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_create_dot_file(self):
 961         c = Collection()
 962         with self.assertRaises(IOError):
 963             with c.open("./dir/\\056", "wb") as f:
 964                 f.write("Should not be allowed")
 965
 966     def test_create_file_inside_dot_dir(self):
 967         c = Collection()
 968         with self.assertRaises(IOError):
 969             with c.open("./dir/\\056/foo", "wb") as f:
 970                 f.write("Should not be allowed")
 971
 972     def test_remove_empty_subdir(self):
 973         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 974         c.remove("foo/count2.txt")
 975         c.remove("foo")
 976         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 977
 978     def test_remove_nonempty_subdir(self):
 979         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 980         with self.assertRaises(IOError):
 981             c.remove("foo")
 982         c.remove("foo", recursive=True)
 983         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
 984
 985     def test_copy_to_file_in_dir(self):
 986         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 987         c.copy("count1.txt", "foo/count2.txt")
 988         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
 989
 990     def test_copy_file(self):
 991         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
 992         c.copy("count1.txt", "count2.txt")
 993         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
 994
 995     def test_copy_to_existing_dir(self):
 996         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
 997         c.copy("count1.txt", "foo")
 998         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())
 999
1000     def test_copy_to_new_dir(self):
1001         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1002         c.copy("count1.txt", "foo/")
1003         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
1004
1005     def test_rename_file(self):
1006         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1007         c.rename("count1.txt", "count2.txt")
1008         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
1009
1010     def test_move_file_to_dir(self):
1011         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1012         c.mkdirs("foo")
1013         c.rename("count1.txt", "foo/count2.txt")
1014         self.assertEqual("./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
1015
1016     def test_move_file_to_other(self):
1017         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1018         c2 = Collection()
1019         c2.rename("count1.txt", "count2.txt", source_collection=c1)
1020         self.assertEqual("", c1.manifest_text())
1021         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c2.manifest_text())
1022
1023     def test_clone(self):
1024         c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
1025         cl = c.clone()
1026         self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", cl.portable_manifest_text())
1027
1028     def test_diff_del_add(self):
1029         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1030         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1031         d = c2.diff(c1)
1032         self.assertEqual(sorted(d), [
1033             ('add', './count1.txt', c1["count1.txt"]),
1034             ('del', './count2.txt', c2["count2.txt"]),
1035         ])
1036         d = c1.diff(c2)
1037         self.assertEqual(sorted(d), [
1038             ('add', './count2.txt', c2["count2.txt"]),
1039             ('del', './count1.txt', c1["count1.txt"]),
1040         ])
1041         self.assertNotEqual(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_same(self):
1046         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1047         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1048         d = c2.diff(c1)
1049         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1050         d = c1.diff(c2)
1051         self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1052
1053         self.assertEqual(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_mod(self):
1058         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1059         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
1060         d = c2.diff(c1)
1061         self.assertEqual(d, [('mod', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
1062         d = c1.diff(c2)
1063         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1064
1065         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1066         c1.apply(d)
1067         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1068
1069     def test_diff_add(self):
1070         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1071         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt 10:20:count2.txt\n')
1072         d = c2.diff(c1)
1073         self.assertEqual(sorted(d), [
1074             ('del', './count2.txt', c2["count2.txt"]),
1075             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1076         ])
1077         d = c1.diff(c2)
1078         self.assertEqual(sorted(d), [
1079             ('add', './count2.txt', c2["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_add_in_subcollection(self):
1088         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1089         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1090         d = c2.diff(c1)
1091         self.assertEqual(sorted(d), [
1092             ('del', './foo', c2["foo"]),
1093             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1094         ])
1095         d = c1.diff(c2)
1096         self.assertEqual(sorted(d), [
1097             ('add', './foo', c2["foo"]),
1098             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1099         ])
1100         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1101         c1.apply(d)
1102         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1103
1104     def test_diff_del_add_in_subcollection(self):
1105         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1106         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:3:count3.txt\n')
1107         d = c2.diff(c1)
1108         self.assertEqual(sorted(d), [
1109             ('add', './foo/count2.txt', c1.find("foo/count2.txt")),
1110             ('del', './foo/count3.txt', c2.find("foo/count3.txt")),
1111             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1112         ])
1113         d = c1.diff(c2)
1114         self.assertEqual(sorted(d), [
1115             ('add', './foo/count3.txt', c2.find("foo/count3.txt")),
1116             ('del', './foo/count2.txt', c1.find("foo/count2.txt")),
1117             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1118         ])
1119
1120         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1121         c1.apply(d)
1122         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1123
1124     def test_diff_mod_in_subcollection(self):
1125         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1126         c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:3:foo\n')
1127         d = c2.diff(c1)
1128         self.assertEqual(sorted(d), [
1129             ('mod', './foo', c2["foo"], c1["foo"]),
1130             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1131         ])
1132         d = c1.diff(c2)
1133         self.assertEqual(sorted(d), [
1134             ('mod', './foo', c1["foo"], c2["foo"]),
1135             ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
1136         ])
1137
1138         self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1139         c1.apply(d)
1140         self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
1141
1142     def test_conflict_keep_local_change(self):
1143         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
1144         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
1145         d = c1.diff(c2)
1146         self.assertEqual(sorted(d), [
1147             ('add', './count2.txt', c2["count2.txt"]),
1148             ('del', './count1.txt', c1["count1.txt"]),
1149         ])
1150         f = c1.open("count1.txt", "wb")
1151         f.write(b"zzzzz")
1152
1153         # c1 changed, so it should not be deleted.
1154         c1.apply(d)
1155         self.assertEqual(c1.portable_manifest_text(), ". 95ebc3c7b3b9f1d2c40fec14415d3cb8+5 5348b82a029fd9e971a811ce1f71360b+43 0:5:count1.txt 5:10:count2.txt\n")
1156
1157     def test_conflict_mod(self):
1158         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1159         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1160         d = c1.diff(c2)
1161         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1162         f = c1.open("count1.txt", "wb")
1163         f.write(b"zzzzz")
1164
1165         # c1 changed, so c2 mod will go to a conflict file
1166         c1.apply(d)
1167         self.assertRegex(
1168             c1.portable_manifest_text(),
1169             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~$")
1170
1171     def test_conflict_add(self):
1172         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
1173         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
1174         d = c1.diff(c2)
1175         self.assertEqual(sorted(d), [
1176             ('add', './count1.txt', c2["count1.txt"]),
1177             ('del', './count2.txt', c1["count2.txt"]),
1178         ])
1179         f = c1.open("count1.txt", "wb")
1180         f.write(b"zzzzz")
1181
1182         # c1 added count1.txt, so c2 add will go to a conflict file
1183         c1.apply(d)
1184         self.assertRegex(
1185             c1.portable_manifest_text(),
1186             r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1187
1188     def test_conflict_del(self):
1189         c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
1190         c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
1191         d = c1.diff(c2)
1192         self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
1193         c1.remove("count1.txt")
1194
1195         # c1 deleted, so c2 mod will go to a conflict file
1196         c1.apply(d)
1197         self.assertRegex(
1198             c1.portable_manifest_text(),
1199             r"\. 5348b82a029fd9e971a811ce1f71360b\+43 0:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
1200
1201     def test_notify(self):
1202         c1 = Collection()
1203         events = []
1204         c1.subscribe(lambda event, collection, name, item: events.append((event, collection, name, item)))
1205         f = c1.open("foo.txt", "wb")
1206         self.assertEqual(events[0], (arvados.collection.ADD, c1, "foo.txt", f.arvadosfile))
1207
1208     def test_open_w(self):
1209         c1 = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n")
1210         self.assertEqual(c1["count1.txt"].size(), 10)
1211         c1.open("count1.txt", "wb").close()
1212         self.assertEqual(c1["count1.txt"].size(), 0)
1213
1214
1215 class NewCollectionTestCaseWithServersAndTokens(run_test_server.TestCaseWithServers):
1216     MAIN_SERVER = {}
1217     KEEP_SERVER = {}
1218     local_locator_re = r"[0-9a-f]{32}\+\d+\+A[a-f0-9]{40}@[a-f0-9]{8}"
1219     remote_locator_re = r"[0-9a-f]{32}\+\d+\+R[a-z]{5}-[a-f0-9]{40}@[a-f0-9]{8}"
1220
1221     def setUp(self):
1222         self.keep_put = getattr(arvados.keep.KeepClient, 'put')
1223
1224     @mock.patch('arvados.keep.KeepClient.put', autospec=True)
1225     def test_repacked_block_submission_get_permission_token(self, mocked_put):
1226         '''
1227         Make sure that those blocks that are committed after repacking small ones,
1228         get their permission tokens assigned on the collection manifest.
1229         '''
1230         def wrapped_keep_put(*args, **kwargs):
1231             # Simulate slow put operations
1232             time.sleep(1)
1233             return self.keep_put(*args, **kwargs)
1234
1235         mocked_put.side_effect = wrapped_keep_put
1236         c = Collection()
1237         # Write 70 files ~1MiB each so we force to produce 1 big block by repacking
1238         # small ones before finishing the upload.
1239         for i in range(70):
1240             f = c.open("file_{}.txt".format(i), 'wb')
1241             f.write(random.choice('abcdefghijklmnopqrstuvwxyz') * (2**20+i))
1242             f.close(flush=False)
1243         # We should get 2 blocks with their tokens
1244         self.assertEqual(len(re.findall(self.local_locator_re, c.manifest_text())), 2)
1245
1246     @mock.patch('arvados.keep.KeepClient.refresh_signature')
1247     def test_copy_remote_blocks_on_save_new(self, rs_mock):
1248         remote_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+Remote-" + "a" * 40 + "@abcdef01"
1249         local_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+A" + "b" * 40 + "@abcdef01"
1250         rs_mock.return_value = local_block_loc
1251         c = Collection(". " + remote_block_loc + " 0:3:foofile.txt\n")
1252         self.assertEqual(
1253             len(re.findall(self.remote_locator_re, c.manifest_text())), 1)
1254         self.assertEqual(
1255             len(re.findall(self.local_locator_re, c.manifest_text())), 0)
1256         c.save_new()
1257         rs_mock.assert_called()
1258         self.assertEqual(
1259             len(re.findall(self.remote_locator_re, c.manifest_text())), 0)
1260         self.assertEqual(
1261             len(re.findall(self.local_locator_re, c.manifest_text())), 1)
1262
1263     @mock.patch('arvados.keep.KeepClient.refresh_signature')
1264     def test_copy_remote_blocks_on_save(self, rs_mock):
1265         remote_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+Remote-" + "a" * 40 + "@abcdef01"
1266         local_block_loc = "acbd18db4cc2f85cedef654fccc4a4d8+3+A" + "b" * 40 + "@abcdef01"
1267         rs_mock.return_value = local_block_loc
1268         # Remote collection
1269         remote_c = Collection(". " + remote_block_loc + " 0:3:foofile.txt\n")
1270         self.assertEqual(
1271             len(re.findall(self.remote_locator_re, remote_c.manifest_text())), 1)
1272         # Local collection
1273         local_c = Collection()
1274         with local_c.open('barfile.txt', 'wb') as f:
1275             f.write('bar')
1276         local_c.save_new()
1277         self.assertEqual(
1278             len(re.findall(self.local_locator_re, local_c.manifest_text())), 1)
1279         self.assertEqual(
1280             len(re.findall(self.remote_locator_re, local_c.manifest_text())), 0)
1281         # Copy remote file to local collection
1282         local_c.copy('./foofile.txt', './copied/foofile.txt', remote_c)
1283         self.assertEqual(
1284             len(re.findall(self.local_locator_re, local_c.manifest_text())), 1)
1285         self.assertEqual(
1286             len(re.findall(self.remote_locator_re, local_c.manifest_text())), 1)
1287         # Save local collection: remote block should be copied
1288         local_c.save()
1289         rs_mock.assert_called()
1290         self.assertEqual(
1291             len(re.findall(self.local_locator_re, local_c.manifest_text())), 2)
1292         self.assertEqual(
1293             len(re.findall(self.remote_locator_re, local_c.manifest_text())), 0)
1294
1295
1296 class NewCollectionTestCaseWithServers(run_test_server.TestCaseWithServers):
1297     def test_get_manifest_text_only_committed(self):
1298         c = Collection()
1299         with c.open("count.txt", "wb") as f:
1300             # One file committed
1301             with c.open("foo.txt", "wb") as foo:
1302                 foo.write(b"foo")
1303                 foo.flush() # Force block commit
1304             f.write(b"0123456789")
1305             # Other file not committed. Block not written to keep yet.
1306             self.assertEqual(
1307                 c._get_manifest_text(".",
1308                                      strip=False,
1309                                      normalize=False,
1310                                      only_committed=True),
1311                 '. acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:count.txt 0:3:foo.txt\n')
1312             # And now with the file closed...
1313             f.flush() # Force block commit
1314         self.assertEqual(
1315             c._get_manifest_text(".",
1316                                  strip=False,
1317                                  normalize=False,
1318                                  only_committed=True),
1319             ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:10:count.txt 10:3:foo.txt\n")
1320
1321     def test_only_small_blocks_are_packed_together(self):
1322         c = Collection()
1323         # Write a couple of small files,
1324         f = c.open("count.txt", "wb")
1325         f.write(b"0123456789")
1326         f.close(flush=False)
1327         foo = c.open("foo.txt", "wb")
1328         foo.write(b"foo")
1329         foo.close(flush=False)
1330         # Then, write a big file, it shouldn't be packed with the ones above
1331         big = c.open("bigfile.txt", "wb")
1332         big.write(b"x" * 1024 * 1024 * 33) # 33 MB > KEEP_BLOCK_SIZE/2
1333         big.close(flush=False)
1334         self.assertEqual(
1335             c.manifest_text("."),
1336             '. 2d303c138c118af809f39319e5d507e9+34603008 a8430a058b8fbf408e1931b794dbd6fb+13 0:34603008:bigfile.txt 34603008:10:count.txt 34603018:3:foo.txt\n')
1337
1338     def test_flush_after_small_block_packing(self):
1339         c = Collection()
1340         # Write a couple of small files,
1341         f = c.open("count.txt", "wb")
1342         f.write(b"0123456789")
1343         f.close(flush=False)
1344         foo = c.open("foo.txt", "wb")
1345         foo.write(b"foo")
1346         foo.close(flush=False)
1347
1348         self.assertEqual(
1349             c.manifest_text(),
1350             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1351
1352         f = c.open("count.txt", "rb+")
1353         f.close(flush=True)
1354
1355         self.assertEqual(
1356             c.manifest_text(),
1357             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1358
1359     def test_write_after_small_block_packing2(self):
1360         c = Collection()
1361         # Write a couple of small files,
1362         f = c.open("count.txt", "wb")
1363         f.write(b"0123456789")
1364         f.close(flush=False)
1365         foo = c.open("foo.txt", "wb")
1366         foo.write(b"foo")
1367         foo.close(flush=False)
1368
1369         self.assertEqual(
1370             c.manifest_text(),
1371             '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
1372
1373         f = c.open("count.txt", "rb+")
1374         f.write(b"abc")
1375         f.close(flush=False)
1376
1377         self.assertEqual(
1378             c.manifest_text(),
1379             '. 900150983cd24fb0d6963f7d28e17f72+3 a8430a058b8fbf408e1931b794dbd6fb+13 0:3:count.txt 6:7:count.txt 13:3:foo.txt\n')
1380
1381
1382     def test_small_block_packing_with_overwrite(self):
1383         c = Collection()
1384         c.open("b1", "wb").close()
1385         c["b1"].writeto(0, b"b1", 0)
1386
1387         c.open("b2", "wb").close()
1388         c["b2"].writeto(0, b"b2", 0)
1389
1390         c["b1"].writeto(0, b"1b", 0)
1391
1392         self.assertEqual(c.manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1 2:2:b2\n")
1393         self.assertEqual(c["b1"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1\n")
1394         self.assertEqual(c["b2"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 2:2:b2\n")
1395
1396
1397 class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers):
1398     MAIN_SERVER = {}
1399     KEEP_SERVER = {}
1400
1401     def create_count_txt(self):
1402         # Create an empty collection, save it to the API server, then write a
1403         # file, but don't save it.
1404
1405         c = Collection()
1406         c.save_new("CollectionCreateUpdateTest", ensure_unique_name=True)
1407         self.assertEqual(c.portable_data_hash(), "d41d8cd98f00b204e9800998ecf8427e+0")
1408         self.assertEqual(c.api_response()["portable_data_hash"], "d41d8cd98f00b204e9800998ecf8427e+0" )
1409
1410         with c.open("count.txt", "wb") as f:
1411             f.write(b"0123456789")
1412
1413         self.assertEqual(c.portable_manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1414
1415         return c
1416
1417     def test_create_and_save(self):
1418         c = self.create_count_txt()
1419         c.save(properties={'type' : 'Intermediate'},
1420                storage_classes=['archive'],
1421                trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111))
1422
1423         self.assertRegex(
1424             c.manifest_text(),
1425             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1426         self.assertEqual(c.api_response()["storage_classes_desired"], ['archive'])
1427         self.assertEqual(c.api_response()["properties"], {'type' : 'Intermediate'})
1428         self.assertEqual(c.api_response()["trash_at"], '2111-01-01T11:11:11.111111000Z')
1429
1430
1431     def test_create_and_save_new(self):
1432         c = self.create_count_txt()
1433         c.save_new(properties={'type' : 'Intermediate'},
1434                    storage_classes=['archive'],
1435                    trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111))
1436
1437         self.assertRegex(
1438             c.manifest_text(),
1439             r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
1440         self.assertEqual(c.api_response()["storage_classes_desired"], ['archive'])
1441         self.assertEqual(c.api_response()["properties"], {'type' : 'Intermediate'})
1442         self.assertEqual(c.api_response()["trash_at"], '2111-01-01T11:11:11.111111000Z')
1443
1444     def test_create_and_save_after_commiting(self):
1445         c = self.create_count_txt()
1446         c.save(properties={'type' : 'Intermediate'},
1447                storage_classes=['hot'],
1448                trash_at=datetime.datetime(2111, 1, 1, 11, 11, 11, 111111))
1449         c.save(properties={'type' : 'Output'},
1450                storage_classes=['cold'],
1451                trash_at=datetime.datetime(2222, 2, 2, 22, 22, 22, 222222))
1452
1453         self.assertEqual(c.api_response()["storage_classes_desired"], ['cold'])
1454         self.assertEqual(c.api_response()["properties"], {'type' : 'Output'})
1455         self.assertEqual(c.api_response()["trash_at"], '2222-02-02T22:22:22.222222000Z')
1456
1457     def test_create_diff_apply(self):
1458         c1 = self.create_count_txt()
1459         c1.save()
1460
1461         c2 = Collection(c1.manifest_locator())
1462         with c2.open("count.txt", "wb") as f:
1463             f.write(b"abcdefg")
1464
1465         diff = c1.diff(c2)
1466
1467         self.assertEqual(diff[0], (arvados.collection.MOD, u'./count.txt', c1["count.txt"], c2["count.txt"]))
1468
1469         c1.apply(diff)
1470         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1471
1472     def test_diff_apply_with_token(self):
1473         baseline = CollectionReader(". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:10:count.txt\n")
1474         c = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
1475         other = CollectionReader(". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1476
1477         diff = baseline.diff(other)
1478         self.assertEqual(diff, [('mod', u'./count.txt', c["count.txt"], other["count.txt"])])
1479
1480         c.apply(diff)
1481
1482         self.assertEqual(c.manifest_text(), ". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
1483
1484
1485     def test_create_and_update(self):
1486         c1 = self.create_count_txt()
1487         c1.save()
1488
1489         c2 = arvados.collection.Collection(c1.manifest_locator())
1490         with c2.open("count.txt", "wb") as f:
1491             f.write(b"abcdefg")
1492
1493         c2.save()
1494
1495         self.assertNotEqual(c1.portable_data_hash(), c2.portable_data_hash())
1496         c1.update()
1497         self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
1498
1499
1500     def test_create_and_update_with_conflict(self):
1501         c1 = self.create_count_txt()
1502         c1.save()
1503
1504         with c1.open("count.txt", "wb") as f:
1505             f.write(b"XYZ")
1506
1507         c2 = arvados.collection.Collection(c1.manifest_locator())
1508         with c2.open("count.txt", "wb") as f:
1509             f.write(b"abcdefg")
1510
1511         c2.save()
1512
1513         c1.update()
1514         self.assertRegex(
1515             c1.manifest_text(),
1516             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~$")
1517
1518     def test_pdh_is_native_str(self):
1519         c1 = self.create_count_txt()
1520         pdh = c1.portable_data_hash()
1521         self.assertEqual(type(''), type(pdh))
1522
1523
1524 if __name__ == '__main__':
1525     unittest.main()