root@db1075.eqiad.wmnet[(none)]> use etwiki
Database changed
root@db1075.eqiad.wmnet[etwiki]> alter table templatelinks add primary key (tl_from,tl_namespace,tl_title);
Query OK, 0 rows affected (10.64 sec)               
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table pagelinks add primary key (pl_from,pl_namespace,pl_title);
Query OK, 0 rows affected (1 min 22.80 sec)         
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table categorylinks drop key cl_from, add primary key (cl_from,cl_to);
Query OK, 0 rows affected (5.76 sec)                
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table ep_users_per_course drop key ep_users_per_course, add primary key (upc_user_id,upc_course_id,upc_role);
ERROR 1146 (42S02): Table 'etwiki.ep_users_per_course' doesn't exist
root@db1075.eqiad.wmnet[etwiki]> alter table flaggedrevs_tracking drop key from_namespace_title, add primary key (ftr_from,ftr_namespace,ftr_title`);
    `> `\c
root@db1075.eqiad.wmnet[etwiki]> alter table flaggedrevs_tracking drop key from_namespace_title, add primary key (ftr_from,ftr_namespace,ftr_title);
ERROR 1146 (42S02): Table 'etwiki.flaggedrevs_tracking' doesn't exist
root@db1075.eqiad.wmnet[etwiki]> alter table imagelinks drop key il_from, add primary key (il_from,il_to);
Query OK, 0 rows affected (2.61 sec)                
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table iwlinks drop key iwl_from, add primary key (iwl_from,iwl_prefix,iwl_title);
Query OK, 0 rows affected (0.60 sec)                
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table langlinks drop key ll_from, add primary key (ll_from,ll_lang);
Query OK, 0 rows affected (25.97 sec)               
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table log_search drop key ls_field_val, add primary key (ls_field,ls_value,ls_log_id);
Query OK, 0 rows affected (0.18 sec)
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table math drop key math_inputhash, add primary key (math_inputhash);
Query OK, 0 rows affected (0.28 sec)                
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table module_deps drop key md_module_skin, add primary key (md_module,md_skin);
Query OK, 0 rows affected (0.14 sec)
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table objectcache drop key keyname, add primary key (keyname);
Query OK, 0 rows affected (0.16 sec)
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table profiling drop key pf_name_server, add primary key (pf_name,pf_server);
ERROR 1146 (42S02): Table 'etwiki.profiling' doesn't exist
root@db1075.eqiad.wmnet[etwiki]> alter table querycache_info drop key  qci_type, add primary key (qci_type);
Query OK, 0 rows affected (0.07 sec)
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table site_stats drop key ss_row_id, add primary key (ss_row_id);
Query OK, 0 rows affected (0.06 sec)
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table text drop key old_id, add primary key (old_id);
Query OK, 0 rows affected (26.58 sec)               
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table transcache drop key tc_url_idx, add primary key (tc_url);
Query OK, 0 rows affected (0.06 sec)
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table user_former_groups drop key ufg_user_group, add primary key (ufg_user,ufg_group);
Query OK, 0 rows affected (0.06 sec)
Records: 0  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table user_properties drop key user_properties_user_property, add primary key (up_user,up_property);
Query OK, 149551 rows affected (1.16 sec)              
Records: 149551  Duplicates: 0  Warnings: 0

root@db1075.eqiad.wmnet[etwiki]> alter table vote_log drop key log_id, add primary key (log_id);
ERROR 1146 (42S02): Table 'etwiki.vote_log' doesn't exist

alter table templatelinks add primary key (tl_from,tl_namespace,tl_title); -- duplicate index, to be fixed on mediawiki later
alter table pagelinks add primary key (pl_from,pl_namespace,pl_title); -- duplicate index, to be fixed on mediawiki later
alter table categorylinks drop key cl_from, add primary key (cl_from,cl_to);
alter table imagelinks drop key il_from, add primary key (il_from,il_to);
alter table iwlinks drop key iwl_from, add primary key (iwl_from,iwl_prefix,iwl_title);
alter table langlinks drop key ll_from, add primary key (ll_from,ll_lang);
alter table log_search drop key ls_field_val, add primary key (ls_field,ls_value,ls_log_id);
alter table math drop key math_inputhash, add primary key (math_inputhash);
alter table module_deps drop key md_module_skin, add primary key (md_module,md_skin);
alter table objectcache drop key keyname, add primary key (keyname);
alter table querycache_info drop key  qci_type, add primary key (qci_type);
alter table site_stats drop key ss_row_id, add primary key (ss_row_id);
alter table text drop key old_id, add primary key (old_id);
alter table transcache drop key tc_url_idx, add primary key (tc_url);
alter table user_former_groups drop key ufg_user_group, add primary key (ufg_user,ufg_group);
alter table user_properties drop key user_properties_user_property, add primary key (up_user,up_property);

cur
hidden
interwiki
l10n_cache
logging_pre_1_10
oldimage
querycache
querycachetwo
searchindex
securepoll_lists
securepoll_msgs
securepoll_properties
site_identifiers
user_newtalk

[Exception Wikimedia\Rdbms\DBQueryError] (/srv/mediawiki/php-1.29.0-wmf.21/includes/libs/rdbms/database/Database.php:1075) A database query error has occurred. Did you forget to run your application's database schema updater after upgrading? 
Query: SELECT  log_id,log_type,log_action,log_timestamp,log_user,log_user_text,log_namespace,log_title,log_comment,log_params,log_deleted,user_id,user_name,user_editcount,(SELECT  GROUP_CONCAT(ct_tag SEPARATOR ',')  FROM `change_tag`    WHERE ct_log_id=log_id  ) AS `ts_tags`  FROM `logging` FORCE INDEX (PRIMARY) LEFT JOIN `user` ON ((log_user=user_id)) INNER JOIN `log_search` FORCE INDEX (ls_field_val) ON ((ls_log_id=log_id))   WHERE log_type = 'delete' AND log_action = 'revision' AND ls_field = 'rev_id' AND ls_value = 'X' AND (log_type != 'suppress') AND log_namespace = 'X' AND log_title = 'X' AND ((log_deleted & 9) != 9)  ORDER BY log_timestamp DESC LIMIT 26  
Function: IndexPager::buildQueryInfo (LogPager)
Error: 1176 Key 'ls_field_val' doesn't exist in table 'log_search' (10.64.0.206)

  #0 /srv/mediawiki/php-1.29.0-wmf.21/includes/libs/rdbms/database/Database.php(933): Wikimedia\Rdbms\Database->reportQueryError(string, integer, string, string, boolean)
  #1 /srv/mediawiki/php-1.29.0-wmf.21/includes/libs/rdbms/database/Database.php(1269): Wikimedia\Rdbms\Database->query(string, string)
  #2 /srv/mediawiki/php-1.29.0-wmf.21/includes/pager/IndexPager.php(368): Wikimedia\Rdbms\Database->select(array, array, array, string, array, array)
  #3 /srv/mediawiki/php-1.29.0-wmf.21/includes/pager/IndexPager.php(225): IndexPager->reallyDoQuery(string, integer, boolean)
  #4 /srv/mediawiki/php-1.29.0-wmf.21/includes/logging/LogPager.php(428): IndexPager->doQuery()
  #5 /srv/mediawiki/php-1.29.0-wmf.21/includes/pager/IndexPager.php(422): LogPager->doQuery()
  #6 /srv/mediawiki/php-1.29.0-wmf.21/includes/logging/LogEventsList.php(623): IndexPager->getBody()
  #7 /srv/mediawiki/php-1.29.0-wmf.21/includes/specials/SpecialRevisiondelete.php(224): LogEventsList::showLogExtract(OutputPage, string, Title, string, array)
  #8 /srv/mediawiki/php-1.29.0-wmf.21/includes/specialpage/SpecialPage.php(522): SpecialRevisionDelete->execute(NULL)
  #9 /srv/mediawiki/php-1.29.0-wmf.21/includes/specialpage/SpecialPageFactory.php(578): SpecialPage->run(NULL)
  #10 /srv/mediawiki/php-1.29.0-wmf.21/includes/MediaWiki.php(287): SpecialPageFactory::executePath(Title, RequestContext)
  #11 /srv/mediawiki/php-1.29.0-wmf.21/includes/MediaWiki.php(862): MediaWiki->performRequest()
  #12 /srv/mediawiki/php-1.29.0-wmf.21/includes/MediaWiki.php(523): MediaWiki->main()
  #13 /srv/mediawiki/php-1.29.0-wmf.21/index.php(43): MediaWiki->run()
  #14 /srv/mediawiki/w/index.php(3): include(string)
  #15 {main}

ALTER TABLE /*_*/pagelinks DROP INDEX /*i*/pl_from;
ALTER TABLE /*_*/templatelinks DROP INDEX /*i*/tl_from;