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authorzsloan2021-06-18 17:33:09 -0500
committerGitHub2021-06-18 17:33:09 -0500
commitd653a635d0efd2291754c18f51d31f91a1c0a25c (patch)
tree309ea800da204f721e92ebc1c725144eab939d0f /tests
parentc553b52e140de1d7e5ed49f07bae2f4a120266f8 (diff)
parentf7becfa11ca857104ecc1b668b4bd3d0a721083c (diff)
downloadgenenetwork3-d653a635d0efd2291754c18f51d31f91a1c0a25c.tar.gz
Merge pull request #13 from zsloan/feature/add_rqtl_endpoints
Feature/add rqtl endpoints
Diffstat (limited to 'tests')
-rw-r--r--tests/unit/computations/test_rqtl.py42
-rw-r--r--tests/unit/test_commands.py25
2 files changed, 67 insertions, 0 deletions
diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py
new file mode 100644
index 0000000..955d0ab
--- /dev/null
+++ b/tests/unit/computations/test_rqtl.py
@@ -0,0 +1,42 @@
+"""Test cases for procedures defined in computations.rqtl"""
+import unittest
+
+from unittest import mock
+from gn3.computations.rqtl import generate_rqtl_cmd
+
+class TestRqtl(unittest.TestCase):
+ """Test cases for computations.rqtl module"""
+ @mock.patch("gn3.computations.rqtl.generate_hash_of_string")
+ @mock.patch("gn3.computations.rqtl.get_hash_of_files")
+ def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
+ """Test computing mapping results with R/qtl"""
+ mock_get_hash_files.return_value = "my-hash1"
+ mock_generate_hash_string.return_value = "my-hash2"
+
+ self.assertEqual(
+ generate_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
+ rqtl_wrapper_kwargs={
+ "g": "genofile",
+ "p": "phenofile",
+ "model": "normal",
+ "method": "hk",
+ "nperm": 1000,
+ "scale": "Mb",
+ "control": "rs123456"
+ },
+ rqtl_wrapper_bool_kwargs=[
+ "addcovar",
+ "interval"
+ ]), {
+ "output_file":
+ "my-hash1my-hash2my-hash2-output.csv",
+ "rqtl_cmd": (
+ "Rscript rqtl-wrapper "
+ "--g genofile --p phenofile "
+ "--model normal --method hk "
+ "--nperm 1000 --scale Mb "
+ "--control rs123456 "
+ "--filename my-hash1my-hash2my-hash2-output.csv "
+ "--addcovar --interval"
+ )
+ })
diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py
index aafb3a2..f36ba55 100644
--- a/tests/unit/test_commands.py
+++ b/tests/unit/test_commands.py
@@ -6,6 +6,7 @@ from datetime import datetime
from typing import Callable
from unittest import mock
from gn3.commands import compose_gemma_cmd
+from gn3.commands import compose_rqtl_cmd
from gn3.commands import queue_cmd
from gn3.commands import run_cmd
from gn3.exceptions import RedisConnectionError
@@ -53,6 +54,30 @@ class TestCommands(unittest.TestCase):
"-p /tmp/gf13Ad0tRX/phenofile.txt"
" -gk"))
+ def test_compose_rqtl_cmd(self):
+ """Test that the R/qtl cmd is composed correctly"""
+ self.assertEqual(
+ compose_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
+ rqtl_wrapper_kwargs={
+ "g": "the_genofile",
+ "p": "the_phenofile",
+ "model": "np",
+ "method": "ehk",
+ "nperm": 2000,
+ "scale": "Mb",
+ "control": "rs234567"
+ },
+ rqtl_wrapper_bool_kwargs=[
+ "addcovar"
+ ]),
+ ("Rscript rqtl-wrapper "
+ "--g the_genofile --p the_phenofile "
+ "--model np --method ehk "
+ "--nperm 2000 --scale Mb "
+ "--control rs234567 "
+ "--addcovar")
+ )
+
def test_queue_cmd_exception_raised_when_redis_is_down(self):
"""Test that the correct error is raised when Redis is unavailable"""
self.assertRaises(RedisConnectionError,