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 RHEL/CentOS, install OpenJDK (devel version) using yum:

# 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 RHEL/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¶

Note: The Dataverse installer need not be run as root, and it is recommended that Glassfish not run as root either. We suggest the creation of a glassfish service account for this purpose.

• 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
  

If you intend to install and run Glassfish under a service account (and we hope you do), chown -R the Glassfish hierarchy to root to protect it but give the service account access to the below directories:

• Set service account permissions:

  # chown -R root:root /usr/local/glassfish4
  # chown glassfish /usr/local/glassfish4/glassfish/lib
  # chown -R glassfish:glassfish /usr/local/glassfish4/glassfish/domains/domain1
  

After installation, you may chown the lib/ directory back to root; the installer only needs write access to copy the JDBC driver into that directory.

Once Glassfish is installed, you’ll need a newer version of the Weld library (v2.2.10.SP1) to fix a serious issue in the library supplied with Glassfish 4.1 (see https://github.com/IQSS/dataverse/issues/647 for details). If you plan to front Glassfish with Apache you must also patch Grizzly as explained in the Shibboleth section.

• 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
  

• Change from -client to -server under <jvm-options>-client</jvm-options>:

  # vim /usr/local/glassfish4/glassfish/domains/domain1/config/domain.xml
  

This recommendation comes from http://www.c2b2.co.uk/middleware-blog/glassfish-4-performance-tuning-monitoring-and-troubleshooting.php among other places.

• Start Glassfish and verify the Weld version:

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

Launching Glassfish on system boot¶

The Dataverse installation script will start Glassfish if necessary, but you may find the following scripts helpful to launch Glassfish start automatically on boot.

• This Systemd file may be serve as a reference for systems using Systemd (such as RHEL/CentOS 7 or Ubuntu 16+)
• This init script may be useful for RHEL/CentOS 6 or Ubuntu >= 14 if you’re using a Glassfish service account, or
• This Glassfish init script may be helpful if you’re just going to run Glassfish as root.

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

Please note that you must run Glassfish in an English locale. If you are using something like LANG=de_DE.UTF-8, ingest of tabular data will fail with the message “RoundRoutines:decimal separator no in right place”.

Installing PostgreSQL¶

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

The version that ships with el7 and above is fine:

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

The standard init script that ships with el7 should work fine. Enable it with this command:

# chkconfig postgresql on

Configuring Database Access for the Dataverse Application (and the Dataverse Installer)¶

• The application and the installer script will be connecting to PostgreSQL over TCP/IP, using password authentication. In this section we explain how to configure PostgreSQL to accept these connections.

• If PostgreSQL is running on the same server as Glassfish, 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 md5
  

  Once you are done with the prerequisites and run the installer script (documented here: Installation) it will ask you to enter the address of the Postgres server. Simply accept the default value 127.0.0.1 there.

• The Dataverse installer script will need to connect to PostgreSQL as the admin user, in order to create and set up the database that the Dataverse will be using. If for whatever reason it is failing to connect (for example, if you don’t know/remember what your Postgres admin password is), you may choose to temporarily disable all the access restrictions on localhost connections, by changing the above line to:

  host all all 127.0.0.1/32 trust
  

  Note that this rule opens access to the database server via localhost only. Still, in a production environment, this may constitute a security risk. So you will likely want to change it back to “md5” once the installer has finished.

• 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 md5
  

  Where [ADDRESS] is the numeric IP address of the Glassfish server. Enter this address when the installer asks for the PostgreSQL server address.

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

  # service postgresql restart
  

  On MacOS X a “Reload Configuration” icon is usually supplied in the PostgreSQL application folder. Or you could look up the process id of the PostgreSQL postmaster process, and send it the SIGHUP signal:

  kill -1 PROCESS_ID
  

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:

# cd /usr/local/solr-4.6.0/example
# 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 letting the system start Solr automatically is recommended.

• This Solr Systemd file will launch Solr on boot as the solr user for RHEL/CentOS 7 or Ubuntu 16+ systems, or
• For systems using init.d, you may attempt to adjust this Solr init script for your needs or write your own.

Solr should be running before the Dataverse 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

Installing and configuring ImageMagick¶

On a Red Hat and similar Linux distributions, you can install ImageMagick with something like:

# yum install ImageMagick

(most RedHat systems will have it pre-installed). When installed using standard yum mechanism, above, the executable for the ImageMagick convert utility will be located at /usr/bin/convert. No further configuration steps will then be required.

On MacOS you can compile ImageMagick from sources, or use one of the popular installation frameworks, such as brew.

If the installed location of the convert executable is different from /usr/bin/convert, you will also need to specify it in your Glassfish configuration using the JVM option, below. For example:

<jvm-options>-Ddataverse.path.imagemagick.convert=/opt/local/bin/convert</jvm-options>

(see the Configuration section for more information on the JVM options)

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