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.portable_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.portable_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.portable_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.portable_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_get_manifest_text_commits(self):
 164          keep = ArvadosFileWriterTestCase.MockKeep({})
 165          with Collection(keep_client=keep) as c:
 166              writer = c.open("count.txt", "w")
 167              writer.write("0123456789")
 168              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
 169              self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 170              self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text())
 171              self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
 172
 173
 174     def test_write_in_middle(self):
 175         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 176         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 177                              keep_client=keep) as c:
 178             writer = c.open("count.txt", "r+")
 179             self.assertEqual("0123456789", writer.readfrom(0, 13))
 180             writer.seek(3, os.SEEK_SET)
 181             writer.write("foo")
 182             self.assertEqual(writer.size(), 10)
 183             self.assertEqual("012foo6789", writer.readfrom(0, 13))
 184             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.portable_manifest_text())
 185
 186     def test_write_at_end(self):
 187         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 188         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 189                              keep_client=keep) as c:
 190             writer = c.open("count.txt", "r+")
 191             self.assertEqual("0123456789", writer.readfrom(0, 13))
 192             writer.seek(7, os.SEEK_SET)
 193             writer.write("foo")
 194             self.assertEqual(writer.size(), 10)
 195             self.assertEqual("0123456foo", writer.readfrom(0, 13))
 196             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text())
 197
 198     def test_write_across_segment_boundary(self):
 199         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 200         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
 201                              keep_client=keep) as c:
 202             writer = c.open("count.txt", "r+")
 203             self.assertEqual("012345678901234", writer.readfrom(0, 15))
 204             writer.seek(7, os.SEEK_SET)
 205             writer.write("foobar")
 206             self.assertEqual(writer.size(), 20)
 207             self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
 208             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text())
 209
 210     def test_write_across_several_segments(self):
 211         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 212         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
 213                              keep_client=keep) as c:
 214             writer = c.open("count.txt", "r+")
 215             self.assertEqual("012301230123", writer.readfrom(0, 15))
 216             writer.seek(2, os.SEEK_SET)
 217             writer.write("abcdefg")
 218             self.assertEqual(writer.size(), 12)
 219             self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
 220             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text())
 221
 222     def test_write_large(self):
 223         keep = ArvadosFileWriterTestCase.MockKeep({})
 224         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 225                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"},
 226                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 227                                                  "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"})
 228         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 229                              api_client=api, keep_client=keep) as c:
 230             writer = c.open("count.txt", "r+")
 231             text = "0123456789" * 100
 232             for b in xrange(0, 100000):
 233                 writer.write(text)
 234             self.assertEqual(writer.size(), 100000000)
 235
 236             self.assertEqual(None, c.manifest_locator())
 237             self.assertEqual(True, c.modified())
 238             c.save_new("test_write_large")
 239             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 240             self.assertEqual(False, c.modified())
 241
 242
 243     def test_large_write(self):
 244         keep = ArvadosFileWriterTestCase.MockKeep({})
 245         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 246                                                  "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n"},
 247                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 248                                                  "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n"})
 249         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 250                              api_client=api, keep_client=keep) as c:
 251             writer = c.open("count.txt", "r+")
 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(None, c.manifest_locator())
 259             self.assertEqual(True, c.modified())
 260             c.save_new("test_write_large")
 261             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 262             self.assertEqual(False, c.modified())
 263
 264     def test_rewrite_on_empty_file(self):
 265         keep = ArvadosFileWriterTestCase.MockKeep({})
 266         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 267                              keep_client=keep) as c:
 268             writer = c.open("count.txt", "r+")
 269             for b in xrange(0, 10):
 270                 writer.seek(0, os.SEEK_SET)
 271                 writer.write("0123456789")
 272
 273             self.assertEqual(writer.size(), 10)
 274             self.assertEqual("0123456789", writer.readfrom(0, 20))
 275             self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.portable_manifest_text())
 276             writer.flush()
 277             self.assertEqual(writer.size(), 10)
 278             self.assertEqual("0123456789", writer.readfrom(0, 20))
 279             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.portable_manifest_text())
 280
 281     def test_rewrite_append_existing_file(self):
 282         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 283         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 284                              keep_client=keep) as c:
 285             writer = c.open("count.txt", "r+")
 286             for b in xrange(0, 10):
 287                 writer.seek(10, os.SEEK_SET)
 288                 writer.write("abcdefghij")
 289
 290             self.assertEqual(writer.size(), 20)
 291             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 292             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 293
 294             writer.arvadosfile.flush()
 295             self.assertEqual(writer.size(), 20)
 296             self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
 297             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.portable_manifest_text())
 298
 299     def test_rewrite_over_existing_file(self):
 300         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 301         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
 302                              keep_client=keep) as c:
 303             writer = c.open("count.txt", "r+")
 304             for b in xrange(0, 10):
 305                 writer.seek(5, os.SEEK_SET)
 306                 writer.write("abcdefghij")
 307
 308             self.assertEqual(writer.size(), 15)
 309             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 310             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.portable_manifest_text())
 311
 312             writer.arvadosfile.flush()
 313
 314             self.assertEqual(writer.size(), 15)
 315             self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
 316             self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.portable_manifest_text())
 317
 318     def test_write_large_rewrite(self):
 319         keep = ArvadosFileWriterTestCase.MockKeep({})
 320         api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
 321                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"},
 322                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 323                                                  "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"})
 324         with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
 325                              api_client=api, keep_client=keep) as c:
 326             writer = c.open("count.txt", "r+")
 327             text = ''.join(["0123456789" for a in xrange(0, 100)])
 328             for b in xrange(0, 100000):
 329                 writer.write(text)
 330             writer.seek(0, os.SEEK_SET)
 331             writer.write("foo")
 332             self.assertEqual(writer.size(), 100000000)
 333
 334             self.assertEqual(None, c.manifest_locator())
 335             self.assertEqual(True, c.modified())
 336             c.save_new("test_write_large")
 337             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 338             self.assertEqual(False, c.modified())
 339
 340     def test_create(self):
 341         keep = ArvadosFileWriterTestCase.MockKeep({})
 342         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 343                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 344                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 345                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 346         with Collection(api_client=api, keep_client=keep) as c:
 347             writer = c.open("count.txt", "w+")
 348             self.assertEqual(writer.size(), 0)
 349             writer.write("01234567")
 350             self.assertEqual(writer.size(), 8)
 351
 352             self.assertEqual(None, c.manifest_locator())
 353             self.assertEqual(True, c.modified())
 354             self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 355             c.save_new("test_create")
 356             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 357             self.assertEqual(False, c.modified())
 358             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 359
 360
 361     def test_create_subdir(self):
 362         keep = ArvadosFileWriterTestCase.MockKeep({})
 363         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
 364                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 365                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 366                                                  "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 367         with Collection(api_client=api, keep_client=keep) as c:
 368             self.assertIsNone(c.api_response())
 369             writer = c.open("foo/bar/count.txt", "w+")
 370             writer.write("01234567")
 371             c.save_new("test_create")
 372             self.assertEqual(c.api_response(), api.response)
 373
 374     def test_overwrite(self):
 375         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 376         api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
 377                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
 378                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 379                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
 380         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
 381                              api_client=api, keep_client=keep) as c:
 382             writer = c.open("count.txt", "w+")
 383             self.assertEqual(writer.size(), 0)
 384             writer.write("01234567")
 385             self.assertEqual(writer.size(), 8)
 386
 387             self.assertEqual(None, c.manifest_locator())
 388             self.assertEqual(True, c.modified())
 389             c.save_new("test_overwrite")
 390             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 391             self.assertEqual(False, c.modified())
 392
 393     def test_file_not_found(self):
 394         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 395             with self.assertRaises(IOError):
 396                 writer = c.open("nocount.txt", "r")
 397
 398     def test_cannot_open_directory(self):
 399         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
 400             with self.assertRaises(IOError):
 401                 writer = c.open(".", "r")
 402
 403     def test_create_multiple(self):
 404         keep = ArvadosFileWriterTestCase.MockKeep({})
 405         api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
 406                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"},
 407                                                 {"uuid":"zzzzz-4zz18-mockcollection0",
 408                                                  "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"})
 409         with Collection(api_client=api, keep_client=keep) as c:
 410             w1 = c.open("count1.txt", "w")
 411             w2 = c.open("count2.txt", "w")
 412             w1.write("01234567")
 413             w2.write("abcdefgh")
 414             self.assertEqual(w1.size(), 8)
 415             self.assertEqual(w2.size(), 8)
 416
 417             self.assertEqual(None, c.manifest_locator())
 418             self.assertEqual(True, c.modified())
 419             self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 420             c.save_new("test_create_multiple")
 421             self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
 422             self.assertEqual(False, c.modified())
 423             self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
 424
 425
 426 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
 427     class MockParent(object):
 428         class MockBlockMgr(object):
 429             def __init__(self, blocks, nocache):
 430                 self.blocks = blocks
 431                 self.nocache = nocache
 432
 433             def block_prefetch(self, loc):
 434                 pass
 435
 436             def get_block_contents(self, loc, num_retries=0, cache_only=False):
 437                 if self.nocache and cache_only:
 438                     return None
 439                 return self.blocks[loc]
 440
 441         def __init__(self, blocks, nocache):
 442             self.blocks = blocks
 443             self.nocache = nocache
 444             self.lock = arvados.arvfile.NoopLock()
 445
 446         def root_collection(self):
 447             return self
 448
 449         def _my_block_manager(self):
 450             return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
 451
 452
 453     def make_count_reader(self, nocache=False):
 454         stream = []
 455         n = 0
 456         blocks = {}
 457         for d in ['01234', '34567', '67890']:
 458             loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d))
 459             blocks[loc] = d
 460             stream.append(Range(loc, n, len(d)))
 461             n += len(d)
 462         af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
 463         return ArvadosFileReader(af, "count.txt")
 464
 465     def test_read_block_crossing_behavior(self):
 466         # read() needs to return all the data requested if possible, even if it
 467         # crosses uncached blocks: https://arvados.org/issues/5856
 468         sfile = self.make_count_reader(nocache=True)
 469         self.assertEqual('12345678', sfile.read(8))
 470
 471     def test_successive_reads(self):
 472         # Override StreamFileReaderTestCase.test_successive_reads
 473         sfile = self.make_count_reader(nocache=True)
 474         self.assertEqual('1234', sfile.read(4))
 475         self.assertEqual('5678', sfile.read(4))
 476         self.assertEqual('9', sfile.read(4))
 477         self.assertEqual('', sfile.read(4))
 478
 479     def test_tell_after_block_read(self):
 480         # Override StreamFileReaderTestCase.test_tell_after_block_read
 481         sfile = self.make_count_reader(nocache=True)
 482         self.assertEqual('12345678', sfile.read(8))
 483         self.assertEqual(8, sfile.tell())
 484
 485     def test_prefetch(self):
 486         keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
 487         with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
 488             r = c.open("count.txt", "r")
 489             self.assertEqual("0123", r.read(4))
 490         self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
 491         self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
 492
 493     def test__eq__from_manifest(self):
 494         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 495             with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
 496                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 497                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 498
 499     def test__eq__from_writes(self):
 500         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 501             with Collection() as c2:
 502                 with c2.open("count1.txt", "w") as f:
 503                     f.write("0123456789")
 504
 505                 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
 506                 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
 507
 508     def test__ne__(self):
 509         with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
 510             with Collection() as c2:
 511                 with c2.open("count1.txt", "w") as f:
 512                     f.write("1234567890")
 513
 514                 self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
 515                 self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
 516
 517
 518 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
 519     def reader_for(self, coll_name, **kwargs):
 520         stream = []
 521         segments = []
 522         n = 0
 523         for d in self.manifest_for(coll_name).split():
 524             try:
 525                 k = KeepLocator(d)
 526                 segments.append(Range(n, n, k.size))
 527                 stream.append(Range(d, n, k.size))
 528                 n += k.size
 529             except ValueError:
 530                 pass
 531
 532         blockmanager = arvados.arvfile._BlockManager(self.keep_client())
 533         blockmanager.prefetch_enabled = False
 534         col = Collection(keep_client=self.keep_client(), block_manager=blockmanager)
 535         af = ArvadosFile(col,
 536                          stream=stream,
 537                          segments=segments)
 538         return ArvadosFileReader(af, "test", **kwargs)
 539
 540     def read_for_test(self, reader, byte_count, **kwargs):
 541         return reader.read(byte_count, **kwargs)
 542
 543
 544 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
 545     def read_for_test(self, reader, byte_count, **kwargs):
 546         return reader.readfrom(0, byte_count, **kwargs)
 547
 548
 549 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
 550     def read_for_test(self, reader, byte_count, **kwargs):
 551         return ''.join(reader.readall(**kwargs))
 552
 553
 554 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
 555     def read_for_test(self, reader, byte_count, **kwargs):
 556         return ''.join(reader.readall_decompressed(**kwargs))
 557
 558
 559 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
 560     def read_for_test(self, reader, byte_count, **kwargs):
 561         return ''.join(reader.readlines(**kwargs))
 562
 563 class BlockManagerTest(unittest.TestCase):
 564     def test_bufferblock_append(self):
 565         keep = ArvadosFileWriterTestCase.MockKeep({})
 566         blockmanager = arvados.arvfile._BlockManager(keep)
 567         bufferblock = blockmanager.alloc_bufferblock()
 568         bufferblock.append("foo")
 569
 570         self.assertEqual(bufferblock.size(), 3)
 571         self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 572         self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 573
 574         bufferblock.append("bar")
 575
 576         self.assertEqual(bufferblock.size(), 6)
 577         self.assertEqual(bufferblock.buffer_view[0:6], "foobar")
 578         self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
 579
 580         bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 581         with self.assertRaises(arvados.errors.AssertionError):
 582             bufferblock.append("bar")
 583
 584     def test_bufferblock_dup(self):
 585         keep = ArvadosFileWriterTestCase.MockKeep({})
 586         blockmanager = arvados.arvfile._BlockManager(keep)
 587         bufferblock = blockmanager.alloc_bufferblock()
 588         bufferblock.append("foo")
 589
 590         self.assertEqual(bufferblock.size(), 3)
 591         self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 592         self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 593         bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
 594
 595         bufferblock2 = blockmanager.dup_block(bufferblock, None)
 596         self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
 597
 598         bufferblock2.append("bar")
 599
 600         self.assertEqual(bufferblock2.size(), 6)
 601         self.assertEqual(bufferblock2.buffer_view[0:6], "foobar")
 602         self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
 603
 604         self.assertEqual(bufferblock.size(), 3)
 605         self.assertEqual(bufferblock.buffer_view[0:3], "foo")
 606         self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
 607
 608     def test_bufferblock_get(self):
 609         keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
 610         blockmanager = arvados.arvfile._BlockManager(keep)
 611         bufferblock = blockmanager.alloc_bufferblock()
 612         bufferblock.append("foo")
 613
 614         self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), "0123456789")
 615         self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), "foo")
 616
 617     def test_bufferblock_commit(self):
 618         mockkeep = mock.MagicMock()
 619         blockmanager = arvados.arvfile._BlockManager(mockkeep)
 620         bufferblock = blockmanager.alloc_bufferblock()
 621         bufferblock.owner = mock.MagicMock()
 622         bufferblock.owner.flush.side_effect = lambda: blockmanager.commit_bufferblock(bufferblock)
 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
 631     def test_bufferblock_commit_with_error(self):
 632         mockkeep = mock.MagicMock()
 633         mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail")
 634         blockmanager = arvados.arvfile._BlockManager(mockkeep)
 635         bufferblock = blockmanager.alloc_bufferblock()
 636         bufferblock.owner = mock.MagicMock()
 637         bufferblock.owner.flush.side_effect = lambda: blockmanager.commit_bufferblock(bufferblock)
 638         bufferblock.append("foo")
 639         with self.assertRaises(arvados.errors.KeepWriteError) as err:
 640             blockmanager.commit_all()
 641         self.assertTrue(bufferblock.owner.flush.called)
 642         self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
 643         self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)