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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: Royal Society of Chemistry
#? www: http://www.rsc.org/
#? urls: http://www.rsc.org/ http://www.chemspider.com/ http://goldbook.iupac.org/
import spineapi
import urllib
import urllib2
from lxml import etree
import utopia.document
class RSCAnnotator(utopia.document.Annotator):
'''Annotate with RSC'''
@utopia.document.buffer
def after_ready_event(self, document):
# Get (if present) the RSCMetadataLink annotation
for annotation in document.annotations():
if annotation.get('concept') == 'RSCMetadataLink':
text = document.text()
doi = annotation['property:doi'].upper()
rscId = annotation['property:rscId'].upper()
xmlquery = '<SearchCriteria><SearchTerm><Category>Journal</Category><ContentType>All</ContentType><Criterias><NameValue><Name>FreeText</Name><Value>"%s"</Value></NameValue></Criterias><Source>Utopia</Source></SearchTerm><PageNo>1</PageNo><PageSize>10</PageSize><SortBy>Relevance</SortBy></SearchCriteria>' % doi
baseurl = 'http://pubs.rsc.org/en/federated/search'
params = { 'federatedsearchname': 'Utopia',
'inputxml': xmlquery }
url = baseurl + '?%s' % urllib.urlencode(params)
searchresult = urllib2.urlopen(url, timeout=14).read()
root = etree.fromstring(searchresult)
#print etree.tostring(root, pretty_print=True, encoding='utf8')
articles = root.findall('./{http://www.rsc.org/schema/rscart38}article')
#print articles
# the search use above can return more than one article, so select out only the one with
# the correct doi
thearticle = None
articleID = None
for article in articles:
found_doi = article.findtext("./{http://www.rsc.org/schema/rscart38}metainfo/{http://www.rsc.org/schema/rscart38}meta[@field='doi']")
if found_doi is None:
found_doi = article.findtext("./{http://www.rsc.org/schema/rscart38}art-admin/{http://www.rsc.org/schema/rscart38}doi")
if found_doi is not None and found_doi.upper() == doi:
thearticle = article
articleIDelem = article.find("./{http://www.rsc.org/schema/rscart38}metainfo/{http://www.rsc.org/schema/rscart38}meta[@field='docid']")
if articleIDelem is not None:
articleID = articleIDelem.text
break
# if we get back a single valid article...
if thearticle != None:
#print articleID
compoundsInArticle = []
compoundText = {}
annotationsInArticle = []
annotationText = {}
# create a list of all the compounds that are mentioned in the article body
compnames = thearticle.findall('./{http://www.rsc.org/schema/rscart38}art-body/{http://www.rsc.org/schema/rscart38}compname')
#print compnames
for compname in compnames:
# This line removes (erroneous?) elements from inside the XML
etree.strip_elements(compname, '{http://www.rsc.org/schema/rscart38}compound', with_tail=False)
#print compname.attrib['idrefs'], compname.text
compoundsInArticle.append(compname.attrib['idrefs'])
compoundText[compname.attrib['idrefs']] = etree.tounicode(compname, method='text')
annotationnames = thearticle.findall('./{http://www.rsc.org/schema/rscart38}art-body/{http://www.rsc.org/schema/rscart38}annref')
#print annotationnames
for annotationname in annotationnames:
# This line removes (erroneous?) elements from inside the XML
etree.strip_elements(annotationname, '{http://www.rsc.org/schema/rscart38}annotation', with_tail=False)
#print annotationname.attrib['idrefs'], annotationname.text
annotationsInArticle.append(annotationname.attrib['idrefs'])
annotationText[annotationname.attrib['idrefs']] = etree.tounicode(annotationname, method='text')
#print compoundText, annotationText
#sprint annotationsInArticle
# then for all the compounds that are defined in the article back
compounds = thearticle.findall('./{http://www.rsc.org/schema/rscart38}art-back/{http://www.rsc.org/schema/rscart38}compound')
for compound in compounds:
id = compound.attrib['id']
if id in compoundsInArticle:
url = None
id = compound.attrib['id']
# if the compound has a CSID, then the URL links to the chemspider page
csid = compound.find("./{http://www.rsc.org/schema/rscart38}link[@type='CSID']" )
# if the compound has a CSID, create a Chemspider URL for it
if csid is not None and csid.text is not None:
url = 'http://www.chemspider.com/Chemical-Structure.%s.html' % csid.text[5:]
else:
# otherwise, use the RSC landing page
url = 'http://www.rsc.org/publishing/journals/prospect/cheminfo.asp?XMLID=%s&compoundtext=%s&MSID=%s' % (id[4:], compoundText[id], articleID)
if url is not None:
options = spineapi.WholeWordsOnly + spineapi.IgnoreCase
matches = document.search(compoundText[id], options)
annotation = spineapi.Annotation()
annotation['concept'] = 'Hyperlink'
annotation['property:webpageUrl'] = url
for match in matches:
annotation.addExtent(match)
document.addAnnotation(annotation)
# similarly, for all the annotations
annotations = thearticle.findall('./{http://www.rsc.org/schema/rscart38}art-back/{http://www.rsc.org/schema/rscart38}annotation')
for annotation in annotations:
id = annotation.attrib['id']
url = None
if id in annotationsInArticle:
id = annotation.attrib['id']
# get the link id
link = annotation.findtext("./{http://www.rsc.org/schema/rscart38}link" )
# if the compound has a link, create an RSC ontology landing page for it
if link is not None:
if link[:3] == 'AU:':
url = 'http://goldbook.iupac.org/%s.html' % link[3:]
else:
url = 'http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=%s&MSID=%s' % (link, articleID)
if url is not None:
matches = document.search(annotationText[id], spineapi.IgnoreCase + spineapi.WholeWordsOnly)
annotation = spineapi.Annotation()
annotation['concept'] = 'Hyperlink'
annotation['property:webpageUrl'] = url
for match in matches:
annotation.addExtent(match)
document.addAnnotation(annotation)
break
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