def createAnnotation(self, domain, document, html, mentions):
annotation = Annotation()
annotation['concept'] = 'Bio3DMInformation'
annotation['property:name'] = '%s: "%s"' % (
mentions[0]['mentionType'].title(),
mentions[0]['formalRepresentation'])
annotation['property:description'] = '3DM %s record' % mentions[0][
'mentionType'].title()
annotation['property:sourceDatabase'] = domain
annotation['property:html'] = mentions[0]['html']
annotation['property:css'] = mentions[0]['css']
annotation['property:js'] = mentions[0]['js']
annotation['property:sourceDatabase'] = 'bioprodict'
annotation[
'property:sourceDescription'] = '<p><a href="http://www.bio-prodict.nl">Bio-Prodict\'s</a> 3DM information systems provide protein family-specific annotations for this article</p>'
annotation['session:overlay'] = 'hyperlink'
annotation['session:color'] = '#336611'
for mention in mentions:
for textRange in mention['textRangeList']:
start = int(textRange['start'])
end = int(textRange['end'])
match = document.substr(start, end - start)
annotation.addExtent(match)
return annotation
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_ready_event(self, document):
username = self.get_config('username')
password = self.get_config('password')
if self.validUsernameAndPassword(username, password):
# Get a new bearer token
basic = 'Basic dXRvcGlhLXBsdWdpbjo=' # base64.encodestring('utopia-plugin:').replace('\n', '')
data = dict(username=username, password=password, grant_type='password')
content = post_for_json(self.tokenurl, basic, data)
self.bearer = 'Bearer ' + content['access_token']
self.proteinJs = self.proteinJs.replace('#TOKEN#', self.bearer)
self.commonJs = self.commonJs.replace('#TOKEN#', self.bearer)
# Get available databases for user
databases = post_for_json(self.databasesurl, self.bearer)
sorted_databases = sorted(databases.items(), key=lambda item: item[1])
databaseIds = [item[0] for item in sorted_databases]
databaseDescriptions = [item[1] for item in sorted_databases]
annotation = Annotation()
annotation['concept'] = 'Bio3DMInformation'
annotation['property:name'] = 'Bio-Prodict 3DM'
annotation['property:html'] = 'html'
annotation['session:overlay'] = 'hyperlink'
annotation['session:color'] = '#336611'
annotation['property:description'] = '''Annotate using one of your 3DM systems'''
annotation['property:databaseIds'] = '|'.join(databaseIds)
annotation['property:databaseDescriptions'] = '|'.join(databaseDescriptions)
annotation['property:sourceDatabase'] = 'bioprodict'
annotation['property:sourceDescription'] = '<p><a href="http://www.bio-prodict.nl">Bio-Prodict\'s</a> 3DM information systems provide protein family-specific annotations for this article</p>'
document.addAnnotation(annotation)
def createAnnotation(self, domain, document, html, mentions):
annotation = Annotation()
annotation["concept"] = "Bio3DMInformation"
annotation["property:name"] = '%s: "%s"' % (mentions[0].mentionType.title(), mentions[0].formalRepresentation)
annotation["property:description"] = "3DM %s record" % mentions[0].mentionType.title()
annotation["property:sourceDatabase"] = domain
annotation["property:html"] = mentions[0].html
annotation["property:css"] = mentions[0].css
annotation["property:js"] = mentions[0].js
annotation["property:sourceDatabase"] = "bioprodict"
annotation[
"property:sourceDescription"
] = '<p><a href="http://www.bio-prodict.nl">Bio-Prodict\'s</a> 3DM information systems provide protein family-specific annotations for this article</p>'
for mention in mentions:
for textRange in mention.textRangeList:
start = int(textRange.start)
end = int(textRange.end)
match = document.substr(start, end - start)
annotation.addExtent(match)
return annotation
def on_activate_event(self, document):
ns = {'r': 'Reflect'}
maxTextFragmentSize = 1000000
textFragments = []
seenItemNames = set()
ignoredEntityTypes = [-11]
# Retrieve the full text of the document, split into fragments
for page in document.pages():
pageText = re.sub(r'\s+', r' ', page.pageText())
if len(textFragments) == 0 or len(textFragments[-1][0]) + len(
pageText) > maxTextFragmentSize:
textFragments.append([pageText, page])
else:
textFragments[-1][0] = textFragments[-1][0] + ' ' + pageText
for text, page in textFragments:
# Package it as URL encoded form encoding
payload = 'document=%s' % urllib.quote(text.encode('utf8'))
# Send it off to the reflect server
response = urllib2.urlopen("http://reflect.ws/REST/GetEntities",
payload,
timeout=8)
# Parse response
root = etree.fromstring(response.read(), self.parser)
reflections = {}
annotations = {}
for item in root.xpath('//r:item', namespaces=ns):
itemName = etree.tostring(item.find('{%s}name' % ns['r']),
method="text",
encoding=unicode,
with_tail=False).lower().strip()
if itemName not in seenItemNames:
for entity in item.xpath('.//r:entity', namespaces=ns):
entityType = entity.findtext('{%s}type' % ns['r'])
if entityType is not None:
entityType = int(entityType)
if entityType not in ignoredEntityTypes:
entityIdentifier = entity.findtext(
'{%s}identifier' % ns['r'])
if itemName not in reflections:
reflections[itemName] = set()
reflections[itemName].add(
(entityType, entityIdentifier))
# For each match, create an annotation that the UI will handle later
regex = '(%s)' % '|'.join(
[re.escape(key) for key in reflections.iterkeys()])
matches = document.search(regex,
IgnoreCase + WholeWordsOnly + RegExp,
start=page)
for match in matches:
if match.begin().wordArea()[1] == 0:
itemName = match.text().lower().strip()
annotation = annotations.get(itemName, None)
if annotation is None and itemName in reflections:
annotation = Annotation()
annotation['concept'] = 'Reflection'
annotation['property:webpageUrl'] = \
'http://reflect.ws/fcgi-bin/solveAmbig.fcgi?entities=%s' % \
';'.join(['%d.%s' % (t, id) for (t, id) in reflections[itemName]])
annotation['property:name'] = itemName
annotation['session:overlay'] = 'hyperlink'
annotation['session:color'] = '#0A0'
annotations[itemName] = annotation
seenItemNames.add(itemName)
if annotation is not None:
annotation.addExtent(match)
else:
print "ERROR: matched '%s' but could not find in reflections map" % itemName.encode(
'utf8')
print reflections.keys()
document.addAnnotations(annotations.values())
def on_activate_event(self, document):
ns = {'r': 'Reflect'}
maxTextFragmentSize = 1000000
textFragments = []
seenItemNames = set()
ignoredEntityTypes = [-11]
# Retrieve the full text of the document, split into fragments
for page in document.pages():
pageText = re.sub(r'\s+', r' ', page.pageText())
if len(textFragments) == 0 or len(textFragments[-1][0]) + len(pageText) > maxTextFragmentSize:
textFragments.append([pageText, page])
else:
textFragments[-1][0] = textFragments[-1][0] + ' ' + pageText
for text, page in textFragments:
# Package it as URL encoded form encoding
payload = 'document=%s' % urllib.quote(text.encode('utf8'))
# Send it off to the reflect server
response = urllib2.urlopen("http://reflect.ws/REST/GetEntities", payload, timeout=8)
# Parse response
root = etree.fromstring(response.read(), self.parser)
reflections = {}
annotations = {}
for item in root.xpath('//r:item', namespaces = ns):
itemName = item.findtext('{%s}name' % ns['r']).lower().strip()
if itemName not in seenItemNames:
for entity in item.xpath('.//r:entity', namespaces = ns):
entityType = entity.findtext('{%s}type' % ns['r'])
if entityType is not None:
entityType = int(entityType)
if entityType not in ignoredEntityTypes:
entityIdentifier = entity.findtext('{%s}identifier' % ns['r'])
if itemName not in reflections:
reflections[itemName] = set()
reflections[itemName].add((entityType, entityIdentifier))
# For each match, create an annotation that the UI will handle later
regex = '(%s)' % '|'.join([re.escape(key) for key in reflections.iterkeys()])
matches = document.search(regex, IgnoreCase + WholeWordsOnly + RegExp, start = page)
for match in matches:
if match.begin().wordArea()[1] == 0:
itemName = match.text().lower().strip()
annotation = annotations.get(itemName, None)
if annotation is None and itemName in reflections:
annotation = Annotation()
annotation['concept'] = 'Reflection'
annotation['property:webpageUrl'] = \
'http://reflect.ws/fcgi-bin/solveAmbig.fcgi?entities=%s' % \
';'.join(['%d.%s' % (t, id) for (t, id) in reflections[itemName]])
annotation['property:name'] = itemName
annotation['session:overlay'] = 'hyperlink'
annotation['session:color'] = '#0A0'
annotations[itemName] = annotation
seenItemNames.add(itemName)
if annotation is not None:
annotation.addExtent(match)
else:
print "ERROR: matched '%s' but could not find in reflections map" % itemName.encode('utf8')
print reflections.keys()
document.addAnnotations(annotations.values())
