import mock
import os
import unittest
-import hashlib
+import time
import arvados
-from arvados import Range, KeepLocator
-from arvados.collection import import_manifest, export_manifest, ReadOnlyCollection, WritableCollection
-from arvados.arvfile import ArvadosFile, ArvadosFileReader, SYNC_READONLY, SYNC_EXPLICIT
+from arvados._ranges import Range
+from arvados.keep import KeepLocator
+from arvados.collection import Collection, CollectionReader
+from arvados.arvfile import ArvadosFile, ArvadosFileReader
import arvados_testutil as tutil
from test_stream import StreamFileReaderTestCase, StreamRetryTestMixin
self.requests.append(locator)
return self.blocks.get(locator)
def put(self, data, num_retries=None):
- pdh = "%s+%i" % (hashlib.md5(data).hexdigest(), len(data))
+ pdh = tutil.str_keep_locator(data)
self.blocks[pdh] = str(data)
return pdh
def __init__(self, b, r):
self.body = b
self.response = r
+ self._schema = ArvadosFileWriterTestCase.MockApi.MockSchema()
+ class MockSchema(object):
+ def __init__(self):
+ self.schemas = {'Collection': {'properties': {'replication_desired': 2}}}
class MockCollections(object):
def __init__(self, b, r):
self.body = b
def test_truncate(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate",
- "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"},
+ "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
+ "replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual(writer.size(), 10)
- writer.seek(5)
- self.assertEqual("56789", writer.read(8))
+ self.assertEqual("0123456789", writer.read(12))
+
writer.truncate(8)
- writer.seek(5, os.SEEK_SET)
- self.assertEqual("567", writer.read(8))
- self.assertEqual(None, c._manifest_locator)
- self.assertEqual(True, c.modified())
+ # Make sure reading off the end doesn't break
+ self.assertEqual("", writer.read(12))
+
+ self.assertEqual(writer.size(), 8)
+ writer.seek(0, os.SEEK_SET)
+ self.assertEqual("01234567", writer.read(12))
+
+ self.assertIsNone(c.manifest_locator())
+ self.assertTrue(c.modified())
c.save_new("test_truncate")
- self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
- self.assertEqual(False, c.modified())
+ self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
+ self.assertFalse(c.modified())
def test_write_to_end(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_append",
- "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"},
+ "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
+ "replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual(writer.size(), 10)
writer.seek(5, os.SEEK_SET)
self.assertEqual("56789foo", writer.read(8))
- self.assertEqual(None, c._manifest_locator)
- self.assertEqual(True, c.modified())
- self.assertEqual(None, keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
+ self.assertIsNone(c.manifest_locator())
+ self.assertTrue(c.modified())
+ self.assertIsNone(keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
c.save_new("test_append")
- self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
- self.assertEqual(False, c.modified())
+ self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
+ self.assertFalse(c.modified())
self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
def test_append(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
- c = WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep)
+ c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep)
writer = c.open("count.txt", "a+")
self.assertEqual(writer.read(20), "0123456789")
writer.seek(0, os.SEEK_SET)
writer.write("world")
self.assertEqual(writer.read(20), "0123456789helloworld")
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", export_manifest(c))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.portable_manifest_text())
def test_write_at_beginning(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual("0123456789", writer.readfrom(0, 13))
writer.write("foo")
self.assertEqual(writer.size(), 10)
self.assertEqual("foo3456789", writer.readfrom(0, 13))
- self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", export_manifest(c))
+ self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", c.portable_manifest_text())
+
+ def test_write_empty(self):
+ keep = ArvadosFileWriterTestCase.MockKeep({})
+ with Collection(keep_client=keep) as c:
+ writer = c.open("count.txt", "w")
+ self.assertEqual(writer.size(), 0)
+ self.assertEqual(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n", c.portable_manifest_text())
+
+ def test_save_manifest_text(self):
+ keep = ArvadosFileWriterTestCase.MockKeep({})
+ with Collection(keep_client=keep) as c:
+ writer = c.open("count.txt", "w")
+ writer.write("0123456789")
+ self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
+ self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
+
+ self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.save_new(create_collection_record=False))
+ self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
+
+ def test_get_manifest_text_commits(self):
+ keep = ArvadosFileWriterTestCase.MockKeep({})
+ with Collection(keep_client=keep) as c:
+ writer = c.open("count.txt", "w")
+ writer.write("0123456789")
+ self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
+ self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
+ self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text())
+ self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
+
def test_write_in_middle(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual("0123456789", writer.readfrom(0, 13))
writer.write("foo")
self.assertEqual(writer.size(), 10)
self.assertEqual("012foo6789", writer.readfrom(0, 13))
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", export_manifest(c))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.portable_manifest_text())
def test_write_at_end(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual("0123456789", writer.readfrom(0, 13))
writer.write("foo")
self.assertEqual(writer.size(), 10)
self.assertEqual("0123456foo", writer.readfrom(0, 13))
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", export_manifest(c))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text())
def test_write_across_segment_boundary(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual("012345678901234", writer.readfrom(0, 15))
writer.write("foobar")
self.assertEqual(writer.size(), 20)
self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", export_manifest(c))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text())
def test_write_across_several_segments(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual("012301230123", writer.readfrom(0, 15))
writer.write("abcdefg")
self.assertEqual(writer.size(), 12)
self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", export_manifest(c))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text())
def test_write_large(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
- "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"},
+ "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
+ "replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"})
- with WritableCollection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
+ with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
- text = ''.join(["0123456789" for a in xrange(0, 100)])
+ text = "0123456789" * 100
for b in xrange(0, 100000):
writer.write(text)
self.assertEqual(writer.size(), 100000000)
- self.assertEqual(None, c._manifest_locator)
- self.assertEqual(True, c.modified())
+ self.assertIsNone(c.manifest_locator())
+ self.assertTrue(c.modified())
c.save_new("test_write_large")
- self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
- self.assertEqual(False, c.modified())
+ self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
+ self.assertFalse(c.modified())
+
+
+ def test_large_write(self):
+ keep = ArvadosFileWriterTestCase.MockKeep({})
+ api = ArvadosFileWriterTestCase.MockApi({}, {})
+ with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
+ api_client=api, keep_client=keep) as c:
+ writer = c.open("count.txt", "r+")
+ self.assertEqual(writer.size(), 0)
+
+ text = "0123456789"
+ writer.write(text)
+ text = "0123456789" * 9999999
+ writer.write(text)
+ self.assertEqual(writer.size(), 100000000)
+
+ self.assertEqual(c.manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n")
def test_rewrite_on_empty_file(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
- with WritableCollection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
+ with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
for b in xrange(0, 10):
writer.seek(0, os.SEEK_SET)
writer.write("0123456789")
- writer.arvadosfile._repack_writes()
+
+ self.assertEqual(writer.size(), 10)
+ self.assertEqual("0123456789", writer.readfrom(0, 20))
+ self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.portable_manifest_text())
+ writer.flush()
self.assertEqual(writer.size(), 10)
self.assertEqual("0123456789", writer.readfrom(0, 20))
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", export_manifest(c))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.portable_manifest_text())
def test_rewrite_append_existing_file(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
for b in xrange(0, 10):
writer.seek(10, os.SEEK_SET)
writer.write("abcdefghij")
- writer.arvadosfile._repack_writes()
+
self.assertEqual(writer.size(), 20)
self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
- self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", export_manifest(c))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.portable_manifest_text())
+
+ writer.arvadosfile.flush()
+ self.assertEqual(writer.size(), 20)
+ self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.portable_manifest_text())
def test_rewrite_over_existing_file(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
for b in xrange(0, 10):
writer.seek(5, os.SEEK_SET)
writer.write("abcdefghij")
- writer.arvadosfile._repack_writes()
+
+ self.assertEqual(writer.size(), 15)
+ self.assertEqual("01234abcdefghij", writer.readfrom(0, 20))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.portable_manifest_text())
+
+ writer.arvadosfile.flush()
+
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", export_manifest(c))
+ self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.portable_manifest_text())
def test_write_large_rewrite(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large",
- "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"},
+ "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n",
+ "replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"})
- with WritableCollection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
+ with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
text = ''.join(["0123456789" for a in xrange(0, 100)])
writer.write("foo")
self.assertEqual(writer.size(), 100000000)
- self.assertEqual(None, c._manifest_locator)
- self.assertEqual(True, c.modified())
+ self.assertIsNone(c.manifest_locator())
+ self.assertTrue(c.modified())
c.save_new("test_write_large")
- self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
- self.assertEqual(False, c.modified())
+ self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
+ self.assertFalse(c.modified())
def test_create(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
- "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
+ "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
+ "replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
- with WritableCollection(api_client=api, keep_client=keep) as c:
+ with Collection(api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "w+")
self.assertEqual(writer.size(), 0)
writer.write("01234567")
self.assertEqual(writer.size(), 8)
- self.assertEqual(None, c._manifest_locator)
- self.assertEqual(True, c.modified())
- self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
+ self.assertIsNone(c.manifest_locator())
+ self.assertTrue(c.modified())
+ self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
c.save_new("test_create")
- self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
- self.assertEqual(False, c.modified())
+ self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
+ self.assertFalse(c.modified())
self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
def test_create_subdir(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_create",
- "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
+ "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
+ "replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
- with WritableCollection(api_client=api, keep_client=keep) as c:
+ with Collection(api_client=api, keep_client=keep) as c:
self.assertIsNone(c.api_response())
writer = c.open("foo/bar/count.txt", "w+")
writer.write("01234567")
+ self.assertFalse(c.committed())
c.save_new("test_create")
+ self.assertTrue(c.committed())
self.assertEqual(c.api_response(), api.response)
def test_overwrite(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite",
- "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"},
+ "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
+ "replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "w+")
self.assertEqual(writer.size(), 0)
writer.write("01234567")
self.assertEqual(writer.size(), 8)
- self.assertEqual(None, c._manifest_locator)
- self.assertEqual(True, c.modified())
+ self.assertIsNone(c.manifest_locator())
+ self.assertTrue(c.modified())
c.save_new("test_overwrite")
- self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
- self.assertEqual(False, c.modified())
+ self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
+ self.assertFalse(c.modified())
def test_file_not_found(self):
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
with self.assertRaises(IOError):
writer = c.open("nocount.txt", "r")
def test_cannot_open_directory(self):
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c:
with self.assertRaises(IOError):
writer = c.open(".", "r")
def test_create_multiple(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple",
- "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"},
+ "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
+ "replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"})
- with WritableCollection(api_client=api, keep_client=keep) as c:
+ with Collection(api_client=api, keep_client=keep) as c:
w1 = c.open("count1.txt", "w")
w2 = c.open("count2.txt", "w")
w1.write("01234567")
self.assertEqual(w1.size(), 8)
self.assertEqual(w2.size(), 8)
- self.assertEqual(None, c._manifest_locator)
- self.assertEqual(True, c.modified())
- self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8"))
+ self.assertIsNone(c.manifest_locator())
+ self.assertTrue(c.modified())
+ self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
c.save_new("test_create_multiple")
- self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator)
- self.assertEqual(False, c.modified())
+ self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
+ self.assertFalse(c.modified())
self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8"))
def _my_block_manager(self):
return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache)
- def sync_mode(self):
- return SYNC_READONLY
-
def make_count_reader(self, nocache=False):
stream = []
n = 0
blocks = {}
for d in ['01234', '34567', '67890']:
- loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d))
+ loc = tutil.str_keep_locator(d)
blocks[loc] = d
stream.append(Range(loc, n, len(d)))
n += len(d)
- af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
- return ArvadosFileReader(af, "count.txt")
+ af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), "count.txt", stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)])
+ return ArvadosFileReader(af)
- def test_read_returns_first_block(self):
- # read() calls will be aligned on block boundaries - see #3663.
+ def test_read_block_crossing_behavior(self):
+ # read() needs to return all the data requested if possible, even if it
+ # crosses uncached blocks: https://arvados.org/issues/5856
sfile = self.make_count_reader(nocache=True)
- self.assertEqual('123', sfile.read(10))
+ self.assertEqual('12345678', sfile.read(8))
def test_successive_reads(self):
+ # Override StreamFileReaderTestCase.test_successive_reads
sfile = self.make_count_reader(nocache=True)
- for expect in ['123', '456', '789', '']:
- self.assertEqual(expect, sfile.read(10))
+ self.assertEqual('1234', sfile.read(4))
+ self.assertEqual('5678', sfile.read(4))
+ self.assertEqual('9', sfile.read(4))
+ self.assertEqual('', sfile.read(4))
def test_tell_after_block_read(self):
+ # Override StreamFileReaderTestCase.test_tell_after_block_read
sfile = self.make_count_reader(nocache=True)
- sfile.read(5)
- self.assertEqual(3, sfile.tell())
+ self.assertEqual('12345678', sfile.read(8))
+ self.assertEqual(8, sfile.tell())
def test_prefetch(self):
keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
- with WritableCollection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
+ with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
r = c.open("count.txt", "r")
self.assertEqual("0123", r.read(4))
self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
def test__eq__from_manifest(self):
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2:
self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
def test__eq__from_writes(self):
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
- with WritableCollection() as c2:
- with c2.open("count1.txt", "w") as f:
- f.write("0123456789")
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
+ with Collection() as c2:
+ f = c2.open("count1.txt", "w")
+ f.write("0123456789")
self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
def test__ne__(self):
- with WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
- with WritableCollection() as c2:
- with c2.open("count1.txt", "w") as f:
- f.write("1234567890")
+ with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
+ with Collection() as c2:
+ f = c2.open("count1.txt", "w")
+ f.write("1234567890")
self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
n += k.size
except ValueError:
pass
- col = ReadOnlyCollection(keep_client=self.keep_client())
- col._my_block_manager().prefetch_enabled = False
- af = ArvadosFile(col,
+
+ blockmanager = arvados.arvfile._BlockManager(self.keep_client())
+ blockmanager.prefetch_enabled = False
+ col = Collection(keep_client=self.keep_client(), block_manager=blockmanager)
+ af = ArvadosFile(col, "test",
stream=stream,
segments=segments)
- return ArvadosFileReader(af, "test", **kwargs)
+ return ArvadosFileReader(af, **kwargs)
def read_for_test(self, reader, byte_count, **kwargs):
return reader.read(byte_count, **kwargs)
class BlockManagerTest(unittest.TestCase):
def test_bufferblock_append(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
- blockmanager = arvados.arvfile.BlockManager(keep)
- bufferblock = blockmanager.alloc_bufferblock()
- bufferblock.append("foo")
+ with arvados.arvfile._BlockManager(keep) as blockmanager:
+ bufferblock = blockmanager.alloc_bufferblock()
+ bufferblock.append("foo")
- self.assertEqual(bufferblock.size(), 3)
- self.assertEqual(bufferblock.buffer_view[0:3], "foo")
- self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
+ self.assertEqual(bufferblock.size(), 3)
+ self.assertEqual(bufferblock.buffer_view[0:3], "foo")
+ self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
- bufferblock.append("bar")
+ bufferblock.append("bar")
- self.assertEqual(bufferblock.size(), 6)
- self.assertEqual(bufferblock.buffer_view[0:6], "foobar")
- self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
+ self.assertEqual(bufferblock.size(), 6)
+ self.assertEqual(bufferblock.buffer_view[0:6], "foobar")
+ self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6")
- bufferblock.set_state(arvados.arvfile.BufferBlock.PENDING)
- with self.assertRaises(arvados.errors.AssertionError):
- bufferblock.append("bar")
+ bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
+ with self.assertRaises(arvados.errors.AssertionError):
+ bufferblock.append("bar")
def test_bufferblock_dup(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
- blockmanager = arvados.arvfile.BlockManager(keep)
- bufferblock = blockmanager.alloc_bufferblock()
- bufferblock.append("foo")
+ with arvados.arvfile._BlockManager(keep) as blockmanager:
+ bufferblock = blockmanager.alloc_bufferblock()
+ bufferblock.append("foo")
- self.assertEqual(bufferblock.size(), 3)
- self.assertEqual(bufferblock.buffer_view[0:3], "foo")
- self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
- bufferblock.set_state(arvados.arvfile.BufferBlock.PENDING)
+ self.assertEqual(bufferblock.size(), 3)
+ self.assertEqual(bufferblock.buffer_view[0:3], "foo")
+ self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
+ bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING)
- bufferblock2 = blockmanager.dup_block(bufferblock, None)
- self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
+ bufferblock2 = blockmanager.dup_block(bufferblock, None)
+ self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid)
- bufferblock2.append("bar")
+ bufferblock2.append("bar")
- self.assertEqual(bufferblock2.size(), 6)
- self.assertEqual(bufferblock2.buffer_view[0:6], "foobar")
- self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
+ self.assertEqual(bufferblock2.size(), 6)
+ self.assertEqual(bufferblock2.buffer_view[0:6], "foobar")
+ self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6")
- self.assertEqual(bufferblock.size(), 3)
- self.assertEqual(bufferblock.buffer_view[0:3], "foo")
- self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
+ self.assertEqual(bufferblock.size(), 3)
+ self.assertEqual(bufferblock.buffer_view[0:3], "foo")
+ self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3")
def test_bufferblock_get(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
- blockmanager = arvados.arvfile.BlockManager(keep)
- bufferblock = blockmanager.alloc_bufferblock()
- bufferblock.append("foo")
+ with arvados.arvfile._BlockManager(keep) as blockmanager:
+ bufferblock = blockmanager.alloc_bufferblock()
+ bufferblock.append("foo")
- self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), "0123456789")
- self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), "foo")
+ self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), "0123456789")
+ self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), "foo")
def test_bufferblock_commit(self):
mockkeep = mock.MagicMock()
- blockmanager = arvados.arvfile.BlockManager(mockkeep)
- bufferblock = blockmanager.alloc_bufferblock()
- bufferblock.append("foo")
- blockmanager.commit_all()
- self.assertTrue(mockkeep.put.called)
- self.assertEqual(bufferblock.state(), arvados.arvfile.BufferBlock.COMMITTED)
- self.assertIsNone(bufferblock.buffer_view)
+ with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
+ bufferblock = blockmanager.alloc_bufferblock()
+ bufferblock.owner = mock.MagicMock()
+ def flush(sync=None):
+ blockmanager.commit_bufferblock(bufferblock, sync)
+ bufferblock.owner.flush.side_effect = flush
+ bufferblock.append("foo")
+ blockmanager.commit_all()
+ self.assertTrue(bufferblock.owner.flush.called)
+ self.assertTrue(mockkeep.put.called)
+ self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
+ self.assertIsNone(bufferblock.buffer_view)
+
+ def test_bufferblock_commit_pending(self):
+ # Test for bug #7225
+ mockkeep = mock.MagicMock()
+ mockkeep.put.side_effect = lambda x: time.sleep(1)
+ with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
+ bufferblock = blockmanager.alloc_bufferblock()
+ bufferblock.append("foo")
+
+ blockmanager.commit_bufferblock(bufferblock, False)
+ self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)
+
+ blockmanager.commit_bufferblock(bufferblock, True)
+ self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED)
def test_bufferblock_commit_with_error(self):
mockkeep = mock.MagicMock()
mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail")
- blockmanager = arvados.arvfile.BlockManager(mockkeep)
- bufferblock = blockmanager.alloc_bufferblock()
- bufferblock.append("foo")
- with self.assertRaises(arvados.errors.KeepWriteError) as err:
- blockmanager.commit_all()
- self.assertEquals(str(err.exception), "Error writing some blocks: acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
- self.assertEqual(bufferblock.state(), arvados.arvfile.BufferBlock.PENDING)
+ with arvados.arvfile._BlockManager(mockkeep) as blockmanager:
+ bufferblock = blockmanager.alloc_bufferblock()
+ bufferblock.owner = mock.MagicMock()
+ def flush(sync=None):
+ blockmanager.commit_bufferblock(bufferblock, sync)
+ bufferblock.owner.flush.side_effect = flush
+ bufferblock.append("foo")
+ with self.assertRaises(arvados.errors.KeepWriteError) as err:
+ blockmanager.commit_all()
+ self.assertTrue(bufferblock.owner.flush.called)
+ self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)")
+ self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.ERROR)
projects / arvados.git / blobdiff