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###############################################################################
#
# This file is part of the Utopia Documents application.
# Copyright (c) 2008-2014 Lost Island Labs
# <info@utopiadocs.com>
#
# Utopia Documents is free software: you can redistribute it and/or modify
# it under the terms of the GNU GENERAL PUBLIC LICENSE VERSION 3 as
# published by the Free Software Foundation.
#
# Utopia Documents is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# In addition, as a special exception, the copyright holders give
# permission to link the code of portions of this program with the OpenSSL
# library under certain conditions as described in each individual source
# file, and distribute linked combinations including the two.
#
# You must obey the GNU General Public License in all respects for all of
# the code used other than OpenSSL. If you modify file(s) with this
# exception, you may extend this exception to your version of the file(s),
# but you are not obligated to do so. If you do not wish to do so, delete
# this exception statement from your version.
#
# You should have received a copy of the GNU General Public License
# along with Utopia Documents. If not, see <http://www.gnu.org/licenses/>
#
###############################################################################
#? name: Dryad
#? www: http://datadryad.org/
#? urls: http://datadryad.org/ https://utopia.cs.man.ac.uk/
import common.utils
import json
import re
import socket
import spineapi
import utopia.document
import urllib2
from lxml import etree
import string
ns = {
'mets': 'http://www.loc.gov/METS/',
'dim': 'http://www.dspace.org/xmlns/dspace/dim',
'kend': 'http://utopia.cs.manchester.ac.uk/kend',
'property': 'http://utopia.cs.manchester.ac.uk/kend/property#'
}
class Dryad(utopia.document.Annotator, utopia.document.Visualiser):
"""Generate Dryad information"""
def on_ready_event(self, document):
#print "RUNNING DRYAD PLUGIN"
doi = common.utils.metadata(document, 'doi')
if doi is not None:
# see if kend knows about this DOI as a Dryad record
response = urllib2.urlopen('https://utopia.cs.man.ac.uk/kend/0.7/define/lookup?database=dryad&term=%s&limit=1000' % doi, timeout=8)
root = etree.fromstring(response.read())
dryadShortHandle = root.findtext('kend:group/kend:annotation/kend:properties/property:databaseTerm', namespaces=ns)
if dryadShortHandle is not None:
# then we have a dryad short-form doi, so can now safely go to dryad to get the rest
response = urllib2.urlopen('http://datadryad.org/solr/search/select/?q=dc.relation.isreferencedby:%s&fl=dc.identifier,dc.title_ac,dc.identifier.uri,dc.contributor.author,dc.date.issued.year,dc.identifier.citation,dc.description' % doi, timeout=8)
root = etree.fromstring(response.read())
#print etree.tostring(root, pretty_print=True, encoding='utf8')
result = root.find('result')
if result.attrib['numFound'] != '0':
# then we have found some datasets for this article DOI
packageDetails = urllib2.urlopen('http://datadryad.org/metadata/handle/%s/mets.xml' % dryadShortHandle, timeout=8)
root = etree.fromstring(packageDetails.read())
#print etree.tostring(root, pretty_print=True, encoding='utf8')
identifiers = root.findall('mets:dmdSec/mets:mdWrap/mets:xmlData/dim:dim/dim:field[@element="identifier"]', namespaces=ns)
packageDOI = None
for identifier in identifiers:
if identifier.text.startswith('doi:'):
packageDOI = identifier.text[4:]
break
contributors = root.findall('mets:dmdSec/mets:mdWrap/mets:xmlData/dim:dim/dim:field[@qualifier="author"]', namespaces=ns)
dataCitation = {
'year': result.findtext("doc/arr[@name='dc.date.issued.year']/int", namespaces=ns),
'title': root.findtext('mets:dmdSec/mets:mdWrap/mets:xmlData/dim:dim/dim:field[@element="title"]', namespaces=ns),
'authors': [string.capwords(a.text) for a in contributors],
'source': 'Dryad Digital Repository',
'doi': packageDOI,
}
articleCitation = root.findtext('mets:dmdSec/mets:mdWrap/mets:xmlData/dim:dim/dim:field[@qualifier="citation"][@element="identifier"]', namespaces=ns)
xhtml = '''
<p>
The data associated with this article are available via Dryad. When using
these data, please cite both the article:
</p>
<div class="box">{0}<br /><a href="http://dx.doi.org/{1}">doi:{1}</a></div>
<p>
and also the data package:
</p>
<div class="box">{2}<br /><a href="http://dx.doi.org/{3}">doi:{3}</a></div>
'''.format(articleCitation, doi, common.utils.format_citation(dataCitation), dataCitation['doi'])
a = spineapi.Annotation()
a['concept'] = 'Dryad'
a['property:name'] = 'Dryad'
a['property:sourceDatabase'] = 'dryad'
a['property:sourceDescription'] = '<p><a href="http://datadryad.org/">Dryad</a> is an international repository of data underlying peer-reviewed articles in the basic and applied biosciences.</p>'
a['property:description'] = 'Data associated with this article'
a['property:xhtml'] = xhtml
document.addAnnotation(a)
def visualisable(self, a):
return a.get('concept') == 'Dryad'
def visualise(self, a):
return a.get('property:xhtml')
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