VIVO Documentation
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Overview
Download the 1.9.x distribution release from the VIVO repository on GitHub. The standard distribution consists of just the projects required to create a home directory for VIVO, and to copy the web application and search index. All of the compiled code , and dependencies are resolved from the Maven central repository at the time you run Maven.
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vivo-1.9.0-rel3/ pom.xml example-settings.xml home/ pom.xml src solr/ pom.xml src webapp/ pom.xml src |
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Preparing the Installation Settings
In order to fully To install VIVO, you need to create a settings file that provides some essential information:
app-name
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This file needs to be created following the Maven Settings Reference. A template file already exists within the VIVO projectstandard distribution, called "example-settings.xml". You may copy this file (it can be called anything you like), and edit the contents to fit your requirements / system configuration.
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Once you have an appropriate settings file (these instructions will assume 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.
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$ cd VIVO VIVO$ mvn install -s example-settings.xml [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [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] .... |
The VIVO home directory will now be created , and the VIVO application installed to Tomcat.
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$ git clone https://github.com/vivo-project/Vitro.git Vitro -b developmaint-rel-1.9 $ git clone https://github.com/vivo-project/VIVO.git VIVO -b developmaint-rel-1.9 $ ls -l drwxr-xr-x user group 1 Dec 12:00 Vitro drwxr-xr-x user group 1 Dec 12:00 VIVO |
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Once you have an appropriate settings file (these instructions will assume that you are using installer/example-settings.xml - replace this with your actual file), you simply need to run Maven, specifying the install goal , and your settings file.
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$ cd VIVO VIVO$ mvn install -s installer/example-settings.xml [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [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] .... |
The VIVO home directory will now be created , and the VIVO application installed to Tomcat.
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Custom InstallerIf you want to use the source code / GitHub clone with your own customisationscustomizations, 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" property. This can be done on the command line , or in the settings.xml. If you are supplying a relative path, it should be relative to the location of the VIVO/pom.xml.
The VIVO home directory will now be created , and the VIVO application installed to Tomcat, including any customizations that are defined in your local installer project. |
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the Installation
Configure the Database Schema
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$ 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 vivodbvitrodb CHARACTER SET utf8; mysql> GRANT ALL ON vivodbvitrodb.* TO 'vitrodbUsername'@'localhost' IDENTIFIED BY 'vitrodbPassword'; |
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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.
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$ cd /usr/local/vivo/home
/usr/local/vivo/home$ cp config/example.runtime.properties runtime.properties
/usr/local/vivo/home$ cd config
/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 the runtime.properties , and ensure that the VitroConnection properties are correct for your database engine. They should look something like this.
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Configure and Start Tomcat
Set JVM parameters
VIVO copies small sections of your RDF database into memory in order to serve Web requests quickly (the in-memory copy and the underlying database are kept in synch as edits are performed).
VIVO may require more memory than that allocated to Tomcat by default. With most installations of Tomcat, the setenv.sh or setenv.bat file in Tomcat's bin directory is a convenient place to set the memory parameters. If this file does not exist in Tomcat's bin directory, you can create it.
For example:
export CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=128m" |
This tells Tomcat to allocate an initial heap of 512 megabytes, a maximum heap of 512 megabytes, and a PermGen space of 128 megs. Larger values may be required, especially for production installations in large enterprises. In general, VIVO runs more quickly if given more memory.
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VIVO is a multithreaded web application that may require more threads than are permitted under your Linux operating system's installation's default configuration. Ensure that your installation can support the required number of threads by making for your application. For a Linux production environment you may wish to make the following edits to /etc/security/limits.conf:, replacing apache and tomcat with the appropriate user or group name for your setup:
apache hard nproc 400 |
tomcat hard nproc 1500 |
Set URI encoding
In order for VIVO to correctly handle international characters, you must configure Tomcat to conform to the URI standard by accepting percent-encoded UTF-8.
Edit Tomcat's conf/server.xml and add the following attribute to each of the Connector elements: URIEncoding="UTF-8".
<Server ...> <Service ...> <Connector ... URIEncoding="UTF-8"/> ... </Connector> </Service> </Server> |
Some versions of Tomcat already include this attribute as the default. |
Take care when creating Context elements
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- When you Start tomcat, you see that Tomcat recognizes the webapp, and that the webapp is able to present the initial page.When you Log in and add RDF data, you verify that you can log in to the root VIVO account.
- The startup status will indicate if the basic configuration of the system was successful. If there were any serious errors, you will see the status screen and will not be allowed to continue with VIVO. If there are warnings, you will see the status screen when you first access VIVO, but after that you may use VIVO without hinderance. In this case, you can review the startup status
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- from siteAdmin -> Startup status.
- Log in as root. Your root username is vivo_root@yourdomainname . The first time root password is rootPassword. You will be asked to change it.
Here is a simple test to see Here is a simple test to see whether the ontology files were loaded:
- Click on the "Index" link on the upper right, below the logo. You should see a "locations" section, with links for "Country" and "Geographic Location." The index is built in a background thread, so on your first login , you may see an empty index instead. Refresh the page periodically to see whether the index will be populated. This may take some time: with VIVO installed on a modest laptop computer, loading the ontology files and building the index took more than 5 minutes from the time that Tomcat was started.
- Click on the "Country" link. You should see an alphabetical list of the countries of the world.
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- Point your browser to the home page of your website , and click the "Log in" link near the upper right corner. Log in with the rootUser.emailAddress you set in runtime.properties. If this is your first time logging in, you will be prompted to change the password.
- After you have successfully logged in, click "site admin" in the upper right corner. In the drop down under "Data Input" select "Faculty Member(core)" and click the "Add individual of this class" button.
- Enter the name "test individual" under the field "Individual Name," scroll to the bottom, and click "Create New Record." You will be taken to the "Individual Control Panel." Make note of the value of the field "URI" - it will be used in the next step.
- Open a new web browser or browser tab to the page http://marbleslodview.sourceforge.netit/. In the pink box on that page enter the Enter the URI of the individual you created in the previous step and click "opengo."
- In the resulting page search for the URI of the "test individual." You should find it towards the bottom of the page next to a red dot followed by "redirect (303)." The page should display information for the individual, including an rdfs:label and rdf:type. This indicates that you are successfully serving linked RDF data. If the URI of the "test individual" is followed by "failed (400)" service returns an error you are not successfully serving linked data.
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- Type the word "Australia" into the search box, and click on the Search button.You should see a page of results, with links to countries that border Australia, individuals that include Australia, and to Australia itself. To trigger a rebuild of the search index, you can log in as a site administrator and go to Site Admin -> Rebuild search index.