Merge branch 'master' of https://github.com/arvados/bh20-seq-resource

1 files changed, 39 insertions, 0 deletions

diff --git a/test/test_sparql.py b/test/test_sparql.py
new file mode 100644
index 0000000..41cf717
--- /dev/null
+++ b/test/test_sparql.py
@@ -0,0 +1,39 @@
+# Run with python3 test/test_sparql.py
+
+import unittest
+import requests
+import logging
+
+
+
+class TestSPARQL(unittest.TestCase):
+
+    def test_sparql(self):
+        sparqlURL='http://sparql.genenetwork.org/sparql/'
+        id = "http://collections.lugli.arvadosapi.com/c=0002e93b86ad77824620bf938b97e134+126/sequence.fasta"
+        id = "MT800005.1"
+        query=f"""
+PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+PREFIX sio: <http://semanticscience.org/resource/>
+select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequenceuri
+{{
+   ?sample sio:SIO_000115 "{id}" .
+   ?sequenceuri pubseq:sample ?sample .
+   ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo .
+   ?geo rdfs:label ?geoname .
+   ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date .
+   OPTIONAL {{ ?sample <http://edamontology.org/data_2091> ?source }}
+   OPTIONAL {{ ?sample <http://purl.obolibrary.org/obo/OBI_0001479> ?sampletype }}
+   OPTIONAL {{ ?sample <http://purl.obolibrary.org/obo/NCIT_C41206> ?institute }}
+}}
+        """
+        print(query)
+        payload = {'query': query, 'format': 'json'}
+        r = requests.get(sparqlURL, params=payload)
+        result = r.json()['results']['bindings']
+        # for now we just take the first one
+        print(result)
+        self.assertEqual(result[0]['geoname']['value'],'Mahuva')
+
+if __name__ == '__main__':
+    unittest.main()