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-rw-r--r--tests/integration/test_gemma.py150
1 files changed, 75 insertions, 75 deletions
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index f4ac685..4573de1 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -187,21 +187,21 @@ class GemmaAPITest(unittest.TestCase):
"-g /tmp/test-data/genofile.txt "
"-p /tmp/test-data/phenofile.txt "
"-a /tmp/test-data/snpfile.txt "
- "-gk > /tmp/test-data/hash-k-output.json"))
- self.assertEqual(response.get_json(), {
- "output_file": "hash-k-output.json",
- "status": "queued",
- "unique_id": "my-unique-id"
- })
+ "-gk > /tmp/test-data/hash-output.json"))
+ self.assertEqual(
+ response.get_json(), {
+ "output_file": "hash-output.json",
+ "status": "queued",
+ "unique_id": "my-unique-id"
+ })
@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_compute_loco(self, mock_redis, mock_path_exist,
- mock_json, mock_hash,
- mock_queue_cmd):
+ def test_k_compute_loco(self, mock_redis, mock_path_exist, mock_json,
+ mock_hash, mock_queue_cmd):
"""Test /gemma/k-compute/loco/<chromosomes>/<token>"""
mock_path_exist.return_value, _redis_conn = True, mock.MagicMock()
mock_redis.return_value = _redis_conn
@@ -223,21 +223,21 @@ class GemmaAPITest(unittest.TestCase):
"-g /tmp/test-data/genofile.txt "
"-p /tmp/test-data/phenofile.txt "
"-a /tmp/test-data/snpfile.txt "
- "-gk > /tmp/test-data/hash-3R77Mz-k-output.json"))
- self.assertEqual(response.get_json(), {
- "output_file": "hash-3R77Mz-k-output.json",
- "status": "queued",
- "unique_id": "my-unique-id"
- })
+ "-gk > /tmp/test-data/hash-3R77Mz-output.json"))
+ self.assertEqual(
+ response.get_json(), {
+ "output_file": "hash-3R77Mz-output.json",
+ "status": "queued",
+ "unique_id": "my-unique-id"
+ })
@mock.patch("gn3.api.gemma.queue_cmd")
- @mock.patch("gn3.api.gemma.get_hash_of_files")
+ @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_gwa_compute(self, mock_redis, mock_path_exist,
- mock_json, mock_hash,
- mock_queue_cmd):
+ def test_gwa_compute(self, mock_redis, mock_path_exist, mock_json,
+ mock_hash, mock_queue_cmd):
"""Test /gemma/gwa-compute/<k-inputfile>/<token>"""
mock_path_exist.return_value, _redis_conn = True, mock.MagicMock()
mock_redis.return_value = _redis_conn
@@ -250,9 +250,10 @@ class GemmaAPITest(unittest.TestCase):
mock_hash.return_value = "hash"
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_hash.assert_called_once_with([
+ '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt',
+ '/tmp/my-token/snpfile.txt'
+ ])
mock_queue_cmd.assert_called_once_with(
conn=_redis_conn,
email=None,
@@ -262,22 +263,21 @@ class GemmaAPITest(unittest.TestCase):
" -- -g /tmp/my-token/genofile.txt "
"-p /tmp/my-token/phenofile.txt "
"-a /tmp/my-token/snpfile.txt "
- "-lmm 9 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"
- })
+ "-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"
+ })
@mock.patch("gn3.api.gemma.queue_cmd")
- @mock.patch("gn3.api.gemma.get_hash_of_files")
+ @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_gwa_compute_with_covars(self, mock_redis,
- mock_path_exist,
- mock_json, mock_hash,
- mock_queue_cmd):
+ def test_gwa_compute_with_covars(self, mock_redis, mock_path_exist,
+ mock_json, mock_hash, mock_queue_cmd):
"""Test /gemma/gwa-compute/covars/<k-inputfile>/<token>"""
mock_path_exist.return_value, _redis_conn = True, mock.MagicMock()
mock_redis.return_value = _redis_conn
@@ -293,10 +293,10 @@ class GemmaAPITest(unittest.TestCase):
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_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_queue_cmd.assert_called_once_with(
conn=_redis_conn,
email=None,
@@ -307,22 +307,21 @@ class GemmaAPITest(unittest.TestCase):
"-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-gwa-output.json"))
- self.assertEqual(response.get_json(), {
- "unique_id": "my-unique-id",
- "status": "queued",
- "output_file": "hash-gwa-output.json"
- })
+ "-gk > /tmp/my-token/hash-output.json"))
+ self.assertEqual(
+ response.get_json(), {
+ "unique_id": "my-unique-id",
+ "status": "queued",
+ "output_file": "hash-output.json"
+ })
@mock.patch("gn3.api.gemma.queue_cmd")
- @mock.patch("gn3.api.gemma.get_hash_of_files")
+ @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_gwa_compute_with_loco_only(self, mock_redis,
- mock_path_exist,
- mock_json, mock_hash,
- mock_queue_cmd):
+ def test_gwa_compute_with_loco_only(self, mock_redis, mock_path_exist,
+ mock_json, mock_hash, mock_queue_cmd):
"""Test /gemma/gwa-compute/<k-inputfile>/loco/maf/<maf>/<token>
"""
@@ -336,35 +335,36 @@ class GemmaAPITest(unittest.TestCase):
}
mock_hash.return_value = "hash"
response = self.app.post(("/api/gemma/gwa-compute/"
- "hash-k-output.json/loco/"
+ "hash-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_hash.assert_called_once_with([
+ '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt',
+ '/tmp/my-token/snpfile.txt'
+ ])
mock_queue_cmd.assert_called_once_with(
conn=_redis_conn,
email=None,
job_queue='GN3::job-queue',
cmd=("gemma-wrapper --json --loco --input "
- "/tmp/my-token/hash-k-output.json -- "
+ "/tmp/my-token/hash-output.json -- "
"-g /tmp/my-token/genofile.txt "
"-p /tmp/my-token/phenofile.txt "
"-a /tmp/my-token/snpfile.txt "
"-lmm 9 -maf 21.0 "
- "-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"
- })
+ "-gk > /tmp/my-token/hash-output.json"))
+ self.assertEqual(
+ response.get_json(), {
+ "unique_id": "my-unique-id",
+ "status": "queued",
+ "output_file": "hash-output.json"
+ })
@mock.patch("gn3.api.gemma.queue_cmd")
- @mock.patch("gn3.api.gemma.get_hash_of_files")
+ @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_gwa_compute_with_loco_covars(self, mock_redis,
- mock_path_exist,
+ def test_gwa_compute_with_loco_covars(self, mock_redis, mock_path_exist,
mock_json, mock_hash,
mock_queue_cmd):
"""Test /gemma/gwa-compute/<k-inputfile>/loco/covariates/maf/<maf><token>
@@ -381,27 +381,27 @@ class GemmaAPITest(unittest.TestCase):
}
mock_hash.return_value = "hash"
response = self.app.post(("/api/gemma/gwa-compute/"
- "hash-k-output.json/loco/"
+ "hash-output.json/loco/"
"covariates/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',
- "/tmp/my-token/covarfile.txt"
- ])
+ 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_queue_cmd.assert_called_once_with(
conn=_redis_conn,
email=None,
job_queue='GN3::job-queue',
cmd=("gemma-wrapper --json --loco --input "
- "/tmp/my-token/hash-k-output.json -- "
+ "/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 -maf 21.0 "
- "-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"
- })
+ "-gk > /tmp/my-token/hash-output.json"))
+ self.assertEqual(
+ response.get_json(), {
+ "unique_id": "my-unique-id",
+ "status": "queued",
+ "output_file": "hash-output.json"
+ })
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 04:53:47 +0000