def render_record(self, c):
if c.resource['format'].lower() != 'dwc':
abort(404, _('Record not in Darwin Core format'))
c.record_title = c.record_dict.get('catalogNumber', None) or c.record_dict.get('occurrenceID')
c.dwc_terms = dwc_terms(c.record_dict.keys())
try:
c.dynamic_properties = c.dwc_terms.pop('dynamicProperties')
except IndexError:
c.dynamic_properties = []
return p.toolkit.render('record/dwc.html')
def _dwc(self):
'''
Yields triples describing the record using DWC (DarWin Core) terms.
:return: yields triples
'''
yield self.record_ref, self.namespaces.dc.identifier, Literal(self.record[u'occurrenceID'])
dwc_terms_dict = dwc_terms(self.record.keys())
groups_to_skip = {u'dynamicProperties'}
terms_to_skip = {u'associatedMedia', u'created', u'modified'}
for group, terms in dwc_terms_dict.items():
if group in groups_to_skip:
continue
for uri, term in terms.items():
if term in terms_to_skip:
continue
yield (self.record_ref, getattr(self.namespaces.dwc, term),
Literal(self.record.get(term)))
# retrieve the dynamic properties and yield them as one JSON dump
dynamic_properties_dict = {}
for properties in dwc_terms_dict.get(u'dynamicProperties', {}).values():
for dynamic_property in properties:
if dynamic_property == u'created':
continue
dynamic_properties_dict[dynamic_property] = self.record.get(dynamic_property)
if dynamic_properties_dict:
yield self.record_ref, self.namespaces.dwc.dynamicProperties, \
Literal(json.dumps(dynamic_properties_dict))
# yield the associatedMedia term as a pipe-separated list of image URIs
media = self.record.get(u'associatedMedia', [])
if media:
yield self.record_ref, self.namespaces.dwc.associatedMedia, \
Literal(as_dwc_list(map(itemgetter(u'identifier'), media)))
# yield the created date in the correct format
yield (self.record_ref, self.namespaces.dc.created,
Literal(epoch_to_datetime(self.record.get(u'created'))))
# yield the modified date in the correct format
yield (self.record_ref, self.namespaces.dwc.modified,
Literal(epoch_to_datetime(self.record.get(u'modified'))))
def graph_from_record(self, record_dict, resource, record_ref):
"""
RDF for an individual record - currently this is a specimen record
Similar approach to: curl -L -H "Accept: application/rdf+ttl" http://data.rbge.org.uk/herb/E00321910
:param record_dict:
:param resource:
:param record_ref:
:return:
"""
context = self.get_context()
namespaces = {
'dc': DC,
'dcat': DCAT,
'dwc': DWC,
'sdwc': SDWC,
'void': VOID,
'cc': CC,
'foaf': FOAF,
'dqv': DQV,
'aiiso': AIISO,
'tdwgi': TDWGI,
'owl': OWL
}
g = self.g
# Add some more namespaces
for prefix, namespace in namespaces.iteritems():
g.bind(prefix, namespace)
# Get the GBIF record if it exists
occurrence_id = record_dict.get('occurrenceID')
package_id = resource.get_package_id()
# Create licences metadata for record
object_uri = URIRef(record_ref + '#object')
# Add publisher - as per BBC we don't need the full org description here
nhm_uri = URIRef('http://nhm.ac.uk')
# Add object description - the metadata and license
g.add((record_ref, RDF.type, FOAF.Document))
g.add((record_ref, CC.license, URIRef(METADATA_LICENCE)))
# This metadata describes #dataset
g.add((record_ref, FOAF.primaryTopic, object_uri))
# Add the de-referenced link to record
record_link = url_for('record', action='view', package_name=package_id, resource_id=resource.id, record_id=record_dict['_id'], qualified=True)
g.add((record_ref, DC.hasVersion, URIRef(record_link)))
# Add institution properties
g.add((record_ref, FOAF.organization, nhm_uri))
g.add((record_ref, AIISO.Department, Literal(get_department(record_dict['collectionCode']))))
try:
sub_dept = record_dict.pop('subDepartment')
except KeyError:
pass
else:
g.add((record_ref, AIISO.Division, Literal(sub_dept)))
# Created and modified belong to the metadata record, not the specimen
for term in ['created', 'modified']:
try:
value = record_dict.get(term)
except KeyError:
pass
else:
# Parse into data format, and add as dates
_date = parse_date(value)
g.add((record_ref, getattr(DWC, term), Literal(_date.isoformat(), datatype=XSD.dateTime)))
try:
gbif_record = toolkit.get_action('gbif_record_show')(context, {
'occurrence_id': occurrence_id
})
except NotFound:
gbif_record = {}
else:
# Assert equivalence with the GBIF record
gbif_uri = os.path.join('http://www.gbif.org/occurrence', gbif_record['gbifID'])
g.add((object_uri, OWL.sameAs, URIRef(gbif_uri)))
# If we have a GBIF country code, add it
# Annoyingly, this seems to be the only geographic element on GBIF with URI
country_code = gbif_record.get('gbifCountryCode')
if country_code:
g.add((object_uri, DWC.countryCode, URIRef(os.path.join('http://www.gbif.org/country', country_code))))
# Now, create the specimen object
# Remove nulls and hidden fields from record_dict
record_dict = dict((k, v) for k, v in record_dict.iteritems() if v)
# Now add the actual specimen object
g.add((object_uri, RDF.type, FOAF.Document))
g.add((object_uri, RDF.type, SDWC.SimpleDarwinRecordSet))
# Make sure decimal latitude and longitude are strings
for d in ['decimalLatitude', 'decimalLongitude']:
try:
record_dict[d] = str(record_dict[d])
except KeyError:
pass
# Adding images as JSON is rubbish! So lets try and do it properly
try:
associated_media = record_dict.pop('associatedMedia')
except KeyError:
pass
else:
images = json.loads(associated_media)
for image in images:
image_uri = URIRef(image['identifier'])
g.set((image_uri, RDF.type, FOAF.Image))
title = image.get('title', None)
if title:
g.set((image_uri, DC.title, Literal(title)))
g.set((image_uri, CC.license, URIRef(image['license'])))
g.set((image_uri, DC.RightsStatement, Literal(image['rightsHolder'])))
g.set((image_uri, DC.Format, Literal(image['format'])))
# Add link from image to object...
g.set((image_uri, FOAF.depicts, object_uri))
# And object to image
g.add((object_uri, FOAF.depiction, image_uri))
# This record belongs in X dataset
dataset_ref = URIRef(dataset_uri({'id': package_id}) + '#dataset')
g.add((object_uri, VOID.inDataset, dataset_ref))
dwc_terms_dict = dwc_terms(record_dict.keys())
# Handle dynamic properties separately
dynamic_properties = dwc_terms_dict.pop('dynamicProperties')
for group, terms in dwc_terms_dict.items():
for uri, term in terms.items():
# Do we have a GBIF key value?
# Uppercase first letter of term, and convert to GBIF key format => gbifGenusKey
uc_term = term[0].upper() + term[1:]
gbif_term_key = 'gbif%sKey' % uc_term
gbif_key = gbif_record.get(gbif_term_key)
# Do we have a GBIF key value? If we do, we can provide a URI to GBIF
if gbif_key:
gbif_uri = URIRef(os.path.join('http://www.gbif.org/species', gbif_key))
# Add the GBIF species URI with label
g.add((gbif_uri, RDFS.label, Literal(record_dict.get(term))))
# And associated our specimen object's DWC term with the GBIF URI
g.add((object_uri, getattr(DWC, term), gbif_uri))
else:
# We do not have a GBIF key, so no URI: Add the term value as a literal
g.add((object_uri, getattr(DWC, term), Literal(record_dict.get(term))))
g.add((object_uri, DC.identifier, Literal(record_dict.get('uuid'))))
dynamic_properties_dict = {}
for properties in dynamic_properties.values():
for property in properties:
dynamic_properties_dict[property] = record_dict.get(property)
if dynamic_properties_dict:
g.add((object_uri, DWC.dynamicProperties, Literal(json.dumps(dynamic_properties_dict))))
