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_pdh_is_native_str(self):
  59         pdh = self.write_foo_bar_baz()
  60         self.assertEqual(type(''), type(pdh))
  61
  62     def test_keep_local_store(self):
  63         self.assertEqual(self.keep_client.put(b'foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
  64         self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), b'foo', 'wrong data from Keep.get')
  65
  66     def test_local_collection_writer(self):
  67         self.assertEqual(self.write_foo_bar_baz(),
  68                          '23ca013983d6239e98931cc779e68426+114',
  69                          'wrong locator hash: ' + self.write_foo_bar_baz())
  70
  71     def test_local_collection_reader(self):
  72         foobarbaz = self.write_foo_bar_baz()
  73         cr = arvados.CollectionReader(
  74             foobarbaz + '+Xzizzle', self.api_client)
  75         got = []
  76         for s in cr.all_streams():
  77             for f in s.all_files():
  78                 got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]]
  79         expected = [[3, '.', 'foo.txt', b'foo'],
  80                     [3, '.', 'bar.txt', b'bar'],
  81                     [3, './baz', 'baz.txt', b'baz']]
  82         self.assertEqual(got,
  83                          expected)
  84         stream0 = cr.all_streams()[0]
  85         self.assertEqual(stream0.readfrom(0, 0),
  86                          b'',
  87                          'reading zero bytes should have returned empty string')
  88         self.assertEqual(stream0.readfrom(0, 2**26),
  89                          b'foobar',
  90                          'reading entire stream failed')
  91         self.assertEqual(stream0.readfrom(2**26, 0),
  92                          b'',
  93                          'reading zero bytes should have returned empty string')
  94
  95     def _test_subset(self, collection, expected):
  96         cr = arvados.CollectionReader(collection, self.api_client)
  97         for s in cr.all_streams():
  98             for ex in expected:
  99                 if ex[0] == s:
 100                     f = s.files()[ex[2]]
 101                     got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))]
 102                     self.assertEqual(got,
 103                                      ex,
 104                                      'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex))
 105
 106     def test_collection_manifest_subset(self):
 107         foobarbaz = self.write_foo_bar_baz()
 108         self._test_subset(foobarbaz,
 109                           [[3, '.',     'bar.txt', b'bar'],
 110                            [3, '.',     'foo.txt', b'foo'],
 111                            [3, './baz', 'baz.txt', b'baz']])
 112         self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" %
 113                            (self.keep_client.put(b"foo"),
 114                             self.keep_client.put(b"bar"))),
 115                           [[3, '.', 'bar.txt', b'bar'],
 116                            [3, '.', 'foo.txt', b'foo']])
 117         self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" %
 118                            (self.keep_client.put(b"foo"),
 119                             self.keep_client.put(b"bar"))),
 120                           [[2, '.', 'fo.txt', b'fo'],
 121                            [4, '.', 'obar.txt', b'obar']])
 122         self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" %
 123                            (self.keep_client.put(b"foo"),
 124                             self.keep_client.put(b"bar"))),
 125                           [[2, '.', 'ar.txt', b'ar'],
 126                            [2, '.', 'fo.txt', b'fo'],
 127                            [2, '.', 'ob.txt', b'ob'],
 128                            [0, '.', 'zero.txt', b'']])
 129
 130     def test_collection_empty_file(self):
 131         cw = arvados.CollectionWriter(self.api_client)
 132         cw.start_new_file('zero.txt')
 133         cw.write(b'')
 134
 135         self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n")
 136         self.check_manifest_file_sizes(cw.manifest_text(), [0])
 137         cw = arvados.CollectionWriter(self.api_client)
 138         cw.start_new_file('zero.txt')
 139         cw.write(b'')
 140         cw.start_new_file('one.txt')
 141         cw.write(b'1')
 142         cw.start_new_stream('foo')
 143         cw.start_new_file('zero.txt')
 144         cw.write(b'')
 145         self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0])
 146
 147     def test_no_implicit_normalize(self):
 148         cw = arvados.CollectionWriter(self.api_client)
 149         cw.start_new_file('b')
 150         cw.write(b'b')
 151         cw.start_new_file('a')
 152         cw.write(b'')
 153         self.check_manifest_file_sizes(cw.manifest_text(), [1,0])
 154         self.check_manifest_file_sizes(
 155             arvados.CollectionReader(
 156                 cw.manifest_text()).manifest_text(normalize=True),
 157             [0,1])
 158
 159     def check_manifest_file_sizes(self, manifest_text, expect_sizes):
 160         cr = arvados.CollectionReader(manifest_text, self.api_client)
 161         got_sizes = []
 162         for f in cr.all_files():
 163             got_sizes += [f.size()]
 164         self.assertEqual(got_sizes, expect_sizes, "got wrong file sizes %s, expected %s" % (got_sizes, expect_sizes))
 165
 166     def test_normalized_collection(self):
 167         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 168 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 169 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 170 """
 171         self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True),
 172                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
 173 """)
 174
 175         m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
 176 """
 177         self.assertEqual(arvados.CollectionReader(m2, self.api_client).manifest_text(normalize=True), m2)
 178
 179         m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
 180 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 181 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 182 """
 183         self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(normalize=True),
 184                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
 185 """)
 186
 187         m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 188 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 189 ./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
 190 """
 191         self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(normalize=True),
 192                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
 193 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 194 """)
 195
 196         m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 197 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 198 ./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar
 199 """
 200         self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(normalize=True),
 201                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
 202 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 203 """)
 204
 205         with self.data_file('1000G_ref_manifest') as f6:
 206             m6 = f6.read()
 207             self.assertEqual(arvados.CollectionReader(m6, self.api_client).manifest_text(normalize=True), m6)
 208
 209         with self.data_file('jlake_manifest') as f7:
 210             m7 = f7.read()
 211             self.assertEqual(arvados.CollectionReader(m7, self.api_client).manifest_text(normalize=True), m7)
 212
 213         m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt
 214 """
 215         self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8)
 216
 217     def test_locators_and_ranges(self):
 218         blocks2 = [Range('a', 0, 10),
 219                    Range('b', 10, 10),
 220                    Range('c', 20, 10),
 221                    Range('d', 30, 10),
 222                    Range('e', 40, 10),
 223                    Range('f', 50, 10)]
 224
 225         self.assertEqual(arvados.locators_and_ranges(blocks2,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 226         self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 227         self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 228         self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 229         self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 230         self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 231         self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), [])
 232         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 233
 234         self.assertEqual(arvados.locators_and_ranges(blocks2,  0,  2), [LocatorAndRange('a', 10, 0, 2)])
 235         self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [LocatorAndRange('b', 10, 0, 2)])
 236         self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [LocatorAndRange('c', 10, 0, 2)])
 237         self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [LocatorAndRange('d', 10, 0, 2)])
 238         self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [LocatorAndRange('e', 10, 0, 2)])
 239         self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [LocatorAndRange('f', 10, 0, 2)])
 240         self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), [])
 241         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 242
 243         self.assertEqual(arvados.locators_and_ranges(blocks2,  9,  2), [LocatorAndRange('a', 10, 9, 1), LocatorAndRange('b', 10, 0, 1)])
 244         self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [LocatorAndRange('b', 10, 9, 1), LocatorAndRange('c', 10, 0, 1)])
 245         self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [LocatorAndRange('c', 10, 9, 1), LocatorAndRange('d', 10, 0, 1)])
 246         self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [LocatorAndRange('d', 10, 9, 1), LocatorAndRange('e', 10, 0, 1)])
 247         self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [LocatorAndRange('e', 10, 9, 1), LocatorAndRange('f', 10, 0, 1)])
 248         self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [LocatorAndRange('f', 10, 9, 1)])
 249
 250
 251         blocks3 = [Range('a', 0, 10),
 252                   Range('b', 10, 10),
 253                   Range('c', 20, 10),
 254                   Range('d', 30, 10),
 255                   Range('e', 40, 10),
 256                   Range('f', 50, 10),
 257                    Range('g', 60, 10)]
 258
 259         self.assertEqual(arvados.locators_and_ranges(blocks3,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 260         self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 261         self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 262         self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 263         self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 264         self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 265         self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [LocatorAndRange('g', 10, 2, 2)])
 266
 267
 268         blocks = [Range('a', 0, 10),
 269                   Range('b', 10, 15),
 270                   Range('c', 25, 5)]
 271         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 0), [])
 272         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [LocatorAndRange('a', 10, 0, 5)])
 273         self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [LocatorAndRange('a', 10, 3, 5)])
 274         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [LocatorAndRange('a', 10, 0, 10)])
 275
 276         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [LocatorAndRange('a', 10, 0, 10),
 277                                                                       LocatorAndRange('b', 15, 0, 1)])
 278         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [LocatorAndRange('a', 10, 1, 9),
 279                                                                       LocatorAndRange('b', 15, 0, 2)])
 280         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [LocatorAndRange('a', 10, 0, 10),
 281                                                                       LocatorAndRange('b', 15, 0, 15)])
 282
 283         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [LocatorAndRange('a', 10, 0, 10),
 284                                                                       LocatorAndRange('b', 15, 0, 15),
 285                                                                       LocatorAndRange('c', 5, 0, 5)])
 286         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [LocatorAndRange('a', 10, 1, 9),
 287                                                                       LocatorAndRange('b', 15, 0, 15),
 288                                                                       LocatorAndRange('c', 5, 0, 5)])
 289         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [LocatorAndRange('a', 10, 0, 10),
 290                                                                       LocatorAndRange('b', 15, 0, 15),
 291                                                                       LocatorAndRange('c', 5, 0, 5)])
 292
 293         self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [LocatorAndRange('b', 15, 5, 5)])
 294
 295         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [LocatorAndRange('a', 10, 8, 2),
 296                                                                       LocatorAndRange('b', 15, 0, 15)])
 297
 298         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [LocatorAndRange('a', 10, 8, 2),
 299                                                                       LocatorAndRange('b', 15, 0, 15),
 300                                                                       LocatorAndRange('c', 5, 0, 3)])
 301
 302         self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [LocatorAndRange('c', 5, 1, 2)])
 303
 304         self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [LocatorAndRange('a', 10, 9, 1),
 305                                                                       LocatorAndRange('b', 15, 0, 14)])
 306         self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [LocatorAndRange('b', 15, 0, 15)])
 307         self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [LocatorAndRange('b', 15, 1, 14),
 308                                                                        LocatorAndRange('c', 5, 0, 1)])
 309
 310     class MockKeep(object):
 311         def __init__(self, content, num_retries=0):
 312             self.content = content
 313
 314         def get(self, locator, num_retries=0):
 315             return self.content[locator]
 316
 317     def test_stream_reader(self):
 318         keepblocks = {
 319             'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': b'abcdefghij',
 320             'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': b'klmnopqrstuvwxy',
 321             'cccccccccccccccccccccccccccccccc+5': b'z0123',
 322         }
 323         mk = self.MockKeep(keepblocks)
 324
 325         sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk)
 326
 327         content = b'abcdefghijklmnopqrstuvwxyz0123456789'
 328
 329         self.assertEqual(sr.readfrom(0, 30), content[0:30])
 330         self.assertEqual(sr.readfrom(2, 30), content[2:30])
 331
 332         self.assertEqual(sr.readfrom(2, 8), content[2:10])
 333         self.assertEqual(sr.readfrom(0, 10), content[0:10])
 334
 335         self.assertEqual(sr.readfrom(0, 5), content[0:5])
 336         self.assertEqual(sr.readfrom(5, 5), content[5:10])
 337         self.assertEqual(sr.readfrom(10, 5), content[10:15])
 338         self.assertEqual(sr.readfrom(15, 5), content[15:20])
 339         self.assertEqual(sr.readfrom(20, 5), content[20:25])
 340         self.assertEqual(sr.readfrom(25, 5), content[25:30])
 341         self.assertEqual(sr.readfrom(30, 5), b'')
 342
 343     def test_extract_file(self):
 344         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 345 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt
 346 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt
 347 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt
 348 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt
 349 """
 350
 351         m2 = arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True)
 352
 353         self.assertEqual(m2,
 354                          ". 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")
 355         files = arvados.CollectionReader(
 356             m2, self.api_client).all_streams()[0].files()
 357
 358         self.assertEqual(files['md5sum.txt'].as_manifest(),
 359                          ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n")
 360         self.assertEqual(files['md6sum.txt'].as_manifest(),
 361                          ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n")
 362         self.assertEqual(files['md7sum.txt'].as_manifest(),
 363                          ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n")
 364         self.assertEqual(files['md9sum.txt'].as_manifest(),
 365                          ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n")
 366
 367     def test_write_directory_tree(self):
 368         cwriter = arvados.CollectionWriter(self.api_client)
 369         cwriter.write_directory_tree(self.build_directory_tree(
 370                 ['basefile', 'subdir/subfile']))
 371         self.assertEqual(cwriter.manifest_text(),
 372                          """. c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 373 ./subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 374
 375     def test_write_named_directory_tree(self):
 376         cwriter = arvados.CollectionWriter(self.api_client)
 377         cwriter.write_directory_tree(self.build_directory_tree(
 378                 ['basefile', 'subdir/subfile']), 'root')
 379         self.assertEqual(
 380             cwriter.manifest_text(),
 381             """./root c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 382 ./root/subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 383
 384     def test_write_directory_tree_in_one_stream(self):
 385         cwriter = arvados.CollectionWriter(self.api_client)
 386         cwriter.write_directory_tree(self.build_directory_tree(
 387                 ['basefile', 'subdir/subfile']), max_manifest_depth=0)
 388         self.assertEqual(cwriter.manifest_text(),
 389                          """. 4ace875ffdc6824a04950f06858f4465+22 0:8:basefile 8:14:subdir/subfile\n""")
 390
 391     def test_write_directory_tree_with_limited_recursion(self):
 392         cwriter = arvados.CollectionWriter(self.api_client)
 393         cwriter.write_directory_tree(
 394             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 395             max_manifest_depth=1)
 396         self.assertEqual(cwriter.manifest_text(),
 397                          """. bd19836ddb62c11c55ab251ccaca5645+2 0:2:f1
 398 ./d1 50170217e5b04312024aa5cd42934494+13 0:8:d2/f3 8:5:f2\n""")
 399
 400     def test_write_directory_tree_with_zero_recursion(self):
 401         cwriter = arvados.CollectionWriter(self.api_client)
 402         content = 'd1/d2/f3d1/f2f1'
 403         blockhash = tutil.str_keep_locator(content)
 404         cwriter.write_directory_tree(
 405             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 406             max_manifest_depth=0)
 407         self.assertEqual(
 408             cwriter.manifest_text(),
 409             ". {} 0:8:d1/d2/f3 8:5:d1/f2 13:2:f1\n".format(blockhash))
 410
 411     def test_write_one_file(self):
 412         cwriter = arvados.CollectionWriter(self.api_client)
 413         with self.make_test_file() as testfile:
 414             cwriter.write_file(testfile.name)
 415             self.assertEqual(
 416                 cwriter.manifest_text(),
 417                 ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:{}\n".format(
 418                     os.path.basename(testfile.name)))
 419
 420     def test_write_named_file(self):
 421         cwriter = arvados.CollectionWriter(self.api_client)
 422         with self.make_test_file() as testfile:
 423             cwriter.write_file(testfile.name, 'foo')
 424             self.assertEqual(cwriter.manifest_text(),
 425                              ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:foo\n")
 426
 427     def test_write_multiple_files(self):
 428         cwriter = arvados.CollectionWriter(self.api_client)
 429         for letter in 'ABC':
 430             with self.make_test_file(letter.encode()) as testfile:
 431                 cwriter.write_file(testfile.name, letter)
 432         self.assertEqual(
 433             cwriter.manifest_text(),
 434             ". 902fbdd2b1df0c4f70b4a5d23525e932+3 0:1:A 1:1:B 2:1:C\n")
 435
 436     def test_basic_resume(self):
 437         cwriter = TestResumableWriter()
 438         with self.make_test_file() as testfile:
 439             cwriter.write_file(testfile.name, 'test')
 440             resumed = TestResumableWriter.from_state(cwriter.current_state())
 441         self.assertEqual(cwriter.manifest_text(), resumed.manifest_text(),
 442                           "resumed CollectionWriter had different manifest")
 443
 444     def test_resume_fails_when_missing_dependency(self):
 445         cwriter = TestResumableWriter()
 446         with self.make_test_file() as testfile:
 447             cwriter.write_file(testfile.name, 'test')
 448         self.assertRaises(arvados.errors.StaleWriterStateError,
 449                           TestResumableWriter.from_state,
 450                           cwriter.current_state())
 451
 452     def test_resume_fails_when_dependency_mtime_changed(self):
 453         cwriter = TestResumableWriter()
 454         with self.make_test_file() as testfile:
 455             cwriter.write_file(testfile.name, 'test')
 456             os.utime(testfile.name, (0, 0))
 457             self.assertRaises(arvados.errors.StaleWriterStateError,
 458                               TestResumableWriter.from_state,
 459                               cwriter.current_state())
 460
 461     def test_resume_fails_when_dependency_is_nonfile(self):
 462         cwriter = TestResumableWriter()
 463         cwriter.write_file('/dev/null', 'empty')
 464         self.assertRaises(arvados.errors.StaleWriterStateError,
 465                           TestResumableWriter.from_state,
 466                           cwriter.current_state())
 467
 468     def test_resume_fails_when_dependency_size_changed(self):
 469         cwriter = TestResumableWriter()
 470         with self.make_test_file() as testfile:
 471             cwriter.write_file(testfile.name, 'test')
 472             orig_mtime = os.fstat(testfile.fileno()).st_mtime
 473             testfile.write(b'extra')
 474             testfile.flush()
 475             os.utime(testfile.name, (orig_mtime, orig_mtime))
 476             self.assertRaises(arvados.errors.StaleWriterStateError,
 477                               TestResumableWriter.from_state,
 478                               cwriter.current_state())
 479
 480     def test_resume_fails_with_expired_locator(self):
 481         cwriter = TestResumableWriter()
 482         state = cwriter.current_state()
 483         # Add an expired locator to the state.
 484         state['_current_stream_locators'].append(''.join([
 485                     'a' * 32, '+1+A', 'b' * 40, '@', '10000000']))
 486         self.assertRaises(arvados.errors.StaleWriterStateError,
 487                           TestResumableWriter.from_state, state)
 488
 489     def test_arbitrary_objects_not_resumable(self):
 490         cwriter = TestResumableWriter()
 491         with open('/dev/null') as badfile:
 492             self.assertRaises(arvados.errors.AssertionError,
 493                               cwriter.write_file, badfile)
 494
 495     def test_arbitrary_writes_not_resumable(self):
 496         cwriter = TestResumableWriter()
 497         self.assertRaises(arvados.errors.AssertionError,
 498                           cwriter.write, "badtext")
 499
 500     def test_read_arbitrary_data_with_collection_reader(self):
 501         # arv-get relies on this to do "arv-get {keep-locator} -".
 502         self.write_foo_bar_baz()
 503         self.assertEqual(
 504             'foobar',
 505             arvados.CollectionReader(
 506                 '3858f62230ac3c915f300c664312c63f+6'
 507                 ).manifest_text())
 508
 509
 510 class CollectionTestMixin(tutil.ApiClientMock):
 511     API_COLLECTIONS = run_test_server.fixture('collections')
 512     DEFAULT_COLLECTION = API_COLLECTIONS['foo_file']
 513     DEFAULT_DATA_HASH = DEFAULT_COLLECTION['portable_data_hash']
 514     DEFAULT_MANIFEST = DEFAULT_COLLECTION['manifest_text']
 515     DEFAULT_UUID = DEFAULT_COLLECTION['uuid']
 516     ALT_COLLECTION = API_COLLECTIONS['bar_file']
 517     ALT_DATA_HASH = ALT_COLLECTION['portable_data_hash']
 518     ALT_MANIFEST = ALT_COLLECTION['manifest_text']
 519
 520     def api_client_mock(self, status=200):
 521         client = super(CollectionTestMixin, self).api_client_mock()
 522         self.mock_keep_services(client, status=status, service_type='proxy', count=1)
 523         return client
 524
 525
 526 @tutil.skip_sleep
 527 class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin):
 528     def mock_get_collection(self, api_mock, code, fixturename):
 529         body = self.API_COLLECTIONS.get(fixturename)
 530         self._mock_api_call(api_mock.collections().get, code, body)
 531
 532     def api_client_mock(self, status=200):
 533         client = super(CollectionReaderTestCase, self).api_client_mock()
 534         self.mock_get_collection(client, status, 'foo_file')
 535         return client
 536
 537     def test_init_no_default_retries(self):
 538         client = self.api_client_mock(200)
 539         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 540         reader.manifest_text()
 541         client.collections().get().execute.assert_called_with(num_retries=0)
 542
 543     def test_uuid_init_success(self):
 544         client = self.api_client_mock(200)
 545         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 546                                           num_retries=3)
 547         self.assertEqual(self.DEFAULT_COLLECTION['manifest_text'],
 548                          reader.manifest_text())
 549         client.collections().get().execute.assert_called_with(num_retries=3)
 550
 551     def test_uuid_init_failure_raises_api_error(self):
 552         client = self.api_client_mock(500)
 553         with self.assertRaises(arvados.errors.ApiError):
 554             reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 555
 556     def test_locator_init(self):
 557         client = self.api_client_mock(200)
 558         # Ensure Keep will not return anything if asked.
 559         with tutil.mock_keep_responses(None, 404):
 560             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 561                                               api_client=client)
 562             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 563
 564     def test_locator_init_fallback_to_keep(self):
 565         # crunch-job needs this to read manifests that have only ever
 566         # been written to Keep.
 567         client = self.api_client_mock(200)
 568         self.mock_get_collection(client, 404, None)
 569         with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 570             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 571                                               api_client=client)
 572             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 573
 574     def test_uuid_init_no_fallback_to_keep(self):
 575         # Do not look up a collection UUID in Keep.
 576         client = self.api_client_mock(404)
 577         with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 578             with self.assertRaises(arvados.errors.ApiError):
 579                 reader = arvados.CollectionReader(self.DEFAULT_UUID,
 580                                                   api_client=client)
 581
 582     def test_try_keep_first_if_permission_hint(self):
 583         # To verify that CollectionReader tries Keep first here, we
 584         # mock API server to return the wrong data.
 585         client = self.api_client_mock(200)
 586         with tutil.mock_keep_responses(self.ALT_MANIFEST, 200):
 587             self.assertEqual(
 588                 self.ALT_MANIFEST,
 589                 arvados.CollectionReader(
 590                     self.ALT_DATA_HASH + '+Affffffffffffffffffffffffffffffffffffffff@fedcba98',
 591                     api_client=client).manifest_text())
 592
 593     def test_init_num_retries_propagated(self):
 594         # More of an integration test...
 595         client = self.api_client_mock(200)
 596         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 597                                           num_retries=3)
 598         with tutil.mock_keep_responses('foo', 500, 500, 200):
 599             self.assertEqual(b'foo',
 600                              b''.join(f.read(9) for f in reader.all_files()))
 601
 602     def test_read_nonnormalized_manifest_with_collection_reader(self):
 603         # client should be able to use CollectionReader on a manifest without normalizing it
 604         client = self.api_client_mock(500)
 605         nonnormal = ". acbd18db4cc2f85cedef654fccc4a4d8+3+Aabadbadbee@abeebdee 0:3:foo.txt 1:0:bar.txt 0:3:foo.txt\n"
 606         reader = arvados.CollectionReader(
 607             nonnormal,
 608             api_client=client, num_retries=0)
 609         # Ensure stripped_manifest() doesn't mangle our manifest in
 610         # any way other than stripping hints.
 611         self.assertEqual(
 612             re.sub('\+[^\d\s\+]+', '', nonnormal),
 613             reader.stripped_manifest())
 614         # Ensure stripped_manifest() didn't mutate our reader.
 615         self.assertEqual(nonnormal, reader.manifest_text())
 616         # Ensure the files appear in the order given in the manifest.
 617         self.assertEqual(
 618             [[6, '.', 'foo.txt'],
 619              [0, '.', 'bar.txt']],
 620             [[f.size(), f.stream_name(), f.name()]
 621              for f in reader.all_streams()[0].all_files()])
 622
 623     def test_read_empty_collection(self):
 624         client = self.api_client_mock(200)
 625         self.mock_get_collection(client, 200, 'empty')
 626         reader = arvados.CollectionReader('d41d8cd98f00b204e9800998ecf8427e+0',
 627                                           api_client=client)
 628         self.assertEqual('', reader.manifest_text())
 629
 630     def test_api_response(self):
 631         client = self.api_client_mock()
 632         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 633         self.assertEqual(self.DEFAULT_COLLECTION, reader.api_response())
 634
 635     def test_api_response_with_collection_from_keep(self):
 636         client = self.api_client_mock()
 637         self.mock_get_collection(client, 404, 'foo')
 638         with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 639             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 640                                               api_client=client)
 641             api_response = reader.api_response()
 642         self.assertIsNone(api_response)
 643
 644     def check_open_file(self, coll_file, stream_name, file_name, file_size):
 645         self.assertFalse(coll_file.closed, "returned file is not open")
 646         self.assertEqual(stream_name, coll_file.stream_name())
 647         self.assertEqual(file_name, coll_file.name)
 648         self.assertEqual(file_size, coll_file.size())
 649
 650     def test_open_collection_file_one_argument(self):
 651         client = self.api_client_mock(200)
 652         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 653         cfile = reader.open('./foo', 'rb')
 654         self.check_open_file(cfile, '.', 'foo', 3)
 655
 656     def test_open_deep_file(self):
 657         coll_name = 'collection_with_files_in_subdir'
 658         client = self.api_client_mock(200)
 659         self.mock_get_collection(client, 200, coll_name)
 660         reader = arvados.CollectionReader(
 661             self.API_COLLECTIONS[coll_name]['uuid'], api_client=client)
 662         cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt', 'rb')
 663         self.check_open_file(cfile, './subdir2/subdir3', 'file2_in_subdir3.txt',
 664                              32)
 665
 666     def test_open_nonexistent_stream(self):
 667         client = self.api_client_mock(200)
 668         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 669         self.assertRaises(IOError, reader.open, './nonexistent/foo')
 670
 671     def test_open_nonexistent_file(self):
 672         client = self.api_client_mock(200)
 673         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 674         self.assertRaises(IOError, reader.open, 'nonexistent')
 675
 676
 677 @tutil.skip_sleep
 678 class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin):
 679     def mock_keep(self, body, *codes, **headers):
 680         headers.setdefault('x-keep-replicas-stored', 2)
 681         return tutil.mock_keep_responses(body, *codes, **headers)
 682
 683     def foo_writer(self, **kwargs):
 684         kwargs.setdefault('api_client', self.api_client_mock())
 685         writer = arvados.CollectionWriter(**kwargs)
 686         writer.start_new_file('foo')
 687         writer.write(b'foo')
 688         return writer
 689
 690     def test_write_whole_collection(self):
 691         writer = self.foo_writer()
 692         with self.mock_keep(self.DEFAULT_DATA_HASH, 200, 200):
 693             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 694
 695     def test_write_no_default(self):
 696         writer = self.foo_writer()
 697         with self.mock_keep(None, 500):
 698             with self.assertRaises(arvados.errors.KeepWriteError):
 699                 writer.finish()
 700
 701     def test_write_insufficient_replicas_via_proxy(self):
 702         writer = self.foo_writer(replication=3)
 703         with self.mock_keep(None, 200, **{'x-keep-replicas-stored': 2}):
 704             with self.assertRaises(arvados.errors.KeepWriteError):
 705                 writer.manifest_text()
 706
 707     def test_write_insufficient_replicas_via_disks(self):
 708         client = mock.MagicMock(name='api_client')
 709         with self.mock_keep(
 710                 None, 200, 200,
 711                 **{'x-keep-replicas-stored': 1}) as keepmock:
 712             self.mock_keep_services(client, status=200, service_type='disk', count=2)
 713             writer = self.foo_writer(api_client=client, replication=3)
 714             with self.assertRaises(arvados.errors.KeepWriteError):
 715                 writer.manifest_text()
 716
 717     def test_write_three_replicas(self):
 718         client = mock.MagicMock(name='api_client')
 719         with self.mock_keep(
 720                 "", 500, 500, 500, 200, 200, 200,
 721                 **{'x-keep-replicas-stored': 1}) as keepmock:
 722             self.mock_keep_services(client, status=200, service_type='disk', count=6)
 723             writer = self.foo_writer(api_client=client, replication=3)
 724             writer.manifest_text()
 725             self.assertEqual(6, keepmock.call_count)
 726
 727     def test_write_whole_collection_through_retries(self):
 728         writer = self.foo_writer(num_retries=2)
 729         with self.mock_keep(self.DEFAULT_DATA_HASH,
 730                             500, 500, 200, 500, 500, 200):
 731             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 732
 733     def test_flush_data_retries(self):
 734         writer = self.foo_writer(num_retries=2)
 735         foo_hash = self.DEFAULT_MANIFEST.split()[1]
 736         with self.mock_keep(foo_hash, 500, 200):
 737             writer.flush_data()
 738         self.assertEqual(self.DEFAULT_MANIFEST, writer.manifest_text())
 739
 740     def test_one_open(self):
 741         client = self.api_client_mock()
 742         writer = arvados.CollectionWriter(client)
 743         with writer.open('out') as out_file:
 744             self.assertEqual('.', writer.current_stream_name())
 745             self.assertEqual('out', writer.current_file_name())
 746             out_file.write(b'test data')
 747             data_loc = tutil.str_keep_locator('test data')
 748         self.assertTrue(out_file.closed, "writer file not closed after context")
 749         self.assertRaises(ValueError, out_file.write, 'extra text')
 750         with self.mock_keep(data_loc, 200) as keep_mock:
 751             self.assertEqual(". {} 0:9:out\n".format(data_loc),
 752                              writer.manifest_text())
 753
 754     def test_open_writelines(self):
 755         client = self.api_client_mock()
 756         writer = arvados.CollectionWriter(client)
 757         with writer.open('six') as out_file:
 758             out_file.writelines(['12', '34', '56'])
 759             data_loc = tutil.str_keep_locator('123456')
 760         with self.mock_keep(data_loc, 200) as keep_mock:
 761             self.assertEqual(". {} 0:6:six\n".format(data_loc),
 762                              writer.manifest_text())
 763
 764     def test_open_flush(self):
 765         client = self.api_client_mock()
 766         data_loc1 = tutil.str_keep_locator('flush1')
 767         data_loc2 = tutil.str_keep_locator('flush2')
 768         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 769             writer = arvados.CollectionWriter(client)
 770             with writer.open('flush_test') as out_file:
 771                 out_file.write(b'flush1')
 772                 out_file.flush()
 773                 out_file.write(b'flush2')
 774             self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1,
 775                                                                 data_loc2),
 776                              writer.manifest_text())
 777
 778     def test_two_opens_same_stream(self):
 779         client = self.api_client_mock()
 780         writer = arvados.CollectionWriter(client)
 781         with writer.open('.', '1') as out_file:
 782             out_file.write(b'1st')
 783         with writer.open('.', '2') as out_file:
 784             out_file.write(b'2nd')
 785         data_loc = tutil.str_keep_locator('1st2nd')
 786         with self.mock_keep(data_loc, 200) as keep_mock:
 787             self.assertEqual(". {} 0:3:1 3:3:2\n".format(data_loc),
 788                              writer.manifest_text())
 789
 790     def test_two_opens_two_streams(self):
 791         client = self.api_client_mock()
 792         data_loc1 = tutil.str_keep_locator('file')
 793         data_loc2 = tutil.str_keep_locator('indir')
 794         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 795             writer = arvados.CollectionWriter(client)
 796             with writer.open('file') as out_file:
 797                 out_file.write(b'file')
 798             with writer.open('./dir', 'indir') as out_file:
 799                 out_file.write(b'indir')
 800             expected = ". {} 0:4:file\n./dir {} 0:5:indir\n".format(
 801                 data_loc1, data_loc2)
 802             self.assertEqual(expected, writer.manifest_text())
 803
 804     def test_dup_open_fails(self):
 805         client = self.api_client_mock()
 806         writer = arvados.CollectionWriter(client)
 807         file1 = writer.open('one')
 808         self.assertRaises(arvados.errors.AssertionError, writer.open, 'two')
 809
 810
 811 class CollectionMethods(run_test_server.TestCaseWithServers):
 812
 813     def test_keys_values_items_support_indexing(self):
 814         c = Collection()
 815         with c.open('foo', 'wb') as f:
 816             f.write(b'foo')
 817         with c.open('bar', 'wb') as f:
 818             f.write(b'bar')
 819         self.assertEqual(2, len(c.keys()))
 820         if sys.version_info < (3, 0):
 821             # keys() supports indexing only for python2 callers.
 822             fn0 = c.keys()[0]
 823             fn1 = c.keys()[1]
 824         else:
 825             fn0, fn1 = c.keys()
 826         self.assertEqual(2, len(c.values()))
 827         f0 = c.values()[0]
 828         f1 = c.values()[1]
 829         self.assertEqual(2, len(c.items()))
 830         self.assertEqual(fn0, c.items()[0][0])
 831         self.assertEqual(fn1, c.items()[1][0])
 832
 833
 834 class CollectionOpenModes(run_test_server.TestCaseWithServers):
 835
 836     def test_open_binary_modes(self):
 837         c = Collection()
 838         for mode in ['wb', 'wb+', 'ab', 'ab+']:
 839             with c.open('foo', mode) as f:
 840                 f.write(b'foo')
 841
 842     def test_open_invalid_modes(self):
 843         c = Collection()
 844         for mode in ['+r', 'aa', '++', 'r+b', 'beer', '', None]:
 845             with self.assertRaises(Exception):
 846                 c.open('foo', mode)
 847
 848     def test_open_text_modes(self):
 849         c = Collection()
 850         with c.open('foo', 'wb') as f:
 851             f.write('foo')
 852         for mode in ['r', 'rt', 'r+', 'rt+', 'w', 'wt', 'a', 'at']:
 853             if sys.version_info >= (3, 0):
 854                 with self.assertRaises(NotImplementedError):
 855                     c.open('foo', mode)
 856             else:
 857                 with c.open('foo', mode) as f:
 858                     if mode[0] == 'r' and '+' not in mode:
 859                         self.assertEqual('foo', f.read(3))
 860                     else:
 861                         f.write('bar')
 862                         f.seek(-3, os.SEEK_CUR)
 863                         self.assertEqual('bar', f.read(3))
 864
 865
 866 class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin):
 867
 868     def test_replication_desired_kept_on_load(self):
 869         m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
 870         c1 = Collection(m, replication_desired=1)
 871         c1.save_new()
 872         loc = c1.manifest_locator()
 873         c2 = Collection(loc)
 874         self.assertEqual(c1.manifest_text, c2.manifest_text)
 875         self.assertEqual(c1.replication_desired, c2.replication_desired)
 876
 877     def test_replication_desired_not_loaded_if_provided(self):
 878         m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
 879         c1 = Collection(m, replication_desired=1)
 880         c1.save_new()
 881         loc = c1.manifest_locator()
 882         c2 = Collection(loc, replication_desired=2)
 883         self.assertEqual(c1.manifest_text, c2.manifest_text)
 884         self.assertNotEqual(c1.replication_desired, c2.replication_desired)
 885
 886     def test_init_manifest(self):
 887         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 888 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 889 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 890 """
 891         self.assertEqual(m1, CollectionReader(m1).manifest_text(normalize=False))
 892         self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", CollectionReader(m1).manifest_text(normalize=True))
 893
 894     def test_init_manifest_with_collision(self):
 895         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 896 ./md5sum.txt 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 897 """
 898         with self.assertRaises(arvados.errors.ArgumentError):
 899             self.assertEqual(m1, CollectionReader(m1))
 900
 901     def test_init_manifest_with_error(self):
 902         m1 = """. 0:43:md5sum.txt"""
 903         with self.assertRaises(arvados.errors.ArgumentError):
 904             self.assertEqual(m1, CollectionReader(m1))
 905
 906     def test_remove(self):
 907         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
 908         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 909         self.assertIn("count1.txt", c)
 910         c.remove("count1.txt")
 911         self.assertNotIn("count1.txt", c)
 912         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
 913         with self.assertRaises(arvados.errors.ArgumentError):
 914             c.remove("")
 915
 916     def test_find(self):
 917         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
 918         self.assertIs(c.find("."), c)
 919         self.assertIs(c.find("./count1.txt"), c["count1.txt"])
 920         self.assertIs(c.find("count1.txt"), c["count1.txt"])
 921         with self.assertRaises(IOError):
 922             c.find("/.")
 923         with self.assertRaises(arvados.errors.ArgumentError):
 924             c.find("")
 925         self.assertIs(c.find("./nonexistant.txt"), None)
 926         self.assertIs(c.find("./nonexistantsubdir/nonexistant.txt"), None)
 927
 928     def test_remove_in_subdir(self):
 929         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 930         c.remove("foo/count2.txt")
 931         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 932
 933     def test_remove_empty_subdir(self):
 934         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 935         c.remove("foo/count2.txt")
 936         c.remove("foo")
 937         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 938
 939     def test_remove_nonempty_subdir(self):
 940         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 941         with self.assertRaises(IOError):
 942             c.remove("foo")
 943         c.remove("foo", recursive=True)
 944         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 945
 946     def test_copy_to_file_in_dir(self):
 947         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 948         c.copy("count1.txt", "foo/count2.txt")
 949         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
 950
 951     def test_copy_file(self):
 952         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 953         c.copy("count1.txt", "count2.txt")
 954         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 955
 956     def test_copy_to_existing_dir(self):
 957         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 958         c.copy("count1.txt", "foo")
 959         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())
 960
 961     def test_copy_to_new_dir(self):
 962         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 963         c.copy("count1.txt", "foo/")
 964         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 965
 966     def test_rename_file(self):
 967         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 968         c.rename("count1.txt", "count2.txt")
 969         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
 970
 971     def test_move_file_to_dir(self):
 972         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 973         c.mkdirs("foo")
 974         c.rename("count1.txt", "foo/count2.txt")
 975         self.assertEqual("./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
 976
 977     def test_move_file_to_other(self):
 978         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 979         c2 = Collection()
 980         c2.rename("count1.txt", "count2.txt", source_collection=c1)
 981         self.assertEqual("", c1.manifest_text())
 982         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c2.manifest_text())
 983
 984     def test_clone(self):
 985         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 986         cl = c.clone()
 987         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", cl.portable_manifest_text())
 988
 989     def test_diff_del_add(self):
 990         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 991         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
 992         d = c2.diff(c1)
 993         self.assertEqual(sorted(d), [
 994             ('add', './count1.txt', c1["count1.txt"]),
 995             ('del', './count2.txt', c2["count2.txt"]),
 996         ])
 997         d = c1.diff(c2)
 998         self.assertEqual(sorted(d), [
 999             ('add', './count2.txt', c2["count2.txt"]),
1000             ('del', './count1.txt', c1["count1.txt"]),
1001         ])
1002         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1003         c1.apply(d)
1004         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1005
1006     def test_diff_same(self):
1007         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1008         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1009         d = c2.diff(c1)
1010         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1011         d = c1.diff(c2)
1012         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1013
1014         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1015         c1.apply(d)
1016         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1017
1018     def test_diff_mod(self):
1019         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1020         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
1021         d = c2.diff(c1)
1022         self.assertEqual(d, [('mod', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1023         d = c1.diff(c2)
1024         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1025
1026         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1027         c1.apply(d)
1028         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1029
1030     def test_diff_add(self):
1031         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1032         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt 10:20:count2.txt\n')
1033         d = c2.diff(c1)
1034         self.assertEqual(sorted(d), [
1035             ('del', './count2.txt', c2["count2.txt"]),
1036             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1037         ])
1038         d = c1.diff(c2)
1039         self.assertEqual(sorted(d), [
1040             ('add', './count2.txt', c2["count2.txt"]),
1041             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1042         ])
1043
1044         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1045         c1.apply(d)
1046         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1047
1048     def test_diff_add_in_subcollection(self):
1049         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1050         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1051         d = c2.diff(c1)
1052         self.assertEqual(sorted(d), [
1053             ('del', './foo', c2["foo"]),
1054             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1055         ])
1056         d = c1.diff(c2)
1057         self.assertEqual(sorted(d), [
1058             ('add', './foo', c2["foo"]),
1059             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1060         ])
1061         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1062         c1.apply(d)
1063         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1064
1065     def test_diff_del_add_in_subcollection(self):
1066         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1067         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:3:count3.txt\n')
1068         d = c2.diff(c1)
1069         self.assertEqual(sorted(d), [
1070             ('add', './foo/count2.txt', c1.find("foo/count2.txt")),
1071             ('del', './foo/count3.txt', c2.find("foo/count3.txt")),
1072             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1073         ])
1074         d = c1.diff(c2)
1075         self.assertEqual(sorted(d), [
1076             ('add', './foo/count3.txt', c2.find("foo/count3.txt")),
1077             ('del', './foo/count2.txt', c1.find("foo/count2.txt")),
1078             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1079         ])
1080
1081         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1082         c1.apply(d)
1083         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1084
1085     def test_diff_mod_in_subcollection(self):
1086         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1087         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:3:foo\n')
1088         d = c2.diff(c1)
1089         self.assertEqual(sorted(d), [
1090             ('mod', './foo', c2["foo"], c1["foo"]),
1091             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1092         ])
1093         d = c1.diff(c2)
1094         self.assertEqual(sorted(d), [
1095             ('mod', './foo', c1["foo"], c2["foo"]),
1096             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1097         ])
1098
1099         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1100         c1.apply(d)
1101         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1102
1103     def test_conflict_keep_local_change(self):
1104         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1105         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1106         d = c1.diff(c2)
1107         self.assertEqual(sorted(d), [
1108             ('add', './count2.txt', c2["count2.txt"]),
1109             ('del', './count1.txt', c1["count1.txt"]),
1110         ])
1111         f = c1.open("count1.txt", "wb")
1112         f.write(b"zzzzz")
1113
1114         # c1 changed, so it should not be deleted.
1115         c1.apply(d)
1116         self.assertEqual(c1.portable_manifest_text(), ". 95ebc3c7b3b9f1d2c40fec14415d3cb8+5 5348b82a029fd9e971a811ce1f71360b+43 0:5:count1.txt 5:10:count2.txt\n")
1117
1118     def test_conflict_mod(self):
1119         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1120         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1121         d = c1.diff(c2)
1122         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1123         f = c1.open("count1.txt", "wb")
1124         f.write(b"zzzzz")
1125
1126         # c1 changed, so c2 mod will go to a conflict file
1127         c1.apply(d)
1128         self.assertRegex(
1129             c1.portable_manifest_text(),
1130             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~$")
1131
1132     def test_conflict_add(self):
1133         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
1134         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
1135         d = c1.diff(c2)
1136         self.assertEqual(sorted(d), [
1137             ('add', './count1.txt', c2["count1.txt"]),
1138             ('del', './count2.txt', c1["count2.txt"]),
1139         ])
1140         f = c1.open("count1.txt", "wb")
1141         f.write(b"zzzzz")
1142
1143         # c1 added count1.txt, so c2 add will go to a conflict file
1144         c1.apply(d)
1145         self.assertRegex(
1146             c1.portable_manifest_text(),
1147             r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1148
1149     def test_conflict_del(self):
1150         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1151         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1152         d = c1.diff(c2)
1153         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1154         c1.remove("count1.txt")
1155
1156         # c1 deleted, so c2 mod will go to a conflict file
1157         c1.apply(d)
1158         self.assertRegex(
1159             c1.portable_manifest_text(),
1160             r"\. 5348b82a029fd9e971a811ce1f71360b\+43 0:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1161
1162     def test_notify(self):
1163         c1 = Collection()
1164         events = []
1165         c1.subscribe(lambda event, collection, name, item: events.append((event, collection, name, item)))
1166         f = c1.open("foo.txt", "wb")
1167         self.assertEqual(events[0], (arvados.collection.ADD, c1, "foo.txt", f.arvadosfile))
1168
1169     def test_open_w(self):
1170         c1 = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n")
1171         self.assertEqual(c1["count1.txt"].size(), 10)
1172         c1.open("count1.txt", "wb").close()
1173         self.assertEqual(c1["count1.txt"].size(), 0)
1174
1175
1176 class NewCollectionTestCaseWithServers(run_test_server.TestCaseWithServers):
1177     def test_get_manifest_text_only_committed(self):
1178         c = Collection()
1179         with c.open("count.txt", "wb") as f:
1180             # One file committed
1181             with c.open("foo.txt", "wb") as foo:
1182                 foo.write(b"foo")
1183                 foo.flush() # Force block commit
1184             f.write(b"0123456789")
1185             # Other file not committed. Block not written to keep yet.
1186             self.assertEqual(
1187                 c._get_manifest_text(".",
1188                                      strip=False,
1189                                      normalize=False,
1190                                      only_committed=True),
1191                 '. acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:count.txt 0:3:foo.txt\n')
1192             # And now with the file closed...
1193             f.flush() # Force block commit
1194         self.assertEqual(
1195             c._get_manifest_text(".",
1196                                  strip=False,
1197                                  normalize=False,
1198                                  only_committed=True),
1199             ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:10:count.txt 10:3:foo.txt\n")
1200
1201     def test_only_small_blocks_are_packed_together(self):
1202         c = Collection()
1203         # Write a couple of small files,
1204         f = c.open("count.txt", "wb")
1205         f.write(b"0123456789")
1206         f.close(flush=False)
1207         foo = c.open("foo.txt", "wb")
1208         foo.write(b"foo")
1209         foo.close(flush=False)
1210         # Then, write a big file, it shouldn't be packed with the ones above
1211         big = c.open("bigfile.txt", "wb")
1212         big.write(b"x" * 1024 * 1024 * 33) # 33 MB > KEEP_BLOCK_SIZE/2
1213         big.close(flush=False)
1214         self.assertEqual(
1215             c.manifest_text("."),
1216             '. 2d303c138c118af809f39319e5d507e9+34603008 a8430a058b8fbf408e1931b794dbd6fb+13 0:34603008:bigfile.txt 34603008:10:count.txt 34603018:3:foo.txt\n')
1217
1218     def test_flush_after_small_block_packing(self):
1219         c = Collection()
1220         # Write a couple of small files,
1221         f = c.open("count.txt", "wb")
1222         f.write(b"0123456789")
1223         f.close(flush=False)
1224         foo = c.open("foo.txt", "wb")
1225         foo.write(b"foo")
1226         foo.close(flush=False)
1227
1228         self.assertEqual(
1229             c.manifest_text(),
1230             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1231
1232         f = c.open("count.txt", "rb+")
1233         f.close(flush=True)
1234
1235         self.assertEqual(
1236             c.manifest_text(),
1237             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1238
1239     def test_write_after_small_block_packing2(self):
1240         c = Collection()
1241         # Write a couple of small files,
1242         f = c.open("count.txt", "wb")
1243         f.write(b"0123456789")
1244         f.close(flush=False)
1245         foo = c.open("foo.txt", "wb")
1246         foo.write(b"foo")
1247         foo.close(flush=False)
1248
1249         self.assertEqual(
1250             c.manifest_text(),
1251             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1252
1253         f = c.open("count.txt", "rb+")
1254         f.write(b"abc")
1255         f.close(flush=False)
1256
1257         self.assertEqual(
1258             c.manifest_text(),
1259             '. 900150983cd24fb0d6963f7d28e17f72+3 a8430a058b8fbf408e1931b794dbd6fb+13 0:3:count.txt 6:7:count.txt 13:3:foo.txt\n')
1260
1261
1262     def test_small_block_packing_with_overwrite(self):
1263         c = Collection()
1264         c.open("b1", "wb").close()
1265         c["b1"].writeto(0, b"b1", 0)
1266
1267         c.open("b2", "wb").close()
1268         c["b2"].writeto(0, b"b2", 0)
1269
1270         c["b1"].writeto(0, b"1b", 0)
1271
1272         self.assertEquals(c.manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1 2:2:b2\n")
1273         self.assertEquals(c["b1"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1\n")
1274         self.assertEquals(c["b2"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 2:2:b2\n")
1275
1276
1277 class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers):
1278     MAIN_SERVER = {}
1279     KEEP_SERVER = {}
1280
1281     def create_count_txt(self):
1282         # Create an empty collection, save it to the API server, then write a
1283         # file, but don't save it.
1284
1285         c = Collection()
1286         c.save_new("CollectionCreateUpdateTest", ensure_unique_name=True)
1287         self.assertEqual(c.portable_data_hash(), "d41d8cd98f00b204e9800998ecf8427e+0")
1288         self.assertEqual(c.api_response()["portable_data_hash"], "d41d8cd98f00b204e9800998ecf8427e+0" )
1289
1290         with c.open("count.txt", "wb") as f:
1291             f.write(b"0123456789")
1292
1293         self.assertEqual(c.portable_manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1294
1295         return c
1296
1297     def test_create_and_save(self):
1298         c = self.create_count_txt()
1299         c.save()
1300         self.assertRegex(
1301             c.manifest_text(),
1302             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1303
1304     def test_create_and_save_new(self):
1305         c = self.create_count_txt()
1306         c.save_new()
1307         self.assertRegex(
1308             c.manifest_text(),
1309             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1310
1311     def test_create_diff_apply(self):
1312         c1 = self.create_count_txt()
1313         c1.save()
1314
1315         c2 = Collection(c1.manifest_locator())
1316         with c2.open("count.txt", "wb") as f:
1317             f.write(b"abcdefg")
1318
1319         diff = c1.diff(c2)
1320
1321         self.assertEqual(diff[0], (arvados.collection.MOD, u'./count.txt', c1["count.txt"], c2["count.txt"]))
1322
1323         c1.apply(diff)
1324         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1325
1326     def test_diff_apply_with_token(self):
1327         baseline = CollectionReader(". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:10:count.txt\n")
1328         c = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1329         other = CollectionReader(". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1330
1331         diff = baseline.diff(other)
1332         self.assertEqual(diff, [('mod', u'./count.txt', c["count.txt"], other["count.txt"])])
1333
1334         c.apply(diff)
1335
1336         self.assertEqual(c.manifest_text(), ". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1337
1338
1339     def test_create_and_update(self):
1340         c1 = self.create_count_txt()
1341         c1.save()
1342
1343         c2 = arvados.collection.Collection(c1.manifest_locator())
1344         with c2.open("count.txt", "wb") as f:
1345             f.write(b"abcdefg")
1346
1347         c2.save()
1348
1349         self.assertNotEqual(c1.portable_data_hash(), c2.portable_data_hash())
1350         c1.update()
1351         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1352
1353
1354     def test_create_and_update_with_conflict(self):
1355         c1 = self.create_count_txt()
1356         c1.save()
1357
1358         with c1.open("count.txt", "wb") as f:
1359             f.write(b"XYZ")
1360
1361         c2 = arvados.collection.Collection(c1.manifest_locator())
1362         with c2.open("count.txt", "wb") as f:
1363             f.write(b"abcdefg")
1364
1365         c2.save()
1366
1367         c1.update()
1368         self.assertRegex(
1369             c1.manifest_text(),
1370             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~$")
1371
1372     def test_pdh_is_native_str(self):
1373         c1 = self.create_count_txt()
1374         pdh = c1.portable_data_hash()
1375         self.assertEqual(type(''), type(pdh))
1376
1377
1378 if __name__ == '__main__':
1379     unittest.main()