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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/>
#
###############################################################################
import datetime
import re
import spineapi
import utopia
def hasprovenance(value):
return hasattr(value, '_provenance') and type(value._provenance) == dict
def provenance(value):
try:
return value._provenance
except AttributeError:
raise RuntimeError('No associated provenance found for this value')
def wrap_provenance(value, **kwargs):
kwargs.setdefault('when', datetime.datetime.now())
if isinstance(kwargs['when'], datetime.datetime):
kwargs['when'] = kwargs['when'].isoformat()
class sourced(type(value)):
_provenance = kwargs
sourced = sourced(value)
return sourced
def metadata(document, needle = None, as_list = False, all = False, whence = None):
# Place to accumulate metadata before returning
data = {}
# Should the value(s) be seen as a list?
if needle is not None and needle[-2:] == '[]':
as_list = True
needle = needle[:-2]
# 'Official' metadata keys (i.e. legacy keys)
alternatives = {
'articleTitle': 'title',
'articleDOI': 'doi',
'articlePMID': 'pmid',
}
# Find all metadata annotations in the appropriate scratch list
for annotation in document.annotations('Document Metadata'):
# Check the two kinds of annotations that hold metadata
if annotation.get('concept') in ('DocumentMetadata', 'DocumentIdentifier'):
# Compile information from annotation
provdata = {}
metadata = {}
for key, value in annotation.iteritems():
if key.startswith('provenance:') and len(value) > 0:
key = key[11:]
provdata[key] = value[0]
elif key.startswith('property:'):
key = key[9:]
key = alternatives.get(key, key)
if needle is None or needle == key:
# Store all the values
if as_list:
metadata[key] = value
elif len(value) > 0:
metadata[key] = value[0]
# Skip unmatching provenance
if whence is not None and provdata.get('whence') != whence:
continue
# Apply provenance and store metadata
for key, value in metadata.iteritems():
data.setdefault(key, [])
data[key].append(wrap_provenance(value, **provdata))
# Sort metadata according to weight / when provenance fields
def cmp_provenance(left, right):
lprov, rprov = provenance(left), provenance(right)
lweight, rweight = int(lprov.get('weight', '1')), int(rprov.get('weight', '0'))
lwhen, rwhen = lprov.get('when'), rprov.get('when')
if lweight > rweight:
return -1
elif lweight == rweight:
return cmp(lwhen, rwhen)
else:
return 1
for key, value in data.iteritems():
value.sort(cmp_provenance)
# If not requesting everything, only choose the highest weighted values
if not all:
data = dict(((k, v[0]) for k, v in data.iteritems()))
# If not searching for a specific key, only choose that key
if needle is not None:
data = data.get(needle)
# Return requested metadata
return data
def _metadata(document, needle = None, default = None, as_list = False, whence = None):
# Place to accumulate metadata before returning
data = {}
# Should the needle be seen as a list?
if needle is not None and needle[-2:] == '[]':
as_list = True
needle = needle[:-2]
def set_data(key, weight, value):
if value is not None:
data.setdefault(key, {})
data[key][weight] = value
def one_or_all(key, value):
if value is not None:
if as_list:
return value
elif isinstance(value, (set, list, tuple)):
if len(value) > 0:
prov = None
if hasprovenance(value):
prov = provenance(value)
value = tuple(value)[0]
if prov is not None:
value = wrap_provenance(value, **prov)
return value
else:
return value
if whence is None and needle is not None:
# Check 'official' metadata
alternatives = {
'title': 'articleTitle',
'doi': 'articleDOI',
'pmid': 'articlePMID',
}
if needle in alternatives:
alternative_key = alternatives.get(needle)
for annotation in document.annotations('Document Metadata'):
if annotation.get('concept') == 'DocumentMetadata':
value = annotation.get('property:{0}'.format(alternative_key))
if value is not None:
value = wrap_provenance(value, whence=annotation.get('provenance:whence'))
set_data(needle, 0, value)
# Check already scraped data
for annotation in document.annotations('Document Metadata'):
if annotation.get('concept') == 'DocumentIdentifier':
if whence is None or annotation.get('provenance:whence') == whence:
for key, value in annotation.iteritems():
if key.startswith('property:'):
key_name = key[9:]
if needle is None or needle == key_name:
weight = int(annotation.get('session:weight', 0))
value = wrap_provenance(value, whence=annotation.get('provenance:whence'))
set_data(key_name, weight, value)
if needle is not None:
data = data.get(needle, {})
if len(data) > 0:
return one_or_all(needle, data[max(data.keys())])
else:
return one_or_all(needle, default)
else:
return dict(((k, one_or_all(k, v[max(v.keys())])) for k, v in data.iteritems() if len(v) > 0))
def store_metadata(document, **kwargs):
special = {
':whence': 'provenance',
':when': 'provenance',
':confidence': 'provenance',
':weight': 'provenance',
}
if len(kwargs) > 0:
# Create an annotation
annotation = spineapi.Annotation()
annotation['concept'] = 'DocumentIdentifier'
for key, value in kwargs.items():
if value is not None:
annotation['{0}:{1}'.format(special.get(key, 'property'), unicode(key).strip(':'))] = kwargs.get(key)
else:
del kwargs[key]
annotation['session:volatile'] = '1'
document.addAnnotation(annotation, 'Document Metadata')
# Log the metadata being stored
for key, value in kwargs.iteritems():
if isinstance(value, str) or isinstance(value, unicode):
if len(value) > 63:
value = value[:60] + '...'
value = value.replace('\n', r'\n').replace('\r', r'\r')
print "Stored metadata '{0}' / {2}: {1}".format(key, value.encode('utf8'), kwargs.get(':weight', '0'))
else:
print "Stored metadata '{0}' / {2}: {1}".format(key, repr(value).encode('utf8'), kwargs.get(':weight', '0'))
return annotation
def format_citation(citation):
def format(string, value):
if value is not None and len(u'{0}'.format(value)) > 0:
return unicode(string).format(value)
else:
return ''
def get(map, key, default = None):
value = map.get('property:{0}'.format(key))
if value is None:
value = map.get(key, default)
if value is None:
return default
return value
type = get(citation, 'type')
html = get(citation, 'unstructured')
label = get(citation, 'label', '')
if html is None:
copy = citation.copy()
if 'label' in copy:
del copy['label']
html = utopia.citation.format(copy)
# title = re.sub(r'([^!?.])$', r'\1.', get(citation, 'title', ''))
# publication = get(citation, 'publication-title')
# volume = get(citation, 'volume')
# year = get(citation, 'year')
# pages = get(citation, 'pages')
# if pages is None and 'pagefrom' in citation and 'pageto' in citation:
# pages = u'{0}-{1}'.format(get(citation, 'pagefrom', ''), get(citation, 'pageto', ''))
# authors = get(citation, 'authors', [])
# if len(authors) > 0:
# author_list = get(citation, 'authors', [])
# author_count = len(author_list)
# max_authors = 4
# authors = u' and '.join(author_list[:max_authors])
# if author_count > max_authors:
# authors += 'u <em>et al.</em>'
#
# data = {
# 'title': format('<em>{0}</em>', title),
# 'publication-title': format('{0}', publication),
# 'volume': format('{0}', volume),
# 'year': format('({0})', year),
# 'pages': format('{0}', pages),
# 'authors': format('{0}.', authors),
# }
# html = u'{authors} {year} {title} {publication-title}, {volume} {pages}'.format(**data).strip(' -,.').replace('()', '')
if len(label) > 0:
html = u'{0}. {1}'.format(format('<strong>{0}</strong>', label), html)
return re.sub(r'([^!?,.])$', r'\1.', re.sub(r'\s+', ' ', html))
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