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