diff options
| -rw-r--r-- | gn3/computations/ctl.py | 4 | ||||
| -rw-r--r-- | gn3/computations/wgcna.py | 6 | ||||
| -rw-r--r-- | tests/unit/computations/test_wgcna.py | 10 |
3 files changed, 10 insertions, 10 deletions
diff --git a/gn3/computations/ctl.py b/gn3/computations/ctl.py index f881410..af1c508 100644 --- a/gn3/computations/ctl.py +++ b/gn3/computations/ctl.py @@ -3,7 +3,7 @@ import json 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: diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py index c985491..01aaedb 100644 --- a/gn3/computations/wgcna.py +++ b/gn3/computations/wgcna.py @@ -55,17 +55,17 @@ def process_image(image_loc: str) -> bytes: return b"" -def compose_wgcna_cmd(rscript_path: str, temp_file_path: str): +def compose_rscript_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}" + cmd = f'"Rscript ./scripts/{rscript_path} {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 diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py index a9108b0..d6d2bf8 100644 --- a/tests/unit/computations/test_wgcna.py +++ b/tests/unit/computations/test_wgcna.py @@ -5,7 +5,7 @@ from unittest import mock import pytest 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 @@ -15,7 +15,7 @@ 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 +100,7 @@ class TestWgcna(TestCase): @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\ @@ -122,9 +122,9 @@ class TestWgcna(TestCase): "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_cmd = compose_rscript_cmd( "wgcna.r", "/tmp/wgcna.json") self.assertEqual( wgcna_cmd, "Rscript ./scripts/wgcna.r /tmp/wgcna.json") |