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Be sure to review S= ystem Requirements before installing VIVO.
Download the distribution from the VIVO repository on GitHub. The standard distribution consists of = the projects required to create a home directory for VIVO, and to copy the = web application and search index. All the compiled code and dependencies ar= e resolved from the Maven central repository at the time you run Maven.
The standard distribution is laid out as follows:
vivo-1.= 10.0/ pom.xml example-settings.xml home/ pom.xml src solr/ pom.xml src webapp/ pom.xml src
In order to fully install VIVO, you need to create a settings file that = provides some essential information:
app-name
vivo-dir
tomcat-dir
This file needs to be created following the Maven = Settings Reference. A template file already exists within = the VIVO standard distribution, called "example-settings.xml". You m= ay copy this file (it can be called anything you like), and edit the conten= ts to fit your requirements / system configuration.
Make sure:
Once you have an appropriate settings file (these instructions will assu= me that you are using example-settings.xml - replace this with your actual = file), you simply need to run Maven, specifying the install goal and your settings file.
$ cd VI= VO VIVO$ mvn install -s example-settings.xml [INFO] Scanning for projects... [INFO] --------------------------------------------------------------------= ---- [INFO] Reactor Build Order: [INFO]=20 [INFO] Vitro [INFO] Vitro Dependencies [INFO] Vitro API [INFO] VIVO [INFO] VIVO API [INFO] Vitro Web App [INFO] VIVO Web App [INFO] Vitro Home [INFO] VIVO Home [INFO] Vitro Solr App [INFO] VIVO Installer [INFO] VIVO Prepare Home [INFO] VIVO Prepare Solr App [INFO] VIVO Prepare Web App [INFO] = =20 ....
The VIVO home directory will now be created and the VIVO application ins= talled to Tomcat.
In order to run VIVO, please read the section below "Completing the Installation".
In order to install the development code from GitHub, you need to clone = both the Vitro and VIVO repositories from the vivo-project organization. Th= ese clones should be in sibling directories called "Vitro" and "VIVO" = respectively:
$ git c= lone https://github.com/vivo-project/Vitro.git Vitro -b rel-1.10-maint $ git clone https://github.com/vivo-project/VIVO.git VIVO -b rel-1.10-maint $ ls -l drwxr-xr-x user group 1 Dec 12:00 Vitro drwxr-xr-x user group 1 Dec 12:00 VIVO
If you do not place the Vitro code in a sibling directory called "Vitro"= , then you will have to supply the "vitro-core" property to Maven - e.g. mv= n package -Dvitro-core=3D~/Vitro
It is expected that the Maven project numbers are kept in sync between t= he Vitro / VIVO projects, however, depending on when you update / sync your= repositories, you may need to adjust the project version numbers for the b= uild to work.
In order to fully install VIVO, you need to create a settings file that = provides some essential information:
app-name
vivo-dir
tomcat-dir
This file needs to be created following the Maven Setti= ngs Reference. A template file already exists in the "installer" direct= ory within the VIVO project, called "example-settings.xml". You may copy th= is file (it can be called anything you like), and edit the contents to fit = your requirements / system configuration.
Make sure:
Once you have an appropriate settings file (these instructions will assu= me that you are using installer/example-settings.xml - replace this with yo= ur actual file), you simply need to run Maven, specifying the install goal = and your settings file.
$ cd VI= VO VIVO$ mvn install -s installer/example-settings.xml [INFO] Scanning for projects... [INFO] --------------------------------------------------------------------= ---- [INFO] Reactor Build Order: [INFO]=20 [INFO] Vitro [INFO] Vitro Dependencies [INFO] Vitro API [INFO] VIVO [INFO] VIVO API [INFO] Vitro Web App [INFO] VIVO Web App [INFO] Vitro Home [INFO] VIVO Home [INFO] Vitro Solr App [INFO] VIVO Installer [INFO] VIVO Prepare Home [INFO] VIVO Prepare Solr App [INFO] VIVO Prepare Web App [INFO] = =20 ....
The VIVO home directory will now be created and the VIVO application ins= talled to Tomcat. To run VIVO, please read the section below "Completing the Installation".
If you want to use the source code / GitHub clone with your own cu= stomizations, you can exclude the supplied installer project, and use your = own customized installer project instead. To do so, you need to supply the = location of your custom installer project as the "vivo-installer-dir" prope= rty. This can be done on the command line or in the settings.xml. If you ar= e supplying a relative path, it should be relative to the location of the V= IVO/pom.xml.
$ cd VI= VO VIVO$ mvn install -s installer/example-settings.xml -Dvivo-installer-dir=3D= ../myedu-vivo [INFO] Scanning for projects... [INFO] --------------------------------------------------------------------= ---- [INFO] Reactor Build Order: [INFO]=20 [INFO] Vitro [INFO] Vitro Dependencies [INFO] Vitro API [INFO] VIVO [INFO] VIVO API [INFO] Vitro Web App [INFO] VIVO Web App [INFO] Vitro Home [INFO] VIVO Home [INFO] Vitro Solr App [INFO] Custom VIVO Installer [INFO] Custom VIVO Prepare Home [INFO] Custom VIVO Prepare Solr App [INFO] Custom VIVO Prepare Web App [INFO] = =20 ....
The VIVO home directory will now be c= reated and the VIVO application installed to Tomcat, including any customiz= ations that are defined in your local installer project. To run = VIVO, please read the section below "Completing the 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 trip= le 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) = p>
$ 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 stateme= nt. mysql> CREATE DATABASE vitrodb CHARACTER SET utf8mb4 COLLATE utf8mb4_uni= code_ci; mysql> GRANT ALL ON vitrodb.* TO 'vitrodbUsername'@'localhost' IDENTIFIE= D BY 'vitrodbPassword';
For MySQL 8+, the second command must be split into two commands like so= :
mysql&g= t; CREATE USER 'vitrodbUsername'@'localhost' IDENTIFIED BY 'vitrodbPassword= '; mysql> GRANT ALL PRIVILEGES ON vitrodb.* TO 'vitrodbUsername'@'localhost= ';
There are two configuration files that are required to be in the home di= rectory. By default, the installer does not create them so that they are no= t overwritten when you redeploy the application. Instead, example files are= created in the home directory, which can be copied and used as the basis f= or your installation.
$ cd /u= sr/local/vivo/home/config /usr/local/vivo/home/config$ cp example.runtime.properties runtime.properti= es /usr/local/vivo/home/config$ cp example.applicationSetup.n3 applicationSetu= p.n3
Minimum Configuration of runtime.prope= rties Required
In order for your installation to work, you will need to edit runt=
ime.properties
and ensure that the VitroConnection properties are co=
rrect for your database engine. They should look something lik=
e this.
VitroCo= nnection.DataSource.url =3D jdbc:mysql://localhost/vitrodb VitroConnection.DataSource.username =3D vitrodbUsername VitroConnection.DataSource.password =3D vitrodbPassword
VIVO copies small sections of your RDF d= atabase into memory in order to serve Web requests quickly (the in-memory c= opy and the underlying database are kept in synch as edits are performed).<= /span>
VIVO may require more memory than alloca=
ted to Tomcat by default. With most installations of Tomcat, the
For example:
expor= t CATALINA_OPTS=3D"-Xms512m -Xmx512m -XX:MaxPermSize=3D128m" |
This tells Tomcat to allocate an initial= heap of 512 megabytes, a maximum heap of 512 megabytes, and a PermGen spac= e of 128 megs. Larger values may be required, especially for production ins= tallations in large enterprises. In general, VIVO runs more quickly if give= n more memory.
If an OutOfMem= oryError occurs during VIVO execution, increase t= he heap parameters and restart Tomcat.
VIVO is a multithreaded web application = that may require more threads than are permitted under the default configur= ation of your operating system. Ensure that your installation can support t= he required number of threads for your application. For a Linux produ= ction environment you may wish to make the following edits to /etc/security/limits.conf, replacing apache and tomcat with th= e appropriate user or group name for your setup:<= /span>
apach= e hard nproc 400 tomcat hard <= /span>nproc 1500= |
In order for VIVO to correctly handle in= ternational characters, you must configure Tomcat to conform to the URI sta= ndard by accepting percent-encoded UTF-8.
Edit Tomcat's = conf/server.xml and add the following attribute t= o each of the Connector elements: URIEncoding=3D"UTF-8".
<S= erver ...> <Service ...> <Connector ... URIEncoding=3D"UTF-8"/><= /strong> = ... &= nbsp; </Connector> </Service> </Server> |
Some = versions of Tomcat already include this attribute as the default.<= /span> |
Each of the webapps in the VIVO distribu= tion (VIVO and Solr) includes a "context fragment" file, containing some of= the deployment information for that webapp.
Tomcat allows you to override these cont= ext fragments by adding Context elements to serve= r.xml. If you decide to do this, be sure that you= r new Context element includes the necessary deployment parameters from the= overridden context fragment.
If everything has been completed successfully, then you should simply be= able to start Tomcat at this point, and VIVO will be available. If you are= using a Tomcat supplied by your operating system / package manager, then u= se your normal means for starting the application server.
Otherwise, start Tomcat by running the startup script - e.g.
$ /usr/= local/tomcat/bin/startup.sh
If you have completed the previous steps= , you have good indications that the installation was successful.
Here is a simple test to see whether the= ontology files were loaded:
Here is a test to see whether your syste= m is configured to serve linked data:
Finally, test the search index.= p>