Chores/ctl wgcna enhancement

gn3/computations/ctl.py

@@ -3,7 +3,7 @@
 from gn3.commands import run_cmd
 
 from gn3.computations.wgcna import dump_wgcna_data
-from gn3.computations.wgcna import compose_wgcna_cmd
+from gn3.computations.wgcna import compose_rscript_cmd
 from gn3.computations.wgcna import process_image
 
 from gn3.settings import TMPDIR
@@ -13,7 +13,7 @@ def call_ctl_script(data):
     """function to call ctl script"""
     data["imgDir"] = TMPDIR
     temp_file_name = dump_wgcna_data(data)
-    cmd = compose_wgcna_cmd("ctl_analysis.R", temp_file_name)
+    cmd = compose_rscript_cmd("ctl_analysis.R", temp_file_name)
 
     cmd_results = run_cmd(cmd)
     with open(temp_file_name, "r", encoding="utf-8") as outputfile:

gn3/computations/wgcna.py

@@ -8,6 +8,7 @@
 
 
 from gn3.settings import TMPDIR
+from gn3.settings import R_SCRIPTS
 from gn3.commands import run_cmd
 
 
@@ -55,17 +56,19 @@ def process_image(image_loc: str) -> bytes:
         return b""
 
 
-def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
-    """function to componse wgcna cmd"""
-    # (todo):issue relative paths to abs paths
-    cmd = f"Rscript ./scripts/{rscript_path}  {temp_file_path}"
+def compose_rscript_cmd(script_path: str,
+                        file_name: str,
+                        temp_file_path: str):
+
+    cmd = f'"Rscript {os.path.join(script_path,file_name)}  {temp_file_path}"'
     return cmd
 
 
 def call_wgcna_script(rscript_path: str, request_data: dict):
     """function to call wgcna script"""
     generated_file = dump_wgcna_data(request_data)
-    cmd = compose_wgcna_cmd(rscript_path, generated_file)
+
+    cmd = compose_rscript_cmd(rscript_path, generated_file)
 
     # stream_cmd_output(request_data, cmd)  disable streaming of data
 

gn3/settings.py

@@ -2,6 +2,7 @@
 
 import tempfile
 import os
+import pathlib
 
 BCRYPT_SALT = "$2b$12$mxLvu9XRLlIaaSeDxt8Sle"  # Change this!
 DATA_DIR = ""
@@ -24,7 +25,9 @@
 
 GN2_BASE_URL = "http://www.genenetwork.org/"
 
-# wgcna script
+# R script
+R_SCRIPTS = pathlib.Path("./scripts/").absolute()
+
 WGCNA_RSCRIPT = "wgcna_analysis.R"
 # qtlreaper command
 REAPER_COMMAND = f"{os.environ.get('GUIX_ENVIRONMENT')}/bin/qtlreaper"

tests/unit/computations/test_wgcna.py

@@ -1,12 +1,16 @@
 """module contains python code for wgcna"""
+
 from unittest import TestCase
 from unittest import mock
 
 import pytest
 
+import os.path
+
 from gn3.computations.wgcna import dump_wgcna_data
-from gn3.computations.wgcna import compose_wgcna_cmd
+from gn3.computations.wgcna import compose_rscript_cmd
 from gn3.computations.wgcna import call_wgcna_script
+from gn3.settings import R_SCRIPTS
 
 
 class TestWgcna(TestCase):
@@ -15,7 +19,7 @@ class TestWgcna(TestCase):
     @pytest.mark.unit_test
     @mock.patch("gn3.computations.wgcna.process_image")
     @mock.patch("gn3.computations.wgcna.run_cmd")
-    @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
+    @mock.patch("gn3.computations.wgcna.compose_rscript_cmd")
     @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
     def test_call_wgcna_script(self,
                                mock_dumping_data,
@@ -100,7 +104,7 @@ def test_call_wgcna_script(self,
 
     @pytest.mark.unit_test
     @mock.patch("gn3.computations.wgcna.run_cmd")
-    @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
+    @mock.patch("gn3.computations.wgcna.compose_rscript_cmd")
     @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
     def test_call_wgcna_script_fails(self, mock_dumping_data, mock_compose_wgcna, mock_run_cmd):
         """test for calling wgcna script\
@@ -122,16 +126,20 @@ def test_call_wgcna_script_fails(self, mock_dumping_data, mock_compose_wgcna, mo
                 "input_file.R", ""), expected_error)
 
     @pytest.mark.unit_test
-    def test_compose_wgcna_cmd(self):
+    def test_compose_rscript_cmd(self):
         """test for composing wgcna cmd"""
-        wgcna_cmd = compose_wgcna_cmd(
-            "wgcna.r", "/tmp/wgcna.json")
-        self.assertEqual(
-            wgcna_cmd, "Rscript ./scripts/wgcna.r  /tmp/wgcna.json")
 
-    @pytest.mark.unit_test
-    @mock.patch("gn3.computations.wgcna.TMPDIR", "/tmp")
-    @mock.patch("gn3.computations.wgcna.uuid.uuid4")
+        expected_cmd = '"Rscript /home/scripts/test_script.R  tmp/wgcna.json"'
+
+        cmd = compose_rscript_cmd(script_path="/home/scripts",
+                                  file_name="test_script.R",
+                                  temp_file_path="tmp/wgcna.json")
+
+        self.assertEqual(cmd, expected_cmd)
+
+    @ pytest.mark.unit_test
+    @ mock.patch("gn3.computations.wgcna.TMPDIR", "/tmp")
+    @ mock.patch("gn3.computations.wgcna.uuid.uuid4")
     def test_create_json_file(self, file_name_generator):
         """test for writing the data to a csv file"""
         # # All the traits we have data for (should not contain duplicates)
@@ -170,3 +178,17 @@ def test_create_json_file(self, file_name_generator):
 
             self.assertEqual(
                 results, "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json")
+
+    def test_if_scripts_file_exists(self):
+        """check if certain script files exists"""
+
+        files_data = [
+            ("wgcna_analysis.R", True),
+            ("ctl_analysis.R", True),
+            ("control_experiment.R", False)
+        ]
+
+        for file_name, file_exists in files_data:
+            file_path = os.path.join(R_SCRIPTS, file_name)
+            self.assertIs(os.path.exists(file_path), file_exists,
+                          f"the file {file_path} doesn't exist in path")