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Note: This page applies only for 5.0.2 and before. For post 5.0.2, refer to the below two pages:
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
- Database: MySQL 5.7 or Oracle 11g/12c
- See database privileges section
- Java 8 JRE and JAVA_HOME is set.
- 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:
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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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If MySQL, remember to perform steps here MySQL prerequisites on Linux
Give executable permission using following command
chmod +xopenspecimen.sh- 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
- Open a browser(Chrome, Firefox, Safari, IE (11 and above only)
- 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.
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./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.
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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
Locale Configuration
For locale configuration, please refer: Locale Configuration
LDAP Integration
For LDAP configuration, please refer: LDAP Configuration