server/checkintegrity.py
author Sylvain Thénault <sylvain.thenault@logilab.fr>
Fri, 18 Dec 2015 09:07:33 +0100
changeset 11030 c1fdd22232d1
parent 10847 ce5403611cbe
child 11033 63d860a14a17
permissions -rw-r--r--
[server] always monkeypatch QuerierHelper to handle dates and times on SQLite The patch prevents problems due to a SQLite bug causing some values to be returned as strings instead of properly typed objects. This should probably be improved to use SQLite connection hooks. But the major improvement is that the monkeypatch is now done all the time, and not just for tests.
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# copyright 2003-2014 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 print_function
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0
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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, VIRTUAL_RTYPES, UNIQUE_CONSTRAINTS
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from cubicweb.server.sqlutils import SQL_PREFIX
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def notify_fixed(fix):
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    if fix:
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        sys.stderr.write(' [FIXED]')
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    sys.stderr.write('\n')
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def has_eid(cnx, 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 FROM entities WHERE eid=%s' % eid)
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    try:
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        etype = sqlcursor.fetchone()[0]
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    except Exception:
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        eids[eid] = False
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        return False
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    if etype not in cnx.vreg.schema:
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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!\n'
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               '  WARNING : Unable to fix this, do it yourself!\n')
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        sys.stderr.write(msg % eid)
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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, cnx, 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 = cnx.repo
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    dbhelper = repo.system_source.dbhelper
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    cursor = cnx.cnxset.cu
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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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                continue
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            indexable_attrs = tuple(eschema.indexable_attributes()) # generator
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            if not indexable_attrs:
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                continue
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            for container in etype_fti_containers(eschema):
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                etypes.add(container)
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        # clear fti table first
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        cnx.system_sql('DELETE FROM %s' % dbhelper.fti_table)
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    else:
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        print('Reindexing entities of type %s' % \
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              ', '.join(sorted(str(e) for e in etypes)))
5954
987086484876 [fti migration] test and fix reindexation of some specific entity types
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 5850
diff changeset
   114
        # clear fti table first. Use subquery for sql compatibility
9574
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parents: 9543
diff changeset
   115
        cnx.system_sql("DELETE FROM %s WHERE EXISTS(SELECT 1 FROM ENTITIES "
2d4c4842bd04 [server] some s/session/cnx/
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parents: 9543
diff changeset
   116
                       "WHERE eid=%s AND type IN (%s))" % (
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parents: 9543
diff changeset
   117
                           dbhelper.fti_table, dbhelper.fti_uid_attr,
2d4c4842bd04 [server] some s/session/cnx/
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parents: 9543
diff changeset
   118
                           ','.join("'%s'" % etype for etype in etypes)))
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9233a8350420 [test] don't display progress bar when testing checkintegrity
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parents: 4252
diff changeset
   119
    if withpb:
6112
913979c79244 [db-fti-index] simple fix fpr progressbar-related crash when etypes is None in reindex_entities()
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents: 5999
diff changeset
   120
        pb = ProgressBar(len(etypes) + 1)
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parents: 4252
diff changeset
   121
        pb.update()
0
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parents:
diff changeset
   122
    # reindex entities by generating rql queries which set all indexable
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parents:
diff changeset
   123
    # attribute to their current value
4816
c02583cb80a9 repair stuff broken by fti handling changes
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4806
diff changeset
   124
    source = repo.system_source
0
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parents:
diff changeset
   125
    for eschema in etypes:
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parents: 9543
diff changeset
   126
        etype_class = cnx.vreg['etypes'].etype_class(str(eschema))
10847
ce5403611cbe [fti] add cw_fti_index_rql_limit method
Julien Cristau <julien.cristau@logilab.fr>
parents: 10846
diff changeset
   127
        for rset in etype_class.cw_fti_index_rql_limit(cnx):
9574
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parents: 9543
diff changeset
   128
            source.fti_index_entities(cnx, rset.entities())
8450
11063635c4e4 [fti] allow usage of custom RQL to fetch entities to index (closes #2410509)
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents: 8447
diff changeset
   129
            # clear entity cache to avoid high memory consumption on big tables
9574
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parents: 9543
diff changeset
   130
            cnx.drop_entity_cache()
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parents: 4252
diff changeset
   131
        if withpb:
9233a8350420 [test] don't display progress bar when testing checkintegrity
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parents: 4252
diff changeset
   132
            pb.update()
9578
68049d53426c [fti] properly close the ProgressBar
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parents: 9577
diff changeset
   133
    if withpb:
68049d53426c [fti] properly close the ProgressBar
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parents: 9577
diff changeset
   134
        pb.finish()
0
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parents:
diff changeset
   135
1802
d628defebc17 delete-trailing-whitespace + some copyright update
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents: 1398
diff changeset
   136
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parents: 9574
diff changeset
   137
def check_schema(schema, cnx, eids, fix=1):
0
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parents:
diff changeset
   138
    """check serialized schema"""
10589
7c23b7de2b8d [py3k] print function
Samuel Trégouët <samuel.tregouet@logilab.fr>
parents: 10365
diff changeset
   139
    print('Checking serialized schema')
5338
3e5a256d17ba [db-check] fix duplicated schema constraint detection
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4835
diff changeset
   140
    rql = ('Any COUNT(X),RN,SN,ON,CTN GROUPBY RN,SN,ON,CTN ORDERBY 1 '
1398
5fe84a5f7035 rename internal entity types to have CW prefix instead of E
sylvain.thenault@logilab.fr
parents: 1263
diff changeset
   141
           'WHERE X is CWConstraint, R constrained_by X, '
5338
3e5a256d17ba [db-check] fix duplicated schema constraint detection
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4835
diff changeset
   142
           'R relation_type RT, RT name RN, R from_entity ST, ST name SN, '
3e5a256d17ba [db-check] fix duplicated schema constraint detection
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4835
diff changeset
   143
           'R to_entity OT, OT name ON, X cstrtype CT, CT name CTN')
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parents: 9574
diff changeset
   144
    for count, rn, sn, on, cstrname in cnx.execute(rql):
0
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   145
        if count == 1:
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parents:
diff changeset
   146
            continue
10813
ab626726a70a [syncschema] don't arbitrarily remove constraints from the in-memory schema
Julien Cristau <julien.cristau@logilab.fr>
parents: 10663
diff changeset
   147
        if cstrname in UNIQUE_CONSTRAINTS:
10589
7c23b7de2b8d [py3k] print function
Samuel Trégouët <samuel.tregouet@logilab.fr>
parents: 10365
diff changeset
   148
            print("ERROR: got %s %r constraints on relation %s.%s.%s" % (
7c23b7de2b8d [py3k] print function
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parents: 10365
diff changeset
   149
                count, cstrname, sn, rn, on))
5523
4bf975c049a6 [db-check] RQLConstraint is not a 'unique' constraint
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 5424
diff changeset
   150
            if fix:
10589
7c23b7de2b8d [py3k] print function
Samuel Trégouët <samuel.tregouet@logilab.fr>
parents: 10365
diff changeset
   151
                print('dunno how to fix, do it yourself')
0
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parents:
diff changeset
   152
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parents:
diff changeset
   153
1802
d628defebc17 delete-trailing-whitespace + some copyright update
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents: 1398
diff changeset
   154
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parents: 9574
diff changeset
   155
def check_text_index(schema, cnx, eids, fix=1):
0
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parents:
diff changeset
   156
    """check all entities registered in the text index"""
10589
7c23b7de2b8d [py3k] print function
Samuel Trégouët <samuel.tregouet@logilab.fr>
parents: 10365
diff changeset
   157
    print('Checking text index')
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   158
    msg = '  Entity with eid %s exists in the text index but in no source (autofix will remove from text index)'
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
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parents: 9574
diff changeset
   159
    cursor = cnx.system_sql('SELECT uid FROM appears;')
0
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   160
    for row in cursor.fetchall():
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   161
        eid = row[0]
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
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parents: 9574
diff changeset
   162
        if not has_eid(cnx, cursor, eid, eids):
7896
4c954e1e73ef [lint] remove uses of "print >> sys.stderr" (closes #1908571)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7815
diff changeset
   163
            sys.stderr.write(msg % eid)
0
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parents:
diff changeset
   164
            if fix:
9577
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parents: 9574
diff changeset
   165
                cnx.system_sql('DELETE FROM appears WHERE uid=%s;' % eid)
7035
8d2cf36bd79d [c-c db-check] factorize code by introducing notify_fixed dumb function
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 6889
diff changeset
   166
            notify_fixed(fix)
0
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Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   167
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   168
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
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parents: 9574
diff changeset
   169
def check_entities(schema, cnx, eids, fix=1):
0
b97547f5f1fa Showtime !
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parents:
diff changeset
   170
    """check all entities registered in the repo system table"""
10589
7c23b7de2b8d [py3k] print function
Samuel Trégouët <samuel.tregouet@logilab.fr>
parents: 10365
diff changeset
   171
    print('Checking entities system table')
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   172
    # system table but no source
9171
be9596750678 Fix two crashes in db-check (closes #3024964)
Denis Laxalde <denis.laxalde@logilab.fr>
parents: 8900
diff changeset
   173
    msg = '  Entity %s with eid %s exists in the system table but in no source (autofix will delete the entity)'
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
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parents: 9574
diff changeset
   174
    cursor = cnx.system_sql('SELECT eid,type FROM entities;')
0
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parents:
diff changeset
   175
    for row in cursor.fetchall():
9171
be9596750678 Fix two crashes in db-check (closes #3024964)
Denis Laxalde <denis.laxalde@logilab.fr>
parents: 8900
diff changeset
   176
        eid, etype = row
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
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parents: 9574
diff changeset
   177
        if not has_eid(cnx, cursor, eid, eids):
9171
be9596750678 Fix two crashes in db-check (closes #3024964)
Denis Laxalde <denis.laxalde@logilab.fr>
parents: 8900
diff changeset
   178
            sys.stderr.write(msg % (etype, eid))
0
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parents:
diff changeset
   179
            if fix:
9577
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parents: 9574
diff changeset
   180
                cnx.system_sql('DELETE FROM entities WHERE eid=%s;' % eid)
7035
8d2cf36bd79d [c-c db-check] factorize code by introducing notify_fixed dumb function
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 6889
diff changeset
   181
            notify_fixed(fix)
7965
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Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   182
    # source in entities, but no relation cw_source
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
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parents: 9574
diff changeset
   183
    # XXX this (get_versions) requires a second connection to the db when we already have one open
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   184
    applcwversion = cnx.repo.get_versions().get('cubicweb')
9468
39b7a91a3f4c [repo] pylint cleanup, mainly of imports, with a bit of style
Julien Cristau <julien.cristau@logilab.fr>
parents: 9463
diff changeset
   185
    if applcwversion >= (3, 13, 1): # entities.asource appeared in 3.13.1
9577
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parents: 9574
diff changeset
   186
        cursor = cnx.system_sql('SELECT e.eid FROM entities as e, cw_CWSource as s '
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   187
                                    'WHERE s.cw_name=e.asource AND '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   188
                                    'NOT EXISTS(SELECT 1 FROM cw_source_relation as cs '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   189
                                    '  WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid) '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   190
                                    'ORDER BY e.eid')
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   191
        msg = ('  Entity with eid %s refers to source in entities table, '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   192
               'but is missing relation cw_source (autofix will create the relation)\n')
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   193
        for row in cursor.fetchall():
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   194
            sys.stderr.write(msg % row[0])
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   195
        if fix:
9577
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Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   196
            cnx.system_sql('INSERT INTO cw_source_relation (eid_from, eid_to) '
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   197
                               'SELECT e.eid, s.cw_eid FROM entities as e, cw_CWSource as s '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   198
                               'WHERE s.cw_name=e.asource AND NOT EXISTS(SELECT 1 FROM cw_source_relation as cs '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   199
                               '  WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid)')
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
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parents: 7896
diff changeset
   200
            notify_fixed(True)
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
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parents: 7896
diff changeset
   201
    # inconsistencies for 'is'
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   202
    msg = '  %s #%s is missing relation "is" (autofix will create the relation)\n'
9577
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parents: 9574
diff changeset
   203
    cursor = cnx.system_sql('SELECT e.type, e.eid FROM entities as e, cw_CWEType as s '
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   204
                                'WHERE s.cw_name=e.type AND NOT EXISTS(SELECT 1 FROM is_relation as cs '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   205
                                '  WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid) '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   206
                                'ORDER BY e.eid')
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   207
    for row in cursor.fetchall():
10625
684dbf6722ef [server] fix checkintegrity with pyodbc
Julien Cristau <julien.cristau@logilab.fr>
parents: 10365
diff changeset
   208
        sys.stderr.write(msg % tuple(row))
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   209
    if fix:
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
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parents: 9574
diff changeset
   210
        cnx.system_sql('INSERT INTO is_relation (eid_from, eid_to) '
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   211
                           'SELECT e.eid, s.cw_eid FROM entities as e, cw_CWEType as s '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   212
                           'WHERE s.cw_name=e.type AND NOT EXISTS(SELECT 1 FROM is_relation as cs '
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
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parents: 7896
diff changeset
   213
                           '  WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid)')
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
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parents: 7896
diff changeset
   214
        notify_fixed(True)
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   215
    # inconsistencies for 'is_instance_of'
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    msg = '  %s #%s is missing relation "is_instance_of" (autofix will create the relation)\n'
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    cursor = cnx.system_sql('SELECT e.type, e.eid FROM entities as e, cw_CWEType as s '
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                                'WHERE s.cw_name=e.type AND NOT EXISTS(SELECT 1 FROM is_instance_of_relation as cs '
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                                '  WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid) '
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                                'ORDER BY e.eid')
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    for row in cursor.fetchall():
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        sys.stderr.write(msg % tuple(row))
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    if fix:
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        cnx.system_sql('INSERT INTO is_instance_of_relation (eid_from, eid_to) '
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                           'SELECT e.eid, s.cw_eid FROM entities as e, cw_CWEType as s '
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                           'WHERE s.cw_name=e.type AND NOT EXISTS(SELECT 1 FROM is_instance_of_relation as cs '
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                           '  WHERE cs.eid_from=e.eid AND cs.eid_to=s.cw_eid)')
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        notify_fixed(True)
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    print('Checking entities tables')
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    msg = '  Entity with eid %s exists in the %s table but not in the system table (autofix will delete the entity)'
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    for eschema in schema.entities():
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        if eschema.final:
0
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            continue
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        table = SQL_PREFIX + eschema.type
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        column = SQL_PREFIX +  'eid'
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        cursor = cnx.system_sql('SELECT %s FROM %s;' % (column, table))
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        for row in cursor.fetchall():
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            eid = row[0]
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            # eids is full since we have fetched everything from the entities table,
0
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            # no need to call has_eid
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            if not eid in eids or not eids[eid]:
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                sys.stderr.write(msg % (eid, eschema.type))
0
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                if fix:
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                    cnx.system_sql('DELETE FROM %s WHERE %s=%s;' % (table, column, eid))
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                notify_fixed(fix)
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0
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def bad_related_msg(rtype, target, eid, fix):
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    msg = '  A relation %s with %s eid %s exists but no such entity in sources'
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    sys.stderr.write(msg % (rtype, target, eid))
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    notify_fixed(fix)
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def bad_inlined_msg(rtype, parent_eid, eid, fix):
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    msg = ('  An inlined relation %s from %s to %s exists but the latter '
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           'entity does not exist')
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    sys.stderr.write(msg % (rtype, parent_eid, eid))
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    notify_fixed(fix)
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   258
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def check_relations(schema, cnx, eids, fix=1):
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    """check that eids referenced by relations are registered in the repo system
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    table
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    """
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    print('Checking relations')
0
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    for rschema in schema.relations():
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        if rschema.final or rschema.type in PURE_VIRTUAL_RTYPES:
0
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            continue
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        if rschema.inlined:
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            for subjtype in rschema.subjects():
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                table = SQL_PREFIX + str(subjtype)
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                column = SQL_PREFIX +  str(rschema)
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                sql = 'SELECT cw_eid,%s FROM %s WHERE %s IS NOT NULL;' % (
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                    column, table, column)
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                cursor = cnx.system_sql(sql)
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                for row in cursor.fetchall():
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                    parent_eid, eid = row
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                    if not has_eid(cnx, cursor, eid, eids):
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                        bad_inlined_msg(rschema, parent_eid, 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)
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                            cnx.system_sql(sql)
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            continue
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        try:
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            cursor = cnx.system_sql('SELECT eid_from FROM %s_relation;' % rschema)
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358d8bed9626 [toward-py3k] rewrite to "except AnException as exc:" (part of #2711624)
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diff changeset
   286
        except Exception as ex:
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   287
            # usually because table doesn't exist
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   288
            print('ERROR', ex)
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   289
            continue
0
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        for row in cursor.fetchall():
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            eid = row[0]
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   292
            if not has_eid(cnx, cursor, eid, eids):
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   293
                bad_related_msg(rschema, 'subject', eid, fix)
0
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   294
                if fix:
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diff changeset
   295
                    sql = 'DELETE FROM %s_relation WHERE eid_from=%s;' % (
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   296
                        rschema, eid)
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   297
                    cnx.system_sql(sql)
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   298
        cursor = cnx.system_sql('SELECT eid_to FROM %s_relation;' % rschema)
0
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   299
        for row in cursor.fetchall():
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            eid = row[0]
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diff changeset
   301
            if not has_eid(cnx, cursor, eid, eids):
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diff changeset
   302
                bad_related_msg(rschema, 'object', eid, fix)
0
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diff changeset
   303
                if fix:
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diff changeset
   304
                    sql = 'DELETE FROM %s_relation WHERE eid_to=%s;' % (
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diff changeset
   305
                        rschema, eid)
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diff changeset
   306
                    cnx.system_sql(sql)
0
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diff changeset
   307
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diff changeset
   308
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diff changeset
   309
def check_mandatory_relations(schema, cnx, eids, fix=1):
7036
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
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diff changeset
   310
    """check entities missing some mandatory relation"""
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   311
    print('Checking mandatory relations')
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diff changeset
   312
    msg = '%s #%s is missing mandatory %s relation %s (autofix will delete the entity)'
7036
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
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diff changeset
   313
    for rschema in schema.relations():
8527
6151b0199bc1 [c-c db-check] don't skip is/is_instance_of mandatory relation to avoid telling two opposite messages when the relation is missing. Closes #2465659
Sylvain Thénault <sylvain.thenault@logilab.fr>
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diff changeset
   314
        if rschema.final or rschema in PURE_VIRTUAL_RTYPES or rschema in ('is', 'is_instance_of'):
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diff changeset
   315
            continue
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diff changeset
   316
        smandatory = set()
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
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diff changeset
   317
        omandatory = set()
10663
54b8a1f249fb [py3k] dict.itervalues → dict.values
Rémi Cardona <remi.cardona@logilab.fr>
parents: 10651
diff changeset
   318
        for rdef in rschema.rdefs.values():
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63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
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diff changeset
   319
            if rdef.cardinality[0] in '1+':
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   320
                smandatory.add(rdef.subject)
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   321
            if rdef.cardinality[1] in '1+':
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   322
                omandatory.add(rdef.object)
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   323
        for role, etypes in (('subject', smandatory), ('object', omandatory)):
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   324
            for etype in etypes:
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   325
                if role == 'subject':
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   326
                    rql = 'Any X WHERE NOT X %s Y, X is %s' % (rschema, etype)
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   327
                else:
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   328
                    rql = 'Any X WHERE NOT Y %s X, X is %s' % (rschema, etype)
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   329
                for entity in cnx.execute(rql).entities():
8900
010a59e12d89 use cw_etype instead of __regid__
Pierre-Yves David <pierre-yves.david@logilab.fr>
parents: 8696
diff changeset
   330
                    sys.stderr.write(msg % (entity.cw_etype, entity.eid, role, rschema))
7036
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   331
                    if fix:
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   332
                        #if entity.cw_describe()['source']['uri'] == 'system': XXX
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   333
                        entity.cw_delete() # XXX this is BRUTAL!
7036
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   334
                    notify_fixed(fix)
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   335
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   336
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   337
def check_mandatory_attributes(schema, cnx, eids, fix=1):
7036
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   338
    """check for entities stored in the system source missing some mandatory
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   339
    attribute
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   340
    """
10589
7c23b7de2b8d [py3k] print function
Samuel Trégouët <samuel.tregouet@logilab.fr>
parents: 10365
diff changeset
   341
    print('Checking mandatory attributes')
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   342
    msg = '%s #%s is missing mandatory attribute %s (autofix will delete the entity)'
7036
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   343
    for rschema in schema.relations():
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   344
        if not rschema.final or rschema in VIRTUAL_RTYPES:
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   345
            continue
10663
54b8a1f249fb [py3k] dict.itervalues → dict.values
Rémi Cardona <remi.cardona@logilab.fr>
parents: 10651
diff changeset
   346
        for rdef in rschema.rdefs.values():
7036
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   347
            if rdef.cardinality[0] in '1+':
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   348
                rql = 'Any X WHERE X %s NULL, X is %s, X cw_source S, S name "system"' % (
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   349
                    rschema, rdef.subject)
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   350
                for entity in cnx.execute(rql).entities():
8900
010a59e12d89 use cw_etype instead of __regid__
Pierre-Yves David <pierre-yves.david@logilab.fr>
parents: 8696
diff changeset
   351
                    sys.stderr.write(msg % (entity.cw_etype, entity.eid, rschema))
7036
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   352
                    if fix:
7682
07b592a62be3 [c-c db-check] drop some deprecation warning
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7473
diff changeset
   353
                        entity.cw_delete()
7036
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   354
                    notify_fixed(fix)
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   355
63386b35ec69 [c-c db-check] new checks for entities missing a mandatory relation/attribute
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 7035
diff changeset
   356
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   357
def check_metadata(schema, cnx, eids, fix=1):
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   358
    """check entities has required metadata
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   359
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   360
    FIXME: rewrite using RQL queries ?
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   361
    """
10589
7c23b7de2b8d [py3k] print function
Samuel Trégouët <samuel.tregouet@logilab.fr>
parents: 10365
diff changeset
   362
    print('Checking metadata')
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   363
    cursor = cnx.system_sql("SELECT DISTINCT type FROM entities;")
1251
af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
sylvain.thenault@logilab.fr
parents: 1161
diff changeset
   364
    eidcolumn = SQL_PREFIX + 'eid'
7965
d45c0eb39e72 [server] fix integrity checks that destroy data (closes #1972842)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7896
diff changeset
   365
    msg = '  %s with eid %s has no %s (autofix will set it to now)'
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   366
    for etype, in cursor.fetchall():
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   367
        if etype not in cnx.vreg.schema:
9171
be9596750678 Fix two crashes in db-check (closes #3024964)
Denis Laxalde <denis.laxalde@logilab.fr>
parents: 8900
diff changeset
   368
            sys.stderr.write('entities table references unknown type %s\n' %
be9596750678 Fix two crashes in db-check (closes #3024964)
Denis Laxalde <denis.laxalde@logilab.fr>
parents: 8900
diff changeset
   369
                             etype)
be9596750678 Fix two crashes in db-check (closes #3024964)
Denis Laxalde <denis.laxalde@logilab.fr>
parents: 8900
diff changeset
   370
            if fix:
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   371
                cnx.system_sql("DELETE FROM entities WHERE type = %(type)s",
9171
be9596750678 Fix two crashes in db-check (closes #3024964)
Denis Laxalde <denis.laxalde@logilab.fr>
parents: 8900
diff changeset
   372
                                   {'type': etype})
be9596750678 Fix two crashes in db-check (closes #3024964)
Denis Laxalde <denis.laxalde@logilab.fr>
parents: 8900
diff changeset
   373
            continue
1251
af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
sylvain.thenault@logilab.fr
parents: 1161
diff changeset
   374
        table = SQL_PREFIX + etype
1016
26387b836099 use datetime instead of mx.DateTime
sylvain.thenault@logilab.fr
parents: 713
diff changeset
   375
        for rel, default in ( ('creation_date', datetime.now()),
26387b836099 use datetime instead of mx.DateTime
sylvain.thenault@logilab.fr
parents: 713
diff changeset
   376
                              ('modification_date', datetime.now()), ):
1251
af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
sylvain.thenault@logilab.fr
parents: 1161
diff changeset
   377
            column = SQL_PREFIX + rel
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   378
            cursor = cnx.system_sql("SELECT %s FROM %s WHERE %s is NULL"
1251
af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
sylvain.thenault@logilab.fr
parents: 1161
diff changeset
   379
                                        % (eidcolumn, table, column))
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   380
            for eid, in cursor.fetchall():
7896
4c954e1e73ef [lint] remove uses of "print >> sys.stderr" (closes #1908571)
Nicolas Chauvat <nicolas.chauvat@logilab.fr>
parents: 7815
diff changeset
   381
                sys.stderr.write(msg % (etype, eid, rel))
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   382
                if fix:
9577
c52441e4a3d7 [serverctl] use repoapi for db-check, add-source, rebuild-fti commands
Julien Cristau <julien.cristau@logilab.fr>
parents: 9574
diff changeset
   383
                    cnx.system_sql("UPDATE %s SET %s=%%(v)s WHERE %s=%s ;"
1251
af40e615dc89 introduce a 'cw_' prefix on entity table and column names so we don't conflict with sql or DBMS specific keywords
sylvain.thenault@logilab.fr
parents: 1161
diff changeset
   384
                                       % (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
sylvain.thenault@logilab.fr
parents: 1161
diff changeset
   385
                                       {'v': 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
   386
                notify_fixed(fix)
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   387
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   388
4675
9233a8350420 [test] don't display progress bar when testing checkintegrity
Sylvain Thénault <sylvain.thenault@logilab.fr>
parents: 4252
diff changeset
   389
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
   390
    """check integrity of instance's repository,
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   391
    using given user and password to locally connect to the repository
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   392
    (no running cubicweb server needed)
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   393
    """
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   394
    # yo, launch checks
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   395
    if checks:
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   396
        eids_cache = {}
9797
4e640ab62f51 [tests/checkintegrity] use the new connection api
Aurelien Campeas <aurelien.campeas@logilab.fr>
parents: 9578
diff changeset
   397
        with cnx.security_enabled(read=False, write=False): # ensure no read security
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
   398
            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
   399
                check_func = globals()['check_%s' % check]
10365
21461f80f348 [connection] remove ensure_cnx_set context manager uses
Aurelien Campeas <aurelien.campeas@logilab.fr>
parents: 9797
diff changeset
   400
                check_func(repo.schema, cnx, eids_cache, fix=fix)
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   401
        if fix:
9797
4e640ab62f51 [tests/checkintegrity] use the new connection api
Aurelien Campeas <aurelien.campeas@logilab.fr>
parents: 9578
diff changeset
   402
            cnx.commit()
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   403
        else:
10589
7c23b7de2b8d [py3k] print function
Samuel Trégouët <samuel.tregouet@logilab.fr>
parents: 10365
diff changeset
   404
            print()
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   405
        if not fix:
10589
7c23b7de2b8d [py3k] print function
Samuel Trégouët <samuel.tregouet@logilab.fr>
parents: 10365
diff changeset
   406
            print('WARNING: Diagnostic run, nothing has been corrected')
0
b97547f5f1fa Showtime !
Adrien Di Mascio <Adrien.DiMascio@logilab.fr>
parents:
diff changeset
   407
    if reindex:
9797
4e640ab62f51 [tests/checkintegrity] use the new connection api
Aurelien Campeas <aurelien.campeas@logilab.fr>
parents: 9578
diff changeset
   408
        cnx.rollback()
10365
21461f80f348 [connection] remove ensure_cnx_set context manager uses
Aurelien Campeas <aurelien.campeas@logilab.fr>
parents: 9797
diff changeset
   409
        reindex_entities(repo.schema, cnx, withpb=withpb)
9797
4e640ab62f51 [tests/checkintegrity] use the new connection api
Aurelien Campeas <aurelien.campeas@logilab.fr>
parents: 9578
diff changeset
   410
        cnx.commit()