def on_activate_event(self, document):
if len(document.annotations('GPCRDB cache')) == 0:
print 'annotating stuff . . .'
pubmedId = utopialib.utils.metadata(document,
'identifiers[pubmed]')
if pubmedId is not None:
print 'found pubmed id: ' + pubmedId
else:
print 'did not find pubmed id'
ns = {'r': 'GPCR'}
textMentions = self.getMentions(document.text(), pubmedId)
objectlist = []
mention_cache = {}
for mention in textMentions:
if mention.mentionType != 'SPECIES':
mention_cache.setdefault(mention.html, [])
mention_cache[mention.html].append(mention)
for html, mentions in mention_cache.iteritems():
annotation = self.createAnnotation(document, html, mentions)
annotation['displayRelevance'] = '2000'
annotation['displayRank'] = '2000'
document.addAnnotation(annotation)
document.addAnnotation(spineapi.Annotation(), 'GPCRDB cache')
def on_activate_event(self, document):
if len(document.annotations('NucleaRDB cache')) == 0:
print 'annotating stuff . . .'
pubmedId = common.utils.metadata(document, 'pmid')
if pubmedId is not None:
print 'found pubmed id: ' + pubmedId
else:
print 'did not find pubmed id'
ns = {'r': 'GPCR'}
textMentions = self.getMentions(document.text(), pubmedId)
objectlist = []
mention_cache = {}
for mention in textMentions:
if mention.mentionType != 'SPECIES':
mention_cache.setdefault(mention.html, [])
mention_cache[mention.html].append(mention)
for html, mentions in mention_cache.iteritems():
annotation = self.createAnnotation(document, html, mentions)
annotation['displayRelevance']='2000'
annotation['displayRank']= '2000'
document.addAnnotation(annotation)
document.addAnnotation(spineapi.Annotation(), 'NucleaRDB cache')
def on_activate_event(self, document, data={}):
action = data.get('action')
domain = data.get('domain')
if self.annotatedDomains is None:
self.annotatedDomains = []
if action == 'annotate':
print 'starting 3DM annotation . . .'
pubmedId = utopia.tools.utils.metadata(document, 'identifiers[pubmed]')
if pubmedId is None:
pubmedId = '0'
print 'sending text to remote server (' + pubmedId + '). . .'
textMentions = self.getMentions(domain, document.text())
print 'received response, adding annotations for domain ' + domain + ' . . .'
mention_cache = {}
for mention in textMentions:
if mention['mentionType'] != 'SPECIES' and mention['mentionType'] != 'PDB':
html, css, js = self.buildHtml(domain, mention)
mention['html'] = html.encode('utf-8')
mention['css'] = css.encode('utf-8')
mention['js'] = js.encode('utf-8')
mention_cache.setdefault(mention['html'], [])
mention_cache[mention['html']].append(mention)
for html, mentions in mention_cache.iteritems():
annotation = self.createAnnotation(domain, document, html, mentions)
annotation['displayRelevance'] = '2000'
annotation['displayRank'] = '2000'
document.addAnnotation(annotation)
document.addAnnotation(Annotation(), domain)
print 'done adding annotations.'
def on_activate_event(self, document):
text = document.text().encode('utf8')
text_hash = hashlib.md5(text).hexdigest()
url = 'http://beta.sciencewise.info/api/utopia'
payload = urllib.urlencode({'text': text, 'chksum': text_hash})
response = urllib2.urlopen(url, payload, timeout=8).read()
results = json.loads(response)
annotations = []
for result in results:
before = result.get('context', {}).get('before', '')
term = result.get('value', '')
after = result.get('context', {}).get('after', '')
link = result.get('link')
definitions = []
for definition in result.get('definitions', []):
definitions.append(
(definition.get('url'), definition.get('title')))
if len(term) > 0 and len(before) + len(term) + len(
after) > 0 and link is not None:
matches = document.findInContext(before, term, after)
if len(matches) > 0:
annotation = spineapi.Annotation()
annotation['concept'] = 'ScienceWISE'
annotation['property:webpageUrl'] = link
annotation['property:term'] = term
annotation['property:name'] = 'Definitions of {0}'.format(
term)
annotation[
'property:description'] = 'ScienceWISE ontology definitions'
annotation['property:sourceDatabase'] = 'sciencewise'
annotation[
'property:sourceDescription'] = '<p><a href="http://sciencewise.info/">ScienceWISE</a> provides phycists with article annotation and scientific bookmarking.</p>'
for url, title in definitions:
annotation.insertProperty('property:definitions',
'{0} {1}'.format(url, title))
for match in matches:
annotation.addExtent(match)
annotations.append(annotation)
if len(annotations) > 0:
document.addAnnotations(annotations)
def on_activate_event(self, document):
text = document.text().encode('utf8')
text_hash = hashlib.md5(text).hexdigest()
url = 'http://beta.sciencewise.info/api/utopia'
payload = urllib.urlencode({ 'text': text, 'chksum': text_hash })
response = urllib2.urlopen(url, payload, timeout=8).read()
results = json.loads(response)
annotations = []
for result in results:
before = result.get('context', {}).get('before', '')
term = result.get('value', '')
after = result.get('context', {}).get('after', '')
link = result.get('link')
definitions = []
for definition in result.get('definitions', []):
definitions.append((definition.get('url'), definition.get('title')))
if len(term) > 0 and len(before) + len(term) + len(after) > 0 and link is not None:
matches = document.findInContext(before, term, after)
if len(matches) > 0:
annotation = spineapi.Annotation()
annotation['concept'] = 'ScienceWISE'
annotation['property:webpageUrl'] = link
annotation['property:term'] = term
annotation['property:name'] = 'Definitions of {0}'.format(term)
annotation['property:description'] = 'ScienceWISE ontology definitions'
annotation['property:sourceDatabase'] = 'sciencewise'
annotation['property:sourceDescription'] = '<p><a href="http://sciencewise.info/">ScienceWISE</a> provides phycists with article annotation and scientific bookmarking.</p>'
for url, title in definitions:
annotation.insertProperty('property:definitions', '{0} {1}'.format(url, title))
for match in matches:
annotation.addExtent(match)
annotations.append(annotation)
if len(annotations) > 0:
document.addAnnotations(annotations)
def on_activate_event(self, document, data={}):
action = data.get("action")
domain = data.get("domain")
if self.annotatedDomains == None:
self.annotatedDomains = []
if action == "annotate":
print "starting 3DM anntotation . . ."
ns = {"r": "GPCR"}
pubmedId = common.utils.metadata(document, "pmid")
if pubmedId == None:
pubmedId = "0"
print "sending text to remote server (" + pubmedId + "). . ."
textMentions = self.getMentions(domain, document.text(), pubmedId)
print "recieved response, adding annotations for domain " + domain + " . . ."
objectlist = []
mention_cache = {}
for mention in textMentions:
if mention.mentionType != "SPECIES" and mention.mentionType != "PDB":
newData = self.rewriteData(mention)
mention.data = newData
html, css, js = self.buildHtml(domain, mention)
mention.html = html.encode("utf-8")
mention.css = css.encode("utf-8")
mention.js = js.encode("utf-8")
mention_cache.setdefault(mention.html, [])
mention_cache[mention.html].append(mention)
for html, mentions in mention_cache.iteritems():
annotation = self.createAnnotation(domain, document, html, mentions)
annotation["displayRelevance"] = "2000"
annotation["displayRank"] = "2000"
document.addAnnotation(annotation)
document.addAnnotation(Annotation(), domain)
print "done adding annotations."
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
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