Dataverse puppet module

Overview - What is the Dataverse module?
[License(#license)]
Module Description - What does the module do?
Setup - The basics of getting started with Dataverse module
Before you begin - Pre setup conditions
Configuring the infrastructure - Installing dataverse
Hieradata - Using hieradata
Known issues - Known issues
To do - Or not to do
[Contributors(#contributors)]

Overview

The Dataverse module allows you to install Dataverse with Puppet.

Licence

Module Description

Dataverse is an open source (code is available on GitHub) web application to share, preserve, cite, explore and analyze research data. It facilitates making data available to others, and allows you to replicate others work. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit via a data citation with a persistent identifier (e.g., DOI, or Handle).The module offers support for basic management of common security settings.

This module will install dataverse with default settings and allow customisation of those settings.

Setup

What this Dataverse setup affects:

package/service/configuration files for Dataverse, R and R packages, PostgreSQL, Solr and TwoRavens.

What this Dataverse setup does not affect:

You need to run the final database and api scripts to populate your dataverse instance. For example, if you deploy on a development environment with the default settings run:

sudo -u dvnApp psql dvndb -f /opt/dataverse/scripts/database/reference_data.sql /opt/dataverse/scripts/api/setup-all.sh
optimizations such as the best settings for java and PostgreSQL.
Shibboleth configurations (as they have an experimental status), although the packages are installed.

Introductory Questions

Before getting started, you will want to consider:

Do you need a development environment ?
Are you installing an acceptance environment or production environment ?

Your answers to these questions will determine on which nodes you will install what classes and their parameters.

Before you begin

These are the dependencies the puppet module needs:

a first-time update of each of the host's package repository ( e.g. using 'apt-get update' or 'yum update' )
the unzip utility
This module depends on the altered fatmcgav-glassfish module which is not part of the puppet forge repository. There is a [PR:fatmcgav/fatmcgav-glassfish#51] to incorporate them. Until that time use the fork and install it on your puppet master or puppetless client environment:

$ wget -O fatmcgav-glassfish-0.6.0.tar.gz https://github.com/IISH/fatmcgav-glassfish/archive/dataverse.tar.gz $ puppet module install fatmcgav-glassfish-0.6.0.tar.gz

Configuring your infrastructure

To install Dataverse and TwoRavens with all the out-of-the-box settings use:

class {
# The global settings
  'iqss::globals':
    ensure  => present;
}->class {
  [
    'iqss::database',
    'iqss::dataverse',
    'iqss::solr',
    'iqss::tworavens'
  ]:
}

To install on different machines you can deploy per server per component. E.g.:

Server A-1: class { 'iqss::globals':}->class { 'iqss::dataverse': }
Server A-2: class { 'iqss::globals':}->class { 'iqss::dataverse': }
Server A-3: class { 'iqss::globals':}->class { 'iqss::dataverse': }
Server B-1: class { 'iqss::globals':}->class { 'iqss::database': }
Server C-1: class { 'iqss::globals':}->class { 'iqss::solr': }
Server D-1: class { 'iqss::globals':}->class { 'iqss::tworavens': }
Server E-1: class { 'iqss::globals':}->class { 'iqss::rserve': }

###Classes and Defined Types

This module modifies configuration files and directories.

####Class: Iqss::Globals

This class allows you to configure the global configuration that contain settings shared amongst classes, most notably the database settings. Example:

class {
  'iqss::globals':
    ensure            => present,
    dataverse_fqdn    => 'mysite.org',
    database_name     => 'dataverse',
    database_user     => 'dataverse',
    database_password => 'Cárammë',
}

It also contains settings for

#####apache_purge_configs

Removes all other Apache configs and vhosts. Setting this to 'false' is a stopgap measure to allow the apache module to coexist with existing or otherwise-managed configuration. Defaults to 'true'.

#####dataverse_fqdn

If the Dataverse server has multiple DNS names, this option specifies the one to be used as the “official” host name. For example, you may want to have dataverse.foobar.edu, and not the less appealling server-123.socsci.foobar.edu to appear exclusively in all the registered global identifiers, Data Deposit API records, etc. Defaults to 'localhost'.

Do note that whenever the system needs to form a service URL, by default, it will be formed with https:// and port 443. I.e., https://{dataverse.fqdn}/

If that does not suit your setup, use the Iqss::Dataverse::dataverse_site_url option.

#####database_host

The domain of the database. Defaults to Globals:dataverse_fqdn.

#####database_port

The port of the database. Defaults to '5432'.

#####database_name

The name of the database. Defaults to 'dvndb'.

#####database_user

The name of the database owner. Defaults to 'dvnApp'.

#####database_password

The password for the database user. Defaults to 'dvnAppPass'.

####Class: Iqss::Dataverse

This class installs Glassfish, the domain settings and depending on the configuration builds a war or pulls a war distribution from a repository. Example:

class {
    'iqss::dataverse':
        repo => 'https://github.com/IQSS/dataverse/releases/download/v4.0.1/dataverse-4.0.1.war',
}

This will create three services:

The glassfish service: $ service dataverse start|stop|status
An R-daemon: $ service rserve start|stop|status
The Apache web server

It also contains settings for

#####dataverse_auth_password_reset_timeout_in_minutes

A JVM option: the time in minutes for a password reset. Defaults to '60'.

#####dataverse_files_directory

The location of the uploaded files and their tabular derivatives. Defaults to '/home/glassfish/dataverse/files'.

#####dataverse_rserve_host

The Rserve service hostname. Defaults to Globals:dataverse_fqdn.

#####dataverse_rserve_password

The password needed to access the Rserve service. Defaults to 'rserve'.

#####dataverse_rserve_port

The Rserve service port. Defaults to 'rserve'. Defaults to '6311'.

#####dataverse_rserve_user

The serve service user. Defaults to 'serve'.

#####dataverse_site_url

Set this to override the default URL construction behaviour of the Global::dataverse_fqdn setting with a custom value.

#####doi_baseurlstring

The DOI endpoint for the EZID Service. Defaults to 'https://ezid.cdlib.org'.

#####doi_username

The username to connect to the EZID Service. Defaults to 'apitest'.

#####doi_password

The password to connect to the EZID Service. Defaults to 'apitest'.

#####glassfish_parent_dir

The Glassfish parent directory. Defaults to '/home/glassfish'.

#####glassfish_domain_name

The domain name. Defaults to 'domain1'.

#####glassfish_fromaddress

The e-mail -from field in the mail header. Defaults to 'do-not-reply@localhost'.

#####glassfish_jvmoption

An array of jvm options. Defaults to ["-Xmx1024m", "-Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl"].

#####glassfish_mailhost

The mail relay hostname. Defaults to Globals:dataverse_fqdn.

#####glassfish_mailuser

The user name that is allowed by the mail relay to sent mails. Defaults to 'dataversenotify'.

#####glassfish_mailproperties

Key-value pairs sent with to the mail relay, such as credentials. Defaults to dummy values 'username=a_username:password=a_password'.

#####glassfish_service_name

The service handle to submit start, stop, status commands. E.g. service dataverse start. Defaults to 'dataverse'

#####glassfish_tmp_dir

The download path of the glassfish package. Defaults to '/opt/glassfish'.

#####glassfish_user

The user running the glassfish domain. Defaults to 'glassfish'.

#####glassfish_version

The Glassfish J2EE Application server version. Defaults to '4.1'.

#####repository

The repository url of a Dataverse war file.

#####trigger

A timer that monitors the Last Modified Date of the url set by repository. Should it change, the trigger scripts will download and deploy a new war. Defaults to three minutes: '*/3.

####Class: Iqss::Database

Installs Postgresql, the database user and database. For example:

class {
  'iqss::database':
    name     => 'dataverse',
    user     => 'dataverse',
    password => 'secret',
}

Use the Iqss::Globals class to override settings. This will create a running Postgresql server with the database, users and access policies.

It also contains settings for

#####createdb

When 'true' the user can create databases. Defaults to 'false'.

#####createrole

When 'true' the user can create roles. Defaults to 'false'.

#####hba_rule

The access rules that determine who can connect to what database from where. Defaults to:

IPv4 local connections => {
    description => 'Open up a IP4 connection from localhost',
    type        => 'host',
    database    => 'dvndb',
    user        => 'dvnApp',
    address     => '127.0.0.1/32',
    auth_method => 'md5'
    },
IPv6 local connections => {
    description => 'Open up a IP6 connection from localhost',
    type        => 'host',
    database    => 'dvndb',
    user        => 'dvnApp',
    address     => '::1/128',
    auth_method => 'md5'
    }

#####host

The url connection string. Defaults to 'localhost'.

#####login

The fact the user can login or not. Defaults to 'true'.

#####name

Name of the database. Inherited by iqss::globals::database_name. Defaults to 'dvndb'.

#####password

The user password. Defaults to 'dvnAppPass'.

#####port

The connection port to the database. Defaults to '5432'

#####replication

When 'true' this role can replicate. Defaults to 'false'.

#####superuser

When 'true' this role is a superuser. Defaults to 'false'.

#####user

The user name. Defaults to 'dvnApp'.

#####version

The version of Postgresql. Defaults to '9.3'.

#####manage_package_repo

If true this will setup the official PostgreSQL repositories on your host. Defaults to true.

#####encoding

This will set the default encoding encoding for all databases created with this module. On certain operating systems this will be used during the template1 initialization as well so it becomes a default outside of the module as well. Defaults to 'UTF-8'.

#####locale

This will set the default database locale for all databases created with this module. Defaults to 'en_US.UTF-8'.

#####listen_addresses

This value defaults to localhost, meaning the postgres server will only accept connections from localhost. If you'd like to be able to connect to postgres from remote machines, you can override this setting. A value of * will tell postgres to accept connections from any remote machine. Alternately, you can specify a comma-separated list of hostnames or IP addresses. (For more info, have a look at the postgresql.conf file from your system's postgres package).

####Class: Iqss::Solr

Installs Solr. Example:

class { 'iqss::solr':
    version => '4.7.1',
}

This will create a Jetty server with a running Solr instance : $ service solr stop|status|start

It also contains settings for

#####core

The solr core. Defaults to 'collection1'.

#####jetty_home

The Jetty home directory which contains start.jar. Defaults to '/home/solr-4.6.0/example'

#####jetty_host

Use 0.0.0.0 as host to accept all connections. Defaults to Globals:dataverse_fqdn.

#####jetty_java_options

JVM options for Jetty. Defaults to '-Xmx512m'.

#####jetty_port

The port Jetty will bind to. Defaults to '8983'.

#####jetty_user

The user running the Jetty Solr instance. Defaults to 'solr'.

#####solr_home

The Solr home used for the jvm setting -Dsolr.solr.home. Defaults to '/home/solr-4.6.0/example/solr'.

#####solr_parent_dir

The home directory of Solr. Defaults to '/home/solr-4.6.0'.

#####url

The download url for solr. Preferably a mirror. Defaults to 'http://archive.apache.org/dist/lucene/solr'.

#####version

The Apache Solr version. Defaults to '4.6.0'.

####Class: Iqss::Tworavens

This class installs the Apache RApache handler and the Tworavens web application. For example:

class {
  'iqss::tworavens':
    tworavens_package => 'https://github.com/IQSS/TwoRavens/archive/master.zip',
    parent_dir        => '/var/www/html',
}

It also contains settings for

#####domain

The public domain name of the TwoRavens web application. Defaults to 'localhost'.

#####package

The download url of TwoRavens. Defaults to 'https://github.com/IQSS/TwoRavens/archive/v0.1.zip'.

#####parent_dir

The installation directory of the TwoRavens web application. Defaults to '/var/www/html'.

#####port

The port TwoRavens can be accessed on. Defaults to '9999'.

#####protocol

The protocol TwoRavens can be accessed on. Defaults to 'https'.

#####rapache_version

The rapache version to be installed. Defaults to '1.2.6'.

#####tworavens_dataverse_fqdn

The domain name of the dataverse web application this TwoRavens web application will connect to. Defaults to 'localhost'.

#####tworavens_dataverse_port

The port of the dataverse web application. Defaults to '9999'.

#####dataverse_site_url

The url to a dataverse web application. Defaults to 'https://dataverse_fqdn:9999'.

Hieradata

This example shows how all default settings can be set with a hieradata document. Note that you can also inject values like the R packages or package_repo:

{
    "iqss::database::createdb": false,
    "iqss::database::createrole": false,
    "iqss::database::encoding": "UTF-8",
    "iqss::database::listen_addresses": "*",
    "iqss::database::locale": "en_US.UTF-8",
    "iqss::database::login": true,
    "iqss::database::manage_package_repo": true,
    "iqss::database::hba_rule": {
        "IPv4 local connections": {
            "description": "Open up a IP4 connection from localhost",
            "type": "host",
            "database": "dvndb",
            "user": "dvnApp",
            "address": "127.0.0.1/32",
            "auth_method": "md5"
        },
        "IPv6 local connections": {
            "description": "Open up a IP6 connection from localhost",
            "type": "host",
            "database": "dvndb",
            "user": "dvnApp",
            "address": "::1/128",
            "auth_method": "md5"
        }
    },
    "iqss::database::superuser": false,
    "iqss::database::version": "9.3",
    "iqss::dataverse::glassfish_domain_name": "domain1",
    "iqss::dataverse::glassfish_parent_dir": "/home/glassfish",
    "iqss::dataverse::glassfish_service_name": "dataverse",
    "iqss::dataverse::glassfish_tmp_dir": "/opt/glassfish",
    "iqss::dataverse::glassfish_user": "glassfish",
    "iqss::dataverse::glassfish_version": "4.1",
    "iqss::dataverse::repository": "local",
    "iqss::dataverse::repository_custom": "https://bamboo.socialhistoryservices.org/browse/DATAVERSE-TEST/latestSuccessful/artifact/JOB1/4.0.1/dataverse-4.0.1.war",
    "iqss::dataverse::trigger": "*/3",
    "iqss::dataverse::dataverse_site_url": "https://localhost:9999",
    "iqss::dataverse::dataverse_files_directory": "/home/glassfish/dataverse/files",
    "iqss::dataverse::dataverse_rserve_host": "localhost",
    "iqss::dataverse::dataverse_rserve_port": "6311",
    "iqss::dataverse::dataverse_rserve_user": "rserve",
    "iqss::dataverse::dataverse_rserve_password": "rserve",
    "iqss::dataverse::dataverse_auth_password_reset_timeout_in_minutes": "60",
    "iqss::dataverse::doi_username": "apitest",
    "iqss::dataverse::doi_password": "apitest",
    "iqss::dataverse::doi_baseurlstring": "https\://ezid.cdlib.org",
    "iqss::dataverse::glassfish_fromaddress": "do-not-reply@localhost",
    "iqss::dataverse::glassfish_jvmoption": [
        "-XX\:MaxPermSize=512m",
        "-XX\:PermSize=256m",
        "-Xmx1024m",
        "-Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl"
    ],
    "iqss::dataverse::glassfish_mailhost": "localhost",
    "iqss::dataverse::glassfish_mailuser": "dataversenotify",
    "iqss::dataverse::glassfish_mailproperties": "username=a_username:password=a_password",
    "iqss::globals::apache2_purge_configs": true,
    "iqss::globals::database_host": "localhost",
    "iqss::globals::dataverse_fqdn": "localhost",
    "iqss::globals::dataverse_port": "9999",
    "iqss::globals::database_port": 5432,
    "iqss::globals::database_name": "dvndb",
    "iqss::globals::database_user": "dvnApp",
    "iqss::globals::database_password": "dvnAppPass",
    "iqss::rserve::packages_r": [ "devtools", "DescTools", "R2HTML", "Rserve", "VGAM", "AER", "dplyr", "quantreg", "geepack", "maxLik", "Amelia", "Rook", "jsonlite", "rjson"],
    "iqss::rserve::packages_zelig": "https://github.com/IQSS/Zelig/archive/master.zip",
    "iqss::rserve::user": "rserve",
    "iqss::rserve::package_repo": "http://cran.r-project.org",
    "iqss::solr::url": "http://archive.apache.org/dist/lucene/solr",
    "iqss::solr::version": "4.6.0",
    "iqss::solr::solr_parent_dir": "/home/solr-4.6.0",
    "iqss::solr::jetty_user": "solr",
    "iqss::solr::jetty_host": "localhost",
    "iqss::solr::jetty_port": "8983",
    "iqss::solr::jetty_java_options": "-Xmx512m",
    "iqss::solr::jetty_home": "/home/solr-4.6.0/example",
    "iqss::solr::solr_home": "/home/solr-4.6.0/example/solr",
    "iqss::solr::core": "collection1",
    "iqss::tworavens::rapache_version": "1.2.6",
    "iqss::tworavens::package": "https://github.com/IQSS/TwoRavens/archive/v0.1.zip",
    "iqss::tworavens::parent_dir": "/var/www/html",
    "iqss::tworavens::domain": "localhost",
    "iqss::tworavens::tworavens_dataverse_port": "9999",
    "iqss::tworavens::port": "9999",
    "iqss::tworavens::protocol": "https"
}

Known issues

The Rserve service does not automatically start when it is installed for the first time.
When installing TwoRavens for the first time, apache does not restart and read in the configuration.
The glassfish installation order is wrong: it sets up glassfish, starts it and then adds library and config dependencies. The service start should be the last step.

To do

The Rserver config uses a static file in files/dataverse/conf/R/ but it should be a template.
Discuss how to move on from here: a dataverse installation module on https://forge.puppetlabs.com/ so developers and IT administrators can setup their DTAP environment ?
Test with Centos 7 ?
Shibboleth
Maintainers and contributors ?

Contributors

Lucien van Wouw, IISH

Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
files		files
lib/puppet/parser/functions		lib/puppet/parser/functions
manifests		manifests
spec		spec
templates		templates
tests		tests
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
Rakefile		Rakefile
Vagrantfile		Vagrantfile
metadata.json		metadata.json
setup.sh		setup.sh

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Dataverse puppet module

Table of Contents

Overview

Licence

Module Description

Setup

Before you begin

Configuring your infrastructure

Hieradata

Known issues

To do

Contributors

About

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License

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Dataverse puppet module

Table of Contents

Overview

Licence

Module Description

Setup

Before you begin

Configuring your infrastructure

Hieradata

Known issues

To do

Contributors

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