#!/usr/bin/env python
+import bz2
+import gzip
+import io
import mock
+import os
import unittest
+import hashlib
import arvados
-from arvados import StreamReader, StreamFileReader
+from arvados import StreamReader, StreamFileReader, StreamWriter, StreamFileWriter
import arvados_testutil as tutil
import run_test_server
+class StreamFileReaderTestCase(unittest.TestCase):
+ def make_count_reader(self):
+ stream = tutil.MockStreamReader('.', '01234', '34567', '67890')
+ return StreamFileReader(stream, [[1, 3, 0], [6, 3, 3], [11, 3, 6]],
+ 'count.txt')
+
+ def test_read_returns_first_block(self):
+ # read() calls will be aligned on block boundaries - see #3663.
+ sfile = self.make_count_reader()
+ self.assertEqual('123', sfile.read(10))
+
+ def test_small_read(self):
+ sfile = self.make_count_reader()
+ self.assertEqual('12', sfile.read(2))
+
+ def test_successive_reads(self):
+ sfile = self.make_count_reader()
+ for expect in ['123', '456', '789', '']:
+ self.assertEqual(expect, sfile.read(10))
+
+ def test_readfrom_spans_blocks(self):
+ sfile = self.make_count_reader()
+ self.assertEqual('6789', sfile.readfrom(5, 12))
+
+ def test_small_readfrom_spanning_blocks(self):
+ sfile = self.make_count_reader()
+ self.assertEqual('2345', sfile.readfrom(1, 4))
+
+ def test_readall(self):
+ sfile = self.make_count_reader()
+ self.assertEqual('123456789', ''.join(sfile.readall()))
+
+ def test_one_arg_seek(self):
+ self.test_relative_seek([])
+
+ def test_absolute_seek(self, args=[os.SEEK_SET]):
+ sfile = self.make_count_reader()
+ sfile.seek(6, *args)
+ self.assertEqual('78', sfile.read(2))
+ sfile.seek(4, *args)
+ self.assertEqual('56', sfile.read(2))
+
+ def test_relative_seek(self, args=[os.SEEK_CUR]):
+ sfile = self.make_count_reader()
+ self.assertEqual('12', sfile.read(2))
+ sfile.seek(2, *args)
+ self.assertEqual('56', sfile.read(2))
+
+ def test_end_seek(self):
+ sfile = self.make_count_reader()
+ sfile.seek(-6, os.SEEK_END)
+ self.assertEqual('45', sfile.read(2))
+
+ def test_seek_min_zero(self):
+ sfile = self.make_count_reader()
+ sfile.seek(-2, os.SEEK_SET)
+ self.assertEqual(0, sfile.tell())
+
+ def test_seek_max_size(self):
+ sfile = self.make_count_reader()
+ sfile.seek(2, os.SEEK_END)
+ self.assertEqual(9, sfile.tell())
+
+ def test_size(self):
+ self.assertEqual(9, self.make_count_reader().size())
+
+ def test_tell_after_block_read(self):
+ sfile = self.make_count_reader()
+ sfile.read(5)
+ self.assertEqual(3, sfile.tell())
+
+ def test_tell_after_small_read(self):
+ sfile = self.make_count_reader()
+ sfile.read(1)
+ self.assertEqual(1, sfile.tell())
+
+ def test_no_read_after_close(self):
+ sfile = self.make_count_reader()
+ sfile.close()
+ self.assertRaises(ValueError, sfile.read, 2)
+
+ def test_context(self):
+ with self.make_count_reader() as sfile:
+ self.assertFalse(sfile.closed, "reader is closed inside context")
+ self.assertEqual('12', sfile.read(2))
+ self.assertTrue(sfile.closed, "reader is open after context")
+
+ def make_newlines_reader(self):
+ stream = tutil.MockStreamReader('.', 'one\ntwo\n\nth', 'ree\nfour\n\n')
+ return StreamFileReader(stream, [[0, 11, 0], [11, 10, 11]], 'count.txt')
+
+ def check_lines(self, actual):
+ self.assertEqual(['one\n', 'two\n', '\n', 'three\n', 'four\n', '\n'],
+ actual)
+
+ def test_readline(self):
+ reader = self.make_newlines_reader()
+ actual = []
+ while True:
+ data = reader.readline()
+ if not data:
+ break
+ actual.append(data)
+ self.check_lines(actual)
+
+ def test_readlines(self):
+ self.check_lines(self.make_newlines_reader().readlines())
+
+ def test_iteration(self):
+ self.check_lines(list(iter(self.make_newlines_reader())))
+
+ def test_readline_size(self):
+ reader = self.make_newlines_reader()
+ self.assertEqual('on', reader.readline(2))
+ self.assertEqual('e\n', reader.readline(4))
+ self.assertEqual('two\n', reader.readline(6))
+ self.assertEqual('\n', reader.readline(8))
+ self.assertEqual('thre', reader.readline(4))
+
+ def test_readlines_sizehint(self):
+ result = self.make_newlines_reader().readlines(8)
+ self.assertEqual(['one\n', 'two\n'], result[:2])
+ self.assertNotIn('three\n', result)
+
+ def test_name_attribute(self):
+ # Test both .name and .name() (for backward compatibility)
+ stream = tutil.MockStreamReader()
+ sfile = StreamFileReader(stream, [[0, 0, 0]], 'nametest')
+ self.assertEqual('nametest', sfile.name)
+ self.assertEqual('nametest', sfile.name())
+
+ def check_decompression(self, compress_ext, compress_func):
+ test_text = 'decompression\ntest\n'
+ test_data = compress_func(test_text)
+ stream = tutil.MockStreamReader('.', test_data)
+ reader = StreamFileReader(stream, [[0, len(test_data), 0]],
+ 'test.' + compress_ext)
+ self.assertEqual(test_text, ''.join(reader.readall_decompressed()))
+
+ @staticmethod
+ def gzip_compress(data):
+ compressed_data = io.BytesIO()
+ with gzip.GzipFile(fileobj=compressed_data, mode='wb') as gzip_file:
+ gzip_file.write(data)
+ return compressed_data.getvalue()
+
+ def test_no_decompression(self):
+ self.check_decompression('log', lambda s: s)
+
+ def test_gzip_decompression(self):
+ self.check_decompression('gz', self.gzip_compress)
+
+ def test_bz2_decompression(self):
+ self.check_decompression('bz2', bz2.compress)
+
+
class StreamRetryTestMixin(object):
# Define reader_for(coll_name, **kwargs)
# and read_for_test(reader, size, **kwargs).
@tutil.skip_sleep
def test_success_without_retries(self):
reader = self.reader_for('bar_file')
- with tutil.mock_responses('bar', 200):
+ with tutil.mock_get_responses('bar', 200):
self.assertEqual('bar', self.read_for_test(reader, 3))
@tutil.skip_sleep
def test_read_no_default_retry(self):
reader = self.reader_for('user_agreement')
- with tutil.mock_responses('', 500):
+ with tutil.mock_get_responses('', 500):
with self.assertRaises(arvados.errors.KeepReadError):
self.read_for_test(reader, 10)
@tutil.skip_sleep
def test_read_with_instance_retries(self):
reader = self.reader_for('foo_file', num_retries=3)
- with tutil.mock_responses('foo', 500, 200):
+ with tutil.mock_get_responses('foo', 500, 200):
self.assertEqual('foo', self.read_for_test(reader, 3))
@tutil.skip_sleep
def test_read_with_method_retries(self):
reader = self.reader_for('foo_file')
- with tutil.mock_responses('foo', 500, 200):
+ with tutil.mock_get_responses('foo', 500, 200):
self.assertEqual('foo',
self.read_for_test(reader, 3, num_retries=3))
@tutil.skip_sleep
def test_read_instance_retries_exhausted(self):
reader = self.reader_for('bar_file', num_retries=3)
- with tutil.mock_responses('bar', 500, 500, 500, 500, 200):
+ with tutil.mock_get_responses('bar', 500, 500, 500, 500, 200):
with self.assertRaises(arvados.errors.KeepReadError):
self.read_for_test(reader, 3)
@tutil.skip_sleep
def test_read_method_retries_exhausted(self):
reader = self.reader_for('bar_file')
- with tutil.mock_responses('bar', 500, 500, 500, 500, 200):
+ with tutil.mock_get_responses('bar', 500, 500, 500, 500, 200):
with self.assertRaises(arvados.errors.KeepReadError):
self.read_for_test(reader, 3, num_retries=3)
@tutil.skip_sleep
def test_method_retries_take_precedence(self):
reader = self.reader_for('user_agreement', num_retries=10)
- with tutil.mock_responses('', 500, 500, 500, 200):
+ with tutil.mock_get_responses('', 500, 500, 500, 200):
with self.assertRaises(arvados.errors.KeepReadError):
self.read_for_test(reader, 10, num_retries=1)
def read_for_test(self, reader, byte_count, **kwargs):
return ''.join(reader.readlines(**kwargs))
+class StreamWriterTestCase(unittest.TestCase):
+ class MockKeep(object):
+ def __init__(self, blocks):
+ self.blocks = blocks
+ def get(self, locator, num_retries=0):
+ return self.blocks[locator]
+ def put(self, data):
+ pdh = "%s+%i" % (hashlib.md5(data).hexdigest(), len(data))
+ self.blocks[pdh] = str(data)
+ return pdh
+
+ def test_init(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ self.assertEqual("01234", stream.readfrom(0, 5))
+
+ def test_append(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ self.assertEqual("56789", stream.readfrom(5, 8))
+ stream.append("foo")
+ self.assertEqual("56789foo", stream.readfrom(5, 8))
+
+
+class StreamFileWriterTestCase(unittest.TestCase):
+ def test_truncate(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ writer = stream.files()["count.txt"]
+ self.assertEqual("56789", writer.readfrom(5, 8))
+ writer.truncate(8)
+ self.assertEqual("567", writer.readfrom(5, 8))
+
+ def test_append(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ writer = stream.files()["count.txt"]
+ self.assertEqual("56789", writer.readfrom(5, 8))
+ writer.seek(10)
+ writer.write("foo")
+ self.assertEqual(writer.size(), 13)
+ self.assertEqual("56789foo", writer.readfrom(5, 8))
+
+ def test_write0(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ writer = stream.files()["count.txt"]
+ self.assertEqual("0123456789", writer.readfrom(0, 13))
+ writer.seek(0)
+ writer.write("foo")
+ self.assertEqual(writer.size(), 10)
+ self.assertEqual("foo3456789", writer.readfrom(0, 13))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 bufferblock0 10:3:count.txt 3:7:count.txt\n", stream.manifest_text())
+
+ def test_write1(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ writer = stream.files()["count.txt"]
+ self.assertEqual("0123456789", writer.readfrom(0, 13))
+ writer.seek(3)
+ writer.write("foo")
+ self.assertEqual(writer.size(), 10)
+ self.assertEqual("012foo6789", writer.readfrom(0, 13))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 bufferblock0 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", stream.manifest_text())
+
+ def test_write2(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ writer = stream.files()["count.txt"]
+ self.assertEqual("0123456789", writer.readfrom(0, 13))
+ writer.seek(7)
+ writer.write("foo")
+ self.assertEqual(writer.size(), 10)
+ self.assertEqual("0123456foo", writer.readfrom(0, 13))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 bufferblock0 0:7:count.txt 10:3:count.txt\n", stream.manifest_text())
+
+ def test_write3(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ writer = stream.files()["count.txt"]
+ self.assertEqual("012345678901234", writer.readfrom(0, 15))
+ writer.seek(7)
+ writer.write("foobar")
+ self.assertEqual(writer.size(), 20)
+ self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 bufferblock0 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", stream.manifest_text())
+
+ def test_write4(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:4:count.txt', '0:4:count.txt', '0:4:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ writer = stream.files()["count.txt"]
+ self.assertEqual("012301230123", writer.readfrom(0, 15))
+ writer.seek(2)
+ writer.write("abcdefg")
+ self.assertEqual(writer.size(), 12)
+ self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 bufferblock0 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", stream.manifest_text())
+
+ def test_write_large(self):
+ stream = StreamWriter(['.', arvados.config.EMPTY_BLOCK_LOCATOR, '0:0:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({}))
+ writer = stream.files()["count.txt"]
+ text = ''.join(["0123456789" for a in xrange(0, 100)])
+ for b in xrange(0, 100000):
+ writer.write(text)
+ self.assertEqual(writer.size(), 100000000)
+ stream.commit()
+ self.assertEqual(". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n", stream.manifest_text())
+
+ def test_write_rewrite0(self):
+ stream = StreamWriter(['.', arvados.config.EMPTY_BLOCK_LOCATOR, '0:0:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({}))
+ writer = stream.files()["count.txt"]
+ for b in xrange(0, 10):
+ writer.seek(0, os.SEEK_SET)
+ writer.write("0123456789")
+ stream.commit()
+ self.assertEqual(writer.size(), 10)
+ self.assertEqual("0123456789", writer.readfrom(0, 20))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", stream.manifest_text())
+
+ def test_write_rewrite1(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ writer = stream.files()["count.txt"]
+ for b in xrange(0, 10):
+ writer.seek(10, os.SEEK_SET)
+ writer.write("abcdefghij")
+ stream.commit()
+ self.assertEqual(writer.size(), 20)
+ self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:10:count.txt 10:10:count.txt\n", stream.manifest_text())
+
+ def test_write_rewrite2(self):
+ stream = StreamWriter(['.', '781e5e245d69b566979b86e28d23f2c7+10', '0:10:count.txt'],
+ keep=StreamWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}))
+ writer = stream.files()["count.txt"]
+ for b in xrange(0, 10):
+ writer.seek(5, os.SEEK_SET)
+ writer.write("abcdefghij")
+ stream.commit()
+ self.assertEqual(writer.size(), 15)
+ self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", stream.manifest_text())
if __name__ == '__main__':
unittest.main()
projects / arvados.git / blobdiff