After upgrading from 1.38 to 1.39
php maintenance/update.php gives error,
Modifying tl_namespace field of table templatelinks...Wikimedia\Rdbms\DBQueryError from line 1618 of /var/www/html/includes/libs/rdbms/database/Database.php: Error 1091: Can't DROP INDEX `PRIMARY`; check that it exists
Function: Wikimedia\Rdbms\Database::sourceFile( /var/www/html/maintenance/archives/patch-templatelinks-tl_title-nullable.sql )
Query: ALTER TABLE `templatelinks`
DROP PRIMARY KEY
mysql> describe templatelinks;
+-------------------+---------------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-------------------+---------------------+------+-----+---------+-------+
| tl_from | int(10) unsigned | NO | | 0 | |
| tl_namespace | int(11) | NO | MUL | 0 | |
| tl_title | varbinary(255) | NO | | | |
| tl_from_namespace | int(11) | NO | MUL | 0 | |
| tl_target_id | bigint(20) unsigned | NO | MUL | NULL | |
+-------------------+---------------------+------+-----+---------+-------+
SHOW INDEXES FROM templatelinks;
+---------------+------------+----------------------------------+--------------+-------------------+-----------+-------------+----------+--------+------+------------+---------+---------------+---------+
| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment | Ignored |
+---------------+------------+----------------------------------+--------------+-------------------+-----------+-------------+----------+--------+------+------------+---------+---------------+---------+
| templatelinks | 1 | tl_namespace | 1 | tl_namespace | A | 3300 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_namespace | 2 | tl_title | A | 2479612 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_namespace | 3 | tl_from | A | 47112645 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_backlinks_namespace | 1 | tl_from_namespace | A | 3686 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_backlinks_namespace | 2 | tl_namespace | A | 14745 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_backlinks_namespace | 3 | tl_title | A | 1346075 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_backlinks_namespace | 4 | tl_from | A | 47112645 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_target_id | 1 | tl_target_id | A | 1624573 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_target_id | 2 | tl_from | A | 47112645 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_backlinks_namespace_target_id | 1 | tl_from_namespace | A | 5130 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_backlinks_namespace_target_id | 2 | tl_target_id | A | 298181 | NULL | NULL | | BTREE | | | NO |
| templatelinks | 1 | tl_backlinks_namespace_target_id | 3 | tl_from | A | 47112645 | NULL | NULL | | BTREE | | | NO |
+---------------+------------+----------------------------------+--------------+-------------------+-----------+-------------+----------+--------+------+------------+---------+---------------+---------+