def link_to_bio2rdf(*args,**kwargs):
# Retrieve the article from the post
article_id = kwargs['article']['id']
match_items = kwargs['inputs']
match_type = kwargs['link']
app.logger.debug("Running Bio2RDF plugin for article {}".format(article_id))
try :
# Initialize the plugin
plugin = SPARQLPlugin(endpoint = endpoints,
template = "bio2rdf.query",
match_type = match_type,
id_base = 'label',
all=True)
# Run the plugin, and retrieve matches using the default label property (rdfs:label)
matches = plugin.match(match_items)
app.logger.debug("Plugin is done, returning the following matches")
app.logger.debug(matches)
# Return the matches
return matches
except Exception as e:
app.logger.error(e.message)
return {'error': e.message }
def link_to_neurolex(*args, **kwargs):
# Retrieve the article from the wrapper
article_id = kwargs['article']['id']
app.logger.debug("Running Neurolex plugin for article {}".format(article_id))
match_items = kwargs['inputs']
try :
# Initialize the plugin
plugin = SPARQLPlugin(endpoint = "http://rdf-stage.neuinfo.org/ds/query",
template = "neurolex.query")
# Run the plugin, and retrieve matches using the default label property (rdfs:label)
matches = plugin.match(match_items)
app.logger.debug(matches)
# Run the plugin with a NeuroLex specific property (namespace is defined in the neurolex.query template)
specific_matches = plugin.match(match_items, property="property:Label")
matches_keys_lower = {k.lower(): k for k,v in matches.items()}
specific_keys_lower = {k.lower(): k for k,v in specific_matches.items()}
app.logger.debug("Removing duplicates from matches")
app.logger.debug(matches_keys_lower.keys())
app.logger.debug(specific_keys_lower.keys())
for k, K in specific_keys_lower.items():
app.logger.debug(k)
if not k in matches_keys_lower.items():
app.logger.debug("{} is not in {}".format(k,matches_keys_lower))
matches[K] = specific_matches[K]
matches_keys_lower = {k.lower(): k for k,v in matches.items()}
unique_matches = {}
for k, K in matches_keys_lower.items():
unique_matches[K] = matches[K]
app.logger.debug(unique_matches)
# Return the matches
return unique_matches
except Exception as e:
return {'error': e.message }
def link_to_wikipedia(*args,**kwargs):
# Retrieve the article from the post
article_id = kwargs['article']['id']
match_items = kwargs['inputs']
match_type = kwargs['link']
app.logger.debug("Running DBPedia plugin for article {}".format(article_id))
# Rewrite the match_items to strip the inchikey= prefix from the tag, if present. This allows the SPARQLPlugin to find additional matches for the dbpprop:inchikey property.
match_items = [{'id': item['id'],
'label': re.findall('^.*?\=(.*)$',item['label'])[0] if item['label'].lower().startswith('inchikey=') else item['label']}
for item in match_items]
try :
# Initialize the plugin
plugin = SPARQLPlugin(endpoint = endpoints,
template = "dbpedia.query",
match_type = match_type,
rewrite_function = lambda x: re.sub('dbpedia.org/resource','en.wikipedia.org/wiki',x),
id_function = lambda x: re.sub('http://dbpedia.org/resource/','',x),
id_base = 'uri')
# Run the plugin, and retrieve matches using the default label property (rdfs:label)
matches = plugin.match(match_items)
# Run the plugin with a specific property for the InchiKeys (namespace is defined in the dbpedia.query template)
matches.update(plugin.match(match_items, property="dbpprop:inchikey"))
app.logger.debug("Plugin is done, returning the following matches")
app.logger.debug(matches)
# Return the matches
return matches
except Exception as e:
app.logger.error(e.message)
return {'error': e.message }