sdk/python/tests/test_collections.py

   1 # usage example:
   2 #
   3 # ARVADOS_API_TOKEN=abc ARVADOS_API_HOST=arvados.local python -m unittest discover
   4
   5 import arvados
   6 import copy
   7 import hashlib
   8 import mock
   9 import os
  10 import pprint
  11 import re
  12 import tempfile
  13 import unittest
  14
  15 import run_test_server
  16 import arvados_testutil as tutil
  17 from arvados.ranges import Range, LocatorAndRange
  18
  19 class TestResumableWriter(arvados.ResumableCollectionWriter):
  20     KEEP_BLOCK_SIZE = 1024  # PUT to Keep every 1K.
  21
  22     def current_state(self):
  23         return self.dump_state(copy.deepcopy)
  24
  25
  26 class ArvadosCollectionsTest(run_test_server.TestCaseWithServers,
  27                              tutil.ArvadosBaseTestCase):
  28     MAIN_SERVER = {}
  29
  30     @classmethod
  31     def setUpClass(cls):
  32         super(ArvadosCollectionsTest, cls).setUpClass()
  33         run_test_server.authorize_with('active')
  34         cls.api_client = arvados.api('v1')
  35         cls.keep_client = arvados.KeepClient(api_client=cls.api_client,
  36                                              local_store=cls.local_store)
  37
  38     def write_foo_bar_baz(self):
  39         cw = arvados.CollectionWriter(self.api_client)
  40         self.assertEqual(cw.current_stream_name(), '.',
  41                          'current_stream_name() should be "." now')
  42         cw.set_current_file_name('foo.txt')
  43         cw.write('foo')
  44         self.assertEqual(cw.current_file_name(), 'foo.txt',
  45                          'current_file_name() should be foo.txt now')
  46         cw.start_new_file('bar.txt')
  47         cw.write('bar')
  48         cw.start_new_stream('baz')
  49         cw.write('baz')
  50         cw.set_current_file_name('baz.txt')
  51         self.assertEqual(cw.manifest_text(),
  52                          ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" +
  53                          "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n",
  54                          "wrong manifest: got {}".format(cw.manifest_text()))
  55         cw.finish()
  56         return cw.portable_data_hash()
  57
  58     def test_keep_local_store(self):
  59         self.assertEqual(self.keep_client.put('foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
  60         self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), 'foo', 'wrong data from Keep.get')
  61
  62     def test_local_collection_writer(self):
  63         self.assertEqual(self.write_foo_bar_baz(),
  64                          '23ca013983d6239e98931cc779e68426+114',
  65                          'wrong locator hash: ' + self.write_foo_bar_baz())
  66
  67     def test_local_collection_reader(self):
  68         foobarbaz = self.write_foo_bar_baz()
  69         cr = arvados.CollectionReader(
  70             foobarbaz + '+Xzizzle', self.api_client)
  71         got = []
  72         for s in cr.all_streams():
  73             for f in s.all_files():
  74                 got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]]
  75         expected = [[3, '.', 'foo.txt', 'foo'],
  76                     [3, '.', 'bar.txt', 'bar'],
  77                     [3, './baz', 'baz.txt', 'baz']]
  78         self.assertEqual(got,
  79                          expected)
  80         stream0 = cr.all_streams()[0]
  81         self.assertEqual(stream0.readfrom(0, 0),
  82                          '',
  83                          'reading zero bytes should have returned empty string')
  84         self.assertEqual(stream0.readfrom(0, 2**26),
  85                          'foobar',
  86                          'reading entire stream failed')
  87         self.assertEqual(stream0.readfrom(2**26, 0),
  88                          '',
  89                          'reading zero bytes should have returned empty string')
  90
  91     def _test_subset(self, collection, expected):
  92         cr = arvados.CollectionReader(collection, self.api_client)
  93         for s in cr.all_streams():
  94             for ex in expected:
  95                 if ex[0] == s:
  96                     f = s.files()[ex[2]]
  97                     got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))]
  98                     self.assertEqual(got,
  99                                      ex,
 100                                      'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex))
 101
 102     def test_collection_manifest_subset(self):
 103         foobarbaz = self.write_foo_bar_baz()
 104         self._test_subset(foobarbaz,
 105                           [[3, '.',     'bar.txt', 'bar'],
 106                            [3, '.',     'foo.txt', 'foo'],
 107                            [3, './baz', 'baz.txt', 'baz']])
 108         self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" %
 109                            (self.keep_client.put("foo"),
 110                             self.keep_client.put("bar"))),
 111                           [[3, '.', 'bar.txt', 'bar'],
 112                            [3, '.', 'foo.txt', 'foo']])
 113         self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" %
 114                            (self.keep_client.put("foo"),
 115                             self.keep_client.put("bar"))),
 116                           [[2, '.', 'fo.txt', 'fo'],
 117                            [4, '.', 'obar.txt', 'obar']])
 118         self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" %
 119                            (self.keep_client.put("foo"),
 120                             self.keep_client.put("bar"))),
 121                           [[2, '.', 'ar.txt', 'ar'],
 122                            [2, '.', 'fo.txt', 'fo'],
 123                            [2, '.', 'ob.txt', 'ob'],
 124                            [0, '.', 'zero.txt', '']])
 125
 126     def test_collection_empty_file(self):
 127         cw = arvados.CollectionWriter(self.api_client)
 128         cw.start_new_file('zero.txt')
 129         cw.write('')
 130
 131         self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n")
 132         self.check_manifest_file_sizes(cw.manifest_text(), [0])
 133         cw = arvados.CollectionWriter(self.api_client)
 134         cw.start_new_file('zero.txt')
 135         cw.write('')
 136         cw.start_new_file('one.txt')
 137         cw.write('1')
 138         cw.start_new_stream('foo')
 139         cw.start_new_file('zero.txt')
 140         cw.write('')
 141         self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0])
 142
 143     def test_no_implicit_normalize(self):
 144         cw = arvados.CollectionWriter(self.api_client)
 145         cw.start_new_file('b')
 146         cw.write('b')
 147         cw.start_new_file('a')
 148         cw.write('')
 149         self.check_manifest_file_sizes(cw.manifest_text(), [1,0])
 150         self.check_manifest_file_sizes(
 151             arvados.CollectionReader(
 152                 cw.manifest_text()).manifest_text(normalize=True),
 153             [0,1])
 154
 155     def check_manifest_file_sizes(self, manifest_text, expect_sizes):
 156         cr = arvados.CollectionReader(manifest_text, self.api_client)
 157         got_sizes = []
 158         for f in cr.all_files():
 159             got_sizes += [f.size()]
 160         self.assertEqual(got_sizes, expect_sizes, "got wrong file sizes %s, expected %s" % (got_sizes, expect_sizes))
 161
 162     def test_normalized_collection(self):
 163         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 164 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 165 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 166 """
 167         self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True),
 168                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
 169 """)
 170
 171         m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
 172 """
 173         self.assertEqual(arvados.CollectionReader(m2, self.api_client).manifest_text(normalize=True), m2)
 174
 175         m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
 176 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 177 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 178 """
 179         self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(normalize=True),
 180                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
 181 """)
 182
 183         m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 184 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 185 ./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
 186 """
 187         self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(normalize=True),
 188                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
 189 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 190 """)
 191
 192         m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 193 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 194 ./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar
 195 """
 196         self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(normalize=True),
 197                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
 198 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 199 """)
 200
 201         with self.data_file('1000G_ref_manifest') as f6:
 202             m6 = f6.read()
 203             self.assertEqual(arvados.CollectionReader(m6, self.api_client).manifest_text(normalize=True), m6)
 204
 205         with self.data_file('jlake_manifest') as f7:
 206             m7 = f7.read()
 207             self.assertEqual(arvados.CollectionReader(m7, self.api_client).manifest_text(normalize=True), m7)
 208
 209         m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt
 210 """
 211         self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8)
 212
 213     def test_locators_and_ranges(self):
 214         blocks2 = [Range('a', 0, 10),
 215                    Range('b', 10, 10),
 216                    Range('c', 20, 10),
 217                    Range('d', 30, 10),
 218                    Range('e', 40, 10),
 219                    Range('f', 50, 10)]
 220
 221         self.assertEqual(arvados.locators_and_ranges(blocks2,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 222         self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 223         self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 224         self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 225         self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 226         self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 227         self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), [])
 228         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 229
 230         self.assertEqual(arvados.locators_and_ranges(blocks2,  0,  2), [LocatorAndRange('a', 10, 0, 2)])
 231         self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [LocatorAndRange('b', 10, 0, 2)])
 232         self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [LocatorAndRange('c', 10, 0, 2)])
 233         self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [LocatorAndRange('d', 10, 0, 2)])
 234         self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [LocatorAndRange('e', 10, 0, 2)])
 235         self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [LocatorAndRange('f', 10, 0, 2)])
 236         self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), [])
 237         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 238
 239         self.assertEqual(arvados.locators_and_ranges(blocks2,  9,  2), [LocatorAndRange('a', 10, 9, 1), LocatorAndRange('b', 10, 0, 1)])
 240         self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [LocatorAndRange('b', 10, 9, 1), LocatorAndRange('c', 10, 0, 1)])
 241         self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [LocatorAndRange('c', 10, 9, 1), LocatorAndRange('d', 10, 0, 1)])
 242         self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [LocatorAndRange('d', 10, 9, 1), LocatorAndRange('e', 10, 0, 1)])
 243         self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [LocatorAndRange('e', 10, 9, 1), LocatorAndRange('f', 10, 0, 1)])
 244         self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [LocatorAndRange('f', 10, 9, 1)])
 245
 246
 247         blocks3 = [Range('a', 0, 10),
 248                   Range('b', 10, 10),
 249                   Range('c', 20, 10),
 250                   Range('d', 30, 10),
 251                   Range('e', 40, 10),
 252                   Range('f', 50, 10),
 253                    Range('g', 60, 10)]
 254
 255         self.assertEqual(arvados.locators_and_ranges(blocks3,  2,  2), [LocatorAndRange('a', 10, 2, 2)])
 256         self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [LocatorAndRange('b', 10, 2, 2)])
 257         self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [LocatorAndRange('c', 10, 2, 2)])
 258         self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [LocatorAndRange('d', 10, 2, 2)])
 259         self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [LocatorAndRange('e', 10, 2, 2)])
 260         self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [LocatorAndRange('f', 10, 2, 2)])
 261         self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [LocatorAndRange('g', 10, 2, 2)])
 262
 263
 264         blocks = [Range('a', 0, 10),
 265                   Range('b', 10, 15),
 266                   Range('c', 25, 5)]
 267         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 0), [])
 268         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [LocatorAndRange('a', 10, 0, 5)])
 269         self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [LocatorAndRange('a', 10, 3, 5)])
 270         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [LocatorAndRange('a', 10, 0, 10)])
 271
 272         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [LocatorAndRange('a', 10, 0, 10),
 273                                                                       LocatorAndRange('b', 15, 0, 1)])
 274         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [LocatorAndRange('a', 10, 1, 9),
 275                                                                       LocatorAndRange('b', 15, 0, 2)])
 276         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [LocatorAndRange('a', 10, 0, 10),
 277                                                                       LocatorAndRange('b', 15, 0, 15)])
 278
 279         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [LocatorAndRange('a', 10, 0, 10),
 280                                                                       LocatorAndRange('b', 15, 0, 15),
 281                                                                       LocatorAndRange('c', 5, 0, 5)])
 282         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [LocatorAndRange('a', 10, 1, 9),
 283                                                                       LocatorAndRange('b', 15, 0, 15),
 284                                                                       LocatorAndRange('c', 5, 0, 5)])
 285         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [LocatorAndRange('a', 10, 0, 10),
 286                                                                       LocatorAndRange('b', 15, 0, 15),
 287                                                                       LocatorAndRange('c', 5, 0, 5)])
 288
 289         self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [LocatorAndRange('b', 15, 5, 5)])
 290
 291         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [LocatorAndRange('a', 10, 8, 2),
 292                                                                       LocatorAndRange('b', 15, 0, 15)])
 293
 294         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [LocatorAndRange('a', 10, 8, 2),
 295                                                                       LocatorAndRange('b', 15, 0, 15),
 296                                                                       LocatorAndRange('c', 5, 0, 3)])
 297
 298         self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [LocatorAndRange('c', 5, 1, 2)])
 299
 300         self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [LocatorAndRange('a', 10, 9, 1),
 301                                                                       LocatorAndRange('b', 15, 0, 14)])
 302         self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [LocatorAndRange('b', 15, 0, 15)])
 303         self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [LocatorAndRange('b', 15, 1, 14),
 304                                                                        LocatorAndRange('c', 5, 0, 1)])
 305
 306     class MockKeep(object):
 307         def __init__(self, content, num_retries=0):
 308             self.content = content
 309
 310         def get(self, locator, num_retries=0):
 311             return self.content[locator]
 312
 313     def test_stream_reader(self):
 314         keepblocks = {'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': 'abcdefghij',
 315                       'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': 'klmnopqrstuvwxy',
 316                       'cccccccccccccccccccccccccccccccc+5': 'z0123'}
 317         mk = self.MockKeep(keepblocks)
 318
 319         sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk)
 320
 321         content = 'abcdefghijklmnopqrstuvwxyz0123456789'
 322
 323         self.assertEqual(sr.readfrom(0, 30), content[0:30])
 324         self.assertEqual(sr.readfrom(2, 30), content[2:30])
 325
 326         self.assertEqual(sr.readfrom(2, 8), content[2:10])
 327         self.assertEqual(sr.readfrom(0, 10), content[0:10])
 328
 329         self.assertEqual(sr.readfrom(0, 5), content[0:5])
 330         self.assertEqual(sr.readfrom(5, 5), content[5:10])
 331         self.assertEqual(sr.readfrom(10, 5), content[10:15])
 332         self.assertEqual(sr.readfrom(15, 5), content[15:20])
 333         self.assertEqual(sr.readfrom(20, 5), content[20:25])
 334         self.assertEqual(sr.readfrom(25, 5), content[25:30])
 335         self.assertEqual(sr.readfrom(30, 5), '')
 336
 337     def test_extract_file(self):
 338         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 339 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt
 340 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt
 341 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt
 342 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt
 343 """
 344
 345         m2 = arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True)
 346
 347         self.assertEqual(m2,
 348                          ". 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")
 349         files = arvados.CollectionReader(
 350             m2, self.api_client).all_streams()[0].files()
 351
 352         self.assertEqual(files['md5sum.txt'].as_manifest(),
 353                          ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n")
 354         self.assertEqual(files['md6sum.txt'].as_manifest(),
 355                          ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n")
 356         self.assertEqual(files['md7sum.txt'].as_manifest(),
 357                          ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n")
 358         self.assertEqual(files['md9sum.txt'].as_manifest(),
 359                          ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n")
 360
 361     def test_write_directory_tree(self):
 362         cwriter = arvados.CollectionWriter(self.api_client)
 363         cwriter.write_directory_tree(self.build_directory_tree(
 364                 ['basefile', 'subdir/subfile']))
 365         self.assertEqual(cwriter.manifest_text(),
 366                          """. c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 367 ./subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 368
 369     def test_write_named_directory_tree(self):
 370         cwriter = arvados.CollectionWriter(self.api_client)
 371         cwriter.write_directory_tree(self.build_directory_tree(
 372                 ['basefile', 'subdir/subfile']), 'root')
 373         self.assertEqual(
 374             cwriter.manifest_text(),
 375             """./root c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 376 ./root/subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 377
 378     def test_write_directory_tree_in_one_stream(self):
 379         cwriter = arvados.CollectionWriter(self.api_client)
 380         cwriter.write_directory_tree(self.build_directory_tree(
 381                 ['basefile', 'subdir/subfile']), max_manifest_depth=0)
 382         self.assertEqual(cwriter.manifest_text(),
 383                          """. 4ace875ffdc6824a04950f06858f4465+22 0:8:basefile 8:14:subdir/subfile\n""")
 384
 385     def test_write_directory_tree_with_limited_recursion(self):
 386         cwriter = arvados.CollectionWriter(self.api_client)
 387         cwriter.write_directory_tree(
 388             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 389             max_manifest_depth=1)
 390         self.assertEqual(cwriter.manifest_text(),
 391                          """. bd19836ddb62c11c55ab251ccaca5645+2 0:2:f1
 392 ./d1 50170217e5b04312024aa5cd42934494+13 0:8:d2/f3 8:5:f2\n""")
 393
 394     def test_write_directory_tree_with_zero_recursion(self):
 395         cwriter = arvados.CollectionWriter(self.api_client)
 396         content = 'd1/d2/f3d1/f2f1'
 397         blockhash = hashlib.md5(content).hexdigest() + '+' + str(len(content))
 398         cwriter.write_directory_tree(
 399             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 400             max_manifest_depth=0)
 401         self.assertEqual(
 402             cwriter.manifest_text(),
 403             ". {} 0:8:d1/d2/f3 8:5:d1/f2 13:2:f1\n".format(blockhash))
 404
 405     def test_write_one_file(self):
 406         cwriter = arvados.CollectionWriter(self.api_client)
 407         with self.make_test_file() as testfile:
 408             cwriter.write_file(testfile.name)
 409             self.assertEqual(
 410                 cwriter.manifest_text(),
 411                 ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:{}\n".format(
 412                     os.path.basename(testfile.name)))
 413
 414     def test_write_named_file(self):
 415         cwriter = arvados.CollectionWriter(self.api_client)
 416         with self.make_test_file() as testfile:
 417             cwriter.write_file(testfile.name, 'foo')
 418             self.assertEqual(cwriter.manifest_text(),
 419                              ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:foo\n")
 420
 421     def test_write_multiple_files(self):
 422         cwriter = arvados.CollectionWriter(self.api_client)
 423         for letter in 'ABC':
 424             with self.make_test_file(letter) as testfile:
 425                 cwriter.write_file(testfile.name, letter)
 426         self.assertEqual(
 427             cwriter.manifest_text(),
 428             ". 902fbdd2b1df0c4f70b4a5d23525e932+3 0:1:A 1:1:B 2:1:C\n")
 429
 430     def test_basic_resume(self):
 431         cwriter = TestResumableWriter()
 432         with self.make_test_file() as testfile:
 433             cwriter.write_file(testfile.name, 'test')
 434             resumed = TestResumableWriter.from_state(cwriter.current_state())
 435         self.assertEquals(cwriter.manifest_text(), resumed.manifest_text(),
 436                           "resumed CollectionWriter had different manifest")
 437
 438     def test_resume_fails_when_missing_dependency(self):
 439         cwriter = TestResumableWriter()
 440         with self.make_test_file() as testfile:
 441             cwriter.write_file(testfile.name, 'test')
 442         self.assertRaises(arvados.errors.StaleWriterStateError,
 443                           TestResumableWriter.from_state,
 444                           cwriter.current_state())
 445
 446     def test_resume_fails_when_dependency_mtime_changed(self):
 447         cwriter = TestResumableWriter()
 448         with self.make_test_file() as testfile:
 449             cwriter.write_file(testfile.name, 'test')
 450             os.utime(testfile.name, (0, 0))
 451             self.assertRaises(arvados.errors.StaleWriterStateError,
 452                               TestResumableWriter.from_state,
 453                               cwriter.current_state())
 454
 455     def test_resume_fails_when_dependency_is_nonfile(self):
 456         cwriter = TestResumableWriter()
 457         cwriter.write_file('/dev/null', 'empty')
 458         self.assertRaises(arvados.errors.StaleWriterStateError,
 459                           TestResumableWriter.from_state,
 460                           cwriter.current_state())
 461
 462     def test_resume_fails_when_dependency_size_changed(self):
 463         cwriter = TestResumableWriter()
 464         with self.make_test_file() as testfile:
 465             cwriter.write_file(testfile.name, 'test')
 466             orig_mtime = os.fstat(testfile.fileno()).st_mtime
 467             testfile.write('extra')
 468             testfile.flush()
 469             os.utime(testfile.name, (orig_mtime, orig_mtime))
 470             self.assertRaises(arvados.errors.StaleWriterStateError,
 471                               TestResumableWriter.from_state,
 472                               cwriter.current_state())
 473
 474     def test_resume_fails_with_expired_locator(self):
 475         cwriter = TestResumableWriter()
 476         state = cwriter.current_state()
 477         # Add an expired locator to the state.
 478         state['_current_stream_locators'].append(''.join([
 479                     'a' * 32, '+1+A', 'b' * 40, '@', '10000000']))
 480         self.assertRaises(arvados.errors.StaleWriterStateError,
 481                           TestResumableWriter.from_state, state)
 482
 483     def test_arbitrary_objects_not_resumable(self):
 484         cwriter = TestResumableWriter()
 485         with open('/dev/null') as badfile:
 486             self.assertRaises(arvados.errors.AssertionError,
 487                               cwriter.write_file, badfile)
 488
 489     def test_arbitrary_writes_not_resumable(self):
 490         cwriter = TestResumableWriter()
 491         self.assertRaises(arvados.errors.AssertionError,
 492                           cwriter.write, "badtext")
 493
 494     def test_read_arbitrary_data_with_collection_reader(self):
 495         # arv-get relies on this to do "arv-get {keep-locator} -".
 496         self.write_foo_bar_baz()
 497         self.assertEqual(
 498             'foobar',
 499             arvados.CollectionReader(
 500                 '3858f62230ac3c915f300c664312c63f+6'
 501                 ).manifest_text())
 502
 503
 504 class CollectionTestMixin(object):
 505     PROXY_RESPONSE = {
 506         'items_available': 1,
 507         'items': [{
 508                 'uuid': 'zzzzz-bi6l4-mockproxy012345',
 509                 'owner_uuid': 'zzzzz-tpzed-mockowner012345',
 510                 'service_host': tutil.TEST_HOST,
 511                 'service_port': 65535,
 512                 'service_ssl_flag': True,
 513                 'service_type': 'proxy',
 514                 }]}
 515     API_COLLECTIONS = run_test_server.fixture('collections')
 516     DEFAULT_COLLECTION = API_COLLECTIONS['foo_file']
 517     DEFAULT_DATA_HASH = DEFAULT_COLLECTION['portable_data_hash']
 518     DEFAULT_MANIFEST = DEFAULT_COLLECTION['manifest_text']
 519     DEFAULT_UUID = DEFAULT_COLLECTION['uuid']
 520     ALT_COLLECTION = API_COLLECTIONS['bar_file']
 521     ALT_DATA_HASH = ALT_COLLECTION['portable_data_hash']
 522     ALT_MANIFEST = ALT_COLLECTION['manifest_text']
 523
 524     def _mock_api_call(self, mock_method, code, body):
 525         mock_method = mock_method().execute
 526         if code == 200:
 527             mock_method.return_value = body
 528         else:
 529             mock_method.side_effect = arvados.errors.ApiError(
 530                 tutil.fake_httplib2_response(code), "{}")
 531
 532     def mock_keep_services(self, api_mock, code, body):
 533         self._mock_api_call(api_mock.keep_services().accessible, code, body)
 534
 535     def api_client_mock(self, code=200):
 536         client = mock.MagicMock(name='api_client')
 537         self.mock_keep_services(client, code, self.PROXY_RESPONSE)
 538         return client
 539
 540
 541 @tutil.skip_sleep
 542 class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin):
 543     def mock_get_collection(self, api_mock, code, body):
 544         body = self.API_COLLECTIONS.get(body)
 545         self._mock_api_call(api_mock.collections().get, code, body)
 546
 547     def api_client_mock(self, code=200):
 548         client = super(CollectionReaderTestCase, self).api_client_mock(code)
 549         self.mock_get_collection(client, code, 'foo_file')
 550         return client
 551
 552     def test_init_no_default_retries(self):
 553         client = self.api_client_mock(200)
 554         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 555         reader.manifest_text()
 556         client.collections().get().execute.assert_called_with(num_retries=0)
 557
 558     def test_uuid_init_success(self):
 559         client = self.api_client_mock(200)
 560         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 561                                           num_retries=3)
 562         self.assertEqual(self.DEFAULT_COLLECTION['manifest_text'],
 563                          reader.manifest_text())
 564         client.collections().get().execute.assert_called_with(num_retries=3)
 565
 566     def test_uuid_init_failure_raises_api_error(self):
 567         client = self.api_client_mock(500)
 568         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 569         with self.assertRaises(arvados.errors.ApiError):
 570             reader.manifest_text()
 571
 572     def test_locator_init(self):
 573         client = self.api_client_mock(200)
 574         # Ensure Keep will not return anything if asked.
 575         with tutil.mock_get_responses(None, 404):
 576             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 577                                               api_client=client)
 578             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 579
 580     def test_locator_init_fallback_to_keep(self):
 581         # crunch-job needs this to read manifests that have only ever
 582         # been written to Keep.
 583         client = self.api_client_mock(200)
 584         self.mock_get_collection(client, 404, None)
 585         with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200):
 586             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 587                                               api_client=client)
 588             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 589
 590     def test_uuid_init_no_fallback_to_keep(self):
 591         # Do not look up a collection UUID in Keep.
 592         client = self.api_client_mock(404)
 593         reader = arvados.CollectionReader(self.DEFAULT_UUID,
 594                                           api_client=client)
 595         with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200):
 596             with self.assertRaises(arvados.errors.ApiError):
 597                 reader.manifest_text()
 598
 599     def test_try_keep_first_if_permission_hint(self):
 600         # To verify that CollectionReader tries Keep first here, we
 601         # mock API server to return the wrong data.
 602         client = self.api_client_mock(200)
 603         with tutil.mock_get_responses(self.ALT_MANIFEST, 200):
 604             self.assertEqual(
 605                 self.ALT_MANIFEST,
 606                 arvados.CollectionReader(
 607                     self.ALT_DATA_HASH + '+Affffffffffffffffffffffffffffffffffffffff@fedcba98',
 608                     api_client=client).manifest_text())
 609
 610     def test_init_num_retries_propagated(self):
 611         # More of an integration test...
 612         client = self.api_client_mock(200)
 613         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 614                                           num_retries=3)
 615         with tutil.mock_get_responses('foo', 500, 500, 200):
 616             self.assertEqual('foo',
 617                              ''.join(f.read(9) for f in reader.all_files()))
 618
 619     def test_read_nonnormalized_manifest_with_collection_reader(self):
 620         # client should be able to use CollectionReader on a manifest without normalizing it
 621         client = self.api_client_mock(500)
 622         nonnormal = ". acbd18db4cc2f85cedef654fccc4a4d8+3+Aabadbadbee@abeebdee 0:3:foo.txt 1:0:bar.txt 0:3:foo.txt\n"
 623         reader = arvados.CollectionReader(
 624             nonnormal,
 625             api_client=client, num_retries=0)
 626         # Ensure stripped_manifest() doesn't mangle our manifest in
 627         # any way other than stripping hints.
 628         self.assertEqual(
 629             re.sub('\+[^\d\s\+]+', '', nonnormal),
 630             reader.stripped_manifest())
 631         # Ensure stripped_manifest() didn't mutate our reader.
 632         self.assertEqual(nonnormal, reader.manifest_text())
 633         # Ensure the files appear in the order given in the manifest.
 634         self.assertEqual(
 635             [[6, '.', 'foo.txt'],
 636              [0, '.', 'bar.txt']],
 637             [[f.size(), f.stream_name(), f.name()]
 638              for f in reader.all_streams()[0].all_files()])
 639
 640     def test_read_empty_collection(self):
 641         client = self.api_client_mock(200)
 642         self.mock_get_collection(client, 200, 'empty')
 643         reader = arvados.CollectionReader('d41d8cd98f00b204e9800998ecf8427e+0',
 644                                           api_client=client)
 645         self.assertEqual('', reader.manifest_text())
 646
 647     def test_api_response(self):
 648         client = self.api_client_mock()
 649         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 650         self.assertEqual(self.DEFAULT_COLLECTION, reader.api_response())
 651
 652     def test_api_response_with_collection_from_keep(self):
 653         client = self.api_client_mock()
 654         self.mock_get_collection(client, 404, 'foo')
 655         with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200):
 656             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 657                                               api_client=client)
 658             api_response = reader.api_response()
 659         self.assertIsNone(api_response)
 660
 661     def check_open_file(self, coll_file, stream_name, file_name, file_size):
 662         self.assertFalse(coll_file.closed, "returned file is not open")
 663         self.assertEqual(stream_name, coll_file.stream_name())
 664         self.assertEqual(file_name, coll_file.name())
 665         self.assertEqual(file_size, coll_file.size())
 666
 667     def test_open_collection_file_one_argument(self):
 668         client = self.api_client_mock(200)
 669         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 670         cfile = reader.open('./foo')
 671         self.check_open_file(cfile, '.', 'foo', 3)
 672
 673     def test_open_collection_file_two_arguments(self):
 674         client = self.api_client_mock(200)
 675         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 676         cfile = reader.open('.', 'foo')
 677         self.check_open_file(cfile, '.', 'foo', 3)
 678
 679     def test_open_deep_file(self):
 680         coll_name = 'collection_with_files_in_subdir'
 681         client = self.api_client_mock(200)
 682         self.mock_get_collection(client, 200, coll_name)
 683         reader = arvados.CollectionReader(
 684             self.API_COLLECTIONS[coll_name]['uuid'], api_client=client)
 685         cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt')
 686         self.check_open_file(cfile, './subdir2/subdir3', 'file2_in_subdir3.txt',
 687                              32)
 688
 689     def test_open_nonexistent_stream(self):
 690         client = self.api_client_mock(200)
 691         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 692         self.assertRaises(ValueError, reader.open, './nonexistent', 'foo')
 693
 694     def test_open_nonexistent_file(self):
 695         client = self.api_client_mock(200)
 696         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 697         self.assertRaises(ValueError, reader.open, '.', 'nonexistent')
 698
 699
 700 @tutil.skip_sleep
 701 class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin):
 702     def mock_keep(self, body, *codes, **headers):
 703         headers.setdefault('x-keep-replicas-stored', 2)
 704         return tutil.mock_put_responses(body, *codes, **headers)
 705
 706     def foo_writer(self, **kwargs):
 707         api_client = self.api_client_mock()
 708         writer = arvados.CollectionWriter(api_client, **kwargs)
 709         writer.start_new_file('foo')
 710         writer.write('foo')
 711         return writer
 712
 713     def test_write_whole_collection(self):
 714         writer = self.foo_writer()
 715         with self.mock_keep(self.DEFAULT_DATA_HASH, 200, 200):
 716             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 717
 718     def test_write_no_default(self):
 719         writer = self.foo_writer()
 720         with self.mock_keep(None, 500):
 721             with self.assertRaises(arvados.errors.KeepWriteError):
 722                 writer.finish()
 723
 724     def test_write_whole_collection_through_retries(self):
 725         writer = self.foo_writer(num_retries=2)
 726         with self.mock_keep(self.DEFAULT_DATA_HASH,
 727                             500, 500, 200, 500, 500, 200):
 728             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 729
 730     def test_flush_data_retries(self):
 731         writer = self.foo_writer(num_retries=2)
 732         foo_hash = self.DEFAULT_MANIFEST.split()[1]
 733         with self.mock_keep(foo_hash, 500, 200):
 734             writer.flush_data()
 735         self.assertEqual(self.DEFAULT_MANIFEST, writer.manifest_text())
 736
 737     def test_one_open(self):
 738         client = self.api_client_mock()
 739         writer = arvados.CollectionWriter(client)
 740         with writer.open('out') as out_file:
 741             self.assertEqual('.', writer.current_stream_name())
 742             self.assertEqual('out', writer.current_file_name())
 743             out_file.write('test data')
 744             data_loc = hashlib.md5('test data').hexdigest() + '+9'
 745         self.assertTrue(out_file.closed, "writer file not closed after context")
 746         self.assertRaises(ValueError, out_file.write, 'extra text')
 747         with self.mock_keep(data_loc, 200) as keep_mock:
 748             self.assertEqual(". {} 0:9:out\n".format(data_loc),
 749                              writer.manifest_text())
 750
 751     def test_open_writelines(self):
 752         client = self.api_client_mock()
 753         writer = arvados.CollectionWriter(client)
 754         with writer.open('six') as out_file:
 755             out_file.writelines(['12', '34', '56'])
 756             data_loc = hashlib.md5('123456').hexdigest() + '+6'
 757         with self.mock_keep(data_loc, 200) as keep_mock:
 758             self.assertEqual(". {} 0:6:six\n".format(data_loc),
 759                              writer.manifest_text())
 760
 761     def test_open_flush(self):
 762         client = self.api_client_mock()
 763         data_loc1 = hashlib.md5('flush1').hexdigest() + '+6'
 764         data_loc2 = hashlib.md5('flush2').hexdigest() + '+6'
 765         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 766             writer = arvados.CollectionWriter(client)
 767             with writer.open('flush_test') as out_file:
 768                 out_file.write('flush1')
 769                 out_file.flush()
 770                 out_file.write('flush2')
 771             self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1,
 772                                                                 data_loc2),
 773                              writer.manifest_text())
 774
 775     def test_two_opens_same_stream(self):
 776         client = self.api_client_mock()
 777         writer = arvados.CollectionWriter(client)
 778         with writer.open('.', '1') as out_file:
 779             out_file.write('1st')
 780         with writer.open('.', '2') as out_file:
 781             out_file.write('2nd')
 782         data_loc = hashlib.md5('1st2nd').hexdigest() + '+6'
 783         with self.mock_keep(data_loc, 200) as keep_mock:
 784             self.assertEqual(". {} 0:3:1 3:3:2\n".format(data_loc),
 785                              writer.manifest_text())
 786
 787     def test_two_opens_two_streams(self):
 788         client = self.api_client_mock()
 789         data_loc1 = hashlib.md5('file').hexdigest() + '+4'
 790         data_loc2 = hashlib.md5('indir').hexdigest() + '+5'
 791         with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
 792             writer = arvados.CollectionWriter(client)
 793             with writer.open('file') as out_file:
 794                 out_file.write('file')
 795             with writer.open('./dir', 'indir') as out_file:
 796                 out_file.write('indir')
 797             expected = ". {} 0:4:file\n./dir {} 0:5:indir\n".format(
 798                 data_loc1, data_loc2)
 799             self.assertEqual(expected, writer.manifest_text())
 800
 801     def test_dup_open_fails(self):
 802         client = self.api_client_mock()
 803         writer = arvados.CollectionWriter(client)
 804         file1 = writer.open('one')
 805         self.assertRaises(arvados.errors.AssertionError, writer.open, 'two')
 806
 807
 808 class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin):
 809     def test_import_manifest(self):
 810         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 811 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 812 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 813 """
 814         self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", arvados.export_manifest(arvados.import_manifest(m1)))
 815
 816     def test_init_manifest(self):
 817         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 818 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 819 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
 820 """
 821         self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", arvados.export_manifest(arvados.Collection(m1)))
 822
 823 if __name__ == '__main__':
 824     unittest.main()