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Enhancement: Structured runtime logging, parameter tracking, and output handling (Issue #6) #25

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Enhancement: Structured runtime logging, parameter tracking, and output handling (Issue #6) #25

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Binary file added dummy.txt
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9 changes: 9 additions & 0 deletions outputs/run_log.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
2026-03-26 02:58:55.197801 - Need pathway list file for heatmap
2026-03-26 03:00:19.381438 - Need pathway list file for heatmap
2026-03-26 03:06:26.609750 - Parameters: {'data': 'dummy.txt', 'heatmap': 'T', 'tsne': False, 'kaplan': False, 'pathway_list': None, 'output': 'output', 'compound': None}
2026-03-26 03:06:26.611719 - MP-BioPath execution started
2026-03-26 03:06:26.612742 - Need pathway list file for heatmap
2026-03-26 03:14:03.942724 - MP-BioPath execution started
2026-03-26 03:14:03.943771 - Parameters: {'data': 'dummy.txt', 'heatmap': 'T', 'tsne': False, 'kaplan': False, 'pathway_list': None, 'output': 'output', 'compound': None}
2026-03-26 03:14:03.944770 - Need pathway list file for heatmap
2026-03-26 03:14:03.946767 - Execution stopped: pathway list missing
36 changes: 32 additions & 4 deletions sandbox/make_output_files.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,17 @@
#################################################################################

import sys, argparse, subprocess
import os
from datetime import datetime

def log_message(message):
if not os.path.exists("outputs"):
os.makedirs("outputs")

with open("outputs/run_log.txt", "a") as f:
f.write(f"{datetime.now()} - {message}\n")


parser = argparse.ArgumentParser(description='Creates output visuals from MP-BioPath output data file')
parser.add_argument("data", help="output file from MP-BioPath")
parser.add_argument("-m", "--heatmap", help="default is 'T' to make heatmap, else specify 'F' for no heatmap",
Expand All @@ -45,9 +55,24 @@
parser.add_argument("-c", "--compound", help="specify compound name")

args = parser.parse_args()

log_message("MP-BioPath execution started")

params = {
"data": args.data,
"heatmap": args.heatmap,
"tsne": args.tsne,
"kaplan": args.kaplan,
"pathway_list": args.pathway_list,
"output": args.output,
"compound": args.compound
}

log_message(f"Parameters: {params}")
if args.pathway_list is None:
print("Need pathway list file for heatmap")
log_message("Need pathway list file for heatmap")
log_message("Execution stopped: pathway list missing")
print("Need pathway list file for heatmap")
sys.exit()
else:
pathway_color_map = {}
with open(args.pathway_list, 'r') as p:
Expand Down Expand Up @@ -81,8 +106,9 @@
output_string = output_string[:-2]
colour_string = colour_string[:-2]

if args.heatmap is "F":
print("heatmap script is not executed")
if args.heatmap == "F":
log_message("Heatmap script is not executed")
print("Heatmap script is not executed")

command = "Rscript" # --vanilla --slave < "
path2script = "sandbox/create_visuals.R"
Expand All @@ -101,5 +127,7 @@

#calls and executes Rscript (create_visuals.R) by passing in arguments
cmd = [command, path2script, args.data, colour_column_string, args.output, output_string, colour_string, switch]#, args.compound]
log_message(f"Running command: {cmd}")
print(cmd)
subprocess.call(cmd, universal_newlines = True)
log_message("MP-BioPath execution completed")