Note: This page applies only for 5.0.2 and before. For post 5.0.2, refer to the below two pages:

Fresh deployment steps (5.0.2 onwards)

Upgrade OpenSpecimen steps (5.0.2 onwards)

Download Latest OpenSpecimen

For Enterprise customers: For download details, please email contact@openspecimen.org

For Community edition: Download the code from Github  and follow steps on How to build from code?)

Prerequisites

1. Database: MySQL 5.7 or Oracle 11g/12c
2. See database privileges section
3. Java 8 JRE and JAVA_HOME is set.
4. MySQL on Linux: MySQL prerequisites on Linux

Please visit the respective download centres and download the latest version available for your operating system:

• MySQL (Ignore if you are going to use Oracle)
• JAVA
• Tomcat
• Apache for Linux
• Apache for Windows

Database Privileges

 Refer to Database Configuration

Database Import/Export

MySQL:

mysqldump -u<username> -p<password> --routines [database_name] > dumpfilename.sql

mysqldump -u<username> -p<password> --routines [database_name] | grep -v 'SQL SECURITY DEFINER' > dump.sql

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1. If MySQL, remember to perform steps here MySQL prerequisites on Linux 

2. Give executable permission using following command
   chmod +xopenspecimen.sh

3. You can install OpenSpecimen using one of below ways:
   

   1) GUI Mode

       With this mode, you can install OpenSpecimen with graphical user interface as follow:

   Code Block
   language bash title Start Installer wizard (Tomcat service will not be installed)
   ./openspecimen.sh

   
   

   2) Unattended mode

       With this mode first you must need to fill all valid values in properties.varfile (present in zip).

   Code Block
   language bash title Command to start installer in Unattended mode
   sudo ./openspecimen.sh -q -varfile properties.varfile

   
   

   Properties.varfile

   install_home	Valid directory path where OpenSpecimen needs to be installed.
   install_service	Whether to install tomcat as a service or not.yes- It will install tomcat service with name 'openspecimen' and will set it as an auto startup (Requires super admin privileges).no- It will not install tomcat service, but will start tomcat normally during installation.
   database_type	DB which you are going to use for installing OpenSpecimen (mysql / oracle).
   database_create	OnlyappliesforMySQLdatabase.yes- It will create a database with the specified name and will use same for OpenSpecimen.no- It won't create a new database, it will use existing database with the name provided in database_name.
   database_name	Name of the database will be used for OpenSpecimen.
   database_host	Hostname of the database server.
   database_port	The port on which database is running (default port are: MySQL - 3306 / Oracle - 1521).
   database_user	Database user name.
   database_password	Database password.
   app_server_port	The port on which Apache tomcat will start.
   app_host	Hostname of the application server.
   deployment_environment	development : It will set tomcat logging to Info, and will enable hibernate query logging. production : It will set tomcat logging to Error only, and will disable hibernate query logging.
   first_name	First name of the super admin user.
   last_name	Last name of the super admin user.
   email	The email address of the super admin user (This will be used as login name as well).
   password	Password for super adminusertologinintoOpenSpecimen.
   institute	Name of the institute whichwillbecreatedinOpenSpecimenon which super admin will get registered.

   
   

Accessing OpenSpecimen

1. Open a browser(Chrome, Firefox, Safari, IE (11 and above only)
2. Type in: http://<SERVER_IP_ADDRESS>:<APP_SERVER_PORT>/openspecimen/
   E.g. http://localhost:8080/openspecimen

Upgrading existing versions of OpenSpecimen via Installer

Below are the few assumptions made during installation/upgradation.

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NOTE: So while upgrading OpenSpecimen using an installer, please make sure the directory structure should be same as described above.

Tomcat Configuration Overwrite Policy

This applies only if you are installing OpenSpecimen on an existing Tomcat OR you have made some configuration changes OR have other applications deployed.

...

./openspecimen.sh -q -varfile properties.varfile -overwrite

Fresh/Upgrade: Data source handling

Data Source property for upgrading OpenSpecimen from OS 1.x to OS X.x via installer is handled automatically, no need to take extra care for this, the installer will automatically use relevant data source property.

Default Data Directory

Installer by default will create data directory with name "os-data" in the installation directory.

...

2) If you want to use existing data directory, make sure directory is present & same location is used in "Settings" menu.

Plugin Directory

Installer by default will create plugin directory with name "os-plugins" in installation directory & will use the plugin from there only.

<installer-dir>/os-plugins

Super Admin Creation Via Installer

The installer will create a super admin only if there is no super admin present in the system.

Start/Stop OpenSpecimen server

OpenSpecimen(v3.3 onwards) installer supports the installation of Apache tomcat service, which is optional.

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Refer to wiki page to create tomcat service manually

Plugin Deployment

Download and copy the plugin jar under ${install_home}/os-plugin directory. After copying the plugin you need to restart the tomcat.

Email Configuration

For email configuration, please refer: Email Configuration