1 # Copyright (C) The Arvados Authors. All rights reserved.
3 # SPDX-License-Identifier: Apache-2.0
5 from __future__ import absolute_import
6 from builtins import hex
7 from builtins import str
8 from builtins import range
9 from builtins import object
20 from arvados._ranges import Range
21 from arvados.keep import KeepLocator
22 from arvados.collection import Collection, CollectionReader
23 from arvados.arvfile import ArvadosFile, ArvadosFileReader
25 from . import arvados_testutil as tutil
26 from .test_stream import StreamFileReaderTestCase, StreamRetryTestMixin
28 class ArvadosFileWriterTestCase(unittest.TestCase):
29 class MockKeep(object):
30 def __init__(self, blocks):
33 def get(self, locator, num_retries=0):
34 self.requests.append(locator)
35 return self.blocks.get(locator)
36 def get_from_cache(self, locator):
37 self.requests.append(locator)
38 return self.blocks.get(locator)
39 def put(self, data, num_retries=None, copies=None):
40 pdh = tutil.str_keep_locator(data)
41 self.blocks[pdh] = bytes(data)
44 class MockApi(object):
45 def __init__(self, b, r):
48 self._schema = ArvadosFileWriterTestCase.MockApi.MockSchema()
50 class MockSchema(object):
52 self.schemas = {'Collection': {'properties': {'replication_desired': {'type':'integer'}}}}
53 class MockCollections(object):
54 def __init__(self, b, r):
57 class Execute(object):
58 def __init__(self, r):
60 def execute(self, num_retries=None):
62 def create(self, ensure_unique_name=False, body=None):
64 raise Exception("Body %s does not match expectation %s" % (body, self.body))
65 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
66 def update(self, uuid=None, body=None):
67 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response)
68 def collections(self):
69 return ArvadosFileWriterTestCase.MockApi.MockCollections(self.body, self.response)
72 def test_truncate(self):
73 keep = ArvadosFileWriterTestCase.MockKeep({
74 "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
76 api = ArvadosFileWriterTestCase.MockApi({
77 "name": "test_truncate",
78 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
79 "replication_desired": None,
81 "uuid": "zzzzz-4zz18-mockcollection0",
82 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
83 "portable_data_hash":"7fcd0eaac3aad4c31a6a0e756475da92+52",
85 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
86 api_client=api, keep_client=keep) as c:
87 writer = c.open("count.txt", "rb+")
88 self.assertEqual(writer.size(), 10)
89 self.assertEqual(b"0123456789", writer.read(12))
93 # Make sure reading off the end doesn't break
94 self.assertEqual(b"", writer.read(12))
96 self.assertEqual(writer.size(), 8)
97 writer.seek(0, os.SEEK_SET)
98 self.assertEqual(b"01234567", writer.read(12))
100 self.assertIsNone(c.manifest_locator())
101 self.assertTrue(c.modified())
102 c.save_new("test_truncate")
103 self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
104 self.assertFalse(c.modified())
107 def test_truncate2(self):
108 keep = ArvadosFileWriterTestCase.MockKeep({
109 "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
111 api = ArvadosFileWriterTestCase.MockApi({
112 "name": "test_truncate2",
113 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n",
114 "replication_desired": None,
116 "uuid": "zzzzz-4zz18-mockcollection0",
117 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n",
118 "portable_data_hash": "272da898abdf86ddc71994835e3155f8+95",
120 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
121 api_client=api, keep_client=keep) as c:
122 writer = c.open("count.txt", "rb+")
123 self.assertEqual(writer.size(), 10)
124 self.assertEqual(b"0123456789", writer.read(12))
129 self.assertEqual(writer.size(), 12)
130 writer.seek(0, os.SEEK_SET)
131 self.assertEqual(b"0123456789\x00\x00", writer.read(12))
133 self.assertIsNone(c.manifest_locator())
134 self.assertTrue(c.modified())
135 c.save_new("test_truncate2")
136 self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
137 self.assertFalse(c.modified())
139 def test_truncate3(self):
140 keep = ArvadosFileWriterTestCase.MockKeep({
141 "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
142 "a925576942e94b2ef57a066101b48876+10": b"abcdefghij",
144 api = ArvadosFileWriterTestCase.MockApi({
145 "name": "test_truncate",
146 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
147 "replication_desired": None,
149 "uuid": "zzzzz-4zz18-mockcollection0",
150 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
151 "portable_data_hash": "7fcd0eaac3aad4c31a6a0e756475da92+52",
153 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n',
154 api_client=api, keep_client=keep) as c:
155 writer = c.open("count.txt", "rb+")
156 self.assertEqual(writer.size(), 20)
157 self.assertEqual(b"0123456789ab", writer.read(12))
158 self.assertEqual(12, writer.tell())
162 # Make sure reading off the end doesn't break
163 self.assertEqual(12, writer.tell())
164 self.assertEqual(b"", writer.read(12))
166 self.assertEqual(writer.size(), 8)
167 self.assertEqual(2, writer.seek(-10, os.SEEK_CUR))
168 self.assertEqual(b"234567", writer.read(12))
170 self.assertIsNone(c.manifest_locator())
171 self.assertTrue(c.modified())
172 c.save_new("test_truncate")
173 self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
174 self.assertFalse(c.modified())
178 def test_write_to_end(self):
179 keep = ArvadosFileWriterTestCase.MockKeep({
180 "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
182 api = ArvadosFileWriterTestCase.MockApi({
183 "name": "test_append",
184 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
185 "replication_desired": None,
187 "uuid": "zzzzz-4zz18-mockcollection0",
188 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
189 "portable_data_hash": "c5c3af76565c8efb6a806546bcf073f3+88",
191 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
192 api_client=api, keep_client=keep) as c:
193 writer = c.open("count.txt", "rb+")
194 self.assertEqual(writer.size(), 10)
196 self.assertEqual(5, writer.seek(5, os.SEEK_SET))
197 self.assertEqual(b"56789", writer.read(8))
199 writer.seek(10, os.SEEK_SET)
201 self.assertEqual(writer.size(), 13)
203 writer.seek(5, os.SEEK_SET)
204 self.assertEqual(b"56789foo", writer.read(8))
206 self.assertIsNone(c.manifest_locator())
207 self.assertTrue(c.modified())
208 self.assertIsNone(keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
210 c.save_new("test_append")
211 self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
212 self.assertFalse(c.modified())
213 self.assertEqual(b"foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
216 def test_append(self):
217 keep = ArvadosFileWriterTestCase.MockKeep({
218 "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
220 for (mode, convert) in (
221 ('a+', lambda data: data.decode(encoding='utf-8')),
222 ('at+', lambda data: data.decode(encoding='utf-8')),
223 ('ab+', lambda data: data)):
224 c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep)
225 writer = c.open("count.txt", mode)
226 self.assertEqual(writer.read(20), convert(b"0123456789"))
228 writer.seek(0, os.SEEK_SET)
229 writer.write(convert(b"hello"))
230 self.assertEqual(writer.read(), convert(b""))
232 writer.seek(-5, os.SEEK_CUR)
233 self.assertEqual(writer.read(3), convert(b"hel"))
234 self.assertEqual(writer.read(), convert(b"lo"))
236 with self.assertRaises(IOError):
237 writer.seek(-5, os.SEEK_CUR)
238 with self.assertRaises(IOError):
239 writer.seek(-3, os.SEEK_END)
240 writer.seek(0, os.SEEK_SET)
242 self.assertEqual(7, writer.tell())
243 self.assertEqual(7, writer.seek(7, os.SEEK_SET))
245 writer.seek(0, os.SEEK_SET)
246 self.assertEqual(writer.read(), convert(b"0123456789hello"))
249 writer.write(convert(b"world"))
250 self.assertEqual(writer.read(), convert(b""))
252 self.assertEqual(writer.read(), convert(b"0123456789helloworld"))
254 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.portable_manifest_text())
256 def test_write_at_beginning(self):
257 keep = ArvadosFileWriterTestCase.MockKeep({
258 "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
260 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
261 keep_client=keep) as c:
262 writer = c.open("count.txt", "rb+")
263 self.assertEqual(b"0123456789", writer.readfrom(0, 13))
264 writer.seek(0, os.SEEK_SET)
266 self.assertEqual(writer.size(), 10)
267 self.assertEqual(b"foo3456789", writer.readfrom(0, 13))
268 self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", c.portable_manifest_text())
270 def test_write_empty(self):
271 keep = ArvadosFileWriterTestCase.MockKeep({})
272 with Collection(keep_client=keep) as c:
273 writer = c.open("count.txt", "wb")
274 self.assertEqual(writer.size(), 0)
275 self.assertEqual(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n", c.portable_manifest_text())
277 def test_save_manifest_text(self):
278 keep = ArvadosFileWriterTestCase.MockKeep({})
279 with Collection(keep_client=keep) as c:
280 writer = c.open("count.txt", "wb")
281 writer.write(b"0123456789")
282 self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
283 self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
285 self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.save_new(create_collection_record=False))
286 self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
288 def test_get_manifest_text_commits(self):
289 keep = ArvadosFileWriterTestCase.MockKeep({})
290 with Collection(keep_client=keep) as c:
291 writer = c.open("count.txt", "wb")
292 writer.write("0123456789")
293 self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
294 self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
295 self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text())
296 self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
299 def test_write_in_middle(self):
300 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
301 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
302 keep_client=keep) as c:
303 writer = c.open("count.txt", "rb+")
304 self.assertEqual(b"0123456789", writer.readfrom(0, 13))
305 writer.seek(3, os.SEEK_SET)
307 self.assertEqual(writer.size(), 10)
308 self.assertEqual(b"012foo6789", writer.readfrom(0, 13))
309 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.portable_manifest_text())
311 def test_write_at_end(self):
312 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
313 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
314 keep_client=keep) as c:
315 writer = c.open("count.txt", "rb+")
316 self.assertEqual(b"0123456789", writer.readfrom(0, 13))
317 writer.seek(7, os.SEEK_SET)
319 self.assertEqual(writer.size(), 10)
320 self.assertEqual(b"0123456foo", writer.readfrom(0, 13))
321 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text())
323 def test_write_across_segment_boundary(self):
324 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
325 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
326 keep_client=keep) as c:
327 writer = c.open("count.txt", "rb+")
328 self.assertEqual(b"012345678901234", writer.readfrom(0, 15))
329 writer.seek(7, os.SEEK_SET)
330 writer.write("foobar")
331 self.assertEqual(writer.size(), 20)
332 self.assertEqual(b"0123456foobar34", writer.readfrom(0, 15))
333 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text())
335 def test_write_across_several_segments(self):
336 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789"})
337 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
338 keep_client=keep) as c:
339 writer = c.open("count.txt", "rb+")
340 self.assertEqual(b"012301230123", writer.readfrom(0, 15))
341 writer.seek(2, os.SEEK_SET)
342 writer.write("abcdefg")
343 self.assertEqual(writer.size(), 12)
344 self.assertEqual(b"01abcdefg123", writer.readfrom(0, 15))
345 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text())
347 def test_write_large(self):
348 keep = ArvadosFileWriterTestCase.MockKeep({})
349 api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
350 "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
351 "replication_desired":None},
352 {"uuid":"zzzzz-4zz18-mockcollection0",
353 "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
354 "portable_data_hash":"9132ca8e3f671c76103a38f5bc24328c+108"})
355 with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
356 api_client=api, keep_client=keep) as c:
357 writer = c.open("count.txt", "rb+")
358 text = "0123456789" * 100
359 for b in range(0, 100000):
361 self.assertEqual(writer.size(), 100000000)
363 self.assertIsNone(c.manifest_locator())
364 self.assertTrue(c.modified())
365 c.save_new("test_write_large")
366 self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
367 self.assertFalse(c.modified())
370 def test_large_write(self):
371 keep = ArvadosFileWriterTestCase.MockKeep({})
372 api = ArvadosFileWriterTestCase.MockApi({}, {})
373 with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
374 api_client=api, keep_client=keep) as c:
375 writer = c.open("count.txt", "rb+")
376 self.assertEqual(writer.size(), 0)
380 text = "0123456789" * 9999999
382 self.assertEqual(writer.size(), 100000000)
384 self.assertEqual(c.manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n")
386 def test_sparse_write(self):
387 keep = ArvadosFileWriterTestCase.MockKeep({})
388 api = ArvadosFileWriterTestCase.MockApi({}, {})
389 with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
390 api_client=api, keep_client=keep) as c:
391 writer = c.open("count.txt", "rb+")
392 self.assertEqual(writer.size(), 0)
397 self.assertEqual(writer.size(), 12)
398 writer.seek(0, os.SEEK_SET)
399 self.assertEqual(writer.read(), b"\x00\x00"+text)
401 self.assertEqual(c.manifest_text(), ". 7f614da9329cd3aebf59b91aadc30bf0+67108864 781e5e245d69b566979b86e28d23f2c7+10 0:2:count.txt 67108864:10:count.txt\n")
404 def test_sparse_write2(self):
405 keep = ArvadosFileWriterTestCase.MockKeep({})
406 api = ArvadosFileWriterTestCase.MockApi({}, {})
407 with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
408 api_client=api, keep_client=keep) as c:
409 writer = c.open("count.txt", "rb+")
410 self.assertEqual(writer.size(), 0)
413 writer.seek((arvados.config.KEEP_BLOCK_SIZE*2) + 2)
415 self.assertEqual(writer.size(), (arvados.config.KEEP_BLOCK_SIZE*2) + 12)
416 writer.seek(0, os.SEEK_SET)
418 self.assertEqual(c.manifest_text(), ". 7f614da9329cd3aebf59b91aadc30bf0+67108864 781e5e245d69b566979b86e28d23f2c7+10 0:67108864:count.txt 0:67108864:count.txt 0:2:count.txt 67108864:10:count.txt\n")
421 def test_sparse_write3(self):
422 keep = ArvadosFileWriterTestCase.MockKeep({})
423 api = ArvadosFileWriterTestCase.MockApi({}, {})
424 for r in [[0, 1, 2, 3, 4], [4, 3, 2, 1, 0], [3, 2, 0, 4, 1]]:
425 with Collection() as c:
426 writer = c.open("count.txt", "rb+")
427 self.assertEqual(writer.size(), 0)
432 writer.write(w.encode())
434 self.assertEqual(writer.read(), b"00000000001111111111222222222233333333334444444444")
436 def test_sparse_write4(self):
437 keep = ArvadosFileWriterTestCase.MockKeep({})
438 api = ArvadosFileWriterTestCase.MockApi({}, {})
439 for r in [[0, 1, 2, 4], [4, 2, 1, 0], [2, 0, 4, 1]]:
440 with Collection() as c:
441 writer = c.open("count.txt", "rb+")
442 self.assertEqual(writer.size(), 0)
447 writer.write(w.encode())
449 self.assertEqual(writer.read(), b"000000000011111111112222222222\x00\x00\x00\x00\x00\x00\x00\x00\x00\x004444444444")
452 def test_rewrite_on_empty_file(self):
453 keep = ArvadosFileWriterTestCase.MockKeep({})
454 with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
455 keep_client=keep) as c:
456 writer = c.open("count.txt", "rb+")
457 for b in range(0, 10):
458 writer.seek(0, os.SEEK_SET)
459 writer.write("0123456789")
461 self.assertEqual(writer.size(), 10)
462 self.assertEqual(b"0123456789", writer.readfrom(0, 20))
463 self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.portable_manifest_text())
465 self.assertEqual(writer.size(), 10)
466 self.assertEqual(b"0123456789", writer.readfrom(0, 20))
467 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.portable_manifest_text())
469 def test_rewrite_append_existing_file(self):
470 keep = ArvadosFileWriterTestCase.MockKeep({
471 "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
473 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
474 keep_client=keep) as c:
475 writer = c.open("count.txt", "rb+")
476 for b in range(0, 10):
477 writer.seek(10, os.SEEK_SET)
478 writer.write("abcdefghij")
480 self.assertEqual(writer.size(), 20)
481 self.assertEqual(b"0123456789abcdefghij", writer.readfrom(0, 20))
482 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.portable_manifest_text())
484 writer.arvadosfile.flush()
485 self.assertEqual(writer.size(), 20)
486 self.assertEqual(b"0123456789abcdefghij", writer.readfrom(0, 20))
487 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.portable_manifest_text())
489 def test_rewrite_over_existing_file(self):
490 keep = ArvadosFileWriterTestCase.MockKeep({
491 "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
493 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
494 keep_client=keep) as c:
495 writer = c.open("count.txt", "rb+")
496 for b in range(0, 10):
497 writer.seek(5, os.SEEK_SET)
498 writer.write("abcdefghij")
500 self.assertEqual(writer.size(), 15)
501 self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20))
502 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.portable_manifest_text())
504 writer.arvadosfile.flush()
506 self.assertEqual(writer.size(), 15)
507 self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20))
508 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.portable_manifest_text())
510 def test_write_large_rewrite(self):
511 keep = ArvadosFileWriterTestCase.MockKeep({})
512 api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
513 "manifest_text": ". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n",
514 "replication_desired":None},
515 {"uuid":"zzzzz-4zz18-mockcollection0",
516 "manifest_text": ". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n",
517 "portable_data_hash":"217665c6b713e1b78dfba7ebd42344db+156"})
518 with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
519 api_client=api, keep_client=keep) as c:
520 writer = c.open("count.txt", "rb+")
521 text = b''.join([b"0123456789" for a in range(0, 100)])
522 for b in range(0, 100000):
524 writer.seek(0, os.SEEK_SET)
526 self.assertEqual(writer.size(), 100000000)
528 self.assertIsNone(c.manifest_locator())
529 self.assertTrue(c.modified())
530 c.save_new("test_write_large")
531 self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
532 self.assertFalse(c.modified())
534 def test_create(self):
535 keep = ArvadosFileWriterTestCase.MockKeep({})
536 api = ArvadosFileWriterTestCase.MockApi({
537 "name":"test_create",
538 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
539 "replication_desired":None,
541 "uuid":"zzzzz-4zz18-mockcollection0",
542 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
543 "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51",
545 with Collection(api_client=api, keep_client=keep) as c:
546 writer = c.open("count.txt", "wb+")
547 self.assertEqual(writer.size(), 0)
548 writer.write("01234567")
549 self.assertEqual(writer.size(), 8)
551 self.assertIsNone(c.manifest_locator())
552 self.assertTrue(c.modified())
553 self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
554 c.save_new("test_create")
555 self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
556 self.assertFalse(c.modified())
557 self.assertEqual(b"01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
560 def test_create_subdir(self):
561 keep = ArvadosFileWriterTestCase.MockKeep({})
562 api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
563 "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
564 "replication_desired":None},
565 {"uuid":"zzzzz-4zz18-mockcollection0",
566 "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
567 "portable_data_hash":"1b02aaa62528d28a5be41651cbb9d7c7+59"})
568 with Collection(api_client=api, keep_client=keep) as c:
569 self.assertIsNone(c.api_response())
570 writer = c.open("foo/bar/count.txt", "wb+")
571 writer.write("01234567")
572 self.assertFalse(c.committed())
573 c.save_new("test_create")
574 self.assertTrue(c.committed())
575 self.assertEqual(c.api_response(), api.response)
577 def test_overwrite(self):
578 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
579 api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
580 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
581 "replication_desired":None},
582 {"uuid":"zzzzz-4zz18-mockcollection0",
583 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
584 "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51"})
585 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
586 api_client=api, keep_client=keep) as c:
587 writer = c.open("count.txt", "wb+")
588 self.assertEqual(writer.size(), 0)
589 writer.write("01234567")
590 self.assertEqual(writer.size(), 8)
592 self.assertIsNone(c.manifest_locator())
593 self.assertTrue(c.modified())
594 c.save_new("test_overwrite")
595 self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
596 self.assertFalse(c.modified())
598 def test_file_not_found(self):
599 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
600 with self.assertRaises(IOError):
601 writer = c.open("nocount.txt", "rb")
603 def test_cannot_open_directory(self):
604 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
605 with self.assertRaises(IOError):
606 writer = c.open(".", "rb")
608 def test_create_multiple(self):
609 keep = ArvadosFileWriterTestCase.MockKeep({})
610 api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
611 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
612 "replication_desired":None},
613 {"uuid":"zzzzz-4zz18-mockcollection0",
614 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
615 "portable_data_hash":"71e7bb6c00d31fc2b4364199fd97be08+102"})
616 with Collection(api_client=api, keep_client=keep) as c:
617 w1 = c.open("count1.txt", "wb")
618 w2 = c.open("count2.txt", "wb")
621 self.assertEqual(w1.size(), 8)
622 self.assertEqual(w2.size(), 8)
624 self.assertIsNone(c.manifest_locator())
625 self.assertTrue(c.modified())
626 self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
627 c.save_new("test_create_multiple")
628 self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
629 self.assertFalse(c.modified())
630 self.assertEqual(b"01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
633 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
634 class MockParent(object):
635 class MockBlockMgr(object):
636 def __init__(self, blocks, nocache):
638 self.nocache = nocache
640 def block_prefetch(self, loc):
643 def get_block_contents(self, loc, num_retries=0, cache_only=False):
644 if self.nocache and cache_only:
646 return self.blocks[loc]
648 def __init__(self, blocks, nocache):
650 self.nocache = nocache
651 self.lock = arvados.arvfile.NoopLock()
653 def root_collection(self):
656 def _my_block_manager(self):
657 return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
660 def make_count_reader(self, nocache=False):
664 for d in [b'01234', b'34567', b'67890']:
665 loc = tutil.str_keep_locator(d)
667 stream.append(Range(loc, n, len(d)))
669 af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), "count.txt", stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
670 return ArvadosFileReader(af, mode="rb")
672 def test_read_block_crossing_behavior(self):
673 # read() needs to return all the data requested if possible, even if it
674 # crosses uncached blocks: https://arvados.org/issues/5856
675 sfile = self.make_count_reader(nocache=True)
676 self.assertEqual(b'12345678', sfile.read(8))
678 def test_successive_reads(self):
679 # Override StreamFileReaderTestCase.test_successive_reads
680 sfile = self.make_count_reader(nocache=True)
681 self.assertEqual(b'1234', sfile.read(4))
682 self.assertEqual(b'5678', sfile.read(4))
683 self.assertEqual(b'9', sfile.read(4))
684 self.assertEqual(b'', sfile.read(4))
686 def test_tell_after_block_read(self):
687 # Override StreamFileReaderTestCase.test_tell_after_block_read
688 sfile = self.make_count_reader(nocache=True)
689 self.assertEqual(b'12345678', sfile.read(8))
690 self.assertEqual(8, sfile.tell())
692 def test_prefetch(self):
693 keep = ArvadosFileWriterTestCase.MockKeep({
694 "2e9ec317e197819358fbc43afca7d837+8": b"01234567",
695 "e8dc4081b13434b45189a720b77b6818+8": b"abcdefgh",
697 with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
698 r = c.open("count.txt", "rb")
699 self.assertEqual(b"0123", r.read(4))
700 self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
701 self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
703 def test__eq__from_manifest(self):
704 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
705 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
706 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
707 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
709 def test__eq__from_writes(self):
710 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
711 with Collection() as c2:
712 f = c2.open("count1.txt", "wb")
713 f.write("0123456789")
715 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
716 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
718 def test__ne__(self):
719 with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
720 with Collection() as c2:
721 f = c2.open("count1.txt", "wb")
722 f.write("1234567890")
724 self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
725 self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
728 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
729 def reader_for(self, coll_name, **kwargs):
733 for d in self.manifest_for(coll_name).split():
736 segments.append(Range(n, n, k.size))
737 stream.append(Range(d, n, k.size))
742 blockmanager = arvados.arvfile._BlockManager(self.keep_client())
743 blockmanager.prefetch_enabled = False
744 col = Collection(keep_client=self.keep_client(), block_manager=blockmanager)
745 af = ArvadosFile(col, "test",
748 kwargs.setdefault('mode', 'rb')
749 return ArvadosFileReader(af, **kwargs)
751 def read_for_test(self, reader, byte_count, **kwargs):
752 return reader.read(byte_count, **kwargs)
755 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
756 def read_for_test(self, reader, byte_count, **kwargs):
757 return reader.readfrom(0, byte_count, **kwargs)
760 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
761 def read_for_test(self, reader, byte_count, **kwargs):
762 return b''.join(reader.readall(**kwargs))
765 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
766 def read_for_test(self, reader, byte_count, **kwargs):
767 return b''.join(reader.readall_decompressed(**kwargs))
770 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
771 def read_for_test(self, reader, byte_count, **kwargs):
772 return ''.join(reader.readlines(**kwargs)).encode()
775 class ArvadosFileTestCase(unittest.TestCase):
776 def datetime_to_hex(self, dt):
777 return hex(int(time.mktime(dt.timetuple())))[2:]
779 def test_permission_expired(self):
780 base_manifest = ". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@{} 0:10:count.txt\n"
781 now = datetime.datetime.now()
782 a_week_ago = now - datetime.timedelta(days=7)
783 a_month_ago = now - datetime.timedelta(days=30)
784 a_week_from_now = now + datetime.timedelta(days=7)
785 with Collection(base_manifest.format(self.datetime_to_hex(a_week_from_now))) as c:
786 self.assertFalse(c.find('count.txt').permission_expired())
787 with Collection(base_manifest.format(self.datetime_to_hex(a_week_ago))) as c:
788 f = c.find('count.txt')
789 self.assertTrue(f.permission_expired())
790 self.assertTrue(f.permission_expired(a_week_from_now))
791 self.assertFalse(f.permission_expired(a_month_ago))
794 class BlockManagerTest(unittest.TestCase):
795 def test_bufferblock_append(self):
796 keep = ArvadosFileWriterTestCase.MockKeep({})
797 with arvados.arvfile._BlockManager(keep) as blockmanager:
798 bufferblock = blockmanager.alloc_bufferblock()
799 bufferblock.append("foo")
801 self.assertEqual(bufferblock.size(), 3)
802 self.assertEqual(bufferblock.buffer_view[0:3], b"foo")
803 self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
805 bufferblock.append("bar")
807 self.assertEqual(bufferblock.size(), 6)
808 self.assertEqual(bufferblock.buffer_view[0:6], b"foobar")
809 self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
811 bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
812 with self.assertRaises(arvados.errors.AssertionError):
813 bufferblock.append("bar")
815 def test_bufferblock_dup(self):
816 keep = ArvadosFileWriterTestCase.MockKeep({})
817 with arvados.arvfile._BlockManager(keep) as blockmanager:
818 bufferblock = blockmanager.alloc_bufferblock()
819 bufferblock.append("foo")
821 self.assertEqual(bufferblock.size(), 3)
822 self.assertEqual(bufferblock.buffer_view[0:3], b"foo")
823 self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
824 bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
826 bufferblock2 = blockmanager.dup_block(bufferblock, None)
827 self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
829 bufferblock2.append("bar")
831 self.assertEqual(bufferblock2.size(), 6)
832 self.assertEqual(bufferblock2.buffer_view[0:6], b"foobar")
833 self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
835 self.assertEqual(bufferblock.size(), 3)
836 self.assertEqual(bufferblock.buffer_view[0:3], b"foo")
837 self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
839 def test_bufferblock_get(self):
840 keep = ArvadosFileWriterTestCase.MockKeep({
841 "781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
843 with arvados.arvfile._BlockManager(keep) as blockmanager:
844 bufferblock = blockmanager.alloc_bufferblock()
845 bufferblock.append("foo")
847 self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), b"0123456789")
848 self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), b"foo")
850 def test_bufferblock_commit(self):
851 mockkeep = mock.MagicMock()
852 with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
853 bufferblock = blockmanager.alloc_bufferblock()
854 bufferblock.owner = mock.MagicMock(spec=arvados.arvfile.ArvadosFile)
855 def flush(sync=None):
856 blockmanager.commit_bufferblock(bufferblock, sync)
857 bufferblock.owner.flush.side_effect = flush
858 bufferblock.append("foo")
859 blockmanager.commit_all()
860 self.assertTrue(bufferblock.owner.flush.called)
861 self.assertTrue(mockkeep.put.called)
862 self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
863 self.assertIsNone(bufferblock.buffer_view)
865 def test_bufferblock_commit_pending(self):
867 mockkeep = mock.MagicMock()
868 mockkeep.put.side_effect = lambda x: time.sleep(1)
869 with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
870 bufferblock = blockmanager.alloc_bufferblock()
871 bufferblock.append("foo")
873 blockmanager.commit_bufferblock(bufferblock, False)
874 self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)
876 blockmanager.commit_bufferblock(bufferblock, True)
877 self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
880 def test_bufferblock_commit_with_error(self):
881 mockkeep = mock.MagicMock()
882 mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail")
883 with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
884 bufferblock = blockmanager.alloc_bufferblock()
885 bufferblock.owner = mock.MagicMock(spec=arvados.arvfile.ArvadosFile)
886 def flush(sync=None):
887 blockmanager.commit_bufferblock(bufferblock, sync)
888 bufferblock.owner.flush.side_effect = flush
889 bufferblock.append("foo")
890 with self.assertRaises(arvados.errors.KeepWriteError) as err:
891 blockmanager.commit_all()
892 self.assertTrue(bufferblock.owner.flush.called)
893 self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
894 self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.ERROR)