From bb622cc5947e6ea896d3b94a1d2c4e0cbd1b26f9 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 22 Mar 2022 16:20:00 +0300
Subject: rename compose_wgcna to general func name
---
gn3/computations/ctl.py | 4 ++--
gn3/computations/wgcna.py | 6 +++---
2 files changed, 5 insertions(+), 5 deletions(-)
(limited to 'gn3')
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
--
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