Sync with NEO/py v1.9

CHANGELOG.rst

 Change History
 ==============
 
+1.9 (2018-03-13)
+----------------
+
+A lot of performance improvements have been done on storage nodes for this
+release, and some of them required changes in the storage format. In short,
+the migration is done automatically, but you may want to read UPGRADE notes
+for more details.
+
+Performance:
+
+- Speed up replication by sending bigger network packets,
+  and by not getting object next_serial for nothing.
+- Speed up reads by indexing 'obj' primarily by 'oid' (instead of 'tid').
+- Optimize storage layout of raw data for replication.
+
+Other storage changes:
+
+- Disable data deduplication by default. --dedup option added.
+- importer: do not crash if a backup cluster tries to replicate.
+- importer: preserve 'packed' flag.
+
+Master:
+
+- Fix possible failure when reading data in a backup cluster with replicas.
+- Fix generation of TID.
+- Fix resumption of backup replication (internal or not).
+
+Client:
+
+- New 'cache-size' Storage option.
+- Cache hit/miss statistics.
+- Fix accounting of cache size.
+- Preserve 'packed' flag on iteration.
+- At startup, or after nodes are back, full load balancing could be prevented
+  until some data are written.
+
+Other:
+
+- neolog: --from option now also tries to parse with `dateutil`_.
+- neolog: add support for xz-compressed logs, using external xzcat commands.
+
+.. _dateutil: https://dateutil.readthedocs.io/
+
 1.8.1 (2017-11-07)
 ------------------
 

UPGRADE.rst

+NEO 1.9
+=======
+
+The `obj` table in MySQL/SQLite backends is automatically upgraded at startup.
+
+Note however that rewritting this table can take a lot of time if you have a
+lot of object records.
+
+This migration is reversible but you'd have to dig into the migration code
+(``DatabaseManager._migrate2()``) and do manually the opposite SQL queries.
+
+The change in the `data` table is such that no migration is done (like for NEO
+1.4, it's optional and it would cost too much). For optimal performance, you
+may prefer to set up new nodes (and drop the old ones once the replication
+is finished).
+
+Because there's no change in the protocol, it's actually possible to mix nodes
+with versions 1.8.1 and 1.9, and avoid any downtime because of the migration.
+
 NEO 1.6
 =======
 

neo/client/Storage.py

@@ -136,9 +136,6 @@ class Storage(BaseStorage.BaseStorage,
     def supportsUndo(self):
         return True
 
-    def supportsTransactionalUndo(self):
-        return True
-
     def loadEx(self, oid, version):
         try:
             data, serial, _ = self.app.load(oid)

neo/client/pool.py

@@ -56,25 +56,28 @@ class ConnectionPool(object):
             logging.info('%r not ready', node)
         else:
             logging.info('Connected %r', node)
+            # Make sure this node will be considered for the next reads
+            # even if there was a previous recent failure.
+            self.node_failure_dict.pop(node.getUUID(), None)
             return conn
         self.node_failure_dict[node.getUUID()] = time.time() + MAX_FAILURE_AGE
 
     def getCellSortKey(self, cell, random=random.random):
-        # The use of 'random' suffles cells to randomise node to access.
-        uuid = cell.getUUID()
-        # First, prefer a connected node.
-        if uuid in self.connection_dict:
-            return random()
-        # Then one that didn't fail recently.
-        failure = self.node_failure_dict.get(uuid)
+        # Prefer a node that didn't fail recently.
+        failure = self.node_failure_dict.get(cell.getUUID())
         if failure:
             if time.time() < failure:
-                # At last, order by date of connection failure.
+                # Or order by date of connection failure.
                 return failure
             # Do not use 'del' statement: we didn't lock, so another
             # thread might have removed uuid from node_failure_dict.
-            self.node_failure_dict.pop(uuid, None)
-        return 1 + random()
+            self.node_failure_dict.pop(cell.getUUID(), None)
+        # A random one, connected or not, is a trivial and quite efficient way
+        # to distribute the load evenly. On write accesses, a client connects
+        # to all nodes of touched cells, but before that, or if a client is
+        # specialized to only do read-only accesses, it should not limit
+        # itself to only use the first connected nodes.
+        return random()
 
     def getConnForNode(self, node):
         """Return a locked connection object to a given node

neo/master/backup_app.py

@@ -206,12 +206,21 @@ class BackupApplication(object):
             except IndexError:
                 last_max_tid = prev_tid
             if offset in partition_set:
-                self.tid_list[offset].append(tid)
+                primary_list = []
                 node_list = []
-                for cell in pt.getCellList(offset, readable=True):
+                cell_list = pt.getCellList(offset, readable=True)
+                for cell in cell_list:
                     node = cell.getNode()
                     assert node.isConnected(), node
                     if cell.backup_tid == prev_tid:
+                        if prev_tid == tid:
+                            # Connecting to upstream: any node is that is
+                            # up-to-date wrt upstream is candidate for being
+                            # primary.
+                            assert self.ignore_invalidations
+                            if app.isStorageReady(node.getUUID()):
+                                primary_list.append(node)
+                            continue
                         # Let's given 4 TID t0,t1,t2,t3: if a cell is only
                         # modified by t0 & t3 and has all data for t0, 4 values
                         # are possible for its 'backup_tid' until it replicates
@@ -231,12 +240,19 @@ class BackupApplication(object):
                             cell.backup_tid, last_max_tid, prev_tid, tid)
                     if app.isStorageReady(node.getUUID()):
                         node_list.append(node)
-                assert node_list
-                trigger_set.update(node_list)
                 # Make sure we have a primary storage for this partition.
                 if offset not in self.primary_partition_dict:
                     self.primary_partition_dict[offset] = \
-                        random.choice(node_list)
+                        random.choice(primary_list or node_list)
+                if node_list:
+                    self.tid_list[offset].append(tid)
+                    if primary_list:
+                        # Resume replication to secondary cells.
+                        self._triggerSecondary(
+                            self.primary_partition_dict[offset],
+                            offset, tid, cell_list)
+                    else:
+                        trigger_set.update(node_list)
             else:
                 # Partition not touched, so increase 'backup_tid' of all
                 # "up-to-date" replicas, without having to replicate.
@@ -335,6 +351,10 @@ class BackupApplication(object):
             if app.getClusterState() == ClusterStates.BACKINGUP:
                 self.triggerBackup(node)
             if primary:
+                self._triggerSecondary(node, offset, tid, cell_list)
+        return result
+
+    def _triggerSecondary(self, node, offset, tid, cell_list):
         # Notify secondary storages that they can replicate from
         # primary ones, even if they are already replicating.
         p = Packets.Replicate(tid, '', {offset: node.getAddress()})
@@ -346,4 +366,3 @@ class BackupApplication(object):
                     uuid_str(cell.getUUID()), offset,
                     dump(tid), uuid_str(node.getUUID()))
                 cell.getNode().send(p)
-        return result

neo/master/handlers/backup.py

@@ -35,7 +35,7 @@ class BackupHandler(EventHandler):
     def answerLastTransaction(self, conn, tid):
         app = self.app
         prev_tid = app.app.getLastTransaction()
-        if prev_tid < tid:
+        if prev_tid <= tid:
             # Since we don't know which partitions were modified during our
             # absence, we must force replication on all storages. As long as
             # they haven't done this first check, our backup tid will remain
@@ -43,8 +43,12 @@ class BackupHandler(EventHandler):
             #   >= app.app.getLastTransaction()
             #   < tid
             # but passing 'tid' is good enough.
+            # A special case is when prev_tid == tid: even in this case, we
+            # must restore the state of the backup app so that any interrupted
+            # replication (internal or not) is resumed, otherwise the global
+            # backup_tid could remain stuck to an old tid if upstream is idle.
             app.invalidatePartitions(tid, tid, xrange(app.pt.getPartitions()))
-        elif prev_tid != tid:
+        else:
             raise RuntimeError("upstream DB truncated")
         app.ignore_invalidations = False
 

neo/master/handlers/client.py

@@ -147,5 +147,5 @@ class ClientReadOnlyServiceHandler(ClientServiceHandler):
     # like in MasterHandler but returns backup_tid instead of last_tid
     def askLastTransaction(self, conn):
         assert self.app.backup_tid is not None   # we are in BACKUPING mode
-        backup_tid = self.app.pt.getBackupTid()
+        backup_tid = self.app.pt.getBackupTid(min)
         conn.answer(Packets.AnswerLastTransaction(backup_tid))

neo/master/transactions.py

@@ -235,28 +235,15 @@ class TransactionManager(EventQueue):
         min_tid = self._last_tid
         if tid <= min_tid:
             tid = addTID(min_tid, 1)
-            # We know we won't have room to adjust by decreasing.
-            try_decrease = False
-        else:
-            try_decrease = True
         if ttid is not None:
-            assert isinstance(ttid, basestring), repr(ttid)
-            assert isinstance(divisor, (int, long)), repr(divisor)
-            ref_remainder = u64(ttid) % divisor
-            remainder = u64(tid) % divisor
-            if ref_remainder != remainder:
-                if try_decrease:
-                    new_tid = addTID(tid, ref_remainder - divisor - remainder)
-                    assert u64(new_tid) % divisor == ref_remainder, (dump(new_tid),
-                        ref_remainder)
-                    if new_tid <= min_tid:
-                        new_tid = addTID(new_tid, divisor)
-                else:
-                    if ref_remainder > remainder:
-                        ref_remainder += divisor
-                    new_tid = addTID(tid, ref_remainder - remainder)
-                assert min_tid < new_tid, (dump(min_tid), dump(tid), dump(new_tid))
-                tid = new_tid
+            remainder = u64(ttid) % divisor
+            delta_remainder = remainder - u64(tid) % divisor
+            if delta_remainder:
+                tid = addTID(tid, delta_remainder)
+                if tid <= min_tid:
+                    tid = addTID(tid, divisor)
+                assert u64(tid) % divisor == remainder, (dump(tid), remainder)
+                assert min_tid < tid, (dump(min_tid), dump(tid))
         self._last_tid = tid
         return self._last_tid
 

neo/storage/database/importer.py

@@ -406,7 +406,7 @@ class ImporterDatabaseManager(DatabaseManager):
                         if compression:
                             data = compressed_data
                     checksum = util.makeChecksum(data)
-                    data_id = self.holdData(util.makeChecksum(data), data,
+                    data_id = self.holdData(util.makeChecksum(data), oid, data,
                                             compression)
                     data_id_list.append(data_id)
                 object_list.append((oid, data_id, data_tid))

neo/storage/database/manager.py

@@ -161,11 +161,14 @@ class DatabaseManager(object):
                 "The database can not be upgraded because you have unfinished"
                 " transactions. Use an older version of NEO to verify them.")
 
-    def _getVersion(self):
+    def migrate(self, *args, **kw):
         version = int(self.getConfiguration("version") or 0)
         if self.VERSION < version:
             raise DatabaseFailure("The database can not be downgraded.")
-        return version
+        while version < self.VERSION:
+            version += 1
+            getattr(self, '_migrate%s' % version)(*args, **kw)
+            self.setConfiguration("version", version)
 
     def doOperation(self, app):
         pass
@@ -485,7 +488,11 @@ class DatabaseManager(object):
         existing data is first thrown away.
         """
 
-    @requires(_changePartitionTable)
+    def _getDataLastId(self, partition):
+        """
+        """
+
+    @requires(_changePartitionTable, _getDataLastId)
     def changePartitionTable(self, ptid, cell_list, reset=False):
         readable_set = self._readable_set
         if reset:
@@ -500,6 +507,10 @@ class DatabaseManager(object):
                 raise NonReadableCell
             self._getPartition = _getPartition
             self._getReadablePartition = _getReadablePartition
+            d = self._data_last_ids = []
+            for p in xrange(np):
+                i = self._getDataLastId(p)
+                d.append(p << 48 if i is None else i + 1)
         me = self.getUUID()
         for offset, nid, state in cell_list:
             if nid == me:
@@ -567,7 +578,7 @@ class DatabaseManager(object):
         """
 
     @abstract
-    def storeData(self, checksum, data, compression):
+    def storeData(self, checksum, oid, data, compression):
         """To be overridden by the backend to store object raw data
 
         If same data was already stored, the storage only has to check there's

neo/storage/handlers/storage.py

@@ -113,7 +113,7 @@ class StorageOperationHandler(EventHandler):
                               checksum, data, data_serial):
         dm = self.app.dm
         if data or checksum != ZERO_HASH:
-            data_id = dm.storeData(checksum, data, compression)
+            data_id = dm.storeData(checksum, oid, data, compression)
         else:
             data_id = None
         # Directly store the transaction.

neo/storage/transactions.py

@@ -470,7 +470,7 @@ class TransactionManager(EventQueue):
         if data is None:
             data_id = None
         else:
-            data_id = self._app.dm.holdData(checksum, data, compression)
+            data_id = self._app.dm.holdData(checksum, oid, data, compression)
         transaction.store(oid, data_id, value_serial)
 
     def rebaseObject(self, ttid, oid):

neo/tests/storage/testStorageDBTests.py

@@ -104,6 +104,7 @@ class StorageDBTests(NeoUnitTestBase):
 
     def test_getPartitionTable(self):
         db = self.getDB()
+        db.setNumPartitions(3)
         uuid1, uuid2 = self.getStorageUUID(), self.getStorageUUID()
         cell1 = (0, uuid1, CellStates.OUT_OF_DATE)
         cell2 = (1, uuid1, CellStates.UP_TO_DATE)
@@ -124,7 +125,7 @@ class StorageDBTests(NeoUnitTestBase):
         self._last_ttid = ttid = add64(self._last_ttid, 1)
         transaction = oid_list, 'user', 'desc', 'ext', False, ttid
         H = "0" * 20
-        object_list = [(oid, self.db.holdData(H, '', 1), None)
+        object_list = [(oid, self.db.holdData(H, oid, '', 1), None)
                        for oid in oid_list]
         return (transaction, object_list)
 
@@ -203,6 +204,7 @@ class StorageDBTests(NeoUnitTestBase):
 
     def test_setPartitionTable(self):
         db = self.getDB()
+        db.setNumPartitions(3)
         ptid = 1
         uuid = self.getStorageUUID()
         cell1 = 0, uuid, CellStates.OUT_OF_DATE
@@ -452,8 +454,8 @@ class StorageDBTests(NeoUnitTestBase):
         tid4 = self.getNextTID()
         tid5 = self.getNextTID()
         oid1 = p64(1)
-        foo = db.holdData("3" * 20, 'foo', 0)
-        bar = db.holdData("4" * 20, 'bar', 0)
+        foo = db.holdData("3" * 20, oid1, 'foo', 0)
+        bar = db.holdData("4" * 20, oid1, 'bar', 0)
         db.releaseData((foo, bar))
         db.storeTransaction(
             tid1, (

neo/tests/storage/testStorageMySQL.py

@@ -19,6 +19,7 @@ from MySQLdb import NotSupportedError, OperationalError
 from MySQLdb.constants.ER import UNKNOWN_STORAGE_ENGINE
 from ..mock import Mock
 from neo.lib.exception import DatabaseFailure
+from neo.lib.protocol import ZERO_OID
 from neo.lib.util import p64
 from .. import DB_PREFIX, DB_SOCKET, DB_USER
 from .testStorageDBTests import StorageDBTests
@@ -114,7 +115,7 @@ class StorageMySQLdbTests(StorageDBTests):
         self.assertEqual(2, max(len(self.db.escape(chr(x)))
                                 for x in xrange(256)))
         self.assertEqual(2, len(self.db.escape('\0')))
-        self.db.storeData('\0' * 20, '\0' * (2**24-1), 0)
+        self.db.storeData('\0' * 20, ZERO_OID, '\0' * (2**24-1), 0)
         size, = query_list
         max_allowed = self.db.__class__._max_allowed_packet
         self.assertTrue(max_allowed - 1024 < size <= max_allowed, size)
@@ -123,7 +124,7 @@ class StorageMySQLdbTests(StorageDBTests):
             self.db._max_allowed_packet = max_allowed_packet
             del query_list[:]
             self.db.storeTransaction(p64(0),
-                ((p64(1<<i),0,None) for i in xrange(10)), None)
+                ((p64(1<<i),1234,None) for i in xrange(10)), None)
             self.assertEqual(max(query_list), max_allowed_packet)
             self.assertEqual(len(query_list), count)
 

neo/tests/storage/testTransactions.py

@@ -57,7 +57,7 @@ class TransactionManagerTests(NeoUnitTestBase):
         self.manager.storeObject(locking_serial, ram_serial, oid, 0, "3" * 20,
             'bar', None)
         holdData = self.app.dm.mockGetNamedCalls('holdData')
-        self.assertEqual(holdData.pop(0).params, ("3" * 20, 'bar', 0))
+        self.assertEqual(holdData.pop(0).params, ("3" * 20, oid, 'bar', 0))
         orig_object = self.manager.getObjectFromTransaction(locking_serial,
             oid)
         self.manager.updateObjectDataForPack(oid, orig_serial, None, checksum)

neo/tests/threaded/test.py

@@ -480,17 +480,18 @@ class Test(NEOThreadedTest):
     def test_notifyNodeInformation(self, cluster):
         # translated from MasterNotificationsHandlerTests
         # (neo.tests.client.testMasterHandler)
+        good = [1, 0].pop
         if 1:
             cluster.db # open DB
             s0, s1 = cluster.client.nm.getStorageList()
             conn = s0.getConnection()
             self.assertFalse(conn.isClosed())
             getCellSortKey = cluster.client.cp.getCellSortKey
-            self.assertEqual(getCellSortKey(s0, int), 0)
+            self.assertEqual(getCellSortKey(s0, good), 0)
             cluster.neoctl.dropNode(s0.getUUID())
             self.assertEqual([s1], cluster.client.nm.getStorageList())
             self.assertTrue(conn.isClosed())
-            self.assertEqual(getCellSortKey(s0, int), 1)
+            self.assertEqual(getCellSortKey(s0, good), 1)
             # XXX: the test originally checked that 'unregister' method
             #      was called (even if it's useless in this case),
             #      but we would need an API to do that easily.
@@ -1438,7 +1439,7 @@ class Test(NEOThreadedTest):
             bad = []
             ok = []
             def data_args(value):
-                return makeChecksum(value), value, 0
+                return makeChecksum(value), ZERO_OID, value, 0
             node_list = []
             for i, s in enumerate(cluster.storage_list):
                 node_list.append(s.uuid)

neo/tests/threaded/testReplication.py

@@ -132,10 +132,14 @@ class ReplicationTests(NEOThreadedTest):
                 self.assertEqual(backup.neoctl.getClusterState(),
                                  ClusterStates.RUNNING)
 
+                # Restart and switch to BACKINGUP mode again.
                 backup.stop()
                 backup.start()
                 backup.neoctl.setClusterState(ClusterStates.STARTING_BACKUP)
                 self.tic()
+
+                # Leave BACKINGUP mode when 1 replica is late. The cluster
+                # remains in STOPPING_BACKUP state until it catches up.
                 with backup.master.filterConnection(*backup.storage_list) as f:
                     f.add(delaySecondary)
                     while not f.filtered_count:
@@ -147,6 +151,8 @@ class ReplicationTests(NEOThreadedTest):
                 self.assertEqual(np*nr, self.checkBackup(backup,
                     max_tid=backup.last_tid))
 
+                # Again but leave BACKINGUP mode when a storage node is
+                # receiving data from the upstream cluster.
                 backup.stop()
                 backup.start()
                 backup.neoctl.setClusterState(ClusterStates.STARTING_BACKUP)
@@ -162,6 +168,48 @@ class ReplicationTests(NEOThreadedTest):
                 self.assertEqual(np*nr, self.checkBackup(backup,
                     max_tid=backup.last_tid))
 
+                storage = upstream.getZODBStorage()
+
+                # Check that replication from upstream is resumed even if
+                # upstream is idle.
+                backup.neoctl.setClusterState(ClusterStates.STARTING_BACKUP)
+                self.tic()
+                x = backup.master.backup_app.primary_partition_dict
+                new_oid_storage = x[0]
+                with upstream.moduloTID(next(p for p, n in x.iteritems()
+                                               if n is not new_oid_storage)), \
+                     ConnectionFilter() as f:
+                    f.delayAddObject()
+                    # Transaction that touches 2 primary cells on 2 different
+                    # nodes.
+                    txn = transaction.Transaction()
+                    tid = storage.load(ZERO_OID)[1]
+                    storage.tpc_begin(txn)
+                    storage.store(ZERO_OID, tid, '', '', txn)
+                    storage.tpc_vote(txn)
+                    storage.tpc_finish(txn)
+                    self.tic()
+                    # Stop when exactly 1 of the 2 cells is synced with
+                    # upstream.
+                    backup.stop()
+                backup.start()
+                self.assertEqual(np*nr, self.checkBackup(backup,
+                    max_tid=backup.last_tid))
+
+                # Check that replication to secondary cells is resumed even if
+                # upstream is idle.
+                with backup.master.filterConnection(*backup.storage_list) as f:
+                    f.add(delaySecondary)
+                    txn = transaction.Transaction()
+                    storage.tpc_begin(txn)
+                    storage.tpc_finish(txn)
+                    self.tic()
+                    backup.stop()
+                backup.start()
+                self.assertEqual(np*nr, self.checkBackup(backup,
+                    max_tid=backup.last_tid))
+
+
     @predictable_random()
     def testBackupNodeLost(self):
         """Check backup cluster can recover after random connection loss

setup.py

@@ -60,7 +60,7 @@ else:
 
 setup(
     name = 'neoppod',
-    version = '1.8.1',
+    version = '1.9',
     description = __doc__.strip(),
     author = 'Nexedi SA',
     author_email = 'neo-dev@erp5.org',