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author | lltommy | 2020-11-11 09:56:12 +0100 |
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committer | lltommy | 2020-11-11 09:56:12 +0100 |
commit | d6aa323b6fc7a82e45cc1df51fc72c2d547146eb (patch) | |
tree | 6e8b77bde4dc34fab3fa8804906f3cb821f61dae /test/test_sparql.py | |
parent | c5fe5de7e4c77bfb48b1ae2f662c2d9cc120c06e (diff) | |
parent | c872248e43c1c66e5fed8ef341f7b4ac21d63e6f (diff) | |
download | bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.gz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.lz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.zip |
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'test/test_sparql.py')
-rw-r--r-- | test/test_sparql.py | 39 |
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() |