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authorBonfaceKilz2021-03-03 12:37:40 +0300
committerBonfaceKilz2021-03-08 21:09:58 +0300
commit62fca4bd4dc433230ce0ad8c2a2c785c3ea5b5b3 (patch)
treefd8c845d9b852b75826680ac6ffc231526d05d6d /tests/integration/test_gemma.py
parent396aeed35a5925cb03cc1569669b257b8ccb07cb (diff)
downloadgenenetwork3-62fca4bd4dc433230ce0ad8c2a2c785c3ea5b5b3.tar.gz
Add new endpoint: "/gemma/k-compute/loco/<chromosomes>/<token>"
Diffstat (limited to 'tests/integration/test_gemma.py')
-rw-r--r--tests/integration/test_gemma.py28
1 files changed, 28 insertions, 0 deletions
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 18e3fb0..3e64987 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -176,3 +176,31 @@ class GemmaAPITest(unittest.TestCase):
"status": "queued",
"unique_id": "my-unique-id"
})
+
+ @mock.patch("gn3.api.gemma.queue_cmd")
+ @mock.patch("gn3.api.gemma.generate_gemma_computation_cmd")
+ @mock.patch("gn3.api.gemma.get_hash_of_files")
+ @mock.patch("gn3.api.gemma.jsonfile_to_dict")
+ def test_k_compute_loco(self, mock_json, mock_hash, mock_cmd,
+ mock_queue_cmd):
+ """Test /gemma/k-compute/<token>"""
+ mock_queue_cmd.return_value = "my-unique-id"
+ mock_json.return_value = {
+ "geno": "genofile.txt",
+ "pheno": "phenofile.txt",
+ "snps": "snpfile.txt",
+ }
+ mock_hash.return_value = "hash"
+ mock_cmd.return_value = ("gemma-wrapper --json -- "
+ "-debug -g "
+ "genotype_name.txt "
+ "-p traitfilename.txt "
+ "-a genotype_snps.txt "
+ "-gk > k_output_filename.json")
+ response = self.app.post(("/api/gemma/k-compute/loco/"
+ "1%2C2%2C3%2C4%2C5%2C6/test-data"))
+ self.assertEqual(response.get_json(), {
+ "output_file": "hash-k-output.json",
+ "status": "queued",
+ "unique_id": "my-unique-id"
+ })