diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/integration/test_gemma.py | 45 |
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" + }) |