diff options
Diffstat (limited to 'tests/integration')
| -rw-r--r-- | tests/integration/test_gemma.py | 43 |
1 files changed, 42 insertions, 1 deletions
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py index 3e64987..746cfb6 100644 --- a/tests/integration/test_gemma.py +++ b/tests/integration/test_gemma.py @@ -183,7 +183,7 @@ class GemmaAPITest(unittest.TestCase): @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>""" + """Test /gemma/k-compute/loco/<chromosomes>/<token>""" mock_queue_cmd.return_value = "my-unique-id" mock_json.return_value = { "geno": "genofile.txt", @@ -204,3 +204,44 @@ 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_gwa_compute(self, mock_json, mock_hash, mock_cmd, + mock_queue_cmd): + """Test /gemma/gwa-compute/<k-inputfile>/<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/gwa-compute/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']) + 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', + '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" + }) |