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Table of Contents

Note: This page applies only for pre-5.0.2. For 5.1 onwards, refer to the below two pages:

Deployment steps (5.1 onwards)

Upgrade OpenSpecimen steps (5.1 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:

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

Note: Use the second command when the test server dump is to be imported into the production database.

Code Block
languagebash
titleMySQL import dump file into database
mysql -u<username> -p<password> [database_name] < dumpfilename.sql

Oracle:

Code Block
languagebash
titleOracle export database user into dump file
expdp <username>/<password> full=y DIRECTORY=<DUMP_DIR> DUMPFILE=<dumpfilename.dmp> logfile=<logfile.log>
Code Block
languagebash
titleOracle import dump file into database user
impdp <username>/<password> DIRECTORY=<DUMP_DIR> DUMPFILE=<dumpfilename.dmp> REMAP_SCHEMA=<from_user>:<to_user> logfile=<logfile.log> transform=oid:n

Deployment Instructions (for Enterprise Edition)

  1. Unzip the installer file. Let's call the new folder OSPM_HOME
  2. Change directory to OSPM_HOME

For Windows:

  1. Double click on "openspecimen.exe" file which will start the installation wizard.
  2. Follow the steps to proceed.

For Linux:

...

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

...

Give executable permission using following command
chmod +xopenspecimen.sh

...

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

...

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.

...

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.

  • Consider installation directory is <install_home>.
  • The installer will check whether tomcat is already present with name ‘tomcat-as’ under <install_home>. If yes, it upgrades existing one, else it will install new tomcat with name ‘tomcat-as’ which will be used for the OpenSpecimen installation.
  • It will create ‘os-plugins’ directory in <install_home>, copy all plugins into this directory and use them for OpenSpecimen.
  • It will create ‘os-data’ directory in <install_home> and use the same for OpenSpecimen.

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.

This should not apply to most installations where Tomcat is used only to deploy OpenSpecimen. 

In GUI mode: Select appropriate overwrite options. 

  1. If "Yes/Yes to all" is selected,then it will use new database and tomcat port configuration.
  2. If "No/No to all" is selected,then it will use existing tomcat configuration for database and port.

For "command line mode"

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-data

If you are having different data directory other than this default one, then please perform any of the following operation:

1)Ifyouwantstousedefault data directory created by the installer, then please update the locations (like sprpath, consent path etc...) via "Settings" menu and move data manually from older location to newer one.

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.

If user wants to install the service (which requires root privileges) then installer will install tomcat service with name "openspecimen" and will set this service to auto-start. 

If the user is not interested in installing service then it will start apache tomcat server once, and user will manually have to setup the service.

- It will start service with max heap size 2 GB.

For Windows:

-Set as service: Service can be started/stopped from windows services.

-Service not set: Use the below command:

  • Open command prompt
  • Go to ${TOMCAT_HOME}/bin
  • ./catalina.bat start
  • ./catalina.bat stop

For Linux:

-Set as a service:

...

-Service not set:

  • Open command prompt
  • Go to ${TOMCAT_HOME}/bin
  • ./catalina.sh start
  • ./catalina.sh stop

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

...

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