cw.set_current_file_name('baz.txt')
hash = cw.finish()
self.assertEqual(hash,
- '23ca013983d6239e98931cc779e68426+114',
- 'resulting manifest hash is not what I expected')
+ 'd6c3b8e571f1b81ebb150a45ed06c884+114',
+ "resulting manifest hash was {0}, expecting d6c3b8e571f1b81ebb150a45ed06c884+114".format(hash))
class LocalCollectionReaderTest(unittest.TestCase):
def setUp(self):
os.environ['KEEP_LOCAL_STORE'] = '/tmp'
LocalCollectionWriterTest().runTest()
def runTest(self):
- cr = arvados.CollectionReader('23ca013983d6239e98931cc779e68426+114')
+ cr = arvados.CollectionReader('d6c3b8e571f1b81ebb150a45ed06c884+114+Xzizzle')
got = []
for s in cr.all_streams():
for f in s.all_files():
got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]]
- expected = [[3, '.', 'foo.txt', 'foo'],
- [3, '.', 'bar.txt', 'bar'],
+ expected = [[3, '.', 'bar.txt', 'bar'],
+ [3, '.', 'foo.txt', 'foo'],
[3, './baz', 'baz.txt', 'baz']]
self.assertEqual(got,
- expected,
- 'resulting file list is not what I expected')
+ expected)
stream0 = cr.all_streams()[0]
- self.assertEqual(stream0.read(0),
+ self.assertEqual(stream0.readfrom(0, 0),
'',
'reading zero bytes should have returned empty string')
- self.assertEqual(stream0.read(2**26),
+ self.assertEqual(stream0.readfrom(0, 2**26),
'foobar',
'reading entire stream failed')
- self.assertEqual(stream0.read(2**26),
- None,
- 'reading past end of stream should have returned None')
- self.assertEqual(stream0.read(0),
+ self.assertEqual(stream0.readfrom(2**26, 0),
'',
'reading zero bytes should have returned empty string')
os.environ['KEEP_LOCAL_STORE'] = '/tmp'
LocalCollectionWriterTest().runTest()
def runTest(self):
- self._runTest('23ca013983d6239e98931cc779e68426+114',
- [[3, '.', 'foo.txt', 'foo'],
- [3, '.', 'bar.txt', 'bar'],
+ self._runTest('d6c3b8e571f1b81ebb150a45ed06c884+114',
+ [[3, '.', 'bar.txt', 'bar'],
+ [3, '.', 'foo.txt', 'foo'],
[3, './baz', 'baz.txt', 'baz']])
self._runTest((". %s %s 0:3:foo.txt 3:3:bar.txt\n" %
(arvados.Keep.put("foo"),
arvados.Keep.put("bar"))),
- [[3, '.', 'foo.txt', 'foo'],
- [3, '.', 'bar.txt', 'bar']])
+ [[3, '.', 'bar.txt', 'bar'],
+ [3, '.', 'foo.txt', 'foo']])
self._runTest((". %s %s 0:2:fo.txt 2:4:obar.txt\n" %
(arvados.Keep.put("foo"),
arvados.Keep.put("bar"))),
self._runTest((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" %
(arvados.Keep.put("foo"),
arvados.Keep.put("bar"))),
- [[2, '.', 'fo.txt', 'fo'],
- [0, '.', 'zero.txt', ''],
+ [[2, '.', 'ar.txt', 'ar'],
+ [2, '.', 'fo.txt', 'fo'],
[2, '.', 'ob.txt', 'ob'],
- [2, '.', 'ar.txt', 'ar']])
+ [0, '.', 'zero.txt', '']])
+
def _runTest(self, collection, expected):
cr = arvados.CollectionReader(collection)
- manifest_subsets = []
for s in cr.all_streams():
- for f in s.all_files():
- manifest_subsets += [f.as_manifest()]
- expect_i = 0
- for m in manifest_subsets:
- cr = arvados.CollectionReader(m)
- for f in cr.all_files():
- got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))]
- self.assertEqual(got,
- expected[expect_i],
- 'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, expected[expect_i]))
- expect_i += 1
+ for ex in expected:
+ if ex[0] == s:
+ f = s.files()[ex[2]]
+ got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))]
+ self.assertEqual(got,
+ ex,
+ 'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex))
class LocalCollectionReadlineTest(unittest.TestCase):
def setUp(self):
cw = arvados.CollectionWriter()
cw.start_new_file('zero.txt')
cw.write('')
+
+ self.assertEqual(cw.manifest_text(), ". 0:0:zero.txt\n")
self.check_manifest_file_sizes(cw.manifest_text(), [0])
cw = arvados.CollectionWriter()
cw.start_new_file('zero.txt')
cw.start_new_stream('foo')
cw.start_new_file('zero.txt')
cw.write('')
- self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0])
+ self.check_manifest_file_sizes(cw.manifest_text(), [1,0,0])
+
def check_manifest_file_sizes(self, manifest_text, expect_sizes):
cr = arvados.CollectionReader(manifest_text)
got_sizes = []
bz2_manifest = cw.manifest_text()
cr = arvados.CollectionReader(bz2_manifest)
+
got = 0
for x in list(cr.all_files())[0].readlines():
self.assertEqual(x, "abc\n", "decompression returned wrong data: %s" % x)
"decompression returned %d lines instead of %d" % (got, n_lines_in))
class NormalizedCollectionTest(unittest.TestCase):
- def setUp(self):
- pass
-
def runTest(self):
m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt"""
- self.assertEqual(arvados.collection.normalize(arvados.CollectionReader(m1)),
+ self.assertEqual(arvados.CollectionReader(m1).manifest_text(),
""". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
""")
m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
"""
- self.assertEqual(arvados.collection.normalize(arvados.CollectionReader(m2)), m2)
+ self.assertEqual(arvados.CollectionReader(m2).manifest_text(), m2)
m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt"""
- self.assertEqual(arvados.collection.normalize(arvados.CollectionReader(m3)),
+ self.assertEqual(arvados.CollectionReader(m3).manifest_text(),
""". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
""")
m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar"""
- self.assertEqual(arvados.collection.normalize(arvados.CollectionReader(m4)),
+ self.assertEqual(arvados.CollectionReader(m4).manifest_text(),
"""./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
""")
m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar"""
- self.assertEqual(arvados.collection.normalize(arvados.CollectionReader(m5)),
+ self.assertEqual(arvados.CollectionReader(m5).manifest_text(),
"""./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
""")
with open('testdata/1000G_ref_manifest') as f6:
m6 = f6.read()
- self.assertEqual(arvados.collection.normalize(arvados.CollectionReader(m6)), m6)
+ self.assertEqual(arvados.CollectionReader(m6).manifest_text(), m6)
with open('testdata/jlake_manifest') as f7:
m7 = f7.read()
- self.assertEqual(arvados.collection.normalize(arvados.CollectionReader(m7)), m7)
+ self.assertEqual(arvados.CollectionReader(m7).manifest_text(), m7)
m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt
"""
- self.assertEqual(arvados.collection.normalize(arvados.CollectionReader(m8)), m8)
+ self.assertEqual(arvados.CollectionReader(m8).manifest_text(), m8)
+
+class LocatorsAndRangesTest(unittest.TestCase):
+ def runTest(self):
+ blocks2 = [['a', 10, 0],
+ ['b', 10, 10],
+ ['c', 10, 20],
+ ['d', 10, 30],
+ ['e', 10, 40],
+ ['f', 10, 50]]
+
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 2, 2), [['a', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [['b', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [['c', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [['d', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [['e', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [['f', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), [])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 0, 2), [['a', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [['b', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [['c', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [['d', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [['e', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [['f', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), [])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 9, 2), [['a', 10, 9, 1], ['b', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [['b', 10, 9, 1], ['c', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [['c', 10, 9, 1], ['d', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [['d', 10, 9, 1], ['e', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [['e', 10, 9, 1], ['f', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [['f', 10, 9, 1]])
+
+
+ blocks3 = [['a', 10, 0],
+ ['b', 10, 10],
+ ['c', 10, 20],
+ ['d', 10, 30],
+ ['e', 10, 40],
+ ['f', 10, 50],
+ ['g', 10, 60]]
+
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 2, 2), [['a', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [['b', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [['c', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [['d', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [['e', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [['f', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [['g', 10, 2, 2]])
+
+
+ blocks = [['a', 10, 0],
+ ['b', 15, 10],
+ ['c', 5, 25]]
+ self.assertEqual(arvados.locators_and_ranges(blocks, 1, 0), [])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [['a', 10, 0, 5]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [['a', 10, 3, 5]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [['a', 10, 0, 10]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [['a', 10, 0, 10],
+ ['b', 15, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [['a', 10, 1, 9],
+ ['b', 15, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [['a', 10, 0, 10],
+ ['b', 15, 0, 15]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [['a', 10, 0, 10],
+ ['b', 15, 0, 15],
+ ['c', 5, 0, 5]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [['a', 10, 1, 9],
+ ['b', 15, 0, 15],
+ ['c', 5, 0, 5]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [['a', 10, 0, 10],
+ ['b', 15, 0, 15],
+ ['c', 5, 0, 5]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [['b', 15, 5, 5]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [['a', 10, 8, 2],
+ ['b', 15, 0, 15]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [['a', 10, 8, 2],
+ ['b', 15, 0, 15],
+ ['c', 5, 0, 3]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [['c', 5, 1, 2]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [['a', 10, 9, 1],
+ ['b', 15, 0, 14]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [['b', 15, 0, 15]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [['b', 15, 1, 14],
+ ['c', 5, 0, 1]])
+
+class FileStreamTest(unittest.TestCase):
+ class MockStreamReader(object):
+ def __init__(self, content):
+ self.content = content
+
+ def readfrom(self, start, size):
+ return self.content[start:start+size]
+
+ def runTest(self):
+ content = 'abcdefghijklmnopqrstuvwxyz0123456789'
+ msr = FileStreamTest.MockStreamReader(content)
+ segments = [[0, 10, 0],
+ [10, 15, 10],
+ [25, 5, 25]]
+
+ sfr = arvados.StreamFileReader(msr, segments, "test")
+
+ self.assertEqual(sfr.name(), "test")
+ self.assertEqual(sfr.size(), 30)
+
+ self.assertEqual(sfr.readfrom(0, 30), content[0:30])
+ self.assertEqual(sfr.readfrom(2, 30), content[2:30])
+
+ self.assertEqual(sfr.readfrom(2, 8), content[2:10])
+ self.assertEqual(sfr.readfrom(0, 10), content[0:10])
+
+ self.assertEqual(sfr.tell(), 0)
+ self.assertEqual(sfr.read(5), content[0:5])
+ self.assertEqual(sfr.tell(), 5)
+ self.assertEqual(sfr.read(5), content[5:10])
+ self.assertEqual(sfr.tell(), 10)
+ self.assertEqual(sfr.read(5), content[10:15])
+ self.assertEqual(sfr.tell(), 15)
+ self.assertEqual(sfr.read(5), content[15:20])
+ self.assertEqual(sfr.tell(), 20)
+ self.assertEqual(sfr.read(5), content[20:25])
+ self.assertEqual(sfr.tell(), 25)
+ self.assertEqual(sfr.read(5), content[25:30])
+ self.assertEqual(sfr.tell(), 30)
+ self.assertEqual(sfr.read(5), '')
+ self.assertEqual(sfr.tell(), 30)
+
+ segments = [[26, 10, 0],
+ [0, 15, 10],
+ [15, 5, 25]]
+
+ sfr = arvados.StreamFileReader(msr, segments, "test")
+
+ self.assertEqual(sfr.size(), 30)
+
+ self.assertEqual(sfr.readfrom(0, 30), content[26:36] + content[0:20])
+ self.assertEqual(sfr.readfrom(2, 30), content[28:36] + content[0:20])
+
+ self.assertEqual(sfr.readfrom(2, 8), content[28:36])
+ self.assertEqual(sfr.readfrom(0, 10), content[26:36])
+
+ self.assertEqual(sfr.tell(), 0)
+ self.assertEqual(sfr.read(5), content[26:31])
+ self.assertEqual(sfr.tell(), 5)
+ self.assertEqual(sfr.read(5), content[31:36])
+ self.assertEqual(sfr.tell(), 10)
+ self.assertEqual(sfr.read(5), content[0:5])
+ self.assertEqual(sfr.tell(), 15)
+ self.assertEqual(sfr.read(5), content[5:10])
+ self.assertEqual(sfr.tell(), 20)
+ self.assertEqual(sfr.read(5), content[10:15])
+ self.assertEqual(sfr.tell(), 25)
+ self.assertEqual(sfr.read(5), content[15:20])
+ self.assertEqual(sfr.tell(), 30)
+ self.assertEqual(sfr.read(5), '')
+ self.assertEqual(sfr.tell(), 30)
+
+
+class StreamReaderTest(unittest.TestCase):
+
+ class MockKeep(object):
+ def __init__(self, content):
+ self.content = content
+
+ def get(self, locator):
+ return self.content[locator]
+
+ def runTest(self):
+ keepblocks = {'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': 'abcdefghij',
+ 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': 'klmnopqrstuvwxy',
+ 'cccccccccccccccccccccccccccccccc+5': 'z0123'}
+ mk = StreamReaderTest.MockKeep(keepblocks)
+
+ sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk)
+
+ content = 'abcdefghijklmnopqrstuvwxyz0123456789'
+
+ self.assertEqual(sr.readfrom(0, 30), content[0:30])
+ self.assertEqual(sr.readfrom(2, 30), content[2:30])
+
+ self.assertEqual(sr.readfrom(2, 8), content[2:10])
+ self.assertEqual(sr.readfrom(0, 10), content[0:10])
+
+ self.assertEqual(sr.readfrom(0, 5), content[0:5])
+ self.assertEqual(sr.readfrom(5, 5), content[5:10])
+ self.assertEqual(sr.readfrom(10, 5), content[10:15])
+ self.assertEqual(sr.readfrom(15, 5), content[15:20])
+ self.assertEqual(sr.readfrom(20, 5), content[20:25])
+ self.assertEqual(sr.readfrom(25, 5), content[25:30])
+ self.assertEqual(sr.readfrom(30, 5), '')
+
+class ExtractFileTest(unittest.TestCase):
+ def runTest(self):
+ m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt
+. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt"""
+
+ m2 = arvados.CollectionReader(m1)
+
+ self.assertEqual(m2.manifest_text(),
+ ". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt 43:41:md6sum.txt 84:43:md7sum.txt 6:37:md8sum.txt 84:43:md8sum.txt 83:1:md9sum.txt 0:43:md9sum.txt 84:36:md9sum.txt\n")
+
+ self.assertEqual(arvados.CollectionReader(m1).all_streams()[0].files()['md5sum.txt'].as_manifest(),
+ ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n")
+ self.assertEqual(arvados.CollectionReader(m1).all_streams()[0].files()['md6sum.txt'].as_manifest(),
+ ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n")
+ self.assertEqual(arvados.CollectionReader(m1).all_streams()[0].files()['md7sum.txt'].as_manifest(),
+ ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n")
+ self.assertEqual(arvados.CollectionReader(m1).all_streams()[0].files()['md9sum.txt'].as_manifest(),
+ ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n")
projects / arvados.git / blobdiff