Merge branch 'master' of https://github.com/CommunityDataScienceCollective/COVID...

[covid19.git] / transliterations / src / wikidata_transliterations.py

diff --git a/transliterations/src/wikidata_transliterations.py b/transliterations/src/wikidata_transliterations.py
index e94742254fe3f19ebdec72e53d95d5cea0cbc514..0856c9cc01d132cd2825522c06ac850eaa48c4f9 100644 (file)
--- a/transliterations/src/wikidata_transliterations.py
+++ b/transliterations/src/wikidata_transliterations.py
@@ -6,11 +6,11 @@ from json import JSONDecodeError
 class LabelData:
     __slots__ = ['entityid','label','langcode','is_alt']
 
-    def __init__(self, wd_res, entityid, is_alt):
+    def __init__(self, wd_res, is_alt):
         obj = wd_res.get('label',None)
         self.label = obj.get('value',None)
         self.langcode = obj.get('xml:lang',None)
-        self.entityid = entityid
+        self.entityid = wd_res.get('entity',None).get('value',None)
         self.is_alt = is_alt
 
     def to_list(self):
@@ -19,19 +19,18 @@ class LabelData:
                 self.langcode,
                 self.is_alt]
 
-
-def GetAllLabels(in_csv, outfile, topN):
+def GetAllLabels(in_csvs, outfile, topNs):
 
     def load_entity_ids(in_csv, topN=5):
         with open(in_csv,'r',newline='') as infile:
-            reader = csv.DictReader(infile)
+            reader = list(csv.DictReader(infile))
             for row in reader:
                 if int(row['search_position']) < topN:
                     yield row["entityid"]
 
-    ids = set(load_entity_ids(in_csv, topN))
+    ids = set(chain(* map(lambda in_csv, topN: load_entity_ids(in_csv, topN), in_csvs, topNs)))
 
-    labeldata = chain(* map(GetEntityLabels, ids))
+    labeldata = GetEntityLabels(ids)
 
     with open(outfile, 'w', newline='') as of:
         writer = csv.writer(of)
@@ -39,41 +38,59 @@ def GetAllLabels(in_csv, outfile, topN):
         writer.writerows(map(LabelData.to_list,labeldata))
 
     
-def GetEntityLabels(entityid):
+def GetEntityLabels(entityids):
 
-    def run_query_and_parse(query, entityid, is_alt):
-        results = run_sparql_query(query % entityid)
+    def run_query_and_parse(query, is_alt):
+        results = run_sparql_query(query)
         try:
             jobj = results.json()
+
             res = jobj.get('results',None)
             if res is not None:
                 res = res.get('bindings',None)
             if res is None:
                 raise requests.APIError(f"got invalid response from wikidata for {query % entityid}")
+
             for info in res:
-                yield LabelData(info, entityid, is_alt)
+                yield LabelData(info, is_alt)
 
         except JSONDecodeError as e:
             print(e)
-            print(query % entityid)
+            print(query)
             
-
-    label_base_query = """
-    SELECT DISTINCT ?label WHERE {
-    wd:%s rdfs:label ?label;
-    }"""
-
-    altLabel_base_query = """
-    SELECT DISTINCT ?label WHERE {
-    wd:%s skos:altLabel ?label;
-    }"""
-
-    label_results = run_query_and_parse(label_base_query, entityid, is_alt=False)
-
-    altLabel_results = run_query_and_parse(altLabel_base_query, entityid, is_alt=True)
-
-    return chain(label_results, altLabel_results)
+    def prep_query(query, prop, entityids):
+        values = ' '.join(('wd:{0}'.format(id) for id in entityids))
+        return query.format(prop, values)
+    
+    base_query = """
+    SELECT DISTINCT ?entity ?label WHERE {{
+    ?entity {0} ?label;
+    VALUES ?entity  {{ {1} }}
+    }}"""
+
+    # we can't get all the entities at once. how about 100 at a time?
+    chunksize = 100
+    entityids = (id for id in entityids)
+    chunk = list(islice(entityids, chunksize))
+    calls = []
+    while len(chunk) > 0:
+        label_query = prep_query(base_query, "rdfs:label", chunk)
+        altLabel_query = prep_query(base_query, "skos:altLabel", chunk)
+        label_results = run_query_and_parse(label_query,  is_alt=False)
+        altLabel_results = run_query_and_parse(altLabel_query, is_alt=True)
+        calls.extend([label_results, altLabel_results])
+        chunk = list(islice(entityids, chunksize))
+
+    return chain(*calls)
         
 
 if __name__ == "__main__":
-    GetAllLabels("../data/output/wikidata_search_results.csv","../data/output/wikidata_entity_labels.csv", topN=20)
+    import argparse
+    parser = argparse.ArgumentParser("Use wikidata to find transliterations of terms")
+    parser.add_argument('inputs', type=str, nargs='+', help='one or more files to read. the inputs are generated by wikidata_search.py')
+    parser.add_argument('--topN', type=int, nargs='+', help='limit number of wikidata search results to use, can pass one arg for each source.')
+    parser.add_argument('--output', type=str, help='an output file. defaults to stdout',default=20)
+
+    args = parser.parse_args()
+
+    GetAllLabels(args.inputs, args.output, topNs=args.topN)