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Table of Contents


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

...

Database Privileges

 Refer to Database Configuration

Database Import/Export

MySQL:


Code Block
languagebash
titleMySQL export database into dump file
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

...

  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
    languagebash
    titleStart 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
    languagebash
    titleCommand 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_serviceWhether 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_typeDB which you are going to use for installing OpenSpecimen (mysql / oracle).
    database_createOnlyappliesforMySQLdatabase.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_nameName of the database will be used for OpenSpecimen.
    database_hostHostname of the database server.
    database_portThe port on which database is running (default port are: MySQL - 3306 / Oracle - 1521).
    database_userDatabase user name.
    database_passwordDatabase password.
    app_server_portThe port on which Apache tomcat will start.
    app_hostHostname 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_nameFirst name of the super admin user.
    last_nameLast name of the super admin user.
    emailThe email address of the super admin user (This will be used as login name as well).
    passwordPassword for super adminusertologinintoOpenSpecimen.
    instituteName 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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Code Block
languagebash
titleInstall OpenSpecimen with overwriting existing tomcat
./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.

...

<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.

...

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

Locale Configuration

For locale configuration, please refer: Locale Configuration

LDAP Integration

For LDAP configuration, please refer: LDAP Configuration