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 bz2
   7 import copy
   8 import mock
   9 import os
  10 import pprint
  11 import subprocess
  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         return cw.finish()
  51
  52     def test_keep_local_store(self):
  53         self.assertEqual(self.keep_client.put('foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
  54         self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), 'foo', 'wrong data from Keep.get')
  55
  56     def test_local_collection_writer(self):
  57         self.assertEqual(self.write_foo_bar_baz(),
  58                          'd6c3b8e571f1b81ebb150a45ed06c884+114',
  59                          "wrong locator hash for files foo, bar, baz")
  60
  61     def test_local_collection_reader(self):
  62         self.write_foo_bar_baz()
  63         cr = arvados.CollectionReader(
  64             'd6c3b8e571f1b81ebb150a45ed06c884+114+Xzizzle', self.api_client)
  65         got = []
  66         for s in cr.all_streams():
  67             for f in s.all_files():
  68                 got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]]
  69         expected = [[3, '.', 'bar.txt', 'bar'],
  70                     [3, '.', 'foo.txt', 'foo'],
  71                     [3, './baz', 'baz.txt', 'baz']]
  72         self.assertEqual(got,
  73                          expected)
  74         stream0 = cr.all_streams()[0]
  75         self.assertEqual(stream0.readfrom(0, 0),
  76                          '',
  77                          'reading zero bytes should have returned empty string')
  78         self.assertEqual(stream0.readfrom(0, 2**26),
  79                          'foobar',
  80                          'reading entire stream failed')
  81         self.assertEqual(stream0.readfrom(2**26, 0),
  82                          '',
  83                          'reading zero bytes should have returned empty string')
  84
  85     def _test_subset(self, collection, expected):
  86         cr = arvados.CollectionReader(collection, self.api_client)
  87         for s in cr.all_streams():
  88             for ex in expected:
  89                 if ex[0] == s:
  90                     f = s.files()[ex[2]]
  91                     got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))]
  92                     self.assertEqual(got,
  93                                      ex,
  94                                      'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex))
  95
  96     def test_collection_manifest_subset(self):
  97         self.write_foo_bar_baz()
  98         self._test_subset('d6c3b8e571f1b81ebb150a45ed06c884+114',
  99                           [[3, '.',     'bar.txt', 'bar'],
 100                            [3, '.',     'foo.txt', 'foo'],
 101                            [3, './baz', 'baz.txt', 'baz']])
 102         self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" %
 103                            (self.keep_client.put("foo"),
 104                             self.keep_client.put("bar"))),
 105                           [[3, '.', 'bar.txt', 'bar'],
 106                            [3, '.', 'foo.txt', 'foo']])
 107         self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" %
 108                            (self.keep_client.put("foo"),
 109                             self.keep_client.put("bar"))),
 110                           [[2, '.', 'fo.txt', 'fo'],
 111                            [4, '.', 'obar.txt', 'obar']])
 112         self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" %
 113                            (self.keep_client.put("foo"),
 114                             self.keep_client.put("bar"))),
 115                           [[2, '.', 'ar.txt', 'ar'],
 116                            [2, '.', 'fo.txt', 'fo'],
 117                            [2, '.', 'ob.txt', 'ob'],
 118                            [0, '.', 'zero.txt', '']])
 119
 120     def _test_readline(self, what_in, what_out):
 121         cw = arvados.CollectionWriter(self.api_client)
 122         cw.start_new_file('test.txt')
 123         cw.write(what_in)
 124         test1 = cw.finish()
 125         cr = arvados.CollectionReader(test1, self.api_client)
 126         got = []
 127         for x in list(cr.all_files())[0].readlines():
 128             got += [x]
 129         self.assertEqual(got,
 130                          what_out,
 131                          "readlines did not split lines correctly: %s" % got)
 132
 133     def test_collection_readline(self):
 134         self._test_readline("\na\nbcd\n\nefg\nz",
 135                             ["\n", "a\n", "bcd\n", "\n", "efg\n", "z"])
 136         self._test_readline("ab\ncd\n",
 137                             ["ab\n", "cd\n"])
 138
 139     def test_collection_empty_file(self):
 140         cw = arvados.CollectionWriter(self.api_client)
 141         cw.start_new_file('zero.txt')
 142         cw.write('')
 143
 144         self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n")
 145         self.check_manifest_file_sizes(cw.manifest_text(), [0])
 146         cw = arvados.CollectionWriter(self.api_client)
 147         cw.start_new_file('zero.txt')
 148         cw.write('')
 149         cw.start_new_file('one.txt')
 150         cw.write('1')
 151         cw.start_new_stream('foo')
 152         cw.start_new_file('zero.txt')
 153         cw.write('')
 154         self.check_manifest_file_sizes(cw.manifest_text(), [1,0,0])
 155
 156     def check_manifest_file_sizes(self, manifest_text, expect_sizes):
 157         cr = arvados.CollectionReader(manifest_text, self.api_client)
 158         got_sizes = []
 159         for f in cr.all_files():
 160             got_sizes += [f.size()]
 161         self.assertEqual(got_sizes, expect_sizes, "got wrong file sizes %s, expected %s" % (got_sizes, expect_sizes))
 162
 163     def test_collection_bz2_decompression(self):
 164         n_lines_in = 2**18
 165         data_in = "abc\n"
 166         for x in xrange(0, 18):
 167             data_in += data_in
 168         compressed_data_in = bz2.compress(data_in)
 169         cw = arvados.CollectionWriter(self.api_client)
 170         cw.start_new_file('test.bz2')
 171         cw.write(compressed_data_in)
 172         bz2_manifest = cw.manifest_text()
 173
 174         cr = arvados.CollectionReader(bz2_manifest, self.api_client)
 175
 176         got = 0
 177         for x in list(cr.all_files())[0].readlines():
 178             self.assertEqual(x, "abc\n", "decompression returned wrong data: %s" % x)
 179             got += 1
 180         self.assertEqual(got,
 181                          n_lines_in,
 182                          "decompression returned %d lines instead of %d" % (got, n_lines_in))
 183
 184     def test_collection_gzip_decompression(self):
 185         n_lines_in = 2**18
 186         data_in = "abc\n"
 187         for x in xrange(0, 18):
 188             data_in += data_in
 189         p = subprocess.Popen(["gzip", "-1cn"],
 190                              stdout=subprocess.PIPE,
 191                              stdin=subprocess.PIPE,
 192                              stderr=subprocess.PIPE,
 193                              shell=False, close_fds=True)
 194         compressed_data_in, stderrdata = p.communicate(data_in)
 195
 196         cw = arvados.CollectionWriter(self.api_client)
 197         cw.start_new_file('test.gz')
 198         cw.write(compressed_data_in)
 199         gzip_manifest = cw.manifest_text()
 200
 201         cr = arvados.CollectionReader(gzip_manifest, self.api_client)
 202         got = 0
 203         for x in list(cr.all_files())[0].readlines():
 204             self.assertEqual(x, "abc\n", "decompression returned wrong data: %s" % x)
 205             got += 1
 206         self.assertEqual(got,
 207                          n_lines_in,
 208                          "decompression returned %d lines instead of %d" % (got, n_lines_in))
 209
 210     def test_normalized_collection(self):
 211         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 212 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 213 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt"""
 214         self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(),
 215                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
 216 """)
 217
 218         m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
 219 """
 220         self.assertEqual(arvados.CollectionReader(m2, self.api_client).manifest_text(), m2)
 221
 222         m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
 223 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
 224 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt"""
 225         self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(),
 226                          """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
 227 """)
 228
 229         m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 230 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 231 ./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar"""
 232         self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(),
 233                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
 234 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 235 """)
 236
 237         m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
 238 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 239 ./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar"""
 240         self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(),
 241                          """./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
 242 ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
 243 """)
 244
 245         with self.data_file('1000G_ref_manifest') as f6:
 246             m6 = f6.read()
 247             self.assertEqual(arvados.CollectionReader(m6, self.api_client).manifest_text(), m6)
 248
 249         with self.data_file('jlake_manifest') as f7:
 250             m7 = f7.read()
 251             self.assertEqual(arvados.CollectionReader(m7, self.api_client).manifest_text(), m7)
 252
 253         m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt
 254 """
 255         self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(), m8)
 256
 257     def test_locators_and_ranges(self):
 258         blocks2 = [['a', 10, 0],
 259                   ['b', 10, 10],
 260                   ['c', 10, 20],
 261                   ['d', 10, 30],
 262                   ['e', 10, 40],
 263                   ['f', 10, 50]]
 264
 265         self.assertEqual(arvados.locators_and_ranges(blocks2,  2,  2), [['a', 10, 2, 2]])
 266         self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [['b', 10, 2, 2]])
 267         self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [['c', 10, 2, 2]])
 268         self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [['d', 10, 2, 2]])
 269         self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [['e', 10, 2, 2]])
 270         self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [['f', 10, 2, 2]])
 271         self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), [])
 272         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 273
 274         self.assertEqual(arvados.locators_and_ranges(blocks2,  0,  2), [['a', 10, 0, 2]])
 275         self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [['b', 10, 0, 2]])
 276         self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [['c', 10, 0, 2]])
 277         self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [['d', 10, 0, 2]])
 278         self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [['e', 10, 0, 2]])
 279         self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [['f', 10, 0, 2]])
 280         self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), [])
 281         self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
 282
 283         self.assertEqual(arvados.locators_and_ranges(blocks2,  9,  2), [['a', 10, 9, 1], ['b', 10, 0, 1]])
 284         self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [['b', 10, 9, 1], ['c', 10, 0, 1]])
 285         self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [['c', 10, 9, 1], ['d', 10, 0, 1]])
 286         self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [['d', 10, 9, 1], ['e', 10, 0, 1]])
 287         self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [['e', 10, 9, 1], ['f', 10, 0, 1]])
 288         self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [['f', 10, 9, 1]])
 289
 290
 291         blocks3 = [['a', 10, 0],
 292                   ['b', 10, 10],
 293                   ['c', 10, 20],
 294                   ['d', 10, 30],
 295                   ['e', 10, 40],
 296                   ['f', 10, 50],
 297                   ['g', 10, 60]]
 298
 299         self.assertEqual(arvados.locators_and_ranges(blocks3,  2,  2), [['a', 10, 2, 2]])
 300         self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [['b', 10, 2, 2]])
 301         self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [['c', 10, 2, 2]])
 302         self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [['d', 10, 2, 2]])
 303         self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [['e', 10, 2, 2]])
 304         self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [['f', 10, 2, 2]])
 305         self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [['g', 10, 2, 2]])
 306
 307
 308         blocks = [['a', 10, 0],
 309                   ['b', 15, 10],
 310                   ['c', 5, 25]]
 311         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 0), [])
 312         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [['a', 10, 0, 5]])
 313         self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [['a', 10, 3, 5]])
 314         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [['a', 10, 0, 10]])
 315
 316         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [['a', 10, 0, 10],
 317                                                                       ['b', 15, 0, 1]])
 318         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [['a', 10, 1, 9],
 319                                                                       ['b', 15, 0, 2]])
 320         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [['a', 10, 0, 10],
 321                                                                       ['b', 15, 0, 15]])
 322
 323         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [['a', 10, 0, 10],
 324                                                                       ['b', 15, 0, 15],
 325                                                                       ['c', 5, 0, 5]])
 326         self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [['a', 10, 1, 9],
 327                                                                       ['b', 15, 0, 15],
 328                                                                       ['c', 5, 0, 5]])
 329         self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [['a', 10, 0, 10],
 330                                                                       ['b', 15, 0, 15],
 331                                                                       ['c', 5, 0, 5]])
 332
 333         self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [['b', 15, 5, 5]])
 334
 335         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [['a', 10, 8, 2],
 336                                                                       ['b', 15, 0, 15]])
 337
 338         self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [['a', 10, 8, 2],
 339                                                                       ['b', 15, 0, 15],
 340                                                                       ['c', 5, 0, 3]])
 341
 342         self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [['c', 5, 1, 2]])
 343
 344         self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [['a', 10, 9, 1],
 345                                                                       ['b', 15, 0, 14]])
 346         self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [['b', 15, 0, 15]])
 347         self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [['b', 15, 1, 14],
 348                                                                        ['c', 5, 0, 1]])
 349
 350     class MockStreamReader(object):
 351         def __init__(self, content):
 352             self.content = content
 353             self.num_retries = 0
 354
 355         def readfrom(self, start, size, num_retries=0):
 356             return self.content[start:start+size]
 357
 358     def test_file_stream(self):
 359         content = 'abcdefghijklmnopqrstuvwxyz0123456789'
 360         msr = self.MockStreamReader(content)
 361         segments = [[0, 10, 0],
 362                     [10, 15, 10],
 363                     [25, 5, 25]]
 364
 365         sfr = arvados.StreamFileReader(msr, segments, "test")
 366
 367         self.assertEqual(sfr.name(), "test")
 368         self.assertEqual(sfr.size(), 30)
 369
 370         self.assertEqual(sfr.readfrom(0, 30), content[0:30])
 371         self.assertEqual(sfr.readfrom(2, 30), content[2:30])
 372
 373         self.assertEqual(sfr.readfrom(2, 8), content[2:10])
 374         self.assertEqual(sfr.readfrom(0, 10), content[0:10])
 375
 376         self.assertEqual(sfr.tell(), 0)
 377         self.assertEqual(sfr.read(5), content[0:5])
 378         self.assertEqual(sfr.tell(), 5)
 379         self.assertEqual(sfr.read(5), content[5:10])
 380         self.assertEqual(sfr.tell(), 10)
 381         self.assertEqual(sfr.read(5), content[10:15])
 382         self.assertEqual(sfr.tell(), 15)
 383         self.assertEqual(sfr.read(5), content[15:20])
 384         self.assertEqual(sfr.tell(), 20)
 385         self.assertEqual(sfr.read(5), content[20:25])
 386         self.assertEqual(sfr.tell(), 25)
 387         self.assertEqual(sfr.read(5), content[25:30])
 388         self.assertEqual(sfr.tell(), 30)
 389         self.assertEqual(sfr.read(5), '')
 390         self.assertEqual(sfr.tell(), 30)
 391
 392         segments = [[26, 10, 0],
 393                     [0, 15, 10],
 394                     [15, 5, 25]]
 395
 396         sfr = arvados.StreamFileReader(msr, segments, "test")
 397
 398         self.assertEqual(sfr.size(), 30)
 399
 400         self.assertEqual(sfr.readfrom(0, 30), content[26:36] + content[0:20])
 401         self.assertEqual(sfr.readfrom(2, 30), content[28:36] + content[0:20])
 402
 403         self.assertEqual(sfr.readfrom(2, 8), content[28:36])
 404         self.assertEqual(sfr.readfrom(0, 10), content[26:36])
 405
 406         self.assertEqual(sfr.tell(), 0)
 407         self.assertEqual(sfr.read(5), content[26:31])
 408         self.assertEqual(sfr.tell(), 5)
 409         self.assertEqual(sfr.read(5), content[31:36])
 410         self.assertEqual(sfr.tell(), 10)
 411         self.assertEqual(sfr.read(5), content[0:5])
 412         self.assertEqual(sfr.tell(), 15)
 413         self.assertEqual(sfr.read(5), content[5:10])
 414         self.assertEqual(sfr.tell(), 20)
 415         self.assertEqual(sfr.read(5), content[10:15])
 416         self.assertEqual(sfr.tell(), 25)
 417         self.assertEqual(sfr.read(5), content[15:20])
 418         self.assertEqual(sfr.tell(), 30)
 419         self.assertEqual(sfr.read(5), '')
 420         self.assertEqual(sfr.tell(), 30)
 421
 422
 423     class MockKeep(object):
 424         def __init__(self, content, num_retries=0):
 425             self.content = content
 426
 427         def get(self, locator, num_retries=0):
 428             return self.content[locator]
 429
 430     def test_stream_reader(self):
 431         keepblocks = {'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': 'abcdefghij',
 432                       'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': 'klmnopqrstuvwxy',
 433                       'cccccccccccccccccccccccccccccccc+5': 'z0123'}
 434         mk = self.MockKeep(keepblocks)
 435
 436         sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk)
 437
 438         content = 'abcdefghijklmnopqrstuvwxyz0123456789'
 439
 440         self.assertEqual(sr.readfrom(0, 30), content[0:30])
 441         self.assertEqual(sr.readfrom(2, 30), content[2:30])
 442
 443         self.assertEqual(sr.readfrom(2, 8), content[2:10])
 444         self.assertEqual(sr.readfrom(0, 10), content[0:10])
 445
 446         self.assertEqual(sr.readfrom(0, 5), content[0:5])
 447         self.assertEqual(sr.readfrom(5, 5), content[5:10])
 448         self.assertEqual(sr.readfrom(10, 5), content[10:15])
 449         self.assertEqual(sr.readfrom(15, 5), content[15:20])
 450         self.assertEqual(sr.readfrom(20, 5), content[20:25])
 451         self.assertEqual(sr.readfrom(25, 5), content[25:30])
 452         self.assertEqual(sr.readfrom(30, 5), '')
 453
 454     def test_file_reader(self):
 455         keepblocks = {'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': 'abcdefghij',
 456                       'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': 'klmnopqrstuvwxy',
 457                       'cccccccccccccccccccccccccccccccc+5': 'z0123'}
 458         mk = self.MockKeep(keepblocks)
 459
 460         sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:10:foo", "15:10:foo"], mk)
 461
 462         content = 'abcdefghijpqrstuvwxy'
 463
 464         f = sr.files()["foo"]
 465
 466         # f.read() calls will be aligned on block boundaries (as a
 467         # result of ticket #3663).
 468
 469         f.seek(0)
 470         self.assertEqual(f.read(20), content[0:10])
 471
 472         f.seek(0)
 473         self.assertEqual(f.read(6), content[0:6])
 474         self.assertEqual(f.read(6), content[6:10])
 475         self.assertEqual(f.read(6), content[10:16])
 476         self.assertEqual(f.read(6), content[16:20])
 477
 478     def test_extract_file(self):
 479         m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
 480 . 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt
 481 . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt
 482 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt
 483 . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt"""
 484
 485         m2 = arvados.CollectionReader(m1, self.api_client)
 486
 487         self.assertEqual(m2.manifest_text(),
 488                          ". 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")
 489
 490         self.assertEqual(arvados.CollectionReader(m1, self.api_client).all_streams()[0].files()['md5sum.txt'].as_manifest(),
 491                          ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n")
 492         self.assertEqual(arvados.CollectionReader(m1, self.api_client).all_streams()[0].files()['md6sum.txt'].as_manifest(),
 493                          ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n")
 494         self.assertEqual(arvados.CollectionReader(m1, self.api_client).all_streams()[0].files()['md7sum.txt'].as_manifest(),
 495                          ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n")
 496         self.assertEqual(arvados.CollectionReader(m1, self.api_client).all_streams()[0].files()['md9sum.txt'].as_manifest(),
 497                          ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n")
 498
 499     def test_write_directory_tree(self):
 500         cwriter = arvados.CollectionWriter(self.api_client)
 501         cwriter.write_directory_tree(self.build_directory_tree(
 502                 ['basefile', 'subdir/subfile']))
 503         self.assertEqual(cwriter.manifest_text(),
 504                          """. c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 505 ./subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 506
 507     def test_write_named_directory_tree(self):
 508         cwriter = arvados.CollectionWriter(self.api_client)
 509         cwriter.write_directory_tree(self.build_directory_tree(
 510                 ['basefile', 'subdir/subfile']), 'root')
 511         self.assertEqual(
 512             cwriter.manifest_text(),
 513             """./root c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
 514 ./root/subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
 515
 516     def test_write_directory_tree_in_one_stream(self):
 517         cwriter = arvados.CollectionWriter(self.api_client)
 518         cwriter.write_directory_tree(self.build_directory_tree(
 519                 ['basefile', 'subdir/subfile']), max_manifest_depth=0)
 520         self.assertEqual(cwriter.manifest_text(),
 521                          """. 4ace875ffdc6824a04950f06858f4465+22 0:8:basefile
 522 ./subdir 4ace875ffdc6824a04950f06858f4465+22 8:14:subfile\n""")
 523
 524     def test_write_directory_tree_with_limited_recursion(self):
 525         cwriter = arvados.CollectionWriter(self.api_client)
 526         cwriter.write_directory_tree(
 527             self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
 528             max_manifest_depth=1)
 529         self.assertEqual(cwriter.manifest_text(),
 530                          """. bd19836ddb62c11c55ab251ccaca5645+2 0:2:f1
 531 ./d1 50170217e5b04312024aa5cd42934494+13 8:5:f2
 532 ./d1/d2 50170217e5b04312024aa5cd42934494+13 0:8:f3\n""")
 533
 534     def test_write_one_file(self):
 535         cwriter = arvados.CollectionWriter(self.api_client)
 536         with self.make_test_file() as testfile:
 537             cwriter.write_file(testfile.name)
 538             self.assertEqual(
 539                 cwriter.manifest_text(),
 540                 ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:{}\n".format(
 541                     os.path.basename(testfile.name)))
 542
 543     def test_write_named_file(self):
 544         cwriter = arvados.CollectionWriter(self.api_client)
 545         with self.make_test_file() as testfile:
 546             cwriter.write_file(testfile.name, 'foo')
 547             self.assertEqual(cwriter.manifest_text(),
 548                              ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:foo\n")
 549
 550     def test_write_multiple_files(self):
 551         cwriter = arvados.CollectionWriter(self.api_client)
 552         for letter in 'ABC':
 553             with self.make_test_file(letter) as testfile:
 554                 cwriter.write_file(testfile.name, letter)
 555         self.assertEqual(
 556             cwriter.manifest_text(),
 557             ". 902fbdd2b1df0c4f70b4a5d23525e932+3 0:1:A 1:1:B 2:1:C\n")
 558
 559     def test_basic_resume(self):
 560         cwriter = TestResumableWriter()
 561         with self.make_test_file() as testfile:
 562             cwriter.write_file(testfile.name, 'test')
 563             resumed = TestResumableWriter.from_state(cwriter.current_state())
 564         self.assertEquals(cwriter.manifest_text(), resumed.manifest_text(),
 565                           "resumed CollectionWriter had different manifest")
 566
 567     def test_resume_fails_when_missing_dependency(self):
 568         cwriter = TestResumableWriter()
 569         with self.make_test_file() as testfile:
 570             cwriter.write_file(testfile.name, 'test')
 571         self.assertRaises(arvados.errors.StaleWriterStateError,
 572                           TestResumableWriter.from_state,
 573                           cwriter.current_state())
 574
 575     def test_resume_fails_when_dependency_mtime_changed(self):
 576         cwriter = TestResumableWriter()
 577         with self.make_test_file() as testfile:
 578             cwriter.write_file(testfile.name, 'test')
 579             os.utime(testfile.name, (0, 0))
 580             self.assertRaises(arvados.errors.StaleWriterStateError,
 581                               TestResumableWriter.from_state,
 582                               cwriter.current_state())
 583
 584     def test_resume_fails_when_dependency_is_nonfile(self):
 585         cwriter = TestResumableWriter()
 586         cwriter.write_file('/dev/null', 'empty')
 587         self.assertRaises(arvados.errors.StaleWriterStateError,
 588                           TestResumableWriter.from_state,
 589                           cwriter.current_state())
 590
 591     def test_resume_fails_when_dependency_size_changed(self):
 592         cwriter = TestResumableWriter()
 593         with self.make_test_file() as testfile:
 594             cwriter.write_file(testfile.name, 'test')
 595             orig_mtime = os.fstat(testfile.fileno()).st_mtime
 596             testfile.write('extra')
 597             testfile.flush()
 598             os.utime(testfile.name, (orig_mtime, orig_mtime))
 599             self.assertRaises(arvados.errors.StaleWriterStateError,
 600                               TestResumableWriter.from_state,
 601                               cwriter.current_state())
 602
 603     def test_resume_fails_with_expired_locator(self):
 604         cwriter = TestResumableWriter()
 605         state = cwriter.current_state()
 606         # Add an expired locator to the state.
 607         state['_current_stream_locators'].append(''.join([
 608                     'a' * 32, '+1+A', 'b' * 40, '@', '10000000']))
 609         self.assertRaises(arvados.errors.StaleWriterStateError,
 610                           TestResumableWriter.from_state, state)
 611
 612     def test_arbitrary_objects_not_resumable(self):
 613         cwriter = TestResumableWriter()
 614         with open('/dev/null') as badfile:
 615             self.assertRaises(arvados.errors.AssertionError,
 616                               cwriter.write_file, badfile)
 617
 618     def test_arbitrary_writes_not_resumable(self):
 619         cwriter = TestResumableWriter()
 620         self.assertRaises(arvados.errors.AssertionError,
 621                           cwriter.write, "badtext")
 622
 623
 624 class CollectionTestMixin(object):
 625     PROXY_RESPONSE = {
 626         'items_available': 1,
 627         'items': [{
 628                 'uuid': 'zzzzz-bi6l4-mockproxy012345',
 629                 'owner_uuid': 'zzzzz-tpzed-mockowner012345',
 630                 'service_host': tutil.TEST_HOST,
 631                 'service_port': 65535,
 632                 'service_ssl_flag': True,
 633                 'service_type': 'proxy',
 634                 }]}
 635     API_COLLECTIONS = run_test_server.fixture('collections')
 636     DEFAULT_COLLECTION = API_COLLECTIONS['foo_file']
 637     DEFAULT_DATA_HASH = DEFAULT_COLLECTION['portable_data_hash']
 638     DEFAULT_MANIFEST = DEFAULT_COLLECTION['manifest_text']
 639     DEFAULT_UUID = DEFAULT_COLLECTION['uuid']
 640
 641     def _mock_api_call(self, mock_method, code, body):
 642         mock_method = mock_method().execute
 643         if code == 200:
 644             mock_method.return_value = body
 645         else:
 646             mock_method.side_effect = arvados.errors.ApiError(
 647                 tutil.fake_httplib2_response(code), "{}")
 648
 649     def mock_keep_services(self, api_mock, code, body):
 650         self._mock_api_call(api_mock.keep_services().accessible, code, body)
 651
 652     def api_client_mock(self, code=200):
 653         client = mock.MagicMock(name='api_client')
 654         self.mock_keep_services(client, code, self.PROXY_RESPONSE)
 655         return client
 656
 657
 658 @tutil.skip_sleep
 659 class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin):
 660     def mock_get_collection(self, api_mock, code, body):
 661         body = self.API_COLLECTIONS.get(body)
 662         self._mock_api_call(api_mock.collections().get, code, body)
 663
 664     def api_client_mock(self, code=200):
 665         client = super(CollectionReaderTestCase, self).api_client_mock(code)
 666         self.mock_get_collection(client, code, 'foo_file')
 667         return client
 668
 669     def test_init_no_default_retries(self):
 670         client = self.api_client_mock(200)
 671         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 672         reader.manifest_text()
 673         client.collections().get().execute.assert_called_with(num_retries=0)
 674
 675     def test_uuid_init_success(self):
 676         client = self.api_client_mock(200)
 677         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 678                                           num_retries=3)
 679         self.assertEqual(self.DEFAULT_COLLECTION['manifest_text'],
 680                          reader.manifest_text())
 681         client.collections().get().execute.assert_called_with(num_retries=3)
 682
 683     def test_uuid_init_failure_raises_api_error(self):
 684         client = self.api_client_mock(500)
 685         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
 686         with self.assertRaises(arvados.errors.ApiError):
 687             reader.manifest_text()
 688
 689     def test_locator_init(self):
 690         client = self.api_client_mock(200)
 691         # Ensure Keep will not return anything if asked.
 692         with tutil.mock_responses(None, 404):
 693             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 694                                               api_client=client)
 695             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 696
 697     def test_locator_init_falls_back_to_keep(self):
 698         # Reading manifests from Keep is deprecated.  Feel free to
 699         # remove this test when we remove the fallback.
 700         client = self.api_client_mock(200)
 701         self.mock_get_collection(client, 404, None)
 702         with tutil.mock_responses(self.DEFAULT_MANIFEST, 200):
 703             reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
 704                                               api_client=client, num_retries=3)
 705             self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
 706
 707     def test_init_num_retries_propagated(self):
 708         # More of an integration test...
 709         client = self.api_client_mock(200)
 710         reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
 711                                           num_retries=3)
 712         with tutil.mock_responses('foo', 500, 500, 200):
 713             self.assertEqual('foo',
 714                              ''.join(f.read(9) for f in reader.all_files()))
 715
 716
 717 @tutil.skip_sleep
 718 class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin):
 719     def mock_keep(self, body, *codes, **headers):
 720         headers.setdefault('x-keep-replicas-stored', 2)
 721         return tutil.mock_responses(body, *codes, **headers)
 722
 723     def foo_writer(self, **kwargs):
 724         api_client = self.api_client_mock()
 725         writer = arvados.CollectionWriter(api_client, **kwargs)
 726         writer.start_new_file('foo')
 727         writer.write('foo')
 728         return writer
 729
 730     def test_write_whole_collection(self):
 731         writer = self.foo_writer()
 732         with self.mock_keep(self.DEFAULT_DATA_HASH, 200, 200):
 733             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 734
 735     def test_write_no_default(self):
 736         writer = self.foo_writer()
 737         with self.mock_keep(None, 500):
 738             with self.assertRaises(arvados.errors.KeepWriteError):
 739                 writer.finish()
 740
 741     def test_write_whole_collection_through_retries(self):
 742         writer = self.foo_writer(num_retries=2)
 743         with self.mock_keep(self.DEFAULT_DATA_HASH,
 744                             500, 500, 200, 500, 500, 200):
 745             self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
 746
 747     def test_flush_data_retries(self):
 748         writer = self.foo_writer(num_retries=2)
 749         foo_hash = self.DEFAULT_MANIFEST.split()[1]
 750         with self.mock_keep(foo_hash, 500, 200):
 751             writer.flush_data()
 752         self.assertEqual(self.DEFAULT_MANIFEST, writer.manifest_text())
 753
 754
 755 if __name__ == '__main__':
 756     unittest.main()