1. Genesys PGR
  2. Genesys Server
  3. genesys2-server

Overview

HTTPS SSH

Genesys PGR - Gateway to genetic resources

Note: This is the source code of the Genesys PGR Portal implementation running at https://www.genesys-pgr.org

These instructions will help you run a copy of the Genesys portal (without the data) for testing and development purposes.

Running genesys2-server with jetty

Obtain a copy of genesys2-server-X.Y.Z-jetty.zip archive by building the project. The zip can be found in target/ directory.

$ mvn clean package

Download a stable-9 copy of jetty and unpack it to your favorite location.

Unpack genesys2-server-X.Y.Z-jetty.zip archive and move its contents into the jetty directory, next to existing demo-base and webapps directories.

Start jetty from the genesys2-server-X.Y.Z-jetty base

$ cd genesys2-server-X.Y.Z-jetty/
$ java -jar ../start.jar

STDOUT is used for logging.

This configuration uses HSQL database and is intended for testing genesys2-server. To change the database settings, edit genesys2-server-X.Y.Z-jetty/resources/genesys.properties file:

# mysql
db.url=jdbc:mysql://localhost/genesys?useUnicode=true&characterEncoding=UTF-8&useFastDateParsing=false
db.driverClassName=com.mysql.jdbc.Driver
db.username=root
db.password=mysql
hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect

The complete list of available configuration options and their default values can be found in spring.properties.

Running genesys2-server with maven

  • Clone genesys2-server to your computer
  • Create a blank mysql database
  • Configure genesys2-server database connection settings
  • Start Jetty with mvn -Dspring.profiles.active=dev jetty:run

Creating a mysql database

Connect to your mysql instance and create a new blank database genesys2:

# Create database
CREATE DATABASE genesys2 DEFAULT CHARSET UTF8;

# Create user genesys with password pwd
GRANT ALL ON genesys2.* TO 'genesys'@'localhost' IDENTIFIED BY 'pwd';

Change the settings in src/main/resources/spring/spring.properties:

# genesys2 with mysql database
db.url=jdbc:mysql://localhost/genesys2?useUnicode=true&characterEncoding=UTF-8&useFastDateParsing=false
db.driverClassName=com.mysql.jdbc.Driver
hibernate.dialect=org.hibernate.dialect.MySQL5Dialect
db.username=genesys
db.password=pwd
db.showSql=false
# Allow hibernate to update database (development/testing mode only)
db.hbm2ddl=update