EPrints Documentation - User contributions [en-gb]

EP2DCOverview

2009-12-24T05:17:06Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. A demonstrator has been integrated with the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], itself presently configured to manage data that comply with the MatDB schema. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Options==
[[Image:ep2dc_eprints_metadata.png|frame|right|||||Screen capture of the metadata section of the EP2DC stage]]

The EP2DC stage for uploading experimental data includes an options (collapsed in the previous figure) that allows metadata associated with the test data to be entered. The fields marked with a red star are mandatory. As shown in the adjacent figure, one of these madatory fields defines the access control. This field affects the data retrieval process, as follows:
* Open—allows data retrieved from the EP2DC EPrints repository to be downloaded by anyone.
* Restricted to registered users—allows data retrieved from the EP2DC EPrints repository to be downloaded by by registered users.
* On demoand—data is supplied on request direct from the owner.

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the page for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=EP2DC Plugin Installation=

Installation of EP2DC at an existing EPrints repository (version 3.1 or higher) 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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx Web Services API documentation].

Further technical information relating to data centre integration is available from the [http://ep2dc.codeplex.com/documentation CodePlex EP2DC Documentation Page].

=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:
* Enable support for SSO.
* Integrate with other data centres in other scientific domains.
* Associate data with a pre-existing EPrints deposit.

EP2DCOverview

2009-12-24T05:16:31Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. A demonstrator has been integrated with a [https://mdc-s1.soton.ac.uk/ Materials Data Centre], which is itself presently configured to manage data that comply with the MatDB schema. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Options==
[[Image:ep2dc_eprints_metadata.png|frame|right|||||Screen capture of the metadata section of the EP2DC stage]]

The EP2DC stage for uploading experimental data includes an options (collapsed in the previous figure) that allows metadata associated with the test data to be entered. The fields marked with a red star are mandatory. As shown in the adjacent figure, one of these madatory fields defines the access control. This field affects the data retrieval process, as follows:
* Open—allows data retrieved from the EP2DC EPrints repository to be downloaded by anyone.
* Restricted to registered users—allows data retrieved from the EP2DC EPrints repository to be downloaded by by registered users.
* On demoand—data is supplied on request direct from the owner.

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the page for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=EP2DC Plugin Installation=

Installation of EP2DC at an existing EPrints repository (version 3.1 or higher) 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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx Web Services API documentation].

Further technical information relating to data centre integration is available from the [http://ep2dc.codeplex.com/documentation CodePlex EP2DC Documentation Page].

=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:
* Enable support for SSO.
* Integrate with other data centres in other scientific domains.
* Associate data with a pre-existing EPrints deposit.

EP2DCOverview

2009-12-24T05:10:13Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Options==
[[Image:ep2dc_eprints_metadata.png|frame|right|||||Screen capture of the metadata section of the EP2DC stage]]

The EP2DC stage for uploading experimental data includes an options (collapsed in the previous figure) that allows metadata associated with the test data to be entered. The fields marked with a red star are mandatory. As shown in the adjacent figure, one of these madatory fields defines the access control. This field affects the data retrieval process, as follows:
* Open—allows data retrieved from the EP2DC EPrints repository to be downloaded by anyone.
* Restricted to registered users—allows data retrieved from the EP2DC EPrints repository to be downloaded by by registered users.
* On demoand—data is supplied on request direct from the owner.

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the page for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=EP2DC Plugin Installation=

Installation of EP2DC at an existing EPrints repository (version 3.1 or higher) 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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx Web Services API documentation].

Further technical information relating to data centre integration is available from the [http://ep2dc.codeplex.com/documentation CodePlex EP2DC Documentation Page].

=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:
* Enable support for SSO.
* Integrate with other data centres in other scientific domains.
* Associate data with a pre-existing EPrints deposit.

EP2DCOverview

2009-12-23T05:16:35Z

Taustin@soton.ac.uk: /* Development Roadmap */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Options==
[[Image:ep2dc_eprints_metadata.png|frame|right|||||Screen capture of the metadata section of the EP2DC stage]]

The EP2DC stage for uploading experimental data includes an options (collapsed in the previous figure) that allows metadata associated with the test data to be entered. The fields marked with a red star are mandatory. As shown in the adjacent figure, one of these madatory fields defines the access control. This field affects the data retrieval process, as follows:
* Open—allows data retrieved from the EP2DC EPrints repository to be downloaded by anyone.
* Restricted to registered users—allows data retrieved from the EP2DC EPrints repository to be downloaded by by registered users.
* On demoand—data is supplied on request direct from the owner.

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the page for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=EP2DC Plugin Installation=

Installation of EP2DC at an existing EPrints repository (version 3.1 or higher) 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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx Web Services API documentation].

Further technical information relating to data centre integration is available from the [http://ep2dc.codeplex.com/documentation CodePlex EP2DC Documentation Page].

=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:
* Enable support for SSO.
* Integrate with other data centres in other scientific domains.
* Associate data with a pre-existing EPrints deposit.

EP2DCOverview

2009-12-23T05:14:09Z

Taustin@soton.ac.uk: /* Data Centre Integration */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Options==
[[Image:ep2dc_eprints_metadata.png|frame|right|||||Screen capture of the metadata section of the EP2DC stage]]

The EP2DC stage for uploading experimental data includes an options (collapsed in the previous figure) that allows metadata associated with the test data to be entered. The fields marked with a red star are mandatory. As shown in the adjacent figure, one of these madatory fields defines the access control. This field affects the data retrieval process, as follows:
* Open—allows data retrieved from the EP2DC EPrints repository to be downloaded by anyone.
* Restricted to registered users—allows data retrieved from the EP2DC EPrints repository to be downloaded by by registered users.
* On demoand—data is supplied on request direct from the owner.

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the page for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=EP2DC Plugin Installation=

Installation of EP2DC at an existing EPrints repository (version 3.1 or higher) 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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx Web Services API documentation].

Further technical information relating to data centre integration is available from the [http://ep2dc.codeplex.com/documentation CodePlex EP2DC Documentation Page].

=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

EP2DCOverview

2009-12-23T05:11:09Z

Taustin@soton.ac.uk: /* EP2DC Plugin Installation */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Options==
[[Image:ep2dc_eprints_metadata.png|frame|right|||||Screen capture of the metadata section of the EP2DC stage]]

The EP2DC stage for uploading experimental data includes an options (collapsed in the previous figure) that allows metadata associated with the test data to be entered. The fields marked with a red star are mandatory. As shown in the adjacent figure, one of these madatory fields defines the access control. This field affects the data retrieval process, as follows:
* Open—allows data retrieved from the EP2DC EPrints repository to be downloaded by anyone.
* Restricted to registered users—allows data retrieved from the EP2DC EPrints repository to be downloaded by by registered users.
* On demoand—data is supplied on request direct from the owner.

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the page for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=EP2DC Plugin Installation=

Installation of EP2DC at an existing EPrints repository (version 3.1 or higher) 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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-23T04:12:33Z

Taustin@soton.ac.uk: /* Data Retrieval */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Options==
[[Image:ep2dc_eprints_metadata.png|frame|right|||||Screen capture of the metadata section of the EP2DC stage]]

The EP2DC stage for uploading experimental data includes an options (collapsed in the previous figure) that allows metadata associated with the test data to be entered. The fields marked with a red star are mandatory. As shown in the adjacent figure, one of these madatory fields defines the access control. This field affects the data retrieval process, as follows:
* Open—allows data retrieved from the EP2DC EPrints repository to be downloaded by anyone.
* Restricted to registered users—allows data retrieved from the EP2DC EPrints repository to be downloaded by by registered users.
* On demoand—data is supplied on request direct from the owner.

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the page for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

File:Retrieving restricted data.png

2009-12-23T04:11:09Z

Taustin@soton.ac.uk:

File:Retrieving unrestricted data.png

2009-12-23T04:06:38Z

Taustin@soton.ac.uk:

File:Deposit eprints stage.png

2009-12-23T03:57:12Z

Taustin@soton.ac.uk: uploaded a new version of "File:Deposit eprints stage.png"

File:Deposit eprints stage.png

2009-12-23T03:54:40Z

Taustin@soton.ac.uk:

EP2DCOverview

2009-12-23T03:44:45Z

Taustin@soton.ac.uk: /* Data Options */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Options==
[[Image:ep2dc_eprints_metadata.png|frame|right|||||Screen capture of the metadata section of the EP2DC stage]]

The EP2DC stage for uploading experimental data includes an options (collapsed in the previous figure) that allows metadata associated with the test data to be entered. The fields marked with a red star are mandatory. As shown in the adjacent figure, one of these madatory fields defines the access control. This field affects the data retrieval process, as follows:
* Open—allows data retrieved from the EP2DC EPrints repository to be downloaded by anyone.
* Restricted to registered users—allows data retrieved from the EP2DC EPrints repository to be downloaded by by registered users.
* On demoand—data is supplied on request direct from the owner.

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the message box for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

File:Ep2dc eprints metadata.png

2009-12-23T03:40:29Z

Taustin@soton.ac.uk:

EP2DCOverview

2009-12-23T03:39:24Z

Taustin@soton.ac.uk:

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Options==
[[Image:ep2dc_eprints_metadata.png|frame|right|||||Screen capture of the metadata section of the EP2DC stage]]

The EP2DC stage for uploading experimental data includes an options (collapsed in the previous figure) that allows metadata associated with the test data to be entered. The fields marked with a red star are mandatory, as shown in the adjacent figure.

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the message box for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

File:Ep2dc eprints stage.png

2009-12-23T03:34:44Z

Taustin@soton.ac.uk: uploaded a new version of "File:Ep2dc eprints stage.png"

File:Ep2dc eprints stage.png

2009-12-21T16:26:07Z

Taustin@soton.ac.uk: uploaded a new version of "File:Ep2dc eprints stage.png": Reverted to version as of 09:36, 15 December 2009

EP2DCOverview

2009-12-21T16:25:46Z

Taustin@soton.ac.uk: /* Data Upload */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the message box for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T16:25:13Z

Taustin@soton.ac.uk: /* Data Upload */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|600px|thumb|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the message box for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

File:Ep2dc eprints stage.png

2009-12-21T16:20:46Z

Taustin@soton.ac.uk: uploaded a new version of "File:Ep2dc eprints stage.png"

EP2DCOverview

2009-12-21T16:11:35Z

Taustin@soton.ac.uk: /* Retrieving the Data */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Data Retrieval==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the message box for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T16:11:13Z

Taustin@soton.ac.uk: /* Depositing the Data */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Data Deposit==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Retrieving the Data==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the message box for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T16:10:53Z

Taustin@soton.ac.uk: /* Uploading the Data */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Data Upload==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Depositing the Data==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Retrieving the Data==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the message box for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T16:10:21Z

Taustin@soton.ac.uk: /* Features */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

The EP2DC module affects the default stages for upload and deposit, as well as the page displayed when a unit of work that includes a remotely stored data set is retrieved.

==Uploading the Data==
[[Image:ep2dc_eprints_stage.png|frame|right|||||Screen capture of the EP2DC stage added to the default EPrints stages]]

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

<div style="clear: both;"></div>

==Depositing the Data==
[[Image:deposit_eprints_stage.png|frame|right|||||Screen capture of the default EPrints deposit stage for a successfully deposited unit of work]]

The last stage in the EPrints default workflow is to deposit the unit of work (meaning all of the documentation, figures, etc. together with the accompanying data). The data will be deposited ataa remoted data centre, which is responsible for validating the data against the corresponding XML Schema Definition. If the data sets is validated and deposited successfully, a page similar to that shown in the adjacent figure is displayed.

<div style="clear: both;"></div>

==Retrieving the Data==
[[Image:retrieving_unrestricted_data.png|frame|right|||||Screen capture of the link to the data set and the disproportionate feedback provided on related data sets]]

As shown in the adjacent figure, when an item that has accompanying data is retrieved, in the case where a data set is unrestricted (meaning open access or accessible to registered users), there is an accompanying link to the data.

<div style="clear: both;"></div>

[[Image:retrieving_restricted_data.png|frame|right|||||Screen capture of the message box for requesting access to restricted data]]

In the case where the data set is available on demand, a message can be sent to the owner requesting that a copy of the data set be provided.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T15:53:41Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set at [[SampleMatDBCompliantDataSet]] can be copy/pasted into an XML file (the XML extension is important because the EP2DC module filters on this file type).
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

SampleMatDBCompliantDataSet

2009-12-21T15:51:24Z

Taustin@soton.ac.uk: Created page with ' <?xml version="1.0" encoding="UTF-8"?> <MatDB:MatDB xsi:schemaLocation="http://odin.jrc.ec.europa.eu matdb.xsd" xmlns:MatDB="http://odin.jrc.ec.europa.eu" xmlns:xsi="http://w…'

<?xml version="1.0" encoding="UTF-8"?>
<MatDB:MatDB xsi:schemaLocation="http://odin.jrc.ec.europa.eu matdb.xsd" xmlns:MatDB="http://odin.jrc.ec.europa.eu" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<MatDB:Source>
<MatDB:Details companyName="University of Southampton" sourceNumber="text" sourceKey="text">
<MatDB:Address state="Hampshire" street="University Road" city="Southampton" postCode="SO17 1BJ" country="United Kingdom"/>
<MatDB:FullSourceTitle>School of Engineering Sciences, University of Southampton</MatDB:FullSourceTitle>
<MatDB:DateOfSourceDelivery>2009-12-14</MatDB:DateOfSourceDelivery>
<MatDB:SourceAdministrator>Tim Austin</MatDB:SourceAdministrator>
<MatDB:Reports>
<MatDB:ReferenceToReport hyperlinkToReport="text" authors="text" year="test" title="text"/>
</MatDB:Reports>
</MatDB:Details>
<MatDB:ProjectResponsibilities name="text"></MatDB:ProjectResponsibilities>
</MatDB:Source>
<MatDB:Materials>
<MatDB:Material materialKey="sample_1" materialName="text" materialClass="text">
<MatDB:Production internalMaterialSpecification="text" combinedMaterialName="text" materialNumber="text" nameOfProducer="text" chemicalAnalysis="text" batchIdentifier="text" productionRemark="text" supplierName="text" referenceToProducer="text" serialNumber="text" metallurgicalProcess="text" formingProcedure="text" productForm="text" grainSizeType="text">
<MatDB:Characterisation/>
<MatDB:ProductSize>text</MatDB:ProductSize>
</MatDB:Production>
<MatDB:ChemicalComposition>
<MatDB:Symbol maximumContent="100.0" minimumContent="100.0" meanContent="100.0" remark="String">Al</MatDB:Symbol>
</MatDB:ChemicalComposition>
<MatDB:ThermoMechanicalHeatTreatment>
<MatDB:Step type="text" quenchingType="water" treatedOn="text" environment="text">
<MatDB:Temperature unit="C" value="0"/>
<MatDB:HoldTime unit="s" value="text"/>
<MatDB:HeatingOrCoolingRate unit="1/s" value="text"/>
<MatDB:ColdWork unit="text" value="text"/>
<MatDB:HipingPressure unit="MPa" value="text"/>
</MatDB:Step>
</MatDB:ThermoMechanicalHeatTreatment>
<MatDB:Hardness meanValue="text" minimumValue="text" maximumValue="text" testMethod="text" measuredAt="text">
<MatDB:TestLoad unit="text" value="text"/>
</MatDB:Hardness>
<MatDB:PhysicalMetallurgicalProperties>
<MatDB:RecrystalisationTemperature unit="text" value="text"/>
<MatDB:SolidusTemperature unit="text" value="text"/>
</MatDB:PhysicalMetallurgicalProperties>
<MatDB:GrainSize>
<MatDB:DirectionallySolidified>text</MatDB:DirectionallySolidified>
</MatDB:GrainSize>
</MatDB:Material>
</MatDB:Materials>
<MatDB:Tests>
<MatDB:Test testID="ID_2" materialKey="ID_1" sourceKey="text">
<MatDB:UniaxialTensile linkToDescription="https://odin.jrc.ec.europa.eu/alcor/docums/uniaxial tensile.pdf">
<MatDB:Specimen>
<MatDB:SpecimenGeometryAndProduction characterisation="text" materialKey="ID_1" standard="text" specimenName="text" sampling="text" remark="text" orientation="text" specimenForm="text" internalSpecimenSpecification="text"/>
<MatDB:SpecimenDimension>
<MatDB:ActiveGaugeLength unit="mm">20</MatDB:ActiveGaugeLength>
<MatDB:ActiveSurface unit="mm2">20</MatDB:ActiveSurface>
<MatDB:DiameterMisalignment unit="text"/>
<MatDB:ThicknessB unit="mm">5</MatDB:ThicknessB>
<MatDB:Width unit="mm">4</MatDB:Width>
</MatDB:SpecimenDimension>
</MatDB:Specimen>
<MatDB:TestResults>
<MatDB:TestData qualityRemark="text" testDate="1967-08-13" testStandard="text" testedBy="text" testResultKey="text" remark="text" testMachine="text">
<MatDB:ReferenceToReport hyperlinkToReport="text" authors="text" year="text" title="text"/>
<MatDB:TestParams>
<MatDB:TestControl>text</MatDB:TestControl>
<MatDB:Temperature unit="C" value="0"/>
<MatDB:DisplacementRate1 unit="m/s" value="0"/>
<MatDB:DisplacementRate2 unit="m/s" value="0"/>
<MatDB:LoadRate1 unit="N/s" value="0"/>
<MatDB:LoadRate2 unit="N/s" value="0"/>
<MatDB:StrainRate1 unit="1/s" value="0"/>
<MatDB:StrainRate2 unit="1/s" value="0"/>
<MatDB:StressRate1 unit="MPa/s" value="0"/>
<MatDB:StressRate2 unit="MPa/s" value="0"/>
</MatDB:TestParams>
<MatDB:Results>
<MatDB:TensileStrength unit="MPa" value="0"/>
<MatDB:YieldStrength unit="MPa" value="0"/>
<MatDB:LowerYStrength unit="MPa" value="0"/>
<MatDB:UpperYStrength unit="MPa" value="0"/>
<MatDB:ElongAfterRupture unit="%" value="0"/>
<MatDB:UniformElongation unit="%" value="0"/>
<MatDB:ReductionOfArea unit="%" value="0"/>
<MatDB:YoungsModulus unit="MPa" value="0"/>
<MatDB:ProofStrength PS0.01perc="text" PS0.1perc="text" PS10perc="text" PS0.5perc="text" unit="MPa" PS2perc="text" PS0.02perc="text" PS0.2perc="text" PS20perc="text" PS1perc="text" PS0.05perc="text" PS5perc="text"/>
</MatDB:Results>
<MatDB:Fracture>
<MatDB:FractureMode>text</MatDB:FractureMode>
<MatDB:FracturePosition>text</MatDB:FracturePosition>
<MatDB:GaugeLengthElong>text</MatDB:GaugeLengthElong>
</MatDB:Fracture>
<MatDB:OrientationDeviationAngle unit="Â°" deviationAngleRho="text" deviationAngleTheta="text"/>
</MatDB:TestData>
<MatDB:CurveData>
<MatDB:SequenceNumber>1</MatDB:SequenceNumber>
<MatDB:EngStrain unit="%">0.0001</MatDB:EngStrain>
<MatDB:EngStress unit="MPa">10</MatDB:EngStress>
<MatDB:TrueStrain unit="%">0.0001</MatDB:TrueStrain>
<MatDB:TrueStress unit="MPa">10</MatDB:TrueStress>
<MatDB:Load unit="N">1</MatDB:Load>
<MatDB:TransStrainEng unit="%">0.000</MatDB:TransStrainEng>
<MatDB:Time unit="s">1</MatDB:Time>
<MatDB:Notes>text</MatDB:Notes>
</MatDB:CurveData>
<MatDB:CurveData>
<MatDB:SequenceNumber>2</MatDB:SequenceNumber>
<MatDB:EngStrain unit="%">0.0002</MatDB:EngStrain>
<MatDB:EngStress unit="MPa">20</MatDB:EngStress>
<MatDB:TrueStrain unit="%">0.0002</MatDB:TrueStrain>
<MatDB:TrueStress unit="MPa">20</MatDB:TrueStress>
<MatDB:Load unit="N">2</MatDB:Load>
<MatDB:TransStrainEng unit="%">0.000</MatDB:TransStrainEng>
<MatDB:Time unit="s">2</MatDB:Time>
<MatDB:Notes>text</MatDB:Notes>
</MatDB:CurveData>
<MatDB:CurveData>
<MatDB:SequenceNumber>3</MatDB:SequenceNumber>
<MatDB:EngStrain unit="%">0.0003</MatDB:EngStrain>
<MatDB:EngStress unit="MPa">30</MatDB:EngStress>
<MatDB:TrueStrain unit="%">0.0003</MatDB:TrueStrain>
<MatDB:TrueStress unit="MPa">30</MatDB:TrueStress>
<MatDB:Load unit="N">3</MatDB:Load>
<MatDB:TransStrainEng unit="%">0.000</MatDB:TransStrainEng>
<MatDB:Time unit="s">3</MatDB:Time>
<MatDB:Notes>text</MatDB:Notes>
</MatDB:CurveData>
<MatDB:CurveData>
<MatDB:SequenceNumber>4</MatDB:SequenceNumber>
<MatDB:EngStrain unit="%">0.0004</MatDB:EngStrain>
<MatDB:EngStress unit="MPa">40</MatDB:EngStress>
<MatDB:TrueStrain unit="%">0.0004</MatDB:TrueStrain>
<MatDB:TrueStress unit="MPa">40</MatDB:TrueStress>
<MatDB:Load unit="N">4</MatDB:Load>
<MatDB:TransStrainEng unit="%">0.000</MatDB:TransStrainEng>
<MatDB:Time unit="s">4</MatDB:Time>
<MatDB:Notes>text</MatDB:Notes>
</MatDB:CurveData>
<MatDB:CurveData>
<MatDB:SequenceNumber>5</MatDB:SequenceNumber>
<MatDB:EngStrain unit="%">0.0005</MatDB:EngStrain>
<MatDB:EngStress unit="MPa">50</MatDB:EngStress>
<MatDB:TrueStrain unit="%">0.0005</MatDB:TrueStrain>
<MatDB:TrueStress unit="MPa">50</MatDB:TrueStress>
<MatDB:Load unit="N">5</MatDB:Load>
<MatDB:TransStrainEng unit="%">0.000</MatDB:TransStrainEng>
<MatDB:Time unit="s">5</MatDB:Time>
<MatDB:Notes>text</MatDB:Notes>
</MatDB:CurveData>
</MatDB:TestResults>
</MatDB:UniaxialTensile>
</MatDB:Test>
</MatDB:Tests>
</MatDB:MatDB>

EP2DCOverview

2009-12-21T15:44:47Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[SampleMatDBCompliantDataSet]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T15:13:16Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[File:sample.ogg]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T15:10:08Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[MatdDBSampleDataSet]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T05:43:49Z

Taustin@soton.ac.uk: /* Introduction */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC EPrints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[File:matdb_data_set.xml]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T05:43:24Z

Taustin@soton.ac.uk: /* Introduction */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre], it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[File:matdb_data_set.xml]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T05:42:38Z

Taustin@soton.ac.uk: /* Introduction */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre] (presently under development at the University of Southampton) it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[File:matdb_data_set.xml]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T05:36:29Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre] that is presently under development at the University of Southampton, it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[File:matdb_data_set.xml]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T05:35:27Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre] that is presently under development at the University of Southampton, it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[Media:matdb_data_set.xml]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T05:34:12Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre] that is presently under development at the University of Southampton, it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[sample.xml]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T05:18:43Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre] that is presently under development at the University of Southampton, it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload a MatDB-compliant data set, add some additional metadata, and set the access rights, which are open, accessible to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[EP2DCSampleDataSet]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

File:EPrints navigable stages.png

2009-12-21T05:14:44Z

Taustin@soton.ac.uk: uploaded a new version of "File:EPrints navigable stages.png"

Screen capture of the EP2DC deposit stages

EP2DCOverview

2009-12-21T05:10:41Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre] that is presently under development at the University of Southampton, it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png||center]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload MatDB-compliant data set, add some additional metadata, and set the access rights, which are either open, accessable to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[EP2DCSampleDataSet]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

File:EPrints navigable stages.png

2009-12-21T05:08:53Z

Taustin@soton.ac.uk: Screen capture of the EP2DC deposit stages

Screen capture of the EP2DC deposit stages

EP2DCOverview

2009-12-21T05:06:34Z

Taustin@soton.ac.uk: /* Trialing the EP2DC Service */

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre] that is presently under development at the University of Southampton, it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:EPrints_navigable_stages.png|frame|center|||||The EP2DC EPrints Workflow]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload MatDB-compliant data set, add some additional metadata, and set the access rights, which are either open, accessable to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[EP2DCSampleDataSet]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-21T05:02:55Z

Taustin@soton.ac.uk: Add trialing instructions

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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx EP2DC Rapid Innovation Project], and the support of JISC, both financial and managerial, is gratefully acknowledged.

An EPrints repository configured for the EP2DC plugin is hosted by the University of Southampton School of Engineering Sciences at [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository]. Whilst the EP2DC plugin has been tested and refined by an integration with the JISC-funded [https://mdc-s1.soton.ac.uk/ Materials Data Centre] that is presently under development at the University of Southampton, it is designed for integration with any data centre.

=Trialing the EP2DC Service=

As already mentioned, EP2DC is a module designed to serve the data capture needs of the scientific community. To trial the service, perhaps in anticipation of installing at your own EPrints repository, or simply to gain an understanding of the direction data management in the UK HE sector is taking, you are invited to upload a sample file and data set, as follows:
* Navigate to [http://ep2dc-s1.soton.ac.uk EP2DC Eprints Repository].
* If not already registered, use the <em>Create Account</em> link at the top left of the landing page to create an account.
* Once logged-in, click the <em>New Item</em> button on the Manage Deposits page. This opens the Edit Item page, which is the entry point for depositing a new item.
* The workflow for creating/editing a deposit is shown in a navigable bar towards the top of the page, as shown in the figure:
[[Image:eprints_stage.png|frame|right|||||The EP2DC EPrints Workflow]]
* The EPrints stages are designed to be intuitive, with Help icons adjacent to each field. Required fields are marked with a red star, but in an effort to simplify the process of depositing an item, these are kept to a minimum.
* The new stage that the EP2DC module introduces is labelled EP2DC Data. At this stage you can upload MatDB-compliant data set, add some additional metadata, and set the access rights, which are either open, accessable to registered users, or available on demand. For the purposes of trialing the service, a sample data set is available at [[EP2DCSampleDataSet]].
* At the <em>Deposit</em>, clicking <em>Deposit</em> will deposit the data set to the MDC repository, and the accompanying manuscript (or other unit of work associated with the data) to the EP2DC EPrints repository.
* Once the data (and the accompanying manuscript or other unit of work associated with the data) are deposited, the standard EPrints search options can be used to retrieve the deposit.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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:

* <code>cd /opt/eprints3/archives/ARCHIVE_ID</code>

* <code>cp mdc-1.0.tar.gz .</code>

* <code>tar zxvf mdc-1.0.tar.gz</code>
This will copy most of the files at the right location.

* <code>cd /opt/eprints3/archives/ARCHIVE_ID/cfg/cfg.d</code>

* Edit '''document_fields_default.pl''', adding the following:
$data->{ep2dc_is_validated} = 'TRUE';
Save the changes.

* Edit '''document_fields.pl''', adding 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 the changes.

* Edit '''eprint_warnings.pl''', adding the following to the end of the file:
push @problems, $session->make_text( "After clicking the deposit button, all EP2DC data files will automatically be transferred to the selected datacentre(s)." );
Save the changes.

* Edit '''eprint_render.pl''' as follows:
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 the changes.

* Update your workflow file in order to enable the upload of XML datasets to your EPrints repository:

Edit '''/opt/eprints3/archives/ARCHIVE_ID/cfg/worklows/eprint/default.xml''', add the following stage definition (between the <flow> tags):

<code>
<stage ref="data"/>
</code>

and add the stage:

<code>
<stage name="data">
<component type="XHTML"><epc:phrase ref="Plugin/InputForm/Component/EP2DCUpload:help" /></component>
<component type="EP2DCUpload">
<upload-methods>
<method>file</method>
</upload-methods>
<field ref="ep2dc_data_centre" required="yes" />
<field ref="ep2dc_test_type" required="yes" />
<field ref="ep2dc_test_date" required="yes" />
<field ref="ep2dc_test_centre" required="yes" />
<field ref="ep2dc_security" required="yes" />
</component>
</stage>
</code>

* Add the new fields to the database with <code>/opt/eprints3/bin/epadmin update_database_structure ARCHIVE_ID</code>

* Link the CGI scripts to EPrints with <code>ln -s /opt/eprints3/archives/ARCHIVE_ID/cgi/* /opt/eprints3/cgi/</code>

* Restart your web server, as root with <code>/etc/init.d/httpd restart</code>
(note that this line might be different depending on which version of Linux you are running).

=Data Centre Integration=

The data centre integration relies on an EP2DC RESTful Web Services API. In the case of the [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-15T10:04:53Z

Taustin@soton.ac.uk: /* Install */

File:Ep2dc eprints stage.png

2009-12-15T09:36:58Z

Taustin@soton.ac.uk:

EP2DCOverview

2009-12-15T09:20:04Z

Taustin@soton.ac.uk: /* Introduction */

EP2DCOverview

2009-12-15T09:10:18Z

Taustin@soton.ac.uk: /* Introduction */

EP2DCOverview

2009-12-15T09:07:38Z

Taustin@soton.ac.uk: /* Introduction */

EP2DCOverview

2009-12-14T22:39:07Z

Taustin@soton.ac.uk:

EP2DCOverview

2009-12-14T22:37:55Z

Taustin@soton.ac.uk: /* Development Roadmap */

The EPrints to Data Centre (EP2DC) plugin extends EPrints to support uploading to a remote data centre any XML-formatted experimental data associated with your 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 experimental 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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx 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 [https://mdc-s1.soton.ac.uk/ Materials Data Centre] that is presently under development at the University of Southampton, it is designed for integration with any data centre.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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 [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx 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

EP2DCOverview

2009-12-14T22:28:31Z

Taustin@soton.ac.uk: first draft of the ep2dc overview

The EPrints to Data Centre (EP2DC) plugin extends EPrints to support uploading to a remote data centre any XML-formatted experimental data associated with your 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 experimental 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 [http://www.jisc.ac.uk/whatwedo/programmes/inf11/jiscri/ep2dc.aspx 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 [https://mdc-s1.soton.ac.uk/ Materials Data Centre] that is presently under development at the University of Southampton, it is designed for integration with any data centre.

=Features=

[[Image:ep2dc_eprints_stage.png|frame|right|||||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.

<div style="clear: both;"></div>

=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 [https://mdc-s1.soton.ac.uk/ Materials Data Centre], the end point is available at [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/MDCSvc.svc 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 [https://mdc-s1.soton.ac.uk:8080/mdc_bin/EP2DC/ServiceDocumentation.aspx Web Services API documentation].

=Development Roadmap=
As mentioned, the module 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

Files/EPrints MDC Layer

2009-12-14T21:15:22Z

Taustin@soton.ac.uk: redirect to EP2DC overview posting

#REDIRECT [[EP2DCOverview]]