diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/wgcna.py | 15 |
1 files changed, 7 insertions, 8 deletions
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py index f7463c5..90db455 100644 --- a/gn3/computations/wgcna.py +++ b/gn3/computations/wgcna.py @@ -66,26 +66,25 @@ def call_wgcna_script(rscript_path: str, request_data: dict): generated_file = dump_wgcna_data(request_data) cmd = compose_wgcna_cmd(rscript_path, generated_file) - stream_cmd_output(request_data, cmd) + # stream_cmd_output(request_data, cmd) disable streaming of data try: - # run_cmd_results = run_cmd(cmd) + run_cmd_results = run_cmd(cmd) with open(generated_file, "r") as outputfile: + if run_cmd_results["code"] != 0: + return run_cmd_results + output_file_data = json.load(outputfile) - # json format only supports unicode string// to get image data reconvert output_file_data["output"]["image_data"] = process_image( output_file_data["output"]["imageLoc"]).decode("ascii") - output_file_data["output"]["image_data2"] = process_image( - output_file_data["output"]["heatMap"]).decode("ascii") + # json format only supports unicode string// to get image data reconvert - # if run_cmd_results["code"] != 0: - # return run_cmd_results return { "data": output_file_data, - "output": "" + **run_cmd_results } except FileNotFoundError: # relook at handling errors gn3 |