sdk/python/tests/test_collections.py

   1 from __future__ import absolute_import
   2
   3 from builtins import object
   4 import arvados
   5 import copy
   6 import mock
   7 import os
   8 import pprint
   9 import re
  10 import sys
  11 import tempfile
  12 import unittest
  13
  14 from . import run_test_server
  15 from arvados._ranges import Range, LocatorAndRange
  16 from arvados.collection import Collection, CollectionReader
  17 from . import arvados_testutil as tutil
  18
  19 class TestResumableWriter(arvados.ResumableCollectionWriter):
  20     KEEP_BLOCK_SIZE = 1024  # PUT to Keep every 1K.
  21
  22     def current_state(self):
  23         return self.dump_state(copy.deepcopy)
  24
  25
  26 class ArvadosCollectionsTest(run_test_server.TestCaseWithServers,
  27                              tutil.ArvadosBaseTestCase):
  28     MAIN_SERVER = {}
  29
  30     @classmethod
  31     def setUpClass(cls):
  32         super(ArvadosCollectionsTest, cls).setUpClass()
  33         run_test_server.authorize_with('active')
  34         cls.api_client = arvados.api('v1')
  35         cls.keep_client = arvados.KeepClient(api_client=cls.api_client,
  36                                              local_store=cls.local_store)
  37
  38     def write_foo_bar_baz(self):
  39         cw = arvados.CollectionWriter(self.api_client)
  40         self.assertEqual(cw.current_stream_name(), '.',
  41                          'current_stream_name() should be "." now')
  42         cw.set_current_file_name('foo.txt')
  43         cw.write(b'foo')
  44         self.assertEqual(cw.current_file_name(), 'foo.txt',
  45                          'current_file_name() should be foo.txt now')
  46         cw.start_new_file('bar.txt')
  47         cw.write(b'bar')
  48         cw.start_new_stream('baz')
  49         cw.write(b'baz')
  50         cw.set_current_file_name('baz.txt')
  51         self.assertEqual(cw.manifest_text(),
  52                          ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" +
  53                          "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n",
  54                          "wrong manifest: got {}".format(cw.manifest_text()))
  55         cw.finish()
  56         return cw.portable_data_hash()
  57
  58     def test_keep_local_store(self):
  59         self.assertEqual(self.keep_client.put(b'foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
  60         self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), b'foo', 'wrong data from Keep.get')
  61
  62     def test_local_collection_writer(self):
  63         self.assertEqual(self.write_foo_bar_baz(),
  64                          '23ca013983d6239e98931cc779e68426+114',
  65                          'wrong locator hash: ' + self.write_foo_bar_baz())
  66
  67     def test_local_collection_reader(self):
  68         foobarbaz = self.write_foo_bar_baz()
  69         cr = arvados.CollectionReader(
  70             foobarbaz + '+Xzizzle', self.api_client)
  71         got = []
  72         for s in cr.all_streams():
  73             for f in s.all_files():
  74                 got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]]
  75         expected = [[3, '.', 'foo.txt', b'foo'],
  76                     [3, '.', 'bar.txt', b'bar'],
  77                     [3, './baz', 'baz.txt', b'baz']]
  78         self.assertEqual(got,
  79                          expected)
  80         stream0 = cr.all_streams()[0]
  81         self.assertEqual(stream0.readfrom(0, 0),
  82                          b'',
  83                          'reading zero bytes should have returned empty string')
  84         self.assertEqual(stream0.readfrom(0, 2**26),
  85                          b'foobar',
  86                          'reading entire stream failed')
  87         self.assertEqual(stream0.readfrom(2**26, 0),
  88                          b'',
  89                          'reading zero bytes should have returned empty string')
  90
  91     def _test_subset(self, collection, expected):
  92         cr = arvados.CollectionReader(collection, self.api_client)
  93         for s in cr.all_streams():
  94             for ex in expected:
  95                 if ex[0] == s:
  96                     f = s.files()[ex[2]]
  97                     got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))]
  98                     self.assertEqual(got,
  99                                      ex,
 100                                      'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex))
 101
 102     def test_collection_manifest_subset(self):
 103         foobarbaz = self.write_foo_bar_baz()
 104         self._test_subset(foobarbaz,
 105                           [[3, '.',     'bar.txt', b'bar'],
 106                            [3, '.',     'foo.txt', b'foo'],
 107                            [3, './baz', 'baz.txt', b'baz']])
 108         self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" %
 109                            (self.keep_client.put(b"foo"),
 110                             self.keep_client.put(b"bar"))),
 111                           [[3, '.', 'bar.txt', b'bar'],
 112                            [3, '.', 'foo.txt', b'foo']])
 113         self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" %
 114                            (self.keep_client.put(b"foo"),
 115                             self.keep_client.put(b"bar"))),
 116                           [[2, '.', 'fo.txt', b'fo'],
 117                            [4, '.', 'obar.txt', b'obar']])
 118         self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" %
 119                            (self.keep_client.put(b"foo"),
 120                             self.keep_client.put(b"bar"))),
 121                           [[2, '.', 'ar.txt', b'ar'],
 122                            [2, '.', 'fo.txt', b'fo'],
 123                            [2, '.', 'ob.txt', b'ob'],
 124                            [0, '.', 'zero.txt', b'']])
 125
 126     def test_collection_empty_file(self):
 127         cw = arvados.CollectionWriter(self.api_client)
 128         cw.start_new_file('zero.txt')
 129         cw.write(b'')
 130
 131         self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n")
 132         self.check_manifest_file_sizes(cw.manifest_text(), [0])
 133         cw = arvados.CollectionWriter(self.api_client)
 134         cw.start_new_file('zero.txt')
 135         cw.write(b'')
 136         cw.start_new_file('one.txt')
 137         cw.write(b'1')
 138         cw.start_new_stream('foo')
 139         cw.start_new_file('zero.txt')
 140         cw.write(b'')
 141         self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0])
 142
 143     def test_no_implicit_normalize(self):
 144         cw = arvados.CollectionWriter(self.api_client)
 145         cw.start_new_file('b')
 146         cw.write(b'b')
 147         cw.start_new_file('a')
 148         cw.write(b'')
 149         self.check_manifest_file_sizes(cw.manifest_text(), [1,0])
 150         self.check_manifest_file_sizes(
 151             arvados.CollectionReader(
 152                 cw.manifest_text()).manifest_text(normalize=True),
 153             [0,1])
 154
 155     def check_manifest_file_sizes(self, manifest_text, expect_sizes):
 156         cr = arvados.CollectionReader(manifest_text, self.api_client)
 157         got_sizes = []
 158         for f in cr.all_files():
 159             got_sizes += [f.size()]
 160         self.assertEqual(got_sizes, expect_sizes, "got wrong file sizes %s, expected %s" % (got_sizes, expect_sizes))
 161
 162     def test_normalized_collection(self):
 163         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 164 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 165 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 166 """
 167         self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True),
 168                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
 169 """)
 170
 171         m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
 172 """
 173         self.assertEqual(arvados.CollectionReader(m2, self.api_client).manifest_text(normalize=True), m2)
 174
 175         m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
 176 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 177 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 178 """
 179         self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(normalize=True),
 180                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
 181 """)
 182
 183         m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 184 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 185 ./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
 186 """
 187         self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(normalize=True),
 188                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
 189 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 190 """)
 191
 192         m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 193 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 194 ./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar
 195 """
 196         self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(normalize=True),
 197                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
 198 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 199 """)
 200
 201         with self.data_file('1000G_ref_manifest') as f6:
 202             m6 = f6.read()
 203             self.assertEqual(arvados.CollectionReader(m6, self.api_client).manifest_text(normalize=True), m6)
 204
 205         with self.data_file('jlake_manifest') as f7:
 206             m7 = f7.read()
 207             self.assertEqual(arvados.CollectionReader(m7, self.api_client).manifest_text(normalize=True), m7)
 208
 209         m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt
 210 """
 211         self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8)
 212
 213     def test_locators_and_ranges(self):
 214         blocks2 = [Range('a', 0, 10),
 215                    Range('b', 10, 10),
 216                    Range('c', 20, 10),
 217                    Range('d', 30, 10),
 218                    Range('e', 40, 10),
 219                    Range('f', 50, 10)]
 220
 221         self.assertEqual(arvados.locators_and_ranges(blocks2,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 222         self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 223         self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 224         self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 225         self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 226         self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 227         self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), [])
 228         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 229
 230         self.assertEqual(arvados.locators_and_ranges(blocks2,  0,  2), [LocatorAndRange('a', 10, 0, 2)])
 231         self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [LocatorAndRange('b', 10, 0, 2)])
 232         self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [LocatorAndRange('c', 10, 0, 2)])
 233         self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [LocatorAndRange('d', 10, 0, 2)])
 234         self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [LocatorAndRange('e', 10, 0, 2)])
 235         self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [LocatorAndRange('f', 10, 0, 2)])
 236         self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), [])
 237         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 238
 239         self.assertEqual(arvados.locators_and_ranges(blocks2,  9,  2), [LocatorAndRange('a', 10, 9, 1), LocatorAndRange('b', 10, 0, 1)])
 240         self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [LocatorAndRange('b', 10, 9, 1), LocatorAndRange('c', 10, 0, 1)])
 241         self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [LocatorAndRange('c', 10, 9, 1), LocatorAndRange('d', 10, 0, 1)])
 242         self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [LocatorAndRange('d', 10, 9, 1), LocatorAndRange('e', 10, 0, 1)])
 243         self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [LocatorAndRange('e', 10, 9, 1), LocatorAndRange('f', 10, 0, 1)])
 244         self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [LocatorAndRange('f', 10, 9, 1)])
 245
 246
 247         blocks3 = [Range('a', 0, 10),
 248                   Range('b', 10, 10),
 249                   Range('c', 20, 10),
 250                   Range('d', 30, 10),
 251                   Range('e', 40, 10),
 252                   Range('f', 50, 10),
 253                    Range('g', 60, 10)]
 254
 255         self.assertEqual(arvados.locators_and_ranges(blocks3,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 256         self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 257         self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 258         self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 259         self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 260         self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 261         self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [LocatorAndRange('g', 10, 2, 2)])
 262
 263
 264         blocks = [Range('a', 0, 10),
 265                   Range('b', 10, 15),
 266                   Range('c', 25, 5)]
 267         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 0), [])
 268         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [LocatorAndRange('a', 10, 0, 5)])
 269         self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [LocatorAndRange('a', 10, 3, 5)])
 270         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [LocatorAndRange('a', 10, 0, 10)])
 271
 272         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [LocatorAndRange('a', 10, 0, 10),
 273                                                                       LocatorAndRange('b', 15, 0, 1)])
 274         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [LocatorAndRange('a', 10, 1, 9),
 275                                                                       LocatorAndRange('b', 15, 0, 2)])
 276         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [LocatorAndRange('a', 10, 0, 10),
 277                                                                       LocatorAndRange('b', 15, 0, 15)])
 278
 279         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [LocatorAndRange('a', 10, 0, 10),
 280                                                                       LocatorAndRange('b', 15, 0, 15),
 281                                                                       LocatorAndRange('c', 5, 0, 5)])
 282         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [LocatorAndRange('a', 10, 1, 9),
 283                                                                       LocatorAndRange('b', 15, 0, 15),
 284                                                                       LocatorAndRange('c', 5, 0, 5)])
 285         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [LocatorAndRange('a', 10, 0, 10),
 286                                                                       LocatorAndRange('b', 15, 0, 15),
 287                                                                       LocatorAndRange('c', 5, 0, 5)])
 288
 289         self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [LocatorAndRange('b', 15, 5, 5)])
 290
 291         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [LocatorAndRange('a', 10, 8, 2),
 292                                                                       LocatorAndRange('b', 15, 0, 15)])
 293
 294         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [LocatorAndRange('a', 10, 8, 2),
 295                                                                       LocatorAndRange('b', 15, 0, 15),
 296                                                                       LocatorAndRange('c', 5, 0, 3)])
 297
 298         self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [LocatorAndRange('c', 5, 1, 2)])
 299
 300         self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [LocatorAndRange('a', 10, 9, 1),
 301                                                                       LocatorAndRange('b', 15, 0, 14)])
 302         self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [LocatorAndRange('b', 15, 0, 15)])
 303         self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [LocatorAndRange('b', 15, 1, 14),
 304                                                                        LocatorAndRange('c', 5, 0, 1)])
 305
 306     class MockKeep(object):
 307         def __init__(self, content, num_retries=0):
 308             self.content = content
 309
 310         def get(self, locator, num_retries=0):
 311             return self.content[locator]
 312
 313     def test_stream_reader(self):
 314         keepblocks = {
 315             'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': b'abcdefghij',
 316             'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': b'klmnopqrstuvwxy',
 317             'cccccccccccccccccccccccccccccccc+5': b'z0123',
 318         }
 319         mk = self.MockKeep(keepblocks)
 320
 321         sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk)
 322
 323         content = b'abcdefghijklmnopqrstuvwxyz0123456789'
 324
 325         self.assertEqual(sr.readfrom(0, 30), content[0:30])
 326         self.assertEqual(sr.readfrom(2, 30), content[2:30])
 327
 328         self.assertEqual(sr.readfrom(2, 8), content[2:10])
 329         self.assertEqual(sr.readfrom(0, 10), content[0:10])
 330
 331         self.assertEqual(sr.readfrom(0, 5), content[0:5])
 332         self.assertEqual(sr.readfrom(5, 5), content[5:10])
 333         self.assertEqual(sr.readfrom(10, 5), content[10:15])
 334         self.assertEqual(sr.readfrom(15, 5), content[15:20])
 335         self.assertEqual(sr.readfrom(20, 5), content[20:25])
 336         self.assertEqual(sr.readfrom(25, 5), content[25:30])
 337         self.assertEqual(sr.readfrom(30, 5), b'')
 338
 339     def test_extract_file(self):
 340         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 341 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt
 342 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt
 343 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt
 344 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt
 345 """
 346
 347         m2 = arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True)
 348
 349         self.assertEqual(m2,
 350                          ". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt 43:41:md6sum.txt 84:43:md7sum.txt 6:37:md8sum.txt 84:43:md8sum.txt 83:1:md9sum.txt 0:43:md9sum.txt 84:36:md9sum.txt\n")
 351         files = arvados.CollectionReader(
 352             m2, self.api_client).all_streams()[0].files()
 353
 354         self.assertEqual(files['md5sum.txt'].as_manifest(),
 355                          ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n")
 356         self.assertEqual(files['md6sum.txt'].as_manifest(),
 357                          ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n")
 358         self.assertEqual(files['md7sum.txt'].as_manifest(),
 359                          ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n")
 360         self.assertEqual(files['md9sum.txt'].as_manifest(),
 361                          ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n")
 362
 363     def test_write_directory_tree(self):
 364         cwriter = arvados.CollectionWriter(self.api_client)
 365         cwriter.write_directory_tree(self.build_directory_tree(
 366                 ['basefile', 'subdir/subfile']))
 367         self.assertEqual(cwriter.manifest_text(),
 368                          """. c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 369 ./subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 370
 371     def test_write_named_directory_tree(self):
 372         cwriter = arvados.CollectionWriter(self.api_client)
 373         cwriter.write_directory_tree(self.build_directory_tree(
 374                 ['basefile', 'subdir/subfile']), 'root')
 375         self.assertEqual(
 376             cwriter.manifest_text(),
 377             """./root c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 378 ./root/subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 379
 380     def test_write_directory_tree_in_one_stream(self):
 381         cwriter = arvados.CollectionWriter(self.api_client)
 382         cwriter.write_directory_tree(self.build_directory_tree(
 383                 ['basefile', 'subdir/subfile']), max_manifest_depth=0)
 384         self.assertEqual(cwriter.manifest_text(),
 385                          """. 4ace875ffdc6824a04950f06858f4465+22 0:8:basefile 8:14:subdir/subfile\n""")
 386
 387     def test_write_directory_tree_with_limited_recursion(self):
 388         cwriter = arvados.CollectionWriter(self.api_client)
 389         cwriter.write_directory_tree(
 390             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 391             max_manifest_depth=1)
 392         self.assertEqual(cwriter.manifest_text(),
 393                          """. bd19836ddb62c11c55ab251ccaca5645+2 0:2:f1
 394 ./d1 50170217e5b04312024aa5cd42934494+13 0:8:d2/f3 8:5:f2\n""")
 395
 396     def test_write_directory_tree_with_zero_recursion(self):
 397         cwriter = arvados.CollectionWriter(self.api_client)
 398         content = 'd1/d2/f3d1/f2f1'
 399         blockhash = tutil.str_keep_locator(content)
 400         cwriter.write_directory_tree(
 401             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 402             max_manifest_depth=0)
 403         self.assertEqual(
 404             cwriter.manifest_text(),
 405             ". {} 0:8:d1/d2/f3 8:5:d1/f2 13:2:f1\n".format(blockhash))
 406
 407     def test_write_one_file(self):
 408         cwriter = arvados.CollectionWriter(self.api_client)
 409         with self.make_test_file() as testfile:
 410             cwriter.write_file(testfile.name)
 411             self.assertEqual(
 412                 cwriter.manifest_text(),
 413                 ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:{}\n".format(
 414                     os.path.basename(testfile.name)))
 415
 416     def test_write_named_file(self):
 417         cwriter = arvados.CollectionWriter(self.api_client)
 418         with self.make_test_file() as testfile:
 419             cwriter.write_file(testfile.name, 'foo')
 420             self.assertEqual(cwriter.manifest_text(),
 421                              ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:foo\n")
 422
 423     def test_write_multiple_files(self):
 424         cwriter = arvados.CollectionWriter(self.api_client)
 425         for letter in 'ABC':
 426             with self.make_test_file(letter.encode()) as testfile:
 427                 cwriter.write_file(testfile.name, letter)
 428         self.assertEqual(
 429             cwriter.manifest_text(),
 430             ". 902fbdd2b1df0c4f70b4a5d23525e932+3 0:1:A 1:1:B 2:1:C\n")
 431
 432     def test_basic_resume(self):
 433         cwriter = TestResumableWriter()
 434         with self.make_test_file() as testfile:
 435             cwriter.write_file(testfile.name, 'test')
 436             resumed = TestResumableWriter.from_state(cwriter.current_state())
 437         self.assertEqual(cwriter.manifest_text(), resumed.manifest_text(),
 438                           "resumed CollectionWriter had different manifest")
 439
 440     def test_resume_fails_when_missing_dependency(self):
 441         cwriter = TestResumableWriter()
 442         with self.make_test_file() as testfile:
 443             cwriter.write_file(testfile.name, 'test')
 444         self.assertRaises(arvados.errors.StaleWriterStateError,
 445                           TestResumableWriter.from_state,
 446                           cwriter.current_state())
 447
 448     def test_resume_fails_when_dependency_mtime_changed(self):
 449         cwriter = TestResumableWriter()
 450         with self.make_test_file() as testfile:
 451             cwriter.write_file(testfile.name, 'test')
 452             os.utime(testfile.name, (0, 0))
 453             self.assertRaises(arvados.errors.StaleWriterStateError,
 454                               TestResumableWriter.from_state,
 455                               cwriter.current_state())
 456
 457     def test_resume_fails_when_dependency_is_nonfile(self):
 458         cwriter = TestResumableWriter()
 459         cwriter.write_file('/dev/null', 'empty')
 460         self.assertRaises(arvados.errors.StaleWriterStateError,
 461                           TestResumableWriter.from_state,
 462                           cwriter.current_state())
 463
 464     def test_resume_fails_when_dependency_size_changed(self):
 465         cwriter = TestResumableWriter()
 466         with self.make_test_file() as testfile:
 467             cwriter.write_file(testfile.name, 'test')
 468             orig_mtime = os.fstat(testfile.fileno()).st_mtime
 469             testfile.write(b'extra')
 470             testfile.flush()
 471             os.utime(testfile.name, (orig_mtime, orig_mtime))
 472             self.assertRaises(arvados.errors.StaleWriterStateError,
 473                               TestResumableWriter.from_state,
 474                               cwriter.current_state())
 475
 476     def test_resume_fails_with_expired_locator(self):
 477         cwriter = TestResumableWriter()
 478         state = cwriter.current_state()
 479         # Add an expired locator to the state.
 480         state['_current_stream_locators'].append(''.join([
 481                     'a' * 32, '+1+A', 'b' * 40, '@', '10000000']))
 482         self.assertRaises(arvados.errors.StaleWriterStateError,
 483                           TestResumableWriter.from_state, state)
 484
 485     def test_arbitrary_objects_not_resumable(self):
 486         cwriter = TestResumableWriter()
 487         with open('/dev/null') as badfile:
 488             self.assertRaises(arvados.errors.AssertionError,
 489                               cwriter.write_file, badfile)
 490
 491     def test_arbitrary_writes_not_resumable(self):
 492         cwriter = TestResumableWriter()
 493         self.assertRaises(arvados.errors.AssertionError,
 494                           cwriter.write, "badtext")
 495
 496     def test_read_arbitrary_data_with_collection_reader(self):
 497         # arv-get relies on this to do "arv-get {keep-locator} -".
 498         self.write_foo_bar_baz()
 499         self.assertEqual(
 500             'foobar',
 501             arvados.CollectionReader(
 502                 '3858f62230ac3c915f300c664312c63f+6'
 503                 ).manifest_text())
 504
 505
 506 class CollectionTestMixin(tutil.ApiClientMock):
 507     API_COLLECTIONS = run_test_server.fixture('collections')
 508     DEFAULT_COLLECTION = API_COLLECTIONS['foo_file']
 509     DEFAULT_DATA_HASH = DEFAULT_COLLECTION['portable_data_hash']
 510     DEFAULT_MANIFEST = DEFAULT_COLLECTION['manifest_text']
 511     DEFAULT_UUID = DEFAULT_COLLECTION['uuid']
 512     ALT_COLLECTION = API_COLLECTIONS['bar_file']
 513     ALT_DATA_HASH = ALT_COLLECTION['portable_data_hash']
 514     ALT_MANIFEST = ALT_COLLECTION['manifest_text']
 515
 516     def api_client_mock(self, status=200):
 517         client = super(CollectionTestMixin, self).api_client_mock()
 518         self.mock_keep_services(client, status=status, service_type='proxy', count=1)
 519         return client
 520
 521
 522 @tutil.skip_sleep
 523 class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin):
 524     def mock_get_collection(self, api_mock, code, fixturename):
 525         body = self.API_COLLECTIONS.get(fixturename)
 526         self._mock_api_call(api_mock.collections().get, code, body)
 527
 528     def api_client_mock(self, status=200):
 529         client = super(CollectionReaderTestCase, self).api_client_mock()
 530         self.mock_get_collection(client, status, 'foo_file')
 531         return client
 532
 533     def test_init_no_default_retries(self):
 534         client = self.api_client_mock(200)
 535         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 536         reader.manifest_text()
 537         client.collections().get().execute.assert_called_with(num_retries=0)
 538
 539     def test_uuid_init_success(self):
 540         client = self.api_client_mock(200)
 541         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 542                                           num_retries=3)
 543         self.assertEqual(self.DEFAULT_COLLECTION['manifest_text'],
 544                          reader.manifest_text())
 545         client.collections().get().execute.assert_called_with(num_retries=3)
 546
 547     def test_uuid_init_failure_raises_api_error(self):
 548         client = self.api_client_mock(500)
 549         with self.assertRaises(arvados.errors.ApiError):
 550             reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 551
 552     def test_locator_init(self):
 553         client = self.api_client_mock(200)
 554         # Ensure Keep will not return anything if asked.
 555         with tutil.mock_keep_responses(None, 404):
 556             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 557                                               api_client=client)
 558             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 559
 560     def test_locator_init_fallback_to_keep(self):
 561         # crunch-job needs this to read manifests that have only ever
 562         # been written to Keep.
 563         client = self.api_client_mock(200)
 564         self.mock_get_collection(client, 404, None)
 565         with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 566             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 567                                               api_client=client)
 568             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 569
 570     def test_uuid_init_no_fallback_to_keep(self):
 571         # Do not look up a collection UUID in Keep.
 572         client = self.api_client_mock(404)
 573         with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 574             with self.assertRaises(arvados.errors.ApiError):
 575                 reader = arvados.CollectionReader(self.DEFAULT_UUID,
 576                                                   api_client=client)
 577
 578     def test_try_keep_first_if_permission_hint(self):
 579         # To verify that CollectionReader tries Keep first here, we
 580         # mock API server to return the wrong data.
 581         client = self.api_client_mock(200)
 582         with tutil.mock_keep_responses(self.ALT_MANIFEST, 200):
 583             self.assertEqual(
 584                 self.ALT_MANIFEST,
 585                 arvados.CollectionReader(
 586                     self.ALT_DATA_HASH + '+Affffffffffffffffffffffffffffffffffffffff@fedcba98',
 587                     api_client=client).manifest_text())
 588
 589     def test_init_num_retries_propagated(self):
 590         # More of an integration test...
 591         client = self.api_client_mock(200)
 592         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 593                                           num_retries=3)
 594         with tutil.mock_keep_responses('foo', 500, 500, 200):
 595             self.assertEqual(b'foo',
 596                              b''.join(f.read(9) for f in reader.all_files()))
 597
 598     def test_read_nonnormalized_manifest_with_collection_reader(self):
 599         # client should be able to use CollectionReader on a manifest without normalizing it
 600         client = self.api_client_mock(500)
 601         nonnormal = ". acbd18db4cc2f85cedef654fccc4a4d8+3+Aabadbadbee@abeebdee 0:3:foo.txt 1:0:bar.txt 0:3:foo.txt\n"
 602         reader = arvados.CollectionReader(
 603             nonnormal,
 604             api_client=client, num_retries=0)
 605         # Ensure stripped_manifest() doesn't mangle our manifest in
 606         # any way other than stripping hints.
 607         self.assertEqual(
 608             re.sub('\+[^\d\s\+]+', '', nonnormal),
 609             reader.stripped_manifest())
 610         # Ensure stripped_manifest() didn't mutate our reader.
 611         self.assertEqual(nonnormal, reader.manifest_text())
 612         # Ensure the files appear in the order given in the manifest.
 613         self.assertEqual(
 614             [[6, '.', 'foo.txt'],
 615              [0, '.', 'bar.txt']],
 616             [[f.size(), f.stream_name(), f.name()]
 617              for f in reader.all_streams()[0].all_files()])
 618
 619     def test_read_empty_collection(self):
 620         client = self.api_client_mock(200)
 621         self.mock_get_collection(client, 200, 'empty')
 622         reader = arvados.CollectionReader('d41d8cd98f00b204e9800998ecf8427e+0',
 623                                           api_client=client)
 624         self.assertEqual('', reader.manifest_text())
 625
 626     def test_api_response(self):
 627         client = self.api_client_mock()
 628         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 629         self.assertEqual(self.DEFAULT_COLLECTION, reader.api_response())
 630
 631     def test_api_response_with_collection_from_keep(self):
 632         client = self.api_client_mock()
 633         self.mock_get_collection(client, 404, 'foo')
 634         with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 635             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 636                                               api_client=client)
 637             api_response = reader.api_response()
 638         self.assertIsNone(api_response)
 639
 640     def check_open_file(self, coll_file, stream_name, file_name, file_size):
 641         self.assertFalse(coll_file.closed, "returned file is not open")
 642         self.assertEqual(stream_name, coll_file.stream_name())
 643         self.assertEqual(file_name, coll_file.name)
 644         self.assertEqual(file_size, coll_file.size())
 645
 646     def test_open_collection_file_one_argument(self):
 647         client = self.api_client_mock(200)
 648         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 649         cfile = reader.open('./foo', 'rb')
 650         self.check_open_file(cfile, '.', 'foo', 3)
 651
 652     def test_open_deep_file(self):
 653         coll_name = 'collection_with_files_in_subdir'
 654         client = self.api_client_mock(200)
 655         self.mock_get_collection(client, 200, coll_name)
 656         reader = arvados.CollectionReader(
 657             self.API_COLLECTIONS[coll_name]['uuid'], api_client=client)
 658         cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt', 'rb')
 659         self.check_open_file(cfile, './subdir2/subdir3', 'file2_in_subdir3.txt',
 660                              32)
 661
 662     def test_open_nonexistent_stream(self):
 663         client = self.api_client_mock(200)
 664         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 665         self.assertRaises(IOError, reader.open, './nonexistent/foo')
 666
 667     def test_open_nonexistent_file(self):
 668         client = self.api_client_mock(200)
 669         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 670         self.assertRaises(IOError, reader.open, 'nonexistent')
 671
 672
 673 @tutil.skip_sleep
 674 class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin):
 675     def mock_keep(self, body, *codes, **headers):
 676         headers.setdefault('x-keep-replicas-stored', 2)
 677         return tutil.mock_keep_responses(body, *codes, **headers)
 678
 679     def foo_writer(self, **kwargs):
 680         kwargs.setdefault('api_client', self.api_client_mock())
 681         writer = arvados.CollectionWriter(**kwargs)
 682         writer.start_new_file('foo')
 683         writer.write(b'foo')
 684         return writer
 685
 686     def test_write_whole_collection(self):
 687         writer = self.foo_writer()
 688         with self.mock_keep(self.DEFAULT_DATA_HASH, 200, 200):
 689             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 690
 691     def test_write_no_default(self):
 692         writer = self.foo_writer()
 693         with self.mock_keep(None, 500):
 694             with self.assertRaises(arvados.errors.KeepWriteError):
 695                 writer.finish()
 696
 697     def test_write_insufficient_replicas_via_proxy(self):
 698         writer = self.foo_writer(replication=3)
 699         with self.mock_keep(None, 200, **{'x-keep-replicas-stored': 2}):
 700             with self.assertRaises(arvados.errors.KeepWriteError):
 701                 writer.manifest_text()
 702
 703     def test_write_insufficient_replicas_via_disks(self):
 704         client = mock.MagicMock(name='api_client')
 705         with self.mock_keep(
 706                 None, 200, 200,
 707                 **{'x-keep-replicas-stored': 1}) as keepmock:
 708             self.mock_keep_services(client, status=200, service_type='disk', count=2)
 709             writer = self.foo_writer(api_client=client, replication=3)
 710             with self.assertRaises(arvados.errors.KeepWriteError):
 711                 writer.manifest_text()
 712
 713     def test_write_three_replicas(self):
 714         client = mock.MagicMock(name='api_client')
 715         with self.mock_keep(
 716                 "", 500, 500, 500, 200, 200, 200,
 717                 **{'x-keep-replicas-stored': 1}) as keepmock:
 718             self.mock_keep_services(client, status=200, service_type='disk', count=6)
 719             writer = self.foo_writer(api_client=client, replication=3)
 720             writer.manifest_text()
 721             self.assertEqual(6, keepmock.call_count)
 722
 723     def test_write_whole_collection_through_retries(self):
 724         writer = self.foo_writer(num_retries=2)
 725         with self.mock_keep(self.DEFAULT_DATA_HASH,
 726                             500, 500, 200, 500, 500, 200):
 727             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 728
 729     def test_flush_data_retries(self):
 730         writer = self.foo_writer(num_retries=2)
 731         foo_hash = self.DEFAULT_MANIFEST.split()[1]
 732         with self.mock_keep(foo_hash, 500, 200):
 733             writer.flush_data()
 734         self.assertEqual(self.DEFAULT_MANIFEST, writer.manifest_text())
 735
 736     def test_one_open(self):
 737         client = self.api_client_mock()
 738         writer = arvados.CollectionWriter(client)
 739         with writer.open('out') as out_file:
 740             self.assertEqual('.', writer.current_stream_name())
 741             self.assertEqual('out', writer.current_file_name())
 742             out_file.write(b'test data')
 743             data_loc = tutil.str_keep_locator('test data')
 744         self.assertTrue(out_file.closed, "writer file not closed after context")
 745         self.assertRaises(ValueError, out_file.write, 'extra text')
 746         with self.mock_keep(data_loc, 200) as keep_mock:
 747             self.assertEqual(". {} 0:9:out\n".format(data_loc),
 748                              writer.manifest_text())
 749
 750     def test_open_writelines(self):
 751         client = self.api_client_mock()
 752         writer = arvados.CollectionWriter(client)
 753         with writer.open('six') as out_file:
 754             out_file.writelines(['12', '34', '56'])
 755             data_loc = tutil.str_keep_locator('123456')
 756         with self.mock_keep(data_loc, 200) as keep_mock:
 757             self.assertEqual(". {} 0:6:six\n".format(data_loc),
 758                              writer.manifest_text())
 759
 760     def test_open_flush(self):
 761         client = self.api_client_mock()
 762         data_loc1 = tutil.str_keep_locator('flush1')
 763         data_loc2 = tutil.str_keep_locator('flush2')
 764         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 765             writer = arvados.CollectionWriter(client)
 766             with writer.open('flush_test') as out_file:
 767                 out_file.write(b'flush1')
 768                 out_file.flush()
 769                 out_file.write(b'flush2')
 770             self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1,
 771                                                                 data_loc2),
 772                              writer.manifest_text())
 773
 774     def test_two_opens_same_stream(self):
 775         client = self.api_client_mock()
 776         writer = arvados.CollectionWriter(client)
 777         with writer.open('.', '1') as out_file:
 778             out_file.write(b'1st')
 779         with writer.open('.', '2') as out_file:
 780             out_file.write(b'2nd')
 781         data_loc = tutil.str_keep_locator('1st2nd')
 782         with self.mock_keep(data_loc, 200) as keep_mock:
 783             self.assertEqual(". {} 0:3:1 3:3:2\n".format(data_loc),
 784                              writer.manifest_text())
 785
 786     def test_two_opens_two_streams(self):
 787         client = self.api_client_mock()
 788         data_loc1 = tutil.str_keep_locator('file')
 789         data_loc2 = tutil.str_keep_locator('indir')
 790         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 791             writer = arvados.CollectionWriter(client)
 792             with writer.open('file') as out_file:
 793                 out_file.write(b'file')
 794             with writer.open('./dir', 'indir') as out_file:
 795                 out_file.write(b'indir')
 796             expected = ". {} 0:4:file\n./dir {} 0:5:indir\n".format(
 797                 data_loc1, data_loc2)
 798             self.assertEqual(expected, writer.manifest_text())
 799
 800     def test_dup_open_fails(self):
 801         client = self.api_client_mock()
 802         writer = arvados.CollectionWriter(client)
 803         file1 = writer.open('one')
 804         self.assertRaises(arvados.errors.AssertionError, writer.open, 'two')
 805
 806
 807 class CollectionOpenModes(run_test_server.TestCaseWithServers):
 808
 809     def test_open_binary_modes(self):
 810         c = Collection()
 811         for mode in ['wb', 'wb+', 'ab', 'ab+']:
 812             with c.open('foo', 'wb') as f:
 813                 f.write(b'foo')
 814
 815     def test_open_invalid_modes(self):
 816         c = Collection()
 817         for mode in ['+r', 'aa', '++', 'r+b', 'beer', '', None]:
 818             with self.assertRaises(Exception):
 819                 c.open('foo', mode)
 820
 821     def test_open_text_modes(self):
 822         c = Collection()
 823         with c.open('foo', 'wb') as f:
 824             f.write('foo')
 825         for mode in ['r', 'rt', 'r+', 'rt+', 'w', 'wt', 'a', 'at']:
 826             if sys.version_info >= (3, 0):
 827                 with self.assertRaises(NotImplementedError):
 828                     c.open('foo', mode)
 829             else:
 830                 with c.open('foo', mode) as f:
 831                     if mode[0] == 'r' and '+' not in mode:
 832                         self.assertEqual('foo', f.read(3))
 833                     else:
 834                         f.write('bar')
 835                         f.seek(-3, os.SEEK_CUR)
 836                         self.assertEqual('bar', f.read(3))
 837
 838
 839 class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin):
 840
 841     def test_replication_desired_kept_on_load(self):
 842         m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
 843         c1 = Collection(m, replication_desired=1)
 844         c1.save_new()
 845         loc = c1.manifest_locator()
 846         c2 = Collection(loc)
 847         self.assertEqual(c1.manifest_text, c2.manifest_text)
 848         self.assertEqual(c1.replication_desired, c2.replication_desired)
 849
 850     def test_replication_desired_not_loaded_if_provided(self):
 851         m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
 852         c1 = Collection(m, replication_desired=1)
 853         c1.save_new()
 854         loc = c1.manifest_locator()
 855         c2 = Collection(loc, replication_desired=2)
 856         self.assertEqual(c1.manifest_text, c2.manifest_text)
 857         self.assertNotEqual(c1.replication_desired, c2.replication_desired)
 858
 859     def test_init_manifest(self):
 860         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 861 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 862 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 863 """
 864         self.assertEqual(m1, CollectionReader(m1).manifest_text(normalize=False))
 865         self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", CollectionReader(m1).manifest_text(normalize=True))
 866
 867     def test_init_manifest_with_collision(self):
 868         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 869 ./md5sum.txt 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 870 """
 871         with self.assertRaises(arvados.errors.ArgumentError):
 872             self.assertEqual(m1, CollectionReader(m1))
 873
 874     def test_init_manifest_with_error(self):
 875         m1 = """. 0:43:md5sum.txt"""
 876         with self.assertRaises(arvados.errors.ArgumentError):
 877             self.assertEqual(m1, CollectionReader(m1))
 878
 879     def test_remove(self):
 880         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
 881         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 882         self.assertIn("count1.txt", c)
 883         c.remove("count1.txt")
 884         self.assertNotIn("count1.txt", c)
 885         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
 886         with self.assertRaises(arvados.errors.ArgumentError):
 887             c.remove("")
 888
 889     def test_find(self):
 890         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
 891         self.assertIs(c.find("."), c)
 892         self.assertIs(c.find("./count1.txt"), c["count1.txt"])
 893         self.assertIs(c.find("count1.txt"), c["count1.txt"])
 894         with self.assertRaises(IOError):
 895             c.find("/.")
 896         with self.assertRaises(arvados.errors.ArgumentError):
 897             c.find("")
 898         self.assertIs(c.find("./nonexistant.txt"), None)
 899         self.assertIs(c.find("./nonexistantsubdir/nonexistant.txt"), None)
 900
 901     def test_remove_in_subdir(self):
 902         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 903         c.remove("foo/count2.txt")
 904         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 905
 906     def test_remove_empty_subdir(self):
 907         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 908         c.remove("foo/count2.txt")
 909         c.remove("foo")
 910         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 911
 912     def test_remove_nonempty_subdir(self):
 913         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 914         with self.assertRaises(IOError):
 915             c.remove("foo")
 916         c.remove("foo", recursive=True)
 917         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 918
 919     def test_copy_to_file_in_dir(self):
 920         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 921         c.copy("count1.txt", "foo/count2.txt")
 922         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
 923
 924     def test_copy_file(self):
 925         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 926         c.copy("count1.txt", "count2.txt")
 927         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 928
 929     def test_copy_to_existing_dir(self):
 930         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 931         c.copy("count1.txt", "foo")
 932         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 933
 934     def test_copy_to_new_dir(self):
 935         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 936         c.copy("count1.txt", "foo/")
 937         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 938
 939     def test_rename_file(self):
 940         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 941         c.rename("count1.txt", "count2.txt")
 942         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
 943
 944     def test_move_file_to_dir(self):
 945         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 946         c.mkdirs("foo")
 947         c.rename("count1.txt", "foo/count2.txt")
 948         self.assertEqual("./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
 949
 950     def test_move_file_to_other(self):
 951         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 952         c2 = Collection()
 953         c2.rename("count1.txt", "count2.txt", source_collection=c1)
 954         self.assertEqual("", c1.manifest_text())
 955         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c2.manifest_text())
 956
 957     def test_clone(self):
 958         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 959         cl = c.clone()
 960         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", cl.portable_manifest_text())
 961
 962     def test_diff_del_add(self):
 963         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 964         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
 965         d = c2.diff(c1)
 966         self.assertEqual(sorted(d), [
 967             ('add', './count1.txt', c1["count1.txt"]),
 968             ('del', './count2.txt', c2["count2.txt"]),
 969         ])
 970         d = c1.diff(c2)
 971         self.assertEqual(sorted(d), [
 972             ('add', './count2.txt', c2["count2.txt"]),
 973             ('del', './count1.txt', c1["count1.txt"]),
 974         ])
 975         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
 976         c1.apply(d)
 977         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
 978
 979     def test_diff_same(self):
 980         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 981         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 982         d = c2.diff(c1)
 983         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
 984         d = c1.diff(c2)
 985         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
 986
 987         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
 988         c1.apply(d)
 989         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
 990
 991     def test_diff_mod(self):
 992         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 993         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
 994         d = c2.diff(c1)
 995         self.assertEqual(d, [('mod', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
 996         d = c1.diff(c2)
 997         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
 998
 999         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1000         c1.apply(d)
1001         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1002
1003     def test_diff_add(self):
1004         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1005         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt 10:20:count2.txt\n')
1006         d = c2.diff(c1)
1007         self.assertEqual(sorted(d), [
1008             ('del', './count2.txt', c2["count2.txt"]),
1009             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1010         ])
1011         d = c1.diff(c2)
1012         self.assertEqual(sorted(d), [
1013             ('add', './count2.txt', c2["count2.txt"]),
1014             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1015         ])
1016
1017         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1018         c1.apply(d)
1019         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1020
1021     def test_diff_add_in_subcollection(self):
1022         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1023         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1024         d = c2.diff(c1)
1025         self.assertEqual(sorted(d), [
1026             ('del', './foo', c2["foo"]),
1027             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1028         ])
1029         d = c1.diff(c2)
1030         self.assertEqual(sorted(d), [
1031             ('add', './foo', c2["foo"]),
1032             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1033         ])
1034         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1035         c1.apply(d)
1036         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1037
1038     def test_diff_del_add_in_subcollection(self):
1039         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1040         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:3:count3.txt\n')
1041         d = c2.diff(c1)
1042         self.assertEqual(sorted(d), [
1043             ('add', './foo/count2.txt', c1.find("foo/count2.txt")),
1044             ('del', './foo/count3.txt', c2.find("foo/count3.txt")),
1045             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1046         ])
1047         d = c1.diff(c2)
1048         self.assertEqual(sorted(d), [
1049             ('add', './foo/count3.txt', c2.find("foo/count3.txt")),
1050             ('del', './foo/count2.txt', c1.find("foo/count2.txt")),
1051             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1052         ])
1053
1054         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1055         c1.apply(d)
1056         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1057
1058     def test_diff_mod_in_subcollection(self):
1059         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1060         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:3:foo\n')
1061         d = c2.diff(c1)
1062         self.assertEqual(sorted(d), [
1063             ('mod', './foo', c2["foo"], c1["foo"]),
1064             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1065         ])
1066         d = c1.diff(c2)
1067         self.assertEqual(sorted(d), [
1068             ('mod', './foo', c1["foo"], c2["foo"]),
1069             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1070         ])
1071
1072         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1073         c1.apply(d)
1074         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1075
1076     def test_conflict_keep_local_change(self):
1077         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1078         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1079         d = c1.diff(c2)
1080         self.assertEqual(sorted(d), [
1081             ('add', './count2.txt', c2["count2.txt"]),
1082             ('del', './count1.txt', c1["count1.txt"]),
1083         ])
1084         f = c1.open("count1.txt", "wb")
1085         f.write(b"zzzzz")
1086
1087         # c1 changed, so it should not be deleted.
1088         c1.apply(d)
1089         self.assertEqual(c1.portable_manifest_text(), ". 95ebc3c7b3b9f1d2c40fec14415d3cb8+5 5348b82a029fd9e971a811ce1f71360b+43 0:5:count1.txt 5:10:count2.txt\n")
1090
1091     def test_conflict_mod(self):
1092         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1093         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1094         d = c1.diff(c2)
1095         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1096         f = c1.open("count1.txt", "wb")
1097         f.write(b"zzzzz")
1098
1099         # c1 changed, so c2 mod will go to a conflict file
1100         c1.apply(d)
1101         self.assertRegex(
1102             c1.portable_manifest_text(),
1103             r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1104
1105     def test_conflict_add(self):
1106         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
1107         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
1108         d = c1.diff(c2)
1109         self.assertEqual(sorted(d), [
1110             ('add', './count1.txt', c2["count1.txt"]),
1111             ('del', './count2.txt', c1["count2.txt"]),
1112         ])
1113         f = c1.open("count1.txt", "wb")
1114         f.write(b"zzzzz")
1115
1116         # c1 added count1.txt, so c2 add will go to a conflict file
1117         c1.apply(d)
1118         self.assertRegex(
1119             c1.portable_manifest_text(),
1120             r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1121
1122     def test_conflict_del(self):
1123         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1124         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1125         d = c1.diff(c2)
1126         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1127         c1.remove("count1.txt")
1128
1129         # c1 deleted, so c2 mod will go to a conflict file
1130         c1.apply(d)
1131         self.assertRegex(
1132             c1.portable_manifest_text(),
1133             r"\. 5348b82a029fd9e971a811ce1f71360b\+43 0:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1134
1135     def test_notify(self):
1136         c1 = Collection()
1137         events = []
1138         c1.subscribe(lambda event, collection, name, item: events.append((event, collection, name, item)))
1139         f = c1.open("foo.txt", "wb")
1140         self.assertEqual(events[0], (arvados.collection.ADD, c1, "foo.txt", f.arvadosfile))
1141
1142     def test_open_w(self):
1143         c1 = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n")
1144         self.assertEqual(c1["count1.txt"].size(), 10)
1145         c1.open("count1.txt", "wb").close()
1146         self.assertEqual(c1["count1.txt"].size(), 0)
1147
1148
1149 class NewCollectionTestCaseWithServers(run_test_server.TestCaseWithServers):
1150     def test_get_manifest_text_only_committed(self):
1151         c = Collection()
1152         with c.open("count.txt", "wb") as f:
1153             # One file committed
1154             with c.open("foo.txt", "wb") as foo:
1155                 foo.write(b"foo")
1156                 foo.flush() # Force block commit
1157             f.write(b"0123456789")
1158             # Other file not committed. Block not written to keep yet.
1159             self.assertEqual(
1160                 c._get_manifest_text(".",
1161                                      strip=False,
1162                                      normalize=False,
1163                                      only_committed=True),
1164                 '. acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:count.txt 0:3:foo.txt\n')
1165             # And now with the file closed...
1166             f.flush() # Force block commit
1167         self.assertEqual(
1168             c._get_manifest_text(".",
1169                                  strip=False,
1170                                  normalize=False,
1171                                  only_committed=True),
1172             ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:10:count.txt 10:3:foo.txt\n")
1173
1174     def test_only_small_blocks_are_packed_together(self):
1175         c = Collection()
1176         # Write a couple of small files,
1177         f = c.open("count.txt", "wb")
1178         f.write(b"0123456789")
1179         f.close(flush=False)
1180         foo = c.open("foo.txt", "wb")
1181         foo.write(b"foo")
1182         foo.close(flush=False)
1183         # Then, write a big file, it shouldn't be packed with the ones above
1184         big = c.open("bigfile.txt", "wb")
1185         big.write(b"x" * 1024 * 1024 * 33) # 33 MB > KEEP_BLOCK_SIZE/2
1186         big.close(flush=False)
1187         self.assertEqual(
1188             c.manifest_text("."),
1189             '. 2d303c138c118af809f39319e5d507e9+34603008 a8430a058b8fbf408e1931b794dbd6fb+13 0:34603008:bigfile.txt 34603008:10:count.txt 34603018:3:foo.txt\n')
1190
1191     def test_flush_after_small_block_packing(self):
1192         c = Collection()
1193         # Write a couple of small files,
1194         f = c.open("count.txt", "w")
1195         f.write("0123456789")
1196         f.close(flush=False)
1197         foo = c.open("foo.txt", "w")
1198         foo.write("foo")
1199         foo.close(flush=False)
1200
1201         self.assertEqual(
1202             c.manifest_text(),
1203             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1204
1205         f = c.open("count.txt", "r+")
1206         f.close(flush=True)
1207
1208         self.assertEqual(
1209             c.manifest_text(),
1210             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1211
1212     def test_write_after_small_block_packing2(self):
1213         c = Collection()
1214         # Write a couple of small files,
1215         f = c.open("count.txt", "w")
1216         f.write("0123456789")
1217         f.close(flush=False)
1218         foo = c.open("foo.txt", "w")
1219         foo.write("foo")
1220         foo.close(flush=False)
1221
1222         self.assertEqual(
1223             c.manifest_text(),
1224             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1225
1226         f = c.open("count.txt", "r+")
1227         f.write("abc")
1228         f.close(flush=False)
1229
1230         self.assertEqual(
1231             c.manifest_text(),
1232             '. 900150983cd24fb0d6963f7d28e17f72+3 a8430a058b8fbf408e1931b794dbd6fb+13 0:3:count.txt 6:7:count.txt 13:3:foo.txt\n')
1233
1234
1235     def test_small_block_packing_with_overwrite(self):
1236         c = Collection()
1237         c.open("b1", "w").close()
1238         c["b1"].writeto(0, "b1", 0)
1239
1240         c.open("b2", "w").close()
1241         c["b2"].writeto(0, "b2", 0)
1242
1243         c["b1"].writeto(0, "1b", 0)
1244
1245         self.assertEquals(c.manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1 2:2:b2\n")
1246         self.assertEquals(c["b1"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1\n")
1247         self.assertEquals(c["b2"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 2:2:b2\n")
1248
1249
1250 class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers):
1251     MAIN_SERVER = {}
1252     KEEP_SERVER = {}
1253
1254     def create_count_txt(self):
1255         # Create an empty collection, save it to the API server, then write a
1256         # file, but don't save it.
1257
1258         c = Collection()
1259         c.save_new("CollectionCreateUpdateTest", ensure_unique_name=True)
1260         self.assertEqual(c.portable_data_hash(), "d41d8cd98f00b204e9800998ecf8427e+0")
1261         self.assertEqual(c.api_response()["portable_data_hash"], "d41d8cd98f00b204e9800998ecf8427e+0" )
1262
1263         with c.open("count.txt", "wb") as f:
1264             f.write(b"0123456789")
1265
1266         self.assertEqual(c.portable_manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1267
1268         return c
1269
1270     def test_create_and_save(self):
1271         c = self.create_count_txt()
1272         c.save()
1273         self.assertRegex(
1274             c.manifest_text(),
1275             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1276
1277     def test_create_and_save_new(self):
1278         c = self.create_count_txt()
1279         c.save_new()
1280         self.assertRegex(
1281             c.manifest_text(),
1282             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1283
1284     def test_create_diff_apply(self):
1285         c1 = self.create_count_txt()
1286         c1.save()
1287
1288         c2 = Collection(c1.manifest_locator())
1289         with c2.open("count.txt", "wb") as f:
1290             f.write(b"abcdefg")
1291
1292         diff = c1.diff(c2)
1293
1294         self.assertEqual(diff[0], (arvados.collection.MOD, u'./count.txt', c1["count.txt"], c2["count.txt"]))
1295
1296         c1.apply(diff)
1297         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1298
1299     def test_diff_apply_with_token(self):
1300         baseline = CollectionReader(". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:10:count.txt\n")
1301         c = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1302         other = CollectionReader(". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1303
1304         diff = baseline.diff(other)
1305         self.assertEqual(diff, [('mod', u'./count.txt', c["count.txt"], other["count.txt"])])
1306
1307         c.apply(diff)
1308
1309         self.assertEqual(c.manifest_text(), ". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1310
1311
1312     def test_create_and_update(self):
1313         c1 = self.create_count_txt()
1314         c1.save()
1315
1316         c2 = arvados.collection.Collection(c1.manifest_locator())
1317         with c2.open("count.txt", "wb") as f:
1318             f.write(b"abcdefg")
1319
1320         c2.save()
1321
1322         self.assertNotEqual(c1.portable_data_hash(), c2.portable_data_hash())
1323         c1.update()
1324         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1325
1326
1327     def test_create_and_update_with_conflict(self):
1328         c1 = self.create_count_txt()
1329         c1.save()
1330
1331         with c1.open("count.txt", "wb") as f:
1332             f.write(b"XYZ")
1333
1334         c2 = arvados.collection.Collection(c1.manifest_locator())
1335         with c2.open("count.txt", "wb") as f:
1336             f.write(b"abcdefg")
1337
1338         c2.save()
1339
1340         c1.update()
1341         self.assertRegex(
1342             c1.manifest_text(),
1343             r"\. e65075d550f9b5bf9992fa1d71a131be\+3\S* 7ac66c0f148de9519b8bd264312c4d64\+7\S* 0:3:count\.txt 3:7:count\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1344
1345
1346 if __name__ == '__main__':
1347     unittest.main()