Problem

Some patches for the ST 5.3.x line, mainly observed with ST 5.3.1 Patch 13, ST 5.3.3 Patch 6 and ST 5.3.6 Patch 1 or 19, can fail to install due to one or both of these issues:

1. Due to a unnecessary file in the Axway Installer folder:

The following errors can be seen in the install.log file:

ERROR javax.xml.parsers.DocumentBuilderFactory.setFeature(Ljava/lang/String;Z)V
ERROR Error on task Adding update  SecureTransport_5.3.1_Patch13: javax.xml.parsers.DocumentBuilderFactory.setFeature(Ljava/lang/String;Z)V

or

ERROR javax.xml.parsers.DocumentBuilderFactory.setFeature(Ljava/lang/String;Z)V
ERROR Error on task Adding update  SecureTransport_5.3.3_Patch6: javax.xml.parsers.DocumentBuilderFactory.setFeature(Ljava/lang/String;Z)V

2. Due to a known issue with MySQL itself.

The following errors can be seen in the install.log file:

Error    : Table 'mysql.innodb_index_stats' doesn't exist
status   : Operation failed
mysql.innodb_table_stats
Error    : Table 'mysql.innodb_table_stats' doesn't exist
status   : Operation failed
mysql.slave_master_info
Error    : Table 'mysql.slave_master_info' doesn't exist
status   : Operation failed
mysql.slave_relay_log_info
Error    : Table 'mysql.slave_relay_log_info' doesn't exist
status   : Operation failed
mysql.slave_worker_info
Error    : Table 'mysql.slave_worker_info' doesn't exist
status   : Operation failed
ERROR Error on task SynJTaskPatchRemove: Unable to backup file: /opt/TMWD/SecureTransport/mysql/bin/mysqld: missing the necessary rights.
ERROR Unable to rollback: Unable to backup file: /opt/TMWD/SecureTransport/mysql/bin/mysqld: missing the necessary rights. Copy the backup files from the directory /opt/TMWD/SecureTransport/synInstall/synPatch/006/ into your product installation /opt/TMWD/SecureTransport/. Delete the backup directory before installing or uninstalling another update.
ERROR Error on task Adding update  SecureTransport_5.3.1_Patch13: An error has occurred during pre-installation: Could not upgrade mysql server. Exiting

Resolution

In order to resolve issue number one:

1. Restore from a backup

2. Navigate to the Axway Installer folder

3. Change to the "Installer" subfolder

4. Delete the xercesImpl-2.6.2.jar file

5. Install the patch again

In order to resolve issue number two:

1. Restore from backup

2. Start only the database

$FILEDRIVEHOME/bin/start_db

3. Login to the MySQL prompt as explained in KB 178322.

4. At the MySQL prompt, change to the mysql database:

use mysql;

5. Execute the following queries:

DROP TABLE innodb_index_stats;
DROP TABLE innodb_table_stats;
DROP TABLE slave_master_info;
DROP TABLE slave_relay_log_info;
DROP TABLE slave_worker_info;
exit

NOTE: If you see errors like these, you can ignore them and still proceed with the next steps:

mysql> DROP TABLE innodb_index_stats;
ERROR 1051 (42S02): Unknown table 'mysql.innodb_index_stats'
mysql> DROP TABLE innodb_table_stats;
ERROR 1051 (42S02): Unknown table 'mysql.innodb_table_stats'
mysql> DROP TABLE slave_master_info;
ERROR 1051 (42S02): Unknown table 'mysql.slave_master_info'
mysql> DROP TABLE slave_relay_log_info;
ERROR 1051 (42S02): Unknown table 'mysql.slave_relay_log_info'
mysql> DROP TABLE slave_worker_info;
ERROR 1051 (42S02): Unknown table 'mysql.slave_worker_info'

6. Navigate to the $FILEDRIVEHOME/var/db/mysql/data/mysql/ folder.

7. Delete any .frm and .ibd files that start with:

innodb_index_stats
innodb_table_stats
slave_master_info
slave_relay_log_info
slave_worker_info

8. Login to the MySQL prompt as explained in KB 178322.

9. At the MySQL prompt, change to the mysql database:

use mysql;

10. Execute the following queries:

CREATE TABLE `innodb_index_stats` (
      `database_name` varchar(64) COLLATE utf8_bin NOT NULL,
      `table_name` varchar(64) COLLATE utf8_bin NOT NULL,
      `index_name` varchar(64) COLLATE utf8_bin NOT NULL,
      `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
      `stat_name` varchar(64) COLLATE utf8_bin NOT NULL,
      `stat_value` bigint(20) unsigned NOT NULL,
      `sample_size` bigint(20) unsigned DEFAULT NULL,
      `stat_description` varchar(1024) COLLATE utf8_bin NOT NULL,
      PRIMARY KEY (`database_name`,`table_name`,`index_name`,`stat_name`)
    ) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin STATS_PERSISTENT=0;

CREATE TABLE `innodb_table_stats` (
      `database_name` varchar(64) COLLATE utf8_bin NOT NULL,
      `table_name` varchar(64) COLLATE utf8_bin NOT NULL,
      `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
      `n_rows` bigint(20) unsigned NOT NULL,
      `clustered_index_size` bigint(20) unsigned NOT NULL,
      `sum_of_other_index_sizes` bigint(20) unsigned NOT NULL,
      PRIMARY KEY (`database_name`,`table_name`)
    ) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin STATS_PERSISTENT=0;

CREATE TABLE `slave_master_info` (
      `Number_of_lines` int(10) unsigned NOT NULL COMMENT 'Number of lines in the file.',
      `Master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL COMMENT 'The name of the master binary log currently being read from the master.',
      `Master_log_pos` bigint(20) unsigned NOT NULL COMMENT 'The master log position of the last read event.',
      `Host` char(64) CHARACTER SET utf8 COLLATE utf8_bin NOT NULL DEFAULT '' COMMENT 'The host name of the master.',
      `User_name` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The user name used to connect to the master.',
      `User_password` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The password used to connect to the master.',
      `Port` int(10) unsigned NOT NULL COMMENT 'The network port used to connect to the master.',
      `Connect_retry` int(10) unsigned NOT NULL COMMENT 'The period (in seconds) that the slave will wait before trying to reconnect to the master.',
      `Enabled_ssl` tinyint(1) NOT NULL COMMENT 'Indicates whether the server supports SSL connections.',
      `Ssl_ca` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The file used for the Certificate Authority (CA) certificate.',
      `Ssl_capath` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The path to the Certificate Authority (CA) certificates.',
      `Ssl_cert` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The name of the SSL certificate file.',
      `Ssl_cipher` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The name of the cipher in use for the SSL connection.',
      `Ssl_key` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The name of the SSL key file.',
      `Ssl_verify_server_cert` tinyint(1) NOT NULL COMMENT 'Whether to verify the server certificate.',
      `Heartbeat` float NOT NULL,
      `Bind` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'Displays which interface is employed when connecting to the MySQL server',
      `Ignored_server_ids` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The number of server IDs to be ignored, followed by the actual server IDs',
      `Uuid` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The master server uuid.',
      `Retry_count` bigint(20) unsigned NOT NULL COMMENT 'Number of reconnect attempts, to the master, before giving up.',
      `Ssl_crl` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The file used for the Certificate Revocation List (CRL)',
      `Ssl_crlpath` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The path used for Certificate Revocation List (CRL) files',
      `Enabled_auto_position` tinyint(1) NOT NULL COMMENT 'Indicates whether GTIDs will be used to retrieve events from the master.',
      PRIMARY KEY (`Host`,`Port`)
    ) ENGINE=InnoDB DEFAULT CHARSET=utf8 STATS_PERSISTENT=0 COMMENT='Master Information';

CREATE TABLE `slave_relay_log_info` (
      `Number_of_lines` int(10) unsigned NOT NULL COMMENT 'Number of lines in the file or rows in the table. Used to version table definitions.',
      `Relay_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL COMMENT 'The name of the current relay log file.',
      `Relay_log_pos` bigint(20) unsigned NOT NULL COMMENT 'The relay log position of the last executed event.',
      `Master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL COMMENT 'The name of the master binary log file from which the events in the relay log file were read.',
      `Master_log_pos` bigint(20) unsigned NOT NULL COMMENT 'The master log position of the last executed event.',
      `Sql_delay` int(11) NOT NULL COMMENT 'The number of seconds that the slave must lag behind the master.',
      `Number_of_workers` int(10) unsigned NOT NULL,
      `Id` int(10) unsigned NOT NULL COMMENT 'Internal Id that uniquely identifies this record.',
      PRIMARY KEY (`Id`)
    ) ENGINE=InnoDB DEFAULT CHARSET=utf8 STATS_PERSISTENT=0 COMMENT='Relay Log Information';

CREATE TABLE `slave_worker_info` (
      `Id` int(10) unsigned NOT NULL,
      `Relay_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
      `Relay_log_pos` bigint(20) unsigned NOT NULL,
      `Master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
      `Master_log_pos` bigint(20) unsigned NOT NULL,
      `Checkpoint_relay_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
      `Checkpoint_relay_log_pos` bigint(20) unsigned NOT NULL,
      `Checkpoint_master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
      `Checkpoint_master_log_pos` bigint(20) unsigned NOT NULL,
      `Checkpoint_seqno` int(10) unsigned NOT NULL,
      `Checkpoint_group_size` int(10) unsigned NOT NULL,
      `Checkpoint_group_bitmap` blob NOT NULL,
      PRIMARY KEY (`Id`)
    ) ENGINE=InnoDB DEFAULT CHARSET=utf8 STATS_PERSISTENT=0 COMMENT='Worker Information';

11. Exit from the prompt and stop the database:

$FILEDRIVEHOME/bin/stop_db

12. Install the patch again