c:
 249             writer = c.open("count.txt", "r+")
 250             self.assertEqual(writer.size(), 0)
 251
 252             text = "0123456789"
 253             writer.write(text)
 254             text = "0123456789" * 9999999
 255             writer.write(text)
 256             self.assertEqual(writer.size(), 100000000)
 257
 258             self.assertEqual(c.manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n")
 259
 260     def test_rewrite_on_empty_file(self):
 261         keep = ArvadosFileWriterTestCase.MockKeep({})
 262         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 263                              keep_client=keep) as c:
 264             writer = c.open("count.txt", "r+")
 265             for b in xrange(0, 10):
 266                 writer.seek(0, os.SEEK_SET)
 267                 writer.write("0123456789")
 268
 269             self.assertEqual(writer.size(), 10)
 270             self.assertEqual("0123456789", writer.readfrom(0, 20))
 271             self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.portable_manifest_text())
 272             writer.flush()
 273             self.assertEqual(writer.size(), 10)
 274             self.assertEqual("0123456789", writer.readfrom(0, 20))
 275             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.portable_manifest_text())
 276
 277     def test_rewrite_append_existing_file(self):
 278         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 279         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 280                              keep_client=keep) as c:
 281             writer = c.open("count.txt", "r+")
 282             for b in xrange(0, 10):
 283                 writer.seek(10, os.SEEK_SET)
 284                 writer.write("abcdefghij")
 285
 286             self.assertEqual(writer.size(), 20)
 287             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 288             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 289
 290             writer.arvadosfile.flush()
 291             self.assertEqual(writer.size(), 20)
 292             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 293             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.portable_manifest_text())
 294
 295     def test_rewrite_over_existing_file(self):
 296         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 297         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 298                              keep_client=keep) as c:
 299             writer = c.open("count.txt", "r+")
 300             for b in xrange(0, 10):
 301                 writer.seek(5, os.SEEK_SET)
 302                 writer.write("abcdefghij")
 303
 304             self.assertEqual(writer.size(), 15)
 305             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 306             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 307
 308             writer.arvadosfile.flush()
 309
 310             self.assertEqual(writer.size(), 15)
 311             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 312             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.portable_manifest_text())
 313
 314     def test_write_large_rewrite(self):
 315         keep = ArvadosFileWriterTestCase.MockKeep({})
 316         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 317                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"},
 318                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 319                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"})
 320         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 321                              api_client=api, keep_client=keep) as c:
 322             writer = c.open("count.txt", "r+")
 323             text = ''.join(["0123456789" for a in xrange(0, 100)])
 324             for b in xrange(0, 100000):
 325                 writer.write(text)
 326             writer.seek(0, os.SEEK_SET)
 327             writer.write("foo")
 328             self.assertEqual(writer.size(), 100000000)
 329
 330             self.assertIsNone(c.manifest_locator())
 331             self.assertTrue(c.modified())
 332             c.save_new("test_write_large")
 333             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 334             self.assertFalse(c.modified())
 335
 336     def test_create(self):
 337         keep = ArvadosFileWriterTestCase.MockKeep({})
 338         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 339                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 340                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 341                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 342         with Collection(api_client=api, keep_client=keep) as c:
 343             writer = c.open("count.txt", "w+")
 344             self.assertEqual(writer.size(), 0)
 345             writer.write("01234567")
 346             self.assertEqual(writer.size(), 8)
 347
 348             self.assertIsNone(c.manifest_locator())
 349             self.assertTrue(c.modified())
 350             self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 351             c.save_new("test_create")
 352             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 353             self.assertFalse(c.modified())
 354             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 355
 356
 357     def test_create_subdir(self):
 358         keep = ArvadosFileWriterTestCase.MockKeep({})
 359         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 360                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 361                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 362                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 363         with Collection(api_client=api, keep_client=keep) as c:
 364             self.assertIsNone(c.api_response())
 365             writer = c.open("foo/bar/count.txt", "w+")
 366             writer.write("01234567")
 367             self.assertFalse(c.committed())
 368             c.save_new("test_create")
 369             self.assertTrue(c.committed())
 370             self.assertEqual(c.api_response(), api.response)
 371
 372     def test_overwrite(self):
 373         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 374         api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
 375                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 376                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 377                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 378         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 379                              api_client=api, keep_client=keep) as c:
 380             writer = c.open("count.txt", "w+")
 381             self.assertEqual(writer.size(), 0)
 382             writer.write("01234567")
 383             self.assertEqual(writer.size(), 8)
 384
 385             self.assertIsNone(c.manifest_locator())
 386             self.assertTrue(c.modified())
 387             c.save_new("test_overwrite")
 388             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 389             self.assertFalse(c.modified())
 390
 391     def test_file_not_found(self):
 392         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 393             with self.assertRaises(IOError):
 394                 writer = c.open("nocount.txt", "r")
 395
 396     def test_cannot_open_directory(self):
 397         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 398             with self.assertRaises(IOError):
 399                 writer = c.open(".", "r")
 400
 401     def test_create_multiple(self):
 402         keep = ArvadosFileWriterTestCase.MockKeep({})
 403         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
 404                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"},
 405                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 406                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"})
 407         with Collection(api_client=api, keep_client=keep) as c:
 408             w1 = c.open("count1.txt", "w")
 409             w2 = c.open("count2.txt", "w")
 410             w1.write("01234567")
 411             w2.write("abcdefgh")
 412             self.assertEqual(w1.size(), 8)
 413             self.assertEqual(w2.size(), 8)
 414
 415             self.assertIsNone(c.manifest_locator())
 416             self.assertTrue(c.modified())
 417             self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 418             c.save_new("test_create_multiple")
 419             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 420             self.assertFalse(c.modified())
 421             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 422
 423
 424 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
 425     class MockParent(object):
 426         class MockBlockMgr(object):
 427             def __init__(self, blocks, nocache):
 428                 self.blocks = blocks
 429                 self.nocache = nocache
 430
 431             def block_prefetch(self, loc):
 432                 pass
 433
 434             def get_block_contents(self, loc, num_retries=0, cache_only=False):
 435                 if self.nocache and cache_only:
 436                     return None
 437                 return self.blocks[loc]
 438
 439         def __init__(self, blocks, nocache):
 440             self.blocks = blocks
 441             self.nocache = nocache
 442             self.lock = arvados.arvfile.NoopLock()
 443
 444         def root_collection(self):
 445             return self
 446
 447         def _my_block_manager(self):
 448             return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
 449
 450
 451     def make_count_reader(self, nocache=False):
 452         stream = []
 453         n = 0
 454         blocks = {}
 455         for d in ['01234', '34567', '67890']:
 456             loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d))
 457             blocks[loc] = d
 458             stream.append(Range(loc, n, len(d)))
 459             n += len(d)
 460         af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), "count.txt", stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
 461         return ArvadosFileReader(af)
 462
 463     def test_read_block_crossing_behavior(self):
 464         # read() needs to return all the data requested if possible, even if it
 465         # crosses uncached blocks: https://arvados.org/issues/5856
 466         sfile = self.make_count_reader(nocache=True)
 467         self.assertEqual('12345678', sfile.read(8))
 468
 469     def test_successive_reads(self):
 470         # Override StreamFileReaderTestCase.test_successive_reads
 471         sfile = self.make_count_reader(nocache=True)
 472         self.assertEqual('1234', sfile.read(4))
 473         self.assertEqual('5678', sfile.read(4))
 474         self.assertEqual('9', sfile.read(4))
 475         self.assertEqual('', sfile.read(4))
 476
 477     def test_tell_after_block_read(self):
 478         # Override StreamFileReaderTestCase.test_tell_after_block_read
 479         sfile = self.make_count_reader(nocache=True)
 480         self.assertEqual('12345678', sfile.read(8))
 481         self.assertEqual(8, sfile.tell())
 482
 483     def test_prefetch(self):
 484         keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
 485         with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
 486             r = c.open("count.txt", "r")
 487             self.assertEqual("0123", r.read(4))
 488         self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
 489         self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
 490
 491     def test__eq__from_manifest(self):
 492         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 493             with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
 494                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 495                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 496
 497     def test__eq__from_writes(self):
 498         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 499             with Collection() as c2:
 500                 f = c2.open("count1.txt", "w")
 501                 f.write("0123456789")
 502
 503                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 504                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 505
 506     def test__ne__(self):
 507         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 508             with Collection() as c2:
 509                 f = c2.open("count1.txt", "w")
 510                 f.write("1234567890")
 511
 512                 self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
 513                 self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
 514
 515
 516 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
 517     def reader_for(self, coll_name, **kwargs):
 518         stream = []
 519         segments = []
 520         n = 0
 521         for d in self.manifest_for(coll_name).split():
 522             try:
 523                 k = KeepLocator(d)
 524                 segments.append(Range(n, n, k.size))
 525                 stream.append(Range(d, n, k.size))
 526                 n += k.size
 527             except ValueError:
 528                 pass
 529
 530         blockmanager = arvados.arvfile._BlockManager(self.keep_client())
 531         blockmanager.prefetch_enabled = False
 532         col = Collection(keep_client=self.keep_client(), block_manager=blockmanager)
 533         af = ArvadosFile(col, "test",
 534                          stream=stream,
 535                          segments=segments)
 536         return ArvadosFileReader(af, **kwargs)
 537
 538     def read_for_test(self, reader, byte_count, **kwargs):
 539         return reader.read(byte_count, **kwargs)
 540
 541
 542 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
 543     def read_for_test(self, reader, byte_count, **kwargs):
 544         return reader.readfrom(0, byte_count, **kwargs)
 545
 546
 547 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
 548     def read_for_test(self, reader, byte_count, **kwargs):
 549         return ''.join(reader.readall(**kwargs))
 550
 551
 552 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
 553     def read_for_test(self, reader, byte_count, **kwargs):
 554         return ''.join(reader.readall_decompressed(**kwargs))
 555
 556
 557 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
 558     def read_for_test(self, reader, byte_count, **kwargs):
 559         return ''.join(reader.readlines(**kwargs))
 560
 561 class BlockManagerTest(unittest.TestCase):
 562     def test_bufferblock_append(self):
 563         keep = ArvadosFileWriterTestCase.MockKeep({})
 564         with arvados.arvfile._BlockManager(keep) as blockmanager:
 565             bufferblock = blockmanager.alloc_bufferblock()
 566             bufferblock.append("foo")
 567
 568             self.assertEqual(bufferblock.size(), 3)
 569             self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 570             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 571
 572             bufferblock.append("bar")
 573
 574             self.assertEqual(bufferblock.size(), 6)
 575             self.assertEqual(bufferblock.buffer_view[0:6], "foobar")
 576             self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
 577
 578             bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 579             with self.assertRaises(arvados.errors.AssertionError):
 580                 bufferblock.append("bar")
 581
 582     def test_bufferblock_dup(self):
 583         keep = ArvadosFileWriterTestCase.MockKeep({})
 584         with arvados.arvfile._BlockManager(keep) as blockmanager:
 585             bufferblock = blockmanager.alloc_bufferblock()
 586             bufferblock.append("foo")
 587
 588             self.assertEqual(bufferblock.size(), 3)
 589             self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 590             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 591             bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 592
 593             bufferblock2 = blockmanager.dup_block(bufferblock, None)
 594             self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
 595
 596             bufferblock2.append("bar")
 597
 598             self.assertEqual(bufferblock2.size(), 6)
 599             self.assertEqual(bufferblock2.buffer_view[0:6], "foobar")
 600             self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
 601
 602             self.assertEqual(bufferblock.size(), 3)
 603             self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 604             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 605
 606     def test_bufferblock_get(self):
 607         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 608         with arvados.arvfile._BlockManager(keep) as blockmanager:
 609             bufferblock = blockmanager.alloc_bufferblock()
 610             bufferblock.append("foo")
 611
 612             self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), "0123456789")
 613             self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), "foo")
 614
 615     def test_bufferblock_commit(self):
 616         mockkeep = mock.MagicMock()
 617         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 618             bufferblock = blockmanager.alloc_bufferblock()
 619             bufferblock.owner = mock.MagicMock()
 620             def flush(sync=None):
 621                 blockmanager.commit_bufferblock(bufferblock, sync)
 622             bufferblock.owner.flush.side_effect = flush
 623             bufferblock.append("foo")
 624             blockmanager.commit_all()
 625             self.assertTrue(bufferblock.owner.flush.called)
 626             self.assertTrue(mockkeep.put.called)
 627             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 628             self.assertIsNone(bufferblock.buffer_view)
 629
 630     def test_bufferblock_commit_pending(self):
 631         # Test for bug #7225
 632         mockkeep = mock.MagicMock()
 633         mockkeep.put.side_effect = lambda x: time.sleep(1)
 634         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 635             bufferblock = blockmanager.alloc_bufferblock()
 636             bufferblock.append("foo")
 637
 638             blockmanager.commit_bufferblock(bufferblock, False)
 639             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)
 640
 641             blockmanager.commit_bufferblock(bufferblock, True)
 642             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 643
 644
 645     def test_bufferblock_commit_with_error(self):
 646         mockkeep = mock.MagicMock()
 647         mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail")
 648         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 649             bufferblock = blockmanager.alloc_bufferblock()
 650             bufferblock.owner = mock.MagicMock()
 651             def flush(sync=None):
 652                 blockmanager.commit_bufferblock(bufferblock, sync)
 653             bufferblock.owner.flush.side_effect = flush
 654             bufferblock.append("foo")
 655             with self.assertRaises(arvados.errors.KeepWriteError) as err:
 656                 blockmanager.commit_all()
 657             self.assertTrue(bufferblock.owner.flush.called)
 658             self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
 659             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.ERROR)