sdk/python/tests/test_arvfile.py

   1 #!/usr/bin/env python
   2
   3 import bz2
   4 import datetime
   5 import gzip
   6 import io
   7 import mock
   8 import os
   9 import unittest
  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, copies=None):
  33             pdh = tutil.str_keep_locator(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             self._schema = ArvadosFileWriterTestCase.MockApi.MockSchema()
  42             self._rootDesc = {}
  43         class MockSchema(object):
  44             def __init__(self):
  45                 self.schemas = {'Collection': {'properties': {'replication_desired': {'type':'integer'}}}}
  46         class MockCollections(object):
  47             def __init__(self, b, r):
  48                 self.body = b
  49                 self.response = r
  50             class Execute(object):
  51                 def __init__(self, r):
  52                     self.response = r
  53                 def execute(self, num_retries=None):
  54                     return self.response
  55             def create(self, ensure_unique_name=False, body=None):
  56                 if body != self.body:
  57                     raise Exception("Body %s does not match expectation %s" % (body, self.body))
  58                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  59             def update(self, uuid=None, body=None):
  60                 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
  61         def collections(self):
  62             return ArvadosFileWriterTestCase.MockApi.MockCollections(self.body, self.response)
  63
  64
  65     def test_truncate(self):
  66         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
  67         api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate",
  68                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
  69                                                  "replication_desired":None},
  70                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
  71                                                  "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"})
  72         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
  73                              api_client=api, keep_client=keep) as c:
  74             writer = c.open("count.txt", "r+")
  75             self.assertEqual(writer.size(), 10)
  76             self.assertEqual("0123456789", writer.read(12))
  77
  78             writer.truncate(8)
  79
  80             # Make sure reading off the end doesn't break
  81             self.assertEqual("", writer.read(12))
  82
  83             self.assertEqual(writer.size(), 8)
  84             writer.seek(0, os.SEEK_SET)
  85             self.assertEqual("01234567", writer.read(12))
  86
  87             self.assertIsNone(c.manifest_locator())
  88             self.assertTrue(c.modified())
  89             c.save_new("test_truncate")
  90             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
  91             self.assertFalse(c.modified())
  92
  93     def test_write_to_end(self):
  94         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
  95         api = ArvadosFileWriterTestCase.MockApi({"name":"test_append",
  96                                                  "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
  97                                                  "replication_desired":None},
  98                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
  99                                                  "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"})
 100         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 101                              api_client=api, keep_client=keep) as c:
 102             writer = c.open("count.txt", "r+")
 103             self.assertEqual(writer.size(), 10)
 104
 105             writer.seek(5, os.SEEK_SET)
 106             self.assertEqual("56789", writer.read(8))
 107
 108             writer.seek(10, os.SEEK_SET)
 109             writer.write("foo")
 110             self.assertEqual(writer.size(), 13)
 111
 112             writer.seek(5, os.SEEK_SET)
 113             self.assertEqual("56789foo", writer.read(8))
 114
 115             self.assertIsNone(c.manifest_locator())
 116             self.assertTrue(c.modified())
 117             self.assertIsNone(keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 118
 119             c.save_new("test_append")
 120             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 121             self.assertFalse(c.modified())
 122             self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
 123
 124
 125     def test_append(self):
 126         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 127         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep)
 128         writer = c.open("count.txt", "a+")
 129         self.assertEqual(writer.read(20), "0123456789")
 130         writer.seek(0, os.SEEK_SET)
 131
 132         writer.write("hello")
 133         self.assertEqual(writer.read(20), "0123456789hello")
 134         writer.seek(0, os.SEEK_SET)
 135
 136         writer.write("world")
 137         self.assertEqual(writer.read(20), "0123456789helloworld")
 138
 139         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.portable_manifest_text())
 140
 141     def test_write_at_beginning(self):
 142         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 143         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 144                              keep_client=keep) as c:
 145             writer = c.open("count.txt", "r+")
 146             self.assertEqual("0123456789", writer.readfrom(0, 13))
 147             writer.seek(0, os.SEEK_SET)
 148             writer.write("foo")
 149             self.assertEqual(writer.size(), 10)
 150             self.assertEqual("foo3456789", writer.readfrom(0, 13))
 151             self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", c.portable_manifest_text())
 152
 153     def test_write_empty(self):
 154         keep = ArvadosFileWriterTestCase.MockKeep({})
 155         with Collection(keep_client=keep) as c:
 156             writer = c.open("count.txt", "w")
 157             self.assertEqual(writer.size(), 0)
 158             self.assertEqual(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n", c.portable_manifest_text())
 159
 160     def test_save_manifest_text(self):
 161         keep = ArvadosFileWriterTestCase.MockKeep({})
 162         with Collection(keep_client=keep) as c:
 163             writer = c.open("count.txt", "w")
 164             writer.write("0123456789")
 165             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
 166             self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 167
 168             self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.save_new(create_collection_record=False))
 169             self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 170
 171     def test_get_manifest_text_commits(self):
 172          keep = ArvadosFileWriterTestCase.MockKeep({})
 173          with Collection(keep_client=keep) as c:
 174              writer = c.open("count.txt", "w")
 175              writer.write("0123456789")
 176              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
 177              self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 178              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text())
 179              self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 180
 181
 182     def test_write_in_middle(self):
 183         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 184         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 185                              keep_client=keep) as c:
 186             writer = c.open("count.txt", "r+")
 187             self.assertEqual("0123456789", writer.readfrom(0, 13))
 188             writer.seek(3, os.SEEK_SET)
 189             writer.write("foo")
 190             self.assertEqual(writer.size(), 10)
 191             self.assertEqual("012foo6789", writer.readfrom(0, 13))
 192             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.portable_manifest_text())
 193
 194     def test_write_at_end(self):
 195         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 196         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 197                              keep_client=keep) as c:
 198             writer = c.open("count.txt", "r+")
 199             self.assertEqual("0123456789", writer.readfrom(0, 13))
 200             writer.seek(7, os.SEEK_SET)
 201             writer.write("foo")
 202             self.assertEqual(writer.size(), 10)
 203             self.assertEqual("0123456foo", writer.readfrom(0, 13))
 204             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text())
 205
 206     def test_write_across_segment_boundary(self):
 207         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 208         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
 209                              keep_client=keep) as c:
 210             writer = c.open("count.txt", "r+")
 211             self.assertEqual("012345678901234", writer.readfrom(0, 15))
 212             writer.seek(7, os.SEEK_SET)
 213             writer.write("foobar")
 214             self.assertEqual(writer.size(), 20)
 215             self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
 216             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text())
 217
 218     def test_write_across_several_segments(self):
 219         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 220         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
 221                              keep_client=keep) as c:
 222             writer = c.open("count.txt", "r+")
 223             self.assertEqual("012301230123", writer.readfrom(0, 15))
 224             writer.seek(2, os.SEEK_SET)
 225             writer.write("abcdefg")
 226             self.assertEqual(writer.size(), 12)
 227             self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
 228             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text())
 229
 230     def test_write_large(self):
 231         keep = ArvadosFileWriterTestCase.MockKeep({})
 232         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 233                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
 234                                                  "replication_desired":None},
 235                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 236                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"})
 237         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 238                              api_client=api, keep_client=keep) as c:
 239             writer = c.open("count.txt", "r+")
 240             text = "0123456789" * 100
 241             for b in xrange(0, 100000):
 242                 writer.write(text)
 243             self.assertEqual(writer.size(), 100000000)
 244
 245             self.assertIsNone(c.manifest_locator())
 246             self.assertTrue(c.modified())
 247             c.save_new("test_write_large")
 248             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 249             self.assertFalse(c.modified())
 250
 251
 252     def test_large_write(self):
 253         keep = ArvadosFileWriterTestCase.MockKeep({})
 254         api = ArvadosFileWriterTestCase.MockApi({}, {})
 255         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 256                              api_client=api, keep_client=keep) as c:
 257             writer = c.open("count.txt", "r+")
 258             self.assertEqual(writer.size(), 0)
 259
 260             text = "0123456789"
 261             writer.write(text)
 262             text = "0123456789" * 9999999
 263             writer.write(text)
 264             self.assertEqual(writer.size(), 100000000)
 265
 266             self.assertEqual(c.manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n")
 267
 268     def test_rewrite_on_empty_file(self):
 269         keep = ArvadosFileWriterTestCase.MockKeep({})
 270         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 271                              keep_client=keep) as c:
 272             writer = c.open("count.txt", "r+")
 273             for b in xrange(0, 10):
 274                 writer.seek(0, os.SEEK_SET)
 275                 writer.write("0123456789")
 276
 277             self.assertEqual(writer.size(), 10)
 278             self.assertEqual("0123456789", writer.readfrom(0, 20))
 279             self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.portable_manifest_text())
 280             writer.flush()
 281             self.assertEqual(writer.size(), 10)
 282             self.assertEqual("0123456789", writer.readfrom(0, 20))
 283             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.portable_manifest_text())
 284
 285     def test_rewrite_append_existing_file(self):
 286         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 287         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 288                              keep_client=keep) as c:
 289             writer = c.open("count.txt", "r+")
 290             for b in xrange(0, 10):
 291                 writer.seek(10, os.SEEK_SET)
 292                 writer.write("abcdefghij")
 293
 294             self.assertEqual(writer.size(), 20)
 295             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 296             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 297
 298             writer.arvadosfile.flush()
 299             self.assertEqual(writer.size(), 20)
 300             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 301             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.portable_manifest_text())
 302
 303     def test_rewrite_over_existing_file(self):
 304         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 305         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 306                              keep_client=keep) as c:
 307             writer = c.open("count.txt", "r+")
 308             for b in xrange(0, 10):
 309                 writer.seek(5, os.SEEK_SET)
 310                 writer.write("abcdefghij")
 311
 312             self.assertEqual(writer.size(), 15)
 313             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 314             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 315
 316             writer.arvadosfile.flush()
 317
 318             self.assertEqual(writer.size(), 15)
 319             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 320             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.portable_manifest_text())
 321
 322     def test_write_large_rewrite(self):
 323         keep = ArvadosFileWriterTestCase.MockKeep({})
 324         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 325                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n",
 326                                                  "replication_desired":None},
 327                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 328                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"})
 329         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 330                              api_client=api, keep_client=keep) as c:
 331             writer = c.open("count.txt", "r+")
 332             text = ''.join(["0123456789" for a in xrange(0, 100)])
 333             for b in xrange(0, 100000):
 334                 writer.write(text)
 335             writer.seek(0, os.SEEK_SET)
 336             writer.write("foo")
 337             self.assertEqual(writer.size(), 100000000)
 338
 339             self.assertIsNone(c.manifest_locator())
 340             self.assertTrue(c.modified())
 341             c.save_new("test_write_large")
 342             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 343             self.assertFalse(c.modified())
 344
 345     def test_create(self):
 346         keep = ArvadosFileWriterTestCase.MockKeep({})
 347         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 348                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 349                                                  "replication_desired":None},
 350                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 351                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 352         with Collection(api_client=api, keep_client=keep) as c:
 353             writer = c.open("count.txt", "w+")
 354             self.assertEqual(writer.size(), 0)
 355             writer.write("01234567")
 356             self.assertEqual(writer.size(), 8)
 357
 358             self.assertIsNone(c.manifest_locator())
 359             self.assertTrue(c.modified())
 360             self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 361             c.save_new("test_create")
 362             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 363             self.assertFalse(c.modified())
 364             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 365
 366
 367     def test_create_subdir(self):
 368         keep = ArvadosFileWriterTestCase.MockKeep({})
 369         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 370                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 371                                                  "replication_desired":None},
 372                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 373                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 374         with Collection(api_client=api, keep_client=keep) as c:
 375             self.assertIsNone(c.api_response())
 376             writer = c.open("foo/bar/count.txt", "w+")
 377             writer.write("01234567")
 378             self.assertFalse(c.committed())
 379             c.save_new("test_create")
 380             self.assertTrue(c.committed())
 381             self.assertEqual(c.api_response(), api.response)
 382
 383     def test_overwrite(self):
 384         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 385         api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
 386                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
 387                                                  "replication_desired":None},
 388                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 389                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 390         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 391                              api_client=api, keep_client=keep) as c:
 392             writer = c.open("count.txt", "w+")
 393             self.assertEqual(writer.size(), 0)
 394             writer.write("01234567")
 395             self.assertEqual(writer.size(), 8)
 396
 397             self.assertIsNone(c.manifest_locator())
 398             self.assertTrue(c.modified())
 399             c.save_new("test_overwrite")
 400             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 401             self.assertFalse(c.modified())
 402
 403     def test_file_not_found(self):
 404         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 405             with self.assertRaises(IOError):
 406                 writer = c.open("nocount.txt", "r")
 407
 408     def test_cannot_open_directory(self):
 409         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 410             with self.assertRaises(IOError):
 411                 writer = c.open(".", "r")
 412
 413     def test_create_multiple(self):
 414         keep = ArvadosFileWriterTestCase.MockKeep({})
 415         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
 416                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
 417                                                  "replication_desired":None},
 418                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 419                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"})
 420         with Collection(api_client=api, keep_client=keep) as c:
 421             w1 = c.open("count1.txt", "w")
 422             w2 = c.open("count2.txt", "w")
 423             w1.write("01234567")
 424             w2.write("abcdefgh")
 425             self.assertEqual(w1.size(), 8)
 426             self.assertEqual(w2.size(), 8)
 427
 428             self.assertIsNone(c.manifest_locator())
 429             self.assertTrue(c.modified())
 430             self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 431             c.save_new("test_create_multiple")
 432             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 433             self.assertFalse(c.modified())
 434             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 435
 436
 437 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
 438     class MockParent(object):
 439         class MockBlockMgr(object):
 440             def __init__(self, blocks, nocache):
 441                 self.blocks = blocks
 442                 self.nocache = nocache
 443
 444             def block_prefetch(self, loc):
 445                 pass
 446
 447             def get_block_contents(self, loc, num_retries=0, cache_only=False):
 448                 if self.nocache and cache_only:
 449                     return None
 450                 return self.blocks[loc]
 451
 452         def __init__(self, blocks, nocache):
 453             self.blocks = blocks
 454             self.nocache = nocache
 455             self.lock = arvados.arvfile.NoopLock()
 456
 457         def root_collection(self):
 458             return self
 459
 460         def _my_block_manager(self):
 461             return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
 462
 463
 464     def make_count_reader(self, nocache=False):
 465         stream = []
 466         n = 0
 467         blocks = {}
 468         for d in ['01234', '34567', '67890']:
 469             loc = tutil.str_keep_locator(d)
 470             blocks[loc] = d
 471             stream.append(Range(loc, n, len(d)))
 472             n += len(d)
 473         af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), "count.txt", stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
 474         return ArvadosFileReader(af)
 475
 476     def test_read_block_crossing_behavior(self):
 477         # read() needs to return all the data requested if possible, even if it
 478         # crosses uncached blocks: https://arvados.org/issues/5856
 479         sfile = self.make_count_reader(nocache=True)
 480         self.assertEqual('12345678', sfile.read(8))
 481
 482     def test_successive_reads(self):
 483         # Override StreamFileReaderTestCase.test_successive_reads
 484         sfile = self.make_count_reader(nocache=True)
 485         self.assertEqual('1234', sfile.read(4))
 486         self.assertEqual('5678', sfile.read(4))
 487         self.assertEqual('9', sfile.read(4))
 488         self.assertEqual('', sfile.read(4))
 489
 490     def test_tell_after_block_read(self):
 491         # Override StreamFileReaderTestCase.test_tell_after_block_read
 492         sfile = self.make_count_reader(nocache=True)
 493         self.assertEqual('12345678', sfile.read(8))
 494         self.assertEqual(8, sfile.tell())
 495
 496     def test_prefetch(self):
 497         keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
 498         with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
 499             r = c.open("count.txt", "r")
 500             self.assertEqual("0123", r.read(4))
 501         self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
 502         self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
 503
 504     def test__eq__from_manifest(self):
 505         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 506             with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
 507                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 508                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 509
 510     def test__eq__from_writes(self):
 511         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 512             with Collection() as c2:
 513                 f = c2.open("count1.txt", "w")
 514                 f.write("0123456789")
 515
 516                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 517                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 518
 519     def test__ne__(self):
 520         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 521             with Collection() as c2:
 522                 f = c2.open("count1.txt", "w")
 523                 f.write("1234567890")
 524
 525                 self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
 526                 self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
 527
 528
 529 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
 530     def reader_for(self, coll_name, **kwargs):
 531         stream = []
 532         segments = []
 533         n = 0
 534         for d in self.manifest_for(coll_name).split():
 535             try:
 536                 k = KeepLocator(d)
 537                 segments.append(Range(n, n, k.size))
 538                 stream.append(Range(d, n, k.size))
 539                 n += k.size
 540             except ValueError:
 541                 pass
 542
 543         blockmanager = arvados.arvfile._BlockManager(self.keep_client())
 544         blockmanager.prefetch_enabled = False
 545         col = Collection(keep_client=self.keep_client(), block_manager=blockmanager)
 546         af = ArvadosFile(col, "test",
 547                          stream=stream,
 548                          segments=segments)
 549         return ArvadosFileReader(af, **kwargs)
 550
 551     def read_for_test(self, reader, byte_count, **kwargs):
 552         return reader.read(byte_count, **kwargs)
 553
 554
 555 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
 556     def read_for_test(self, reader, byte_count, **kwargs):
 557         return reader.readfrom(0, byte_count, **kwargs)
 558
 559
 560 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
 561     def read_for_test(self, reader, byte_count, **kwargs):
 562         return ''.join(reader.readall(**kwargs))
 563
 564
 565 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
 566     def read_for_test(self, reader, byte_count, **kwargs):
 567         return ''.join(reader.readall_decompressed(**kwargs))
 568
 569
 570 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
 571     def read_for_test(self, reader, byte_count, **kwargs):
 572         return ''.join(reader.readlines(**kwargs))
 573
 574
 575 class ArvadosFileTestCase(unittest.TestCase):
 576     def datetime_to_hex(self, dt):
 577         return hex(int(time.mktime(dt.timetuple())))[2:]
 578
 579     def test_permission_expired(self):
 580         base_manifest = ". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@{} 0:10:count.txt\n"
 581         now = datetime.datetime.now()
 582         a_week_ago = now - datetime.timedelta(days=7)
 583         a_month_ago = now - datetime.timedelta(days=30)
 584         a_week_from_now = now + datetime.timedelta(days=7)
 585         with Collection(base_manifest.format(self.datetime_to_hex(a_week_from_now))) as c:
 586             self.assertFalse(c.find('count.txt').permission_expired())
 587         with Collection(base_manifest.format(self.datetime_to_hex(a_week_ago))) as c:
 588             f = c.find('count.txt')
 589             self.assertTrue(f.permission_expired())
 590             self.assertTrue(f.permission_expired(a_week_from_now))
 591             self.assertFalse(f.permission_expired(a_month_ago))
 592
 593
 594 class BlockManagerTest(unittest.TestCase):
 595     def test_bufferblock_append(self):
 596         keep = ArvadosFileWriterTestCase.MockKeep({})
 597         with arvados.arvfile._BlockManager(keep) as blockmanager:
 598             bufferblock = blockmanager.alloc_bufferblock()
 599             bufferblock.append("foo")
 600
 601             self.assertEqual(bufferblock.size(), 3)
 602             self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 603             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 604
 605             bufferblock.append("bar")
 606
 607             self.assertEqual(bufferblock.size(), 6)
 608             self.assertEqual(bufferblock.buffer_view[0:6], "foobar")
 609             self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
 610
 611             bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 612             with self.assertRaises(arvados.errors.AssertionError):
 613                 bufferblock.append("bar")
 614
 615     def test_bufferblock_dup(self):
 616         keep = ArvadosFileWriterTestCase.MockKeep({})
 617         with arvados.arvfile._BlockManager(keep) as blockmanager:
 618             bufferblock = blockmanager.alloc_bufferblock()
 619             bufferblock.append("foo")
 620
 621             self.assertEqual(bufferblock.size(), 3)
 622             self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 623             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 624             bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 625
 626             bufferblock2 = blockmanager.dup_block(bufferblock, None)
 627             self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
 628
 629             bufferblock2.append("bar")
 630
 631             self.assertEqual(bufferblock2.size(), 6)
 632             self.assertEqual(bufferblock2.buffer_view[0:6], "foobar")
 633             self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
 634
 635             self.assertEqual(bufferblock.size(), 3)
 636             self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 637             self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 638
 639     def test_bufferblock_get(self):
 640         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 641         with arvados.arvfile._BlockManager(keep) as blockmanager:
 642             bufferblock = blockmanager.alloc_bufferblock()
 643             bufferblock.append("foo")
 644
 645             self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), "0123456789")
 646             self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), "foo")
 647
 648     def test_bufferblock_commit(self):
 649         mockkeep = mock.MagicMock()
 650         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 651             bufferblock = blockmanager.alloc_bufferblock()
 652             bufferblock.owner = mock.MagicMock()
 653             def flush(sync=None):
 654                 blockmanager.commit_bufferblock(bufferblock, sync)
 655             bufferblock.owner.flush.side_effect = flush
 656             bufferblock.append("foo")
 657             blockmanager.commit_all()
 658             self.assertTrue(bufferblock.owner.flush.called)
 659             self.assertTrue(mockkeep.put.called)
 660             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 661             self.assertIsNone(bufferblock.buffer_view)
 662
 663     def test_bufferblock_commit_pending(self):
 664         # Test for bug #7225
 665         mockkeep = mock.MagicMock()
 666         mockkeep.put.side_effect = lambda x: time.sleep(1)
 667         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 668             bufferblock = blockmanager.alloc_bufferblock()
 669             bufferblock.append("foo")
 670
 671             blockmanager.commit_bufferblock(bufferblock, False)
 672             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)
 673
 674             blockmanager.commit_bufferblock(bufferblock, True)
 675             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
 676
 677
 678     def test_bufferblock_commit_with_error(self):
 679         mockkeep = mock.MagicMock()
 680         mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail")
 681         with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
 682             bufferblock = blockmanager.alloc_bufferblock()
 683             bufferblock.owner = mock.MagicMock()
 684             def flush(sync=None):
 685                 blockmanager.commit_bufferblock(bufferblock, sync)
 686             bufferblock.owner.flush.side_effect = flush
 687             bufferblock.append("foo")
 688             with self.assertRaises(arvados.errors.KeepWriteError) as err:
 689                 blockmanager.commit_all()
 690             self.assertTrue(bufferblock.owner.flush.called)
 691             self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
 692             self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.ERROR)