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Completing the Installation

Configure the

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Home Directory

There are two configuration files that are required to be in the home directory. By default, the installer does not create them so that they are not overwritten when you redeploy the application. Instead, example files are created in the home directory, which can be copied and used as the basis for your installation.The default configuration of VIVO is to use MySQL as a backing store for Jena SDB. Whilst VIVO / Jena will create the necessary tables for the triple store, a database (schema) and authentication details need to have been created first. To do so, log in to MySQL as a superuser (e.g. root) 

$ mysql -u root -p
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 2
Server version: 5.7.9 MySQL Community Server (GPL)
Copyright (c) 2000, 2015, Oracle and/or its affiliates. All rights reserved.
Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
 
mysql> CREATE DATABASE vitrodb CHARACTER SET utf8;
mysql> GRANT ALL ON vitrodb.* TO 'vitrodbUsername'@'localhost' IDENTIFIED BY 'vitrodbPassword';
mysql> FLUSH PRIVILEGES;

For MySQL 8+, the second command must be split into two commands like so:

mysql> CREATE USER 'vitrodbUsername'@'localhost' IDENTIFIED BY 'vitrodbPassword';
mysql> GRANT ALL PRIVILEGES ON vitrodb.* TO 'vitrodbUsername'@'localhost';
mysql> FLUSH PRIVILEGES;

Configure the Home Directory

There are two configuration files that are required to be in the home directory. By default, the installer does not create them so that they are not overwritten when you redeploy the application. Instead, example files are created in the home directory, which can be copied and used as the basis for your installation.

$ cd /usr/local/vivo/home/config
/usr/local/vivo/home/config$ cp example.runtime.properties runtime.properties
/usr/local/vivo/home/config$ cp example.applicationSetup.n3 applicationSetup.n3

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In order for your installation to work, you will need to edit runtime.properties and ensure that the VitroConnection properties are correct for your database engine. They should look something like this.

VitroConnection.DataSource.url = jdbc:mysql://localhost/vitrodb
VitroConnection.DataSource.username = vitrodbUsername
VitroConnection.DataSource.password = vitrodbPassword

cd /usr/local/vivo/home/config
/usr/local/vivo/home/config$ cp example.runtime.properties runtime.properties
/usr/local/vivo/home/config$ cp example.applicationSetup.n3 applicationSetup.n3

Configure the Database Schema

Optionally, you may choose to use the older Jena SDB database backed by MySQL. SDB is not recommended for new installations, however it may offer some situation-dependent advantages for some users. For more information on SDB setup, see Jena SDB and MySQL setup.

Configure and Start Solr

Configure and Start Solr

Starting with the 1.11.0 release of VIVO, Solr must be independently deployed and configured with the schema expected by VIVO. VIVO must then be configured to connect to the external Solr.

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