-# usage example:
+# Copyright (C) The Arvados Authors. All rights reserved.
#
-# ARVADOS_API_TOKEN=abc ARVADOS_API_HOST=arvados.local python -m unittest discover
+# SPDX-License-Identifier: Apache-2.0
+from __future__ import absolute_import
+
+from builtins import object
import arvados
import copy
-import hashlib
import mock
import os
import pprint
+import random
import re
+import sys
import tempfile
+import time
import unittest
-import run_test_server
-import arvados_testutil as tutil
-from arvados.ranges import Range, LocatorAndRange
-from arvados import import_manifest, export_manifest
-from arvados.arvfile import SYNC_EXPLICIT
+from . import run_test_server
+from arvados._ranges import Range, LocatorAndRange
+from arvados.collection import Collection, CollectionReader
+from . import arvados_testutil as tutil
class TestResumableWriter(arvados.ResumableCollectionWriter):
KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K.
self.assertEqual(cw.current_stream_name(), '.',
'current_stream_name() should be "." now')
cw.set_current_file_name('foo.txt')
- cw.write('foo')
+ cw.write(b'foo')
self.assertEqual(cw.current_file_name(), 'foo.txt',
'current_file_name() should be foo.txt now')
cw.start_new_file('bar.txt')
- cw.write('bar')
+ cw.write(b'bar')
cw.start_new_stream('baz')
- cw.write('baz')
+ cw.write(b'baz')
cw.set_current_file_name('baz.txt')
self.assertEqual(cw.manifest_text(),
". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" +
cw.finish()
return cw.portable_data_hash()
+ def test_pdh_is_native_str(self):
+ pdh = self.write_foo_bar_baz()
+ self.assertEqual(type(''), type(pdh))
+
def test_keep_local_store(self):
- self.assertEqual(self.keep_client.put('foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
- self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), 'foo', 'wrong data from Keep.get')
+ self.assertEqual(self.keep_client.put(b'foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
+ self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), b'foo', 'wrong data from Keep.get')
def test_local_collection_writer(self):
self.assertEqual(self.write_foo_bar_baz(),
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'],
- [3, './baz', 'baz.txt', 'baz']]
+ expected = [[3, '.', 'foo.txt', b'foo'],
+ [3, '.', 'bar.txt', b'bar'],
+ [3, './baz', 'baz.txt', b'baz']]
self.assertEqual(got,
expected)
stream0 = cr.all_streams()[0]
self.assertEqual(stream0.readfrom(0, 0),
- '',
+ b'',
'reading zero bytes should have returned empty string')
self.assertEqual(stream0.readfrom(0, 2**26),
- 'foobar',
+ b'foobar',
'reading entire stream failed')
self.assertEqual(stream0.readfrom(2**26, 0),
- '',
+ b'',
'reading zero bytes should have returned empty string')
def _test_subset(self, collection, expected):
def test_collection_manifest_subset(self):
foobarbaz = self.write_foo_bar_baz()
self._test_subset(foobarbaz,
- [[3, '.', 'bar.txt', 'bar'],
- [3, '.', 'foo.txt', 'foo'],
- [3, './baz', 'baz.txt', 'baz']])
+ [[3, '.', 'bar.txt', b'bar'],
+ [3, '.', 'foo.txt', b'foo'],
+ [3, './baz', 'baz.txt', b'baz']])
self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" %
- (self.keep_client.put("foo"),
- self.keep_client.put("bar"))),
- [[3, '.', 'bar.txt', 'bar'],
- [3, '.', 'foo.txt', 'foo']])
+ (self.keep_client.put(b"foo"),
+ self.keep_client.put(b"bar"))),
+ [[3, '.', 'bar.txt', b'bar'],
+ [3, '.', 'foo.txt', b'foo']])
self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" %
- (self.keep_client.put("foo"),
- self.keep_client.put("bar"))),
- [[2, '.', 'fo.txt', 'fo'],
- [4, '.', 'obar.txt', 'obar']])
+ (self.keep_client.put(b"foo"),
+ self.keep_client.put(b"bar"))),
+ [[2, '.', 'fo.txt', b'fo'],
+ [4, '.', 'obar.txt', b'obar']])
self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" %
- (self.keep_client.put("foo"),
- self.keep_client.put("bar"))),
- [[2, '.', 'ar.txt', 'ar'],
- [2, '.', 'fo.txt', 'fo'],
- [2, '.', 'ob.txt', 'ob'],
- [0, '.', 'zero.txt', '']])
+ (self.keep_client.put(b"foo"),
+ self.keep_client.put(b"bar"))),
+ [[2, '.', 'ar.txt', b'ar'],
+ [2, '.', 'fo.txt', b'fo'],
+ [2, '.', 'ob.txt', b'ob'],
+ [0, '.', 'zero.txt', b'']])
def test_collection_empty_file(self):
cw = arvados.CollectionWriter(self.api_client)
cw.start_new_file('zero.txt')
- cw.write('')
+ cw.write(b'')
self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n")
self.check_manifest_file_sizes(cw.manifest_text(), [0])
cw = arvados.CollectionWriter(self.api_client)
cw.start_new_file('zero.txt')
- cw.write('')
+ cw.write(b'')
cw.start_new_file('one.txt')
- cw.write('1')
+ cw.write(b'1')
cw.start_new_stream('foo')
cw.start_new_file('zero.txt')
- cw.write('')
+ cw.write(b'')
self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0])
def test_no_implicit_normalize(self):
cw = arvados.CollectionWriter(self.api_client)
cw.start_new_file('b')
- cw.write('b')
+ cw.write(b'b')
cw.start_new_file('a')
- cw.write('')
+ cw.write(b'')
self.check_manifest_file_sizes(cw.manifest_text(), [1,0])
self.check_manifest_file_sizes(
arvados.CollectionReader(
return self.content[locator]
def test_stream_reader(self):
- keepblocks = {'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': 'abcdefghij',
- 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': 'klmnopqrstuvwxy',
- 'cccccccccccccccccccccccccccccccc+5': 'z0123'}
+ keepblocks = {
+ 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': b'abcdefghij',
+ 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': b'klmnopqrstuvwxy',
+ 'cccccccccccccccccccccccccccccccc+5': b'z0123',
+ }
mk = self.MockKeep(keepblocks)
sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk)
- content = 'abcdefghijklmnopqrstuvwxyz0123456789'
+ content = b'abcdefghijklmnopqrstuvwxyz0123456789'
self.assertEqual(sr.readfrom(0, 30), content[0:30])
self.assertEqual(sr.readfrom(2, 30), content[2:30])
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), '')
+ self.assertEqual(sr.readfrom(30, 5), b'')
def test_extract_file(self):
m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
def test_write_directory_tree_with_zero_recursion(self):
cwriter = arvados.CollectionWriter(self.api_client)
content = 'd1/d2/f3d1/f2f1'
- blockhash = hashlib.md5(content).hexdigest() + '+' + str(len(content))
+ blockhash = tutil.str_keep_locator(content)
cwriter.write_directory_tree(
self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
max_manifest_depth=0)
def test_write_multiple_files(self):
cwriter = arvados.CollectionWriter(self.api_client)
for letter in 'ABC':
- with self.make_test_file(letter) as testfile:
+ with self.make_test_file(letter.encode()) as testfile:
cwriter.write_file(testfile.name, letter)
self.assertEqual(
cwriter.manifest_text(),
with self.make_test_file() as testfile:
cwriter.write_file(testfile.name, 'test')
resumed = TestResumableWriter.from_state(cwriter.current_state())
- self.assertEquals(cwriter.manifest_text(), resumed.manifest_text(),
+ self.assertEqual(cwriter.manifest_text(), resumed.manifest_text(),
"resumed CollectionWriter had different manifest")
def test_resume_fails_when_missing_dependency(self):
with self.make_test_file() as testfile:
cwriter.write_file(testfile.name, 'test')
orig_mtime = os.fstat(testfile.fileno()).st_mtime
- testfile.write('extra')
+ testfile.write(b'extra')
testfile.flush()
os.utime(testfile.name, (orig_mtime, orig_mtime))
self.assertRaises(arvados.errors.StaleWriterStateError,
).manifest_text())
-class CollectionTestMixin(object):
- PROXY_RESPONSE = {
- 'items_available': 1,
- 'items': [{
- 'uuid': 'zzzzz-bi6l4-mockproxy012345',
- 'owner_uuid': 'zzzzz-tpzed-mockowner012345',
- 'service_host': tutil.TEST_HOST,
- 'service_port': 65535,
- 'service_ssl_flag': True,
- 'service_type': 'proxy',
- }]}
+class CollectionTestMixin(tutil.ApiClientMock):
API_COLLECTIONS = run_test_server.fixture('collections')
DEFAULT_COLLECTION = API_COLLECTIONS['foo_file']
DEFAULT_DATA_HASH = DEFAULT_COLLECTION['portable_data_hash']
ALT_DATA_HASH = ALT_COLLECTION['portable_data_hash']
ALT_MANIFEST = ALT_COLLECTION['manifest_text']
- def _mock_api_call(self, mock_method, code, body):
- mock_method = mock_method().execute
- if code == 200:
- mock_method.return_value = body
- else:
- mock_method.side_effect = arvados.errors.ApiError(
- tutil.fake_httplib2_response(code), "{}")
-
- def mock_keep_services(self, api_mock, code, body):
- self._mock_api_call(api_mock.keep_services().accessible, code, body)
-
- def api_client_mock(self, code=200):
- client = mock.MagicMock(name='api_client')
- self.mock_keep_services(client, code, self.PROXY_RESPONSE)
+ def api_client_mock(self, status=200):
+ client = super(CollectionTestMixin, self).api_client_mock()
+ self.mock_keep_services(client, status=status, service_type='proxy', count=1)
return client
@tutil.skip_sleep
class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin):
- def mock_get_collection(self, api_mock, code, body):
- body = self.API_COLLECTIONS.get(body)
+ def mock_get_collection(self, api_mock, code, fixturename):
+ body = self.API_COLLECTIONS.get(fixturename)
self._mock_api_call(api_mock.collections().get, code, body)
- def api_client_mock(self, code=200):
- client = super(CollectionReaderTestCase, self).api_client_mock(code)
- self.mock_get_collection(client, code, 'foo_file')
+ def api_client_mock(self, status=200):
+ client = super(CollectionReaderTestCase, self).api_client_mock()
+ self.mock_get_collection(client, status, 'foo_file')
return client
def test_init_no_default_retries(self):
def test_uuid_init_failure_raises_api_error(self):
client = self.api_client_mock(500)
- reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
with self.assertRaises(arvados.errors.ApiError):
- reader.manifest_text()
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
def test_locator_init(self):
client = self.api_client_mock(200)
# Ensure Keep will not return anything if asked.
- with tutil.mock_get_responses(None, 404):
+ with tutil.mock_keep_responses(None, 404):
reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
api_client=client)
self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
# been written to Keep.
client = self.api_client_mock(200)
self.mock_get_collection(client, 404, None)
- with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200):
+ with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
api_client=client)
self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
def test_uuid_init_no_fallback_to_keep(self):
# Do not look up a collection UUID in Keep.
client = self.api_client_mock(404)
- reader = arvados.CollectionReader(self.DEFAULT_UUID,
- api_client=client)
- with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200):
+ with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
with self.assertRaises(arvados.errors.ApiError):
- reader.manifest_text()
+ reader = arvados.CollectionReader(self.DEFAULT_UUID,
+ api_client=client)
def test_try_keep_first_if_permission_hint(self):
# To verify that CollectionReader tries Keep first here, we
# mock API server to return the wrong data.
client = self.api_client_mock(200)
- with tutil.mock_get_responses(self.ALT_MANIFEST, 200):
+ with tutil.mock_keep_responses(self.ALT_MANIFEST, 200):
self.assertEqual(
self.ALT_MANIFEST,
arvados.CollectionReader(
client = self.api_client_mock(200)
reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
num_retries=3)
- with tutil.mock_get_responses('foo', 500, 500, 200):
- self.assertEqual('foo',
- ''.join(f.read(9) for f in reader.all_files()))
+ with tutil.mock_keep_responses('foo', 500, 500, 200):
+ self.assertEqual(b'foo',
+ b''.join(f.read(9) for f in reader.all_files()))
def test_read_nonnormalized_manifest_with_collection_reader(self):
# client should be able to use CollectionReader on a manifest without normalizing it
def test_api_response_with_collection_from_keep(self):
client = self.api_client_mock()
self.mock_get_collection(client, 404, 'foo')
- with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200):
+ with tutil.mock_keep_responses(self.DEFAULT_MANIFEST, 200):
reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
api_client=client)
api_response = reader.api_response()
def check_open_file(self, coll_file, stream_name, file_name, file_size):
self.assertFalse(coll_file.closed, "returned file is not open")
self.assertEqual(stream_name, coll_file.stream_name())
- self.assertEqual(file_name, coll_file.name())
+ self.assertEqual(file_name, coll_file.name)
self.assertEqual(file_size, coll_file.size())
def test_open_collection_file_one_argument(self):
client = self.api_client_mock(200)
reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
- cfile = reader.open('./foo')
- self.check_open_file(cfile, '.', 'foo', 3)
-
- def test_open_collection_file_two_arguments(self):
- client = self.api_client_mock(200)
- reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
- cfile = reader.open('.', 'foo')
+ cfile = reader.open('./foo', 'rb')
self.check_open_file(cfile, '.', 'foo', 3)
def test_open_deep_file(self):
self.mock_get_collection(client, 200, coll_name)
reader = arvados.CollectionReader(
self.API_COLLECTIONS[coll_name]['uuid'], api_client=client)
- cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt')
+ cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt', 'rb')
self.check_open_file(cfile, './subdir2/subdir3', 'file2_in_subdir3.txt',
32)
def test_open_nonexistent_stream(self):
client = self.api_client_mock(200)
reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
- self.assertRaises(ValueError, reader.open, './nonexistent', 'foo')
+ self.assertRaises(IOError, reader.open, './nonexistent/foo')
def test_open_nonexistent_file(self):
client = self.api_client_mock(200)
reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
- self.assertRaises(ValueError, reader.open, '.', 'nonexistent')
+ self.assertRaises(IOError, reader.open, 'nonexistent')
@tutil.skip_sleep
class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin):
def mock_keep(self, body, *codes, **headers):
headers.setdefault('x-keep-replicas-stored', 2)
- return tutil.mock_put_responses(body, *codes, **headers)
+ return tutil.mock_keep_responses(body, *codes, **headers)
def foo_writer(self, **kwargs):
- api_client = self.api_client_mock()
- writer = arvados.CollectionWriter(api_client, **kwargs)
+ kwargs.setdefault('api_client', self.api_client_mock())
+ writer = arvados.CollectionWriter(**kwargs)
writer.start_new_file('foo')
- writer.write('foo')
+ writer.write(b'foo')
return writer
def test_write_whole_collection(self):
with self.assertRaises(arvados.errors.KeepWriteError):
writer.finish()
+ def test_write_insufficient_replicas_via_proxy(self):
+ writer = self.foo_writer(replication=3)
+ with self.mock_keep(None, 200, **{'x-keep-replicas-stored': 2}):
+ with self.assertRaises(arvados.errors.KeepWriteError):
+ writer.manifest_text()
+
+ def test_write_insufficient_replicas_via_disks(self):
+ client = mock.MagicMock(name='api_client')
+ with self.mock_keep(
+ None, 200, 200,
+ **{'x-keep-replicas-stored': 1}) as keepmock:
+ self.mock_keep_services(client, status=200, service_type='disk', count=2)
+ writer = self.foo_writer(api_client=client, replication=3)
+ with self.assertRaises(arvados.errors.KeepWriteError):
+ writer.manifest_text()
+
+ def test_write_three_replicas(self):
+ client = mock.MagicMock(name='api_client')
+ with self.mock_keep(
+ "", 500, 500, 500, 200, 200, 200,
+ **{'x-keep-replicas-stored': 1}) as keepmock:
+ self.mock_keep_services(client, status=200, service_type='disk', count=6)
+ writer = self.foo_writer(api_client=client, replication=3)
+ writer.manifest_text()
+ self.assertEqual(6, keepmock.call_count)
+
def test_write_whole_collection_through_retries(self):
writer = self.foo_writer(num_retries=2)
with self.mock_keep(self.DEFAULT_DATA_HASH,
with writer.open('out') as out_file:
self.assertEqual('.', writer.current_stream_name())
self.assertEqual('out', writer.current_file_name())
- out_file.write('test data')
- data_loc = hashlib.md5('test data').hexdigest() + '+9'
+ out_file.write(b'test data')
+ data_loc = tutil.str_keep_locator('test data')
self.assertTrue(out_file.closed, "writer file not closed after context")
self.assertRaises(ValueError, out_file.write, 'extra text')
with self.mock_keep(data_loc, 200) as keep_mock:
writer = arvados.CollectionWriter(client)
with writer.open('six') as out_file:
out_file.writelines(['12', '34', '56'])
- data_loc = hashlib.md5('123456').hexdigest() + '+6'
+ data_loc = tutil.str_keep_locator('123456')
with self.mock_keep(data_loc, 200) as keep_mock:
self.assertEqual(". {} 0:6:six\n".format(data_loc),
writer.manifest_text())
def test_open_flush(self):
client = self.api_client_mock()
- data_loc1 = hashlib.md5('flush1').hexdigest() + '+6'
- data_loc2 = hashlib.md5('flush2').hexdigest() + '+6'
+ data_loc1 = tutil.str_keep_locator('flush1')
+ data_loc2 = tutil.str_keep_locator('flush2')
with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
writer = arvados.CollectionWriter(client)
with writer.open('flush_test') as out_file:
- out_file.write('flush1')
+ out_file.write(b'flush1')
out_file.flush()
- out_file.write('flush2')
+ out_file.write(b'flush2')
self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1,
data_loc2),
writer.manifest_text())
client = self.api_client_mock()
writer = arvados.CollectionWriter(client)
with writer.open('.', '1') as out_file:
- out_file.write('1st')
+ out_file.write(b'1st')
with writer.open('.', '2') as out_file:
- out_file.write('2nd')
- data_loc = hashlib.md5('1st2nd').hexdigest() + '+6'
+ out_file.write(b'2nd')
+ data_loc = tutil.str_keep_locator('1st2nd')
with self.mock_keep(data_loc, 200) as keep_mock:
self.assertEqual(". {} 0:3:1 3:3:2\n".format(data_loc),
writer.manifest_text())
def test_two_opens_two_streams(self):
client = self.api_client_mock()
- data_loc1 = hashlib.md5('file').hexdigest() + '+4'
- data_loc2 = hashlib.md5('indir').hexdigest() + '+5'
+ data_loc1 = tutil.str_keep_locator('file')
+ data_loc2 = tutil.str_keep_locator('indir')
with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock:
writer = arvados.CollectionWriter(client)
with writer.open('file') as out_file:
- out_file.write('file')
+ out_file.write(b'file')
with writer.open('./dir', 'indir') as out_file:
- out_file.write('indir')
+ out_file.write(b'indir')
expected = ". {} 0:4:file\n./dir {} 0:5:indir\n".format(
data_loc1, data_loc2)
self.assertEqual(expected, writer.manifest_text())
self.assertRaises(arvados.errors.AssertionError, writer.open, 'two')
+class CollectionMethods(run_test_server.TestCaseWithServers):
+
+ def test_keys_values_items_support_indexing(self):
+ c = Collection()
+ with c.open('foo', 'wb') as f:
+ f.write(b'foo')
+ with c.open('bar', 'wb') as f:
+ f.write(b'bar')
+ self.assertEqual(2, len(c.keys()))
+ if sys.version_info < (3, 0):
+ # keys() supports indexing only for python2 callers.
+ fn0 = c.keys()[0]
+ fn1 = c.keys()[1]
+ else:
+ fn0, fn1 = c.keys()
+ self.assertEqual(2, len(c.values()))
+ f0 = c.values()[0]
+ f1 = c.values()[1]
+ self.assertEqual(2, len(c.items()))
+ self.assertEqual(fn0, c.items()[0][0])
+ self.assertEqual(fn1, c.items()[1][0])
+
+
+class CollectionOpenModes(run_test_server.TestCaseWithServers):
+
+ def test_open_binary_modes(self):
+ c = Collection()
+ for mode in ['wb', 'wb+', 'ab', 'ab+']:
+ with c.open('foo', mode) as f:
+ f.write(b'foo')
+
+ def test_open_invalid_modes(self):
+ c = Collection()
+ for mode in ['+r', 'aa', '++', 'r+b', 'beer', '', None]:
+ with self.assertRaises(Exception):
+ c.open('foo', mode)
+
+ def test_open_text_modes(self):
+ c = Collection()
+ with c.open('foo', 'wb') as f:
+ f.write('foo')
+ for mode in ['r', 'rt', 'r+', 'rt+', 'w', 'wt', 'a', 'at']:
+ if sys.version_info >= (3, 0):
+ with self.assertRaises(NotImplementedError):
+ c.open('foo', mode)
+ else:
+ with c.open('foo', mode) as f:
+ if mode[0] == 'r' and '+' not in mode:
+ self.assertEqual('foo', f.read(3))
+ else:
+ f.write('bar')
+ f.seek(-3, os.SEEK_CUR)
+ self.assertEqual('bar', f.read(3))
+
+
class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin):
- def test_import_manifest(self):
+
+ def test_replication_desired_kept_on_load(self):
+ m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
+ c1 = Collection(m, replication_desired=1)
+ c1.save_new()
+ loc = c1.manifest_locator()
+ c2 = Collection(loc)
+ self.assertEqual(c1.manifest_text, c2.manifest_text)
+ self.assertEqual(c1.replication_desired, c2.replication_desired)
+
+ def test_replication_desired_not_loaded_if_provided(self):
+ m = '. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n'
+ c1 = Collection(m, replication_desired=1)
+ c1.save_new()
+ loc = c1.manifest_locator()
+ c2 = Collection(loc, replication_desired=2)
+ self.assertEqual(c1.manifest_text, c2.manifest_text)
+ self.assertNotEqual(c1.replication_desired, c2.replication_desired)
+
+ def test_init_manifest(self):
m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
"""
- self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", arvados.export_manifest(arvados.import_manifest(m1)))
+ self.assertEqual(m1, CollectionReader(m1).manifest_text(normalize=False))
+ self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", CollectionReader(m1).manifest_text(normalize=True))
- def test_init_manifest(self):
+ def test_init_manifest_with_collision(self):
m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
-. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
-. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
+./md5sum.txt 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
"""
- self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", arvados.export_manifest(arvados.Collection(m1)))
+ with self.assertRaises(arvados.errors.ArgumentError):
+ self.assertEqual(m1, CollectionReader(m1))
+ def test_init_manifest_with_error(self):
+ m1 = """. 0:43:md5sum.txt"""
+ with self.assertRaises(arvados.errors.ArgumentError):
+ self.assertEqual(m1, CollectionReader(m1))
def test_remove(self):
- with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c:
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", export_manifest(c))
- self.assertTrue("count1.txt" in c)
- c.remove("count1.txt")
- self.assertFalse("count1.txt" in c)
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", export_manifest(c))
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
+ self.assertIn("count1.txt", c)
+ c.remove("count1.txt")
+ self.assertNotIn("count1.txt", c)
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
+ with self.assertRaises(arvados.errors.ArgumentError):
+ c.remove("")
+
+ def test_find(self):
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n')
+ self.assertIs(c.find("."), c)
+ self.assertIs(c.find("./count1.txt"), c["count1.txt"])
+ self.assertIs(c.find("count1.txt"), c["count1.txt"])
+ with self.assertRaises(IOError):
+ c.find("/.")
+ with self.assertRaises(arvados.errors.ArgumentError):
+ c.find("")
+ self.assertIs(c.find("./nonexistant.txt"), None)
+ self.assertIs(c.find("./nonexistantsubdir/nonexistant.txt"), None)
def test_remove_in_subdir(self):
- with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c:
- c.remove("foo/count2.txt")
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c))
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
+ c.remove("foo/count2.txt")
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
def test_remove_empty_subdir(self):
- with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c:
- c.remove("foo/count2.txt")
- c.remove("foo")
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c))
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
+ c.remove("foo/count2.txt")
+ c.remove("foo")
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
def test_remove_nonempty_subdir(self):
- with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c:
- with self.assertRaises(IOError):
- c.remove("foo")
- c.remove("foo", rm_r=True)
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c))
-
- def test_copy_to_dir1(self):
- with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n', sync=SYNC_EXPLICIT) as c:
- c.copy("count1.txt", "foo/count2.txt")
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", export_manifest(c))
-
- def test_copy_to_dir2(self):
- with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n', sync=SYNC_EXPLICIT) as c:
- c.copy("count1.txt", "foo")
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c))
-
- def test_copy_to_dir2(self):
- with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n', sync=SYNC_EXPLICIT) as c:
- c.copy("count1.txt", "foo/")
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c))
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
+ with self.assertRaises(IOError):
+ c.remove("foo")
+ c.remove("foo", recursive=True)
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
+
+ def test_copy_to_file_in_dir(self):
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c.copy("count1.txt", "foo/count2.txt")
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.portable_manifest_text())
def test_copy_file(self):
- with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n', sync=SYNC_EXPLICIT) as c:
- c.copy("count1.txt", "count2.txt")
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", export_manifest(c))
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c.copy("count1.txt", "count2.txt")
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
+
+ def test_copy_to_existing_dir(self):
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
+ c.copy("count1.txt", "foo")
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", c.portable_manifest_text())
+
+ def test_copy_to_new_dir(self):
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c.copy("count1.txt", "foo/")
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", c.portable_manifest_text())
+
+ def test_rename_file(self):
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c.rename("count1.txt", "count2.txt")
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
+
+ def test_move_file_to_dir(self):
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c.mkdirs("foo")
+ c.rename("count1.txt", "foo/count2.txt")
+ self.assertEqual("./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c.manifest_text())
+
+ def test_move_file_to_other(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c2 = Collection()
+ c2.rename("count1.txt", "count2.txt", source_collection=c1)
+ self.assertEqual("", c1.manifest_text())
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", c2.manifest_text())
+
+ def test_clone(self):
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
+ cl = c.clone()
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", cl.portable_manifest_text())
+
+ def test_diff_del_add(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
+ d = c2.diff(c1)
+ self.assertEqual(sorted(d), [
+ ('add', './count1.txt', c1["count1.txt"]),
+ ('del', './count2.txt', c2["count2.txt"]),
+ ])
+ d = c1.diff(c2)
+ self.assertEqual(sorted(d), [
+ ('add', './count2.txt', c2["count2.txt"]),
+ ('del', './count1.txt', c1["count1.txt"]),
+ ])
+ self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+ c1.apply(d)
+ self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+
+ def test_diff_same(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ d = c2.diff(c1)
+ self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
+ d = c1.diff(c2)
+ self.assertEqual(d, [('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
+
+ self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+ c1.apply(d)
+ self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+
+ def test_diff_mod(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
+ d = c2.diff(c1)
+ self.assertEqual(d, [('mod', './count1.txt', c2["count1.txt"], c1["count1.txt"])])
+ d = c1.diff(c2)
+ self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
+
+ self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+ c1.apply(d)
+ self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+
+ def test_diff_add(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt 10:20:count2.txt\n')
+ d = c2.diff(c1)
+ self.assertEqual(sorted(d), [
+ ('del', './count2.txt', c2["count2.txt"]),
+ ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
+ ])
+ d = c1.diff(c2)
+ self.assertEqual(sorted(d), [
+ ('add', './count2.txt', c2["count2.txt"]),
+ ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
+ ])
+
+ self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+ c1.apply(d)
+ self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+
+ def test_diff_add_in_subcollection(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
+ d = c2.diff(c1)
+ self.assertEqual(sorted(d), [
+ ('del', './foo', c2["foo"]),
+ ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
+ ])
+ d = c1.diff(c2)
+ self.assertEqual(sorted(d), [
+ ('add', './foo', c2["foo"]),
+ ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
+ ])
+ self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+ c1.apply(d)
+ self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+
+ def test_diff_del_add_in_subcollection(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
+ c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:3:count3.txt\n')
+ d = c2.diff(c1)
+ self.assertEqual(sorted(d), [
+ ('add', './foo/count2.txt', c1.find("foo/count2.txt")),
+ ('del', './foo/count3.txt', c2.find("foo/count3.txt")),
+ ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
+ ])
+ d = c1.diff(c2)
+ self.assertEqual(sorted(d), [
+ ('add', './foo/count3.txt', c2.find("foo/count3.txt")),
+ ('del', './foo/count2.txt', c1.find("foo/count2.txt")),
+ ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
+ ])
+
+ self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+ c1.apply(d)
+ self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+
+ def test_diff_mod_in_subcollection(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
+ c2 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:3:foo\n')
+ d = c2.diff(c1)
+ self.assertEqual(sorted(d), [
+ ('mod', './foo', c2["foo"], c1["foo"]),
+ ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
+ ])
+ d = c1.diff(c2)
+ self.assertEqual(sorted(d), [
+ ('mod', './foo', c1["foo"], c2["foo"]),
+ ('tok', './count1.txt', c2["count1.txt"], c1["count1.txt"]),
+ ])
+
+ self.assertNotEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+ c1.apply(d)
+ self.assertEqual(c1.portable_manifest_text(), c2.portable_manifest_text())
+
+ def test_conflict_keep_local_change(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n')
+ c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count2.txt\n')
+ d = c1.diff(c2)
+ self.assertEqual(sorted(d), [
+ ('add', './count2.txt', c2["count2.txt"]),
+ ('del', './count1.txt', c1["count1.txt"]),
+ ])
+ f = c1.open("count1.txt", "wb")
+ f.write(b"zzzzz")
+
+ # c1 changed, so it should not be deleted.
+ c1.apply(d)
+ self.assertEqual(c1.portable_manifest_text(), ". 95ebc3c7b3b9f1d2c40fec14415d3cb8+5 5348b82a029fd9e971a811ce1f71360b+43 0:5:count1.txt 5:10:count2.txt\n")
+
+ def test_conflict_mod(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
+ c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
+ d = c1.diff(c2)
+ self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
+ f = c1.open("count1.txt", "wb")
+ f.write(b"zzzzz")
+
+ # c1 changed, so c2 mod will go to a conflict file
+ c1.apply(d)
+ self.assertRegex(
+ c1.portable_manifest_text(),
+ r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
+
+ def test_conflict_add(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n')
+ c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt\n')
+ d = c1.diff(c2)
+ self.assertEqual(sorted(d), [
+ ('add', './count1.txt', c2["count1.txt"]),
+ ('del', './count2.txt', c1["count2.txt"]),
+ ])
+ f = c1.open("count1.txt", "wb")
+ f.write(b"zzzzz")
+
+ # c1 added count1.txt, so c2 add will go to a conflict file
+ c1.apply(d)
+ self.assertRegex(
+ c1.portable_manifest_text(),
+ r"\. 95ebc3c7b3b9f1d2c40fec14415d3cb8\+5 5348b82a029fd9e971a811ce1f71360b\+43 0:5:count1\.txt 5:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
+
+ def test_conflict_del(self):
+ c1 = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt')
+ c2 = Collection('. 5348b82a029fd9e971a811ce1f71360b+43 0:10:count1.txt')
+ d = c1.diff(c2)
+ self.assertEqual(d, [('mod', './count1.txt', c1["count1.txt"], c2["count1.txt"])])
+ c1.remove("count1.txt")
+
+ # c1 deleted, so c2 mod will go to a conflict file
+ c1.apply(d)
+ self.assertRegex(
+ c1.portable_manifest_text(),
+ r"\. 5348b82a029fd9e971a811ce1f71360b\+43 0:10:count1\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
+
+ def test_notify(self):
+ c1 = Collection()
+ events = []
+ c1.subscribe(lambda event, collection, name, item: events.append((event, collection, name, item)))
+ f = c1.open("foo.txt", "wb")
+ self.assertEqual(events[0], (arvados.collection.ADD, c1, "foo.txt", f.arvadosfile))
+
+ def test_open_w(self):
+ c1 = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n")
+ self.assertEqual(c1["count1.txt"].size(), 10)
+ c1.open("count1.txt", "wb").close()
+ self.assertEqual(c1["count1.txt"].size(), 0)
+
+
+class NewCollectionTestCaseWithServersAndTokens(run_test_server.TestCaseWithServers):
+ MAIN_SERVER = {}
+ KEEP_SERVER = {}
+
+ def setUp(self):
+ self.keep_put = getattr(arvados.keep.KeepClient, 'put')
+
+ def test_repacked_block_submission_get_permission_token(self):
+ '''
+ Make sure that those blocks that are committed after repacking small ones,
+ get their permission tokens assigned on the collection manifest.
+ '''
+ def wrapped_keep_put(*args, **kwargs):
+ # Simulate slow put operations
+ time.sleep(1)
+ return self.keep_put(*args, **kwargs)
+
+ re_locator = "[0-9a-f]{32}\+\d+\+A[a-f0-9]{40}@[a-f0-9]{8}"
+
+ with mock.patch('arvados.keep.KeepClient.put', autospec=True) as mocked_put:
+ mocked_put.side_effect = wrapped_keep_put
+ c = Collection()
+ # Write 70 files ~1MiB each so we force to produce 1 big block by repacking
+ # small ones before finishing the upload.
+ for i in range(70):
+ f = c.open("file_{}.txt".format(i), 'wb')
+ f.write(random.choice('abcdefghijklmnopqrstuvwxyz') * (2**20+i))
+ f.close(flush=False)
+ # We should get 2 blocks with their tokens
+ self.assertEqual(len(re.findall(re_locator, c.manifest_text())), 2)
+
+
+class NewCollectionTestCaseWithServers(run_test_server.TestCaseWithServers):
+ def test_get_manifest_text_only_committed(self):
+ c = Collection()
+ with c.open("count.txt", "wb") as f:
+ # One file committed
+ with c.open("foo.txt", "wb") as foo:
+ foo.write(b"foo")
+ foo.flush() # Force block commit
+ f.write(b"0123456789")
+ # Other file not committed. Block not written to keep yet.
+ self.assertEqual(
+ c._get_manifest_text(".",
+ strip=False,
+ normalize=False,
+ only_committed=True),
+ '. acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:count.txt 0:3:foo.txt\n')
+ # And now with the file closed...
+ f.flush() # Force block commit
+ self.assertEqual(
+ c._get_manifest_text(".",
+ strip=False,
+ normalize=False,
+ only_committed=True),
+ ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:10:count.txt 10:3:foo.txt\n")
+
+ def test_only_small_blocks_are_packed_together(self):
+ c = Collection()
+ # Write a couple of small files,
+ f = c.open("count.txt", "wb")
+ f.write(b"0123456789")
+ f.close(flush=False)
+ foo = c.open("foo.txt", "wb")
+ foo.write(b"foo")
+ foo.close(flush=False)
+ # Then, write a big file, it shouldn't be packed with the ones above
+ big = c.open("bigfile.txt", "wb")
+ big.write(b"x" * 1024 * 1024 * 33) # 33 MB > KEEP_BLOCK_SIZE/2
+ big.close(flush=False)
+ self.assertEqual(
+ c.manifest_text("."),
+ '. 2d303c138c118af809f39319e5d507e9+34603008 a8430a058b8fbf408e1931b794dbd6fb+13 0:34603008:bigfile.txt 34603008:10:count.txt 34603018:3:foo.txt\n')
+
+ def test_flush_after_small_block_packing(self):
+ c = Collection()
+ # Write a couple of small files,
+ f = c.open("count.txt", "wb")
+ f.write(b"0123456789")
+ f.close(flush=False)
+ foo = c.open("foo.txt", "wb")
+ foo.write(b"foo")
+ foo.close(flush=False)
+
+ self.assertEqual(
+ c.manifest_text(),
+ '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
+
+ f = c.open("count.txt", "rb+")
+ f.close(flush=True)
+
+ self.assertEqual(
+ c.manifest_text(),
+ '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
+
+ def test_write_after_small_block_packing2(self):
+ c = Collection()
+ # Write a couple of small files,
+ f = c.open("count.txt", "wb")
+ f.write(b"0123456789")
+ f.close(flush=False)
+ foo = c.open("foo.txt", "wb")
+ foo.write(b"foo")
+ foo.close(flush=False)
+
+ self.assertEqual(
+ c.manifest_text(),
+ '. a8430a058b8fbf408e1931b794dbd6fb+13 0:10:count.txt 10:3:foo.txt\n')
+
+ f = c.open("count.txt", "rb+")
+ f.write(b"abc")
+ f.close(flush=False)
+
+ self.assertEqual(
+ c.manifest_text(),
+ '. 900150983cd24fb0d6963f7d28e17f72+3 a8430a058b8fbf408e1931b794dbd6fb+13 0:3:count.txt 6:7:count.txt 13:3:foo.txt\n')
+
+
+ def test_small_block_packing_with_overwrite(self):
+ c = Collection()
+ c.open("b1", "wb").close()
+ c["b1"].writeto(0, b"b1", 0)
+
+ c.open("b2", "wb").close()
+ c["b2"].writeto(0, b"b2", 0)
+
+ c["b1"].writeto(0, b"1b", 0)
+
+ self.assertEquals(c.manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1 2:2:b2\n")
+ self.assertEquals(c["b1"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 0:2:b1\n")
+ self.assertEquals(c["b2"].manifest_text(), ". ed4f3f67c70b02b29c50ce1ea26666bd+4 2:2:b2\n")
+
+
+class CollectionCreateUpdateTest(run_test_server.TestCaseWithServers):
+ MAIN_SERVER = {}
+ KEEP_SERVER = {}
+
+ def create_count_txt(self):
+ # Create an empty collection, save it to the API server, then write a
+ # file, but don't save it.
+
+ c = Collection()
+ c.save_new("CollectionCreateUpdateTest", ensure_unique_name=True)
+ self.assertEqual(c.portable_data_hash(), "d41d8cd98f00b204e9800998ecf8427e+0")
+ self.assertEqual(c.api_response()["portable_data_hash"], "d41d8cd98f00b204e9800998ecf8427e+0" )
+
+ with c.open("count.txt", "wb") as f:
+ f.write(b"0123456789")
+
+ self.assertEqual(c.portable_manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
+
+ return c
+
+ def test_create_and_save(self):
+ c = self.create_count_txt()
+ c.save()
+ self.assertRegex(
+ c.manifest_text(),
+ r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
+
+ def test_create_and_save_new(self):
+ c = self.create_count_txt()
+ c.save_new()
+ self.assertRegex(
+ c.manifest_text(),
+ r"^\. 781e5e245d69b566979b86e28d23f2c7\+10\+A[a-f0-9]{40}@[a-f0-9]{8} 0:10:count\.txt$",)
+
+ def test_create_diff_apply(self):
+ c1 = self.create_count_txt()
+ c1.save()
+
+ c2 = Collection(c1.manifest_locator())
+ with c2.open("count.txt", "wb") as f:
+ f.write(b"abcdefg")
+
+ diff = c1.diff(c2)
+
+ self.assertEqual(diff[0], (arvados.collection.MOD, u'./count.txt', c1["count.txt"], c2["count.txt"]))
+
+ c1.apply(diff)
+ self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
+
+ def test_diff_apply_with_token(self):
+ baseline = CollectionReader(". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:10:count.txt\n")
+ c = Collection(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n")
+ other = CollectionReader(". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
+
+ diff = baseline.diff(other)
+ self.assertEqual(diff, [('mod', u'./count.txt', c["count.txt"], other["count.txt"])])
+
+ c.apply(diff)
+
+ self.assertEqual(c.manifest_text(), ". 7ac66c0f148de9519b8bd264312c4d64+7+A715fd31f8111894f717eb1003c1b0216799dd9ec@54f5dd1a 0:7:count.txt\n")
+
+
+ def test_create_and_update(self):
+ c1 = self.create_count_txt()
+ c1.save()
+
+ c2 = arvados.collection.Collection(c1.manifest_locator())
+ with c2.open("count.txt", "wb") as f:
+ f.write(b"abcdefg")
+
+ c2.save()
+
+ self.assertNotEqual(c1.portable_data_hash(), c2.portable_data_hash())
+ c1.update()
+ self.assertEqual(c1.portable_data_hash(), c2.portable_data_hash())
+
+
+ def test_create_and_update_with_conflict(self):
+ c1 = self.create_count_txt()
+ c1.save()
+
+ with c1.open("count.txt", "wb") as f:
+ f.write(b"XYZ")
+
+ c2 = arvados.collection.Collection(c1.manifest_locator())
+ with c2.open("count.txt", "wb") as f:
+ f.write(b"abcdefg")
+
+ c2.save()
+
+ c1.update()
+ self.assertRegex(
+ c1.manifest_text(),
+ r"\. e65075d550f9b5bf9992fa1d71a131be\+3\S* 7ac66c0f148de9519b8bd264312c4d64\+7\S* 0:3:count\.txt 3:7:count\.txt~\d\d\d\d\d\d\d\d-\d\d\d\d\d\d~conflict~$")
+
+ def test_pdh_is_native_str(self):
+ c1 = self.create_count_txt()
+ pdh = c1.portable_data_hash()
+ self.assertEqual(type(''), type(pdh))
if __name__ == '__main__':
projects / arvados.git / blobdiff