--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cubicweb/server/checkintegrity.py Sat Jan 16 13:48:51 2016 +0100
@@ -0,0 +1,410 @@
+# copyright 2003-2014 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
+# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
+#
+# This file is part of CubicWeb.
+#
+# CubicWeb is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 2.1 of the License, or (at your option)
+# any later version.
+#
+# CubicWeb 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with CubicWeb. If not, see <http://www.gnu.org/licenses/>.
+"""Integrity checking tool for instances:
+
+* integrity of a CubicWeb repository. Hum actually only the system database is
+ checked.
+"""
+from __future__ import print_function
+
+__docformat__ = "restructuredtext en"
+
+import sys
+from datetime import datetime
+
+from logilab.common.shellutils import ProgressBar
+
+from cubicweb.schema import PURE_VIRTUAL_RTYPES, VIRTUAL_RTYPES, UNIQUE_CONSTRAINTS
+from cubicweb.server.sqlutils import SQL_PREFIX
+
+def notify_fixed(fix):
+ if fix:
+ sys.stderr.write(' [FIXED]')
+ sys.stderr.write('\n')
+
+def has_eid(cnx, sqlcursor, eid, eids):
+ """return true if the eid is a valid eid"""
+ if eid in eids:
+ return eids[eid]
+ sqlcursor.execute('SELECT type FROM entities WHERE eid=%s' % eid)
+ try:
+ etype = sqlcursor.fetchone()[0]
+ except Exception:
+ eids[eid] = False
+ return False
+ if etype not in cnx.vreg.schema:
+ eids[eid] = False
+ return False
+ sqlcursor.execute('SELECT * FROM %s%s WHERE %seid=%s' % (SQL_PREFIX, etype,
+ SQL_PREFIX, eid))
+ result = sqlcursor.fetchall()
+ if len(result) == 0:
+ eids[eid] = False
+ return False
+ elif len(result) > 1:
+ msg = (' More than one entity with eid %s exists in source!\n'
+ ' WARNING : Unable to fix this, do it yourself!\n')
+ sys.stderr.write(msg % eid)
+ eids[eid] = True
+ return True
+
+# XXX move to yams?
+def etype_fti_containers(eschema, _done=None):
+ if _done is None:
+ _done = set()
+ _done.add(eschema)
+ containers = tuple(eschema.fulltext_containers())
+ if containers:
+ for rschema, target in containers:
+ if target == 'object':
+ targets = rschema.objects(eschema)
+ else:
+ targets = rschema.subjects(eschema)
+ for targeteschema in targets:
+ if targeteschema in _done:
+ continue
+ _done.add(targeteschema)
+ for container in etype_fti_containers(targeteschema, _done):
+ yield container
+ else:
+ yield eschema
+
+def reindex_entities(schema, cnx, withpb=True, etypes=None):
+ """reindex all entities in the repository"""
+ # deactivate modification_date hook since we don't want them
+ # to be updated due to the reindexation
+ repo = cnx.repo
+ dbhelper = repo.system_source.dbhelper
+ cursor = cnx.cnxset.cu
+ if not dbhelper.has_fti_table(cursor):
+ print('no text index table')
+ dbhelper.init_fti(cursor)
+ repo.system_source.do_fti = True # ensure full-text indexation is activated
+ if etypes is None:
+ print('Reindexing entities')
+ etypes = set()
+ for eschema in schema.entities():
+ if eschema.final:
+ continue
+ indexable_attrs = tuple(eschema.indexable_attributes()) # generator
+ if not indexable_attrs:
+ continue
+ for container in etype_fti_containers(eschema):
+ etypes.add(container)
+ # clear fti table first
+ cnx.system_sql('DELETE FROM %s' % dbhelper.fti_table)
+ else:
+ print('Reindexing entities of type %s' % \
+ ', '.join(sorted(str(e) for e in etypes)))
+ # clear fti table first. Use subquery for sql compatibility
+ cnx.system_sql("DELETE FROM %s WHERE EXISTS(SELECT 1 FROM ENTITIES "
+ "WHERE eid=%s AND type IN (%s))" % (
+ dbhelper.fti_table, dbhelper.fti_uid_attr,
+ ','.join("'%s'" % etype for etype in etypes)))
+ if withpb:
+ pb = ProgressBar(len(etypes) + 1)
+ pb.update()
+ # reindex entities by generating rql queries which set all indexable
+ # attribute to their current value
+ source = repo.system_source
+ for eschema in etypes:
+ etype_class = cnx.vreg['etypes'].etype_class(str(eschema))
+ for rset in etype_class.cw_fti_index_rql_limit(cnx):
+ source.fti_index_entities(cnx, rset.entities())
+ # clear entity cache to avoid high memory consumption on big tables
+ cnx.drop_entity_cache()
+ if withpb:
+ pb.update()
+ if withpb:
+ pb.finish()
+
+
+def check_schema(schema, cnx, eids, fix=1):
+ """check serialized schema"""
+ print('Checking serialized schema')
+ rql = ('Any COUNT(X),RN,SN,ON,CTN GROUPBY RN,SN,ON,CTN ORDERBY 1 '
+ 'WHERE X is CWConstraint, R constrained_by X, '
+ 'R relation_type RT, RT name RN, R from_entity ST, ST name SN, '
+ 'R to_entity OT, OT name ON, X cstrtype CT, CT name CTN')
+ for count, rn, sn, on, cstrname in cnx.execute(rql):
+ if count == 1:
+ continue
+ if cstrname in UNIQUE_CONSTRAINTS:
+ print("ERROR: got %s %r constraints on relation %s.%s.%s" % (
+ count, cstrname, sn, rn, on))
+ if fix:
+ print('dunno how to fix, do it yourself')
+
+
+
+def check_text_index(schema, cnx, eids, fix=1):
+ """check all entities registered in the text index"""
+ print('Checking text index')
+ msg = ' Entity with eid %s exists in the text index but in no source (autofix will remove from text index)'
+ cursor = cnx.system_sql('SELECT uid FROM appears;')
+ for row in cursor.fetchall():
+ eid = row[0]
+ if not has_eid(cnx, cursor, eid, eids):
+ sys.stderr.write(msg % eid)
+ if fix:
+ cnx.system_sql('DELETE FROM appears WHERE uid=%s;' % eid)
+ notify_fixed(fix)
+
+
+def check_entities(schema, cnx, eids, fix=1):
+ """check all entities registered in the repo system table"""
+ print('Checking entities system table')
+ # system table but no source
+ msg = ' Entity %s with eid %s exists in the system table but in no source (autofix will delete the entity)'
+ cursor = cnx.system_sql('SELECT eid,type FROM entities;')
+ for row in cursor.fetchall():
+ eid, etype = row
+ if not has_eid(cnx, cursor, eid, eids):
+ sys.stderr.write(msg % (etype, eid))
+ if fix:
+ cnx.system_sql('DELETE FROM entities WHERE eid=%s;' % eid)
+ notify_fixed(fix)
+ # source in entities, but no relation cw_source
+ # XXX this (get_versions) requires a second connection to the db when we already have one open
+ applcwversion = cnx.repo.get_versions().get('cubicweb')
+ if applcwversion >= (3, 13, 1): # entities.asource appeared in 3.13.1
+ cursor = cnx.system_sql('SELECT e.eid FROM entities as e, cw_CWSource as s '
+ 'WHERE s.cw_name=e.asource AND '
+ 'NOT EXISTS(SELECT 1 FROM cw_source_relation as cs '
+ ' WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid) '
+ 'ORDER BY e.eid')
+ msg = (' Entity with eid %s refers to source in entities table, '
+ 'but is missing relation cw_source (autofix will create the relation)\n')
+ for row in cursor.fetchall():
+ sys.stderr.write(msg % row[0])
+ if fix:
+ cnx.system_sql('INSERT INTO cw_source_relation (eid_from, eid_to) '
+ 'SELECT e.eid, s.cw_eid FROM entities as e, cw_CWSource as s '
+ 'WHERE s.cw_name=e.asource AND NOT EXISTS(SELECT 1 FROM cw_source_relation as cs '
+ ' WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid)')
+ notify_fixed(True)
+ # inconsistencies for 'is'
+ msg = ' %s #%s is missing relation "is" (autofix will create the relation)\n'
+ cursor = cnx.system_sql('SELECT e.type, e.eid FROM entities as e, cw_CWEType as s '
+ 'WHERE s.cw_name=e.type AND NOT EXISTS(SELECT 1 FROM is_relation as cs '
+ ' WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid) '
+ 'ORDER BY e.eid')
+ for row in cursor.fetchall():
+ sys.stderr.write(msg % tuple(row))
+ if fix:
+ cnx.system_sql('INSERT INTO is_relation (eid_from, eid_to) '
+ 'SELECT e.eid, s.cw_eid FROM entities as e, cw_CWEType as s '
+ 'WHERE s.cw_name=e.type AND NOT EXISTS(SELECT 1 FROM is_relation as cs '
+ ' WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid)')
+ notify_fixed(True)
+ # inconsistencies for 'is_instance_of'
+ msg = ' %s #%s is missing relation "is_instance_of" (autofix will create the relation)\n'
+ cursor = cnx.system_sql('SELECT e.type, e.eid FROM entities as e, cw_CWEType as s '
+ 'WHERE s.cw_name=e.type AND NOT EXISTS(SELECT 1 FROM is_instance_of_relation as cs '
+ ' WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid) '
+ 'ORDER BY e.eid')
+ for row in cursor.fetchall():
+ sys.stderr.write(msg % tuple(row))
+ if fix:
+ cnx.system_sql('INSERT INTO is_instance_of_relation (eid_from, eid_to) '
+ 'SELECT e.eid, s.cw_eid FROM entities as e, cw_CWEType as s '
+ 'WHERE s.cw_name=e.type AND NOT EXISTS(SELECT 1 FROM is_instance_of_relation as cs '
+ ' WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid)')
+ notify_fixed(True)
+ print('Checking entities tables')
+ msg = ' Entity with eid %s exists in the %s table but not in the system table (autofix will delete the entity)'
+ for eschema in schema.entities():
+ if eschema.final:
+ continue
+ table = SQL_PREFIX + eschema.type
+ column = SQL_PREFIX + 'eid'
+ cursor = cnx.system_sql('SELECT %s FROM %s;' % (column, table))
+ for row in cursor.fetchall():
+ eid = row[0]
+ # eids is full since we have fetched everything from the entities table,
+ # no need to call has_eid
+ if not eid in eids or not eids[eid]:
+ sys.stderr.write(msg % (eid, eschema.type))
+ if fix:
+ cnx.system_sql('DELETE FROM %s WHERE %s=%s;' % (table, column, eid))
+ notify_fixed(fix)
+
+
+def bad_related_msg(rtype, target, eid, fix):
+ msg = ' A relation %s with %s eid %s exists but no such entity in sources'
+ sys.stderr.write(msg % (rtype, target, eid))
+ notify_fixed(fix)
+
+def bad_inlined_msg(rtype, parent_eid, eid, fix):
+ msg = (' An inlined relation %s from %s to %s exists but the latter '
+ 'entity does not exist')
+ sys.stderr.write(msg % (rtype, parent_eid, eid))
+ notify_fixed(fix)
+
+
+def check_relations(schema, cnx, eids, fix=1):
+ """check that eids referenced by relations are registered in the repo system
+ table
+ """
+ print('Checking relations')
+ for rschema in schema.relations():
+ if rschema.final or rschema.type in PURE_VIRTUAL_RTYPES:
+ continue
+ if rschema.inlined:
+ for subjtype in rschema.subjects():
+ table = SQL_PREFIX + str(subjtype)
+ column = SQL_PREFIX + str(rschema)
+ sql = 'SELECT cw_eid,%s FROM %s WHERE %s IS NOT NULL;' % (
+ column, table, column)
+ cursor = cnx.system_sql(sql)
+ for row in cursor.fetchall():
+ parent_eid, eid = row
+ if not has_eid(cnx, cursor, eid, eids):
+ bad_inlined_msg(rschema, parent_eid, eid, fix)
+ if fix:
+ sql = 'UPDATE %s SET %s=NULL WHERE %s=%s;' % (
+ table, column, column, eid)
+ cnx.system_sql(sql)
+ continue
+ try:
+ cursor = cnx.system_sql('SELECT eid_from FROM %s_relation;' % rschema)
+ except Exception as ex:
+ # usually because table doesn't exist
+ print('ERROR', ex)
+ continue
+ for row in cursor.fetchall():
+ eid = row[0]
+ if not has_eid(cnx, cursor, eid, eids):
+ bad_related_msg(rschema, 'subject', eid, fix)
+ if fix:
+ sql = 'DELETE FROM %s_relation WHERE eid_from=%s;' % (
+ rschema, eid)
+ cnx.system_sql(sql)
+ cursor = cnx.system_sql('SELECT eid_to FROM %s_relation;' % rschema)
+ for row in cursor.fetchall():
+ eid = row[0]
+ if not has_eid(cnx, cursor, eid, eids):
+ bad_related_msg(rschema, 'object', eid, fix)
+ if fix:
+ sql = 'DELETE FROM %s_relation WHERE eid_to=%s;' % (
+ rschema, eid)
+ cnx.system_sql(sql)
+
+
+def check_mandatory_relations(schema, cnx, eids, fix=1):
+ """check entities missing some mandatory relation"""
+ print('Checking mandatory relations')
+ msg = '%s #%s is missing mandatory %s relation %s (autofix will delete the entity)'
+ for rschema in schema.relations():
+ if rschema.final or rschema in PURE_VIRTUAL_RTYPES or rschema in ('is', 'is_instance_of'):
+ continue
+ smandatory = set()
+ omandatory = set()
+ for rdef in rschema.rdefs.values():
+ if rdef.cardinality[0] in '1+':
+ smandatory.add(rdef.subject)
+ if rdef.cardinality[1] in '1+':
+ omandatory.add(rdef.object)
+ for role, etypes in (('subject', smandatory), ('object', omandatory)):
+ for etype in etypes:
+ if role == 'subject':
+ rql = 'Any X WHERE NOT X %s Y, X is %s' % (rschema, etype)
+ else:
+ rql = 'Any X WHERE NOT Y %s X, X is %s' % (rschema, etype)
+ for entity in cnx.execute(rql).entities():
+ sys.stderr.write(msg % (entity.cw_etype, entity.eid, role, rschema))
+ if fix:
+ #if entity.cw_describe()['source']['uri'] == 'system': XXX
+ entity.cw_delete() # XXX this is BRUTAL!
+ notify_fixed(fix)
+
+
+def check_mandatory_attributes(schema, cnx, eids, fix=1):
+ """check for entities stored in the system source missing some mandatory
+ attribute
+ """
+ print('Checking mandatory attributes')
+ msg = '%s #%s is missing mandatory attribute %s (autofix will delete the entity)'
+ for rschema in schema.relations():
+ if not rschema.final or rschema in VIRTUAL_RTYPES:
+ continue
+ for rdef in rschema.rdefs.values():
+ if rdef.cardinality[0] in '1+':
+ rql = 'Any X WHERE X %s NULL, X is %s, X cw_source S, S name "system"' % (
+ rschema, rdef.subject)
+ for entity in cnx.execute(rql).entities():
+ sys.stderr.write(msg % (entity.cw_etype, entity.eid, rschema))
+ if fix:
+ entity.cw_delete()
+ notify_fixed(fix)
+
+
+def check_metadata(schema, cnx, eids, fix=1):
+ """check entities has required metadata
+
+ FIXME: rewrite using RQL queries ?
+ """
+ print('Checking metadata')
+ cursor = cnx.system_sql("SELECT DISTINCT type FROM entities;")
+ eidcolumn = SQL_PREFIX + 'eid'
+ msg = ' %s with eid %s has no %s (autofix will set it to now)'
+ for etype, in cursor.fetchall():
+ if etype not in cnx.vreg.schema:
+ sys.stderr.write('entities table references unknown type %s\n' %
+ etype)
+ if fix:
+ cnx.system_sql("DELETE FROM entities WHERE type = %(type)s",
+ {'type': etype})
+ continue
+ table = SQL_PREFIX + etype
+ for rel, default in ( ('creation_date', datetime.utcnow()),
+ ('modification_date', datetime.utcnow()), ):
+ column = SQL_PREFIX + rel
+ cursor = cnx.system_sql("SELECT %s FROM %s WHERE %s is NULL"
+ % (eidcolumn, table, column))
+ for eid, in cursor.fetchall():
+ sys.stderr.write(msg % (etype, eid, rel))
+ if fix:
+ cnx.system_sql("UPDATE %s SET %s=%%(v)s WHERE %s=%s ;"
+ % (table, column, eidcolumn, eid),
+ {'v': default})
+ notify_fixed(fix)
+
+
+def check(repo, cnx, checks, reindex, fix, withpb=True):
+ """check integrity of instance's repository,
+ using given user and password to locally connect to the repository
+ (no running cubicweb server needed)
+ """
+ # yo, launch checks
+ if checks:
+ eids_cache = {}
+ with cnx.security_enabled(read=False, write=False): # ensure no read security
+ for check in checks:
+ check_func = globals()['check_%s' % check]
+ check_func(repo.schema, cnx, eids_cache, fix=fix)
+ if fix:
+ cnx.commit()
+ else:
+ print()
+ if not fix:
+ print('WARNING: Diagnostic run, nothing has been corrected')
+ if reindex:
+ cnx.rollback()
+ reindex_entities(repo.schema, cnx, withpb=withpb)
+ cnx.commit()