Prerequisites¶

Installing Java¶

Dataverse should run fine with only the Java Runtime Environment (JRE) installed, but installing the Java Development Kit (JDK) is recommended so that useful tools for troubleshooting production environments are available. We recommend using Oracle JDK or OpenJDK.

The Oracle JDK can be downloaded from http://www.oracle.com/technetwork/java/javase/downloads/index.html

On a Red Hat and similar Linux distributions, install OpenJDK with something like:

# yum install java-1.8.0-openjdk-devel

If you have multiple versions of Java installed, Java 8 should be the default when java is invoked from the command line. You can test this by running java -version.

On Red Hat/CentOS you can make Java 8 the default with the alternatives command, having it prompt you to select the version of Java from a list:

# alternatives --config java

If you don’t want to be prompted, here is an example of the non-interactive invocation:

# alternatives --set java /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java

Installing Glassfish¶

Important: once Glassfish is installed, a new version of the Weld library (v2.2.10.SP1) must be downloaded and installed. This fixes a serious issue in the library supplied with Glassfish 4.1 ( see https://github.com/IQSS/dataverse/issues/647 for details). Please note that if you plan to front Glassfish with Apache you must also patch Grizzly as explained in the Shibboleth section.

• Download and install Glassfish (installed in /usr/local/glassfish4 in the example commands below):

  # wget http://dlc-cdn.sun.com/glassfish/4.1/release/glassfish-4.1.zip
  # unzip glassfish-4.1.zip
  # mv glassfish4 /usr/local
  

• Remove the stock Weld jar; download Weld v2.2.10.SP1 and install it in the modules folder:

  # cd /usr/local/glassfish4/glassfish/modules
  # rm weld-osgi-bundle.jar
  # wget http://central.maven.org/maven2/org/jboss/weld/weld-osgi-bundle/2.2.10.SP1/weld-osgi-bundle-2.2.10.SP1-glassfish4.jar
  # /usr/local/glassfish4/bin/asadmin start-domain
  

• Verify the Weld version:

  # /usr/local/glassfish4/bin/asadmin osgi lb | grep 'Weld OSGi Bundle'
  

• Stop Glassfish and change from -client to -server under <jvm-options>-client</jvm-options>:

  # /usr/local/glassfish4/bin/asadmin stop-domain
  # vim /usr/local/glassfish4/glassfish/domains/domain1/config/domain.xml
  

This recommendation comes from http://blog.c2b2.co.uk/2013/07/glassfish-4-performance-tuning.html among other places.

Glassfish Init Script¶

The Dataverse installation script will start Glassfish if necessary, but while you’re configuring Glassfish, you might find the following init script helpful to have Glassfish start on boot.

Adjust this Glassfish init script for your needs or write your own.

It is not necessary to have Glassfish running before you execute the Dataverse installation script because it will start Glassfish for you.

Installing PostgreSQL¶

Version 9.x is required. Previous versions have not been tested.

The version that ships with RHEL 6 and above is fine:

# yum install postgresql-server
# service postgresql initdb
# service postgresql start

Configure Access to PostgreSQL for the Installer Script¶

• When using localhost for the database server, the installer script needs to have direct access to the local PostgreSQL server via Unix domain sockets. This is configured by the line that starts with local all all in the pg_hba.conf file. The location of this file may vary depending on the distribution. But if you followed the suggested installation instructions above, it will be /var/lib/pgsql/data/pg_hba.conf on RHEL and similar. Make sure the line looks like this (it will likely be pre-configured like this already):

  local all all       peer

• If the installer still fails to connect to the databse, we recommend changing this configuration entry to trust:

  local all all      trust

This is a security risk, as it opens your database to anyone with a shell on your server. It does not however compromise remote access to your system. Plus you only need this configuration in place to run the installer. After it’s done, you can safely reset it to how it was configured before.

Configure Database Access for the Dataverse Application¶

• The application will be talking to PostgreSQL over TCP/IP, using password authentication. If you are running PostgreSQL on the same server as Glassfish, we strongly recommend that you use the localhost interface to connect to the database. Make you sure you accept the default value localhost when the installer asks you for the PostgreSQL server address. Then find the localhost (127.0.0.1) entry that’s already in the pg_hba.conf and modify it to look like this:

  host all all 127.0.0.1/32 password

• If the Dataverse application is running on a different server, you will need to add a new entry to the pg_hba.conf granting it access by its network address:

  host all all [ADDRESS]      255.255.255.255 password

  ([ADDRESS] should be the numeric IP address of the Glassfish server).

• In some distributions, PostgreSQL is pre-configured so that it doesn’t accept network connections at all. Check that the listen_address line in the configuration file postgresql.conf is not commented-out and looks like this:

  listen_addresses='*'
  

  The file postgresql.conf will be located in the same directory as the pg_hba.conf above.

• Important: you must restart Postgres for the configuration changes to take effect! On RHEL and similar (provided you installed Postgres as instructed above):

  # service postgresql restart
  

PostgreSQL Init Script¶

The standard init script that ships RHEL 6 and similar should work fine. Enable it with this command:

# chkconfig postgresql on

Installing Solr¶

Download and install Solr with these commands:

# wget https://archive.apache.org/dist/lucene/solr/4.6.0/solr-4.6.0.tgz
# tar xvzf solr-4.6.0.tgz
# rsync -auv solr-4.6.0 /usr/local/
# cd /usr/local/solr-4.6.0/example/solr/collection1/conf/
# cp -a schema.xml schema.xml.orig

The reason for backing up the schema.xml file is that Dataverse requires a custom Solr schema to operate. This schema.xml file is contained in the “dvinstall” zip supplied in each Dataverse release at https://github.com/IQSS/dataverse/releases . Download this zip file, extract schema.xml from it, and put it into place (in the same directory as above):

# cp /tmp/schema.xml schema.xml

With the Dataverse-specific schema in place, you can now start Solr:

# java -jar start.jar

Solr Init Script¶

The command above will start Solr in the foreground which is good for a quick sanity check that Solr accepted the schema file, but starting Solr with an init script is recommended. You can attempt to adjust this Solr init script for your needs or write your own.

Solr should be running before the installation script is executed.

Securing Solr¶

Solr must be firewalled off from all hosts except the server(s) running Dataverse. Otherwise, any host that can reach the Solr port (8983 by default) can add or delete data, search unpublished data, and even reconfigure Solr. For more information, please see https://wiki.apache.org/solr/SolrSecurity

You may want to poke a temporary hole in your firewall to play with the Solr GUI. More information on this can be found in the Development Environment section of the Developer Guide.

Installing jq¶

jq is a command line tool for parsing JSON output that is used by the Dataverse installation script. https://stedolan.github.io/jq explains various ways of installing it, but a relatively straightforward method is described below. Please note that you must download the 64- or 32-bit version based on your architecture. In the example below, the 64-bit version is installed. We confirm it’s executable and in our $PATH by checking the version (1.4 or higher should be fine):

# cd /usr/bin
# wget http://stedolan.github.io/jq/download/linux64/jq
# chmod +x jq
# jq --version

Now that you have all the prerequisites in place, you can proceed to the Installation section.