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 random
  10 import re
  11 import sys
  12 import tempfile
  13 import time
  14 import unittest
  15
  16 from . import run_test_server
  17 from arvados._ranges import Range, LocatorAndRange
  18 from arvados.collection import Collection, CollectionReader
  19 from . import arvados_testutil as tutil
  20
  21 class TestResumableWriter(arvados.ResumableCollectionWriter):
  22     KEEP_BLOCK_SIZE = 1024  # PUT to Keep every 1K.
  23
  24     def current_state(self):
  25         return self.dump_state(copy.deepcopy)
  26
  27
  28 class ArvadosCollectionsTest(run_test_server.TestCaseWithServers,
  29                              tutil.ArvadosBaseTestCase):
  30     MAIN_SERVER = {}
  31
  32     @classmethod
  33     def setUpClass(cls):
  34         super(ArvadosCollectionsTest, cls).setUpClass()
  35         run_test_server.authorize_with('active')
  36         cls.api_client = arvados.api('v1')
  37         cls.keep_client = arvados.KeepClient(api_client=cls.api_client,
  38                                              local_store=cls.local_store)
  39
  40     def write_foo_bar_baz(self):
  41         cw = arvados.CollectionWriter(self.api_client)
  42         self.assertEqual(cw.current_stream_name(), '.',
  43                          'current_stream_name() should be "." now')
  44         cw.set_current_file_name('foo.txt')
  45         cw.write(b'foo')
  46         self.assertEqual(cw.current_file_name(), 'foo.txt',
  47                          'current_file_name() should be foo.txt now')
  48         cw.start_new_file('bar.txt')
  49         cw.write(b'bar')
  50         cw.start_new_stream('baz')
  51         cw.write(b'baz')
  52         cw.set_current_file_name('baz.txt')
  53         self.assertEqual(cw.manifest_text(),
  54                          ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" +
  55                          "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n",
  56                          "wrong manifest: got {}".format(cw.manifest_text()))
  57         cw.finish()
  58         return cw.portable_data_hash()
  59
  60     def test_pdh_is_native_str(self):
  61         pdh = self.write_foo_bar_baz()
  62         self.assertEqual(type(''), type(pdh))
  63
  64     def test_keep_local_store(self):
  65         self.assertEqual(self.keep_client.put(b'foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
  66         self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), b'foo', 'wrong data from Keep.get')
  67
  68     def test_local_collection_writer(self):
  69         self.assertEqual(self.write_foo_bar_baz(),
  70                          '23ca013983d6239e98931cc779e68426+114',
  71                          'wrong locator hash: ' + self.write_foo_bar_baz())
  72
  73     def test_local_collection_reader(self):
  74         foobarbaz = self.write_foo_bar_baz()
  75         cr = arvados.CollectionReader(
  76             foobarbaz + '+Xzizzle', self.api_client)
  77         got = []
  78         for s in cr.all_streams():
  79             for f in s.all_files():
  80                 got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]]
  81         expected = [[3, '.', 'foo.txt', b'foo'],
  82                     [3, '.', 'bar.txt', b'bar'],
  83                     [3, './baz', 'baz.txt', b'baz']]
  84         self.assertEqual(got,
  85                          expected)
  86         stream0 = cr.all_streams()[0]
  87         self.assertEqual(stream0.readfrom(0, 0),
  88                          b'',
  89                          'reading zero bytes should have returned empty string')
  90         self.assertEqual(stream0.readfrom(0, 2**26),
  91                          b'foobar',
  92                          'reading entire stream failed')
  93         self.assertEqual(stream0.readfrom(2**26, 0),
  94                          b'',
  95                          'reading zero bytes should have returned empty string')
  96
  97     def _test_subset(self, collection, expected):
  98         cr = arvados.CollectionReader(collection, self.api_client)
  99         for s in cr.all_streams():
 100             for ex in expected:
 101                 if ex[0] == s:
 102                     f = s.files()[ex[2]]
 103                     got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))]
 104                     self.assertEqual(got,
 105                                      ex,
 106                                      'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex))
 107
 108     def test_collection_manifest_subset(self):
 109         foobarbaz = self.write_foo_bar_baz()
 110         self._test_subset(foobarbaz,
 111                           [[3, '.',     'bar.txt', b'bar'],
 112                            [3, '.',     'foo.txt', b'foo'],
 113                            [3, './baz', 'baz.txt', b'baz']])
 114         self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" %
 115                            (self.keep_client.put(b"foo"),
 116                             self.keep_client.put(b"bar"))),
 117                           [[3, '.', 'bar.txt', b'bar'],
 118                            [3, '.', 'foo.txt', b'foo']])
 119         self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" %
 120                            (self.keep_client.put(b"foo"),
 121                             self.keep_client.put(b"bar"))),
 122                           [[2, '.', 'fo.txt', b'fo'],
 123                            [4, '.', 'obar.txt', b'obar']])
 124         self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" %
 125                            (self.keep_client.put(b"foo"),
 126                             self.keep_client.put(b"bar"))),
 127                           [[2, '.', 'ar.txt', b'ar'],
 128                            [2, '.', 'fo.txt', b'fo'],
 129                            [2, '.', 'ob.txt', b'ob'],
 130                            [0, '.', 'zero.txt', b'']])
 131
 132     def test_collection_empty_file(self):
 133         cw = arvados.CollectionWriter(self.api_client)
 134         cw.start_new_file('zero.txt')
 135         cw.write(b'')
 136
 137         self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n")
 138         self.check_manifest_file_sizes(cw.manifest_text(), [0])
 139         cw = arvados.CollectionWriter(self.api_client)
 140         cw.start_new_file('zero.txt')
 141         cw.write(b'')
 142         cw.start_new_file('one.txt')
 143         cw.write(b'1')
 144         cw.start_new_stream('foo')
 145         cw.start_new_file('zero.txt')
 146         cw.write(b'')
 147         self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0])
 148
 149     def test_no_implicit_normalize(self):
 150         cw = arvados.CollectionWriter(self.api_client)
 151         cw.start_new_file('b')
 152         cw.write(b'b')
 153         cw.start_new_file('a')
 154         cw.write(b'')
 155         self.check_manifest_file_sizes(cw.manifest_text(), [1,0])
 156         self.check_manifest_file_sizes(
 157             arvados.CollectionReader(
 158                 cw.manifest_text()).manifest_text(normalize=True),
 159             [0,1])
 160
 161     def check_manifest_file_sizes(self, manifest_text, expect_sizes):
 162         cr = arvados.CollectionReader(manifest_text, self.api_client)
 163         got_sizes = []
 164         for f in cr.all_files():
 165             got_sizes += [f.size()]
 166         self.assertEqual(got_sizes, expect_sizes, "got wrong file sizes %s, expected %s" % (got_sizes, expect_sizes))
 167
 168     def test_normalized_collection(self):
 169         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 170 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 171 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 172 """
 173         self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True),
 174                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
 175 """)
 176
 177         m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
 178 """
 179         self.assertEqual(arvados.CollectionReader(m2, self.api_client).manifest_text(normalize=True), m2)
 180
 181         m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
 182 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 183 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 184 """
 185         self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(normalize=True),
 186                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
 187 """)
 188
 189         m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 190 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 191 ./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
 192 """
 193         self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(normalize=True),
 194                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
 195 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 196 """)
 197
 198         m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 199 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 200 ./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar
 201 """
 202         self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(normalize=True),
 203                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
 204 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 205 """)
 206
 207         with self.data_file('1000G_ref_manifest') as f6:
 208             m6 = f6.read()
 209             self.assertEqual(arvados.CollectionReader(m6, self.api_client).manifest_text(normalize=True), m6)
 210
 211         with self.data_file('jlake_manifest') as f7:
 212             m7 = f7.read()
 213             self.assertEqual(arvados.CollectionReader(m7, self.api_client).manifest_text(normalize=True), m7)
 214
 215         m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt
 216 """
 217         self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8)
 218
 219     def test_locators_and_ranges(self):
 220         blocks2 = [Range('a', 0, 10),
 221                    Range('b', 10, 10),
 222                    Range('c', 20, 10),
 223                    Range('d', 30, 10),
 224                    Range('e', 40, 10),
 225                    Range('f', 50, 10)]
 226
 227         self.assertEqual(arvados.locators_and_ranges(blocks2,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 228         self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 229         self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 230         self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 231         self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 232         self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 233         self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), [])
 234         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 235
 236         self.assertEqual(arvados.locators_and_ranges(blocks2,  0,  2), [LocatorAndRange('a', 10, 0, 2)])
 237         self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [LocatorAndRange('b', 10, 0, 2)])
 238         self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [LocatorAndRange('c', 10, 0, 2)])
 239         self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [LocatorAndRange('d', 10, 0, 2)])
 240         self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [LocatorAndRange('e', 10, 0, 2)])
 241         self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [LocatorAndRange('f', 10, 0, 2)])
 242         self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), [])
 243         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 244
 245         self.assertEqual(arvados.locators_and_ranges(blocks2,  9,  2), [LocatorAndRange('a', 10, 9, 1), LocatorAndRange('b', 10, 0, 1)])
 246         self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [LocatorAndRange('b', 10, 9, 1), LocatorAndRange('c', 10, 0, 1)])
 247         self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [LocatorAndRange('c', 10, 9, 1), LocatorAndRange('d', 10, 0, 1)])
 248         self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [LocatorAndRange('d', 10, 9, 1), LocatorAndRange('e', 10, 0, 1)])
 249         self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [LocatorAndRange('e', 10, 9, 1), LocatorAndRange('f', 10, 0, 1)])
 250         self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [LocatorAndRange('f', 10, 9, 1)])
 251
 252
 253         blocks3 = [Range('a', 0, 10),
 254                   Range('b', 10, 10),
 255                   Range('c', 20, 10),
 256                   Range('d', 30, 10),
 257                   Range('e', 40, 10),
 258                   Range('f', 50, 10),
 259                    Range('g', 60, 10)]
 260
 261         self.assertEqual(arvados.locators_and_ranges(blocks3,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 262         self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 263         self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 264         self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 265         self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 266         self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 267         self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [LocatorAndRange('g', 10, 2, 2)])
 268
 269
 270         blocks = [Range('a', 0, 10),
 271                   Range('b', 10, 15),
 272                   Range('c', 25, 5)]
 273         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 0), [])
 274         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [LocatorAndRange('a', 10, 0, 5)])
 275         self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [LocatorAndRange('a', 10, 3, 5)])
 276         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [LocatorAndRange('a', 10, 0, 10)])
 277
 278         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [LocatorAndRange('a', 10, 0, 10),
 279                                                                       LocatorAndRange('b', 15, 0, 1)])
 280         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [LocatorAndRange('a', 10, 1, 9),
 281                                                                       LocatorAndRange('b', 15, 0, 2)])
 282         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [LocatorAndRange('a', 10, 0, 10),
 283                                                                       LocatorAndRange('b', 15, 0, 15)])
 284
 285         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [LocatorAndRange('a', 10, 0, 10),
 286                                                                       LocatorAndRange('b', 15, 0, 15),
 287                                                                       LocatorAndRange('c', 5, 0, 5)])
 288         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [LocatorAndRange('a', 10, 1, 9),
 289                                                                       LocatorAndRange('b', 15, 0, 15),
 290                                                                       LocatorAndRange('c', 5, 0, 5)])
 291         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [LocatorAndRange('a', 10, 0, 10),
 292                                                                       LocatorAndRange('b', 15, 0, 15),
 293                                                                       LocatorAndRange('c', 5, 0, 5)])
 294
 295         self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [LocatorAndRange('b', 15, 5, 5)])
 296
 297         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [LocatorAndRange('a', 10, 8, 2),
 298                                                                       LocatorAndRange('b', 15, 0, 15)])
 299
 300         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [LocatorAndRange('a', 10, 8, 2),
 301                                                                       LocatorAndRange('b', 15, 0, 15),
 302                                                                       LocatorAndRange('c', 5, 0, 3)])
 303
 304         self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [LocatorAndRange('c', 5, 1, 2)])
 305
 306         self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [LocatorAndRange('a', 10, 9, 1),
 307                                                                       LocatorAndRange('b', 15, 0, 14)])
 308         self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [LocatorAndRange('b', 15, 0, 15)])
 309         self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [LocatorAndRange('b', 15, 1, 14),
 310                                                                        LocatorAndRange('c', 5, 0, 1)])
 311
 312     class MockKeep(object):
 313         def __init__(self, content, num_retries=0):
 314             self.content = content
 315
 316         def get(self, locator, num_retries=0):
 317             return self.content[locator]
 318
 319     def test_stream_reader(self):
 320         keepblocks = {
 321             'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': b'abcdefghij',
 322             'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': b'klmnopqrstuvwxy',
 323             'cccccccccccccccccccccccccccccccc+5': b'z0123',
 324         }
 325         mk = self.MockKeep(keepblocks)
 326
 327         sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk)
 328
 329         content = b'abcdefghijklmnopqrstuvwxyz0123456789'
 330
 331         self.assertEqual(sr.readfrom(0, 30), content[0:30])
 332         self.assertEqual(sr.readfrom(2, 30), content[2:30])
 333
 334         self.assertEqual(sr.readfrom(2, 8), content[2:10])
 335         self.assertEqual(sr.readfrom(0, 10), content[0:10])
 336
 337         self.assertEqual(sr.readfrom(0, 5), content[0:5])
 338         self.assertEqual(sr.readfrom(5, 5), content[5:10])
 339         self.assertEqual(sr.readfrom(10, 5), content[10:15])
 340         self.assertEqual(sr.readfrom(15, 5), content[15:20])
 341         self.assertEqual(sr.readfrom(20, 5), content[20:25])
 342         self.assertEqual(sr.readfrom(25, 5), content[25:30])
 343         self.assertEqual(sr.readfrom(30, 5), b'')
 344
 345     def test_extract_file(self):
 346         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 347 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt
 348 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt
 349 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt
 350 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt
 351 """
 352
 353         m2 = arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True)
 354
 355         self.assertEqual(m2,
 356                          ". 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")
 357         files = arvados.CollectionReader(
 358             m2, self.api_client).all_streams()[0].files()
 359
 360         self.assertEqual(files['md5sum.txt'].as_manifest(),
 361                          ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n")
 362         self.assertEqual(files['md6sum.txt'].as_manifest(),
 363                          ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n")
 364         self.assertEqual(files['md7sum.txt'].as_manifest(),
 365                          ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n")
 366         self.assertEqual(files['md9sum.txt'].as_manifest(),
 367                          ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n")
 368
 369     def test_write_directory_tree(self):
 370         cwriter = arvados.CollectionWriter(self.api_client)
 371         cwriter.write_directory_tree(self.build_directory_tree(
 372                 ['basefile', 'subdir/subfile']))
 373         self.assertEqual(cwriter.manifest_text(),
 374                          """. c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 375 ./subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 376
 377     def test_write_named_directory_tree(self):
 378         cwriter = arvados.CollectionWriter(self.api_client)
 379         cwriter.write_directory_tree(self.build_directory_tree(
 380                 ['basefile', 'subdir/subfile']), 'root')
 381         self.assertEqual(
 382             cwriter.manifest_text(),
 383             """./root c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 384 ./root/subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 385
 386     def test_write_directory_tree_in_one_stream(self):
 387         cwriter = arvados.CollectionWriter(self.api_client)
 388         cwriter.write_directory_tree(self.build_directory_tree(
 389                 ['basefile', 'subdir/subfile']), max_manifest_depth=0)
 390         self.assertEqual(cwriter.manifest_text(),
 391                          """. 4ace875ffdc6824a04950f06858f4465+22 0:8:basefile 8:14:subdir/subfile\n""")
 392
 393     def test_write_directory_tree_with_limited_recursion(self):
 394         cwriter = arvados.CollectionWriter(self.api_client)
 395         cwriter.write_directory_tree(
 396             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 397             max_manifest_depth=1)
 398         self.assertEqual(cwriter.manifest_text(),
 399                          """. bd19836ddb62c11c55ab251ccaca5645+2 0:2:f1
 400 ./d1 50170217e5b04312024aa5cd42934494+13 0:8:d2/f3 8:5:f2\n""")
 401
 402     def test_write_directory_tree_with_zero_recursion(self):
 403         cwriter = arvados.CollectionWriter(self.api_client)
 404         content = 'd1/d2/f3d1/f2f1'
 405         blockhash = tutil.str_keep_locator(content)
 406         cwriter.write_directory_tree(
 407             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 408             max_manifest_depth=0)
 409         self.assertEqual(
 410             cwriter.manifest_text(),
 411             ". {} 0:8:d1/d2/f3 8:5:d1/f2 13:2:f1\n".format(blockhash))
 412
 413     def test_write_one_file(self):
 414         cwriter = arvados.CollectionWriter(self.api_client)
 415         with self.make_test_file() as testfile:
 416             cwriter.write_file(testfile.name)
 417             self.assertEqual(
 418                 cwriter.manifest_text(),
 419                 ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:{}\n".format(
 420                     os.path.basename(testfile.name)))
 421
 422     def test_write_named_file(self):
 423         cwriter = arvados.CollectionWriter(self.api_client)
 424         with self.make_test_file() as testfile:
 425             cwriter.write_file(testfile.name, 'foo')
 426             self.assertEqual(cwriter.manifest_text(),
 427                              ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:foo\n")
 428
 429     def test_write_multiple_files(self):
 430         cwriter = arvados.CollectionWriter(self.api_client)
 431         for letter in 'ABC':
 432             with self.make_test_file(letter.encode()) as testfile:
 433                 cwriter.write_file(testfile.name, letter)
 434         self.assertEqual(
 435             cwriter.manifest_text(),
 436             ". 902fbdd2b1df0c4f70b4a5d23525e932+3 0:1:A 1:1:B 2:1:C\n")
 437
 438     def test_basic_resume(self):
 439         cwriter = TestResumableWriter()
 440         with self.make_test_file() as testfile:
 441             cwriter.write_file(testfile.name, 'test')
 442             resumed = TestResumableWriter.from_state(cwriter.current_state())
 443         self.assertEqual(cwriter.manifest_text(), resumed.manifest_text(),
 444                           "resumed CollectionWriter had different manifest")
 445
 446     def test_resume_fails_when_missing_dependency(self):
 447         cwriter = TestResumableWriter()
 448         with self.make_test_file() as testfile:
 449             cwriter.write_file(testfile.name, 'test')
 450         self.assertRaises(arvados.errors.StaleWriterStateError,
 451                           TestResumableWriter.from_state,
 452                           cwriter.current_state())
 453
 454     def test_resume_fails_when_dependency_mtime_changed(self):
 455         cwriter = TestResumableWriter()
 456         with self.make_test_file() as testfile:
 457             cwriter.write_file(testfile.name, 'test')
 458             os.utime(testfile.name, (0, 0))
 459             self.assertRaises(arvados.errors.StaleWriterStateError,
 460                               TestResumableWriter.from_state,
 461                               cwriter.current_state())
 462
 463     def test_resume_fails_when_dependency_is_nonfile(self):
 464         cwriter = TestResumableWriter()
 465         cwriter.write_file('/dev/null', 'empty')
 466         self.assertRaises(arvados.errors.StaleWriterStateError,
 467                           TestResumableWriter.from_state,
 468                           cwriter.current_state())
 469
 470     def test_resume_fails_when_dependency_size_changed(self):
 471         cwriter = TestResumableWriter()
 472         with self.make_test_file() as testfile:
 473             cwriter.write_file(testfile.name, 'test')
 474             orig_mtime = os.fstat(testfile.fileno()).st_mtime
 475             testfile.write(b'extra')
 476             testfile.flush()
 477             os.utime(testfile.name, (orig_mtime, orig_mtime))
 478             self.assertRaises(arvados.errors.StaleWriterStateError,
 479                               TestResumableWriter.from_state,
 480                               cwriter.current_state())
 481
 482     def test_resume_fails_with_expired_locator(self):
 483         cwriter = TestResumableWriter()
 484         state = cwriter.current_state()
 485         # Add an expired locator to the state.
 486         state['_current_stream_locators'].append(''.join([
 487                     'a' * 32, '+1+A', 'b' * 40, '@', '10000000']))
 488         self.assertRaises(arvados.errors.StaleWriterStateError,
 489                           TestResumableWriter.from_state, state)
 490
 491     def test_arbitrary_objects_not_resumable(self):
 492         cwriter = TestResumableWriter()
 493         with open('/dev/null') as badfile:
 494             self.assertRaises(arvados.errors.AssertionError,
 495                               cwriter.write_file, badfile)
 496
 497     def test_arbitrary_writes_not_resumable(self):
 498         cwriter = TestResumableWriter()
 499         self.assertRaises(arvados.errors.AssertionError,
 500                           cwriter.write, "badtext")
 501
 502     def test_read_arbitrary_data_with_collection_reader(self):
 503         # arv-get relies on this to do "arv-get {keep-locator} -".
 504         self.write_foo_bar_baz()
 505         self.assertEqual(
 506             'foobar',
 507             arvados.CollectionReader(
 508                 '3858f62230ac3c915f300c664312c63f+6'
 509                 ).manifest_text())
 510
 511
 512 class CollectionTestMixin(tutil.ApiClientMock):
 513     API_COLLECTIONS = run_test_server.fixture('collections')
 514     DEFAULT_COLLECTION = API_COLLECTIONS['foo_file']
 515     DEFAULT_DATA_HASH = DEFAULT_COLLECTION['portable_data_hash']
 516     DEFAULT_MANIFEST = DEFAULT_COLLECTION['manifest_text']
 517     DEFAULT_UUID = DEFAULT_COLLECTION['uuid']
 518     ALT_COLLECTION = API_COLLECTIONS['bar_file']
 519     ALT_DATA_HASH = ALT_COLLECTION['portable_data_hash']
 520     ALT_MANIFEST = ALT_COLLECTION['manifest_text']
 521
 522     def api_client_mock(self, status=200):
 523         client = super(CollectionTestMixin, self).api_client_mock()
 524         self.mock_keep_services(client, status=status, service_type='proxy', count=1)
 525         return client
 526
 527
 528 @tutil.skip_sleep
 529 class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin):
 530     def mock_get_collection(self, api_mock, code, fixturename):
 531         body = self.API_COLLECTIONS.get(fixturename)
 532         self._mock_api_call(api_mock.collections().get, code, body)
 533
 534     def api_client_mock(self, status=200):
 535         client = super(CollectionReaderTestCase, self).api_client_mock()
 536         self.mock_get_collection(client, status, 'foo_file')
 537         return client
 538
 539     def test_init_no_default_retries(self):
 540         client = self.api_client_mock(200)
 541         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 542         reader.manifest_text()
 543         client.collections().get().execute.assert_called_with(num_retries=0)
 544
 545     def test_uuid_init_success(self):
 546         client = self.api_client_mock(200)
 547         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 548                                           num_retries=3)
 549         self.assertEqual(self.DEFAULT_COLLECTION['manifest_text'],
 550                          reader.manifest_text())
 551         client.collections().get().execute.assert_called_with(num_retries=3)
 552
 553     def test_uuid_init_failure_raises_api_error(self):
 554         client = self.api_client_mock(500)
 555         with self.assertRaises(arvados.errors.ApiError):
 556             reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 557
 558     def test_locator_init(self):
 559         client = self.api_client_mock(200)
 560         # Ensure Keep will not return anything if asked.
 561         with tutil.mock_keep_responses(None, 404):
 562             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 563                                               api_client=client)
 564             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 565
 566     def test_locator_init_fallback_to_keep(self):
 567         # crunch-job needs this to read manifests that have only ever
 568         # been written to Keep.
 569         client = self.api_client_mock(200)
 570         self.mock_get_collection(client, 404, None)
 571         with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 572             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 573                                               api_client=client)
 574             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 575
 576     def test_uuid_init_no_fallback_to_keep(self):
 577         # Do not look up a collection UUID in Keep.
 578         client = self.api_client_mock(404)
 579         with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 580             with self.assertRaises(arvados.errors.ApiError):
 581                 reader = arvados.CollectionReader(self.DEFAULT_UUID,
 582                                                   api_client=client)
 583
 584     def test_try_keep_first_if_permission_hint(self):
 585         # To verify that CollectionReader tries Keep first here, we
 586         # mock API server to return the wrong data.
 587         client = self.api_client_mock(200)
 588         with tutil.mock_keep_responses(self.ALT_MANIFEST, 200):
 589             self.assertEqual(
 590                 self.ALT_MANIFEST,
 591                 arvados.CollectionReader(
 592                     self.ALT_DATA_HASH + '+Affffffffffffffffffffffffffffffffffffffff@fedcba98',
 593                     api_client=client).manifest_text())
 594
 595     def test_init_num_retries_propagated(self):
 596         # More of an integration test...
 597         client = self.api_client_mock(200)
 598         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 599                                           num_retries=3)
 600         with tutil.mock_keep_responses('foo', 500, 500, 200):
 601             self.assertEqual(b'foo',
 602                              b''.join(f.read(9) for f in reader.all_files()))
 603
 604     def test_read_nonnormalized_manifest_with_collection_reader(self):
 605         # client should be able to use CollectionReader on a manifest without normalizing it
 606         client = self.api_client_mock(500)
 607         nonnormal = ". acbd18db4cc2f85cedef654fccc4a4d8+3+Aabadbadbee@abeebdee 0:3:foo.txt 1:0:bar.txt 0:3:foo.txt\n"
 608         reader = arvados.CollectionReader(
 609             nonnormal,
 610             api_client=client, num_retries=0)
 611         # Ensure stripped_manifest() doesn't mangle our manifest in
 612         # any way other than stripping hints.
 613         self.assertEqual(
 614             re.sub('\+[^\d\s\+]+', '', nonnormal),
 615             reader.stripped_manifest())
 616         # Ensure stripped_manifest() didn't mutate our reader.
 617         self.assertEqual(nonnormal, reader.manifest_text())
 618         # Ensure the files appear in the order given in the manifest.
 619         self.assertEqual(
 620             [[6, '.', 'foo.txt'],
 621              [0, '.', 'bar.txt']],
 622             [[f.size(), f.stream_name(), f.name()]
 623              for f in reader.all_streams()[0].all_files()])
 624
 625     def test_read_empty_collection(self):
 626         client = self.api_client_mock(200)
 627         self.mock_get_collection(client, 200, 'empty')
 628         reader = arvados.CollectionReader('d41d8cd98f00b204e9800998ecf8427e+0',
 629                                           api_client=client)
 630         self.assertEqual('', reader.manifest_text())
 631
 632     def test_api_response(self):
 633         client = self.api_client_mock()
 634         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 635         self.assertEqual(self.DEFAULT_COLLECTION, reader.api_response())
 636
 637     def test_api_response_with_collection_from_keep(self):
 638         client = self.api_client_mock()
 639         self.mock_get_collection(client, 404, 'foo')
 640         with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 641             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 642                                               api_client=client)
 643             api_response = reader.api_response()
 644         self.assertIsNone(api_response)
 645
 646     def check_open_file(self, coll_file, stream_name, file_name, file_size):
 647         self.assertFalse(coll_file.closed, "returned file is not open")
 648         self.assertEqual(stream_name, coll_file.stream_name())
 649         self.assertEqual(file_name, coll_file.name)
 650         self.assertEqual(file_size, coll_file.size())
 651
 652     def test_open_collection_file_one_argument(self):
 653         client = self.api_client_mock(200)
 654         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 655         cfile = reader.open('./foo', 'rb')
 656         self.check_open_file(cfile, '.', 'foo', 3)
 657
 658     def test_open_deep_file(self):
 659         coll_name = 'collection_with_files_in_subdir'
 660         client = self.api_client_mock(200)
 661         self.mock_get_collection(client, 200, coll_name)
 662         reader = arvados.CollectionReader(
 663             self.API_COLLECTIONS[coll_name]['uuid'], api_client=client)
 664         cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt', 'rb')
 665         self.check_open_file(cfile, './subdir2/subdir3', 'file2_in_subdir3.txt',
 666                              32)
 667
 668     def test_open_nonexistent_stream(self):
 669         client = self.api_client_mock(200)
 670         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 671         self.assertRaises(IOError, reader.open, './nonexistent/foo')
 672
 673     def test_open_nonexistent_file(self):
 674         client = self.api_client_mock(200)
 675         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 676         self.assertRaises(IOError, reader.open, 'nonexistent')
 677
 678
 679 @tutil.skip_sleep
 680 class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin):
 681     def mock_keep(self, body, *codes, **headers):
 682         headers.setdefault('x-keep-replicas-stored', 2)
 683         return tutil.mock_keep_responses(body, *codes, **headers)
 684
 685     def foo_writer(self, **kwargs):
 686         kwargs.setdefault('api_client', self.api_client_mock())
 687         writer = arvados.CollectionWriter(**kwargs)
 688         writer.start_new_file('foo')
 689         writer.write(b'foo')
 690         return writer
 691
 692     def test_write_whole_collection(self):
 693         writer = self.foo_writer()
 694         with self.mock_keep(self.DEFAULT_DATA_HASH, 200, 200):
 695             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 696
 697     def test_write_no_default(self):
 698         writer = self.foo_writer()
 699         with self.mock_keep(None, 500):
 700             with self.assertRaises(arvados.errors.KeepWriteError):
 701                 writer.finish()
 702
 703     def test_write_insufficient_replicas_via_proxy(self):
 704         writer = self.foo_writer(replication=3)
 705         with self.mock_keep(None, 200, **{'x-keep-replicas-stored': 2}):
 706             with self.assertRaises(arvados.errors.KeepWriteError):
 707                 writer.manifest_text()
 708
 709     def test_write_insufficient_replicas_via_disks(self):
 710         client = mock.MagicMock(name='api_client')
 711         with self.mock_keep(
 712                 None, 200, 200,
 713                 **{'x-keep-replicas-stored': 1}) as keepmock:
 714             self.mock_keep_services(client, status=200, service_type='disk', count=2)
 715             writer = self.foo_writer(api_client=client, replication=3)
 716             with self.assertRaises(arvados.errors.KeepWriteError):
 717                 writer.manifest_text()
 718
 719     def test_write_three_replicas(self):
 720         client = mock.MagicMock(name='api_client')
 721         with self.mock_keep(
 722                 "", 500, 500, 500, 200, 200, 200,
 723                 **{'x-keep-replicas-stored': 1}) as keepmock:
 724             self.mock_keep_services(client, status=200, service_type='disk', count=6)
 725             writer = self.foo_writer(api_client=client, replication=3)
 726             writer.manifest_text()
 727             self.assertEqual(6, keepmock.call_count)
 728
 729     def test_write_whole_collection_through_retries(self):
 730         writer = self.foo_writer(num_retries=2)
 731         with self.mock_keep(self.DEFAULT_DATA_HASH,
 732                             500, 500, 200, 500, 500, 200):
 733             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 734
 735     def test_flush_data_retries(self):
 736         writer = self.foo_writer(num_retries=2)
 737         foo_hash = self.DEFAULT_MANIFEST.split()[1]
 738         with self.mock_keep(foo_hash, 500, 200):
 739             writer.flush_data()
 740         self.assertEqual(self.DEFAULT_MANIFEST, writer.manifest_text())
 741
 742     def test_one_open(self):
 743         client = self.api_client_mock()
 744         writer = arvados.CollectionWriter(client)
 745         with writer.open('out') as out_file:
 746             self.assertEqual('.', writer.current_stream_name())
 747             self.assertEqual('out', writer.current_file_name())
 748             out_file.write(b'test data')
 749             data_loc = tutil.str_keep_locator('test data')
 750         self.assertTrue(out_file.closed, "writer file not closed after context")
 751         self.assertRaises(ValueError, out_file.write, 'extra text')
 752         with self.mock_keep(data_loc, 200) as keep_mock:
 753             self.assertEqual(". {} 0:9:out\n".format(data_loc),
 754                              writer.manifest_text())
 755
 756     def test_open_writelines(self):
 757         client = self.api_client_mock()
 758         writer = arvados.CollectionWriter(client)
 759         with writer.open('six') as out_file:
 760             out_file.writelines(['12', '34', '56'])
 761             data_loc = tutil.str_keep_locator('123456')
 762         with self.mock_keep(data_loc, 200) as keep_mock:
 763             self.assertEqual(". {} 0:6:six\n".format(data_loc),
 764                              writer.manifest_text())
 765
 766     def test_open_flush(self):
 767         client = self.api_client_mock()
 768         data_loc1 = tutil.str_keep_locator('flush1')
 769         data_loc2 = tutil.str_keep_locator('flush2')
 770         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 771             writer = arvados.CollectionWriter(client)
 772             with writer.open('flush_test') as out_file:
 773                 out_file.write(b'flush1')
 774                 out_file.flush()
 775                 out_file.write(b'flush2')
 776             self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1,
 777                                                                 data_loc2),
 778                              writer.manifest_text())
 779
 780     def test_two_opens_same_stream(self):
 781         client = self.api_client_mock()
 782         writer = arvados.CollectionWriter(client)
 783         with writer.open('.', '1') as out_file:
 784             out_file.write(b'1st')
 785         with writer.open('.', '2') as out_file:
 786             out_file.write(b'2nd')
 787         data_loc = tutil.str_keep_locator('1st2nd')
 788         with self.mock_keep(data_loc, 200) as keep_mock:
 789             self.assertEqual(". {} 0:3:1 3:3:2\n".format(data_loc),
 790                              writer.manifest_text())
 791
 792     def test_two_opens_two_streams(self):
 793         client = self.api_client_mock()
 794         data_loc1 = tutil.str_keep_locator('file')
 795         data_loc2 = tutil.str_keep_locator('indir')
 796         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 797             writer = arvados.CollectionWriter(client)
 798             with writer.open('file') as out_file:
 799                 out_file.write(b'file')
 800             with writer.open('./dir', 'indir') as out_file:
 801                 out_file.write(b'indir')
 802             expected = ". {} 0:4:file\n./dir {} 0:5:indir\n".format(
 803                 data_loc1, data_loc2)
 804             self.assertEqual(expected, writer.manifest_text())
 805
 806     def test_dup_open_fails(self):
 807         client = self.api_client_mock()
 808         writer = arvados.CollectionWriter(client)
 809         file1 = writer.open('one')
 810         self.assertRaises(arvados.errors.AssertionError, writer.open, 'two')
 811
 812
 813 class CollectionMethods(run_test_server.TestCaseWithServers):
 814
 815     def test_keys_values_items_support_indexing(self):
 816         c = Collection()
 817         with c.open('foo', 'wb') as f:
 818             f.write(b'foo')
 819         with c.open('bar', 'wb') as f:
 820             f.write(b'bar')
 821         self.assertEqual(2, len(c.keys()))
 822         if sys.version_info < (3, 0):
 823             # keys() supports indexing only for python2 callers.
 824             fn0 = c.keys()[0]
 825             fn1 = c.keys()[1]
 826         else:
 827             fn0, fn1 = c.keys()
 828         self.assertEqual(2, len(c.values()))
 829         f0 = c.values()[0]
 830         f1 = c.values()[1]
 831         self.assertEqual(2, len(c.items()))
 832         self.assertEqual(fn0, c.items()[0][0])
 833         self.assertEqual(fn1, c.items()[1][0])
 834
 835
 836 class CollectionOpenModes(run_test_server.TestCaseWithServers):
 837
 838     def test_open_binary_modes(self):
 839         c = Collection()
 840         for mode in ['wb', 'wb+', 'ab', 'ab+']:
 841             with c.open('foo', mode) as f:
 842                 f.write(b'foo')
 843
 844     def test_open_invalid_modes(self):
 845         c = Collection()
 846         for mode in ['+r', 'aa', '++', 'r+b', 'beer', '', None]:
 847             with self.assertRaises(Exception):
 848                 c.open('foo', mode)
 849
 850     def test_open_text_modes(self):
 851         c = Collection()
 852         with c.open('foo', 'wb') as f:
 853             f.write('foo')
 854         for mode in ['r', 'rt', 'r+', 'rt+', 'w', 'wt', 'a', 'at']:
 855             if sys.version_info >= (3, 0):
 856                 with self.assertRaises(NotImplementedError):
 857                     c.open('foo', mode)
 858             else:
 859                 with c.open('foo', mode) as f:
 860                     if mode[0] == 'r' and '+' not in mode:
 861                         self.assertEqual('foo', f.read(3))
 862                     else:
 863                         f.write('bar')
 864                         f.seek(-3, os.SEEK_CUR)
 865                         self.assertEqual('bar', f.read(3))
 866
 867
 868 class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin):
 869
 870     def test_replication_desired_kept_on_load(self):
 871         m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
 872         c1 = Collection(m, replication_desired=1)
 873         c1.save_new()
 874         loc = c1.manifest_locator()
 875         c2 = Collection(loc)
 876         self.assertEqual(c1.manifest_text, c2.manifest_text)
 877         self.assertEqual(c1.replication_desired, c2.replication_desired)
 878
 879     def test_replication_desired_not_loaded_if_provided(self):
 880         m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
 881         c1 = Collection(m, replication_desired=1)
 882         c1.save_new()
 883         loc = c1.manifest_locator()
 884         c2 = Collection(loc, replication_desired=2)
 885         self.assertEqual(c1.manifest_text, c2.manifest_text)
 886         self.assertNotEqual(c1.replication_desired, c2.replication_desired)
 887
 888     def test_init_manifest(self):
 889         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 890 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 891 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 892 """
 893         self.assertEqual(m1, CollectionReader(m1).manifest_text(normalize=False))
 894         self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", CollectionReader(m1).manifest_text(normalize=True))
 895
 896     def test_init_manifest_with_collision(self):
 897         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 898 ./md5sum.txt 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 899 """
 900         with self.assertRaises(arvados.errors.ArgumentError):
 901             self.assertEqual(m1, CollectionReader(m1))
 902
 903     def test_init_manifest_with_error(self):
 904         m1 = """. 0:43:md5sum.txt"""
 905         with self.assertRaises(arvados.errors.ArgumentError):
 906             self.assertEqual(m1, CollectionReader(m1))
 907
 908     def test_remove(self):
 909         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
 910         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 911         self.assertIn("count1.txt", c)
 912         c.remove("count1.txt")
 913         self.assertNotIn("count1.txt", c)
 914         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
 915         with self.assertRaises(arvados.errors.ArgumentError):
 916             c.remove("")
 917
 918     def test_find(self):
 919         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
 920         self.assertIs(c.find("."), c)
 921         self.assertIs(c.find("./count1.txt"), c["count1.txt"])
 922         self.assertIs(c.find("count1.txt"), c["count1.txt"])
 923         with self.assertRaises(IOError):
 924             c.find("/.")
 925         with self.assertRaises(arvados.errors.ArgumentError):
 926             c.find("")
 927         self.assertIs(c.find("./nonexistant.txt"), None)
 928         self.assertIs(c.find("./nonexistantsubdir/nonexistant.txt"), None)
 929
 930     def test_remove_in_subdir(self):
 931         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 932         c.remove("foo/count2.txt")
 933         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 934
 935     def test_remove_empty_subdir(self):
 936         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 937         c.remove("foo/count2.txt")
 938         c.remove("foo")
 939         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 940
 941     def test_remove_nonempty_subdir(self):
 942         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 943         with self.assertRaises(IOError):
 944             c.remove("foo")
 945         c.remove("foo", recursive=True)
 946         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 947
 948     def test_copy_to_file_in_dir(self):
 949         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 950         c.copy("count1.txt", "foo/count2.txt")
 951         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
 952
 953     def test_copy_file(self):
 954         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 955         c.copy("count1.txt", "count2.txt")
 956         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 957
 958     def test_copy_to_existing_dir(self):
 959         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 960         c.copy("count1.txt", "foo")
 961         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())
 962
 963     def test_copy_to_new_dir(self):
 964         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 965         c.copy("count1.txt", "foo/")
 966         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 967
 968     def test_rename_file(self):
 969         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 970         c.rename("count1.txt", "count2.txt")
 971         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
 972
 973     def test_move_file_to_dir(self):
 974         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 975         c.mkdirs("foo")
 976         c.rename("count1.txt", "foo/count2.txt")
 977         self.assertEqual("./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
 978
 979     def test_move_file_to_other(self):
 980         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 981         c2 = Collection()
 982         c2.rename("count1.txt", "count2.txt", source_collection=c1)
 983         self.assertEqual("", c1.manifest_text())
 984         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c2.manifest_text())
 985
 986     def test_clone(self):
 987         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 988         cl = c.clone()
 989         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", cl.portable_manifest_text())
 990
 991     def test_diff_del_add(self):
 992         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 993         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
 994         d = c2.diff(c1)
 995         self.assertEqual(sorted(d), [
 996             ('add', './count1.txt', c1["count1.txt"]),
 997             ('del', './count2.txt', c2["count2.txt"]),
 998         ])
 999         d = c1.diff(c2)
1000         self.assertEqual(sorted(d), [
1001             ('add', './count2.txt', c2["count2.txt"]),
1002             ('del', './count1.txt', c1["count1.txt"]),
1003         ])
1004         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1005         c1.apply(d)
1006         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1007
1008     def test_diff_same(self):
1009         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1010         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1011         d = c2.diff(c1)
1012         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1013         d = c1.diff(c2)
1014         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1015
1016         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1017         c1.apply(d)
1018         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1019
1020     def test_diff_mod(self):
1021         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1022         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
1023         d = c2.diff(c1)
1024         self.assertEqual(d, [('mod', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1025         d = c1.diff(c2)
1026         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1027
1028         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1029         c1.apply(d)
1030         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1031
1032     def test_diff_add(self):
1033         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1034         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt 10:20:count2.txt\n')
1035         d = c2.diff(c1)
1036         self.assertEqual(sorted(d), [
1037             ('del', './count2.txt', c2["count2.txt"]),
1038             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1039         ])
1040         d = c1.diff(c2)
1041         self.assertEqual(sorted(d), [
1042             ('add', './count2.txt', c2["count2.txt"]),
1043             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1044         ])
1045
1046         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1047         c1.apply(d)
1048         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1049
1050     def test_diff_add_in_subcollection(self):
1051         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1052         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1053         d = c2.diff(c1)
1054         self.assertEqual(sorted(d), [
1055             ('del', './foo', c2["foo"]),
1056             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1057         ])
1058         d = c1.diff(c2)
1059         self.assertEqual(sorted(d), [
1060             ('add', './foo', c2["foo"]),
1061             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1062         ])
1063         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1064         c1.apply(d)
1065         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1066
1067     def test_diff_del_add_in_subcollection(self):
1068         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1069         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:3:count3.txt\n')
1070         d = c2.diff(c1)
1071         self.assertEqual(sorted(d), [
1072             ('add', './foo/count2.txt', c1.find("foo/count2.txt")),
1073             ('del', './foo/count3.txt', c2.find("foo/count3.txt")),
1074             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1075         ])
1076         d = c1.diff(c2)
1077         self.assertEqual(sorted(d), [
1078             ('add', './foo/count3.txt', c2.find("foo/count3.txt")),
1079             ('del', './foo/count2.txt', c1.find("foo/count2.txt")),
1080             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1081         ])
1082
1083         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1084         c1.apply(d)
1085         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1086
1087     def test_diff_mod_in_subcollection(self):
1088         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1089         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:3:foo\n')
1090         d = c2.diff(c1)
1091         self.assertEqual(sorted(d), [
1092             ('mod', './foo', c2["foo"], c1["foo"]),
1093             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1094         ])
1095         d = c1.diff(c2)
1096         self.assertEqual(sorted(d), [
1097             ('mod', './foo', c1["foo"], c2["foo"]),
1098             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1099         ])
1100
1101         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1102         c1.apply(d)
1103         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1104
1105     def test_conflict_keep_local_change(self):
1106         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1107         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1108         d = c1.diff(c2)
1109         self.assertEqual(sorted(d), [
1110             ('add', './count2.txt', c2["count2.txt"]),
1111             ('del', './count1.txt', c1["count1.txt"]),
1112         ])
1113         f = c1.open("count1.txt", "wb")
1114         f.write(b"zzzzz")
1115
1116         # c1 changed, so it should not be deleted.
1117         c1.apply(d)
1118         self.assertEqual(c1.portable_manifest_text(), ". 95ebc3c7b3b9f1d2c40fec14415d3cb8+5 5348b82a029fd9e971a811ce1f71360b+43 0:5:count1.txt 5:10:count2.txt\n")
1119
1120     def test_conflict_mod(self):
1121         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1122         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1123         d = c1.diff(c2)
1124         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1125         f = c1.open("count1.txt", "wb")
1126         f.write(b"zzzzz")
1127
1128         # c1 changed, so c2 mod will go to a conflict file
1129         c1.apply(d)
1130         self.assertRegex(
1131             c1.portable_manifest_text(),
1132             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~$")
1133
1134     def test_conflict_add(self):
1135         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
1136         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
1137         d = c1.diff(c2)
1138         self.assertEqual(sorted(d), [
1139             ('add', './count1.txt', c2["count1.txt"]),
1140             ('del', './count2.txt', c1["count2.txt"]),
1141         ])
1142         f = c1.open("count1.txt", "wb")
1143         f.write(b"zzzzz")
1144
1145         # c1 added count1.txt, so c2 add will go to a conflict file
1146         c1.apply(d)
1147         self.assertRegex(
1148             c1.portable_manifest_text(),
1149             r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1150
1151     def test_conflict_del(self):
1152         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1153         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1154         d = c1.diff(c2)
1155         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1156         c1.remove("count1.txt")
1157
1158         # c1 deleted, so c2 mod will go to a conflict file
1159         c1.apply(d)
1160         self.assertRegex(
1161             c1.portable_manifest_text(),
1162             r"\. 5348b82a029fd9e971a811ce1f71360b\+43 0:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1163
1164     def test_notify(self):
1165         c1 = Collection()
1166         events = []
1167         c1.subscribe(lambda event, collection, name, item: events.append((event, collection, name, item)))
1168         f = c1.open("foo.txt", "wb")
1169         self.assertEqual(events[0], (arvados.collection.ADD, c1, "foo.txt", f.arvadosfile))
1170
1171     def test_open_w(self):
1172         c1 = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n")
1173         self.assertEqual(c1["count1.txt"].size(), 10)
1174         c1.open("count1.txt", "wb").close()
1175         self.assertEqual(c1["count1.txt"].size(), 0)
1176
1177
1178 class NewCollectionTestCaseWithServersAndTokens(run_test_server.TestCaseWithServers):
1179     MAIN_SERVER = {}
1180     KEEP_SERVER = {}
1181
1182     def setUp(self):
1183         self.keep_put = getattr(arvados.keep.KeepClient, 'put')
1184
1185     def test_repacked_block_submission_get_permission_token(self):
1186         '''
1187         Make sure that those blocks that are committed after repacking small ones,
1188         get their permission tokens assigned on the collection manifest.
1189         '''
1190         def wrapped_keep_put(*args, **kwargs):
1191             # Simulate slow put operations
1192             time.sleep(1)
1193             return self.keep_put(*args, **kwargs)
1194
1195         re_locator = "[0-9a-f]{32}\+\d+\+A[a-f0-9]{40}@[a-f0-9]{8}"
1196
1197         with mock.patch('arvados.keep.KeepClient.put', autospec=True) as mocked_put:
1198             mocked_put.side_effect = wrapped_keep_put
1199             c = Collection()
1200             # Write 70 files ~1MiB each so we force to produce 1 big block by repacking
1201             # small ones before finishing the upload.
1202             for i in range(70):
1203                 f = c.open("file_{}.txt".format(i), 'wb')
1204                 f.write(random.choice('abcdefghijklmnopqrstuvwxyz') * (2**20+i))
1205                 f.close(flush=False)
1206             # We should get 2 blocks with their tokens
1207             self.assertEqual(len(re.findall(re_locator, c.manifest_text())), 2)
1208
1209
1210 class NewCollectionTestCaseWithServers(run_test_server.TestCaseWithServers):
1211     def test_get_manifest_text_only_committed(self):
1212         c = Collection()
1213         with c.open("count.txt", "wb") as f:
1214             # One file committed
1215             with c.open("foo.txt", "wb") as foo:
1216                 foo.write(b"foo")
1217                 foo.flush() # Force block commit
1218             f.write(b"0123456789")
1219             # Other file not committed. Block not written to keep yet.
1220             self.assertEqual(
1221                 c._get_manifest_text(".",
1222                                      strip=False,
1223                                      normalize=False,
1224                                      only_committed=True),
1225                 '. acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:count.txt 0:3:foo.txt\n')
1226             # And now with the file closed...
1227             f.flush() # Force block commit
1228         self.assertEqual(
1229             c._get_manifest_text(".",
1230                                  strip=False,
1231                                  normalize=False,
1232                                  only_committed=True),
1233             ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:10:count.txt 10:3:foo.txt\n")
1234
1235     def test_only_small_blocks_are_packed_together(self):
1236         c = Collection()
1237         # Write a couple of small files,
1238         f = c.open("count.txt", "wb")
1239         f.write(b"0123456789")
1240         f.close(flush=False)
1241         foo = c.open("foo.txt", "wb")
1242         foo.write(b"foo")
1243         foo.close(flush=False)
1244         # Then, write a big file, it shouldn't be packed with the ones above
1245         big = c.open("bigfile.txt", "wb")
1246         big.write(b"x" * 1024 * 1024 * 33) # 33 MB > KEEP_BLOCK_SIZE/2
1247         big.close(flush=False)
1248         self.assertEqual(
1249             c.manifest_text("."),
1250             '. 2d303c138c118af809f39319e5d507e9+34603008 a8430a058b8fbf408e1931b794dbd6fb+13 0:34603008:bigfile.txt 34603008:10:count.txt 34603018:3:foo.txt\n')
1251
1252     def test_flush_after_small_block_packing(self):
1253         c = Collection()
1254         # Write a couple of small files,
1255         f = c.open("count.txt", "wb")
1256         f.write(b"0123456789")
1257         f.close(flush=False)
1258         foo = c.open("foo.txt", "wb")
1259         foo.write(b"foo")
1260         foo.close(flush=False)
1261
1262         self.assertEqual(
1263             c.manifest_text(),
1264             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1265
1266         f = c.open("count.txt", "rb+")
1267         f.close(flush=True)
1268
1269         self.assertEqual(
1270             c.manifest_text(),
1271             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1272
1273     def test_write_after_small_block_packing2(self):
1274         c = Collection()
1275         # Write a couple of small files,
1276         f = c.open("count.txt", "wb")
1277         f.write(b"0123456789")
1278         f.close(flush=False)
1279         foo = c.open("foo.txt", "wb")
1280         foo.write(b"foo")
1281         foo.close(flush=False)
1282
1283         self.assertEqual(
1284             c.manifest_text(),
1285             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1286
1287         f = c.open("count.txt", "rb+")
1288         f.write(b"abc")
1289         f.close(flush=False)
1290
1291         self.assertEqual(
1292             c.manifest_text(),
1293             '. 900150983cd24fb0d6963f7d28e17f72+3 a8430a058b8fbf408e1931b794dbd6fb+13 0:3:count.txt 6:7:count.txt 13:3:foo.txt\n')
1294
1295
1296     def test_small_block_packing_with_overwrite(self):
1297         c = Collection()
1298         c.open("b1", "wb").close()
1299         c["b1"].writeto(0, b"b1", 0)
1300
1301         c.open("b2", "wb").close()
1302         c["b2"].writeto(0, b"b2", 0)
1303
1304         c["b1"].writeto(0, b"1b", 0)
1305
1306         self.assertEquals(c.manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1 2:2:b2\n")
1307         self.assertEquals(c["b1"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1\n")
1308         self.assertEquals(c["b2"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 2:2:b2\n")
1309
1310
1311 class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers):
1312     MAIN_SERVER = {}
1313     KEEP_SERVER = {}
1314
1315     def create_count_txt(self):
1316         # Create an empty collection, save it to the API server, then write a
1317         # file, but don't save it.
1318
1319         c = Collection()
1320         c.save_new("CollectionCreateUpdateTest", ensure_unique_name=True)
1321         self.assertEqual(c.portable_data_hash(), "d41d8cd98f00b204e9800998ecf8427e+0")
1322         self.assertEqual(c.api_response()["portable_data_hash"], "d41d8cd98f00b204e9800998ecf8427e+0" )
1323
1324         with c.open("count.txt", "wb") as f:
1325             f.write(b"0123456789")
1326
1327         self.assertEqual(c.portable_manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1328
1329         return c
1330
1331     def test_create_and_save(self):
1332         c = self.create_count_txt()
1333         c.save()
1334         self.assertRegex(
1335             c.manifest_text(),
1336             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1337
1338     def test_create_and_save_new(self):
1339         c = self.create_count_txt()
1340         c.save_new()
1341         self.assertRegex(
1342             c.manifest_text(),
1343             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1344
1345     def test_create_diff_apply(self):
1346         c1 = self.create_count_txt()
1347         c1.save()
1348
1349         c2 = Collection(c1.manifest_locator())
1350         with c2.open("count.txt", "wb") as f:
1351             f.write(b"abcdefg")
1352
1353         diff = c1.diff(c2)
1354
1355         self.assertEqual(diff[0], (arvados.collection.MOD, u'./count.txt', c1["count.txt"], c2["count.txt"]))
1356
1357         c1.apply(diff)
1358         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1359
1360     def test_diff_apply_with_token(self):
1361         baseline = CollectionReader(". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:10:count.txt\n")
1362         c = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1363         other = CollectionReader(". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1364
1365         diff = baseline.diff(other)
1366         self.assertEqual(diff, [('mod', u'./count.txt', c["count.txt"], other["count.txt"])])
1367
1368         c.apply(diff)
1369
1370         self.assertEqual(c.manifest_text(), ". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1371
1372
1373     def test_create_and_update(self):
1374         c1 = self.create_count_txt()
1375         c1.save()
1376
1377         c2 = arvados.collection.Collection(c1.manifest_locator())
1378         with c2.open("count.txt", "wb") as f:
1379             f.write(b"abcdefg")
1380
1381         c2.save()
1382
1383         self.assertNotEqual(c1.portable_data_hash(), c2.portable_data_hash())
1384         c1.update()
1385         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1386
1387
1388     def test_create_and_update_with_conflict(self):
1389         c1 = self.create_count_txt()
1390         c1.save()
1391
1392         with c1.open("count.txt", "wb") as f:
1393             f.write(b"XYZ")
1394
1395         c2 = arvados.collection.Collection(c1.manifest_locator())
1396         with c2.open("count.txt", "wb") as f:
1397             f.write(b"abcdefg")
1398
1399         c2.save()
1400
1401         c1.update()
1402         self.assertRegex(
1403             c1.manifest_text(),
1404             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~$")
1405
1406     def test_pdh_is_native_str(self):
1407         c1 = self.create_count_txt()
1408         pdh = c1.portable_data_hash()
1409         self.assertEqual(type(''), type(pdh))
1410
1411
1412 if __name__ == '__main__':
1413     unittest.main()