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-rw-r--r--tests/integration/test_gemma.py45
1 files changed, 45 insertions, 0 deletions
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 746cfb6..0c2afdc 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -245,3 +245,48 @@ class GemmaAPITest(unittest.TestCase):
"status": "queued",
"output_file": "hash-gwa-output.json"
})
+
+ @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_gwa_compute_with_covars(self, mock_json, mock_hash, mock_cmd,
+ mock_queue_cmd):
+ """Test /gemma/gwa-compute/covars/<k-inputfile>/<token>"""
+ mock_queue_cmd.return_value = "my-unique-id"
+ mock_json.return_value = {
+ "geno": "genofile.txt",
+ "pheno": "phenofile.txt",
+ "snps": "snpfile.txt",
+ "covar": "covarfile.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/gwa-compute/"
+ "covars/hash-k-output.json/"
+ "my-token"))
+ mock_hash.assert_called_once_with(['/tmp/my-token/genofile.txt',
+ '/tmp/my-token/phenofile.txt',
+ '/tmp/my-token/snpfile.txt',
+ '/tmp/my-token/covarfile.txt'])
+ mock_cmd.assert_called_once_with(
+ gemma_cmd='gemma-wrapper',
+ gemma_wrapper_kwargs={
+ 'input': '/tmp/my-token/hash-k-output.json'
+ },
+ gemma_kwargs={'g': '/tmp/my-token/genofile.txt',
+ 'p': '/tmp/my-token/phenofile.txt',
+ 'a': '/tmp/my-token/snpfile.txt',
+ 'c': '/tmp/my-token/covarfile.txt',
+ 'lmm': 9},
+ output_file='/tmp/my-token/hash-gwa-output.json')
+ self.assertEqual(response.get_json(), {
+ "unique_id": "my-unique-id",
+ "status": "queued",
+ "output_file": "hash-gwa-output.json"
+ })