server/checkintegrity.py
author Florent Cayré <florent.cayre@gmail.com>
Wed, 25 May 2011 08:35:20 +0200
branchstable
changeset 7425 7e9d1d6fcba7
parent 7040 9b1f9bc74f5d
child 7398 26695dd703d8
child 7468 c202aaf71489
permissions -rw-r--r--
[entity fetch_attrs] remove ambiguous relations on different etypes from fetched attrs or it may produce wrong related results; closes #1700896
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# copyright 2003-2010 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
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# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
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#
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# This file is part of CubicWeb.
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#
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# CubicWeb is free software: you can redistribute it and/or modify it under the
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# terms of the GNU Lesser General Public License as published by the Free
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# Software Foundation, either version 2.1 of the License, or (at your option)
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# any later version.
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#
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# CubicWeb is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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# FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
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# details.
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#
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# You should have received a copy of the GNU Lesser General Public License along
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# with CubicWeb.  If not, see <http://www.gnu.org/licenses/>.
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"""Integrity checking tool for instances:
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* integrity of a CubicWeb repository. Hum actually only the system database is
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  checked.
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"""
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from __future__ import with_statement
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__docformat__ = "restructuredtext en"
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import sys
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from datetime import datetime
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from logilab.common.shellutils import ProgressBar
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from cubicweb.schema import PURE_VIRTUAL_RTYPES
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from cubicweb.server.sqlutils import SQL_PREFIX
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from cubicweb.server.session import security_enabled
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def notify_fixed(fix):
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    if fix:
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        print >> sys.stderr, ' [FIXED]'
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    else:
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        print >> sys.stderr
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def has_eid(session, sqlcursor, eid, eids):
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    """return true if the eid is a valid eid"""
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    if eid in eids:
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        return eids[eid]
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    sqlcursor.execute('SELECT type, source FROM entities WHERE eid=%s' % eid)
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    try:
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        etype, source = sqlcursor.fetchone()
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    except:
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        eids[eid] = False
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        return False
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    if source and source != 'system':
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        try:
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            # insert eid *and* etype to attempt checking entity has not been
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            # replaced by another subsquently to a restore of an old dump
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            if session.execute('Any X WHERE X is %s, X eid %%(x)s' % etype,
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                               {'x': eid}):
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                eids[eid] = True
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                return True
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        except: # TypeResolverError, Unauthorized...
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            pass
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        eids[eid] = False
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        return False
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    sqlcursor.execute('SELECT * FROM %s%s WHERE %seid=%s' % (SQL_PREFIX, etype,
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                                                             SQL_PREFIX, eid))
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    result = sqlcursor.fetchall()
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    if len(result) == 0:
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        eids[eid] = False
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        return False
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    elif len(result) > 1:
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        msg = '  More than one entity with eid %s exists in source !'
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        print >> sys.stderr, msg % eid
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        print >> sys.stderr, '  WARNING : Unable to fix this, do it yourself !'
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    eids[eid] = True
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    return True
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# XXX move to yams?
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def etype_fti_containers(eschema, _done=None):
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    if _done is None:
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        _done = set()
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    _done.add(eschema)
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    containers = tuple(eschema.fulltext_containers())
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    if containers:
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        for rschema, target in containers:
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            if target == 'object':
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                targets = rschema.objects(eschema)
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            else:
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                targets = rschema.subjects(eschema)
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            for targeteschema in targets:
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                if targeteschema in _done:
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                    continue
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                _done.add(targeteschema)
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                for container in etype_fti_containers(targeteschema, _done):
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                    yield container
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    else:
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        yield eschema
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def reindex_entities(schema, session, withpb=True, etypes=None):
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    """reindex all entities in the repository"""
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    # deactivate modification_date hook since we don't want them
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    # to be updated due to the reindexation
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    repo = session.repo
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    cursor = session.pool['system']
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    dbhelper = session.repo.system_source.dbhelper
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    if not dbhelper.has_fti_table(cursor):
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        print 'no text index table'
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        dbhelper.init_fti(cursor)
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    repo.system_source.do_fti = True  # ensure full-text indexation is activated
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    if etypes is None:
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        print 'Reindexing entities'
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        etypes = set()
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        for eschema in schema.entities():
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            if eschema.final:
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   115
                continue
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   116
            indexable_attrs = tuple(eschema.indexable_attributes()) # generator
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   117
            if not indexable_attrs:
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   118
                continue
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   119
            for container in etype_fti_containers(eschema):
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   120
                etypes.add(container)
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   121
        # clear fti table first
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   122
        session.system_sql('DELETE FROM %s' % dbhelper.fti_table)
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diff changeset
   123
    else:
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   124
        print 'Reindexing entities of type %s' % \
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   125
              ', '.join(sorted(str(e) for e in etypes))
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   126
        # clear fti table first. Use subquery for sql compatibility
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   127
        session.system_sql("DELETE FROM %s WHERE EXISTS(SELECT 1 FROM ENTITIES "
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   128
                           "WHERE eid=%s AND type IN (%s))" % (
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diff changeset
   129
                               dbhelper.fti_table, dbhelper.fti_uid_attr,
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   130
                               ','.join("'%s'" % etype for etype in etypes)))
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   131
    if withpb:
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   132
        pb = ProgressBar(len(etypes) + 1)
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   133
        pb.update()
0
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   134
    # reindex entities by generating rql queries which set all indexable
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   135
    # attribute to their current value
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   136
    source = repo.system_source
0
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   137
    for eschema in etypes:
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diff changeset
   138
        rset = session.execute('Any X WHERE X is %s' % eschema)
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diff changeset
   139
        source.fti_index_entities(session, rset.entities())
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   140
        if withpb:
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   141
            pb.update()
0
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   142
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diff changeset
   143
380
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   144
def check_schema(schema, session, eids, fix=1):
0
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   145
    """check serialized schema"""
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   146
    print 'Checking serialized schema'
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   147
    unique_constraints = ('SizeConstraint', 'FormatConstraint',
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   148
                          'VocabularyConstraint',
0
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                          'RQLVocabularyConstraint')
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diff changeset
   150
    rql = ('Any COUNT(X),RN,SN,ON,CTN GROUPBY RN,SN,ON,CTN ORDERBY 1 '
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5fe84a5f7035 rename internal entity types to have CW prefix instead of E
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diff changeset
   151
           'WHERE X is CWConstraint, R constrained_by X, '
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diff changeset
   152
           'R relation_type RT, RT name RN, R from_entity ST, ST name SN, '
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diff changeset
   153
           'R to_entity OT, OT name ON, X cstrtype CT, CT name CTN')
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diff changeset
   154
    for count, rn, sn, on, cstrname in session.execute(rql):
0
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   155
        if count == 1:
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   156
            continue
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   157
        if cstrname in unique_constraints:
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diff changeset
   158
            print "ERROR: got %s %r constraints on relation %s.%s.%s" % (
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diff changeset
   159
                count, cstrname, sn, rn, on)
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parents: 5424
diff changeset
   160
            if fix:
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diff changeset
   161
                print 'dunno how to fix, do it yourself'
0
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diff changeset
   162
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   163
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diff changeset
   164
0
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diff changeset
   165
def check_text_index(schema, session, eids, fix=1):
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   166
    """check all entities registered in the text index"""
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   167
    print 'Checking text index'
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   168
    cursor = session.system_sql('SELECT uid FROM appears;')
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   169
    for row in cursor.fetchall():
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   170
        eid = row[0]
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diff changeset
   171
        if not has_eid(session, cursor, eid, eids):
0
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   172
            msg = '  Entity with eid %s exists in the text index but in no source'
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   173
            print >> sys.stderr, msg % eid,
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   174
            if fix:
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   175
                session.system_sql('DELETE FROM appears WHERE uid=%s;' % eid)
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8d2cf36bd79d [c-c db-check] factorize code by introducing notify_fixed dumb function
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diff changeset
   176
            notify_fixed(fix)
0
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parents:
diff changeset
   177
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parents:
diff changeset
   178
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   179
def check_entities(schema, session, eids, fix=1):
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   180
    """check all entities registered in the repo system table"""
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   181
    print 'Checking entities system table'
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diff changeset
   182
    cursor = session.system_sql('SELECT eid FROM entities;')
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diff changeset
   183
    for row in cursor.fetchall():
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diff changeset
   184
        eid = row[0]
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diff changeset
   185
        if not has_eid(session, cursor, eid, eids):
0
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diff changeset
   186
            msg = '  Entity with eid %s exists in the system table but in no source'
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   187
            print >> sys.stderr, msg % eid,
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   188
            if fix:
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diff changeset
   189
                session.system_sql('DELETE FROM entities WHERE eid=%s;' % eid)
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8d2cf36bd79d [c-c db-check] factorize code by introducing notify_fixed dumb function
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diff changeset
   190
            notify_fixed(fix)
0
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   191
    print 'Checking entities tables'
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diff changeset
   192
    for eschema in schema.entities():
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diff changeset
   193
        if eschema.final:
0
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diff changeset
   194
            continue
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af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
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diff changeset
   195
        table = SQL_PREFIX + eschema.type
af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
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diff changeset
   196
        column = SQL_PREFIX +  'eid'
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diff changeset
   197
        cursor = session.system_sql('SELECT %s FROM %s;' % (column, table))
0
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   198
        for row in cursor.fetchall():
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diff changeset
   199
            eid = row[0]
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0de53140bd29 [db-check] cleanup
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diff changeset
   200
            # eids is full since we have fetched everything from the entities table,
0
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diff changeset
   201
            # no need to call has_eid
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   202
            if not eid in eids or not eids[eid]:
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diff changeset
   203
                msg = '  Entity with eid %s exists in the %s table but not in the system table'
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diff changeset
   204
                print >> sys.stderr, msg % (eid, eschema.type),
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diff changeset
   205
                if fix:
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af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
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diff changeset
   206
                    session.system_sql('DELETE FROM %s WHERE %s=%s;' % (table, column, eid))
7035
8d2cf36bd79d [c-c db-check] factorize code by introducing notify_fixed dumb function
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diff changeset
   207
                notify_fixed(fix)
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diff changeset
   208
d628defebc17 delete-trailing-whitespace + some copyright update
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diff changeset
   209
0
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diff changeset
   210
def bad_related_msg(rtype, target, eid, fix):
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diff changeset
   211
    msg = '  A relation %s with %s eid %s exists but no such entity in sources'
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diff changeset
   212
    print >> sys.stderr, msg % (rtype, target, eid),
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diff changeset
   213
    notify_fixed(fix)
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diff changeset
   214
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diff changeset
   215
0
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diff changeset
   216
def check_relations(schema, session, eids, fix=1):
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8d2cf36bd79d [c-c db-check] factorize code by introducing notify_fixed dumb function
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diff changeset
   217
    """check that eids referenced by relations are registered in the repo system
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diff changeset
   218
    table
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diff changeset
   219
    """
0
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   220
    print 'Checking relations'
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diff changeset
   221
    for rschema in schema.relations():
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diff changeset
   222
        if rschema.final or rschema in PURE_VIRTUAL_RTYPES:
0
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   223
            continue
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diff changeset
   224
        if rschema.inlined:
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   225
            for subjtype in rschema.subjects():
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af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
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diff changeset
   226
                table = SQL_PREFIX + str(subjtype)
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diff changeset
   227
                column = SQL_PREFIX +  str(rschema)
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diff changeset
   228
                sql = 'SELECT %s FROM %s WHERE %s IS NOT NULL;' % (
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diff changeset
   229
                    column, table, column)
380
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diff changeset
   230
                cursor = session.system_sql(sql)
0
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                for row in cursor.fetchall():
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                    eid = row[0]
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                    if not has_eid(session, cursor, eid, eids):
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                        bad_related_msg(rschema, 'object', eid, fix)
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                        if fix:
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                            sql = 'UPDATE %s SET %s=NULL WHERE %s=%s;' % (
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                                table, column, column, eid)
381
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                            session.system_sql(sql)
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            continue
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        try:
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            cursor = session.system_sql('SELECT eid_from FROM %s_relation;' % rschema)
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        except Exception, ex:
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            # usually because table doesn't exist
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            print 'ERROR', ex
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            continue
0
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        for row in cursor.fetchall():
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            eid = row[0]
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            if not has_eid(session, cursor, eid, eids):
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                bad_related_msg(rschema, 'subject', eid, fix)
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                if fix:
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                    sql = 'DELETE FROM %s_relation WHERE eid_from=%s;' % (
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                        rschema, eid)
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                    session.system_sql(sql)
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        cursor = session.system_sql('SELECT eid_to FROM %s_relation;' % rschema)
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        for row in cursor.fetchall():
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            eid = row[0]
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            if not has_eid(session, cursor, eid, eids):
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                bad_related_msg(rschema, 'object', eid, fix)
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                if fix:
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                    sql = 'DELETE FROM %s_relation WHERE eid_to=%s;' % (
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                        rschema, eid)
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                    session.system_sql(sql)
0
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def check_mandatory_relations(schema, session, eids, fix=1):
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    """check entities missing some mandatory relation"""
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    print 'Checking mandatory relations'
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    for rschema in schema.relations():
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        if rschema.final or rschema in PURE_VIRTUAL_RTYPES:
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            continue
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        smandatory = set()
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        omandatory = set()
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        for rdef in rschema.rdefs.values():
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            if rdef.cardinality[0] in '1+':
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                smandatory.add(rdef.subject)
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            if rdef.cardinality[1] in '1+':
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                omandatory.add(rdef.object)
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        for role, etypes in (('subject', smandatory), ('object', omandatory)):
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            for etype in etypes:
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                if role == 'subject':
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                    rql = 'Any X WHERE NOT X %s Y, X is %s' % (rschema, etype)
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                else:
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                    rql = 'Any X WHERE NOT Y %s X, X is %s' % (rschema, etype)
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                for entity in session.execute(rql).entities():
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                    print >> sys.stderr, '%s #%s is missing mandatory %s relation %s' % (
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                        entity.__regid__, entity.eid, role, rschema)
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                    if fix:
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                        #if entity.cw_describe()['source']['uri'] == 'system': XXX
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                        entity.delete()
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                    notify_fixed(fix)
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   292
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   293
def check_mandatory_attributes(schema, session, eids, fix=1):
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   294
    """check for entities stored in the system source missing some mandatory
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    attribute
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   296
    """
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   297
    print 'Checking mandatory attributes'
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   298
    for rschema in schema.relations():
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   299
        if not rschema.final or rschema in VIRTUAL_RTYPES:
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            continue
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   301
        for rdef in rschema.rdefs.values():
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   302
            if rdef.cardinality[0] in '1+':
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   303
                rql = 'Any X WHERE X %s NULL, X is %s, X cw_source S, S name "system"' % (
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   304
                    rschema, rdef.subject)
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diff changeset
   305
                for entity in session.execute(rql).entities():
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diff changeset
   306
                    print >> sys.stderr, '%s #%s is missing mandatory attribute %s' % (
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diff changeset
   307
                        entity.__regid__, entity.eid, rschema)
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diff changeset
   308
                    if fix:
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diff changeset
   309
                        entity.delete()
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   310
                    notify_fixed(fix)
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diff changeset
   311
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   312
0
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def check_metadata(schema, session, eids, fix=1):
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    """check entities has required metadata
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    FIXME: rewrite using RQL queries ?
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    """
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   318
    print 'Checking metadata'
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   319
    cursor = session.system_sql("SELECT DISTINCT type FROM entities;")
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diff changeset
   320
    eidcolumn = SQL_PREFIX + 'eid'
0
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   321
    for etype, in cursor.fetchall():
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   322
        table = SQL_PREFIX + etype
1016
26387b836099 use datetime instead of mx.DateTime
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diff changeset
   323
        for rel, default in ( ('creation_date', datetime.now()),
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   324
                              ('modification_date', datetime.now()), ):
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diff changeset
   325
            column = SQL_PREFIX + rel
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diff changeset
   326
            cursor = session.system_sql("SELECT %s FROM %s WHERE %s is NULL"
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diff changeset
   327
                                        % (eidcolumn, table, column))
0
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   328
            for eid, in cursor.fetchall():
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   329
                msg = '  %s with eid %s has no %s'
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   330
                print >> sys.stderr, msg % (etype, eid, rel),
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   331
                if fix:
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diff changeset
   332
                    session.system_sql("UPDATE %s SET %s=%%(v)s WHERE %s=%s ;"
af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
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diff changeset
   333
                                       % (table, column, eidcolumn, eid),
af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
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diff changeset
   334
                                       {'v': default})
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8d2cf36bd79d [c-c db-check] factorize code by introducing notify_fixed dumb function
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diff changeset
   335
                notify_fixed(fix)
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5fe84a5f7035 rename internal entity types to have CW prefix instead of E
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parents: 1263
diff changeset
   336
    cursor = session.system_sql('SELECT MIN(%s) FROM %sCWUser;' % (eidcolumn,
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af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
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diff changeset
   337
                                                                  SQL_PREFIX))
0
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diff changeset
   338
    default_user_eid = cursor.fetchone()[0]
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diff changeset
   339
    assert default_user_eid is not None, 'no user defined !'
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diff changeset
   340
    for rel, default in ( ('owned_by', default_user_eid), ):
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   341
        cursor = session.system_sql("SELECT eid, type FROM entities "
5340
4de474016568 [db-check] don't check entities from external sources have owned_by
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 5339
diff changeset
   342
                                    "WHERE source='system' AND NOT EXISTS "
0
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   343
                                    "(SELECT 1 FROM %s_relation WHERE eid_from=eid);"
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   344
                                    % rel)
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   345
        for eid, etype in cursor.fetchall():
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   346
            msg = '  %s with eid %s has no %s relation'
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   347
            print >> sys.stderr, msg % (etype, eid, rel),
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   348
            if fix:
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   349
                session.system_sql('INSERT INTO %s_relation VALUES (%s, %s) ;'
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   350
                                   % (rel, eid, default))
7035
8d2cf36bd79d [c-c db-check] factorize code by introducing notify_fixed dumb function
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 6889
diff changeset
   351
            notify_fixed(fix)
0
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   352
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   353
4675
9233a8350420 [test] don't display progress bar when testing checkintegrity
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4252
diff changeset
   354
def check(repo, cnx, checks, reindex, fix, withpb=True):
2476
1294a6bdf3bf application -> instance where it makes sense
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 2248
diff changeset
   355
    """check integrity of instance's repository,
0
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   356
    using given user and password to locally connect to the repository
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   357
    (no running cubicweb server needed)
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   358
    """
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   359
    session = repo._get_session(cnx.sessionid, setpool=True)
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   360
    # yo, launch checks
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   361
    if checks:
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   362
        eids_cache = {}
4835
13b0b96d7982 [repo] enhanced security handling: deprecates unsafe_execute, in favor of explicit read/write security control using the `enabled_security` context manager. Also code executed on the repository side is now unsafe by default.
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4834
diff changeset
   363
        with security_enabled(session, read=False): # ensure no read security
13b0b96d7982 [repo] enhanced security handling: deprecates unsafe_execute, in favor of explicit read/write security control using the `enabled_security` context manager. Also code executed on the repository side is now unsafe by default.
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4834
diff changeset
   364
            for check in checks:
13b0b96d7982 [repo] enhanced security handling: deprecates unsafe_execute, in favor of explicit read/write security control using the `enabled_security` context manager. Also code executed on the repository side is now unsafe by default.
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4834
diff changeset
   365
                check_func = globals()['check_%s' % check]
13b0b96d7982 [repo] enhanced security handling: deprecates unsafe_execute, in favor of explicit read/write security control using the `enabled_security` context manager. Also code executed on the repository side is now unsafe by default.
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4834
diff changeset
   366
                check_func(repo.schema, session, eids_cache, fix=fix)
0
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   367
        if fix:
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   368
            cnx.commit()
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   369
        else:
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   370
            print
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   371
        if not fix:
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   372
            print 'WARNING: Diagnostic run, nothing has been corrected'
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   373
    if reindex:
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   374
        cnx.rollback()
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   375
        session.set_pool()
4675
9233a8350420 [test] don't display progress bar when testing checkintegrity
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4252
diff changeset
   376
        reindex_entities(repo.schema, session, withpb=withpb)
0
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   377
        cnx.commit()