Versions Compared

Old Version 1

changes.mady.by.user Jim Blake

Saved on

compared with

New Version 2

changes.mady.by.user Jim Blake

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Excerpt

This section describes the process of getting VIVO up and running on your computer, for testing or experimentation, or just to gain familiarity with the process.

If you want to install VIVO on a production server, or if you want to develop VIVO code, you should also read the section on Installation options.

Table of Contents

Preparing for VIVO

Install required software

Before installing VIVO, make sure that the following software is installed on the desired machine:

...

  • Mac:
    • Chrome 30.0.1599.69 and above
    • FireFox 3.6.28, 10.0.12, 24
    • Opera 12.02
    • Safari 5.0.3
  • PC:
    • Chrome 25.1364.2 and above
    • FireFox 10.0.12, 24
    • Internet Explorer 8, 9, 10
    • Opera 12.02

Did it work?

You can test the software installation by typing these commands:

...

Each of these command should print a response that tells you what version is installed. If any of these commands prints an error message, or reports an unexpected version number, you should review your installation.

Create an empty database and a database account

Decide on a database name, username, and password.You will need these values for this step, and again when you Specify runtime properties.

...

Code Block
CREATE DATABASE dbname CHARACTER SET utf8;
GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';

Building VIVO

Download the VIVO source code

Download the VIVO application source as either rel-1.6.zip or rel-1.6.gz file and unpack it on your web server:
http://vivoweb.org/download

Specify build properties

At the top level of the VIVO distribution directory, copy the file example.build.properties to a file named simply build.properties. Edit the file to suit your installation, as described in the following table.

...

Property name

vitro.home

DescriptionThe directory where VIVO will store the data that it creates. This includes uploaded files (usually images) and the Solr search index. Be sure this directory exists and is writable by the Tomcat service.
Default valueNONE
Example value/usr/local/vivo/home

Compile and deploy

In the previous step, you defined the location of the VIVO home directory, by specifying vitro.home in the build.properties file. If that directory does not exist, create it now.

...

  • collecting the source files from the distribution directory,
  • compiling the Java source code,
  • compiling and running unit tests,
  • preparing the Solr search engine,
  • deploying VIVO and Solr to Tomcat.

Did it work?

The output of the build may include a variety of warning messages. The Java compiler may warn of code that is outdated. Unit tests may produce warning messages, and some tests may be ignored if they do not produce consistent results.

...

If the output ends with a failure message, the build has failed. Find the cause of the failure, fix the problem, and run the script again.

Running VIVO

Configure 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).

...

If an OutOfMemoryError is encountered during VIVO execution, it can be remedied by increasing the heap parameters and restarting Tomcat.

Set security limits

VIVO is a multithreaded web application that may require more threads than are permitted under your Linux installation's default configuration. Ensure that your installation can support the required number of threads by making the following edits to /etc/security/limits.conf:

Code Block
apache	hard	nproc	400
tomcat6	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.

...

Note

Some versions of Tomcat already include this attribute as the default.

Take care when creating Context elements

Each of the webapps in the VIVO distribution (VIVO and Solr) includes a "context fragment" file, containing some of the deployment information for that webapp.

...

See the section entitled Running VIVO behind an Apache server for an example of overriding the VIVO context fragment.

Specify runtime properties

The build process in the Compile and deploy step created a file called example.runtime.properties in your VIVO home directory (specified by vitro.home in the build.properties file). Rename this file to runtime.properties and edit the file to suit your installation, as described below.

...

Note

Windows: For those installing on Windows operating system, include the windows drive and use the forward slash "/" and not the back slash "\" in the directory locations, e.g. c:/tomcat.

Basic properties

These properties define some fundamental aspects of your VIVO installation. Most sites will need to modify all of these values.

...

Property name

email.replyTo

DescriptionSpecify an email address which will appear as the sender in e-mail notifications to users (Optional). If a user replies to the notification, this address will receive the reply. If a user's e-mail address is invalid, this address will receive the error notice. If this is left blank, users will not be notified of changes to their accounts.
Default valueNONE
Example valuevivoAdmin@my.domain.edu

Extended properties

These are properties that many sites will not need to modify.

...

Property name

proxy.eligibleTypeList

Description Types of individual for which we can create proxy editors. If this is omitted, defaults to http://www.w3.org/2002/07/owl#Thing
Default valueNONE
Example valuehttp://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization

Additional properties

The runtime.properties file can accept many additional properties, but most of them don't apply to the standard installation. If you choose any of the Installation options, you may need to set some of those properties.

Start Tomcat

Most Tomcat installations can be started by running startup.sh or startup.bat in Tomcat's bin directory. Start Tomcat and direct your browser to http://localhost:8080/vivo to test the application. Note that Tomcat may require several minutes to start VIVO.

...

If Tomcat does not start up, or the VIVO application is not visible, check the files in Tomcat's logs directory. Error messages are commonly found in [tomcat]/logs/catalina.out, [tomcat]/logs/vivo.all.log or [tomcat]/logs/localhost.log

Get started using VIVO

Log in and add RDF data

Direct your browser to the VIVO home page. Click the "Log in" link near the upper right corner. Log in with the rootUser.emailAddress that you set in the runtime.properties file. The initial password for the root account is rootPassword. When you first log in, VIVO will require you to change the password. When login is complete, the search index is checked and, if it is empty, a full index build will be triggered in the background, in order to ensure complete functionality throughout the site.

...

See more documentation for configuring VIVO, ingesting data, and manually adding data at http://vivoweb.org/support.

Set the Contact Email Address

If you have configured your application to use the "Contact Us" feature (email.smtpHost is set in the runtime.properties file), you will also need to add an email address to the VIVO application.  This is the email to which the contact form will submit. It can be a list server or an individual's email address.

...

If you set the email.smtpHost in the runtime.properties file, and do NOT provide an email address in this step, your users will see an error message instead of the expected contact form.

Review the VIVO terms of use

VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name" you assign in the "Site Information" form under the Site Admin area will be inserted into the "Terms of Use" statement. If you want to edit the text content more than just the "Site Name", the file can be found here:

...

Be sure to make the changes in your source files and deploy them to your tomcat so you don't lose your changes next time you deploy for another reason.

Was the installation successful?

If you have completed the previous steps, you have good indications that the installation was successful.

...