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# 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/'
sparqlURL='http://127.0.0.1:8890//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()
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