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| author | Frederick Muriuki Muriithi | 2024-09-27 16:20:18 -0500 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-09-27 16:21:21 -0500 |
| commit | 6e86be5910d01b8d682e217c0e53e49cf709a237 (patch) | |
| tree | 2c7cfcb6a3443223b148245a9696b5a1a34aa0e2 | |
| parent | e2883e55b47f062b2d3d6ae50d6fe533ba8d841d (diff) | |
| download | genenetwork3-6e86be5910d01b8d682e217c0e53e49cf709a237.tar.gz | |
Bug: Use absolute paths in place of relative paths.
Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51
| -rw-r--r-- | gn3/computations/ctl.py | 2 | ||||
| -rw-r--r-- | gn3/computations/wgcna.py | 9 |
2 files changed, 7 insertions, 4 deletions
diff --git a/gn3/computations/ctl.py b/gn3/computations/ctl.py index eb34656..f881410 100644 --- a/gn3/computations/ctl.py +++ b/gn3/computations/ctl.py @@ -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("scripts/ctl_analysis.R", temp_file_name) + cmd = compose_wgcna_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 a86c9ab..d1f7b32 100644 --- a/gn3/computations/wgcna.py +++ b/gn3/computations/wgcna.py @@ -1,10 +1,10 @@ """module contains code to preprocess and call wgcna script""" - import os import json import uuid -import subprocess import base64 +import subprocess +from pathlib import Path from gn3.settings import TMPDIR @@ -58,7 +58,10 @@ def process_image(image_loc: str) -> bytes: 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}" + abs_rscript_path = str( + Path(__file__).absolute().parent.parent.parent.joinpath( + f"scripts/{rscript_path}")) + cmd = f"Rscript {abs_rscript_path} {temp_file_path}" return cmd |