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authorBonfaceKilz2021-03-04 21:46:24 +0300
committerBonfaceKilz2021-03-08 21:09:58 +0300
commit47684b060649695f32a7fe465f018b8ffb53cf37 (patch)
tree8a117da944423d286e8160aea52f49e838d0bd6a /tests/integration
parentd072471bc353663149203d29a82fa9b7b2b95a1d (diff)
downloadgenenetwork3-47684b060649695f32a7fe465f018b8ffb53cf37.tar.gz
Add new endpoint: "/gwa-compute/<k_filename>/loco/maf/<maf>/<token>"
Diffstat (limited to 'tests/integration')
-rw-r--r--tests/integration/test_gemma.py52
1 files changed, 52 insertions, 0 deletions
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 0c2afdc..45c9148 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -290,3 +290,55 @@ class GemmaAPITest(unittest.TestCase):
"status": "queued",
"output_file": "hash-gwa-output.json"
})
+
+ # pylint: disable=R0913
+ @mock.patch("gn3.api.gemma.queue_cmd")
+ @mock.patch("gn3.api.gemma.compose_gemma_cmd")
+ @mock.patch("gn3.api.gemma.get_hash_of_files")
+ @mock.patch("gn3.api.gemma.jsonfile_to_dict")
+ @mock.patch("gn3.api.gemma.do_paths_exist")
+ def test_gwa_compute_with_loco_only(self, mock_path_exist,
+ mock_json, mock_hash,
+ mock_cmd,
+ mock_queue_cmd):
+ """Test /gemma/gwa-compute/<k-inputfile>/loco/maf/<maf>/<token>
+
+ """
+ mock_path_exist.return_value = True
+ 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/"
+ "hash-k-output.json/loco/"
+ "maf/21/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_wrapper_cmd='gemma-wrapper',
+ gemma_wrapper_kwargs={
+ 'loco': '--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,
+ 'maf': 21},
+ gemma_args=["-gk", ">",
+ '/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"
+ })