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| author | BonfaceKilz | 2021-03-08 14:23:53 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-03-08 21:09:58 +0300 |
| commit | 504cd5748e5fa71a539b095958fe71a20f5ca443 (patch) | |
| tree | 150f8b829c19dc0e239e4fbba3b67296dcb8fe8e /tests/integration | |
| parent | 79f931b0fbe0712954201a15278f9088fd7cdb8a (diff) | |
| download | genenetwork3-504cd5748e5fa71a539b095958fe71a20f5ca443.tar.gz | |
Add "/k-gwa-compute/covars/<token>"
Diffstat (limited to 'tests/integration')
| -rw-r--r-- | tests/integration/test_gemma.py | 55 |
1 files changed, 55 insertions, 0 deletions
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py index 5b03cc4..2055829 100644 --- a/tests/integration/test_gemma.py +++ b/tests/integration/test_gemma.py @@ -452,3 +452,58 @@ class GemmaAPITest(unittest.TestCase): "status": "queued", "output_file": "hash-output.json" }) + + @mock.patch("gn3.api.gemma.queue_cmd") + @mock.patch("gn3.computations.gemma.get_hash_of_files") + @mock.patch("gn3.api.gemma.jsonfile_to_dict") + @mock.patch("gn3.api.gemma.do_paths_exist") + @mock.patch("gn3.api.gemma.redis.Redis") + def test_k_gwa_compute_with_covars_only(self, mock_redis, mock_path_exist, + mock_json, mock_hash, + mock_queue_cmd): + """Test /gemma/k-gwa-compute/covars/<token> + + """ + mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() + mock_redis.return_value = _redis_conn + 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" + response = self.app.post("/api/gemma/k-gwa-compute/covars/my-token") + mock_hash.assert_has_calls([ + mock.call([ + '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + '/tmp/my-token/snpfile.txt' + ]), + mock.call([ + '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + '/tmp/my-token/snpfile.txt', "/tmp/my-token/covarfile.txt" + ]) + ]) + mock_queue_cmd.assert_called_once_with( + conn=_redis_conn, + email=None, + job_queue='GN3::job-queue', + cmd=("gemma-wrapper --json -- " + "-g /tmp/my-token/genofile.txt " + "-p /tmp/my-token/phenofile.txt " + "-a /tmp/my-token/snpfile.txt " + "-gk > /tmp/my-token/hash-output.json " + "&& gemma-wrapper --json " + "--input /tmp/my-token/hash-output.json -- " + "-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 " + "-gk > /tmp/my-token/hash-output.json")) + self.assertEqual( + response.get_json(), { + "unique_id": "my-unique-id", + "status": "queued", + "output_file": "hash-output.json" + }) |