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wikidata_extension.py
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import re
import sys
import ror_data
from SPARQLWrapper import SPARQLWrapper, JSON
from time import sleep
# Following probably should be its own class with caching etc.
def my_get_sparql_results(queryString):
sparql = SPARQLWrapper("https://query.wikidata.org/sparql",
agent='extendror (https://extendror.toolforge.org) SPARQLWrapper'
)
sparql.setReturnFormat(JSON)
sparql.setQuery(queryString)
try:
results = sparql.query().convert()
except urllib.error.HTTPError as err:
retry_after = None
if err.code == 429:
retry_after = err.headers.get("Retry-After")
if retry_after is None:
retry_after = 5
sleep(retry_after)
try:
results = sparql.query().convert()
except:
results = None
except:
results = None
return results
def wikidata_metadata(id):
id_parts = id.split('/')
ror_id = id_parts[0]
ror_root_metadata = ror_data.metadata_for_ror(ror_id)
extension = ''
if (len(id_parts) > 1):
extension = id_parts[1]
if not verify_wikidata_relation(ror_id, extension):
return {'ror_id': ror_id, 'extension': extension, 'error': 'Unrelated'}
children = []
self_metadata = {}
ror_self_metadata = {}
qid_pattern = re.compile(r'Q\d+$')
if extension == '':
# Fetch all children of ror_id from Wikidata:
sparql_query = """
SELECT DISTINCT ?parent ?item ?itemLabel WHERE {{
?parent wdt:P6782 '{0}' ; wdt:P355|wdt:P527 ?item .
SERVICE wikibase:label {{ bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }}
}} ORDER BY ?itemLabel
""".format(ror_id)
results = my_get_sparql_results(sparql_query)
parent_item = ''
if results:
for result in results['results']['bindings']:
item = result['item']['value']
parent_item = result['parent']['value']
name = result['itemLabel']['value']
qid_match = qid_pattern.search(item)
if qid_match:
qid = qid_match.group(0)
children.append({'id': qid, 'name': name})
qid_match = qid_pattern.search(parent_item)
if qid_match:
extension = qid_match.group(0)
self_metadata = wikidata_self_metadata(extension)
ror_self_metadata = ror_root_metadata
self_metadata['is_top_level'] = True
else:
self_metadata = wikidata_self_metadata(extension)
self_ror_id = self_metadata['ror_id']
if self_ror_id != '':
ror_self_metadata = ror_data.metadata_for_ror(self_ror_id)
if self_ror_id == ror_id:
self_metadata['is_top_level'] = True
# Fetch all children of extension id from Wikidata:
query_string = """
SELECT DISTINCT ?item ?itemLabel WHERE {{
wd:{0} wdt:P355|wdt:P527 ?item .
SERVICE wikibase:label {{ bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }}
}} ORDER BY ?itemLabel
""".format(extension)
results = my_get_sparql_results(query_string)
if results:
for result in results['results']['bindings']:
item = result['item']['value']
name = result['itemLabel']['value']
qid_match = qid_pattern.search(item)
if qid_match:
qid = qid_match.group(0)
children.append({'id': qid, 'name': name})
return {
'ror_id': ror_id,
'extension': extension,
'metadata': self_metadata,
'ror_self': ror_self_metadata,
'children': children,
'ror_root': ror_root_metadata
}
# Verify there is a path from parent to child found:
def verify_wikidata_relation(ror_id, qid):
if qid == '':
return True
query_string = """
SELECT (count(*) as ?count) WHERE {{
?parent wdt:P6782 '{0}' ; (wdt:P355|wdt:P527)* wd:{1} .
}}
""".format(ror_id, qid)
results = my_get_sparql_results(query_string)
if results:
for result in results['results']['bindings']:
path_count = int(result['count']['value'])
if (path_count > 0):
return True
return False
# Fetch name, parent, any ror_id, for given id
def wikidata_self_metadata(qid):
self_metadata = {'id': qid}
query_string = """
SELECT DISTINCT ?itemLabel ?classLabel ?ror_id ?parent ?parentLabel ?parent_ror_id WHERE {{
VALUES ?item {{ wd:{0} }}
OPTIONAL {{ ?parent wdt:P355|wdt:P527 ?item }}
OPTIONAL {{ ?parent wdt:P355|wdt:P527 ?item; wdt:P6782 ?parent_ror_id }}
OPTIONAL {{ ?item wdt:P6782 ?ror_id }}
OPTIONAL {{ ?item wdt:P31 ?class }}
SERVICE wikibase:label {{ bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }}
}}
""".format(qid)
results = my_get_sparql_results(query_string)
if results:
result = results['results']['bindings'][0]
self_metadata['name'] = result['itemLabel']['value']
if 'ror_id' in result:
self_metadata['ror_id'] = result['ror_id']['value']
else:
self_metadata['ror_id'] = ''
classes = {}
parents = {}
has_ror_parent = False
for result in results['results']['bindings']:
if 'parent' in result:
parent_item = result['parent']['value']
parent_match = re.search(r'Q\d+$', parent_item)
parent_id = None
if parent_match:
parent_id = parent_match.group(0)
parent_name = result['parentLabel']['value']
parent_ror_id = ''
if 'parent_ror_id' in result:
parent_ror_id = result['parent_ror_id']['value']
has_ror_parent = True
parents[parent_id] = {'id': parent_id, 'name': parent_name, 'ror_id': parent_ror_id}
if 'classLabel' in result:
classes[result['classLabel']['value']] = 1
self_metadata['parents'] = parents.values()
self_metadata['classes'] = classes.keys()
self_metadata['has_ror_parent'] = has_ror_parent
return self_metadata
# Perform a search using WDQS and wikibase EntitySearch api
def search(query):
matches = []
qid_pattern = re.compile(r'Q\d+$')
query_string = """
SELECT ?item ?itemLabel ?ror_id WHERE {{
hint:Query hint:optimizer "None" .
SERVICE wikibase:mwapi {{
bd:serviceParam wikibase:api "EntitySearch";
wikibase:endpoint "www.wikidata.org";
mwapi:search "{0}" ;
mwapi:language "en" .
?item wikibase:apiOutputItem mwapi:item .
}}
?item (wdt:P361/wdt:P749)*/wdt:P6782 ?ror_id .
SERVICE wikibase:label {{ bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }}
}}
""".format(query)
results = my_get_sparql_results(query_string)
if results:
for result in results['results']['bindings']:
item = result['item']['value']
name = result['itemLabel']['value']
ror_id = result['ror_id']['value']
qid_match = qid_pattern.search(item)
if qid_match:
qid = qid_match.group(0)
matches.append({'id': qid, 'name': name, 'ror_id': ror_id})
return matches