############################################################################### # # This file is part of the Utopia Documents application. # Copyright (c) 2008-2014 Lost Island Labs # # # 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 # ############################################################################### #? 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 = 'JournalAllFreeText"%s"Utopia110Relevance' % 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