merge master into beta

.gitignore

@@ -11,3 +11,4 @@ michael-local
 .Trashes
 ehthumbs.db
 Thumbs.db
+.vagrant

README.md

@@ -0,0 +1,14 @@
+Dataverse 
+==========
+
+Dataverse is an open source web application for sharing, citing, analyzing, and preserving research data.
+
+Institutions and organizations can choose to install the Dataverse software for their own use. 
+In this case, the institution will be responsible for maintaining the application; installing upgrades, 
+setting up backups and data replication as needed. For more general information about Dataverse please visit our 
+[Data Science site] (http://datascience.iq.harvard.edu/dataverse).
+
+The Dataverse code is *open-source* and *free*. 
+
+Installation packages are in Sourceforge for installers. [Download the latest production stable 
+version of the Dataverse application] (http://sourceforge.net/projects/dvn/files/dvn/).

Vagrantfile

@@ -0,0 +1,124 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  # All Vagrant configuration is done here. The most common configuration
+  # options are documented and commented below. For a complete reference,
+  # please see the online documentation at vagrantup.com.
+
+  # Every Vagrant virtual environment requires a box to build off of.
+  config.vm.box = "puppet-vagrant-boxes.puppetlabs.com-centos-65-x64-virtualbox-puppet.box"
+
+  # The url from where the 'config.vm.box' box will be fetched if it
+  # doesn't already exist on the user's system.
+  config.vm.box_url = "http://puppet-vagrant-boxes.puppetlabs.com/centos-65-x64-virtualbox-puppet.box"
+
+  config.vm.provision "shell", path: "scripts/setup/asadmin-setup.sh"
+  config.vm.provision "shell", path: "scripts/vagrant/deploy.sh"
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  config.vm.network "forwarded_port", guest: 8080, host: 8888
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # If true, then any SSH connections made will enable agent forwarding.
+  # Default value: false
+  # config.ssh.forward_agent = true
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  config.vm.synced_folder "downloads", "/downloads"
+  config.vm.synced_folder "target", "/builds"
+  config.vm.synced_folder "conf", "/conf"
+  config.vm.synced_folder "scripts", "/scripts"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  # config.vm.provider "virtualbox" do |vb|
+  #   # Don't boot with headless mode
+  #   vb.gui = true
+  #
+  #   # Use VBoxManage to customize the VM. For example to change memory:
+  #   vb.customize ["modifyvm", :id, "--memory", "1024"]
+  # end
+  #
+  # View the documentation for the provider you're using for more
+  # information on available options.
+
+  # Enable provisioning with Puppet stand alone.  Puppet manifests
+  # are contained in a directory path relative to this Vagrantfile.
+  # You will need to create the manifests directory and a manifest in
+  # the file base.pp in the manifests_path directory.
+  #
+  # An example Puppet manifest to provision the message of the day:
+  #
+  # # group { "puppet":
+  # #   ensure => "present",
+  # # }
+  # #
+  # # File { owner => 0, group => 0, mode => 0644 }
+  # #
+  # # file { '/etc/motd':
+  # #   content => "Welcome to your Vagrant-built virtual machine!
+  # #               Managed by Puppet.\n"
+  # # }
+  #
+  # config.vm.provision "puppet" do |puppet|
+  #   puppet.manifests_path = "manifests"
+  #   puppet.manifest_file  = "site.pp"
+  # end
+
+  # Enable provisioning with chef solo, specifying a cookbooks path, roles
+  # path, and data_bags path (all relative to this Vagrantfile), and adding
+  # some recipes and/or roles.
+  #
+  # config.vm.provision "chef_solo" do |chef|
+  #   chef.cookbooks_path = "../my-recipes/cookbooks"
+  #   chef.roles_path = "../my-recipes/roles"
+  #   chef.data_bags_path = "../my-recipes/data_bags"
+  #   chef.add_recipe "mysql"
+  #   chef.add_role "web"
+  #
+  #   # You may also specify custom JSON attributes:
+  #   chef.json = { :mysql_password => "foo" }
+  # end
+
+  # Enable provisioning with chef server, specifying the chef server URL,
+  # and the path to the validation key (relative to this Vagrantfile).
+  #
+  # The Opscode Platform uses HTTPS. Substitute your organization for
+  # ORGNAME in the URL and validation key.
+  #
+  # If you have your own Chef Server, use the appropriate URL, which may be
+  # HTTP instead of HTTPS depending on your configuration. Also change the
+  # validation key to validation.pem.
+  #
+  # config.vm.provision "chef_client" do |chef|
+  #   chef.chef_server_url = "https://api.opscode.com/organizations/ORGNAME"
+  #   chef.validation_key_path = "ORGNAME-validator.pem"
+  # end
+  #
+  # If you're using the Opscode platform, your validator client is
+  # ORGNAME-validator, replacing ORGNAME with your organization name.
+  #
+  # If you have your own Chef Server, the default validation client name is
+  # chef-validator, unless you changed the configuration.
+  #
+  #   chef.validation_client_name = "ORGNAME-validator"
+end

conf/jhove/README.txt

@@ -0,0 +1,2 @@
+This config file, jhove.conf should be placed into the <GLASSFISH DOMAIN>/config directoy. 
+

conf/jhove/jhove.conf

@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jhoveConfig version="1.1"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns="http://hul.harvard.edu/ois/xml/ns/jhove/jhoveConfig"
+ xsi:schemaLocation="http://hul.harvard.edu/ois/xml/ns/jhove/jhoveConfig
+                     http://hul.harvard.edu/ois/xml/xsd/jhove/1.4/jhoveConfig.xsd">
+ <jhoveHome>/usr/local/src/jhove</jhoveHome>
+ <defaultEncoding>utf-8</defaultEncoding>
+ <tempDirectory>/tmp</tempDirectory>
+ <bufferSize>131072</bufferSize>
+ <mixVersion>1.0</mixVersion>
+ <sigBytes>1024</sigBytes>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.AiffModule</class>
+ </module>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.WaveModule</class>
+ </module>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.PdfModule</class>
+ </module>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.Jpeg2000Module</class>
+ </module>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.JpegModule</class>
+ </module>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.GifModule</class>
+ </module>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.TiffModule</class>
+ </module>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.HtmlModule</class>
+ </module>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.AsciiModule</class>
+ </module>
+ <module>
+  <class>edu.harvard.hul.ois.jhove.module.Utf8Module</class>
+ </module>
+</jhoveConfig>

conf/solr/4.6.0/schema.xml

@@ -278,10 +278,8 @@
    <field name="contributor" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="contributorAbbreviation" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="contributorAffiliation" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="contributorLogo" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="contributorName" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="contributorType" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="contributorURL" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="controlOperations" type="text_general" multiValued="false" stored="true" indexed="true"/>
    <field name="country" type="text_general" multiValued="false" stored="true" indexed="true"/>
    <field name="coverage" type="text_general" multiValued="true" stored="true" indexed="true"/>
@@ -303,10 +301,7 @@
    <field name="dataCollectionSituation" type="text_general" multiValued="false" stored="true" indexed="true"/>
    <field name="dataCollector" type="text_general" multiValued="false" stored="true" indexed="true"/>
    <field name="dataSources" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="datasetId" type="text_general" multiValued="false" stored="true" indexed="true"/>
    <field name="datasetLevelErrorNotes" type="text_general" multiValued="false" stored="true" indexed="true"/>
-   <field name="datasetVersion" type="text_general" multiValued="false" stored="true" indexed="true"/>
-   <field name="datasetVersionValue" type="text_general" multiValued="false" stored="true" indexed="true"/>
    <field name="dateOfCollectionEnd" type="int" multiValued="false" stored="true" indexed="true"/>
    <field name="dateOfCollectionStart" type="int" multiValued="false" stored="true" indexed="true"/>
    <field name="dateOfDeposit" type="int" multiValued="false" stored="true" indexed="true"/>
@@ -361,39 +356,11 @@
    <field name="softwareName" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="softwareVersion" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="southLongitude" type="text_general" multiValued="false" stored="true" indexed="true"/>
-   <field name="studyAssay" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyAssayFileName" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyAssayMeasurementTermAccessionNumber" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyAssayMeasurementTermSourceREF" type="text_general" multiValued="true" stored="true" indexed="true"/>
+   <field name="studyAssayCellType" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="studyAssayMeasurementType" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyAssayTechnologyPlatform" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyAssayTechnologyType" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyAssayTechnologyTypeTermAccessionNumber" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyAssayTechnologyTypeTermSourceREF" type="text_general" multiValued="true" stored="true" indexed="true"/>
+   <field name="studyAssayOrganism" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="studyDesignType" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyDesignTypeValue" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyFactor" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyFactorName" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyFactorTermAccessionNumber" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyFactorTermSourceREF" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="studyFactorType" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolComponentsName" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolComponentsType" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolComponentsTypeTermAccessionNumber" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolComponentsTypeTermSourceREF" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolDescription" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolName" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolParametersName" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolParametersNameTermAccessionNumber" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolParametersNameTermSourceREF" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolType" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolTypeTermAccessionNumber" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolTypeTermSourceREF" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolURI" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocolVersion" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyProtocols" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyTermAccessionNumber" type="text_general" multiValued="true" stored="true" indexed="true"/>
-   <field name="studyTermSourceREF" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="subject" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="targetSampleSize" type="text_general" multiValued="false" stored="true" indexed="true"/>
    <field name="timeMethod" type="text_general" multiValued="false" stored="true" indexed="true"/>
@@ -408,7 +375,6 @@
    <field name="ucd" type="text_general" multiValued="true" stored="true" indexed="true"/>
    <field name="unitOfAnalysis" type="text_general" multiValued="false" stored="true" indexed="true"/>
    <field name="universe" type="text_general" multiValued="false" stored="true" indexed="true"/>
-   <field name="versionDate" type="int" multiValued="false" stored="true" indexed="true"/>
    <field name="weighting" type="text_general" multiValued="false" stored="true" indexed="true"/>
    <field name="westLongitude" type="text_general" multiValued="false" stored="true" indexed="true"/>
  </fields>
@@ -488,10 +454,8 @@
    <copyField source="contributor" dest="text" maxChars="3000"/>
    <copyField source="contributorAbbreviation" dest="text" maxChars="3000"/>
    <copyField source="contributorAffiliation" dest="text" maxChars="3000"/>
-   <copyField source="contributorLogo" dest="text" maxChars="3000"/>
    <copyField source="contributorName" dest="text" maxChars="3000"/>
    <copyField source="contributorType" dest="text" maxChars="3000"/>
-   <copyField source="contributorURL" dest="text" maxChars="3000"/>
    <copyField source="controlOperations" dest="text" maxChars="3000"/>
    <copyField source="country" dest="text" maxChars="3000"/>
    <copyField source="coverage" dest="text" maxChars="3000"/>
@@ -513,10 +477,7 @@
    <copyField source="dataCollectionSituation" dest="text" maxChars="3000"/>
    <copyField source="dataCollector" dest="text" maxChars="3000"/>
    <copyField source="dataSources" dest="text" maxChars="3000"/>
-   <copyField source="datasetId" dest="text" maxChars="3000"/>
    <copyField source="datasetLevelErrorNotes" dest="text" maxChars="3000"/>
-   <copyField source="datasetVersion" dest="text" maxChars="3000"/>
-   <copyField source="datasetVersionValue" dest="text" maxChars="3000"/>
    <copyField source="dateOfCollectionEnd" dest="text" maxChars="3000"/>
    <copyField source="dateOfCollectionStart" dest="text" maxChars="3000"/>
    <copyField source="dateOfDeposit" dest="text" maxChars="3000"/>
@@ -571,39 +532,11 @@
    <copyField source="softwareName" dest="text" maxChars="3000"/>
    <copyField source="softwareVersion" dest="text" maxChars="3000"/>
    <copyField source="southLongitude" dest="text" maxChars="3000"/>
-   <copyField source="studyAssay" dest="text" maxChars="3000"/>
-   <copyField source="studyAssayFileName" dest="text" maxChars="3000"/>
-   <copyField source="studyAssayMeasurementTermAccessionNumber" dest="text" maxChars="3000"/>
-   <copyField source="studyAssayMeasurementTermSourceREF" dest="text" maxChars="3000"/>
+   <copyField source="studyAssayCellType" dest="text" maxChars="3000"/>
    <copyField source="studyAssayMeasurementType" dest="text" maxChars="3000"/>
-   <copyField source="studyAssayTechnologyPlatform" dest="text" maxChars="3000"/>
-   <copyField source="studyAssayTechnologyType" dest="text" maxChars="3000"/>
-   <copyField source="studyAssayTechnologyTypeTermAccessionNumber" dest="text" maxChars="3000"/>
-   <copyField source="studyAssayTechnologyTypeTermSourceREF" dest="text" maxChars="3000"/>
+   <copyField source="studyAssayOrganism" dest="text" maxChars="3000"/>
    <copyField source="studyDesignType" dest="text" maxChars="3000"/>
-   <copyField source="studyDesignTypeValue" dest="text" maxChars="3000"/>
-   <copyField source="studyFactor" dest="text" maxChars="3000"/>
-   <copyField source="studyFactorName" dest="text" maxChars="3000"/>
-   <copyField source="studyFactorTermAccessionNumber" dest="text" maxChars="3000"/>
-   <copyField source="studyFactorTermSourceREF" dest="text" maxChars="3000"/>
    <copyField source="studyFactorType" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolComponentsName" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolComponentsType" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolComponentsTypeTermAccessionNumber" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolComponentsTypeTermSourceREF" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolDescription" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolName" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolParametersName" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolParametersNameTermAccessionNumber" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolParametersNameTermSourceREF" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolType" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolTypeTermAccessionNumber" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolTypeTermSourceREF" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolURI" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocolVersion" dest="text" maxChars="3000"/>
-   <copyField source="studyProtocols" dest="text" maxChars="3000"/>
-   <copyField source="studyTermAccessionNumber" dest="text" maxChars="3000"/>
-   <copyField source="studyTermSourceREF" dest="text" maxChars="3000"/>
    <copyField source="subject" dest="text" maxChars="3000"/>
    <copyField source="targetSampleSize" dest="text" maxChars="3000"/>
    <copyField source="timeMethod" dest="text" maxChars="3000"/>
@@ -618,7 +551,6 @@
    <copyField source="ucd" dest="text" maxChars="3000"/>
    <copyField source="unitOfAnalysis" dest="text" maxChars="3000"/>
    <copyField source="universe" dest="text" maxChars="3000"/>
-   <copyField source="versionDate" dest="text" maxChars="3000"/>
    <copyField source="weighting" dest="text" maxChars="3000"/>
    <copyField source="westLongitude" dest="text" maxChars="3000"/>