diff options
Diffstat (limited to 'gn3/computations/wgcna.py')
| -rw-r--r-- | gn3/computations/wgcna.py | 11 |
1 files changed, 5 insertions, 6 deletions
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py index d1f7b32..3229a0e 100644 --- a/gn3/computations/wgcna.py +++ b/gn3/computations/wgcna.py @@ -7,17 +7,16 @@ import subprocess from pathlib import Path -from gn3.settings import TMPDIR from gn3.commands import run_cmd -def dump_wgcna_data(request_data: dict): +def dump_wgcna_data(request_data: dict, tmpdir: str): """function to dump request data to json file""" filename = f"{str(uuid.uuid4())}.json" - temp_file_path = os.path.join(TMPDIR, filename) + temp_file_path = os.path.join(tmpdir, filename) - request_data["TMPDIR"] = TMPDIR + request_data["TMPDIR"] = tmpdir with open(temp_file_path, "w", encoding="utf-8") as output_file: json.dump(request_data, output_file) @@ -65,9 +64,9 @@ def compose_wgcna_cmd(rscript_path: str, temp_file_path: str): return cmd -def call_wgcna_script(rscript_path: str, request_data: dict): +def call_wgcna_script(rscript_path: str, request_data: dict, tmpdir: str): """function to call wgcna script""" - generated_file = dump_wgcna_data(request_data) + generated_file = dump_wgcna_data(request_data, tmpdir) cmd = compose_wgcna_cmd(rscript_path, generated_file) # stream_cmd_output(request_data, cmd) disable streaming of data |