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-rw-r--r--gn3/api/gemma.py19
-rw-r--r--gn3/computations/gemma.py14
-rw-r--r--tests/integration/test_gemma.py69
-rw-r--r--tests/unit/computations/test_gemma.py1
4 files changed, 83 insertions, 20 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index effae8a..7c76f2f 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -35,10 +35,12 @@ file output is returned.
"""
data = request.get_json()
app_defaults = current_app.config.get('APP_DEFAULTS')
- __hash = generate_hash_of_string("".join(data.get("values")))
+ __hash = generate_hash_of_string(
+ f"{data.get('genofile_name')}_"
+ ''.join(data.get("values", "")))
gemma_kwargs = {
"geno_filename": os.path.join(app_defaults.get("GENODIR"), "bimbam",
- f"{data.get('genofile_name')}.txt"),
+ f"{data.get('geno_filename')}"),
"trait_filename": generate_pheno_txt_file(
tmpdir=app_defaults.get("TMPDIR"),
values=data.get("values"),
@@ -46,18 +48,21 @@ file output is returned.
trait_filename=(f"{data.get('dataset_groupname')}_"
f"{data.get('trait_name')}_"
f"{__hash}.txt"))}
+ gemma_wrapper_kwargs = {}
+ if data.get("loco"):
+ gemma_wrapper_kwargs["loco"] = f"--input {data.get('loco')}"
k_computation_cmd = generate_gemma_computation_cmd(
- gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
+ gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD") + "_haha",
+ gemma_wrapper_kwargs={"loco": f"--input {data.get('loco')}"},
gemma_kwargs=gemma_kwargs,
output_file=(f"{app_defaults.get('TMPDIR')}/gn2/"
f"{data.get('dataset_name')}_K_"
f"{__hash}.json"))
- if data.get("covariates"):
- gemma_kwargs["c"] = os.path.join(app_defaults.get("GENODIR"),
- "bimbam",
- data.get("covariates"))
gemma_kwargs["lmm"] = data.get("lmm", 9)
+ gemma_wrapper_kwargs["input"] = (f"{data.get('dataset_name')}_K_"
+ f"{__hash}.json")
gwa_cmd = generate_gemma_computation_cmd(
+ gemma_wrapper_kwargs=gemma_wrapper_kwargs,
gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
gemma_kwargs=gemma_kwargs,
output_file=(f"{data.get('dataset_name')}_GWA_"
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 5741692..528f888 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -55,10 +55,12 @@ def do_paths_exist(paths: ValuesView) -> bool:
return True
-def generate_gemma_computation_cmd(gemma_cmd: str,
- gemma_kwargs: Dict[str, str],
- output_file: str) -> Optional[str]:
- """Create a higher order function that generates a command"""
+def generate_gemma_computation_cmd(
+ gemma_cmd: str,
+ gemma_kwargs: Dict[str, str],
+ output_file: str,
+ gemma_wrapper_kwargs: Dict[str, str]) -> Optional[str]:
+ """Create a computation cmd"""
geno_filename = gemma_kwargs.get("geno_filename", "")
trait_filename = gemma_kwargs.get("trait_filename")
ext, snps_filename = geno_filename.partition(".")[-1], ""
@@ -66,13 +68,13 @@ def generate_gemma_computation_cmd(gemma_cmd: str,
snps_filename = geno_filename.replace(f".{ext}", "")
snps_filename += f"_snps.{ext}"
_kwargs = {"g": geno_filename, "p": trait_filename}
- if gemma_kwargs.get("covar_filename"):
- _kwargs["a"] = gemma_kwargs.get("covar_filename")
+ _kwargs["a"] = snps_filename
if not do_paths_exist(_kwargs.values()): # Prevents injection!
return None
if _kwargs.get("lmm"):
_kwargs["lmm"] = gemma_kwargs.get("lmm")
return compose_gemma_cmd(gemma_wrapper_cmd=gemma_cmd,
+ gemma_wrapper_kwargs=gemma_wrapper_kwargs,
gemma_kwargs=_kwargs,
gemma_args=["-gk", ">",
output_file])
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 598c91f..1f59530 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -1,4 +1,5 @@
"""Integration tests for gemma API endpoints"""
+import os
import unittest
from dataclasses import dataclass
@@ -17,7 +18,14 @@ class MockRedis:
class GemmaAPITest(unittest.TestCase):
"""Test cases for the Gemma API"""
def setUp(self):
- self.app = create_app().test_client()
+ self.app = create_app({
+ "APP_DEFAULTS": {
+ "GENODIR": os.path.abspath(
+ os.path.join(os.path.dirname(__file__),
+ "test_data/")),
+ "TMPDIR": "/tmp",
+ "REDIS_JOB_QUEUE": "GN3::job-queue",
+ "GEMMA_WRAPPER_CMD": "gemma-wrapper"}}).test_client()
@mock.patch("gn3.api.gemma.run_cmd")
def test_get_version(self, mock_run_cmd):
@@ -31,9 +39,9 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.api.gemma.generate_gemma_computation_cmd")
- def test_run_gemma(self, mock_gemma_computation_cmd,
- mock_queue_cmd, mock_redis):
- """Test that gemma composes the command correctly"""
+ def test_run_gemma_no_loco(self, mock_gemma_computation_cmd,
+ mock_queue_cmd, mock_redis):
+ """Test that gemma composes the command correctly without loco"""
_redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock())
mock_redis.return_value = _redis_conn
mock_gemma_computation_cmd.side_effect = [
@@ -42,7 +50,9 @@ class GemmaAPITest(unittest.TestCase):
"test.txt -a genofile_snps.txt "
"-gk > /tmp/gn2/"
"bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"),
- ("gemma-wrapper --json -- "
+ ("gemma-wrapper --json --input /tmp/gn2/"
+ "bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt -- "
+ "-a genofile_snps.txt -lmm 9 "
"-g genofile.txt -p "
"test.txt -a genofile_snps.txt "
"-gk > /tmp/gn2/"
@@ -66,7 +76,9 @@ class GemmaAPITest(unittest.TestCase):
"genofile.txt -p test.txt "
"-a genofile_snps.txt -gk > "
"/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt "
- "&& gemma-wrapper --json -- -g "
+ "&& gemma-wrapper --json --input "
+ "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
+ " -- -a genofile_snps.txt -lmm 9 -g "
"genofile.txt -p test.txt "
"-a genofile_snps.txt "
"-gk > "
@@ -78,7 +90,50 @@ class GemmaAPITest(unittest.TestCase):
response.get_json(),
{"unique_id": 'my-unique-id',
"status": "queued",
- "output_file": "BXD_GWA_9lo8zwOOXbfB73EcyXxAYQ.txt"})
+ "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"})
+
+ @mock.patch("gn3.api.gemma.redis.Redis")
+ @mock.patch("gn3.api.gemma.queue_cmd")
+ def test_run_gemma_with_loco(self,
+ mock_queue_cmd, mock_redis):
+ """Test that gemma composes the command correctly with loco"""
+ _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock())
+ mock_redis.return_value = _redis_conn
+ mock_queue_cmd.return_value = "my-unique-id"
+ response = self.app.post("/gemma/k-gwa-computation", json={
+ "trait_filename": os.path.abspath(os.path.join(
+ os.path.dirname(__file__),
+ "test_data/"
+ )),
+ "geno_filename": "BXD_geno.txt.gz",
+ "values": ["X", "N/A", "X"],
+ "dataset_groupname": "BXD",
+ "trait_name": "Height",
+ "email": "me@me.com",
+ "dataset_name": "BXD",
+ "loco": "1,2,3,4,5,6"
+ })
+ mock_queue_cmd.called_with(
+ conn=_redis_conn,
+ email="me@me.com",
+ job_queue="GN3::job-queue",
+ cmd=("gemma-wrapper --json -- -g "
+ "genofile.txt -p test.txt "
+ "-a genofile_snps.txt -gk > "
+ "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt "
+ "&& gemma-wrapper --json --input "
+ "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
+ " -- -a genofile_snps.txt -lmm 9 -g "
+ "genofile.txt -p test.txt "
+ "-a genofile_snps.txt "
+ "-gk > "
+ "/tmp/gn2/"
+ "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))
+ self.assertEqual(
+ response.get_json(),
+ {"unique_id": 'my-unique-id',
+ "status": "queued",
+ "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"})
@mock.patch("gn3.api.gemma.redis.Redis")
def test_check_cmd_status(self, mock_redis):
diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py
index a7884ea..b5ffbfd 100644
--- a/tests/unit/computations/test_gemma.py
+++ b/tests/unit/computations/test_gemma.py
@@ -38,6 +38,7 @@ class TestGemma(unittest.TestCase):
self.assertEqual(
generate_gemma_computation_cmd(
gemma_cmd="gemma-wrapper",
+ gemma_wrapper_kwargs=None,
gemma_kwargs={
"geno_filename": "genofile.txt",
"trait_filename": "test.txt",
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 16:56:32 +0000