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Excerpt

How to get VIVO up and running on your computer, for testing or experimentation, or just to gain familiarity with the processlearn how to do it.

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.

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

Be sure to set Set up the environment variables for JAVA_HOME and ANT_HOME and add the executables to your path, as required. This requirement depends on the operating system you are using. Consult the installation directions from the software support websites.

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Log into your MySQL server and create a new database in MySQL that uses UTF-8 encoding. At the MySQL command line you can create the database and user with these commands substituting your values for dbname, username, and password. Most of the time, the hostname will be localhost.

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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

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

These properties are used in compiling VIVO and deploying it to Tomcat. They will be incorporated into VIVO when it is compiled. If you want to change these properties at a later date, you will need to stop Tomcat, repeat the Compile and deploy step, and restart Tomcat.

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Property name

vitro.core.dir

DescriptionThe directory where Vitro code is located. In most deploymentsthe simple installation, this is set to ./vitro-core (It is not uncommon for this setting to point elsewhere in development environments).
Default valueNONE
Example value./vitro-core

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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.

 

At the command line, from the top level of the VIVO distribution directory, type:

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The build script may run for as much as five minutes, and creates more than 100 lines of output. The process comprises includes several steps:

  • 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?

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If the output ends with a success message, the build was successful. Proceed to the next step.

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BUILD SUCCESSFUL

Total time: 1 minute 49 seconds

If the output ends with a success failure message, the build was successful. Proceed to the next step.

BUILD FAILED
Total time: 35 seconds

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has failed. Find the cause of the failure, fix the problem, and run the script again.

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BUILD FAILED

Total time: 35 seconds

The output of the build may include 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 success message, these warnings may be ignored.

Note

What user account owns the VIVO directories?

In many operating systems, the issue of file permissions is important. Who owns the files? Who is authorized to read them, or to write new files?

When running the VIVO build script, it must have permission to read and write to:

  • the VIVO distribution directory
  • the Tomcat webapps directory
  • the VIVO home directory

When VIVO is started under Tomcat, Tomcat must have permission to read and write to:

  • the Tomcat webapps directory
  • the VIVO home directory

There are several ways to make this work. People who are experimenting with VIVO often use their own account to create the VIVO distribution directory, to run the build script, and to run Tomcat.

In more formal environments, it may be necessary to run Tomcat as a service, under its own account. In that case, some people choose to run the build script with root privilege, and then assign the resulting files to Tomcat:

Code Block
sudo ant all
sudo chown -R tomcat /usr/local/vivo/home
sudo chown -R tomcat /usr/local/tomcat/webapps/vivo*

When installing on Microsoft Windows, this is not usually a problem.

Running VIVO

Configure Tomcat

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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:

Code Block
titlesetenv.sh
export CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=128m"

This configures tells Tomcat to allocate an initial heap of 512 megabytes, a maximum heap of 512 megabytes, and a PermGen space of 128 megs. Lower values may be sufficient, especially for small test installations.

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

Set security limits

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Property name

Vitro.defaultNamespace

Description

The default RDF namespace for this installation.

VIVO installations make their RDF resources available for harvest using linked data. Requests for RDF resource URIs redirect to HTML or RDF representations as specified by the client. To make this possible, VIVO's default namespace must have a certain structure and begin with the public web address of the VIVO installation. For example, if the web address of a VIVO installation is "http://vivo.example.edu/" the default namespace must be set to "http://vivo.example.edu/individual/" in order to support linked data. Similarly, if VIVO is installed at "http://www.example.edu/vivo" the default namespace must be set to "http://www.example.edu/vivo/individual/"

* The namespace must end with "individual/" (including the trailing slash).

Default valueNONE
Example valuehttp://vivo.mydomain.edu/individual/

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Property name

VitroConnection.DataSource.url

Description Specify the JDBC URL of your database. Change the end of the URL to reflect your database name (if it is not "vivovitrodb").
Default valueNONE
Example valuejdbc:mysql://localhost/vivo

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The runtime.properties file can accept many additional properties, but they aren't necessary for this simple installation. If you choose any of the Installation options, you will likely probably need to set some of those properties.

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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

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Note

Remember that Tomcat must have permission to read and write its own files, and the files in the VIVO home directory. This may mean that you must use a particular script or a particular user account to start Tomcat.

 

Start 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.

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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 up in Step IVin 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://marbles.sourceforge.net/. In the pink box on that page enter the URI of the individual you created in the previous step and click "open."
  • 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)." This indicates that you are successfully serving linked RDF data. If the URI of the "test individual" is followed by "failed (400)" you are not successfully serving linked data.

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