EP2DCOverview

The EPrints to Data Centre (EP2DC) plugin extends EPrints to support uploading to a remote data centre any XML-formatted experimental data associated with a deposit.

Introduction

EP2DC is a prototype plugin designed to enable EPrints to support the submission of XML-formatted experimental data sets together with the manuscript to which they correspond. The work recognizes the worth and potential for reuse of high quality experimental data, and is consistent with trends in scientific publishing and funding policy that advocate a more responsible approach to managing research data.

The EP2DC plugin is the realization of the JISC-funded EP2DC Rapid Innovation Project, and the support of JISC, both financial and managerial, is gratefully acknowledged.

Whilst the EP2DC module has been tested and refined by an integration with the JISC-funded Materials Data Centre that is presently under development at the University of Southampton, it is designed for integration with any data centre.

Features

Screen capture of the EP2DC stage added to the default EPrints stages

As shown in the figure, the EP2DC plugin extends the default EPrints stages with an additional EP2DC stage for uploading experimental data.

EP2DC Plugin Installation

Installation of EP2DC at an existing EPrints 3.3 repository has been designed to be a simple as possible.

Prerequisites

PERL modules, all of which are available from CPAN:

• LWP::UserAgent
• HTTP::Request::Common
• Authen::NTLM
• LWP::Authen::Ntlm
• HTML::Entities

Install

Assuming the EPrints install path is /opt/eprints3, and that the name of your archive is ARCHIVE_ID, the following actions are required to install the EP2DC plugin:

1-cd /opt/eprints3/archives/ARCHIVE_ID

2-cp mdc-1.0.tar.gz .

3-tar zxvf mdc-1.0.tar.gz This will copy most of the files at the right location.

4-cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d

5-vim document_fields_default.pl, add the following:

       $data->{ep2dc_is_validated} = 'TRUE';

save & exit vim.

6-vim document_fields.pl, add the following field definitions:

       {
               name => "ep2dc_is_data",
               type => "boolean",
       },
       {
               name => "ep2dc_is_validated",
               type => "boolean",
       },
       {
               name => "ep2dc_data_centre",
               type => "set",
               options => [ "mdc", "ndc", "amcc" ],
       },
       {
               name => "ep2dc_test_type",
               type => "set",
               options => [ "tensile", "creep", "fatigue", "impact", "fcg", "ccg" ],
       },
       {
               name => "ep2dc_test_date",
               type => "date",
       },
       {
               name => "ep2dc_test_centre",
               type => "longtext",
       },
       {
               name => "ep2dc_object_id",
               type => "text",
       },
       {
               name => "ep2dc_security",
               type => "set",
               options => [ "openaccess", "restricted", "ondemand" ]
       }

save & exit vim.

7-vim eprint_warnings.pl, add the following at the end:

       push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );

save & exit vim.

8-vim eprint_render.pl Look for the following piece of code:

       my @documents = $eprint->get_all_documents();

Replace with:

       my @documents = $eprint->get_all_documents(0);

Look for the following piece of code:

       if( defined $files{$doc->get_main} )

Replace with:

       if( defined $files{$doc->get_main} && !$doc->is_data() )

Where you want to display the EP2DC datasets, add the following:

       my $data_container = $session->make_element( "div", id => "ep_datadocs_container", style=>"width:80%;margin:auto;" );
       $page->appendChild( $data_container );
       my $wait_p = $session->make_element( "p", style=>"vertical-align: middle;width:100%;text-align:center;" );
       $data_container->appendChild( $wait_p );
       my $wait_img = $session->make_element( "img", border => "0", src => "/images/ajax_waiting.gif" );
       $wait_p->appendChild( $session->make_text( "Loading datasets...   " ) );
       $wait_p->appendChild( $wait_img );
       $page->appendChild( $session->make_javascript( "var datadocs = new Ajax.Updater( 'ep_datadocs_container', '/cgi/render_data_docs?eprintid=".$eprint->get_id."', { method:'get', onComplete: function(req) { \$('ep_datadocs_container').innerHTML = req.responseText;} } );" ) );

save and exit vim.

9-Add the new fields to the database:

       /opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID

10-Link the CGI scripts to EPrints:

       ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/

11-Restart your web server, as root (note that this line might be different depending on which version of Linux you are running):

       /etc/init.d/httpd restart

Data Centre Integration

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the Materials Data Centre, the end point is available at EP2DC Endpoint.

The out-of-the-box EP2DC module is designed to work with the EP2DC Web Services API. Documentation for implementing this API is available from Web Services API documentation.

Development Roadmap

The EP2DC plugin is a prototype, and reports, and suggestions for improvements are welcomed. Presently, the roadmap for further development includes the following:

• Associate data with a pre-existing EPrints deposit