Merge tag 'v1.10' into master

NEO 1.10

* tag 'v1.10': (55 commits)
  Release version 1.10
  Maximize resiliency by taking into account the topology of storage nodes
  storage: also commit updated cell TID at each replicated chunk of 'obj' records
  storage: skip useless work when unlocking transactions
  qa: flush logs at the end of each test when -L is not used
  qa: add a log in case that a mysterious bug happens again
  storage: clarify log about data deletion of discarded cells
  debug: new example to run the profiler for 1 minute
  mysql: fix replication of big oids (> 16M)
  tests/cluster: speedup waiting a bit
  protocol: update packet docstrings
  Bump protocol version
  protocol: a single byte is more than enough to encode enums
  protocol: small cleanup in packet registration
  Optimize resumption of replication by starting from a greater TID
  importer: update comment about a workaround for ZODB3
  Micro-optimization of p64/u64
  qa: add a log in testBackupNodeLost for easier debugging
  Document that the bug when checking replicas may also cause the master to crash
  storage: stop logging 'Abort TXN' for txn that have been locked
  storage: split _migrate2() for reusable _alterTable()
  qa: new testStorageUpgrade
  qa: update testStorageUpgrade data for what is not automatically upgraded
  qa: original data for the future testStorageUpgrade
  sqlite: fix indexes of upgraded db
  importer: fix NameError when recovering during tpc_finish
  fixup! importer: fetch and process the data to import in a separate process
  Serialize empty transaction extension with an empty string
  client: fix partial import from a source storage
  qa: give a title to subprocesses of functional tests
  importer: give a title to the 'import' and 'writeback' subprocesses
  importer: fetch and process the data to import in a separate process
  importer: new option to write back new transactions to the source database
  importer: log when the transaction index for FileStorage DB is built
  importer: open imported zodb in read-only whenever possible
  fixup! mysql: fix remaining places where a server disconnection was not catched
  fixup! storage: speed up replication by sending bigger network packets
  mysql: do not full-scan for duplicates of big oids if deduplication is disabled
  mysql: fix remaining places where a server disconnection was not catched
  fixup! Add support for custom compression levels
  importer: reenable compression by default
  qa: review testImporter
  qa: remove a few uses of 'chr'
  Fix a few issues with ZODB5
  importer: small code cleanup in speedupFileStorageTxnLookup patch
  importer: do not trigger speedupFileStorageTxnLookup uselessly
  Add support for custom compression levels
  setup: update MANIFEST.in
  importer: do not checksum data twice
  client: store uncompressed if compressed size is equal
  fixup! master: automatically discard feeding cells that get out-of-date
  master: automatically discard feeding cells that get out-of-date
  qa: remove useless indentation in testSafeTweak
  bench: new option to mesure ZEO perfs in matrix test
  bench: reduce number of partitions in matrix test
  storage: fix replication of creation undone

BUGS.rst

@@ -16,6 +16,19 @@ This happens in the following conditions:
 4. the cell is checked completely before it could replicate up to the max tid
    to check
 
+Sometimes, it causes the master to crash::
+
+    File "neo/lib/handler.py", line 72, in dispatch
+      method(conn, *args, **kw)
+    File "neo/master/handlers/storage.py", line 93, in notifyReplicationDone
+      cell_list = app.backup_app.notifyReplicationDone(node, offset, tid)
+    File "neo/master/backup_app.py", line 337, in notifyReplicationDone
+      assert cell.isReadable()
+  AssertionError
+
 Workaround: make sure all cells are up-to-date before checking replicas.
 
-Found by running testBackupNodeLost many times.
+Found by running testBackupNodeLost many times:
+
+- either a failureException: 12 != 11
+- or the above assert failure, in which case the unit test freezes

CHANGELOG.rst

 Change History
 ==============
 
+1.10 (2018-07-16)
+-----------------
+
+A important performance improvement is that the replication now remembers where
+it was interrupted: a storage node that gets disconnected for a short time now
+gets fully operational quite instantaneously because it only has to replicate
+the new data. Before, the time to recover depended on the size of the DB, just
+to verify that most of the data are already transferred.
+
+As a small optimization, an empty transaction extension is now serialized with
+an empty string.
+
+The above 2 changes required a bump of the protocol version, as well as an
+upgrade of the storage format. Once upgraded (this is done automatically as
+usual), databases can't be opened anymore by older versions of NEO.
+
+Other general changes:
+
+- Add support for custom compression levels.
+- Maximize resiliency by taking into account the topology of storage nodes.
+- Fix a few issues with ZODB5. Note however that merging several DB with the
+  Importer backend only works if they were only used with ZODB < 5.
+
+Master:
+
+- Automatically discard feeding cells that get out-of-date.
+
+Client:
+
+- Fix partial import from a source storage.
+- Store uncompressed if compressed size is equal.
+
+Storage:
+
+- Fixed v1.9 code that sped up the replication by sending bigger network
+  packets.
+- Fix replication of creation undone.
+- Stop logging 'Abort TXN' for txn that have been locked.
+- Clarify log about data deletion of discarded cells.
+
+MySQL backend:
+
+- Fix replication of big OIDs (> 16M).
+- Do not full-scan for duplicates of big OIDs if deduplication is disabled.
+- Fix remaining places where a server disconnection was not catched.
+
+SQlite backend:
+
+- Fix indexes of upgraded databases.
+
+Importer backend:
+
+- Fetch and process the data to import in a separate process. It is even
+  usually free to use the best compression level.
+- New option to write back new transactions to the source database.
+  See 'importer.conf' for more information.
+- Give a title to the 'import' and 'writeback' subprocesses,
+  if the 'setproctitle' egg is installed.
+- Log when the transaction index for FileStorage DB is built.
+- Open imported database in read-only whenever possible.
+- Do not trigger speedupFileStorageTxnLookup uselessly.
+- Do not checksum data twice.
+- Fix NameError when recovering during tpc_finish.
+
 1.9 (2018-03-13)
 ----------------
 

MANIFEST.in

 graft tools
-include neo.conf CHANGELOG.rst TODO TESTS.txt ZODB3.patch
+include neo.conf CHANGELOG.rst TODO ZODB3.patch

importer.conf

@@ -14,6 +14,8 @@
 # directly to a NEO cluster with replicas or several storage nodes.
 # Importer backend can only be used with a single storage node.
 #
+# WARNING: Merging several DB only works if they were only used with ZODB < 5.
+#
 # Here is how to proceed once this file is ready:
 # 1. Restart ZODB clients to connect to new NEO cluster (not started yet).
 # 2. Start NEO cluster (use 'neoctl -a <admin> start' command if necessary).
@@ -43,6 +45,12 @@
 # (instead of adapter=Importer & database=/path_to_this_file).
 adapter=MySQL
 database=neo
+# Keep writing back new transactions to the source database, provided it is
+# not splitted. In case of any issue, the import can be aborted without losing
+# data. Note however that it is asynchronous so don't stop the storage node
+# too quickly after the last committed transaction (e.g. check with tools like
+# fstail).
+writeback=true
 
 # The other sections are for source databases.
 [root]
@@ -50,7 +58,8 @@ database=neo
 # ZEO is possible but less efficient: ZEO servers must be stopped
 # if NEO opens FileStorage DBs directly.
 # Note that NEO uses 'new_oid' method to get the last OID, that's why the
-# source DB can't be open read-only. NEO never modifies a FileStorage DB.
+# source DB can't be open read-only. Unless 'writeback' is enabled, NEO never
+# modifies a FileStorage DB.
 storage=
   <filestorage>
     path /path/to/root.fs

neo/client/Storage.py

@@ -160,11 +160,7 @@ class Storage(BaseStorage.BaseStorage,
 
     def copyTransactionsFrom(self, source, verbose=False):
         """ Zope compliant API """
-        return self.importFrom(source)
-
-    def importFrom(self, source, start=None, stop=None, preindex=None):
-        """ Allow import only a part of the source storage """
-        return self.app.importFrom(self, source, start, stop, preindex)
+        return self.app.importFrom(self, source)
 
     def pack(self, t, referencesf, gc=False):
         if gc:

neo/client/__init__.py

@@ -44,7 +44,7 @@ def patch():
         # <patch>
         serial = self._storage.tpc_finish(transaction, callback)
         if serial is not None:
-            assert isinstance(serial, str), repr(serial)
+            assert isinstance(serial, bytes), repr(serial)
             for oid_iterator in (self._modified, self._creating):
                 for oid in oid_iterator:
                     obj = self._cache.get(oid, None)

neo/client/app.py

@@ -14,11 +14,14 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-from cPickle import dumps, loads
-from zlib import compress, decompress
 import heapq
 import time
 
+try:
+    from ZODB._compat import dumps, loads, _protocol
+except ImportError:
+    from cPickle import dumps, loads
+    _protocol = 1
 from ZODB.POSException import UndoError, ConflictError, ReadConflictError
 from . import OLD_ZODB
 if OLD_ZODB:
@@ -26,6 +29,7 @@ if OLD_ZODB:
 from persistent.TimeStamp import TimeStamp
 
 from neo.lib import logging
+from neo.lib.compress import decompress_list, getCompress
 from neo.lib.protocol import NodeTypes, Packets, \
     INVALID_PARTITION, MAX_TID, ZERO_HASH, ZERO_TID
 from neo.lib.util import makeChecksum, dump
@@ -50,7 +54,6 @@ if SignalHandler:
     import signal
     SignalHandler.registerHandler(signal.SIGUSR2, logging.reopen)
 
-
 class Application(ThreadedApplication):
     """The client node application."""
 
@@ -99,7 +102,7 @@ class Application(ThreadedApplication):
         # _connecting_to_master_node is used to prevent simultaneous master
         # node connection attempts
         self._connecting_to_master_node = Lock()
-        self.compress = compress
+        self.compress = getCompress(compress)
 
     def __getattr__(self, attr):
         if attr in ('last_tid', 'pt'):
@@ -215,7 +218,7 @@ class Application(ThreadedApplication):
                         node=node,
                         dispatcher=self.dispatcher)
                 p = Packets.RequestIdentification(
-                    NodeTypes.CLIENT, self.uuid, None, self.name, None)
+                    NodeTypes.CLIENT, self.uuid, None, self.name, (), None)
                 try:
                     ask(conn, p, handler=handler)
                 except ConnectionClosed:
@@ -273,7 +276,8 @@ class Application(ThreadedApplication):
     def _askStorageForRead(self, object_id, packet, askStorage=None):
         cp = self.cp
         pt = self.pt
-        if type(object_id) is str:
+        # BBB: On Py2, it can be a subclass of bytes (binary from zodbpickle).
+        if isinstance(object_id, bytes):
             object_id = pt.getPartition(object_id)
         if askStorage is None:
             askStorage = self._askStorage
@@ -387,7 +391,7 @@ class Application(ThreadedApplication):
                     logging.error('wrong checksum from %s for oid %s',
                               conn, dump(oid))
                     raise NEOStorageReadRetry(False)
-                return (decompress(data) if compression else data,
+                return (decompress_list[compression](data),
                         tid, next_tid, data_tid)
             raise NEOStorageCreationUndoneError(dump(oid))
         return self._askStorageForRead(oid,
@@ -434,17 +438,7 @@ class Application(ThreadedApplication):
             checksum = ZERO_HASH
         else:
             assert data_serial is None
-            size = len(data)
-            if self.compress:
-                compressed_data = compress(data)
-                if size < len(compressed_data):
-                    compressed_data = data
-                    compression = 0
-                else:
-                    compression = 1
-            else:
-                compression = 0
-                compressed_data = data
+            size, compression, compressed_data = self.compress(data)
             checksum = makeChecksum(compressed_data)
             txn_context.data_size += size
         # Store object in tmp cache
@@ -553,9 +547,12 @@ class Application(ThreadedApplication):
         txn_context = self._txn_container.get(transaction)
         self.waitStoreResponses(txn_context)
         ttid = txn_context.ttid
+        ext = transaction._extension
+        ext = dumps(ext, _protocol) if ext else ''
+        # user and description are cast to str in case they're unicode.
+        # BBB: This is not required anymore with recent ZODB.
         packet = Packets.AskStoreTransaction(ttid, str(transaction.user),
-            str(transaction.description), dumps(transaction._extension),
-            txn_context.cache_dict)
+            str(transaction.description), ext, txn_context.cache_dict)
         queue = txn_context.queue
         involved_nodes = txn_context.involved_nodes
         # Ask in parallel all involved storage nodes to commit object metadata.
@@ -785,10 +782,6 @@ class Application(ThreadedApplication):
         self.waitStoreResponses(txn_context)
         return None, txn_oid_list
 
-    def _insertMetadata(self, txn_info, extension):
-        for k, v in loads(extension).items():
-            txn_info[k] = v
-
     def _getTransactionInformation(self, tid):
         return self._askStorageForRead(tid,
             Packets.AskTransactionInformation(tid))
@@ -828,7 +821,8 @@ class Application(ThreadedApplication):
             if filter is None or filter(txn_info):
                 txn_info.pop('packed')
                 txn_info.pop("oids")
-                self._insertMetadata(txn_info, txn_ext)
+                if txn_ext:
+                    txn_info.update(loads(txn_ext))
                 append(txn_info)
                 if len(undo_info) >= last - first:
                     break
@@ -856,7 +850,7 @@ class Application(ThreadedApplication):
         tid = None
         for tid in tid_list:
             (txn_info, txn_ext) = self._getTransactionInformation(tid)
-            txn_info['ext'] = loads(txn_ext)
+            txn_info['ext'] = loads(txn_ext) if txn_ext else {}
             append(txn_info)
         return (tid, txn_list)
 
@@ -875,23 +869,29 @@ class Application(ThreadedApplication):
                 txn_info['size'] = size
                 if filter is None or filter(txn_info):
                     result.append(txn_info)
-                self._insertMetadata(txn_info, txn_ext)
+                if txn_ext:
+                    txn_info.update(loads(txn_ext))
         return result
 
-    def importFrom(self, storage, source, start, stop, preindex=None):
+    def importFrom(self, storage, source):
         # TODO: The main difference with BaseStorage implementation is that
         #       preindex can't be filled with the result 'store' (tid only
         #       known after 'tpc_finish'. This method could be dropped if we
         #       implemented IStorageRestoreable (a wrapper around source would
         #       still be required for partial import).
-        if preindex is None:
         preindex = {}
-        for transaction in source.iterator(start, stop):
+        for transaction in source.iterator():
             tid = transaction.tid
             self.tpc_begin(storage, transaction, tid, transaction.status)
             for r in transaction:
                 oid = r.oid
-                pre = preindex.get(oid)
+                try:
+                    pre = preindex[oid]
+                except KeyError:
+                    try:
+                        pre = self.load(oid)[1]
+                    except NEOStorageNotFoundError:
+                        pre = ZERO_TID
                 self.store(oid, pre, r.data, r.version, transaction)
                 preindex[oid] = tid
             conflicted = self.tpc_vote(transaction)

neo/client/component.xml

@@ -14,10 +14,14 @@
         Give the name of the cluster
       </description>
     </key>
-    <key name="compress" datatype="boolean">
+    <key name="compress" datatype=".compress">
       <description>
-        If true, data is automatically compressed (unless compressed size is
-        not smaller). This is the default behaviour.
+        The value is either of 'boolean' type or an explicit algorithm that
+        matches the regex 'zlib(=\d+)?', where the optional number is
+        the compression level.
+        Any record that is not smaller once compressed is stored uncompressed.
+        True is the default and its meaning may change over time:
+        currently, it is the same as 'zlib'.
       </description>
     </key>
     <key name="read-only" datatype="boolean">

neo/client/config.py

@@ -23,3 +23,11 @@ class NeoStorage(BaseConfig):
         config = self.config
         return Storage(**{k: getattr(config, k)
                           for k in config.getSectionAttributes()})
+
+def compress(value):
+    from ZConfig.datatypes import asBoolean
+    try:
+        return asBoolean(value)
+    except ValueError:
+        from neo.lib.compress import parseOption
+    return parseOption(value)

neo/client/handlers/storage.py

@@ -14,10 +14,10 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-from zlib import decompress
 from ZODB.TimeStamp import TimeStamp
 
 from neo.lib import logging
+from neo.lib.compress import decompress_list
 from neo.lib.protocol import Packets, uuid_str
 from neo.lib.util import dump, makeChecksum
 from neo.lib.exception import NodeNotReady
@@ -129,8 +129,7 @@ class StorageAnswersHandler(AnswerBaseHandler):
                             'wrong checksum while getting back data for'
                             ' object %s during rebase of transaction %s'
                             % (dump(oid), dump(txn_context.ttid)))
-                    if compression:
-                        data = decompress(data)
+                    data = decompress_list[compression](data)
                     size = len(data)
                     txn_context.data_size += size
                     if cached:

neo/client/pool.py

@@ -47,7 +47,7 @@ class ConnectionPool(object):
         conn = MTClientConnection(app, app.storage_event_handler, node,
                                   dispatcher=app.dispatcher)
         p = Packets.RequestIdentification(NodeTypes.CLIENT,
-            app.uuid, None, app.name, app.id_timestamp)
+            app.uuid, None, app.name, (), app.id_timestamp)
         try:
             app._ask(conn, p, handler=app.storage_bootstrap_handler)
         except ConnectionClosed:

neo/client/transactions.py

@@ -117,7 +117,7 @@ class Transaction(object):
         if uuid_list:
             return
         del self.data_dict[oid]
-        if type(data) is str:
+        if type(data) is bytes:
             size = len(data)
             self.data_size -= size
             size += self.cache_size

neo/debug.py

@@ -164,3 +164,17 @@ elif IF == 'frames':
         write("Thread %s:\n" % thread_id)
         traceback.print_stack(frame)
     write("End of dump\n")
+
+elif IF == 'profile':
+    DURATION = 60
+    def stop(prof, path):
+        prof.disable()
+        prof.dump_stats(path)
+    @defer
+    def profile(app):
+        import cProfile, threading, time
+        from .lib.protocol import uuid_str
+        path = 'neo-%s-%s.prof' % (uuid_str(app.uuid), time.time())
+        prof = cProfile.Profile()
+        threading.Timer(DURATION, stop, (prof, path)).start()
+        prof.enable()

neo/lib/bootstrap.py

@@ -26,13 +26,14 @@ class BootstrapManager(EventHandler):
     Manage the bootstrap stage, lookup for the primary master then connect to it
     """
 
-    def __init__(self, app, node_type, server=None):
+    def __init__(self, app, node_type, server=None, devpath=()):
         """
         Manage the bootstrap stage of a non-master node, it lookup for the
         primary master node, connect to it then returns when the master node
         is ready.
         """
         self.server = server
+        self.devpath = devpath
         self.node_type = node_type
         self.num_replicas = None
         self.num_partitions = None
@@ -43,7 +44,7 @@ class BootstrapManager(EventHandler):
     def connectionCompleted(self, conn):
         EventHandler.connectionCompleted(self, conn)
         conn.ask(Packets.RequestIdentification(self.node_type, self.uuid,
-            self.server, self.app.name, None))
+            self.server, self.app.name, self.devpath, None))
 
     def connectionFailed(self, conn):
         EventHandler.connectionFailed(self, conn)

neo/lib/compress.py

+#
+# Copyright (C) 2018  Nexedi SA
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import zlib
+
+decompress_list = (
+    lambda data: data,
+    zlib.decompress,
+)
+
+def parseOption(value):
+    x = value.split('=', 1)
+    try:
+        alg = ('zlib',).index(x[0])
+        if len(x) == 1:
+            return alg, None
+        level = int(x[1])
+    except Exception:
+        raise ValueError("not a valid 'compress' option: %r" % value)
+    if 0 < level <= zlib.Z_BEST_COMPRESSION:
+        return alg, level
+    raise ValueError("invalid compression level: %r" % level)
+
+def getCompress(value):
+    if value:
+        alg, level = (0, None) if value is True else value
+        _compress = zlib.compress
+        if level:
+            zlib_compress = _compress
+            _compress = lambda data: zlib_compress(data, level)
+        alg += 1
+        assert 0 < alg < len(decompress_list), 'invalid compression algorithm'
+        def compress(data):
+            size = len(data)
+            compressed = _compress(data)
+            if len(compressed) < size:
+                return size, alg, compressed
+            return size, 0, data
+        compress._compress = _compress # for testBasicStore
+        return compress
+    return lambda data: (len(data), 0, data)

neo/lib/connector.py

@@ -34,6 +34,7 @@ class SocketConnector(object):
     is_closed = is_server = None
     connect_limit = {}
     CONNECT_LIMIT = 1
+    SOMAXCONN = 5 # for threaded tests
 
     def __new__(cls, addr, s=None):
         if s is None:
@@ -78,6 +79,7 @@ class SocketConnector(object):
     def queue(self, data):
         was_empty = not self.queued
         self.queued += data
+        for data in data:
             self.queue_size += len(data)
         return was_empty
 
@@ -123,7 +125,7 @@ class SocketConnector(object):
         try:
             self.socket.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
             self._bind(self.addr)
-            self.socket.listen(5)
+            self.socket.listen(self.SOMAXCONN)
         except socket.error, e:
             self.socket.close()
             self._error('listen', e)

neo/lib/exception.py

@@ -26,9 +26,6 @@ class PrimaryFailure(NeoException):
 class StoppedOperation(NeoException):
     pass
 
-class DatabaseFailure(NeoException):
-    pass
-
 class NodeNotReady(NeoException):
     pass
 

neo/lib/interfaces.py

@@ -22,14 +22,13 @@ def check_signature(reference, function):
     a, b, c, d = inspect.getargspec(function)
     x = len(A) - len(a)
     if x < 0: # ignore extra default parameters
-        if x + len(d) < 0:
+        if B or x + len(d) < 0:
             return False
         del a[x:]
         d = d[:x] or None
     elif x: # different signature
-        # We have no need yet to support methods with default parameters.
-        return a == A[:-x] and (b or a and c) and not (d or D)
-    return a == A and b == B and c == C and d == D
+        return a == A[:-x] and (b or a and c) and (d or ()) == (D or ())[:-x]
+    return a == A and (b or not B) and (c or not C) and d == D
 
 def implements(obj, ignore=()):
     ignore = set(ignore)
@@ -55,7 +54,7 @@ def implements(obj, ignore=()):
         while 1:
             name, func = base.pop()
             x = getattr(obj, name)
-            if x.im_class is tobj:
+            if type(getattr(x, '__self__', None)) is tobj:
                 x = x.__func__
                 if x is func:
                     try:

neo/lib/logger.py

@@ -281,3 +281,16 @@ class NEOLogger(Logger):
 logging = NEOLogger()
 signal.signal(signal.SIGRTMIN, lambda signum, frame: logging.flush())
 signal.signal(signal.SIGRTMIN+1, lambda signum, frame: logging.reopen())
+
+def patch():
+    def fork():
+        with logging:
+            pid = os_fork()
+            if not pid:
+                logging._setup()
+        return pid
+    os_fork = os.fork
+    os.fork = fork
+
+patch()
+del patch

neo/lib/node.py

@@ -28,6 +28,7 @@ class Node(object):
 
     _connection = None
     _identified = False
+    devpath = ()
     id_timestamp = None
 
     def __init__(self, manager, address=None, uuid=None, state=NodeStates.DOWN):

neo/lib/patch.py

@@ -25,6 +25,7 @@ def speedupFileStorageTxnLookup():
     from array import array
     from bisect import bisect
     from collections import defaultdict
+    from neo.lib import logging
     from ZODB.FileStorage.FileStorage import FileStorage, FileIterator
 
     typecode = 'L' if array('I').itemsize < 4 else 'I'
@@ -44,6 +45,8 @@ def speedupFileStorageTxnLookup():
             try:
                 index = self._tidindex
             except AttributeError:
+                logging.info("Building index for faster lookup of"
+                             " transactions in the FileStorage DB.")
                 # Cache a sorted list of all the file pos from oid index.
                 # To reduce memory usage, the list is splitted in arrays of
                 # low order 32-bit words.
@@ -52,10 +55,10 @@ def speedupFileStorageTxnLookup():
                     tindex[x >> 32].append(x & 0xffffffff)
                 index = self._tidindex = []
                 for h, l in sorted(tindex.iteritems()):
-                    x = array('I')
-                    x.fromlist(sorted(l))
-                    l = self._read_data_header(h << 32 | x[0])
-                    index.append((l.tid, h, x))
+                    l = array(typecode, sorted(l))
+                    x = self._read_data_header(h << 32 | l[0])
+                    index.append((x.tid, h, l))
+                logging.info("... index built")
             x = bisect(index, (start,)) - 1
             if x >= 0:
                 x, h, index = index[x]

neo/lib/util.py

@@ -15,12 +15,12 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 
-import socket
+import os, socket
 from binascii import a2b_hex, b2a_hex
 from datetime import timedelta, datetime
 from hashlib import sha1
 from Queue import deque
-from struct import pack, unpack
+from struct import pack, unpack, Struct
 from time import gmtime
 
 TID_LOW_OVERFLOW = 2**32
@@ -102,11 +102,10 @@ def addTID(ptid, offset):
         higher = (d.year, d.month, d.day, d.hour, d.minute)
     return packTID(higher, lower)
 
-def u64(s):
-    return unpack('!Q', s)[0]
-
-def p64(n):
-    return pack('!Q', n)
+p64, u64 = (lambda unpack: (
+    unpack.__self__.pack,
+    lambda s: unpack(s)[0]
+))(Struct('!Q').unpack)
 
 def add64(packed, offset):
     """Add a python number to a 64-bits packed value"""
@@ -115,7 +114,7 @@ def add64(packed, offset):
 def dump(s):
     """Dump a binary string in hex."""
     if s is not None:
-        if isinstance(s, str):
+        if isinstance(s, bytes):
             return b2a_hex(s)
         return repr(s)
 
@@ -226,3 +225,25 @@ class cached_property(object):
         if obj is None: return self
         value = obj.__dict__[self.func.__name__] = self.func(obj)
         return value
+
+# This module is always imported before multiprocessing is used, and the
+# main process does not want to change name when task are run in threads.
+spt_pid = os.getpid()
+
+def setproctitle(title):
+    global spt_pid
+    pid = os.getpid()
+    if spt_pid == pid:
+        return
+    spt_pid = pid
+    # Try using https://pypi.org/project/setproctitle/
+    try:
+        # On Linux, this is done by clobbering argv, and the main process
+        # usually has a longer command line than the title of subprocesses.
+        os.environ['SPT_NOENV'] = '1'
+        from setproctitle import setproctitle
+    except ImportError:
+        return
+    finally:
+        del os.environ['SPT_NOENV']
+    setproctitle(title)

neo/master/handlers/identification.py

@@ -24,7 +24,7 @@ from ..app import monotonic_time
 class IdentificationHandler(EventHandler):
 
     def requestIdentification(self, conn, node_type, uuid,
-                              address, name, id_timestamp):
+                              address, name, devpath, id_timestamp):
         app = self.app
         self.checkClusterName(name)
         if address == app.server:
@@ -101,6 +101,8 @@ class IdentificationHandler(EventHandler):
                 uuid=uuid, address=address)
         else:
             node.setUUID(uuid)
+        if devpath:
+            node.devpath = tuple(devpath)
         node.id_timestamp = monotonic_time()
         node.setState(state)
         conn.setHandler(handler)
@@ -120,7 +122,7 @@ class IdentificationHandler(EventHandler):
 class SecondaryIdentificationHandler(EventHandler):
 
     def requestIdentification(self, conn, node_type, uuid,
-                              address, name, id_timestamp):
+                              address, name, devpath, id_timestamp):
         app = self.app
         self.checkClusterName(name)
         if address == app.server:

neo/master/handlers/master.py

@@ -38,7 +38,7 @@ class ElectionHandler(MasterHandler):
             super(ElectionHandler, self).connectionCompleted(conn)
             app = self.app
             conn.ask(Packets.RequestIdentification(NodeTypes.MASTER,
-                app.uuid, app.server, app.name, app.election))
+                app.uuid, app.server, app.name, (), app.election))
 
     def connectionFailed(self, conn):
         super(ElectionHandler, self).connectionFailed(conn)

neo/master/pt.py

@@ -178,7 +178,7 @@ class PartitionTable(neo.lib.pt.PartitionTable):
     def tweak(self, drop_list=()):
         """Optimize partition table
 
-        This reassigns cells in 3 ways:
+        This reassigns cells in 4 ways:
         - Discard cells of nodes listed in 'drop_list'. For partitions with too
           few readable cells, some cells are instead marked as FEEDING. This is
           a preliminary step to drop these nodes, otherwise the partition table
@@ -187,6 +187,8 @@ class PartitionTable(neo.lib.pt.PartitionTable):
         - When a transaction creates new objects (oids are roughly allocated
           sequentially), we expect better performance by maximizing the number
           of involved nodes (i.e. parallelizing writes).
+        - For maximum resiliency, cells of each partition are assigned as far
+          as possible from each other, by checking the topology path of nodes.
 
         Examples of optimal partition tables with np=10, nr=1 and 5 nodes:
 
@@ -215,6 +217,17 @@ class PartitionTable(neo.lib.pt.PartitionTable):
           U.  .U  U.
           .U  U.  U.
           U.  U.  .U
+
+        For the topology, let's consider an example with paths of the form
+        (room, machine, disk):
+        - if there are more rooms than the number of replicas, 2 cells of the
+          same partition must not be assigned in the same room;
+        - otherwise, topology paths are checked at a deeper depth,
+          e.g. not on the same machine and distributed evenly
+               (off by 1) among rooms.
+        But the topology is expected to be optimal, otherwise it is ignored.
+        In some cases, we could fall back to a non-optimal topology but
+        that would cause extra replication if the user wants to fix it.
         """
         # Collect some data in a usable form for the rest of the method.
         node_list = {node: {} for node in self.count_dict
@@ -242,6 +255,67 @@ class PartitionTable(neo.lib.pt.PartitionTable):
                 i += 1
         option_dict = Counter(map(tuple, x))
 
+        # Initialize variables/functions to optimize the topology.
+        devpath_max = []
+        devpaths = [()] * node_count
+        if repeats > 1:
+            _devpaths = [x[0].devpath for x in node_list]
+            max_depth = min(map(len, _devpaths))
+            depth = 0
+            while 1:
+                if depth < max_depth:
+                    depth += 1
+                    x = Counter(x[:depth] for x in _devpaths)
+                    n = len(x)
+                    x = set(x.itervalues())
+                    # TODO: Prove it works. If the code turns out to be:
+                    #       - too pessimistic, the topology is ignored when
+                    #         resiliency could be maximized;
+                    #       - or worse too optimistic, in which case this
+                    #         method raises, possibly after a very long time.
+                    if len(x) == 1 or max(x) * repeats <= node_count:
+                        i, x = divmod(repeats, n)
+                        devpath_max.append((i + 1, x) if x else (i, n))
+                        if n < repeats:
+                            continue
+                        devpaths = [x[:depth] for x in _devpaths]
+                        break
+                logging.warning("Can't maximize resiliency: fix the topology"
+                    " of your storage nodes and make sure they're all running."
+                    " %s storage device failure(s) may be enough to lose all"
+                    " the database." % (repeats - 1))
+                break
+        topology = [{} for _ in xrange(self.np)]
+        def update_topology():
+            for offset in option:
+                n = topology[offset]
+                for i, (j, k) in zip(devpath, devpath_max):
+                    try:
+                        i, x = n[i]
+                    except KeyError:
+                        n[i] = i, x = [0, {}]
+                    if i == j or i + 1 == j and k == sum(
+                          1 for i in n.itervalues() if i[0] == j):
+                        # Too many cells would be assigned at this topology
+                        # node.
+                        return False
+                    n = x
+            # The topology may be optimal with this option. Apply it.
+            for offset in option:
+                n = topology[offset]
+                for i in devpath:
+                    n = n[i]
+                    n[0] += 1
+                    n = n[1]
+            return True
+        def revert_topology():
+            for offset in option:
+                n = topology[offset]
+                for i in devpath:
+                    n = n[i]
+                    n[0] -= 1
+                    n = n[1]
+
         # Strategies to find the "best" permutation of nodes.
         def node_options():
             # The second part of the key goes with the above cosmetic sort.
@@ -291,24 +365,27 @@ class PartitionTable(neo.lib.pt.PartitionTable):
         new = []   # the solution
         stack = [] # data recursion
         def options():
-            return iter(node_options[len(new)][-1])
+            x = node_options[len(new)]
+            return devpaths[x[-2]], iter(x[-1])
         for node_options in node_options(): # for each strategy
-            iter_option = options()
+            devpath, iter_option = options()
             while 1:
                 try:
                     option = next(iter_option)
-                except StopIteration: # 1st strategy only
+                except StopIteration:
                     if new:
-                        iter_option = stack.pop()
-                        option_dict[new.pop()] += 1
+                        devpath, iter_option = stack.pop()
+                        option = new.pop()
+                        revert_topology()
+                        option_dict[option] += 1
                         continue
                     break
-                if option_dict[option]:
+                if option_dict[option] and update_topology():
                     new.append(option)
-                    if len(new) == len(node_list):
+                    if len(new) == node_count:
                         break
-                    stack.append(iter_option)
-                    iter_option = options()
+                    stack.append((devpath, iter_option))
+                    devpath, iter_option = options()
                     option_dict[option] -= 1
             if new:
                 break
@@ -384,13 +461,18 @@ class PartitionTable(neo.lib.pt.PartitionTable):
                 if cell.isReadable():
                     if cell.getNode().isRunning():
                         lost = None
-                    else :
+                    else:
                         cell_list.append(cell)
             for cell in cell_list:
-                if cell.getNode() is not lost:
-                    cell.setState(CellStates.OUT_OF_DATE)
-                    change_list.append((offset, cell.getUUID(),
-                        CellStates.OUT_OF_DATE))
+                node = cell.getNode()
+                if node is not lost:
+                    if cell.isFeeding():
+                        self.removeCell(offset, node)
+                        state = CellStates.DISCARDED
+                    else:
+                        state = CellStates.OUT_OF_DATE
+                        cell.setState(state)
+                    change_list.append((offset, node.getUUID(), state))
         if fully_readable and change_list:
             logging.warning(self._first_outdated_message)
         return change_list

neo/scripts/runner.py

@@ -65,6 +65,7 @@ UNIT_TEST_MODULES = [
     'neo.tests.client.testZODBURI',
     # light functional tests
     'neo.tests.threaded.test',
+    'neo.tests.threaded.testConfig',
     'neo.tests.threaded.testImporter',
     'neo.tests.threaded.testReplication',
     'neo.tests.threaded.testSSL',

neo/storage/app.py

@@ -71,6 +71,7 @@ class Application(BaseApplication):
 
         self.dm.setup(reset=config.getReset(), dedup=config.getDedup())
         self.loadConfiguration()
+        self.devpath = self.dm.getTopologyPath()
 
         # force node uuid from command line argument, for testing purpose only
         if config.getUUID() is not None:
@@ -203,7 +204,8 @@ class Application(BaseApplication):
         pt = self.pt
 
         # search, find, connect and identify to the primary master
-        bootstrap = BootstrapManager(self, NodeTypes.STORAGE, self.server)
+        bootstrap = BootstrapManager(self, NodeTypes.STORAGE, self.server,
+                                     self.devpath)
         self.master_node, self.master_conn, num_partitions, num_replicas = \
             bootstrap.getPrimaryConnection()
         uuid = self.uuid

neo/storage/checker.py

@@ -51,7 +51,7 @@ class Checker(object):
             else:
                 conn = ClientConnection(app, StorageOperationHandler(app), node)
                 conn.ask(Packets.RequestIdentification(NodeTypes.STORAGE,
-                    uuid, app.server, name, app.id_timestamp))
+                    uuid, app.server, name, (), app.id_timestamp))
             self.conn_dict[conn] = node.isIdentified()
         conn_set = set(self.conn_dict)
         conn_set.discard(None)

neo/storage/database/__init__.py

@@ -16,8 +16,6 @@
 
 LOG_QUERIES = False
 
-from neo.lib.exception import DatabaseFailure
-
 DATABASE_MANAGER_DICT = {
     'Importer': 'importer.ImporterDatabaseManager',
     'MySQL': 'mysqldb.MySQLDatabaseManager',
@@ -33,3 +31,6 @@ def getAdapterKlass(name):
 
 def buildDatabaseManager(name, args=(), kw={}):
     return getAdapterKlass(name)(*args, **kw)
+
+class DatabaseFailure(Exception):
+    pass

neo/storage/database/sqlite.py

@@ -25,7 +25,7 @@ from . import LOG_QUERIES
 from .manager import DatabaseManager, splitOIDField
 from neo.lib import logging, util
 from neo.lib.interfaces import implements
-from neo.lib.protocol import CellStates, ZERO_OID, ZERO_TID, ZERO_HASH
+from neo.lib.protocol import ZERO_OID, ZERO_TID, ZERO_HASH
 
 def unique_constraint_message(table, *columns):
     c = sqlite3.connect(":memory:")
@@ -68,7 +68,7 @@ class SQLiteDatabaseManager(DatabaseManager):
              never be used for small requests.
     """
 
-    VERSION = 2
+    VERSION = 3
 
     def _parse(self, database):
         self.db = os.path.expanduser(database)
@@ -86,6 +86,9 @@ class SQLiteDatabaseManager(DatabaseManager):
             q("PRAGMA journal_mode = MEMORY")
         self._config = {}
 
+    def _getDevPath(self):
+        return self.db
+
     def _commit(self):
         retry_if_locked(self.conn.commit)
 
@@ -113,23 +116,33 @@ class SQLiteDatabaseManager(DatabaseManager):
             if not e.args[0].startswith("no such table:"):
                 raise
 
-    def _migrate1(self, *_):
-        self._checkNoUnfinishedTransactions()
-        self.query("DROP TABLE IF EXISTS ttrans")
-
-    def _migrate2(self, schema_dict, index_dict):
+    def _alterTable(self, schema_dict, table, select="*"):
         # BBB: As explained in _setup, no transactional DDL
         #      so let's do the same dance as for MySQL.
         q = self.query
-        if self.nonempty('obj') is None:
-            if self.nonempty('new_obj') is None:
+        new = 'new_' + table
+        if self.nonempty(table) is None:
+            if self.nonempty(new) is None:
                 return
         else:
-            q("DROP TABLE IF EXISTS new_obj")
-            q(schema_dict.pop('obj') % 'new_obj')
-            q("INSERT INTO new_obj SELECT * FROM obj")
-            q("DROP TABLE obj")
-        q("ALTER TABLE new_obj RENAME TO obj")
+            q("DROP TABLE IF EXISTS " + new)
+            q(schema_dict.pop(table) % new)
+            q("INSERT INTO %s SELECT %s FROM %s" % (new, select, table))
+            q("DROP TABLE " + table)
+        q("ALTER TABLE %s RENAME TO %s" % (new, table))
+
+    def _migrate1(self, *_):
+        self._checkNoUnfinishedTransactions()
+        self.query("DROP TABLE IF EXISTS ttrans")
+
+    def _migrate2(self, schema_dict, index_dict):
+        self._alterTable(schema_dict, 'obj')
+
+    def _migrate3(self, schema_dict, index_dict):
+        self._alterTable(schema_dict, 'pt', "rid, nid, CASE state"
+            " WHEN 0 THEN -1"  # UP_TO_DATE
+            " WHEN 2 THEN -2"  # FEEDING
+            " ELSE 1-state END")
 
     def _setup(self, dedup=False):
         # BBB: SQLite has transactional DDL but before Python 3.6,
@@ -150,10 +163,10 @@ class SQLiteDatabaseManager(DatabaseManager):
 
         # The table "pt" stores a partition table.
         schema_dict['pt'] = """CREATE TABLE %s (
-                 rid INTEGER NOT NULL,
+                 partition INTEGER NOT NULL,
                  nid INTEGER NOT NULL,
-                 state INTEGER NOT NULL,
-                 PRIMARY KEY (rid, nid))
+                 tid INTEGER NOT NULL,
+                 PRIMARY KEY (partition, nid))
             """
 
         # The table "trans" stores information on committed transactions.
@@ -223,7 +236,8 @@ class SQLiteDatabaseManager(DatabaseManager):
 
         for table, schema in schema_dict.iteritems():
             q(schema % ('IF NOT EXISTS ' + table))
-            for i, index in enumerate(index_dict.get(table, ()), 1):
+        for table, index in index_dict.iteritems():
+            for i, index in enumerate(index, 1):
                 q(index % ('IF NOT EXISTS _%s_i%s' % (table, i), table))
 
         self._uncommitted_data.update(q("SELECT data_id, count(*)"
@@ -249,42 +263,23 @@ class SQLiteDatabaseManager(DatabaseManager):
         else:
             q("REPLACE INTO config VALUES (?,?)", (key, str(value)))
 
-    def getPartitionTable(self, *nid):
-        if nid:
-            return self.query("SELECT rid, state FROM pt WHERE nid=?", nid)
+    def _getPartitionTable(self):
         return self.query("SELECT * FROM pt")
 
-    # A test with a table of 20 million lines and SQLite 3.8.7.1 shows that
-    # it's not worth changing getLastTID:
-    # - It already returns the result in less than 2 seconds, without reading
-    #   the whole table (this is 4-7 times faster than MySQL).
-    # - Strangely, a "GROUP BY partition" clause makes SQLite almost twice
-    #   slower.
-    # - Getting MAX(tid) is immediate with a "AND partition=?" condition so one
-    #   way to speed up the following 2 methods is to repeat the queries for
-    #   each partition (and finish in Python with max() for getLastTID).
-
-    def getLastTID(self, max_tid):
-        return self.query(
-            "SELECT MAX(tid) FROM pt, trans"
-            " WHERE nid=? AND rid=partition AND tid<=?",
-            (self.getUUID(), max_tid,)).next()[0]
-
-    def _getLastIDs(self):
-        p64 = util.p64
+    def _getLastTID(self, partition, max_tid=None):
+        x = self.query
+        if max_tid is None:
+            x = x("SELECT MAX(tid) FROM trans WHERE partition=?", (partition,))
+        else:
+            x = x("SELECT MAX(tid) FROM trans WHERE partition=? AND tid<=?",
+                  (partition, max_tid))
+        return x.next()[0]
+
+    def _getLastIDs(self, *args):
         q = self.query
-        args = self.getUUID(),
-        trans = {partition: p64(tid)
-            for partition, tid in q(
-                "SELECT partition, MAX(tid) FROM pt, trans"
-                " WHERE nid=? AND rid=partition GROUP BY partition", args)}
-        obj = {partition: p64(tid)
-            for partition, tid in q(
-                "SELECT partition, MAX(tid) FROM pt, obj"
-                " WHERE nid=? AND rid=partition GROUP BY partition", args)}
-        oid = q("SELECT MAX(oid) oid FROM pt, obj"
-                " WHERE nid=? AND rid=partition", args).next()[0]
-        return trans, obj, None if oid is None else p64(oid)
+        (oid,), = q("SELECT MAX(oid) FROM obj WHERE `partition`=?", args)
+        (tid,), = q("SELECT MAX(tid) FROM obj WHERE `partition`=?", args)
+        return tid, oid
 
     def _getDataLastId(self, partition):
         return self.query("SELECT MAX(id) FROM data WHERE %s <= id AND id < %s"
@@ -352,8 +347,8 @@ class SQLiteDatabaseManager(DatabaseManager):
             #       whereas we try to replace only 1 value ?
             #       We don't want to remove the 'NOT NULL' constraint
             #       so we must simulate a "REPLACE OR FAIL".
-            q("DELETE FROM pt WHERE rid=? AND nid=?", (offset, nid))
-            if state != CellStates.DISCARDED:
+            q("DELETE FROM pt WHERE partition=? AND nid=?", (offset, nid))
+            if state is not None:
                 q("INSERT OR FAIL INTO pt VALUES (?,?,?)",
                   (offset, nid, int(state)))
 
@@ -478,10 +473,15 @@ class SQLiteDatabaseManager(DatabaseManager):
                    (u64(tid), u64(ttid)))
         self.commit()
 
-    def unlockTransaction(self, tid, ttid):
+    def unlockTransaction(self, tid, ttid, trans, obj):
         q = self.query
         u64 = util.u64
         tid = u64(tid)
+        if trans:
+            q("INSERT INTO trans SELECT * FROM ttrans WHERE tid=?", (tid,))
+            q("DELETE FROM ttrans WHERE tid=?", (tid,))
+            if not obj:
+                return
         ttid = u64(ttid)
         sql = " FROM tobj WHERE tid=?"
         data_id_list = [x for x, in q("SELECT data_id%s AND data_id IS NOT NULL"
@@ -489,8 +489,6 @@ class SQLiteDatabaseManager(DatabaseManager):
         q("INSERT INTO obj SELECT partition, oid, ?, data_id, value_tid" + sql,
           (tid, ttid))
         q("DELETE" + sql, (ttid,))
-        q("INSERT INTO trans SELECT * FROM ttrans WHERE tid=?", (tid,))
-        q("DELETE FROM ttrans WHERE tid=?", (tid,))
         self.releaseData(data_id_list)
 
     def abortTransaction(self, ttid):
@@ -520,12 +518,12 @@ class SQLiteDatabaseManager(DatabaseManager):
     def _deleteRange(self, partition, min_tid=None, max_tid=None):
         sql = " WHERE partition=?"
         args = [partition]
-        if min_tid:
+        if min_tid is not None:
             sql += " AND ? < tid"
-            args.append(util.u64(min_tid))
-        if max_tid:
+            args.append(min_tid)
+        if max_tid is not None:
             sql += " AND tid <= ?"
-            args.append(util.u64(max_tid))
+            args.append(max_tid)
         q = self.query
         q("DELETE FROM trans" + sql, args)
         sql = " FROM obj" + sql
@@ -693,3 +691,24 @@ class SQLiteDatabaseManager(DatabaseManager):
                     sha1(','.join(str(x[1]) for x in r)).digest(),
                     p64(r[-1][1]))
         return 0, ZERO_HASH, ZERO_TID, ZERO_HASH, ZERO_OID
+
+    def dump(self):
+        main = []
+        data = []
+        for line in self.conn.iterdump():
+            if line.startswith('INSERT '):
+                assert line.endswith(';'), line
+                data.append(line)
+                continue
+            if line.startswith('CREATE TABLE '):
+                # ALTER TABLE adds quotes.
+                create, table, name, tail = line.split(' ', 3)
+                line = ' '.join((create, table, name.strip('"'), tail))
+            main.append(line)
+        assert line == 'COMMIT;', line
+        data.sort()
+        main[-1:-1] = data
+        return '\n'.join(main) + '\n'
+
+    def restore(self, sql):
+        self.conn.executescript(sql)

neo/storage/handlers/client.py

@@ -42,11 +42,11 @@ class ClientOperationHandler(BaseHandler):
         # for read rpc
         return self.app.tm.read_queue
 
-    def askObject(self, conn, oid, serial, tid):
+    def askObject(self, conn, oid, at, before):
         app = self.app
         if app.tm.loadLocked(oid):
             raise DelayEvent
-        o = app.dm.getObject(oid, serial, tid)
+        o = app.dm.getObject(oid, at, before)
         try:
             serial, next_serial, compression, checksum, data, data_serial = o
         except TypeError:

neo/storage/handlers/identification.py

@@ -32,7 +32,7 @@ class IdentificationHandler(EventHandler):
         return self.app.nm
 
     def requestIdentification(self, conn, node_type, uuid, address, name,
-                              id_timestamp):
+                              devpath, id_timestamp):
         self.checkClusterName(name)
         app = self.app
         # reject any incoming connections if not ready

neo/storage/handlers/initialization.py

@@ -28,21 +28,21 @@ class InitializationHandler(BaseMasterHandler):
             raise ProtocolError('Partial partition table received')
         # Install the partition table into the database for persistence.
         cell_list = []
-        offset_list = xrange(pt.getPartitions())
-        unassigned_set = set(offset_list)
-        for offset in offset_list:
+        unassigned = range(pt.getPartitions())
+        for offset in reversed(unassigned):
             for cell in pt.getCellList(offset):
                 cell_list.append((offset, cell.getUUID(), cell.getState()))
                 if cell.getUUID() == app.uuid:
-                    unassigned_set.remove(offset)
+                    unassigned.remove(offset)
         # delete objects database
         dm = app.dm
-        if unassigned_set:
+        if unassigned:
           if app.disable_drop_partitions:
-            logging.info("don't drop data for partitions %r", unassigned_set)
+            logging.info('partitions %r are discarded but actual deletion'
+                         ' of data is disabled', unassigned)
           else:
-            logging.debug('drop data for partitions %r', unassigned_set)
-            dm.dropPartitions(unassigned_set)
+            logging.debug('drop data for partitions %r', unassigned)
+            dm.dropPartitions(unassigned)
 
         dm.changePartitionTable(ptid, cell_list, reset=True)
         dm.commit()
@@ -63,7 +63,7 @@ class InitializationHandler(BaseMasterHandler):
     def askLastIDs(self, conn):
         dm = self.app.dm
         dm.truncate()
-        ltid, _, _, loid = dm.getLastIDs()
+        ltid, loid = dm.getLastIDs()
         conn.answer(Packets.AnswerLastIDs(loid, ltid))
 
     def askPartitionTable(self, conn):
@@ -77,18 +77,10 @@ class InitializationHandler(BaseMasterHandler):
     def validateTransaction(self, conn, ttid, tid):
         dm = self.app.dm
         dm.lockTransaction(tid, ttid)
-        dm.unlockTransaction(tid, ttid)
+        dm.unlockTransaction(tid, ttid, True, True)
         dm.commit()
 
     def startOperation(self, conn, backup):
-        self.app.operational = True
         # XXX: see comment in protocol
-        dm = self.app.dm
-        if backup:
-            if dm.getBackupTID():
-                return
-            tid = dm.getLastIDs()[0] or ZERO_TID
-        else:
-            tid = None
-        dm._setBackupTID(tid)
-        dm.commit()
+        self.app.operational = True
+        self.app.replicator.startOperation(backup)

neo/storage/handlers/master.py

@@ -26,10 +26,7 @@ class MasterOperationHandler(BaseMasterHandler):
     def startOperation(self, conn, backup):
         # XXX: see comment in protocol
         assert self.app.operational and backup
-        dm = self.app.dm
-        if not dm.getBackupTID():
-            dm._setBackupTID(dm.getLastIDs()[0] or ZERO_TID)
-            dm.commit()
+        self.app.replicator.startOperation(backup)
 
     def askLockInformation(self, conn, ttid, tid):
         self.app.tm.lock(ttid, tid)

neo/storage/handlers/storage.py

@@ -75,9 +75,6 @@ class StorageOperationHandler(EventHandler):
                 deleteTransaction(tid)
         assert not pack_tid, "TODO"
         if next_tid:
-            # More than one chunk ? This could be a full replication so avoid
-            # restarting from the beginning by committing now.
-            self.app.dm.commit()
             self.app.replicator.fetchTransactions(next_tid)
         else:
             self.app.replicator.fetchObjects()
@@ -97,15 +94,12 @@ class StorageOperationHandler(EventHandler):
             for serial, oid_list in object_dict.iteritems():
                 for oid in oid_list:
                     deleteObject(oid, serial)
-        # XXX: It should be possible not to commit here if it was the last
-        #      chunk, because we'll either commit again when updating
-        #      'backup_tid' or the partition table.
-        self.app.dm.commit()
         assert not pack_tid, "TODO"
         if next_tid:
             # TODO also provide feedback to master about current replication state (tid)
             self.app.replicator.fetchObjects(next_tid, next_oid)
         else:
+            # This will also commit.
             self.app.replicator.finish()
 
     @checkConnectionIsReplicatorConnection
@@ -267,6 +261,8 @@ class StorageOperationHandler(EventHandler):
                             "partition %u dropped or truncated"
                             % partition), msg_id)
                         return
+                    if not object[2]: # creation undone
+                        object = object[0], 0, ZERO_HASH, '', object[4]
                     # Same as in askFetchTransactions.
                     conn.send(Packets.AddObject(oid, *object), msg_id)
                     yield conn.buffering

neo/storage/replicator.py

@@ -93,7 +93,7 @@ from neo.lib import logging
 from neo.lib.protocol import CellStates, NodeTypes, NodeStates, \
     Packets, INVALID_TID, ZERO_TID, ZERO_OID
 from neo.lib.connection import ClientConnection, ConnectionClosed
-from neo.lib.util import add64, dump
+from neo.lib.util import add64, dump, p64
 from .handlers.storage import StorageOperationHandler
 
 FETCH_COUNT = 1000
@@ -190,41 +190,50 @@ class Replicator(object):
             return add64(tid, -1)
         return ZERO_TID
 
-    def updateBackupTID(self):
+    def updateBackupTID(self, commit=False):
         dm = self.app.dm
         tid = dm.getBackupTID()
         if tid:
             new_tid = self.getBackupTID()
             if tid != new_tid:
                 dm._setBackupTID(new_tid)
+                if commit:
                     dm.commit()
 
+    def startOperation(self, backup):
+        dm = self.app.dm
+        if backup:
+            if dm.getBackupTID():
+                assert not hasattr(self, 'partition_dict'), self.partition_dict
+                return
+            tid = dm.getLastIDs()[0] or ZERO_TID
+        else:
+            tid = None
+        dm._setBackupTID(tid)
+        dm.commit()
+        try:
+            partition_dict = self.partition_dict
+        except AttributeError:
+            return
+        for offset, next_tid in dm.iterCellNextTIDs():
+            if type(next_tid) is not bytes: # readable
+                p = partition_dict[offset]
+                p.next_trans, p.next_obj = next_tid
+
     def populate(self):
-        app = self.app
-        pt = app.pt
-        uuid = app.uuid
         self.partition_dict = {}
         self.replicate_dict = {}
         self.source_dict = {}
         self.ttid_set = set()
-        last_tid, last_trans_dict, last_obj_dict, _ = app.dm.getLastIDs()
-        next_tid = app.dm.getBackupTID() or last_tid
-        next_tid = add64(next_tid, 1) if next_tid else ZERO_TID
         outdated_list = []
-        for offset in xrange(pt.getPartitions()):
-            for cell in pt.getCellList(offset):
-                if cell.getUUID() == uuid and not cell.isCorrupted():
+        for offset, next_tid in self.app.dm.iterCellNextTIDs():
             self.partition_dict[offset] = p = Partition()
-                    if cell.isOutOfDate():
+            if type(next_tid) is bytes: # OUT_OF_DATE
                 outdated_list.append(offset)
-                        try:
-                            p.next_trans = add64(last_trans_dict[offset], 1)
-                        except KeyError:
-                            p.next_trans = ZERO_TID
-                        p.next_obj = last_obj_dict.get(offset, ZERO_TID)
-                        p.max_ttid = INVALID_TID
-                    else:
                 p.next_trans = p.next_obj = next_tid
+                p.max_ttid = INVALID_TID
+            else: # readable
+                p.next_trans, p.next_obj = next_tid or (None, None)
                 p.max_ttid = None
         if outdated_list:
             self.app.tm.replicating(outdated_list)
@@ -236,7 +245,6 @@ class Replicator(object):
         discarded_list = []
         readable_list = []
         app = self.app
-        last_tid, last_trans_dict, last_obj_dict, _ = app.dm.getLastIDs()
         for offset, uuid, state in cell_list:
             if uuid == app.uuid:
                 if state in (CellStates.DISCARDED, CellStates.CORRUPTED):
@@ -251,11 +259,9 @@ class Replicator(object):
                 elif state == CellStates.OUT_OF_DATE:
                     assert offset not in self.partition_dict
                     self.partition_dict[offset] = p = Partition()
-                    try:
-                        p.next_trans = add64(last_trans_dict[offset], 1)
-                    except KeyError:
-                        p.next_trans = ZERO_TID
-                    p.next_obj = last_obj_dict.get(offset, ZERO_TID)
+                    # New cell. 0 is also what should be stored by the backend.
+                    # Nothing to optimize.
+                    p.next_trans = p.next_obj = ZERO_TID
                     p.max_ttid = INVALID_TID
                     added_list.append(offset)
                 else:
@@ -289,7 +295,7 @@ class Replicator(object):
                     next_tid = add64(tid, 1)
                 p.next_trans = p.next_obj = next_tid
         if next_tid:
-            self.updateBackupTID()
+            self.updateBackupTID(True)
         self._nextPartition()
 
     def _nextPartitionSortKey(self, offset):
@@ -344,7 +350,7 @@ class Replicator(object):
             try:
                 conn.ask(Packets.RequestIdentification(NodeTypes.STORAGE,
                     None if name else app.uuid, app.server, name or app.name,
-                    app.id_timestamp))
+                    (), app.id_timestamp))
             except ConnectionClosed:
                 if previous_node is self.current_node:
                     return
@@ -360,6 +366,9 @@ class Replicator(object):
         offset = self.current_partition
         p = self.partition_dict[offset]
         if min_tid:
+            # More than one chunk ? This could be a full replication so avoid
+            # restarting from the beginning by committing now.
+            self.app.dm.commit()
             p.next_trans = min_tid
         else:
             try:
@@ -384,13 +393,17 @@ class Replicator(object):
         offset = self.current_partition
         p = self.partition_dict[offset]
         max_tid = self.replicate_tid
+        dm = self.app.dm
         if min_tid:
             p.next_obj = min_tid
+            self.updateBackupTID()
+            dm.updateCellTID(offset, add64(min_tid, -1))
+            dm.commit() # like in fetchTransactions
         else:
             min_tid = p.next_obj
             p.next_trans = add64(max_tid, 1)
         object_dict = {}
-        for serial, oid in self.app.dm.getReplicationObjectList(min_tid,
+        for serial, oid in dm.getReplicationObjectList(min_tid,
                 max_tid, FETCH_COUNT, offset, min_oid):
             try:
                 object_dict[serial].append(oid)
@@ -406,11 +419,14 @@ class Replicator(object):
         p = self.partition_dict[offset]
         p.next_obj = add64(tid, 1)
         self.updateBackupTID()
+        app = self.app
+        app.dm.updateCellTID(offset, tid)
+        app.dm.commit()
         if p.max_ttid or offset in self.replicate_dict and \
                          offset not in self.source_dict:
             logging.debug("unfinished transactions: %r", self.ttid_set)
         else:
-            self.app.tm.replicated(offset, tid)
+            app.tm.replicated(offset, tid)
         logging.debug("partition %u replicated up to %s from %r",
                       offset, dump(tid), self.current_node)
         self.getCurrentConnection().setReconnectionNoDelay()

neo/storage/shared_queue.py

+#
+# Copyright (C) 2018  Nexedi SA
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from msgpack import Packer, Unpacker
+
+class Queue(object):
+    """Unidirectional pipe for asynchronous and fast exchange of big amounts
+    of data between 2 processes.
+
+    It is implemented using shared memory, a few locks and msgpack
+    serialization. While the latter is faster than C pickle, it was mainly
+    chosen for its streaming API while deserializing, which greatly reduces
+    the locking overhead for the consumer process.
+
+    There is no mechanism to end a communication, so this information must be
+    in the exchanged data, for example by choosing a marker object like None:
+    - the last object sent by the producer is this marker
+    - the consumer stops iterating when it gets this marker
+
+    As long as there are data being exchanged, the 2 processes can't change
+    roles (producer/consumer).
+    """
+
+    def __init__(self, max_size):
+        from multiprocessing import Lock, RawArray, RawValue
+        self._max_size = max_size
+        self._array = RawArray('c', max_size)
+        self._pos = RawValue('L')
+        self._size = RawValue('L')
+        self._locks = Lock(), Lock(), Lock()
+
+    def __repr__(self):
+        return "<%s pos=%s size=%s max_size=%s>" % (self.__class__.__name__,
+            self._pos.value, self._size.value, self._max_size)
+
+    def __iter__(self):
+        """Iterate endlessly over all objects sent by the producer
+
+        Internally, this method uses a receiving buffer that is lost if
+        interrupted (GeneratorExit). If this buffer was not empty, the queue
+        is left in a inconsistent state and this method can't be called again.
+
+        So the correct way to split a loop is to first get an iterator
+        explicitly:
+            iq = iter(queue)
+            for x in iq:
+                if ...:
+                    break
+            for x in iq:
+                ...
+        """
+        unpacker = Unpacker(use_list=False, raw=True)
+        feed = unpacker.feed
+        max_size = self._max_size
+        array = self._array
+        pos = self._pos
+        size = self._size
+        lock, get_lock, put_lock = self._locks
+        left = 0
+        while 1:
+            for data in unpacker:
+                yield data
+            while 1:
+                with lock:
+                    p = pos.value
+                    s = size.value
+                if s:
+                    break
+                get_lock.acquire()
+            e = p + s
+            if e < max_size:
+                feed(array[p:e])
+            else:
+                feed(array[p:])
+                e -= max_size
+                feed(array[:e])
+            with lock:
+                pos.value = e
+                n = size.value
+                size.value = n - s
+            if n == max_size:
+                put_lock.acquire(0)
+                put_lock.release()
+
+    def __call__(self, iterable):
+        """Fill the queue with given objects
+
+        Hoping than msgpack.Packer gets a streaming API, 'iterable' should not
+        be split (i.e. this method should be called only once, like __iter__).
+        """
+        pack = Packer(use_bin_type=True).pack
+        max_size = self._max_size
+        array = self._array
+        pos = self._pos
+        size = self._size
+        lock, get_lock, put_lock = self._locks
+        left = 0
+        for data in iterable:
+            data = pack(data)
+            n = len(data)
+            i = 0
+            while 1:
+                if not left:
+                    while 1:
+                        with lock:
+                            p = pos.value
+                            j = size.value
+                        left = max_size - j
+                        if left:
+                            break
+                        put_lock.acquire()
+                    p += j
+                    if p >= max_size:
+                        p -= max_size
+                e = min(p + min(n, left), max_size)
+                j = e - p
+                array[p:e] = data[i:i+j]
+                n -= j
+                i += j
+                with lock:
+                    p = pos.value
+                    s = size.value
+                    j += s
+                    size.value = j
+                if not s:
+                    get_lock.acquire(0)
+                    get_lock.release()
+                p += j
+                if p >= max_size:
+                    p -= max_size
+                left = max_size - j
+                if not n:
+                    break
+
+
+def test(self):
+    import multiprocessing, random, sys, threading
+    from traceback import print_tb
+    r = range(50)
+    random.shuffle(r)
+    for P in threading.Thread, multiprocessing.Process:
+        q = Queue(23)
+        def t():
+            for n in xrange(len(r)):
+                yield '.' * n
+            yield
+            for n in r:
+                yield '.' * n
+        i = j = 0
+        p = P(target=q, args=(t(),))
+        p.daemon = 1
+        p.start()
+        try:
+            q = iter(q)
+            for i, x in enumerate(q):
+                if x is None:
+                    break
+                self.assertEqual(x, '.' * i)
+            self.assertEqual(i, len(r))
+            for j in r:
+                self.assertEqual(next(q), '.' * j)
+        except KeyboardInterrupt:
+            print_tb(sys.exc_info()[2])
+            self.fail((i, j))
+        p.join()
+
+if __name__ == '__main__':
+    import unittest
+    unittest.TextTestRunner().run(type('', (unittest.TestCase,), {
+        'runTest': test})())

neo/storage/transactions.py

@@ -314,12 +314,15 @@ class TransactionManager(EventQueue):
             Unlock transaction
         """
         try:
-            tid = self._transaction_dict[ttid].tid
+            transaction = self._transaction_dict[ttid]
         except KeyError:
             raise ProtocolError("unknown ttid %s" % dump(ttid))
+        tid = transaction.tid
         logging.debug('Unlock TXN %s (ttid=%s)', dump(tid), dump(ttid))
         dm = self._app.dm
-        dm.unlockTransaction(tid, ttid)
+        dm.unlockTransaction(tid, ttid,
+            transaction.voted == 2,
+            transaction.store_dict)
         self._app.em.setTimeout(time() + 1, dm.deferCommit())
         self.abort(ttid, even_if_locked=True)
 
@@ -521,7 +524,6 @@ class TransactionManager(EventQueue):
             assert not even_if_locked
             # See how the master processes AbortTransaction from the client.
             return
-        logging.debug('Abort TXN %s', dump(ttid))
         transaction = self._transaction_dict[ttid]
         locked = transaction.tid
         # if the transaction is locked, ensure we can drop it
@@ -529,6 +531,7 @@ class TransactionManager(EventQueue):
             if not even_if_locked:
                 return
         else:
+            logging.debug('Abort TXN %s', dump(ttid))
             dm = self._app.dm
             dm.abortTransaction(ttid)
             dm.releaseData([x[1] for x in transaction.store_dict.itervalues()],

neo/tests/__init__.py

@@ -28,8 +28,12 @@ import weakref
 import MySQLdb
 import transaction
 
+from ConfigParser import SafeConfigParser
 from cStringIO import StringIO
-from cPickle import Unpickler
+try:
+    from ZODB._compat import Unpickler
+except ImportError:
+    from cPickle import Unpickler
 from functools import wraps
 from inspect import isclass
 from .mock import Mock
@@ -152,8 +156,22 @@ def setupMySQLdb(db_list, user=DB_USER, password='', clear_databases=True):
     conn.commit()
     conn.close()
 
+def ImporterConfigParser(adapter, zodb, **kw):
+    cfg = SafeConfigParser()
+    cfg.add_section("neo")
+    cfg.set("neo", "adapter", adapter)
+    for x in kw.iteritems():
+        cfg.set("neo", *x)
+    for name, zodb in zodb:
+        cfg.add_section(name)
+        for x in zodb.iteritems():
+            cfg.set(name, *x)
+    return cfg
+
 class NeoTestBase(unittest.TestCase):
 
+    maxDiff = None
+
     def setUp(self):
         logging.name = self.setupLog()
         unittest.TestCase.setUp(self)
@@ -172,6 +190,8 @@ class NeoTestBase(unittest.TestCase):
         # Note we don't even abort them because it may require a valid
         # connection to a master node (see Storage.sync()).
         transaction.manager.__init__()
+        if logging._max_size is not None:
+            logging.flush()
 
     class failureException(AssertionError):
         def __init__(self, msg=None):

neo/tests/client/testClientApp.py

@@ -21,6 +21,7 @@ from .. import NeoUnitTestBase, buildUrlFromString
 from neo.client.app import Application
 from neo.client.cache import test as testCache
 from neo.client.exception import NEOStorageError
+from neo.lib.util import p64
 
 class ClientApplicationTests(NeoUnitTestBase):
 
@@ -51,9 +52,7 @@ class ClientApplicationTests(NeoUnitTestBase):
 
     def makeOID(self, value=None):
         from random import randint
-        if value is None:
-            value = randint(1, 255)
-        return '\00' * 7 + chr(value)
+        return p64(randint(1, 255) if value is None else value)
     makeTID = makeOID
 
     def makeTransactionObject(self, user='u', description='d', _extension='e'):

neo/tests/cluster.py

@@ -221,7 +221,7 @@ class ClusterPdb(object):
 
     def wait(self, test, timeout):
         end_time = time() + timeout
-        period = 0.1
+        period = 0.01
         while not test():
             cluster_dict.acquire()
             try:
@@ -232,7 +232,6 @@ class ClusterPdb(object):
                     next_sleep = max(last_pdb + timeout, end_time) - time()
                     if next_sleep > period:
                         next_sleep = period
-                        period *= 1.5
                     elif next_sleep < 0:
                         return False
             finally:

neo/tests/fs2zodb.py

-#
-# Copyright (C) 2014-2017  Nexedi SA
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-import os, stat, time
-from persistent import Persistent
-from BTrees.OOBTree import OOBTree
-
-class Inode(OOBTree):
-
-    data = None
-
-    def __init__(self, up=None, mode=stat.S_IFDIR):
-        self[os.pardir] = self if up is None else up
-        self.mode = mode
-        self.mtime = time.time()
-
-    def __getstate__(self):
-        return Persistent.__getstate__(self), OOBTree.__getstate__(self)
-
-    def __setstate__(self, state):
-        Persistent.__setstate__(self, state[0])
-        OOBTree.__setstate__(self, state[1])
-
-    def edit(self, data=None, mtime=None):
-        fmt = stat.S_IFMT(self.mode)
-        if data is None:
-            assert fmt == stat.S_IFDIR, oct(fmt)
-        else:
-            assert fmt == stat.S_IFREG or fmt == stat.S_IFLNK, oct(fmt)
-            if self.data != data:
-                self.data = data
-        if self.mtime != mtime:
-            self.mtime = mtime or time.time()
-
-    def root(self):
-        try:
-            self = self[os.pardir]
-        except KeyError:
-            return self
-        return self.root()
-
-    def traverse(self, path, followlinks=True):
-        path = iter(path.split(os.sep) if isinstance(path, basestring) and path
-                    else path)
-        for d in path:
-            if not d:
-                return self.root().traverse(path, followlinks)
-            if d != os.curdir:
-                d = self[d]
-                if followlinks and stat.S_ISLNK(d.mode):
-                    d = self.traverse(d.data, True)
-                return d.traverse(path, followlinks)
-        return self
-
-    def inodeFromFs(self, path):
-        s = os.lstat(path)
-        mode = s.st_mode
-        name = os.path.basename(path)
-        try:
-            i = self[name]
-            assert stat.S_IFMT(i.mode) == stat.S_IFMT(mode)
-            changed = False
-        except KeyError:
-            i = self[name] = self.__class__(self, mode)
-            changed = True
-        i.edit(open(path).read() if stat.S_ISREG(mode) else
-                      os.readlink(p) if stat.S_ISLNK(mode) else
-                      None, s.st_mtime)
-        return changed or i._p_changed
-
-    def treeFromFs(self, path, yield_interval=None, filter=None):
-        prefix_len = len(path) + len(os.sep)
-        n = 0
-        for dirpath, dirnames, filenames in os.walk(path):
-            inodeFromFs = self.traverse(dirpath[prefix_len:]).inodeFromFs
-            for names in dirnames, filenames:
-                skipped = []
-                for j, name in enumerate(names):
-                    p = os.path.join(dirpath, name)
-                    if filter and not filter(p[prefix_len:]):
-                        skipped.append(j)
-                    elif inodeFromFs(p):
-                        n += 1
-                        if n == yield_interval:
-                            n = 0
-                            yield self
-                while skipped:
-                    del names[skipped.pop()]
-        if n:
-            yield self
-
-    def walk(self):
-        s = [(None, self)]
-        while s:
-            top, self = s.pop()
-            dirs = []
-            nondirs = []
-            for name, inode in self.iteritems():
-                if name != os.pardir:
-                    (dirs if stat.S_ISDIR(inode.mode) else nondirs).append(name)
-            yield top or os.curdir, dirs, nondirs
-            for name in dirs:
-                s.append((os.path.join(top, name) if top else name, self[name]))

neo/tests/functional/__init__.py

@@ -29,17 +29,16 @@ import tempfile
 import traceback
 import threading
 import psutil
-from ConfigParser import SafeConfigParser
 
 import neo.scripts
 from neo.neoctl.neoctl import NeoCTL, NotReadyException
 from neo.lib import logging
 from neo.lib.protocol import ClusterStates, NodeTypes, CellStates, NodeStates, \
     UUID_NAMESPACES
-from neo.lib.util import dump
+from neo.lib.util import dump, setproctitle
 from .. import (ADDRESS_TYPE, DB_SOCKET, DB_USER, IP_VERSION_FORMAT_DICT, SSL,
-    buildUrlFromString, cluster, getTempDirectory, NeoTestBase, Patch,
-    setupMySQLdb)
+    buildUrlFromString, cluster, getTempDirectory, setupMySQLdb,
+    ImporterConfigParser, NeoTestBase, Patch)
 from neo.client.Storage import Storage
 from neo.storage.database import manager, buildDatabaseManager
 
@@ -116,36 +115,31 @@ class PortAllocator(object):
     __del__ = release
 
 
-class NEOProcess(object):
+class Process(object):
 
     _coverage_fd = None
     _coverage_prefix = os.path.join(getTempDirectory(), 'coverage-')
     _coverage_index = 0
     pid = 0
 
-    def __init__(self, command, uuid, arg_dict):
-        try:
-            __import__('neo.scripts.' + command, level=0)
-        except ImportError:
-            raise NotFound, '%s not found' % (command)
+    def __init__(self, command, arg_dict={}):
         self.command = command
         self.arg_dict = arg_dict
-        self.with_uuid = True
-        self.setUUID(uuid)
 
-    def start(self, with_uuid=True):
-        # Prevent starting when already forked and wait wasn't called.
-        if self.pid != 0:
-            raise AlreadyRunning, 'Already running with PID %r' % (self.pid, )
-        command = self.command
+    def _args(self):
         args = []
-        self.with_uuid = with_uuid
         for arg, param in self.arg_dict.iteritems():
             args.append('--' + arg)
             if param is not None:
                 args.append(str(param))
-        if with_uuid:
-            args += '--uuid', str(self.uuid)
+        return args
+
+    def start(self):
+        # Prevent starting when already forked and wait wasn't called.
+        if self.pid != 0:
+            raise AlreadyRunning('Already running with PID %r' % self.pid)
+        command = self.command
+        args = self._args()
         global coverage
         if coverage:
             cls = self.__class__
@@ -159,7 +153,7 @@ class NEOProcess(object):
             if args:
                 os.close(w)
                 os.kill(os.getpid(), signal.SIGSTOP)
-        self.pid = logging.fork()
+        self.pid = os.fork()
         if self.pid:
             # Wait that the signal to kill the child is set up.
             os.close(w)
@@ -179,7 +173,8 @@ class NEOProcess(object):
                 os.close(self._coverage_fd)
                 os.write(w, '\0')
                 sys.argv = [command] + args
-                getattr(neo.scripts,  command).main()
+                setproctitle(self.command)
+                self.run()
                 status = 0
             except SystemExit, e:
                 status = e.code
@@ -203,6 +198,9 @@ class NEOProcess(object):
         logging.info('pid %u: %s %s',
             self.pid, command, ' '.join(map(repr, args)))
 
+    def run(self):
+        raise NotImplementedError
+
     def child_coverage(self):
         r = self._coverage_fd
         if r is not None:
@@ -249,11 +247,32 @@ class NEOProcess(object):
         self.kill()
         self.wait()
 
-    def getPID(self):
-        return self.pid
+    def isAlive(self):
+        try:
+            return psutil.Process(self.pid).status() != psutil.STATUS_ZOMBIE
+        except psutil.NoSuchProcess:
+            return False
+
+class NEOProcess(Process):
+
+    def __init__(self, command, uuid, arg_dict):
+        try:
+            __import__('neo.scripts.' + command, level=0)
+        except ImportError:
+            raise NotFound(command + ' not found')
+        super(NEOProcess, self).__init__(command, arg_dict)
+        self.setUUID(uuid)
+
+    def _args(self):
+        args = super(NEOProcess, self)._args()
+        if self.uuid:
+            args += '--uuid', str(self.uuid)
+        return args
+
+    def run(self):
+        getattr(neo.scripts,  self.command).main()
 
     def getUUID(self):
-        assert self.with_uuid, 'UUID disabled on this process'
         return self.uuid
 
     def setUUID(self, uuid):
@@ -262,12 +281,6 @@ class NEOProcess(object):
         """
         self.uuid = uuid
 
-    def isAlive(self):
-        try:
-            return psutil.Process(self.pid).status() != psutil.STATUS_ZOMBIE
-        except psutil.NoSuchProcess:
-            return False
-
 class NEOCluster(object):
 
     SSL = None
@@ -304,14 +317,8 @@ class NEOCluster(object):
             IP_VERSION_FORMAT_DICT[self.address_type]
         self.setupDB(clear_databases)
         if importer:
-            cfg = SafeConfigParser()
-            cfg.add_section("neo")
-            cfg.set("neo", "adapter", adapter)
+            cfg = ImporterConfigParser(adapter, **importer)
             cfg.set("neo", "database", self.db_template(*db_list))
-            for name, zodb in importer:
-                cfg.add_section(name)
-                for x in zodb.iteritems():
-                    cfg.set(name, *x)
             importer_conf = os.path.join(temp_dir, 'importer.cfg')
             with open(importer_conf, 'w') as f:
                 cfg.write(f)

neo/tests/functional/testClient.py

@@ -202,9 +202,9 @@ class ClientTests(NEOFunctionalTest):
         self.neo.stop()
 
         self.neo = NEOCluster(db_list=['test_neo1'], partitions=3,
-            importer=[("root", {
+            importer={"zodb": [("root", {
                 "storage": "<filestorage>\npath %s\n</filestorage>"
-                            % dfs_storage.getName()})],
+                            % dfs_storage.getName()})]},
             temp_dir=self.getTempDirectory())
         self.neo.start()
         neo_db, neo_conn = self.neo.getZODBConnection()

neo/tests/master/testMasterPT.py

@@ -15,7 +15,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import random, time, unittest
-from collections import defaultdict
+from collections import Counter, defaultdict
 from .. import NeoUnitTestBase
 from neo.lib import logging
 from neo.lib.protocol import NodeStates, CellStates
@@ -291,13 +291,17 @@ class MasterPartitionTableTests(NeoUnitTestBase):
         self.update(pt, self.tweak(pt, sn[:1]))
         self.assertPartitionTable(pt, '.U.|..U|.U.|..U|.U.|..U|.U.')
 
-    def test_18_tweak(self):
-        s = repr(time.time())
-        logging.info("using seed %r", s)
-        r = random.Random(s)
+    def test_18_tweakBigPT(self):
+        seed = repr(time.time())
+        logging.info("using seed %r", seed)
         sn_count = 11
         sn = [self.createStorage(None, i + 1, NodeStates.RUNNING)
               for i in xrange(sn_count)]
+        for topo in 0, 1:
+            r = random.Random(seed)
+            if topo:
+                for i, s in enumerate(sn, sn_count):
+                    s.devpath = str(i % 5),
             pt = PartitionTable(1000, 2)
             pt.setID(1)
             for offset in xrange(pt.np):
@@ -311,6 +315,70 @@ class MasterPartitionTableTests(NeoUnitTestBase):
             self.tweak(pt)
             self.update(pt)
 
+    def test_19_topology(self):
+        sn_count = 16
+        sn = [self.createStorage(None, i + 1, NodeStates.RUNNING)
+              for i in xrange(sn_count)]
+        pt = PartitionTable(48, 2)
+        pt.make(sn)
+        pt.log()
+        for i, s in enumerate(sn, sn_count):
+            s.devpath = tuple(bin(i)[3:-1])
+        self.assertEqual(Counter(x[2] for x in self.tweak(pt)), {
+            CellStates.OUT_OF_DATE: 96,
+            CellStates.FEEDING: 96,
+        })
+        self.update(pt)
+        x = lambda n, *x: ('|'.join(x[:1]*n), '|'.join(x[1:]*n))
+        for even, np, i, topo, expected in (
+            ## Optimal topology.
+            # All nodes have same number of cells.
+            (1, 2, 2, ("00", "01", "02", "10", "11", "12"), ('UU...U|..UUU.',
+                                                             'UU.U..|..U.UU')),
+            (1, 7, 1, "0001122", (
+                'U.....U|.U.U...|..U.U..|U....U.|.U....U|..UU...|....UU.',
+                'U..U...|.U...U.|..U.U..|U.....U|.U.U...|..U..U.|....U.U')),
+            (1, 4, 1, "00011122", ('U......U|.U.U....|..U.U...|.....UU.',
+                                   'U..U....|.U..U...|..U...U.|.....U.U')),
+            (1, 9, 1, "000111222", ('U.......U|.U.U.....|..U.U....|'
+                                    '.....UU..|U......U.|.U......U|'
+                                    '..UU.....|....U.U..|.....U.U.',
+                                    'U..U.....|.U....U..|..U.U....|'
+                                    '.....U.U.|U.......U|.U.U.....|'
+                                    '..U...U..|....U..U.|.....U..U')),
+            # Some nodes have a extra cell.
+            (0, 8, 1, "0001122", ('U.....U|.U.U...|..U.U..|U....U.|'
+                                  '.U....U|..UU...|....UU.|U.....U',
+                                  'U..U...|.U...U.|..U.U..|U.....U|'
+                                  '.U.U...|..U..U.|....U.U|U..U...')),
+            ## Topology ignored.
+            (1, 6, 1, ("00", "01", "1"), 'UU.|U.U|.UU|UU.|U.U|.UU'),
+            (1, 5, 2, "01233", 'UUU..|U..UU|.UUU.|UU..U|..UUU'),
+        ):
+            assert len(topo) <= sn_count
+            sn2 = sn[:len(topo)]
+            for s in sn2:
+                s.devpath = ()
+            k = (1,7)[even]
+            pt = PartitionTable(np*k, i)
+            pt.make(sn2)
+            for devpath, s in zip(topo, sn2):
+                s.devpath = tuple(devpath)
+            if type(expected) is tuple:
+                self.assertTrue(self.tweak(pt))
+                self.update(pt)
+                self.assertPartitionTable(pt, '|'.join(expected[:1]*k))
+                pt.clear()
+                pt.make(sn2)
+                self.assertPartitionTable(pt, '|'.join(expected[1:]*k))
+                self.assertFalse(pt.tweak())
+            else:
+                expected = '|'.join((expected,)*k)
+                self.assertFalse(pt.tweak())
+                self.assertPartitionTable(pt, expected)
+                pt.clear()
+                pt.make(sn2)
+                self.assertPartitionTable(pt, expected)
 
 if __name__ == '__main__':
     unittest.main()

neo/tests/random_tree.py

+#
+# Copyright (C) 2018  Nexedi SA
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import hashlib, random
+from collections import deque
+from itertools import islice
+from persistent import Persistent
+from BTrees.IOBTree import IOBTree
+from .stat_zodb import _DummyData
+
+def generateTree(random=random):
+    tree = []
+    N = 5
+    fifo = deque()
+    path = ()
+    size = lambda: max(int(random.gauss(40,30)), 0)
+    while 1:
+        tree.extend(path + (i, size())
+            for i in xrange(-random.randrange(N), 0))
+        n = N * (1 - len(path)) + random.randrange(N)
+        for i in xrange(n):
+            fifo.append(path + (i,))
+        try:
+            path = fifo.popleft()
+        except IndexError:
+            break
+    change = tree
+    while change:
+        change = [x[:-1] + (size(),) for x in change if random.randrange(2)]
+        tree += change
+    random.shuffle(tree)
+    return tree
+
+class Leaf(Persistent):
+    pass
+
+Node = IOBTree
+
+def importTree(root, tree, yield_interval=None, filter=None):
+    n = 0
+    for path in tree:
+        node = root
+        for i, x in enumerate(path[:-1], 1):
+            if filter and not filter(path[:i]):
+                break
+            if x < 0:
+                try:
+                    node = node[x]
+                except KeyError:
+                    node[x] = node = Leaf()
+                node.data = bytes(_DummyData(random.Random(path), path[-1]))
+            else:
+                try:
+                    node = node[x]
+                    continue
+                except KeyError:
+                    node[x] = node = Node()
+            n += 1
+            if n == yield_interval:
+                n = 0
+                yield root
+    if n:
+        yield root
+
+class hashTree(object):
+
+    _hash = None
+    _new = hashlib.md5
+
+    def __init__(self, node):
+        s = [((), node)]
+        def walk():
+            h = self._new()
+            update = h.update
+            while s:
+                top, node = s.pop()
+                try:
+                    update('%s %s %s\n' % (top, len(node.data),
+                        self._new(node.data).hexdigest()))
+                    yield
+                except AttributeError:
+                    update('%s %s\n' % (top, tuple(node.keys())))
+                    yield
+                    for k, v in reversed(node.items()):
+                        s.append((top + (k,), v))
+            del self._walk
+            self._hash = h
+        self._walk = walk()
+
+    def __getattr__(self, attr):
+        return getattr(self._hash, attr)
+
+    def __call__(self, n=None):
+        if n is None:
+            return sum(1 for _ in self._walk)
+        next(islice(self._walk, n - 1, None))

neo/tests/stat_zodb.py

@@ -19,11 +19,13 @@ PROD1 = lambda random=random: DummyZODB(6.04237779991, 1.55811487853,
                                         1.04108991045, 0.906703192546,
                                         0.810080409164, random)
 
-def DummyData(random=random):
+def _DummyData(random, size):
     # returns data that gzip at about 28.5 %
+    return bytearray(int(random.gauss(0, .8)) % 256 for x in xrange(size))
+
+def DummyData(random=random):
     # make sure sample is bigger than dictionary of compressor
-    data = ''.join(chr(int(random.gauss(0, .8)) % 256) for x in xrange(100000))
-    return StringIO(data)
+    return StringIO(_DummyData(random, 100000))
 
 
 class DummyZODB(object):

neo/tests/storage/testStorageDBTests.py

@@ -89,7 +89,7 @@ class StorageDBTests(NeoUnitTestBase):
         self.db.lockTransaction(tid, ttid)
         yield
         if commit:
-            self.db.unlockTransaction(tid, ttid)
+            self.db.unlockTransaction(tid, ttid, True, objs)
             self.db.commit()
         elif commit is not None:
             self.db.abortTransaction(ttid)
@@ -227,6 +227,7 @@ class StorageDBTests(NeoUnitTestBase):
 
     def test_changePartitionTable(self):
         db = self.getDB()
+        db.setNumPartitions(3)
         ptid = 1
         uuid = self.getStorageUUID()
         cell1 = 0, uuid, CellStates.OUT_OF_DATE
@@ -253,7 +254,7 @@ class StorageDBTests(NeoUnitTestBase):
         txn1, objs1 = self.getTransaction([oid1])
         txn2, objs2 = self.getTransaction([oid2])
         # nothing in database
-        self.assertEqual(self.db.getLastIDs(), (None, {}, {}, None))
+        self.assertEqual(self.db.getLastIDs(), (None, None))
         self.assertEqual(self.db.getUnfinishedTIDDict(), {})
         self.assertEqual(self.db.getObject(oid1), None)
         self.assertEqual(self.db.getObject(oid2), None)
@@ -319,13 +320,17 @@ class StorageDBTests(NeoUnitTestBase):
             expected = [(t, oid_list[offset+i]) for t in tids for i in (0, np)]
             self.assertEqual(self.db.getReplicationObjectList(ZERO_TID,
                 MAX_TID, len(expected) + 1, offset, ZERO_OID), expected)
-        self.db._deleteRange(0, MAX_TID)
-        self.db._deleteRange(0, max_tid=ZERO_TID)
+        def deleteRange(partition, min_tid=None, max_tid=None):
+            self.db._deleteRange(partition,
+                None if min_tid is None else u64(min_tid),
+                None if max_tid is None else u64(max_tid))
+        deleteRange(0, MAX_TID)
+        deleteRange(0, max_tid=ZERO_TID)
         check(0, [], t1, t2, t3)
-        self.db._deleteRange(0);             check(0, [])
-        self.db._deleteRange(1, t2);         check(1, [t1], t1, t2)
-        self.db._deleteRange(2, max_tid=t2); check(2, [], t3)
-        self.db._deleteRange(3, t1, t2);     check(3, [t3], t1, t3)
+        deleteRange(0);             check(0, [])
+        deleteRange(1, t2);         check(1, [t1], t1, t2)
+        deleteRange(2, max_tid=t2); check(2, [], t3)
+        deleteRange(3, t1, t2);     check(3, [t3], t1, t3)
 
     def test_getTransaction(self):
         oid1, oid2 = self.getOIDs(2)

neo/tests/storage/testStorageMySQL.py

@@ -15,17 +15,32 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import unittest
-from MySQLdb import NotSupportedError, OperationalError
+from contextlib import contextmanager
+from MySQLdb import NotSupportedError, OperationalError, ProgrammingError
+from MySQLdb.constants.CR import SERVER_GONE_ERROR
 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 .. import DB_PREFIX, DB_SOCKET, DB_USER, Patch
 from .testStorageDBTests import StorageDBTests
+from neo.storage.database import DatabaseFailure
 from neo.storage.database.mysqldb import MySQLDatabaseManager
 
 
+class ServerGone(object):
+
+    @contextmanager
+    def __new__(cls, db):
+        self = object.__new__(cls)
+        with Patch(db, conn=self) as self._p:
+            yield self._p
+
+    def query(self, *args):
+        self._p.revert()
+        raise OperationalError(SERVER_GONE_ERROR, 'this is a test')
+
+
 class StorageMySQLdbTests(StorageDBTests):
 
     engine = None
@@ -67,23 +82,9 @@ class StorageMySQLdbTests(StorageDBTests):
         calls[0].checkArgs('SELECT ')
 
     def test_query2(self):
-        # test the OperationalError exception
-        # fake object, raise exception during the first call
-        from MySQLdb.constants.CR import SERVER_GONE_ERROR
-        class FakeConn(object):
-            def query(*args):
-                raise OperationalError(SERVER_GONE_ERROR, 'this is a test')
-        self.db.conn = FakeConn()
-        self.connect_called = False
-        def connect_hook():
-            # mock object, break raise/connect loop
-            self.db.conn = Mock()
-            self.connect_called = True
-        self.db._connect = connect_hook
-        # make a query, exception will be raised then connect() will be
-        # called and the second query will use the mock object
-        self.db.query('INSERT')
-        self.assertTrue(self.connect_called)
+        with ServerGone(self.db) as p:
+            self.assertRaises(ProgrammingError, self.db.query, 'QUERY')
+            self.assertFalse(p.applied)
 
     def test_query3(self):
         # OperationalError > raise DatabaseFailure exception

neo/tests/testUtil.py

@@ -21,6 +21,8 @@ from neo.lib.util import ReadBuffer, parseNodeAddress
 
 class UtilTests(NeoUnitTestBase):
 
+    from neo.storage.shared_queue import test as testSharedQueue
+
     def test_parseNodeAddress(self):
         """ Parsing of addresses """
         def test(parsed, *args):

neo/tests/threaded/__init__.py

@@ -19,7 +19,6 @@
 import os, random, select, socket, sys, tempfile
 import thread, threading, time, traceback, weakref
 from collections import deque
-from ConfigParser import SafeConfigParser
 from contextlib import contextmanager
 from itertools import count
 from functools import partial, wraps
@@ -37,8 +36,9 @@ from neo.lib.handler import EventHandler
 from neo.lib.locking import SimpleQueue
 from neo.lib.protocol import ClusterStates, Enum, NodeStates, NodeTypes, Packets
 from neo.lib.util import cached_property, parseMasterList, p64
-from .. import NeoTestBase, Patch, getTempDirectory, setupMySQLdb, \
-    ADDRESS_TYPE, IP_VERSION_FORMAT_DICT, DB_PREFIX, DB_SOCKET, DB_USER
+from .. import (getTempDirectory, setupMySQLdb,
+    ImporterConfigParser, NeoTestBase, Patch,
+    ADDRESS_TYPE, IP_VERSION_FORMAT_DICT, DB_PREFIX, DB_SOCKET, DB_USER)
 
 BIND = IP_VERSION_FORMAT_DICT[ADDRESS_TYPE], 0
 LOCAL_IP = socket.inet_pton(ADDRESS_TYPE, IP_VERSION_FORMAT_DICT[ADDRESS_TYPE])
@@ -171,6 +171,8 @@ class Serialized(object):
             #      a single-core CPU, other threads are still busy and haven't
             #      sent anything yet on the network. This causes tic() to
             #      return prematurely. Passing a non-zero value is a hack.
+            #      We also increase SocketConnector.SOMAXCONN in tests so that
+            #      a connection attempt is never delayed inside the kernel.
             timeout=0):
         # If you're in a pdb here, 'n' switches to another thread
         # (the following lines are not supposed to be debugged into)
@@ -612,6 +614,7 @@ class NEOCluster(object):
         Patch(BaseConnection, getTimeout=lambda orig, self: None),
         Patch(SimpleQueue, __init__=__init__),
         Patch(SocketConnector, CONNECT_LIMIT=0),
+        Patch(SocketConnector, SOMAXCONN=128), # see Serialized.tic comment
         Patch(SocketConnector, _bind=lambda orig, self, addr: orig(self, BIND)),
         Patch(SocketConnector, _connect = lambda orig, self, addr:
             orig(self, ServerNode.resolv(addr))))
@@ -652,8 +655,8 @@ class NEOCluster(object):
                        adapter=os.getenv('NEO_TESTS_ADAPTER', 'SQLite'),
                        storage_count=None, db_list=None, clear_databases=True,
                        db_user=DB_USER, db_password='', compress=True,
-                       importer=None, autostart=None, dedup=False):
-        self.name = 'neo_%s' % self._allocate('name',
+                       importer=None, autostart=None, dedup=False, name=None):
+        self.name = name or 'neo_%s' % self._allocate('name',
             lambda: random.randint(0, 100))
         self.compress = compress
         self.num_partitions = partitions
@@ -685,14 +688,8 @@ class NEOCluster(object):
         else:
             assert False, adapter
         if importer:
-            cfg = SafeConfigParser()
-            cfg.add_section("neo")
-            cfg.set("neo", "adapter", adapter)
+            cfg = ImporterConfigParser(adapter, **importer)
             cfg.set("neo", "database", db % tuple(db_list))
-            for name, zodb in importer:
-                cfg.add_section(name)
-                for x in zodb.iteritems():
-                    cfg.set(name, *x)
             db = os.path.join(getTempDirectory(), '%s.conf')
             with open(db % tuple(db_list), "w") as f:
                 cfg.write(f)
@@ -777,7 +774,7 @@ class NEOCluster(object):
             else NodeStates.RUNNING)
         for node in self.storage_list if storage_list is None else storage_list:
             state = self.getNodeState(node)
-            assert state == expected_state, (node, state)
+            assert state == expected_state, (repr(node), state)
 
     def stop(self, clear_database=False, __print_exc=traceback.print_exc, **kw):
         if self.started:
@@ -897,10 +894,9 @@ class NEOCluster(object):
         if dummy_zodb is None:
             from ..stat_zodb import PROD1
             dummy_zodb = PROD1(random)
-        preindex = {}
         as_storage = dummy_zodb.as_storage
-        return lambda count: self.getZODBStorage().importFrom(
-            as_storage(count), preindex=preindex)
+        return lambda count: self.getZODBStorage().copyTransactionsFrom(
+            as_storage(count))
 
     def populate(self, transaction_list, tid=lambda i: p64(i+1),
                                          oid=lambda i: p64(i+1)):
@@ -1025,7 +1021,11 @@ class NEOThreadedTest(NeoTestBase):
         with Patch(client, _getFinalTID=lambda *_: None):
             self.assertRaises(ConnectionClosed, txn.commit)
 
-    def assertPartitionTable(self, cluster, expected, pt_node=None):
+    def assertPartitionTable(self, cluster, expected, pt_node=None,
+                                   sort_by_nid=False):
+        if sort_by_nid:
+            index = lambda x: x
+        else:
             index = [x.uuid for x in cluster.storage_list].index
         super(NEOThreadedTest, self).assertPartitionTable(
             (pt_node or cluster.admin).pt, expected,

neo/tests/threaded/test.py

@@ -23,7 +23,6 @@ import unittest
 from collections import defaultdict
 from contextlib import contextmanager
 from thread import get_ident
-from zlib import compress
 from persistent import Persistent, GHOST
 from transaction.interfaces import TransientError
 from ZODB import DB, POSException
@@ -31,7 +30,7 @@ from ZODB.DB import TransactionalUndo
 from neo.storage.transactions import TransactionManager, ConflictError
 from neo.lib.connection import ConnectionClosed, \
     ServerConnection, MTClientConnection
-from neo.lib.exception import DatabaseFailure, StoppedOperation
+from neo.lib.exception import StoppedOperation
 from neo.lib.handler import DelayEvent, EventHandler
 from neo.lib import logging
 from neo.lib.protocol import (CellStates, ClusterStates, NodeStates, NodeTypes,
@@ -43,6 +42,7 @@ from neo.lib.util import add64, makeChecksum, p64, u64
 from neo.client.exception import NEOPrimaryMasterLost, NEOStorageError
 from neo.client.transactions import Transaction
 from neo.master.handlers.client import ClientServiceHandler
+from neo.storage.database import DatabaseFailure
 from neo.storage.handlers.client import ClientOperationHandler
 from neo.storage.handlers.identification import IdentificationHandler
 from neo.storage.handlers.initialization import InitializationHandler
@@ -60,12 +60,13 @@ class PCounterWithResolution(PCounter):
 
 class Test(NEOThreadedTest):
 
-    @with_cluster()
-    def testBasicStore(self, cluster):
-        if 1:
+    def testBasicStore(self, dedup=False):
+        with NEOCluster(dedup=dedup) as cluster:
+            cluster.start()
             storage = cluster.getZODBStorage()
             storage.sync()
             storage.app.max_reconnection_to_master = 0
+            compress = storage.app.compress._compress
             data_info = {}
             compressible = 'x' * 20
             compressed = compress(compressible)
@@ -137,27 +138,6 @@ class Test(NEOThreadedTest):
                     self.assertRaises(POSException.POSKeyError,
                         storage.load, oid, '')
 
-    @with_cluster()
-    def testCreationUndoneHistory(self, cluster):
-        if 1:
-            storage = cluster.getZODBStorage()
-            oid = storage.new_oid()
-            txn = transaction.Transaction()
-            storage.tpc_begin(txn)
-            storage.store(oid, None, 'foo', '', txn)
-            storage.tpc_vote(txn)
-            tid1 = storage.tpc_finish(txn)
-            storage.tpc_begin(txn)
-            storage.undo(tid1, txn)
-            tid2 = storage.tpc_finish(txn)
-            storage.tpc_begin(txn)
-            storage.undo(tid2, txn)
-            tid3 = storage.tpc_finish(txn)
-            expected = [(tid1, 3), (tid2, 0), (tid3, 3)]
-            for x in storage.history(oid, 10):
-                self.assertEqual((x['tid'], x['size']), expected.pop())
-            self.assertFalse(expected)
-
     def _testUndoConflict(self, cluster, *inc):
         def waitResponses(orig, *args):
             orig(*args)
@@ -738,8 +718,9 @@ class Test(NEOThreadedTest):
 
     @with_cluster()
     def testStorageUpgrade1(self, cluster):
-        if 1:
         storage = cluster.storage
+        # Disable migration steps that aren't idempotent.
+        with Patch(storage.dm.__class__, _migrate3=lambda *_: None):
             t, c = cluster.getTransaction()
             storage.dm.setConfiguration("version", None)
             c.root()._p_changed = 1
@@ -1309,7 +1290,7 @@ class Test(NEOThreadedTest):
             s1.resetNode()
             with Patch(s1.dm, truncate=dieFirst(1)):
                 s1.start()
-                self.assertEqual(s0.dm.getLastIDs()[0], truncate_tid)
+                self.assertFalse(s0.dm.getLastIDs()[0])
                 self.assertEqual(s1.dm.getLastIDs()[0], r._p_serial)
                 self.tic()
                 self.assertEqual(calls, [1, 2])
@@ -1723,7 +1704,18 @@ class Test(NEOThreadedTest):
                     x.value += 1
                     c2.root()['x'].value += 2
                     TransactionalResource(t1, 1, tpc_begin=begin1)
-                    s1m, = s1.getConnectionList(cluster.master)
+                    # BUG: Very rarely, getConnectionList returns more that 1
+                    #      connection ("too many values to unpack"), which is
+                    #       a mystery and impossible to reproduce:
+                    #      - 1st time: v1.8.1 on a test machine (no SSL)
+                    #      - last: current revision on my laptop (SSL),
+                    #              at the first iteration of this loop
+                    _sm = list(s1.getConnectionList(cluster.master))
+                    try:
+                        s1m, = _sm
+                    except ValueError:
+                        self.fail((_sm, list(
+                            s1.getConnectionList(cluster.master))))
                     try:
                         s1.em.removeReader(s1m)
                         with ConnectionFilter() as f, \
@@ -2371,7 +2363,7 @@ class Test(NEOThreadedTest):
             oid, tid = big_id_list[i]
             for j, expected in (
                     (1 - i, (dm.getLastTID(u64(MAX_TID)), dm.getLastIDs())),
-                    (i, (u64(tid), (tid, {}, {}, oid)))):
+                    (i, (u64(tid), (tid, oid)))):
                 oid, tid = big_id_list[j]
                 # Somehow we abuse 'storeTransaction' because we ask it to
                 # write data for unassigned partitions. This is not checked
@@ -2381,6 +2373,44 @@ class Test(NEOThreadedTest):
                 self.assertEqual(expected,
                     (dm.getLastTID(u64(MAX_TID)), dm.getLastIDs()))
 
+    def testStorageUpgrade(self):
+        path = os.path.join(os.path.dirname(__file__),
+                            self._testMethodName + '-%s',
+                            's%s.sql')
+        dump_dict = {}
+        def switch(s):
+            dm = s.dm
+            dm.commit()
+            dump_dict[s.uuid] = dm.dump()
+            dm.erase()
+            with open(path % (s.getAdapter(), s.uuid)) as f:
+                dm.restore(f.read())
+        with NEOCluster(storage_count=3, partitions=3, replicas=1,
+                        name=self._testMethodName) as cluster:
+            s1, s2, s3 = cluster.storage_list
+            cluster.start(storage_list=(s1,))
+            for s in s2, s3:
+                s.start()
+                self.tic()
+                cluster.neoctl.enableStorageList([s.uuid])
+                cluster.neoctl.tweakPartitionTable()
+            self.tic()
+            nid_list = [s.uuid for s in cluster.storage_list]
+            switch(s3)
+            s3.stop()
+            storage = cluster.getZODBStorage()
+            txn = transaction.Transaction()
+            storage.tpc_begin(txn, p64(85**9)) # partition 1
+            storage.store(p64(0), None, 'foo', '', txn)
+            storage.tpc_vote(txn)
+            storage.tpc_finish(txn)
+            self.tic()
+            switch(s1)
+            switch(s2)
+            cluster.stop()
+            for i, s in zip(nid_list, cluster.storage_list):
+                self.assertMultiLineEqual(s.dm.dump(), dump_dict[i])
+
 
 if __name__ == "__main__":
     unittest.main()

neo/tests/threaded/testConfig.py

+#
+# Copyright (C) 2018  Nexedi SA
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import unittest
+from contextlib import contextmanager
+from ZConfig import ConfigurationSyntaxError
+from ZODB.config import databaseFromString
+from .. import Patch
+from . import ClientApplication, NEOThreadedTest, with_cluster
+from neo.client import Storage
+
+def databaseFromDict(**kw):
+    return databaseFromString("%%import neo.client\n"
+        "<zodb>\n <NEOStorage>\n%s </NEOStorage>\n</zodb>\n"
+        % ''.join('  %s %s\n' % x for x in kw.iteritems()))
+
+class ConfigTests(NEOThreadedTest):
+
+    dummy_required = {'name': 'cluster', 'master_nodes': '127.0.0.1:10000'}
+
+    @contextmanager
+    def _db(self, cluster, **kw):
+        kw['name'] = cluster.name
+        kw['master_nodes'] = cluster.master_nodes
+        def newClient(_, *args, **kw):
+            client = ClientApplication(*args, **kw)
+            t.append(client.poll_thread)
+            return client
+        t = []
+        with Patch(Storage, Application=newClient):
+            db = databaseFromDict(**kw)
+        try:
+            yield db
+        finally:
+            db.close()
+            cluster.join(t)
+
+    @with_cluster()
+    def testCompress(self, cluster):
+        kw = self.dummy_required.copy()
+        valid = ['false', 'true', 'zlib', 'zlib=9']
+        for kw['compress'] in '9', 'best', 'zlib=0', 'zlib=100':
+            self.assertRaises(ConfigurationSyntaxError, databaseFromDict, **kw)
+        for compress in valid:
+            with self._db(cluster, compress=compress) as db:
+                self.assertEqual((0,0,''), db.storage.app.compress(''))
+
+if __name__ == "__main__":
+    unittest.main()

neo/tests/threaded/testSSL.py

@@ -37,6 +37,11 @@ class SSLTests(SSLMixin, test.Test):
     testStorageDataLock2 = None
     testUndoConflictDuringStore = None
 
+    # With MySQL, this test is expensive.
+    # Let's check deduplication of big oids here.
+    def testBasicStore(self):
+        super(SSLTests, self).testBasicStore(True)
+
     def testAbortConnection(self, after_handshake=1):
         with self.getLoopbackConnection() as conn:
             conn.ask(Packets.Ping())

neo/tests/threaded/testStorageUpgrade-MySQL/s1.sql

+CREATE TABLE `bigdata` (
+  `id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `value` mediumblob NOT NULL,
+  PRIMARY KEY (`id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+CREATE TABLE `config` (
+  `name` varbinary(255) NOT NULL,
+  `value` varbinary(255) DEFAULT NULL,
+  PRIMARY KEY (`name`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+INSERT INTO `config` VALUES ('name','testStorageUpgrade'),('nid','1'),('partitions','3'),('ptid','9'),('replicas','1');
+CREATE TABLE `data` (
+  `id` bigint(20) unsigned NOT NULL,
+  `hash` binary(20) NOT NULL,
+  `compression` tinyint(3) unsigned DEFAULT NULL,
+  `value` mediumblob NOT NULL,
+  PRIMARY KEY (`id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+INSERT INTO `data` VALUES (0,0x0BEEC7B5EA3F0FDBC95D0DD47F3C5BC275DA8A33,0,0x666F6F);
+CREATE TABLE `obj` (
+  `partition` smallint(5) unsigned NOT NULL,
+  `oid` bigint(20) unsigned NOT NULL,
+  `tid` bigint(20) unsigned NOT NULL,
+  `data_id` bigint(20) unsigned DEFAULT NULL,
+  `value_tid` bigint(20) unsigned DEFAULT NULL,
+  PRIMARY KEY (`partition`,`tid`,`oid`),
+  KEY `partition` (`partition`,`oid`,`tid`),
+  KEY `data_id` (`data_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+INSERT INTO `obj` VALUES (0,0,231616946283203125,0,NULL);
+CREATE TABLE `pt` (
+  `rid` int(10) unsigned NOT NULL,
+  `nid` int(11) NOT NULL,
+  `state` tinyint(3) unsigned NOT NULL,
+  PRIMARY KEY (`rid`,`nid`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+INSERT INTO `pt` VALUES (0,1,0),(0,2,0),(1,1,0),(1,3,1),(2,2,0),(2,3,1);
+CREATE TABLE `tobj` (
+  `partition` smallint(5) unsigned NOT NULL,
+  `oid` bigint(20) unsigned NOT NULL,
+  `tid` bigint(20) unsigned NOT NULL,
+  `data_id` bigint(20) unsigned DEFAULT NULL,
+  `value_tid` bigint(20) unsigned DEFAULT NULL,
+  PRIMARY KEY (`tid`,`oid`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+CREATE TABLE `trans` (
+  `partition` smallint(5) unsigned NOT NULL,
+  `tid` bigint(20) unsigned NOT NULL,
+  `packed` tinyint(1) NOT NULL,
+  `oids` mediumblob NOT NULL,
+  `user` blob NOT NULL,
+  `description` blob NOT NULL,
+  `ext` blob NOT NULL,
+  `ttid` bigint(20) unsigned NOT NULL,
+  PRIMARY KEY (`partition`,`tid`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+INSERT INTO `trans` VALUES (1,231616946283203125,0,'\0\0\0\0\0\0\0\0','','','',231616946283203125);
+CREATE TABLE `ttrans` (
+  `partition` smallint(5) unsigned NOT NULL,
+  `tid` bigint(20) unsigned NOT NULL,
+  `packed` tinyint(1) NOT NULL,
+  `oids` mediumblob NOT NULL,
+  `user` blob NOT NULL,
+  `description` blob NOT NULL,
+  `ext` blob NOT NULL,
+  `ttid` bigint(20) unsigned NOT NULL
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;

neo/tests/threaded/testStorageUpgrade-MySQL/s2.sql

+CREATE TABLE `bigdata` (
+  `id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `value` mediumblob NOT NULL,
+  PRIMARY KEY (`id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+CREATE TABLE `config` (
+  `name` varbinary(255) NOT NULL,
+  `value` varbinary(255) DEFAULT NULL,
+  PRIMARY KEY (`name`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+INSERT INTO `config` VALUES ('name','testStorageUpgrade'),('nid','2'),('partitions','3'),('ptid','9'),('replicas','1');
+CREATE TABLE `data` (
+  `id` bigint(20) unsigned NOT NULL,
+  `hash` binary(20) NOT NULL,
+  `compression` tinyint(3) unsigned DEFAULT NULL,
+  `value` mediumblob NOT NULL,
+  PRIMARY KEY (`id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+INSERT INTO `data` VALUES (0,0x0BEEC7B5EA3F0FDBC95D0DD47F3C5BC275DA8A33,0,0x666F6F);
+CREATE TABLE `obj` (
+  `partition` smallint(5) unsigned NOT NULL,
+  `oid` bigint(20) unsigned NOT NULL,
+  `tid` bigint(20) unsigned NOT NULL,
+  `data_id` bigint(20) unsigned DEFAULT NULL,
+  `value_tid` bigint(20) unsigned DEFAULT NULL,
+  PRIMARY KEY (`partition`,`tid`,`oid`),
+  KEY `partition` (`partition`,`oid`,`tid`),
+  KEY `data_id` (`data_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+INSERT INTO `obj` VALUES (0,0,231616946283203125,0,NULL);
+CREATE TABLE `pt` (
+  `rid` int(10) unsigned NOT NULL,
+  `nid` int(11) NOT NULL,
+  `state` tinyint(3) unsigned NOT NULL,
+  PRIMARY KEY (`rid`,`nid`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+INSERT INTO `pt` VALUES (0,1,0),(0,2,0),(1,1,0),(1,3,1),(2,2,0),(2,3,1);
+CREATE TABLE `tobj` (
+  `partition` smallint(5) unsigned NOT NULL,
+  `oid` bigint(20) unsigned NOT NULL,
+  `tid` bigint(20) unsigned NOT NULL,
+  `data_id` bigint(20) unsigned DEFAULT NULL,
+  `value_tid` bigint(20) unsigned DEFAULT NULL,
+  PRIMARY KEY (`tid`,`oid`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+CREATE TABLE `trans` (
+  `partition` smallint(5) unsigned NOT NULL,
+  `tid` bigint(20) unsigned NOT NULL,
+  `packed` tinyint(1) NOT NULL,
+  `oids` mediumblob NOT NULL,
+  `user` blob NOT NULL,
+  `description` blob NOT NULL,
+  `ext` blob NOT NULL,
+  `ttid` bigint(20) unsigned NOT NULL,
+  PRIMARY KEY (`partition`,`tid`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+CREATE TABLE `ttrans` (
+  `partition` smallint(5) unsigned NOT NULL,
+  `tid` bigint(20) unsigned NOT NULL,
+  `packed` tinyint(1) NOT NULL,
+  `oids` mediumblob NOT NULL,
+  `user` blob NOT NULL,
+  `description` blob NOT NULL,
+  `ext` blob NOT NULL,
+  `ttid` bigint(20) unsigned NOT NULL
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;

neo/tests/zeo_cluster.py

+from __future__ import print_function
+import os
+import signal
+import tempfile
+import ZEO.runzeo
+from ZEO.ClientStorage import ClientStorage as _ClientStorage
+from . import buildUrlFromString, ADDRESS_TYPE, IP_VERSION_FORMAT_DICT
+from .functional import AlreadyStopped, PortAllocator, Process
+
+class ZEOProcess(Process):
+
+    def __init__(self, **kw):
+        super(ZEOProcess, self).__init__('runzeo', kw)
+
+    def run(self):
+        from ZEO.runzeo import ZEOServer
+        del ZEOServer.handle_sigusr2
+        getattr(ZEO, self.command).main()
+
+class ClientStorage(_ClientStorage):
+
+    @property
+    def restore(self):
+        raise AttributeError('IStorageRestoreable disabled')
+
+class ZEOCluster(object):
+
+    def start(self):
+        self.zodb_storage_list = []
+        local_ip = IP_VERSION_FORMAT_DICT[ADDRESS_TYPE]
+        port_allocator = PortAllocator()
+        port = port_allocator.allocate(ADDRESS_TYPE, local_ip)
+        self.address = buildUrlFromString(local_ip), port
+        temp_dir = tempfile.mkdtemp(prefix='neo_')
+        print('Using temp directory', temp_dir)
+        self.zeo = ZEOProcess(address='%s:%s' % self.address,
+                              filename=os.path.join(temp_dir, 'Data.fs'))
+        port_allocator.release()
+        self.zeo.start()
+
+    def stop(self):
+        storage_list = self.zodb_storage_list
+        zeo = self.zeo
+        del self.zeo, self.zodb_storage_list
+        try:
+            for storage in storage_list:
+                storage.close()
+            zeo.kill(signal.SIGUSR2)
+        except AlreadyStopped:
+            pass
+        else:
+            zeo.child_coverage()
+            zeo.kill(signal.SIGKILL)
+            zeo.wait()
+
+    def getZODBStorage(self):
+        storage = ClientStorage(self.address)
+        self.zodb_storage_list.append(storage)
+        return storage
+
+    def setupDB(self):
+        pass