sdk/python/tests/test_collections.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 from __future__ import absolute_import
   6
   7 from builtins import object
   8 import arvados
   9 import copy
  10 import mock
  11 import os
  12 import pprint
  13 import random
  14 import re
  15 import sys
  16 import tempfile
  17 import datetime
  18 import ciso8601
  19 import time
  20 import unittest
  21
  22 from . import run_test_server
  23 from arvados._ranges import Range, LocatorAndRange
  24 from arvados.collection import Collection, CollectionReader
  25 from . import arvados_testutil as tutil
  26
  27 class TestResumableWriter(arvados.ResumableCollectionWriter):
  28     KEEP_BLOCK_SIZE = 1024  # PUT to Keep every 1K.
  29
  30     def current_state(self):
  31         return self.dump_state(copy.deepcopy)
  32
  33
  34 class ArvadosCollectionsTest(run_test_server.TestCaseWithServers,
  35                              tutil.ArvadosBaseTestCase):
  36     MAIN_SERVER = {}
  37
  38     @classmethod
  39     def setUpClass(cls):
  40         super(ArvadosCollectionsTest, cls).setUpClass()
  41         # need admin privileges to make collections with unsigned blocks
  42         run_test_server.authorize_with('admin')
  43         cls.api_client = arvados.api('v1')
  44         cls.keep_client = arvados.KeepClient(api_client=cls.api_client,
  45                                              local_store=cls.local_store)
  46
  47     def write_foo_bar_baz(self):
  48         cw = arvados.CollectionWriter(self.api_client)
  49         self.assertEqual(cw.current_stream_name(), '.',
  50                          'current_stream_name() should be "." now')
  51         cw.set_current_file_name('foo.txt')
  52         cw.write(b'foo')
  53         self.assertEqual(cw.current_file_name(), 'foo.txt',
  54                          'current_file_name() should be foo.txt now')
  55         cw.start_new_file('bar.txt')
  56         cw.write(b'bar')
  57         cw.start_new_stream('baz')
  58         cw.write(b'baz')
  59         cw.set_current_file_name('baz.txt')
  60         self.assertEqual(cw.manifest_text(),
  61                          ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" +
  62                          "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n",
  63                          "wrong manifest: got {}".format(cw.manifest_text()))
  64         cw.save_new()
  65         return cw.portable_data_hash()
  66
  67     def test_pdh_is_native_str(self):
  68         pdh = self.write_foo_bar_baz()
  69         self.assertEqual(type(''), type(pdh))
  70
  71     def test_keep_local_store(self):
  72         self.assertEqual(self.keep_client.put(b'foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
  73         self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), b'foo', 'wrong data from Keep.get')
  74
  75     def test_local_collection_writer(self):
  76         self.assertEqual(self.write_foo_bar_baz(),
  77                          '23ca013983d6239e98931cc779e68426+114',
  78                          'wrong locator hash: ' + self.write_foo_bar_baz())
  79
  80     def test_local_collection_reader(self):
  81         foobarbaz = self.write_foo_bar_baz()
  82         cr = arvados.CollectionReader(
  83             foobarbaz + '+Xzizzle', self.api_client)
  84         got = []
  85         for s in cr.all_streams():
  86             for f in s.all_files():
  87                 got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]]
  88         expected = [[3, '.', 'foo.txt', b'foo'],
  89                     [3, '.', 'bar.txt', b'bar'],
  90                     [3, './baz', 'baz.txt', b'baz']]
  91         self.assertEqual(got,
  92                          expected)
  93         stream0 = cr.all_streams()[0]
  94         self.assertEqual(stream0.readfrom(0, 0),
  95                          b'',
  96                          'reading zero bytes should have returned empty string')
  97         self.assertEqual(stream0.readfrom(0, 2**26),
  98                          b'foobar',
  99                          'reading entire stream failed')
 100         self.assertEqual(stream0.readfrom(2**26, 0),
 101                          b'',
 102                          'reading zero bytes should have returned empty string')
 103         self.assertEqual(3, len(cr))
 104         self.assertTrue(cr)
 105
 106     def _test_subset(self, collection, expected):
 107         cr = arvados.CollectionReader(collection, self.api_client)
 108         for s in cr.all_streams():
 109             for ex in expected:
 110                 if ex[0] == s:
 111                     f = s.files()[ex[2]]
 112                     got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))]
 113                     self.assertEqual(got,
 114                                      ex,
 115                                      'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex))
 116
 117     def test_collection_manifest_subset(self):
 118         foobarbaz = self.write_foo_bar_baz()
 119         self._test_subset(foobarbaz,
 120                           [[3, '.',     'bar.txt', b'bar'],
 121                            [3, '.',     'foo.txt', b'foo'],
 122                            [3, './baz', 'baz.txt', b'baz']])
 123         self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" %
 124                            (self.keep_client.put(b"foo"),
 125                             self.keep_client.put(b"bar"))),
 126                           [[3, '.', 'bar.txt', b'bar'],
 127                            [3, '.', 'foo.txt', b'foo']])
 128         self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" %
 129                            (self.keep_client.put(b"foo"),
 130                             self.keep_client.put(b"bar"))),
 131                           [[2, '.', 'fo.txt', b'fo'],
 132                            [4, '.', 'obar.txt', b'obar']])
 133         self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" %
 134                            (self.keep_client.put(b"foo"),
 135                             self.keep_client.put(b"bar"))),
 136                           [[2, '.', 'ar.txt', b'ar'],
 137                            [2, '.', 'fo.txt', b'fo'],
 138                            [2, '.', 'ob.txt', b'ob'],
 139                            [0, '.', 'zero.txt', b'']])
 140
 141     def test_collection_empty_file(self):
 142         cw = arvados.CollectionWriter(self.api_client)
 143         cw.start_new_file('zero.txt')
 144         cw.write(b'')
 145
 146         self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n")
 147         self.check_manifest_file_sizes(cw.manifest_text(), [0])
 148         cw = arvados.CollectionWriter(self.api_client)
 149         cw.start_new_file('zero.txt')
 150         cw.write(b'')
 151         cw.start_new_file('one.txt')
 152         cw.write(b'1')
 153         cw.start_new_stream('foo')
 154         cw.start_new_file('zero.txt')
 155         cw.write(b'')
 156         self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0])
 157
 158     def test_no_implicit_normalize(self):
 159         cw = arvados.CollectionWriter(self.api_client)
 160         cw.start_new_file('b')
 161         cw.write(b'b')
 162         cw.start_new_file('a')
 163         cw.write(b'')
 164         self.check_manifest_file_sizes(cw.manifest_text(), [1,0])
 165         self.check_manifest_file_sizes(
 166             arvados.CollectionReader(
 167                 cw.manifest_text()).manifest_text(normalize=True),
 168             [0,1])
 169
 170     def check_manifest_file_sizes(self, manifest_text, expect_sizes):
 171         cr = arvados.CollectionReader(manifest_text, self.api_client)
 172         got_sizes = []
 173         for f in cr.all_files():
 174             got_sizes += [f.size()]
 175         self.assertEqual(got_sizes, expect_sizes, "got wrong file sizes %s, expected %s" % (got_sizes, expect_sizes))
 176
 177     def test_normalized_collection(self):
 178         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 179 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 180 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 181 """
 182         self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True),
 183                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
 184 """)
 185
 186         m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
 187 """
 188         self.assertEqual(arvados.CollectionReader(m2, self.api_client).manifest_text(normalize=True), m2)
 189
 190         m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
 191 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 192 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 193 """
 194         self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(normalize=True),
 195                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
 196 """)
 197
 198         m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 199 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 200 ./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
 201 """
 202         self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(normalize=True),
 203                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
 204 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 205 """)
 206
 207         m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 208 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 209 ./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar
 210 """
 211         self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(normalize=True),
 212                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
 213 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 214 """)
 215
 216         with self.data_file('1000G_ref_manifest') as f6:
 217             m6 = f6.read()
 218             self.assertEqual(arvados.CollectionReader(m6, self.api_client).manifest_text(normalize=True), m6)
 219
 220         with self.data_file('jlake_manifest') as f7:
 221             m7 = f7.read()
 222             self.assertEqual(arvados.CollectionReader(m7, self.api_client).manifest_text(normalize=True), m7)
 223
 224         m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt
 225 """
 226         self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8)
 227
 228     def test_locators_and_ranges(self):
 229         blocks2 = [Range('a', 0, 10),
 230                    Range('b', 10, 10),
 231                    Range('c', 20, 10),
 232                    Range('d', 30, 10),
 233                    Range('e', 40, 10),
 234                    Range('f', 50, 10)]
 235
 236         self.assertEqual(arvados.locators_and_ranges(blocks2,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 237         self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 238         self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 239         self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 240         self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 241         self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 242         self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), [])
 243         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 244
 245         self.assertEqual(arvados.locators_and_ranges(blocks2,  0,  2), [LocatorAndRange('a', 10, 0, 2)])
 246         self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [LocatorAndRange('b', 10, 0, 2)])
 247         self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [LocatorAndRange('c', 10, 0, 2)])
 248         self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [LocatorAndRange('d', 10, 0, 2)])
 249         self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [LocatorAndRange('e', 10, 0, 2)])
 250         self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [LocatorAndRange('f', 10, 0, 2)])
 251         self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), [])
 252         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 253
 254         self.assertEqual(arvados.locators_and_ranges(blocks2,  9,  2), [LocatorAndRange('a', 10, 9, 1), LocatorAndRange('b', 10, 0, 1)])
 255         self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [LocatorAndRange('b', 10, 9, 1), LocatorAndRange('c', 10, 0, 1)])
 256         self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [LocatorAndRange('c', 10, 9, 1), LocatorAndRange('d', 10, 0, 1)])
 257         self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [LocatorAndRange('d', 10, 9, 1), LocatorAndRange('e', 10, 0, 1)])
 258         self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [LocatorAndRange('e', 10, 9, 1), LocatorAndRange('f', 10, 0, 1)])
 259         self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [LocatorAndRange('f', 10, 9, 1)])
 260
 261
 262         blocks3 = [Range('a', 0, 10),
 263                   Range('b', 10, 10),
 264                   Range('c', 20, 10),
 265                   Range('d', 30, 10),
 266                   Range('e', 40, 10),
 267                   Range('f', 50, 10),
 268                    Range('g', 60, 10)]
 269
 270         self.assertEqual(arvados.locators_and_ranges(blocks3,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 271         self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 272         self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 273         self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 274         self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 275         self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 276         self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [LocatorAndRange('g', 10, 2, 2)])
 277
 278
 279         blocks = [Range('a', 0, 10),
 280                   Range('b', 10, 15),
 281                   Range('c', 25, 5)]
 282         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 0), [])
 283         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [LocatorAndRange('a', 10, 0, 5)])
 284         self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [LocatorAndRange('a', 10, 3, 5)])
 285         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [LocatorAndRange('a', 10, 0, 10)])
 286
 287         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [LocatorAndRange('a', 10, 0, 10),
 288                                                                       LocatorAndRange('b', 15, 0, 1)])
 289         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [LocatorAndRange('a', 10, 1, 9),
 290                                                                       LocatorAndRange('b', 15, 0, 2)])
 291         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [LocatorAndRange('a', 10, 0, 10),
 292                                                                       LocatorAndRange('b', 15, 0, 15)])
 293
 294         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [LocatorAndRange('a', 10, 0, 10),
 295                                                                       LocatorAndRange('b', 15, 0, 15),
 296                                                                       LocatorAndRange('c', 5, 0, 5)])
 297         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [LocatorAndRange('a', 10, 1, 9),
 298                                                                       LocatorAndRange('b', 15, 0, 15),
 299                                                                       LocatorAndRange('c', 5, 0, 5)])
 300         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [LocatorAndRange('a', 10, 0, 10),
 301                                                                       LocatorAndRange('b', 15, 0, 15),
 302                                                                       LocatorAndRange('c', 5, 0, 5)])
 303
 304         self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [LocatorAndRange('b', 15, 5, 5)])
 305
 306         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [LocatorAndRange('a', 10, 8, 2),
 307                                                                       LocatorAndRange('b', 15, 0, 15)])
 308
 309         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [LocatorAndRange('a', 10, 8, 2),
 310                                                                       LocatorAndRange('b', 15, 0, 15),
 311                                                                       LocatorAndRange('c', 5, 0, 3)])
 312
 313         self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [LocatorAndRange('c', 5, 1, 2)])
 314
 315         self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [LocatorAndRange('a', 10, 9, 1),
 316                                                                       LocatorAndRange('b', 15, 0, 14)])
 317         self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [LocatorAndRange('b', 15, 0, 15)])
 318         self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [LocatorAndRange('b', 15, 1, 14),
 319                                                                        LocatorAndRange('c', 5, 0, 1)])
 320
 321     class MockKeep(object):
 322         def __init__(self, content, num_retries=0):
 323             self.content = content
 324
 325         def get(self, locator, num_retries=0):
 326             return self.content[locator]
 327
 328     def test_stream_reader(self):
 329         keepblocks = {
 330             'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': b'abcdefghij',
 331             'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': b'klmnopqrstuvwxy',
 332             'cccccccccccccccccccccccccccccccc+5': b'z0123',
 333         }
 334         mk = self.MockKeep(keepblocks)
 335
 336         sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk)
 337
 338         content = b'abcdefghijklmnopqrstuvwxyz0123456789'
 339
 340         self.assertEqual(sr.readfrom(0, 30), content[0:30])
 341         self.assertEqual(sr.readfrom(2, 30), content[2:30])
 342
 343         self.assertEqual(sr.readfrom(2, 8), content[2:10])
 344         self.assertEqual(sr.readfrom(0, 10), content[0:10])
 345
 346         self.assertEqual(sr.readfrom(0, 5), content[0:5])
 347         self.assertEqual(sr.readfrom(5, 5), content[5:10])
 348         self.assertEqual(sr.readfrom(10, 5), content[10:15])
 349         self.assertEqual(sr.readfrom(15, 5), content[15:20])
 350         self.assertEqual(sr.readfrom(20, 5), content[20:25])
 351         self.assertEqual(sr.readfrom(25, 5), content[25:30])
 352         self.assertEqual(sr.readfrom(30, 5), b'')
 353
 354     def test_extract_file(self):
 355         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 356 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt
 357 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt
 358 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt
 359 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt
 360 """
 361
 362         m2 = arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True)
 363
 364         self.assertEqual(m2,
 365                          ". 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")
 366         files = arvados.CollectionReader(
 367             m2, self.api_client).all_streams()[0].files()
 368
 369         self.assertEqual(files['md5sum.txt'].as_manifest(),
 370                          ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n")
 371         self.assertEqual(files['md6sum.txt'].as_manifest(),
 372                          ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n")
 373         self.assertEqual(files['md7sum.txt'].as_manifest(),
 374                          ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n")
 375         self.assertEqual(files['md9sum.txt'].as_manifest(),
 376                          ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n")
 377
 378     def test_write_directory_tree(self):
 379         cwriter = arvados.CollectionWriter(self.api_client)
 380         cwriter.write_directory_tree(self.build_directory_tree(
 381                 ['basefile', 'subdir/subfile']))
 382         self.assertEqual(cwriter.manifest_text(),
 383                          """. c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 384 ./subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 385
 386     def test_write_named_directory_tree(self):
 387         cwriter = arvados.CollectionWriter(self.api_client)
 388         cwriter.write_directory_tree(self.build_directory_tree(
 389                 ['basefile', 'subdir/subfile']), 'root')
 390         self.assertEqual(
 391             cwriter.manifest_text(),
 392             """./root c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 393 ./root/subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 394
 395     def test_write_directory_tree_in_one_stream(self):
 396         cwriter = arvados.CollectionWriter(self.api_client)
 397         cwriter.write_directory_tree(self.build_directory_tree(
 398                 ['basefile', 'subdir/subfile']), max_manifest_depth=0)
 399         self.assertEqual(cwriter.manifest_text(),
 400                          """. 4ace875ffdc6824a04950f06858f4465+22 0:8:basefile 8:14:subdir/subfile\n""")
 401
 402     def test_write_directory_tree_with_limited_recursion(self):
 403         cwriter = arvados.CollectionWriter(self.api_client)
 404         cwriter.write_directory_tree(
 405             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 406             max_manifest_depth=1)
 407         self.assertEqual(cwriter.manifest_text(),
 408                          """. bd19836ddb62c11c55ab251ccaca5645+2 0:2:f1
 409 ./d1 50170217e5b04312024aa5cd42934494+13 0:8:d2/f3 8:5:f2\n""")
 410
 411     def test_write_directory_tree_with_zero_recursion(self):
 412         cwriter = arvados.CollectionWriter(self.api_client)
 413         content = 'd1/d2/f3d1/f2f1'
 414         blockhash = tutil.str_keep_locator(content)
 415         cwriter.write_directory_tree(
 416             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 417             max_manifest_depth=0)
 418         self.assertEqual(
 419             cwriter.manifest_text(),
 420             ". {} 0:8:d1/d2/f3 8:5:d1/f2 13:2:f1\n".format(blockhash))
 421
 422     def test_write_one_file(self):
 423         cwriter = arvados.CollectionWriter(self.api_client)
 424         with self.make_test_file() as testfile:
 425             cwriter.write_file(testfile.name)
 426             self.assertEqual(
 427                 cwriter.manifest_text(),
 428                 ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:{}\n".format(
 429                     os.path.basename(testfile.name)))
 430
 431     def test_write_named_file(self):
 432         cwriter = arvados.CollectionWriter(self.api_client)
 433         with self.make_test_file() as testfile:
 434             cwriter.write_file(testfile.name, 'foo')
 435             self.assertEqual(cwriter.manifest_text(),
 436                              ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:foo\n")
 437
 438     def test_write_multiple_files(self):
 439         cwriter = arvados.CollectionWriter(self.api_client)
 440         for letter in 'ABC':
 441             with self.make_test_file(letter.encode()) as testfile:
 442                 cwriter.write_file(testfile.name, letter)
 443         self.assertEqual(
 444             cwriter.manifest_text(),
 445             ". 902fbdd2b1df0c4f70b4a5d23525e932+3 0:1:A 1:1:B 2:1:C\n")
 446
 447     def test_basic_resume(self):
 448         cwriter = TestResumableWriter()
 449         with self.make_test_file() as testfile:
 450             cwriter.write_file(testfile.name, 'test')
 451             resumed = TestResumableWriter.from_state(cwriter.current_state())
 452         self.assertEqual(cwriter.manifest_text(), resumed.manifest_text(),
 453                           "resumed CollectionWriter had different manifest")
 454
 455     def test_resume_fails_when_missing_dependency(self):
 456         cwriter = TestResumableWriter()
 457         with self.make_test_file() as testfile:
 458             cwriter.write_file(testfile.name, 'test')
 459         self.assertRaises(arvados.errors.StaleWriterStateError,
 460                           TestResumableWriter.from_state,
 461                           cwriter.current_state())
 462
 463     def test_resume_fails_when_dependency_mtime_changed(self):
 464         cwriter = TestResumableWriter()
 465         with self.make_test_file() as testfile:
 466             cwriter.write_file(testfile.name, 'test')
 467             os.utime(testfile.name, (0, 0))
 468             self.assertRaises(arvados.errors.StaleWriterStateError,
 469                               TestResumableWriter.from_state,
 470                               cwriter.current_state())
 471
 472     def test_resume_fails_when_dependency_is_nonfile(self):
 473         cwriter = TestResumableWriter()
 474         cwriter.write_file('/dev/null', 'empty')
 475         self.assertRaises(arvados.errors.StaleWriterStateError,
 476                           TestResumableWriter.from_state,
 477                           cwriter.current_state())
 478
 479     def test_resume_fails_when_dependency_size_changed(self):
 480         cwriter = TestResumableWriter()
 481         with self.make_test_file() as testfile:
 482             cwriter.write_file(testfile.name, 'test')
 483             orig_mtime = os.fstat(testfile.fileno()).st_mtime
 484             testfile.write(b'extra')
 485             testfile.flush()
 486             os.utime(testfile.name, (orig_mtime, orig_mtime))
 487             self.assertRaises(arvados.errors.StaleWriterStateError,
 488                               TestResumableWriter.from_state,
 489                               cwriter.current_state())
 490
 491     def test_resume_fails_with_expired_locator(self):
 492         cwriter = TestResumableWriter()
 493         state = cwriter.current_state()
 494         # Add an expired locator to the state.
 495         state['_current_stream_locators'].append(''.join([
 496                     'a' * 32, '+1+A', 'b' * 40, '@', '10000000']))
 497         self.assertRaises(arvados.errors.StaleWriterStateError,
 498                           TestResumableWriter.from_state, state)
 499
 500     def test_arbitrary_objects_not_resumable(self):
 501         cwriter = TestResumableWriter()
 502         with open('/dev/null') as badfile:
 503             self.assertRaises(arvados.errors.AssertionError,
 504                               cwriter.write_file, badfile)
 505
 506     def test_arbitrary_writes_not_resumable(self):
 507         cwriter = TestResumableWriter()
 508         self.assertRaises(arvados.errors.AssertionError,
 509                           cwriter.write, "badtext")
 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_init_no_fallback_to_keep(self):
 567         # Do not look up a collection UUID or PDH in Keep.
 568         for key in [self.DEFAULT_UUID, self.DEFAULT_DATA_HASH]:
 569             client = self.api_client_mock(404)
 570             with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
 571                 with self.assertRaises(arvados.errors.ApiError):
 572                     reader = arvados.CollectionReader(key, api_client=client)
 573
 574     def test_init_num_retries_propagated(self):
 575         # More of an integration test...
 576         client = self.api_client_mock(200)
 577         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 578                                           num_retries=3)
 579         with tutil.mock_keep_responses('foo', 500, 500, 200):
 580             self.assertEqual(b'foo',
 581                              b''.join(f.read(9) for f in reader.all_files()))
 582
 583     def test_read_nonnormalized_manifest_with_collection_reader(self):
 584         # client should be able to use CollectionReader on a manifest without normalizing it
 585         client = self.api_client_mock(500)
 586         nonnormal = ". acbd18db4cc2f85cedef654fccc4a4d8+3+Aabadbadbee@abeebdee 0:3:foo.txt 1:0:bar.txt 0:3:foo.txt\n"
 587         reader = arvados.CollectionReader(
 588             nonnormal,
 589             api_client=client, num_retries=0)
 590         # Ensure stripped_manifest() doesn't mangle our manifest in
 591         # any way other than stripping hints.
 592         self.assertEqual(
 593             re.sub('\+[^\d\s\+]+', '', nonnormal),
 594             reader.stripped_manifest())
 595         # Ensure stripped_manifest() didn't mutate our reader.
 596         self.assertEqual(nonnormal, reader.manifest_text())
 597         # Ensure the files appear in the order given in the manifest.
 598         self.assertEqual(
 599             [[6, '.', 'foo.txt'],
 600              [0, '.', 'bar.txt']],
 601             [[f.size(), f.stream_name(), f.name()]
 602              for f in reader.all_streams()[0].all_files()])
 603
 604     def test_read_empty_collection(self):
 605         client = self.api_client_mock(200)
 606         self.mock_get_collection(client, 200, 'empty')
 607         reader = arvados.CollectionReader('d41d8cd98f00b204e9800998ecf8427e+0',
 608                                           api_client=client)
 609         self.assertEqual('', reader.manifest_text())
 610         self.assertEqual(0, len(reader))
 611         self.assertFalse(reader)
 612
 613     def test_api_response(self):
 614         client = self.api_client_mock()
 615         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 616         self.assertEqual(self.DEFAULT_COLLECTION, reader.api_response())
 617
 618     def check_open_file(self, coll_file, stream_name, file_name, file_size):
 619         self.assertFalse(coll_file.closed, "returned file is not open")
 620         self.assertEqual(stream_name, coll_file.stream_name())
 621         self.assertEqual(file_name, coll_file.name)
 622         self.assertEqual(file_size, coll_file.size())
 623
 624     def test_open_collection_file_one_argument(self):
 625         client = self.api_client_mock(200)
 626         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 627         cfile = reader.open('./foo', 'rb')
 628         self.check_open_file(cfile, '.', 'foo', 3)
 629
 630     def test_open_deep_file(self):
 631         coll_name = 'collection_with_files_in_subdir'
 632         client = self.api_client_mock(200)
 633         self.mock_get_collection(client, 200, coll_name)
 634         reader = arvados.CollectionReader(
 635             self.API_COLLECTIONS[coll_name]['uuid'], api_client=client)
 636         cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt', 'rb')
 637         self.check_open_file(cfile, './subdir2/subdir3', 'file2_in_subdir3.txt',
 638                              32)
 639
 640     def test_open_nonexistent_stream(self):
 641         client = self.api_client_mock(200)
 642         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 643         self.assertRaises(IOError, reader.open, './nonexistent/foo')
 644
 645     def test_open_nonexistent_file(self):
 646         client = self.api_client_mock(200)
 647         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 648         self.assertRaises(IOError, reader.open, 'nonexistent')
 649
 650
 651 @tutil.skip_sleep
 652 class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin):
 653     def mock_keep(self, body, *codes, **headers):
 654         headers.setdefault('x-keep-replicas-stored', 2)
 655         return tutil.mock_keep_responses(body, *codes, **headers)
 656
 657     def foo_writer(self, **kwargs):
 658         kwargs.setdefault('api_client', self.api_client_mock())
 659         writer = arvados.CollectionWriter(**kwargs)
 660         writer.start_new_file('foo')
 661         writer.write(b'foo')
 662         return writer
 663
 664     def test_write_whole_collection(self):
 665         writer = self.foo_writer()
 666         with self.mock_keep(self.DEFAULT_DATA_HASH, 200, 200):
 667             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 668
 669     def test_write_no_default(self):
 670         writer = self.foo_writer()
 671         with self.mock_keep(None, 500):
 672             with self.assertRaises(arvados.errors.KeepWriteError):
 673                 writer.finish()
 674
 675     def test_write_insufficient_replicas_via_proxy(self):
 676         writer = self.foo_writer(replication=3)
 677         with self.mock_keep(None, 200, **{'x-keep-replicas-stored': 2}):
 678             with self.assertRaises(arvados.errors.KeepWriteError):
 679                 writer.manifest_text()
 680
 681     def test_write_insufficient_replicas_via_disks(self):
 682         client = mock.MagicMock(name='api_client')
 683         with self.mock_keep(
 684                 None, 200, 200,
 685                 **{'x-keep-replicas-stored': 1}) as keepmock:
 686             self.mock_keep_services(client, status=200, service_type='disk', count=2)
 687             writer = self.foo_writer(api_client=client, replication=3)
 688             with self.assertRaises(arvados.errors.KeepWriteError):
 689                 writer.manifest_text()
 690
 691     def test_write_three_replicas(self):
 692         client = mock.MagicMock(name='api_client')
 693         with self.mock_keep(
 694                 "", 500, 500, 500, 200, 200, 200,
 695                 **{'x-keep-replicas-stored': 1}) as keepmock:
 696             self.mock_keep_services(client, status=200, service_type='disk', count=6)
 697             writer = self.foo_writer(api_client=client, replication=3)
 698             writer.manifest_text()
 699             self.assertEqual(6, keepmock.call_count)
 700
 701     def test_write_whole_collection_through_retries(self):
 702         writer = self.foo_writer(num_retries=2)
 703         with self.mock_keep(self.DEFAULT_DATA_HASH,
 704                             500, 500, 200, 500, 500, 200):
 705             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 706
 707     def test_flush_data_retries(self):
 708         writer = self.foo_writer(num_retries=2)
 709         foo_hash = self.DEFAULT_MANIFEST.split()[1]
 710         with self.mock_keep(foo_hash, 500, 200):
 711             writer.flush_data()
 712         self.assertEqual(self.DEFAULT_MANIFEST, writer.manifest_text())
 713
 714     def test_one_open(self):
 715         client = self.api_client_mock()
 716         writer = arvados.CollectionWriter(client)
 717         with writer.open('out') as out_file:
 718             self.assertEqual('.', writer.current_stream_name())
 719             self.assertEqual('out', writer.current_file_name())
 720             out_file.write(b'test data')
 721             data_loc = tutil.str_keep_locator('test data')
 722         self.assertTrue(out_file.closed, "writer file not closed after context")
 723         self.assertRaises(ValueError, out_file.write, 'extra text')
 724         with self.mock_keep(data_loc, 200) as keep_mock:
 725             self.assertEqual(". {} 0:9:out\n".format(data_loc),
 726                              writer.manifest_text())
 727
 728     def test_open_writelines(self):
 729         client = self.api_client_mock()
 730         writer = arvados.CollectionWriter(client)
 731         with writer.open('six') as out_file:
 732             out_file.writelines(['12', '34', '56'])
 733             data_loc = tutil.str_keep_locator('123456')
 734         with self.mock_keep(data_loc, 200) as keep_mock:
 735             self.assertEqual(". {} 0:6:six\n".format(data_loc),
 736                              writer.manifest_text())
 737
 738     def test_open_flush(self):
 739         client = self.api_client_mock()
 740         data_loc1 = tutil.str_keep_locator('flush1')
 741         data_loc2 = tutil.str_keep_locator('flush2')
 742         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 743             writer = arvados.CollectionWriter(client)
 744             with writer.open('flush_test') as out_file:
 745                 out_file.write(b'flush1')
 746                 out_file.flush()
 747                 out_file.write(b'flush2')
 748             self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1,
 749                                                                 data_loc2),
 750                              writer.manifest_text())
 751
 752     def test_two_opens_same_stream(self):
 753         client = self.api_client_mock()
 754         writer = arvados.CollectionWriter(client)
 755         with writer.open('.', '1') as out_file:
 756             out_file.write(b'1st')
 757         with writer.open('.', '2') as out_file:
 758             out_file.write(b'2nd')
 759         data_loc = tutil.str_keep_locator('1st2nd')
 760         with self.mock_keep(data_loc, 200) as keep_mock:
 761             self.assertEqual(". {} 0:3:1 3:3:2\n".format(data_loc),
 762                              writer.manifest_text())
 763
 764     def test_two_opens_two_streams(self):
 765         client = self.api_client_mock()
 766         data_loc1 = tutil.str_keep_locator('file')
 767         data_loc2 = tutil.str_keep_locator('indir')
 768         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 769             writer = arvados.CollectionWriter(client)
 770             with writer.open('file') as out_file:
 771                 out_file.write(b'file')
 772             with writer.open('./dir', 'indir') as out_file:
 773                 out_file.write(b'indir')
 774             expected = ". {} 0:4:file\n./dir {} 0:5:indir\n".format(
 775                 data_loc1, data_loc2)
 776             self.assertEqual(expected, writer.manifest_text())
 777
 778     def test_dup_open_fails(self):
 779         client = self.api_client_mock()
 780         writer = arvados.CollectionWriter(client)
 781         file1 = writer.open('one')
 782         self.assertRaises(arvados.errors.AssertionError, writer.open, 'two')
 783
 784
 785 class CollectionMethods(run_test_server.TestCaseWithServers):
 786
 787     def test_keys_values_items_support_indexing(self):
 788         c = Collection()
 789         with c.open('foo', 'wb') as f:
 790             f.write(b'foo')
 791         with c.open('bar', 'wb') as f:
 792             f.write(b'bar')
 793         self.assertEqual(2, len(c.keys()))
 794         if sys.version_info < (3, 0):
 795             # keys() supports indexing only for python2 callers.
 796             fn0 = c.keys()[0]
 797             fn1 = c.keys()[1]
 798         else:
 799             fn0, fn1 = c.keys()
 800         self.assertEqual(2, len(c.values()))
 801         f0 = c.values()[0]
 802         f1 = c.values()[1]
 803         self.assertEqual(2, len(c.items()))
 804         self.assertEqual(fn0, c.items()[0][0])
 805         self.assertEqual(fn1, c.items()[1][0])
 806
 807     def test_get_properties(self):
 808         c = Collection()
 809         self.assertEqual(c.get_properties(), {})
 810         c.save_new(properties={"foo":"bar"})
 811         self.assertEqual(c.get_properties(), {"foo":"bar"})
 812
 813     def test_get_trash_at(self):
 814         c = Collection()
 815         self.assertEqual(c.get_trash_at(), None)
 816         c.save_new(trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111))
 817         self.assertEqual(c.get_trash_at(), ciso8601.parse_datetime('2111-01-01T11:11:11.111111000Z'))
 818
 819
 820 class CollectionOpenModes(run_test_server.TestCaseWithServers):
 821
 822     def test_open_binary_modes(self):
 823         c = Collection()
 824         for mode in ['wb', 'wb+', 'ab', 'ab+']:
 825             with c.open('foo', mode) as f:
 826                 f.write(b'foo')
 827
 828     def test_open_invalid_modes(self):
 829         c = Collection()
 830         for mode in ['+r', 'aa', '++', 'r+b', 'beer', '', None]:
 831             with self.assertRaises(Exception):
 832                 c.open('foo', mode)
 833
 834     def test_open_text_modes(self):
 835         c = Collection()
 836         with c.open('foo', 'wb') as f:
 837             f.write('foo')
 838         for mode in ['r', 'rt', 'r+', 'rt+', 'w', 'wt', 'a', 'at']:
 839             with c.open('foo', mode) as f:
 840                 if mode[0] == 'r' and '+' not in mode:
 841                     self.assertEqual('foo', f.read(3))
 842                 else:
 843                     f.write('bar')
 844                     f.seek(0, os.SEEK_SET)
 845                     self.assertEqual('bar', f.read(3))
 846
 847
 848 class TextModes(run_test_server.TestCaseWithServers):
 849
 850     def setUp(self):
 851         arvados.config.KEEP_BLOCK_SIZE = 4
 852         if sys.version_info < (3, 0):
 853             import unicodedata
 854             self.sailboat = unicodedata.lookup('SAILBOAT')
 855             self.snowman = unicodedata.lookup('SNOWMAN')
 856         else:
 857             self.sailboat = '\N{SAILBOAT}'
 858             self.snowman = '\N{SNOWMAN}'
 859
 860     def tearDown(self):
 861         arvados.config.KEEP_BLOCK_SIZE = 2 ** 26
 862
 863     def test_read_sailboat_across_block_boundary(self):
 864         c = Collection()
 865         f = c.open('sailboats', 'wb')
 866         data = self.sailboat.encode('utf-8')
 867         f.write(data)
 868         f.write(data[:1])
 869         f.write(data[1:])
 870         f.write(b'\n')
 871         f.close()
 872         self.assertRegex(c.portable_manifest_text(), r'\+4 .*\+3 ')
 873
 874         f = c.open('sailboats', 'r')
 875         string = f.readline()
 876         self.assertEqual(string, self.sailboat+self.sailboat+'\n')
 877         f.close()
 878
 879     def test_write_snowman_across_block_boundary(self):
 880         c = Collection()
 881         f = c.open('snowmany', 'w')
 882         data = self.snowman
 883         f.write(data+data+'\n'+data+'\n')
 884         f.close()
 885         self.assertRegex(c.portable_manifest_text(), r'\+4 .*\+4 .*\+3 ')
 886
 887         f = c.open('snowmany', 'r')
 888         self.assertEqual(f.readline(), self.snowman+self.snowman+'\n')
 889         self.assertEqual(f.readline(), self.snowman+'\n')
 890         f.close()
 891
 892
 893 class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin):
 894
 895     def test_replication_desired_kept_on_load(self):
 896         m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
 897         c1 = Collection(m, replication_desired=1)
 898         c1.save_new()
 899         loc = c1.manifest_locator()
 900         c2 = Collection(loc)
 901         self.assertEqual(c1.manifest_text, c2.manifest_text)
 902         self.assertEqual(c1.replication_desired, c2.replication_desired)
 903
 904     def test_replication_desired_not_loaded_if_provided(self):
 905         m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
 906         c1 = Collection(m, replication_desired=1)
 907         c1.save_new()
 908         loc = c1.manifest_locator()
 909         c2 = Collection(loc, replication_desired=2)
 910         self.assertEqual(c1.manifest_text, c2.manifest_text)
 911         self.assertNotEqual(c1.replication_desired, c2.replication_desired)
 912
 913     def test_init_manifest(self):
 914         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 915 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 916 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 917 """
 918         self.assertEqual(m1, CollectionReader(m1).manifest_text(normalize=False))
 919         self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", CollectionReader(m1).manifest_text(normalize=True))
 920
 921     def test_init_manifest_with_collision(self):
 922         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 923 ./md5sum.txt 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 924 """
 925         with self.assertRaises(arvados.errors.ArgumentError):
 926             self.assertEqual(m1, CollectionReader(m1))
 927
 928     def test_init_manifest_with_error(self):
 929         m1 = """. 0:43:md5sum.txt"""
 930         with self.assertRaises(arvados.errors.ArgumentError):
 931             self.assertEqual(m1, CollectionReader(m1))
 932
 933     def test_remove(self):
 934         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
 935         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 936         self.assertIn("count1.txt", c)
 937         c.remove("count1.txt")
 938         self.assertNotIn("count1.txt", c)
 939         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
 940         with self.assertRaises(arvados.errors.ArgumentError):
 941             c.remove("")
 942
 943     def test_find(self):
 944         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
 945         self.assertIs(c.find("."), c)
 946         self.assertIs(c.find("./count1.txt"), c["count1.txt"])
 947         self.assertIs(c.find("count1.txt"), c["count1.txt"])
 948         with self.assertRaises(IOError):
 949             c.find("/.")
 950         with self.assertRaises(arvados.errors.ArgumentError):
 951             c.find("")
 952         self.assertIs(c.find("./nonexistant.txt"), None)
 953         self.assertIs(c.find("./nonexistantsubdir/nonexistant.txt"), None)
 954
 955     def test_remove_in_subdir(self):
 956         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 957         c.remove("foo/count2.txt")
 958         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\056\n", c.portable_manifest_text())
 959
 960     def test_remove_empty_subdir(self):
 961         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 962         c.remove("foo/count2.txt")
 963         c.remove("foo")
 964         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 965
 966     def test_remove_nonempty_subdir(self):
 967         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 968         with self.assertRaises(IOError):
 969             c.remove("foo")
 970         c.remove("foo", recursive=True)
 971         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 972
 973     def test_copy_to_file_in_dir(self):
 974         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 975         c.copy("count1.txt", "foo/count2.txt")
 976         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
 977
 978     def test_copy_file(self):
 979         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 980         c.copy("count1.txt", "count2.txt")
 981         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 982
 983     def test_copy_to_existing_dir(self):
 984         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 985         c.copy("count1.txt", "foo")
 986         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())
 987
 988     def test_copy_to_new_dir(self):
 989         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 990         c.copy("count1.txt", "foo/")
 991         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 992
 993     def test_rename_file(self):
 994         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 995         c.rename("count1.txt", "count2.txt")
 996         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
 997
 998     def test_move_file_to_dir(self):
 999         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1000         c.mkdirs("foo")
1001         c.rename("count1.txt", "foo/count2.txt")
1002         self.assertEqual("./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
1003
1004     def test_move_file_to_other(self):
1005         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1006         c2 = Collection()
1007         c2.rename("count1.txt", "count2.txt", source_collection=c1)
1008         self.assertEqual("", c1.manifest_text())
1009         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c2.manifest_text())
1010
1011     def test_clone(self):
1012         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
1013         cl = c.clone()
1014         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", cl.portable_manifest_text())
1015
1016     def test_diff_del_add(self):
1017         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1018         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1019         d = c2.diff(c1)
1020         self.assertEqual(sorted(d), [
1021             ('add', './count1.txt', c1["count1.txt"]),
1022             ('del', './count2.txt', c2["count2.txt"]),
1023         ])
1024         d = c1.diff(c2)
1025         self.assertEqual(sorted(d), [
1026             ('add', './count2.txt', c2["count2.txt"]),
1027             ('del', './count1.txt', c1["count1.txt"]),
1028         ])
1029         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1030         c1.apply(d)
1031         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1032
1033     def test_diff_same(self):
1034         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1035         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1036         d = c2.diff(c1)
1037         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1038         d = c1.diff(c2)
1039         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1040
1041         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1042         c1.apply(d)
1043         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1044
1045     def test_diff_mod(self):
1046         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1047         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
1048         d = c2.diff(c1)
1049         self.assertEqual(d, [('mod', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1050         d = c1.diff(c2)
1051         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1052
1053         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1054         c1.apply(d)
1055         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1056
1057     def test_diff_add(self):
1058         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1059         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt 10:20:count2.txt\n')
1060         d = c2.diff(c1)
1061         self.assertEqual(sorted(d), [
1062             ('del', './count2.txt', c2["count2.txt"]),
1063             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1064         ])
1065         d = c1.diff(c2)
1066         self.assertEqual(sorted(d), [
1067             ('add', './count2.txt', c2["count2.txt"]),
1068             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1069         ])
1070
1071         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1072         c1.apply(d)
1073         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1074
1075     def test_diff_add_in_subcollection(self):
1076         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1077         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1078         d = c2.diff(c1)
1079         self.assertEqual(sorted(d), [
1080             ('del', './foo', c2["foo"]),
1081             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1082         ])
1083         d = c1.diff(c2)
1084         self.assertEqual(sorted(d), [
1085             ('add', './foo', c2["foo"]),
1086             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1087         ])
1088         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1089         c1.apply(d)
1090         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1091
1092     def test_diff_del_add_in_subcollection(self):
1093         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1094         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:3:count3.txt\n')
1095         d = c2.diff(c1)
1096         self.assertEqual(sorted(d), [
1097             ('add', './foo/count2.txt', c1.find("foo/count2.txt")),
1098             ('del', './foo/count3.txt', c2.find("foo/count3.txt")),
1099             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1100         ])
1101         d = c1.diff(c2)
1102         self.assertEqual(sorted(d), [
1103             ('add', './foo/count3.txt', c2.find("foo/count3.txt")),
1104             ('del', './foo/count2.txt', c1.find("foo/count2.txt")),
1105             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1106         ])
1107
1108         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1109         c1.apply(d)
1110         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1111
1112     def test_diff_mod_in_subcollection(self):
1113         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1114         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:3:foo\n')
1115         d = c2.diff(c1)
1116         self.assertEqual(sorted(d), [
1117             ('mod', './foo', c2["foo"], c1["foo"]),
1118             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1119         ])
1120         d = c1.diff(c2)
1121         self.assertEqual(sorted(d), [
1122             ('mod', './foo', c1["foo"], c2["foo"]),
1123             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1124         ])
1125
1126         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1127         c1.apply(d)
1128         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1129
1130     def test_conflict_keep_local_change(self):
1131         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1132         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1133         d = c1.diff(c2)
1134         self.assertEqual(sorted(d), [
1135             ('add', './count2.txt', c2["count2.txt"]),
1136             ('del', './count1.txt', c1["count1.txt"]),
1137         ])
1138         f = c1.open("count1.txt", "wb")
1139         f.write(b"zzzzz")
1140
1141         # c1 changed, so it should not be deleted.
1142         c1.apply(d)
1143         self.assertEqual(c1.portable_manifest_text(), ". 95ebc3c7b3b9f1d2c40fec14415d3cb8+5 5348b82a029fd9e971a811ce1f71360b+43 0:5:count1.txt 5:10:count2.txt\n")
1144
1145     def test_conflict_mod(self):
1146         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1147         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1148         d = c1.diff(c2)
1149         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1150         f = c1.open("count1.txt", "wb")
1151         f.write(b"zzzzz")
1152
1153         # c1 changed, so c2 mod will go to a conflict file
1154         c1.apply(d)
1155         self.assertRegex(
1156             c1.portable_manifest_text(),
1157             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~$")
1158
1159     def test_conflict_add(self):
1160         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
1161         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
1162         d = c1.diff(c2)
1163         self.assertEqual(sorted(d), [
1164             ('add', './count1.txt', c2["count1.txt"]),
1165             ('del', './count2.txt', c1["count2.txt"]),
1166         ])
1167         f = c1.open("count1.txt", "wb")
1168         f.write(b"zzzzz")
1169
1170         # c1 added count1.txt, so c2 add will go to a conflict file
1171         c1.apply(d)
1172         self.assertRegex(
1173             c1.portable_manifest_text(),
1174             r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1175
1176     def test_conflict_del(self):
1177         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1178         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1179         d = c1.diff(c2)
1180         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1181         c1.remove("count1.txt")
1182
1183         # c1 deleted, so c2 mod will go to a conflict file
1184         c1.apply(d)
1185         self.assertRegex(
1186             c1.portable_manifest_text(),
1187             r"\. 5348b82a029fd9e971a811ce1f71360b\+43 0:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1188
1189     def test_notify(self):
1190         c1 = Collection()
1191         events = []
1192         c1.subscribe(lambda event, collection, name, item: events.append((event, collection, name, item)))
1193         f = c1.open("foo.txt", "wb")
1194         self.assertEqual(events[0], (arvados.collection.ADD, c1, "foo.txt", f.arvadosfile))
1195
1196     def test_open_w(self):
1197         c1 = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n")
1198         self.assertEqual(c1["count1.txt"].size(), 10)
1199         c1.open("count1.txt", "wb").close()
1200         self.assertEqual(c1["count1.txt"].size(), 0)
1201
1202
1203 class NewCollectionTestCaseWithServersAndTokens(run_test_server.TestCaseWithServers):
1204     MAIN_SERVER = {}
1205     KEEP_SERVER = {}
1206     local_locator_re = r"[0-9a-f]{32}\+\d+\+A[a-f0-9]{40}@[a-f0-9]{8}"
1207     remote_locator_re = r"[0-9a-f]{32}\+\d+\+R[a-z]{5}-[a-f0-9]{40}@[a-f0-9]{8}"
1208
1209     def setUp(self):
1210         self.keep_put = getattr(arvados.keep.KeepClient, 'put')
1211
1212     @mock.patch('arvados.keep.KeepClient.put', autospec=True)
1213     def test_repacked_block_submission_get_permission_token(self, mocked_put):
1214         '''
1215         Make sure that those blocks that are committed after repacking small ones,
1216         get their permission tokens assigned on the collection manifest.
1217         '''
1218         def wrapped_keep_put(*args, **kwargs):
1219             # Simulate slow put operations
1220             time.sleep(1)
1221             return self.keep_put(*args, **kwargs)
1222
1223         mocked_put.side_effect = wrapped_keep_put
1224         c = Collection()
1225         # Write 70 files ~1MiB each so we force to produce 1 big block by repacking
1226         # small ones before finishing the upload.
1227         for i in range(70):
1228             f = c.open("file_{}.txt".format(i), 'wb')
1229             f.write(random.choice('abcdefghijklmnopqrstuvwxyz') * (2**20+i))
1230             f.close(flush=False)
1231         # We should get 2 blocks with their tokens
1232         self.assertEqual(len(re.findall(self.local_locator_re, c.manifest_text())), 2)
1233
1234     @mock.patch('arvados.keep.KeepClient.refresh_signature')
1235     def test_copy_remote_blocks_on_save_new(self, rs_mock):
1236         remote_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+Remote-" + "a" * 40 + "@abcdef01"
1237         local_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+A" + "b" * 40 + "@abcdef01"
1238         rs_mock.return_value = local_block_loc
1239         c = Collection(". " + remote_block_loc + " 0:3:foofile.txt\n")
1240         self.assertEqual(
1241             len(re.findall(self.remote_locator_re, c.manifest_text())), 1)
1242         self.assertEqual(
1243             len(re.findall(self.local_locator_re, c.manifest_text())), 0)
1244         c.save_new()
1245         rs_mock.assert_called()
1246         self.assertEqual(
1247             len(re.findall(self.remote_locator_re, c.manifest_text())), 0)
1248         self.assertEqual(
1249             len(re.findall(self.local_locator_re, c.manifest_text())), 1)
1250
1251     @mock.patch('arvados.keep.KeepClient.refresh_signature')
1252     def test_copy_remote_blocks_on_save(self, rs_mock):
1253         remote_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+Remote-" + "a" * 40 + "@abcdef01"
1254         local_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+A" + "b" * 40 + "@abcdef01"
1255         rs_mock.return_value = local_block_loc
1256         # Remote collection
1257         remote_c = Collection(". " + remote_block_loc + " 0:3:foofile.txt\n")
1258         self.assertEqual(
1259             len(re.findall(self.remote_locator_re, remote_c.manifest_text())), 1)
1260         # Local collection
1261         local_c = Collection()
1262         with local_c.open('barfile.txt', 'wb') as f:
1263             f.write('bar')
1264         local_c.save_new()
1265         self.assertEqual(
1266             len(re.findall(self.local_locator_re, local_c.manifest_text())), 1)
1267         self.assertEqual(
1268             len(re.findall(self.remote_locator_re, local_c.manifest_text())), 0)
1269         # Copy remote file to local collection
1270         local_c.copy('./foofile.txt', './copied/foofile.txt', remote_c)
1271         self.assertEqual(
1272             len(re.findall(self.local_locator_re, local_c.manifest_text())), 1)
1273         self.assertEqual(
1274             len(re.findall(self.remote_locator_re, local_c.manifest_text())), 1)
1275         # Save local collection: remote block should be copied
1276         local_c.save()
1277         rs_mock.assert_called()
1278         self.assertEqual(
1279             len(re.findall(self.local_locator_re, local_c.manifest_text())), 2)
1280         self.assertEqual(
1281             len(re.findall(self.remote_locator_re, local_c.manifest_text())), 0)
1282
1283
1284 class NewCollectionTestCaseWithServers(run_test_server.TestCaseWithServers):
1285     def test_get_manifest_text_only_committed(self):
1286         c = Collection()
1287         with c.open("count.txt", "wb") as f:
1288             # One file committed
1289             with c.open("foo.txt", "wb") as foo:
1290                 foo.write(b"foo")
1291                 foo.flush() # Force block commit
1292             f.write(b"0123456789")
1293             # Other file not committed. Block not written to keep yet.
1294             self.assertEqual(
1295                 c._get_manifest_text(".",
1296                                      strip=False,
1297                                      normalize=False,
1298                                      only_committed=True),
1299                 '. acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:count.txt 0:3:foo.txt\n')
1300             # And now with the file closed...
1301             f.flush() # Force block commit
1302         self.assertEqual(
1303             c._get_manifest_text(".",
1304                                  strip=False,
1305                                  normalize=False,
1306                                  only_committed=True),
1307             ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:10:count.txt 10:3:foo.txt\n")
1308
1309     def test_only_small_blocks_are_packed_together(self):
1310         c = Collection()
1311         # Write a couple of small files,
1312         f = c.open("count.txt", "wb")
1313         f.write(b"0123456789")
1314         f.close(flush=False)
1315         foo = c.open("foo.txt", "wb")
1316         foo.write(b"foo")
1317         foo.close(flush=False)
1318         # Then, write a big file, it shouldn't be packed with the ones above
1319         big = c.open("bigfile.txt", "wb")
1320         big.write(b"x" * 1024 * 1024 * 33) # 33 MB > KEEP_BLOCK_SIZE/2
1321         big.close(flush=False)
1322         self.assertEqual(
1323             c.manifest_text("."),
1324             '. 2d303c138c118af809f39319e5d507e9+34603008 a8430a058b8fbf408e1931b794dbd6fb+13 0:34603008:bigfile.txt 34603008:10:count.txt 34603018:3:foo.txt\n')
1325
1326     def test_flush_after_small_block_packing(self):
1327         c = Collection()
1328         # Write a couple of small files,
1329         f = c.open("count.txt", "wb")
1330         f.write(b"0123456789")
1331         f.close(flush=False)
1332         foo = c.open("foo.txt", "wb")
1333         foo.write(b"foo")
1334         foo.close(flush=False)
1335
1336         self.assertEqual(
1337             c.manifest_text(),
1338             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1339
1340         f = c.open("count.txt", "rb+")
1341         f.close(flush=True)
1342
1343         self.assertEqual(
1344             c.manifest_text(),
1345             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1346
1347     def test_write_after_small_block_packing2(self):
1348         c = Collection()
1349         # Write a couple of small files,
1350         f = c.open("count.txt", "wb")
1351         f.write(b"0123456789")
1352         f.close(flush=False)
1353         foo = c.open("foo.txt", "wb")
1354         foo.write(b"foo")
1355         foo.close(flush=False)
1356
1357         self.assertEqual(
1358             c.manifest_text(),
1359             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1360
1361         f = c.open("count.txt", "rb+")
1362         f.write(b"abc")
1363         f.close(flush=False)
1364
1365         self.assertEqual(
1366             c.manifest_text(),
1367             '. 900150983cd24fb0d6963f7d28e17f72+3 a8430a058b8fbf408e1931b794dbd6fb+13 0:3:count.txt 6:7:count.txt 13:3:foo.txt\n')
1368
1369
1370     def test_small_block_packing_with_overwrite(self):
1371         c = Collection()
1372         c.open("b1", "wb").close()
1373         c["b1"].writeto(0, b"b1", 0)
1374
1375         c.open("b2", "wb").close()
1376         c["b2"].writeto(0, b"b2", 0)
1377
1378         c["b1"].writeto(0, b"1b", 0)
1379
1380         self.assertEqual(c.manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1 2:2:b2\n")
1381         self.assertEqual(c["b1"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1\n")
1382         self.assertEqual(c["b2"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 2:2:b2\n")
1383
1384
1385 class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers):
1386     MAIN_SERVER = {}
1387     KEEP_SERVER = {}
1388
1389     def create_count_txt(self):
1390         # Create an empty collection, save it to the API server, then write a
1391         # file, but don't save it.
1392
1393         c = Collection()
1394         c.save_new("CollectionCreateUpdateTest", ensure_unique_name=True)
1395         self.assertEqual(c.portable_data_hash(), "d41d8cd98f00b204e9800998ecf8427e+0")
1396         self.assertEqual(c.api_response()["portable_data_hash"], "d41d8cd98f00b204e9800998ecf8427e+0" )
1397
1398         with c.open("count.txt", "wb") as f:
1399             f.write(b"0123456789")
1400
1401         self.assertEqual(c.portable_manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1402
1403         return c
1404
1405     def test_create_and_save(self):
1406         c = self.create_count_txt()
1407         c.save(properties={'type' : 'Intermediate'},
1408                storage_classes=['archive'],
1409                trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111))
1410
1411         self.assertRegex(
1412             c.manifest_text(),
1413             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1414         self.assertEqual(c.api_response()["storage_classes_desired"], ['archive'])
1415         self.assertEqual(c.api_response()["properties"], {'type' : 'Intermediate'})
1416         self.assertEqual(c.api_response()["trash_at"], '2111-01-01T11:11:11.111111000Z')
1417
1418
1419     def test_create_and_save_new(self):
1420         c = self.create_count_txt()
1421         c.save_new(properties={'type' : 'Intermediate'},
1422                    storage_classes=['archive'],
1423                    trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111))
1424
1425         self.assertRegex(
1426             c.manifest_text(),
1427             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1428         self.assertEqual(c.api_response()["storage_classes_desired"], ['archive'])
1429         self.assertEqual(c.api_response()["properties"], {'type' : 'Intermediate'})
1430         self.assertEqual(c.api_response()["trash_at"], '2111-01-01T11:11:11.111111000Z')
1431
1432     def test_create_and_save_after_commiting(self):
1433         c = self.create_count_txt()
1434         c.save(properties={'type' : 'Intermediate'},
1435                storage_classes=['hot'],
1436                trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111))
1437         c.save(properties={'type' : 'Output'},
1438                storage_classes=['cold'],
1439                trash_at=datetime.datetime(2222, 2, 2, 22, 22, 22, 222222))
1440
1441         self.assertEqual(c.api_response()["storage_classes_desired"], ['cold'])
1442         self.assertEqual(c.api_response()["properties"], {'type' : 'Output'})
1443         self.assertEqual(c.api_response()["trash_at"], '2222-02-02T22:22:22.222222000Z')
1444
1445     def test_create_diff_apply(self):
1446         c1 = self.create_count_txt()
1447         c1.save()
1448
1449         c2 = Collection(c1.manifest_locator())
1450         with c2.open("count.txt", "wb") as f:
1451             f.write(b"abcdefg")
1452
1453         diff = c1.diff(c2)
1454
1455         self.assertEqual(diff[0], (arvados.collection.MOD, u'./count.txt', c1["count.txt"], c2["count.txt"]))
1456
1457         c1.apply(diff)
1458         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1459
1460     def test_diff_apply_with_token(self):
1461         baseline = CollectionReader(". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:10:count.txt\n")
1462         c = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1463         other = CollectionReader(". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1464
1465         diff = baseline.diff(other)
1466         self.assertEqual(diff, [('mod', u'./count.txt', c["count.txt"], other["count.txt"])])
1467
1468         c.apply(diff)
1469
1470         self.assertEqual(c.manifest_text(), ". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1471
1472
1473     def test_create_and_update(self):
1474         c1 = self.create_count_txt()
1475         c1.save()
1476
1477         c2 = arvados.collection.Collection(c1.manifest_locator())
1478         with c2.open("count.txt", "wb") as f:
1479             f.write(b"abcdefg")
1480
1481         c2.save()
1482
1483         self.assertNotEqual(c1.portable_data_hash(), c2.portable_data_hash())
1484         c1.update()
1485         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1486
1487
1488     def test_create_and_update_with_conflict(self):
1489         c1 = self.create_count_txt()
1490         c1.save()
1491
1492         with c1.open("count.txt", "wb") as f:
1493             f.write(b"XYZ")
1494
1495         c2 = arvados.collection.Collection(c1.manifest_locator())
1496         with c2.open("count.txt", "wb") as f:
1497             f.write(b"abcdefg")
1498
1499         c2.save()
1500
1501         c1.update()
1502         self.assertRegex(
1503             c1.manifest_text(),
1504             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~$")
1505
1506     def test_pdh_is_native_str(self):
1507         c1 = self.create_count_txt()
1508         pdh = c1.portable_data_hash()
1509         self.assertEqual(type(''), type(pdh))
1510
1511
1512 if __name__ == '__main__':
1513     unittest.main()