New 'Importer' storage backend

README

@@ -33,7 +33,9 @@ ZODB API is fully implemented except:
         (full implementation is considered)
 - blobs: not implemented (not considered yet)
 
-There is a simple way to convert FileStorage to NEO and back again.
+Any ZODB like FileStorage can be converted to NEO instanteously,
+which means the database is operational before all data are imported.
+There's also a tool to convert back to FileStorage.
 
 See also http://www.neoppod.org/links for more detailed information about
 features related to scalability.
@@ -88,7 +90,7 @@ e. Clients can connect when the cluster is in RUNNING state::
     $ neoctl -a <admin> print cluster
     RUNNING
 
-f. See `neomigrate` command to import an existing FileStorage database,
+f. See `importer.conf` file to import an existing database,
    or `neoctl` command for more administrative tasks.
 
 Alternatively, you can use `neosimple` command to quickly setup a cluster for

importer.conf

+# This file describes how to use the NEO Importer storage backend,
+# which is the recommended way to import the data of an existing Zope database
+# into a NEO cluster.
+#
+# Note that the 'neomigrate' command is another way to migrate to NEO but:
+# - the database is unusable as long as migration is not finished;
+# - it can not merge bases at mountpoints;
+# - it can not resume an interrupted migration;
+# - it does not preserve metadata that are specific to "undo" transactions
+#   (which would then behave like normal transactions);
+# - it only supports conversion from FileStorage;
+# - it is slower.
+# The only advantage of 'neomigrate' over Importer is that data can be imported
+# directly to a NEO cluster with replicas or several storage nodes.
+# Importer backend can only be used with a single storage node.
+#
+# Here is how to proceed once this file ready:
+# 1. Restart ZODB clients to connect to new NEO cluster (not started yet).
+# 2. Start NEO cluster and use 'neoctl -a <admin> start' command.
+# 3. Your Zope applications should work and background migration of data
+#    started automatically. The only downtime depends on how fast you are to do
+#    the first 2 steps. The only limitations in this mode are that:
+#    - pack is not supported
+#    - IStorage.history() is not implemented (this is used for example by
+#      history tab in Zope Management Interface)
+# 4. A warning message reporting that "All data are imported"
+#    is emitted to storage node's log when the migration is finished.
+#    This can take days with big databases.
+# The following steps can be scheduled any time after migration is over,
+# at your convenience:
+# 5. Change NEO configuration to stop using Importer backend.
+# 6. Stop clients.
+# 7. Restart NEO cluster.
+# 8. Start clients. This was the second, very short, downtime.
+# 9. Optionally, add storage nodes and balance partitions.
+#
+# Data are migrated even if your ZODB clients are stopped.
+
+# The first section describes the destination NEO storage.
+# See neo.conf for description of parameters.
+[neo]
+# Once migration is finished, restart NEO storage to use the below directly
+# (instead of adapter=Importer & database=/path_to_this_file).
+adapter=MySQL
+database=neo
+
+# The other sections are for source databases.
+[root]
+# Example with FileStorage but this can be anything else.
+# ZEO is possible but less efficient: ZEO servers must be stopped
+# if NEO opens FileStorage DBs directly.
+storage=
+  <filestorage>
+    path /path/to/root.fs
+  </filestorage>
+# (leading spaces indicate value continuation)
+
+# This file can stop here if your source DB is not splitted.
+# Otherwise, you need to describe mountpoints and other ZODB.
+# OID mapping can't be changed once the NEO cluster is started with this
+# configuration.
+
+# Mountpoints for this ZODB (see the use case at the end of this file).
+# <section_name>=<oid>
+foo=421
+bar=666
+
+# Following sections must define 'oid' parameter.
+[foo]
+# Any reference to oid 421 in 'root' is changed to point to oid 123 of 'foo'.
+# Of course, original oid 421 in 'root' will become unreferenced.
+oid=123
+
+storage=
+  <filestorage>
+    path /path/to/foo.fs
+  </filestorage>
+baz=1000
+
+[bar]
+oid=4567
+storage=
+  <filestorage>
+    path /path/to/bar.fs
+  </filestorage>
+
+[baz]
+oid=2000
+storage=
+  <filestorage>
+    path /path/to/baz.fs
+  </filestorage>
+
+
+## Case of several databases linked with MountedObject objects
+#
+# MountedObject is provided by ZODBMountPoint Zope product.
+# It relies on IAcquirer and ITraversable to fetch the real object.
+#
+# Given the following multi-base:
+# - in 'foo', /a/b is the real object
+# - in 'root', /c/d is a MountedObject object configured to point to
+#   /a/b in 'foo'
+#
+# So you need to get the oid of /a/b in 'foo':
+#   unrestrictedTraverse("/a/b")._p_oid
+# which equals to 123 in the above example
+#
+# And that of /c/d in 'root':
+#   unrestrictedTraverse("/c").__dict__["d"]._p_oid -> 421
+# The way to retrieve the mount point depends on the container type.
+# For a BTreeFolder2, it would be: c._tree["d"]._p_oid

neo.conf

@@ -2,6 +2,9 @@
 # must be identical for all nodes in a given cluster.
 # This file is optionnal: parameters can be given at the command line.
 
+# See SafeConfigParser at https://docs.python.org/2/library/configparser.html
+# for more information about the syntax.
+
 # Common parameters.
 [DEFAULT]
 # The cluster name

neo/client/Storage.py

@@ -122,6 +122,11 @@ class Storage(BaseStorage.BaseStorage,
             raise POSException.POSKeyError(oid)
 
     def loadBefore(self, oid, tid):
+        # XXX: FileStorage return an empty string for a deleted object
+        #      but it may cause EOFError exceptions in ZODB.Connection
+        #      and it makes impossible to store empty values.
+        #      We think it's wrong behaviour and raise POSKeyError instead.
+        #      Or maybe we should return None?
         try:
             return self.app.load(oid, None, tid)
         except NEOStorageDoesNotExistError:

neo/scripts/neomigrate.py

@@ -46,9 +46,12 @@ def main(args=None):
     from ZODB.FileStorage import FileStorage
     from neo.client.Storage import Storage as NEOStorage
     if os.path.exists(source):
-        print("NOTE: NEO does not implement IStorageRestoreable interface,"
-              " which means that undo information is not preserved: conflict"
-              " resolution could happen when undoing an old transaction.")
+        print("WARNING: This is not the recommended way to import data to NEO:"
+              " you should use Imported backend instead.\n"
+              "NEO also does not implement IStorageRestoreable interface,"
+              " which means that undo information is not preserved when using"
+              " this tool: conflict resolution could happen when undoing an"
+              " old transaction.")
         src = FileStorage(file_name=source, read_only=True)
         dst = NEOStorage(master_nodes=destination, name=cluster,
                          logfile=options.logfile)

neo/scripts/runner.py

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

neo/storage/app.py

@@ -289,7 +289,8 @@ class Application(object):
         """Handle everything, including replications and transactions."""
         logging.info('doing operation')
 
-        _poll = self._poll
+        poll = self._poll
+        _poll = self.em._poll
         isIdle = self.em.isIdle
 
         handler = master.MasterOperationHandler(self)
@@ -301,14 +302,18 @@ class Application(object):
 
         self.task_queue = task_queue = deque()
         try:
+            self.dm.doOperation(self)
             while True:
-                while task_queue and isIdle():
+                while task_queue:
                     try:
-                        task_queue[-1].next()
-                        task_queue.rotate()
+                        while isIdle():
+                            if task_queue[-1].next():
+                                _poll(0)
+                            task_queue.rotate()
+                        break
                     except StopIteration:
                         task_queue.pop()
-                _poll()
+                poll()
         finally:
             del self.task_queue
             # XXX: Although no handled exception should happen between

neo/storage/database/__init__.py

@@ -20,6 +20,7 @@ from neo.lib.exception import DatabaseFailure
 from .manager import DatabaseManager
 
 DATABASE_MANAGER_DICT = {
+    'Importer': 'importer.ImporterDatabaseManager',
     'MySQL': 'mysqldb.MySQLDatabaseManager',
     'SQLite': 'sqlite.SQLiteDatabaseManager',
 }

neo/storage/database/importer.py

+#
+# Copyright (C) 2014  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 cPickle as pickle
+from bisect import bisect, insort
+from collections import defaultdict
+from ConfigParser import SafeConfigParser
+from ZODB.config import storageFromString
+from ZODB.POSException import POSKeyError
+
+from . import buildDatabaseManager, DatabaseManager
+from neo.lib import logging, util
+from neo.lib.exception import DatabaseFailure
+from neo.lib.protocol import CellStates, ZERO_OID, ZERO_TID, ZERO_HASH, MAX_TID
+
+
+class Reference(object):
+
+    __slots__ = "value",
+    def __init__(self, value):
+        self.value = value
+
+
+class ZODB(object):
+
+    def __init__(self, storage, oid=0, **kw):
+        self.oid = int(oid)
+        self.mountpoints = {k: int(v) for k, v in kw.iteritems()}
+        self.connect(storage)
+        self.ltid = util.u64(self.lastTransaction())
+        if not self.ltid:
+            raise DatabaseFailure("Can not import empty storage: %s" % storage)
+        self.mapping = {}
+
+    def __getstate__(self):
+        state = self.__dict__.copy()
+        del state["data_tid"], state["storage"]
+        return state
+
+    def connect(self, storage):
+        self.data_tid = {}
+        self.storage = storageFromString(storage)
+
+    def setup(self, zodb_dict, shift_oid=0):
+        self.shift_oid = shift_oid
+        self.next_oid = util.u64(self.new_oid())
+        shift_oid += self.next_oid
+        for mp, oid in self.mountpoints.iteritems():
+            mp = zodb_dict[mp]
+            new_oid = mp.oid
+            try:
+                new_oid += mp.shift_oid
+            except AttributeError:
+                new_oid += shift_oid
+                shift_oid = mp.setup(zodb_dict, shift_oid)
+            self.mapping[oid] = new_oid
+        del self.mountpoints
+        return shift_oid
+
+    def translate(self, data):
+        if not (self.shift_oid or self.mapping):
+            self.translate = lambda x: x
+            return data
+        # We'll have to map oids, so define a reusable pickler for this,
+        # and also a method that will transform pickles.
+        pickler = pickle.Pickler(1)
+        u64 = util.u64
+        p64 = util.p64
+        def persistent_id(obj):
+            if type(obj) is Reference:
+                obj = obj.value
+                if isinstance(obj, tuple):
+                    oid = u64(obj[0])
+                    cls = obj[1]
+                    assert not hasattr(cls, '__getnewargs__'), cls
+                    try:
+                        return p64(self.mapping[oid]), cls
+                    except KeyError:
+                        if not self.shift_oid:
+                            return obj # common case for root db
+                elif isinstance(obj, str):
+                    oid = u64(obj)
+                else:
+                    raise NotImplementedError(
+                        "Unsupported external reference: %r" % obj)
+                return p64(self.mapping.get(oid, oid + self.shift_oid))
+        pickler.inst_persistent_id = persistent_id
+        dump = pickler.dump
+        from cStringIO import StringIO
+        from ZODB.broken import find_global
+        Unpickler = pickle.Unpickler
+        def translate(data):
+            u = Unpickler(StringIO(data))
+            u.persistent_load = Reference
+            u.find_global = find_global
+            return dump(u.load()).dump(u.load()).getvalue()
+        self.translate = translate
+        return translate(data)
+
+    def __getattr__(self, attr):
+        return getattr(self.storage, attr)
+
+    def getDataTid(self, oid, tid):
+        try:
+            return self.data_tid[tid][oid]
+        except KeyError:
+            assert tid not in self.data_tid, (oid, tid)
+            p_tid = util.p64(tid)
+            txn = next(self.storage.iterator(p_tid))
+            if txn.tid != p_tid:
+                raise
+        u64 = util.u64
+        txn = self.data_tid[tid] = {u64(x.oid): x.data_txn for x in txn}
+        return txn[oid]
+
+
+class ZODBIterator(object):
+
+    def __init__(self, zodb, *args, **kw):
+        iterator = zodb.iterator(*args, **kw)
+        def _next():
+            self.transaction = next(iterator)
+        _next()
+        self.zodb = zodb
+        self.next = _next
+
+    tid = property(lambda self: self.transaction.tid)
+
+    def __lt__(self, other):
+        return self.tid < other.tid or self.tid == other.tid \
+            and self.zodb.shift_oid < other.zodb.shift_oid
+
+
+class ImporterDatabaseManager(DatabaseManager):
+    """Proxy that transparently imports data from a ZODB storage
+    """
+    def __init__(self, *args, **kw):
+        super(ImporterDatabaseManager, self).__init__(*args, **kw)
+        self.db._connect()
+
+    _uncommitted_data = property(
+        lambda self: self.db._uncommitted_data,
+        lambda self, value: setattr(self.db, "_uncommitted_data", value))
+
+    def _parse(self, database):
+        config = SafeConfigParser()
+        config.read(database)
+        sections = config.sections()
+        # XXX: defaults copy & pasted from elsewhere - refactoring needed
+        main = {'adapter': 'MySQL', 'wait': 0}
+        main.update(config.items(sections.pop(0)))
+        self.zodb = ((x, dict(config.items(x))) for x in sections)
+        self.compress = main.get('compress', 1)
+        self.db = buildDatabaseManager(main['adapter'],
+            (main['database'], main['wait']))
+        for x in """commit query erase getConfiguration _setConfiguration
+                    getPartitionTable changePartitionTable getUnfinishedTIDList
+                    dropUnfinishedData storeTransaction finishTransaction
+                    storeData
+                 """.split():
+            setattr(self, x, getattr(self.db, x))
+
+    def setNumPartitions(self, num_partitions):
+        self.db.setNumPartitions(num_partitions)
+        try:
+            del self._getPartition
+        except AttributeError:
+            pass
+
+    def close(self):
+        self.db.close()
+        if isinstance(self.zodb, list): # _setup called
+            for zodb in self.zodb:
+                zodb.close()
+
+    def _setup(self):
+        self.db._setup()
+        zodb_state = self.getConfiguration("zodb")
+        if zodb_state:
+            logging.warning("Ignoring configuration file for oid mapping."
+                            " Reloading it from NEO storage.")
+            zodb = pickle.loads(zodb_state)
+            for k, v in self.zodb:
+                zodb[k].connect(v["storage"])
+        else:
+            zodb = {k: ZODB(**v) for k, v in self.zodb}
+            x, = (x for x in zodb.itervalues() if not x.oid)
+            x.setup(zodb)
+            self.setConfiguration("zodb", pickle.dumps(zodb))
+        self.zodb_index, self.zodb = zip(*sorted(
+            (x.shift_oid, x) for x in zodb.itervalues()))
+        self.zodb_ltid = max(x.ltid for x in self.zodb)
+        zodb = self.zodb[-1]
+        self.zodb_loid = zodb.shift_oid + zodb.next_oid - 1
+        self.zodb_tid = self.db.getLastTID(self.zodb_ltid) or 0
+        self._import = self._import()
+
+    def doOperation(self, app):
+        if self._import:
+            app.newTask(self._import)
+
+    def _import(self):
+        p64 = util.p64
+        u64 = util.u64
+        tid = p64(self.zodb_tid + 1)
+        zodb_list = []
+        for zodb in self.zodb:
+            try:
+                zodb_list.append(ZODBIterator(zodb, tid, p64(self.zodb_ltid)))
+            except StopIteration:
+                pass
+        tid = None
+        def finish():
+            if tid:
+                self.storeTransaction(tid, (), (oid_list,
+                    str(txn.user), str(txn.description),
+                    pickle.dumps(txn.extension), False, tid), False)
+                logging.debug("TXN %s imported (user=%r, desc=%r, len(oid)=%s)",
+                    util.dump(tid), txn.user, txn.description, len(oid_list))
+                self.commit()
+                self.zodb_tid = u64(tid)
+        if self.compress:
+            from zlib import compress
+        else:
+            compress = None
+            compression = 0
+        while zodb_list:
+            zodb_list.sort()
+            z = zodb_list[0]
+            # Merge transactions with same tid. Only
+            # user/desc/ext from first ZODB are kept.
+            if tid != z.tid:
+                finish()
+                oid_list = []
+                txn = z.transaction
+                tid = txn.tid
+                yield 1
+            zodb = z.zodb
+            for r in z.transaction:
+                oid = p64(u64(r.oid) + zodb.shift_oid)
+                data_tid = r.data_txn
+                if data_tid or r.data is None:
+                    data_id = None
+                else:
+                    data = zodb.translate(r.data)
+                    if compress:
+                        compressed_data = compress(data)
+                        compression = len(compressed_data) < len(data)
+                        if compression:
+                            data = compressed_data
+                    checksum = util.makeChecksum(data)
+                    data_id = self.storeData(util.makeChecksum(data), data,
+                                             compression)
+                # Write metadata before next yield. This may not be efficient
+                # but if they were written at the same time as the transaction,
+                # _pruneData could delete imported but not yet referenced data.
+                self.storeTransaction(tid, ((oid, data_id, data_tid),), (),
+                                      False)
+                oid_list.append(oid)
+                yield 1
+            try:
+                z.next()
+            except StopIteration:
+                del zodb_list[0]
+        finish()
+        logging.warning("All data are imported. You should change"
+            " your configuration to use the native backend and restart.")
+        self._import = None
+        for x in """getObject objectPresent getReplicationTIDList
+                 """.split():
+            setattr(self, x, getattr(self.db, x))
+
+    def inZodb(self, oid, tid=None, before_tid=None):
+        return oid <= self.zodb_loid and (
+            self.zodb_tid < before_tid if before_tid else
+            tid is None or self.zodb_tid < tid <= self.zodb_ltid)
+
+    def zodbFromOid(self, oid):
+        zodb = self.zodb[bisect(self.zodb_index, oid) - 1]
+        return zodb, oid - zodb.shift_oid
+
+    def getLastIDs(self, all=True):
+        tid, _, _, oid = self.db.getLastIDs(all)
+        return (util.p64(max(tid, self.zodb_ltid)), None, None,
+                util.p64(max(oid, self.zodb_loid)))
+
+    def objectPresent(self, oid, tid, all=True):
+        r = self.db.objectPresent(oid, tid, all)
+        if not r:
+            u_oid = util.u64(oid)
+            u_tid = util.u64(tid)
+            if self.inZodb(u_oid, u_tid):
+                zodb, oid = self.zodbFromOid(u_oid)
+                try:
+                    return zodb.loadSerial(util.p64(oid), tid)
+                except POSKeyError:
+                    pass
+
+    def getObject(self, oid, tid=None, before_tid=None):
+        u64 = util.u64
+        u_oid = u64(oid)
+        u_tid = tid and u64(tid)
+        u_before_tid = before_tid and u64(before_tid)
+        db = self.db
+        if self.zodb_tid < (u_before_tid - 1 if before_tid else
+                            u_tid or 0) <= self.zodb_ltid:
+            o = None
+        else:
+            o = db.getObject(oid, tid, before_tid)
+            if o and self.zodb_ltid < u64(o[0]) or \
+               not self.inZodb(u_oid, u_tid, u_before_tid):
+                return o
+        p64 = util.p64
+        zodb, z_oid = self.zodbFromOid(u_oid)
+        try:
+            value, serial, next_serial = zodb.loadBefore(p64(z_oid),
+                before_tid or (util.p64(u_tid + 1) if tid else MAX_TID))
+        except TypeError: # loadBefore returned None
+            return False
+        except POSKeyError:
+            assert not o, o
+            return o
+        if serial != tid:
+            if tid:
+                return False
+            u_tid = u64(serial)
+        if u_tid <= self.zodb_tid and o:
+            return o
+        if value:
+            value = zodb.translate(value)
+            checksum = util.makeChecksum(value)
+        else:
+            # CAVEAT: Although we think loadBefore should not return an empty
+            #         value for a deleted object (see comment in NEO Storage),
+            #         there's no need to distinguish this case in the above
+            #         except clause because it would be crazy to import a
+            #         NEO DB using this backend.
+            checksum = None
+        return (serial, next_serial or
+            db._getNextTID(db._getPartition(u_oid), u_oid, u_tid),
+            0, checksum, value, zodb.getDataTid(z_oid, u_tid))
+
+    def getTransaction(self, tid, all=False):
+        u64 = util.u64
+        if self.zodb_tid < u64(tid) <= self.zodb_ltid:
+            for zodb in self.zodb:
+                for txn in zodb.iterator(tid, tid):
+                    p64 = util.p64
+                    shift_oid = zodb.shift_oid
+                    return ([p64(u64(x.oid) + shift_oid) for x in txn],
+                        txn.user, txn.description,
+                        pickle.dumps(txn.extension), 0, tid)
+        else:
+            return self.db.getTransaction(tid, all)
+
+    def getReplicationTIDList(self, min_tid, max_tid, length, partition):
+        p64 = util.p64
+        tid = p64(self.zodb_tid)
+        if min_tid <= tid:
+            r = self.db.getReplicationTIDList(min_tid, min(max_tid, tid),
+                                              length, partition)
+            if max_tid <= tid:
+                return r
+            length -= len(r)
+            min_tid = p64(self.zodb_tid + 1)
+        else:
+            r = []
+        if length:
+            tid = p64(self.zodb_ltid)
+            if min_tid <= tid:
+                u64 = util.u64
+                def next_tid(i):
+                    for txn in i:
+                        tid = u64(txn.tid)
+                        if self._getPartition(tid) == partition:
+                            insort(z, (-tid, i))
+                            break
+                z = []
+                for zodb in self.zodb:
+                    next_tid(zodb.iterator(min_tid, min(max_tid, tid)))
+                while z:
+                    t, i = z.pop()
+                    r.append(p64(-t))
+                    length -= 1
+                    if not length:
+                        return r
+                    next_tid(i)
+            if tid < max_tid:
+                r += self.db.getReplicationTIDList(max(min_tid, tid), max_tid,
+                                                   length, partition)
+        return r
+

neo/storage/database/manager.py

@@ -81,6 +81,9 @@ class DatabaseManager(object):
         """
         raise NotImplementedError
 
+    def doOperation(self, app):
+        pass
+
     def commit(self):
         pass
 
@@ -198,6 +201,14 @@ class DatabaseManager(object):
         node, and a cell state."""
         raise NotImplementedError
 
+    def getLastTID(self, max_tid):
+        """Return greatest tid in trans table that is <= given 'max_tid'
+
+        Required only to import a DB using Importer backend.
+        max_tid must be in unpacked format.
+        """
+        raise NotImplementedError
+
     def _getLastIDs(self, all=True):
         raise NotImplementedError
 
@@ -228,6 +239,19 @@ class DatabaseManager(object):
         r = self.getObject(oid)
         return r and r[0]
 
+    def _getNextTID(self, partition, oid, tid):
+        """
+        partition (int)
+            Must be the result of (oid % self.getPartition(oid))
+        oid (int)
+            Identifier of object to retrieve.
+        tid (int)
+            Exact serial to retrieve.
+
+        If tid is the last revision of oid, None is returned.
+        """
+        raise NotImplementedError
+
     def _getObject(self, oid, tid=None, before_tid=None):
         """
         oid (int)

neo/storage/database/mysqldb.py

@@ -16,9 +16,9 @@
 
 from binascii import a2b_hex
 import MySQLdb
-from MySQLdb import IntegrityError, OperationalError
+from MySQLdb import DataError, IntegrityError, OperationalError
 from MySQLdb.constants.CR import SERVER_GONE_ERROR, SERVER_LOST
-from MySQLdb.constants.ER import DUP_ENTRY
+from MySQLdb.constants.ER import DATA_TOO_LONG, DUP_ENTRY
 from array import array
 from hashlib import sha1
 import re
@@ -237,16 +237,27 @@ class MySQLDatabaseManager(DatabaseManager):
         q = self.query
         e = self.escape
         self._config[key] = value
-        key = e(str(key))
+        k = e(str(key))
         if value is None:
-            q("DELETE FROM config WHERE name = '%s'" % key)
-        else:
-            value = e(str(value))
-            q("REPLACE INTO config VALUES ('%s', '%s')" % (key, value))
+            q("DELETE FROM config WHERE name = '%s'" % k)
+            return
+        value = str(value)
+        sql = "REPLACE INTO config VALUES ('%s', '%s')" % (k, e(value))
+        try:
+            q(sql)
+        except DataError, (code, _):
+            if code != DATA_TOO_LONG or len(value) < 256 or key != "zodb":
+                raise
+            q("ALTER TABLE config MODIFY value VARBINARY(%s) NULL" % len(value))
+            q(sql)
 
     def getPartitionTable(self):
         return self.query("SELECT * FROM pt")
 
+    def getLastTID(self, max_tid):
+        return self.query("SELECT MAX(tid) FROM trans WHERE tid<=%s"
+                          % max_tid)[0][0]
+
     def _getLastIDs(self, all=True):
         p64 = util.p64
         q = self.query
@@ -290,6 +301,12 @@ class MySQLDatabaseManager(DatabaseManager):
                        % (self._getPartition(oid), oid))
         return util.p64(r[0][0]) if r else None
 
+    def _getNextTID(self, *args): # partition, oid, tid
+        r = self.query("SELECT tid FROM obj"
+                       " WHERE partition=%d AND oid=%d AND tid>%d"
+                       " ORDER BY tid LIMIT 1" % args)
+        return r[0][0] if r else None
+
     def _getObject(self, oid, tid=None, before_tid=None):
         q = self.query
         partition = self._getPartition(oid)
@@ -309,10 +326,8 @@ class MySQLDatabaseManager(DatabaseManager):
             serial, compression, checksum, data, value_serial = r[0]
         except IndexError:
             return None
-        r = q("SELECT tid FROM obj WHERE partition=%d AND oid=%d AND tid>%d"
-              " ORDER BY tid LIMIT 1" % (partition, oid, serial))
-        return (serial, r[0][0] if r else None, compression, checksum, data,
-            value_serial)
+        return (serial, self._getNextTID(partition, oid, serial),
+                compression, checksum, data, value_serial)
 
     def changePartitionTable(self, ptid, cell_list, reset=False):
         offset_list = []

neo/storage/database/sqlite.py

@@ -208,6 +208,10 @@ class SQLiteDatabaseManager(DatabaseManager):
     def getPartitionTable(self):
         return self.query("SELECT * FROM pt")
 
+    def getLastTID(self, max_tid):
+        return self.query("SELECT MAX(tid) FROM trans WHERE tid<=?",
+                          (max_tid,)).next()[0]
+
     def _getLastIDs(self, all=True):
         p64 = util.p64
         q = self.query
@@ -252,6 +256,12 @@ class SQLiteDatabaseManager(DatabaseManager):
                        (self._getPartition(oid), oid)).fetchone()
         return r and util.p64(r[0])
 
+    def _getNextTID(self, *args): # partition, oid, tid
+        r = self.query("""SELECT tid FROM obj
+                          WHERE partition=? AND oid=? AND tid>?
+                          ORDER BY tid LIMIT 1""", args).fetchone()
+        return r and r[0]
+
     def _getObject(self, oid, tid=None, before_tid=None):
         q = self.query
         partition = self._getPartition(oid)
@@ -269,14 +279,11 @@ class SQLiteDatabaseManager(DatabaseManager):
             serial, compression, checksum, data, value_serial = r.fetchone()
         except TypeError:
             return None
-        r = q("""SELECT tid FROM obj
-                 WHERE partition=? AND oid=? AND tid>?
-                 ORDER BY tid LIMIT 1""",
-              (partition, oid, serial)).fetchone()
         if checksum:
             checksum = str(checksum)
             data = str(data)
-        return serial, r and r[0], compression, checksum, data, value_serial
+        return (serial, self._getNextTID(partition, oid, serial),
+                compression, checksum, data, value_serial)
 
     def changePartitionTable(self, ptid, cell_list, reset=False):
         q = self.query

neo/tests/fs2zodb.py

+#
+# Copyright (C) 2014  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 persistent.TimeStamp import TimeStamp
+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

@@ -30,6 +30,7 @@ import tempfile
 import traceback
 import threading
 import psutil
+from ConfigParser import SafeConfigParser
 
 import neo.scripts
 from neo.neoctl.neoctl import NeoCTL, NotReadyException
@@ -238,7 +239,7 @@ class NEOCluster(object):
                  cleanup_on_delete=False, temp_dir=None, clear_databases=True,
                  adapter=os.getenv('NEO_TESTS_ADAPTER'),
                  address_type=ADDRESS_TYPE, bind_ip=None, logger=True,
-        ):
+                 importer=None):
         if not adapter:
             adapter = 'MySQL'
         self.adapter = adapter
@@ -263,6 +264,21 @@ class NEOCluster(object):
         self.local_ip = local_ip = bind_ip or \
             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.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)
+            adapter = "Importer"
+            self.db_template = str
+            db_list = importer_conf,
         self.process_dict = {}
         self.temp_dir = temp_dir
         self.port_allocator = PortAllocator()

neo/tests/functional/testClient.py

@@ -22,6 +22,7 @@ import socket
 
 from struct import pack
 from neo.neoctl.neoctl import NeoCTL
+from neo.lib.util import makeChecksum, u64
 from ZODB.FileStorage import FileStorage
 from ZODB.POSException import ConflictError
 from ZODB.tests.StorageTestBase import zodb_pickle
@@ -168,9 +169,7 @@ class ClientTests(NEOFunctionalTest):
         name = os.path.join(self.getTempDirectory(), 'data.fs')
         if reset and os.path.exists(name):
             os.remove(name)
-        storage = FileStorage(file_name=name)
-        db = ZODB.DB(storage=storage)
-        return (db, storage)
+        return FileStorage(file_name=name)
 
     def __populate(self, db, tree_size=TREE_SIZE):
         if isinstance(db.storage, FileStorage):
@@ -204,7 +203,8 @@ class ClientTests(NEOFunctionalTest):
     def testImport(self):
 
         # source database
-        dfs_db, dfs_storage  = self.__getDataFS()
+        dfs_storage  = self.__getDataFS()
+        dfs_db = ZODB.DB(dfs_storage)
         self.__populate(dfs_db)
 
         # create a neo storage
@@ -213,28 +213,48 @@ class ClientTests(NEOFunctionalTest):
 
         # copy data fs to neo
         neo_storage.copyTransactionsFrom(dfs_storage, verbose=0)
+        dfs_db.close()
 
         # check neo content
         (neo_db, neo_conn) = self.neo.getZODBConnection()
         self.__checkTree(neo_conn.root()['trees'])
 
+    def __dump(self, storage):
+        return {u64(t.tid): [(u64(o.oid), o.data_txn and u64(o.data_txn),
+                              None if o.data is None else makeChecksum(o.data))
+                             for o in t]
+                for t in storage.iterator()}
+
     def testExport(self):
 
         # create a neo storage
         self.neo.start()
         (neo_db, neo_conn) = self.neo.getZODBConnection()
         self.__populate(neo_db)
+        dump = self.__dump(neo_db.storage)
 
         # copy neo to data fs
-        dfs_db, dfs_storage  = self.__getDataFS(reset=True)
+        dfs_storage  = self.__getDataFS(reset=True)
         neo_storage = self.neo.getZODBStorage()
         dfs_storage.copyTransactionsFrom(neo_storage)
 
         # check data fs content
-        conn = dfs_db.open()
-        root = conn.root()
+        dfs_db = ZODB.DB(dfs_storage)
+        root = dfs_db.open().root()
 
         self.__checkTree(root['trees'])
+        dfs_db.close()
+        self.neo.stop()
+
+        self.neo = NEOCluster(db_list=['test_neo1'], partitions=3,
+            importer=[("root", {
+                "storage": "<filestorage>\npath %s\n</filestorage>"
+                            % dfs_storage.getName()})],
+            temp_dir=self.getTempDirectory())
+        self.neo.start()
+        neo_db, neo_conn = self.neo.getZODBConnection()
+        self.__checkTree(neo_conn.root()['trees'])
+        self.assertEqual(dump, self.__dump(neo_db.storage))
 
     def testLockTimeout(self):
         """ Hold a lock on an object to block a second transaction """

neo/tests/threaded/__init__.py

@@ -19,6 +19,7 @@
 import os, random, socket, sys, tempfile, threading, time, types, weakref
 import traceback
 from collections import deque
+from ConfigParser import SafeConfigParser
 from contextlib import contextmanager
 from itertools import count
 from functools import wraps
@@ -545,7 +546,8 @@ class NEOCluster(object):
     def __init__(self, master_count=1, partitions=1, replicas=0, upstream=None,
                        adapter=os.getenv('NEO_TESTS_ADAPTER', 'SQLite'),
                        storage_count=None, db_list=None, clear_databases=True,
-                       db_user=DB_USER, db_password='', compress=True):
+                       db_user=DB_USER, db_password='', compress=True,
+                       importer=None):
         self.name = 'neo_%s' % self._allocate('name',
             lambda: random.randint(0, 100))
         master_list = [MasterApplication.newAddress()
@@ -573,6 +575,19 @@ class NEOCluster(object):
             db = os.path.join(getTempDirectory(), '%s.sqlite')
         else:
             assert False, adapter
+        if importer:
+            cfg = SafeConfigParser()
+            cfg.add_section("neo")
+            cfg.set("neo", "adapter", adapter)
+            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)
+            kw["getAdapter"] = "Importer"
         self.storage_list = [StorageApplication(getDatabase=db % x, **kw)
                              for x in db_list]
         self.admin_list = [AdminApplication(**kw)]

neo/tests/threaded/testImporter.py

+#
+# Copyright (C) 2014  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 collections import deque
+from itertools import islice, izip_longest
+import os, time, unittest
+import neo, transaction, ZODB
+from neo.lib import logging
+from neo.lib.util import u64
+from ..fs2zodb import Inode
+from .. import getTempDirectory
+from . import NEOCluster, NEOThreadedTest
+from ZODB.FileStorage import FileStorage
+
+
+class ImporterTests(NEOThreadedTest):
+
+    def test(self):
+        importer = []
+        fs_dir = os.path.join(getTempDirectory(), self.id())
+        os.mkdir(fs_dir)
+        src_root, = neo.__path__
+        fs_list = "root", "client", "master", "tests"
+        def root_filter(name):
+            if not name.endswith(".pyc"):
+                i = name.find(os.sep)
+                return i < 0 or name[:i] not in fs_list
+        def sub_filter(name):
+            return lambda n: n[-4:] != '.pyc' and \
+                n.split(os.sep, 1)[0] in (name, "scripts")
+        conn_list = []
+        iter_list = []
+        # Setup several FileStorage databases.
+        for i, name in enumerate(fs_list):
+            fs_path = os.path.join(fs_dir, name + ".fs")
+            c = ZODB.DB(FileStorage(fs_path)).open()
+            r = c.root()["neo"] = Inode()
+            transaction.commit()
+            conn_list.append(c)
+            iter_list.append(r.treeFromFs(src_root, 10,
+                sub_filter(name) if i else root_filter))
+            importer.append((name, {
+                "storage": "<filestorage>\npath %s\n</filestorage>" % fs_path
+                }))
+        # Populate FileStorage databases.
+        for iter_list in izip_longest(*iter_list):
+            for i in iter_list:
+                if i:
+                    transaction.commit()
+        del iter_list
+        # Get oids of mount points and close.
+        for (name, cfg), c in zip(importer, conn_list):
+            r = c.root()["neo"]
+            if name == "root":
+                for name in fs_list[1:]:
+                    cfg[name] = str(u64(r[name]._p_oid))
+            else:
+                cfg["oid"] = str(u64(r[name]._p_oid))
+            c.db().close()
+        #del importer[0][1][importer.pop()[0]]
+        # Start NEO cluster with transparent import of a multi-base ZODB.
+        cluster = NEOCluster(compress=False, importer=importer)
+        try:
+            # Suspend import for a while, so that import
+            # is finished in the middle of the below 'for' loop.
+            # Use a slightly different main loop for storage so that it
+            # does not import data too fast and we test read/write access
+            # by the client during the import.
+            dm = cluster.storage.dm
+            def doOperation(app):
+                del dm.doOperation
+                try:
+                    while True:
+                        if app.task_queue:
+                            app.task_queue[-1].next()
+                        app._poll()
+                except StopIteration:
+                    app.task_queue.pop()
+            dm.doOperation = doOperation
+            cluster.start()
+            t, c = cluster.getTransaction()
+            r = c.root()["neo"]
+            i = r.walk()
+            next(islice(i, 9, None))
+            dm.doOperation(cluster.storage) # resume
+            deque(i, maxlen=0)
+            last_import = None
+            for i, r in enumerate(r.treeFromFs(src_root, 10)):
+                t.commit()
+                if cluster.storage.dm._import:
+                    last_import = i
+            self.assertTrue(last_import and not cluster.storage.dm._import)
+            i = len(src_root) + 1
+            self.assertEqual(sorted(r.walk()), sorted(
+                (x[i:] or '.', sorted(y), sorted(z))
+                for x, y, z in os.walk(src_root)))
+            t.commit()
+        finally:
+            cluster.stop()
+
+
+if __name__ == "__main__":
+    unittest.main()

setup.py

@@ -23,13 +23,16 @@ if not os.path.exists('mock.py'):
         raise EnvironmentError("MD5 checksum mismatch downloading 'mock.py'")
     open('mock.py', 'w').write(mock_py)
 
+zodb_require = ['ZODB3>=3.10', 'ZODB3<3.11dev']
+
 extras_require = {
     'admin': [],
-    'client': ['ZODB3>=3.10', 'ZODB3<3.11dev'],
+    'client': zodb_require,
     'ctl': [],
     'master': [],
     'storage-sqlite': [],
     'storage-mysqldb': ['MySQL-python'],
+    'storage-importer': zodb_require,
 }
 extras_require['tests'] = ['zope.testing', 'psutil>=2',
     'neoppod[%s]' % ', '.join(extras_require)]