Merge pull request #13 from zsloan/feature/add_rqtl_endpoints

Feature/add rqtl endpoints

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,