Merge branch 'master' into 4823-python-sdk-writable-collection-api
[arvados.git] / sdk / python / tests / test_arvfile.py
1 #!/usr/bin/env python
2
3 import bz2
4 import gzip
5 import io
6 import mock
7 import os
8 import unittest
9 import hashlib
10
11 import arvados
12 from arvados import ArvadosFile, ArvadosFileReader, Range, import_manifest, export_manifest, KeepLocator
13 from arvados.arvfile import SYNC_READONLY, SYNC_EXPLICIT
14
15 import arvados_testutil as tutil
16 from test_stream import StreamFileReaderTestCase, StreamRetryTestMixin
17
18 class ArvadosFileWriterTestCase(unittest.TestCase):
19     class MockKeep(object):
20         def __init__(self, blocks):
21             self.blocks = blocks
22             self.requests = []
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)
32             return pdh
33
34     class MockApi(object):
35         def __init__(self, b, r):
36             self.b = b
37             self.r = r
38         class MockCollections(object):
39             def __init__(self, b, r):
40                 self.b = b
41                 self.r = r
42             class Execute(object):
43                 def __init__(self, r):
44                     self.r = r
45                 def execute(self, num_retries=None):
46                     return self.r
47             def create(self, ensure_unique_name=False, body=None):
48                 if body != self.b:
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)
55
56
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)
66             writer.seek(5)
67             self.assertEqual("56789", writer.read(8))
68             writer.truncate(8)
69             writer.seek(5, os.SEEK_SET)
70             self.assertEqual("567", writer.read(8))
71
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())
77
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)
89             writer.write("foo")
90             self.assertEqual(writer.size(), 13)
91             writer.seek(5, os.SEEK_SET)
92             self.assertEqual("56789foo", writer.read(8))
93
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"))
101
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)
109             writer.write("foo")
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))
113
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)
121             writer.write("foo")
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))
125
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)
133             writer.write("foo")
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))
137
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))
149
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))
161
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):
172                 writer.write(text)
173             self.assertEqual(writer.size(), 100000000)
174
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())
180
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))
193
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))
206
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))
219
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):
230                 writer.write(text)
231             writer.seek(0, os.SEEK_SET)
232             writer.write("foo")
233             self.assertEqual(writer.size(), 100000000)
234
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())
240
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)
251
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"))
259
260
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")
270
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)
282
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())
288
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")
293
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")
298
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")
307             w1.write("01234567")
308             w2.write("abcdefgh")
309             self.assertEqual(w1.size(), 8)
310             self.assertEqual(w2.size(), 8)
311
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"))
319
320
321 class ArvadosFileReaderTestCase(StreamFileReaderTestCase):
322     class MockParent(object):
323         class MockBlockMgr(object):
324             def __init__(self, blocks, nocache):
325                 self.blocks = blocks
326                 self.nocache = nocache
327
328             def block_prefetch(self, loc):
329                 pass
330
331             def get_block(self, loc, num_retries=0, cache_only=False):
332                 if self.nocache and cache_only:
333                     return None
334                 return self.blocks[loc]
335
336         def __init__(self, blocks, nocache):
337             self.blocks = blocks
338             self.nocache = nocache
339             self.lock = arvados.arvfile.NoopLock()
340
341         def root_collection(self):
342             return self
343
344         def _my_block_manager(self):
345             return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
346
347         def sync_mode(self):
348             return SYNC_READONLY
349
350
351     def make_count_reader(self, nocache=False):
352         stream = []
353         n = 0
354         blocks = {}
355         for d in ['01234', '34567', '67890']:
356             loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d))
357             blocks[loc] = d
358             stream.append(Range(loc, n, len(d)))
359             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")
362
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))
367
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))
372
373     def test_tell_after_block_read(self):
374         sfile = self.make_count_reader(nocache=True)
375         sfile.read(5)
376         self.assertEqual(3, sfile.tell())
377
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)
385
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"])
391
392
393 class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
394     def reader_for(self, coll_name, **kwargs):
395         stream = []
396         segments = []
397         n = 0
398         for d in self.manifest_for(coll_name).split():
399             try:
400                 k = KeepLocator(d)
401                 segments.append(Range(n, n, k.size))
402                 stream.append(Range(d, n, k.size))
403                 n += k.size
404             except ValueError:
405                 pass
406         col = arvados.ReadOnlyCollection(keep_client=self.keep_client())
407         col._my_block_manager().prefetch_enabled = False
408         af = ArvadosFile(col,
409                          stream=stream,
410                          segments=segments)
411         return ArvadosFileReader(af, "test", **kwargs)
412
413     def read_for_test(self, reader, byte_count, **kwargs):
414         return reader.read(byte_count, **kwargs)
415
416
417 class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase):
418     def read_for_test(self, reader, byte_count, **kwargs):
419         return reader.readfrom(0, byte_count, **kwargs)
420
421
422 class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase):
423     def read_for_test(self, reader, byte_count, **kwargs):
424         return ''.join(reader.readall(**kwargs))
425
426
427 class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase):
428     def read_for_test(self, reader, byte_count, **kwargs):
429         return ''.join(reader.readall_decompressed(**kwargs))
430
431
432 class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase):
433     def read_for_test(self, reader, byte_count, **kwargs):
434         return ''.join(reader.readlines(**kwargs))