Add generic fn for computing k and gwa values

2 files changed, 50 insertions, 4 deletions

diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 822f088..f4ac685 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -162,7 +162,7 @@ class GemmaAPITest(unittest.TestCase):
         self.assertEqual(response.get_json(), {"status": "test"})
 
     @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")
@@ -195,7 +195,7 @@ class GemmaAPITest(unittest.TestCase):
         })
 
     @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")
@@ -223,9 +223,9 @@ 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"))
+                 "-gk > /tmp/test-data/hash-3R77Mz-k-output.json"))
         self.assertEqual(response.get_json(), {
-            "output_file": "hash-k-output.json",
+            "output_file": "hash-3R77Mz-k-output.json",
             "status": "queued",
             "unique_id": "my-unique-id"
         })
diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py
index 2d2fbf9..d3fb7aa 100644
--- a/tests/unit/computations/test_gemma.py
+++ b/tests/unit/computations/test_gemma.py
@@ -2,6 +2,7 @@
 import unittest
 
 from unittest import mock
+from gn3.computations.gemma import compute_k_values
 from gn3.computations.gemma import generate_hash_of_string
 from gn3.computations.gemma import generate_pheno_txt_file
 from gn3.computations.gemma import generate_gemma_computation_cmd
@@ -50,3 +51,48 @@ class TestGemma(unittest.TestCase):
                 "test.txt -a genofile_snps.txt "
                 "-gk > /tmp/gn2/"
                 "k_output_gUFhGu4rLG7k+CXLPk1OUg.txt"))
+
+    @mock.patch("gn3.computations.gemma.get_hash_of_files")
+    def test_compute_k_values_without_loco(self, mock_get_hash):
+        """Test computing k valuse without loco"""
+        mock_get_hash.return_value = "my-hash"
+        self.assertEqual(
+            compute_k_values(gemma_cmd="gemma-wrapper",
+                             output_dir="/tmp",
+                             token="my-token",
+                             gemma_kwargs={
+                                 "g": "genofile",
+                                 "p": "phenofile",
+                                 "a": "snpsfile"
+                             }), {
+                                 "output_file":
+                                 "my-hash-k-output.json",
+                                 "gemma_cmd":
+                                 ("gemma-wrapper --json -- -g genofile "
+                                  "-p phenofile -a snpsfile "
+                                  "-gk > /tmp/my-token/my-hash-k-output.json")
+                             })
+
+    @mock.patch("gn3.computations.gemma.get_hash_of_files")
+    def test_compute_k_values_with_loco(self, mock_get_hash):
+        """Test computing k valuse with loco"""
+        mock_get_hash.return_value = "my-hash"
+        self.assertEqual(
+            compute_k_values(gemma_cmd="gemma-wrapper",
+                             output_dir="/tmp",
+                             token="my-token",
+                             chromosomes="1,2,3,4,5",
+                             gemma_kwargs={
+                                 "g": "genofile",
+                                 "p": "phenofile",
+                                 "a": "snpsfile"
+                             }), {
+                                 "output_file":
+                                 "my-hash-r+gF5a-k-output.json",
+                                 "gemma_cmd": ("gemma-wrapper --json "
+                                               "--loco --input 1,2,3,4,5 "
+                                               "-- -g genofile "
+                                               "-p phenofile -a snpsfile "
+                                               "-gk > /tmp/my-token/"
+                                               "my-hash-r+gF5a-k-output.json")
+                             })