2025-05-31-survival.sh

#!/bin/bash

# first, install jq: on macOS, brew install jq 

wget https://raw.githubusercontent.com/Techtonique/datasets/refs/heads/main/tabular/survival/gbsg2_2.csv

# === CONFIG ===
JSON_FILE="survival_curves.json"
CSV_FILE="survival_curves.csv"
PLOT_FILE="survival_plot.png"

# Prompt for auth token
read -p "Enter your Bearer token: " AUTH_TOKEN

# === 1. Submit requests for multiple patients ===
python3 <<END
import subprocess
import sys

try:
    # Use --user to install in the user's site-packages if direct install is restricted (PEP 668)
    subprocess.run([sys.executable, '-m', 'pip', 'install', 'requests'], check=True)
except subprocess.CalledProcessError:
    print("Failed to install requests package")
    sys.exit(1)

import requests
import json

headers = {'Authorization': 'Bearer $AUTH_TOKEN'}
responses = []

for patient_id in range(4):
    params = {'method': 'RidgeCV', 'patient_id': str(patient_id)}
    files = {'file': ('gbsg2_2.csv', open('gbsg2_2.csv', 'rb'), 'text/csv')}
    print(f"Sending request for patient {patient_id}")
    response = requests.post('https://www.techtonique.net/survivalcurve',  params=params, headers=headers, files=files)
    print(response)
    responses.append(response.json())

with open('$JSON_FILE', 'w') as f:
    json.dump(responses, f)
END

# === 2. Convert JSON to CSV ===
jq -r '.[] | .times as $t | .survival_probabilities as $s | range(0; $t|length) | "\(.),\($t[.]),\($s[.])"' "$JSON_FILE" > "$CSV_FILE"
echo "patient_id,time,survival" > temp.csv && tail -n +2 "$CSV_FILE" >> temp.csv && mv temp.csv "$CSV_FILE"

# === 3. Plot with rush ===
rush plot \
  --x time \
  --y survival \
  --group patient_id \
  --color patient_id \
  --title "Patient Survival Curves" \
  "$CSV_FILE" > "$PLOT_FILE"

echo "✅ Final plot saved to: $PLOT_FILE"