example to test sparql endpoint; refs #46

sparql_test.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+# -*- coding: utf8 -*-
+# vim: ts=4 sw=4:
+from json import dumps
+from urllib.error import HTTPError
+from SPARQLWrapper import SPARQLWrapper, GET, JSON
+
+
+def query(query, endpoint):
+    sparql = SPARQLWrapper(endpoint)
+    sparql.setQuery(query)
+    sparql.setReturnFormat(JSON)
+    sparql.setMethod(GET)
+
+    try:
+        result = sparql.query()
+        return result.convert()
+    except HTTPError as e:
+        print(str(e))
+
+if __name__ == '__main__':
+    import sys
+
+    if len(sys.argv) != 2:
+        sys.stderr.write('usage: sparql_test.py [SPARQL_ENDPOINT_URL]\n')
+        sys.exit(1)
+
+    endpoint_url = sys.argv[1]
+    EXACT_MATCH_ORPHANS = """
+    prefix skos: <http://www.w3.org/2004/02/skos/core#>
+    select (count(distinct ?uri2) as ?count)
+    where {
+      ?uri1 skos:exactMatch ?uri2 .
+      minus { ?uri2 skos:inScheme ?scheme .}
+    }
+    """
+    ORTHOLOGOUS_MATCH_ORPHANS = """
+    prefix skos: <http://www.w3.org/2004/02/skos/core#>
+    prefix belv: <http://www.openbel.org/vocabulary/>
+    select (count(distinct ?uri2) as ?count)
+    where {
+      ?uri1 belv:orthologousMatch ?uri2 .
+      minus { ?uri2 skos:inScheme ?scheme .}
+    }
+    """
+
+    print("Orphans for exactMatch:")
+    print(dumps(query(EXACT_MATCH_ORPHANS, endpoint_url), indent=4))
+
+    print("Orphans for orthologousMatch:")
+    print(dumps(query(ORTHOLOGOUS_MATCH_ORPHANS, endpoint_url), indent=4))