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, cache_only=False):
24 self.requests.append(locator)
25 return self.blocks.get(locator)
27 pdh = "%s+%i" % (hashlib.md5(data).hexdigest(), len(data))
28 self.blocks[pdh] = str(data)
31 class MockApi(object):
32 def __init__(self, b, r):
35 class MockCollections(object):
36 def __init__(self, b, r):
39 class Execute(object):
40 def __init__(self, r):
42 def execute(self, num_retries=None):
44 def create(self, ensure_unique_name=False, body=None):
46 raise Exception("Body %s does not match expectation %s" % (body, self.b))
47 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.r)
48 def update(self, uuid=None, body=None):
49 return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.r)
50 def collections(self):
51 return ArvadosFileWriterTestCase.MockApi.MockCollections(self.b, self.r)
54 def test_truncate(self):
55 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
56 api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate",
57 "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"},
58 {"uuid":"zzzzz-4zz18-mockcollection0"})
59 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
60 api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
61 writer = c.open("count.txt", "r+")
62 self.assertEqual(writer.size(), 10)
64 self.assertEqual("56789", writer.read(8))
66 writer.seek(5, os.SEEK_SET)
67 self.assertEqual("567", writer.read(8))
69 self.assertEqual(None, c._manifest_locator)
70 self.assertEqual(True, c.modified())
71 c.save_as("test_truncate")
72 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
73 self.assertEqual(False, c.modified())
75 def test_append(self):
76 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
77 api = ArvadosFileWriterTestCase.MockApi({"name":"test_append",
78 "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"},
79 {"uuid":"zzzzz-4zz18-mockcollection0"})
80 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
81 api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
82 writer = c.open("count.txt", "r+")
83 writer.seek(5, os.SEEK_SET)
84 self.assertEqual("56789", writer.read(8))
85 writer.seek(10, os.SEEK_SET)
87 self.assertEqual(writer.size(), 13)
88 writer.seek(5, os.SEEK_SET)
89 self.assertEqual("56789foo", writer.read(8))
91 self.assertEqual(None, c._manifest_locator)
92 self.assertEqual(True, c.modified())
93 self.assertEqual(None, keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
94 c.save_as("test_append")
95 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
96 self.assertEqual(False, c.modified())
97 self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
99 def test_write0(self):
100 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
101 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
102 keep=keep, sync=SYNC_EXPLICIT) as c:
103 writer = c.open("count.txt", "r+")
104 self.assertEqual("0123456789", writer.readfrom(0, 13))
105 writer.seek(0, os.SEEK_SET)
107 self.assertEqual(writer.size(), 10)
108 self.assertEqual("foo3456789", writer.readfrom(0, 13))
109 self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", export_manifest(c))
111 def test_write1(self):
112 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
113 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
114 keep=keep, sync=SYNC_EXPLICIT) as c:
115 writer = c.open("count.txt", "r+")
116 self.assertEqual("0123456789", writer.readfrom(0, 13))
117 writer.seek(3, os.SEEK_SET)
119 self.assertEqual(writer.size(), 10)
120 self.assertEqual("012foo6789", writer.readfrom(0, 13))
121 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", export_manifest(c))
123 def test_write2(self):
124 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
125 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
126 keep=keep, sync=SYNC_EXPLICIT) as c:
127 writer = c.open("count.txt", "r+")
128 self.assertEqual("0123456789", writer.readfrom(0, 13))
129 writer.seek(7, os.SEEK_SET)
131 self.assertEqual(writer.size(), 10)
132 self.assertEqual("0123456foo", writer.readfrom(0, 13))
133 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", export_manifest(c))
135 def test_write3(self):
136 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
137 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
138 keep=keep, sync=SYNC_EXPLICIT) as c:
139 writer = c.open("count.txt", "r+")
140 self.assertEqual("012345678901234", writer.readfrom(0, 15))
141 writer.seek(7, os.SEEK_SET)
142 writer.write("foobar")
143 self.assertEqual(writer.size(), 20)
144 self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
145 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", export_manifest(c))
147 def test_write4(self):
148 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
149 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
150 keep=keep, sync=SYNC_EXPLICIT) as c:
151 writer = c.open("count.txt", "r+")
152 self.assertEqual("012301230123", writer.readfrom(0, 15))
153 writer.seek(2, os.SEEK_SET)
154 writer.write("abcdefg")
155 self.assertEqual(writer.size(), 12)
156 self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
157 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", export_manifest(c))
159 def test_write_large(self):
160 keep = ArvadosFileWriterTestCase.MockKeep({})
161 api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
162 "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"},
163 {"uuid":"zzzzz-4zz18-mockcollection0"})
164 with import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
165 api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
166 writer = c.open("count.txt", "r+")
167 text = ''.join(["0123456789" for a in xrange(0, 100)])
168 for b in xrange(0, 100000):
170 self.assertEqual(writer.size(), 100000000)
172 self.assertEqual(None, c._manifest_locator)
173 self.assertEqual(True, c.modified())
174 c.save_as("test_write_large")
175 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
176 self.assertEqual(False, c.modified())
178 def test_write_rewrite0(self):
179 keep = ArvadosFileWriterTestCase.MockKeep({})
180 with import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
181 keep=keep, sync=SYNC_EXPLICIT) as c:
182 writer = c.open("count.txt", "r+")
183 for b in xrange(0, 10):
184 writer.seek(0, os.SEEK_SET)
185 writer.write("0123456789")
186 writer.arvadosfile._repack_writes()
187 self.assertEqual(writer.size(), 10)
188 self.assertEqual("0123456789", writer.readfrom(0, 20))
189 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", export_manifest(c))
191 def test_write_rewrite1(self):
192 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
193 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
194 keep=keep, sync=SYNC_EXPLICIT) as c:
195 writer = c.open("count.txt", "r+")
196 for b in xrange(0, 10):
197 writer.seek(10, os.SEEK_SET)
198 writer.write("abcdefghij")
199 writer.arvadosfile._repack_writes()
200 self.assertEqual(writer.size(), 20)
201 self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
202 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", export_manifest(c))
204 def test_write_rewrite2(self):
205 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
206 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
207 keep=keep, sync=SYNC_EXPLICIT) as c:
208 writer = c.open("count.txt", "r+")
209 for b in xrange(0, 10):
210 writer.seek(5, os.SEEK_SET)
211 writer.write("abcdefghij")
212 writer.arvadosfile._repack_writes()
213 self.assertEqual(writer.size(), 15)
214 self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
215 self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", export_manifest(c))
217 def test_write_large_rewrite0(self):
218 keep = ArvadosFileWriterTestCase.MockKeep({})
219 api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
220 "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"},
221 {"uuid":"zzzzz-4zz18-mockcollection0"})
222 with import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
223 api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
224 writer = c.open("count.txt", "r+")
225 text = ''.join(["0123456789" for a in xrange(0, 100)])
226 for b in xrange(0, 100000):
228 writer.seek(0, os.SEEK_SET)
230 self.assertEqual(writer.size(), 100000000)
232 self.assertEqual(None, c._manifest_locator)
233 self.assertEqual(True, c.modified())
234 c.save_as("test_write_large")
235 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
236 self.assertEqual(False, c.modified())
238 def test_create(self):
239 keep = ArvadosFileWriterTestCase.MockKeep({})
240 api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
241 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
242 {"uuid":"zzzzz-4zz18-mockcollection0"})
243 with arvados.Collection(api_client=api, keep_client=keep, sync=SYNC_EXPLICIT) as c:
244 writer = c.open("count.txt", "w+")
245 self.assertEqual(writer.size(), 0)
246 writer.write("01234567")
247 self.assertEqual(writer.size(), 8)
249 self.assertEqual(None, c._manifest_locator)
250 self.assertEqual(True, c.modified())
251 self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
252 c.save_as("test_create")
253 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
254 self.assertEqual(False, c.modified())
255 self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
258 def test_create_subdir(self):
259 keep = ArvadosFileWriterTestCase.MockKeep({})
260 api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
261 "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
262 {"uuid":"zzzzz-4zz18-mockcollection0"})
263 with arvados.Collection(api_client=api, keep_client=keep, sync=SYNC_EXPLICIT) as c:
264 writer = c.open("foo/bar/count.txt", "w+")
265 writer.write("01234567")
266 c.save_as("test_create")
268 def test_overwrite(self):
269 keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
270 api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
271 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
272 {"uuid":"zzzzz-4zz18-mockcollection0"})
273 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
274 api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c:
275 writer = c.open("count.txt", "w+")
276 self.assertEqual(writer.size(), 0)
277 writer.write("01234567")
278 self.assertEqual(writer.size(), 8)
280 self.assertEqual(None, c._manifest_locator)
281 self.assertEqual(True, c.modified())
282 c.save_as("test_overwrite")
283 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
284 self.assertEqual(False, c.modified())
286 def test_file_not_found(self):
287 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
288 with self.assertRaises(IOError):
289 writer = c.open("nocount.txt", "r")
291 def test_cannot_open_directory(self):
292 with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
293 with self.assertRaises(IOError):
294 writer = c.open(".", "r")
296 def test_create_multiple(self):
297 keep = ArvadosFileWriterTestCase.MockKeep({})
298 api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
299 "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"},
300 {"uuid":"zzzzz-4zz18-mockcollection0"})
301 with arvados.Collection(api_client=api, keep_client=keep, sync=SYNC_EXPLICIT) as c:
302 w1 = c.open("count1.txt", "w")
303 w2 = c.open("count2.txt", "w")
306 self.assertEqual(w1.size(), 8)
307 self.assertEqual(w2.size(), 8)
309 self.assertEqual(None, c._manifest_locator)
310 self.assertEqual(True, c.modified())
311 self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
312 c.save_as("test_create_multiple")
313 self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
314 self.assertEqual(False, c.modified())
315 self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
318 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
319 class MockParent(object):
320 class MockBlockMgr(object):
321 def __init__(self, blocks, nocache):
323 self.nocache = nocache
325 def block_prefetch(self, loc):
328 def get_block(self, loc, num_retries=0, cache_only=False):
329 if self.nocache and cache_only:
331 return self.blocks[loc]
333 def __init__(self, blocks, nocache):
335 self.nocache = nocache
337 def _my_block_manager(self):
338 return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
343 def make_count_reader(self, nocache=False):
347 for d in ['01234', '34567', '67890']:
348 loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d))
350 stream.append(Range(loc, n, len(d)))
352 af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
353 return ArvadosFileReader(af, "count.txt")
355 def test_read_returns_first_block(self):
356 # read() calls will be aligned on block boundaries - see #3663.
357 sfile = self.make_count_reader(nocache=True)
358 self.assertEqual('123', sfile.read(10))
360 def test_successive_reads(self):
361 sfile = self.make_count_reader(nocache=True)
362 for expect in ['123', '456', '789', '']:
363 self.assertEqual(expect, sfile.read(10))
365 def test_tell_after_block_read(self):
366 sfile = self.make_count_reader(nocache=True)
368 self.assertEqual(3, sfile.tell())
370 def test_prefetch(self):
371 keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
372 with import_manifest(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep=keep) as c:
373 r = c.open("count.txt", "r")
374 self.assertEqual("0123", r.read(4))
375 self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
376 self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
378 def test__eq__(self):
379 with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
380 with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
381 self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
382 self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
385 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
386 def reader_for(self, coll_name, **kwargs):
390 for d in self.manifest_for(coll_name).split():
393 segments.append(Range(n, n, k.size))
394 stream.append(Range(d, n, k.size))
398 col = arvados.Collection(keep_client=self.keep_client())
399 col._my_block_manager().prefetch_enabled = False
400 af = ArvadosFile(col,
403 return ArvadosFileReader(af, "test", **kwargs)
405 def read_for_test(self, reader, byte_count, **kwargs):
406 return reader.read(byte_count, **kwargs)
409 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
410 def read_for_test(self, reader, byte_count, **kwargs):
411 return reader.readfrom(0, byte_count, **kwargs)
414 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
415 def read_for_test(self, reader, byte_count, **kwargs):
416 return ''.join(reader.readall(**kwargs))
419 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
420 def read_for_test(self, reader, byte_count, **kwargs):
421 return ''.join(reader.readall_decompressed(**kwargs))
424 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
425 def read_for_test(self, reader, byte_count, **kwargs):
426 return ''.join(reader.readlines(**kwargs))