Please ensure that the database user used to deploy Open Specimen has the following privileges. Failing to grant any of the mentioned privileges will result in deployment failure. The attribute username on this page defines the username of the database and not the login name used to log on to Open Specimen.

MySQL

Port

Default port: 3306

If MySQL is on a different server then you also need to open the MySQL port for communicating with OpenSpecimen

Privileges

Either the user should be a MySQL root user or have the following privileges

ALTER
ALTER ROUTINE
CREATE
CREATE ROUTINE
CREATE VIEW
DELETE
DROP
EXECUTE
INDEX
INSERT
LOCK TABLES
SELECT
TRIGGER
UPDATE
REFERENCES

SQL:

GRANT ALTER, ALTER ROUTINE, CREATE, CREATE ROUTINE, CREATE VIEW, DELETE, DROP, EXECUTE, INDEX, INSERT, LOCK TABLES, SELECT, TRIGGER, UPDATE, REFERENCES ON <DATABASE-NAME>.* TO <USERNAME>

Setting INNODB

Please set the property default-storage-engine=INNODB. After the changes made, the Mysql server restart is needed.

This property is available in my.ini file in case of Windows and my.cnf in the case of Linux.

Backup

In the case of an upgrade, take a manual backup of the database, this will create a backup dump on the database server machine.

mysqldump -u<user> -p<password> --single-transaction --skip-lock-tables --routines database name | gzip > OPENSPECIMEN_`date +\%d-\%m-\%Y`.SQL.gz

Oracle

Port

Default port: 1521

If Oracle is on different servers, then you also need to open the Oracle port for communicating with OpenSpecimen.

Privileges

Either the user should be an Oracle sysdba user or have the following privileges

CONNECT
RESOURCE
CREATE ANY TABLE
DROP ANY TABLE
CREATE ANY TRIGGER
DROP ANY TRIGGER
CREATE ANY VIEW
DROP ANY VIEW
CREATE ANY PROCEDURE
DROP ANY PROCEDURE
CREATE ANY SEQUENCE
DROP ANY SEQUENCE

The use of ANY allows user to perform the operation in any schema. Droping ANY will restrict users to perform the aforementioned operations only within their own schema.

SQL:

GRANT CONNECT, RESOURCE, CREATE ANY TABLE, DROP ANY TABLE, CREATE ANY TRIGGER, DROP ANY TRIGGER, CREATE ANY VIEW, DROP ANY VIEW, CREATE ANY PROCEDURE, DROP ANY PROCEDURE, CREATE ANY SEQUENCE, DROP ANY SEQUENCE TO <USERNAME>

Note: If you are using the ORACLE database, it is mandatory to install the Oracle client on the machine that is hosting the Tomcat/JBoss server. Ensure that the system variable ORACLE_HOME is set properly and the system variable PATH contains ORACLE_HOME/bin.

Backup

In case of an upgrade, take the manual of the database backup, this will create a backup dump on the database server machine.

expdp <user name>/<password here>@<database name> schemas=<user name> DIRECTORY=DATA_PUMP_DIR DUMPFILE=<filename> flashback_time=systimestamp

Import the dump and check the table count and records count per table, should match with original DB.

Best practices to follow

Set a strong password (the combination of alphanumeric and special characters) for the database user.

MySQL

Do not use root user for connection from OpenSpecimen.
Create a separate user for the database for OpenSpecimen and provide access to this database only. Use below command:

GRANT ALL PRIVILEGES ON <DataBase name>.* To '<user>'@'<db host>' IDENTIFIED BY '<password>';
  
Note: DB host could be localhost or actual server name or IP. Specify '%' to give access for any host.

Oracle:

Create and assign separate tablespace to the OpenSpecimen user.