12 from arvados import ArvadosFile, ArvadosFileReader, Range, import_manifest, export_manifest, KeepLocator
13 from arvados.arvfile import SYNC_READONLY, SYNC_EXPLICIT
15 import arvados_testutil as tutil
16 from test_stream import StreamFileReaderTestCase, StreamRetryTestMixin
18 class ArvadosFileWriterTestCase(unittest.TestCase):
19 class MockKeep(object):
20 def __init__(self, blocks):
23 def get(self, locator, num_retries=0):
24 self.requests.append(locator)
25 return self.blocks.get(locator)
26 def get_from_cache(self, locator):
27 self.requests.append(locator)
28 return self.blocks.get(locator)
29 def put(self, data, num_retries=None):
30 pdh = "%s+%i" % (hashlib.md5(data).hexdigest(), len(data))
31 self.blocks[pdh] = str(data)
34 class MockApi(object):
35 def __init__(self, b, r):
38 class MockCollections(object):
39 def __init__(self, b, r):
42 class Execute(object):
43 def __init__(self, r):
45 def execute(self, num_retries=None):
47 def create(self, ensure_unique_name=False, body=None):
49 raise Exception("Body %s does not match expectation %s" % (body, self.b))
50 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.r)
51 def update(self, uuid=None, body=None):
52 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.r)
53 def collections(self):
54 return ArvadosFileWriterTestCase.MockApi.MockCollections(self.b, self.r)
57 def test_truncate(self):
58 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
59 api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate",
60 "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"},
61 {"uuid":"zzzzz-4zz18-mockcollection0"})
62 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
63 api_client=api, keep_client=keep) as c:
64 writer = c.open("count.txt", "r+")
65 self.assertEqual(writer.size(), 10)
67 self.assertEqual("56789", writer.read(8))
69 writer.seek(5, os.SEEK_SET)
70 self.assertEqual("567", writer.read(8))
72 self.assertEqual(None, c._manifest_locator)
73 self.assertEqual(True, c.modified())
74 c.save_new("test_truncate")
75 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
76 self.assertEqual(False, c.modified())
78 def test_append(self):
79 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
80 api = ArvadosFileWriterTestCase.MockApi({"name":"test_append",
81 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"},
82 {"uuid":"zzzzz-4zz18-mockcollection0"})
83 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
84 api_client=api, keep_client=keep) as c:
85 writer = c.open("count.txt", "r+")
86 writer.seek(5, os.SEEK_SET)
87 self.assertEqual("56789", writer.read(8))
88 writer.seek(10, os.SEEK_SET)
90 self.assertEqual(writer.size(), 13)
91 writer.seek(5, os.SEEK_SET)
92 self.assertEqual("56789foo", writer.read(8))
94 self.assertEqual(None, c._manifest_locator)
95 self.assertEqual(True, c.modified())
96 self.assertEqual(None, keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
97 c.save_new("test_append")
98 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
99 self.assertEqual(False, c.modified())
100 self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
102 def test_write0(self):
103 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
104 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
105 keep_client=keep) as c:
106 writer = c.open("count.txt", "r+")
107 self.assertEqual("0123456789", writer.readfrom(0, 13))
108 writer.seek(0, os.SEEK_SET)
110 self.assertEqual(writer.size(), 10)
111 self.assertEqual("foo3456789", writer.readfrom(0, 13))
112 self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", export_manifest(c))
114 def test_write1(self):
115 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
116 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
117 keep_client=keep) as c:
118 writer = c.open("count.txt", "r+")
119 self.assertEqual("0123456789", writer.readfrom(0, 13))
120 writer.seek(3, os.SEEK_SET)
122 self.assertEqual(writer.size(), 10)
123 self.assertEqual("012foo6789", writer.readfrom(0, 13))
124 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", export_manifest(c))
126 def test_write2(self):
127 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
128 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
129 keep_client=keep) as c:
130 writer = c.open("count.txt", "r+")
131 self.assertEqual("0123456789", writer.readfrom(0, 13))
132 writer.seek(7, os.SEEK_SET)
134 self.assertEqual(writer.size(), 10)
135 self.assertEqual("0123456foo", writer.readfrom(0, 13))
136 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", export_manifest(c))
138 def test_write3(self):
139 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
140 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
141 keep_client=keep) as c:
142 writer = c.open("count.txt", "r+")
143 self.assertEqual("012345678901234", writer.readfrom(0, 15))
144 writer.seek(7, os.SEEK_SET)
145 writer.write("foobar")
146 self.assertEqual(writer.size(), 20)
147 self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
148 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", export_manifest(c))
150 def test_write4(self):
151 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
152 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
153 keep_client=keep) as c:
154 writer = c.open("count.txt", "r+")
155 self.assertEqual("012301230123", writer.readfrom(0, 15))
156 writer.seek(2, os.SEEK_SET)
157 writer.write("abcdefg")
158 self.assertEqual(writer.size(), 12)
159 self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
160 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", export_manifest(c))
162 def test_write_large(self):
163 keep = ArvadosFileWriterTestCase.MockKeep({})
164 api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
165 "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"},
166 {"uuid":"zzzzz-4zz18-mockcollection0"})
167 with arvados.WritableCollection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
168 api_client=api, keep_client=keep) as c:
169 writer = c.open("count.txt", "r+")
170 text = ''.join(["0123456789" for a in xrange(0, 100)])
171 for b in xrange(0, 100000):
173 self.assertEqual(writer.size(), 100000000)
175 self.assertEqual(None, c._manifest_locator)
176 self.assertEqual(True, c.modified())
177 c.save_new("test_write_large")
178 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
179 self.assertEqual(False, c.modified())
181 def test_write_rewrite0(self):
182 keep = ArvadosFileWriterTestCase.MockKeep({})
183 with arvados.WritableCollection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
184 keep_client=keep) as c:
185 writer = c.open("count.txt", "r+")
186 for b in xrange(0, 10):
187 writer.seek(0, os.SEEK_SET)
188 writer.write("0123456789")
189 writer.arvadosfile._repack_writes()
190 self.assertEqual(writer.size(), 10)
191 self.assertEqual("0123456789", writer.readfrom(0, 20))
192 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", export_manifest(c))
194 def test_write_rewrite1(self):
195 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
196 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
197 keep_client=keep) as c:
198 writer = c.open("count.txt", "r+")
199 for b in xrange(0, 10):
200 writer.seek(10, os.SEEK_SET)
201 writer.write("abcdefghij")
202 writer.arvadosfile._repack_writes()
203 self.assertEqual(writer.size(), 20)
204 self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
205 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", export_manifest(c))
207 def test_write_rewrite2(self):
208 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
209 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
210 keep_client=keep) as c:
211 writer = c.open("count.txt", "r+")
212 for b in xrange(0, 10):
213 writer.seek(5, os.SEEK_SET)
214 writer.write("abcdefghij")
215 writer.arvadosfile._repack_writes()
216 self.assertEqual(writer.size(), 15)
217 self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
218 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", export_manifest(c))
220 def test_write_large_rewrite0(self):
221 keep = ArvadosFileWriterTestCase.MockKeep({})
222 api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
223 "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"},
224 {"uuid":"zzzzz-4zz18-mockcollection0"})
225 with arvados.WritableCollection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
226 api_client=api, keep_client=keep) as c:
227 writer = c.open("count.txt", "r+")
228 text = ''.join(["0123456789" for a in xrange(0, 100)])
229 for b in xrange(0, 100000):
231 writer.seek(0, os.SEEK_SET)
233 self.assertEqual(writer.size(), 100000000)
235 self.assertEqual(None, c._manifest_locator)
236 self.assertEqual(True, c.modified())
237 c.save_new("test_write_large")
238 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
239 self.assertEqual(False, c.modified())
241 def test_create(self):
242 keep = ArvadosFileWriterTestCase.MockKeep({})
243 api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
244 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
245 {"uuid":"zzzzz-4zz18-mockcollection0"})
246 with arvados.WritableCollection(api_client=api, keep_client=keep) as c:
247 writer = c.open("count.txt", "w+")
248 self.assertEqual(writer.size(), 0)
249 writer.write("01234567")
250 self.assertEqual(writer.size(), 8)
252 self.assertEqual(None, c._manifest_locator)
253 self.assertEqual(True, c.modified())
254 self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
255 c.save_new("test_create")
256 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
257 self.assertEqual(False, c.modified())
258 self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
261 def test_create_subdir(self):
262 keep = ArvadosFileWriterTestCase.MockKeep({})
263 api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
264 "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
265 {"uuid":"zzzzz-4zz18-mockcollection0"})
266 with arvados.WritableCollection(api_client=api, keep_client=keep) as c:
267 writer = c.open("foo/bar/count.txt", "w+")
268 writer.write("01234567")
269 c.save_new("test_create")
271 def test_overwrite(self):
272 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
273 api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
274 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
275 {"uuid":"zzzzz-4zz18-mockcollection0"})
276 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
277 api_client=api, keep_client=keep) as c:
278 writer = c.open("count.txt", "w+")
279 self.assertEqual(writer.size(), 0)
280 writer.write("01234567")
281 self.assertEqual(writer.size(), 8)
283 self.assertEqual(None, c._manifest_locator)
284 self.assertEqual(True, c.modified())
285 c.save_new("test_overwrite")
286 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
287 self.assertEqual(False, c.modified())
289 def test_file_not_found(self):
290 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
291 with self.assertRaises(IOError):
292 writer = c.open("nocount.txt", "r")
294 def test_cannot_open_directory(self):
295 with arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
296 with self.assertRaises(IOError):
297 writer = c.open(".", "r")
299 def test_create_multiple(self):
300 keep = ArvadosFileWriterTestCase.MockKeep({})
301 api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
302 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"},
303 {"uuid":"zzzzz-4zz18-mockcollection0"})
304 with arvados.WritableCollection(api_client=api, keep_client=keep) as c:
305 w1 = c.open("count1.txt", "w")
306 w2 = c.open("count2.txt", "w")
309 self.assertEqual(w1.size(), 8)
310 self.assertEqual(w2.size(), 8)
312 self.assertEqual(None, c._manifest_locator)
313 self.assertEqual(True, c.modified())
314 self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
315 c.save_new("test_create_multiple")
316 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
317 self.assertEqual(False, c.modified())
318 self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
321 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
322 class MockParent(object):
323 class MockBlockMgr(object):
324 def __init__(self, blocks, nocache):
326 self.nocache = nocache
328 def block_prefetch(self, loc):
331 def get_block(self, loc, num_retries=0, cache_only=False):
332 if self.nocache and cache_only:
334 return self.blocks[loc]
336 def __init__(self, blocks, nocache):
338 self.nocache = nocache
339 self.lock = arvados.arvfile.NoopLock()
341 def root_collection(self):
344 def _my_block_manager(self):
345 return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
351 def make_count_reader(self, nocache=False):
355 for d in ['01234', '34567', '67890']:
356 loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d))
358 stream.append(Range(loc, n, len(d)))
360 af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
361 return ArvadosFileReader(af, "count.txt")
363 def test_read_returns_first_block(self):
364 # read() calls will be aligned on block boundaries - see #3663.
365 sfile = self.make_count_reader(nocache=True)
366 self.assertEqual('123', sfile.read(10))
368 def test_successive_reads(self):
369 sfile = self.make_count_reader(nocache=True)
370 for expect in ['123', '456', '789', '']:
371 self.assertEqual(expect, sfile.read(10))
373 def test_tell_after_block_read(self):
374 sfile = self.make_count_reader(nocache=True)
376 self.assertEqual(3, sfile.tell())
378 def test_prefetch(self):
379 keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
380 with arvados.WritableCollection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
381 r = c.open("count.txt", "r")
382 self.assertEqual("0123", r.read(4))
383 self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
384 self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
386 def test__eq__(self):
387 with arvados.arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
388 with arvados.arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
389 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
390 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
393 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
394 def reader_for(self, coll_name, **kwargs):
398 for d in self.manifest_for(coll_name).split():
401 segments.append(Range(n, n, k.size))
402 stream.append(Range(d, n, k.size))
406 col = arvados.ReadOnlyCollection(keep_client=self.keep_client())
407 col._my_block_manager().prefetch_enabled = False
408 af = ArvadosFile(col,
411 return ArvadosFileReader(af, "test", **kwargs)
413 def read_for_test(self, reader, byte_count, **kwargs):
414 return reader.read(byte_count, **kwargs)
417 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
418 def read_for_test(self, reader, byte_count, **kwargs):
419 return reader.readfrom(0, byte_count, **kwargs)
422 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
423 def read_for_test(self, reader, byte_count, **kwargs):
424 return ''.join(reader.readall(**kwargs))
427 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
428 def read_for_test(self, reader, byte_count, **kwargs):
429 return ''.join(reader.readall_decompressed(**kwargs))
432 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
433 def read_for_test(self, reader, byte_count, **kwargs):
434 return ''.join(reader.readlines(**kwargs))