File size: 4,787 Bytes
32c143f | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 | import argparse
import os
import subprocess
import sys
from pathlib import Path
def main():
parser = argparse.ArgumentParser(description="Azure ML Driver for CAFA Evaluator")
parser.add_argument("--data_dir", type=str, required=True, help="Mount point for the data asset")
parser.add_argument("--prediction_path", type=str, required=True, help="Relative path to prediction files inside data asset")
parser.add_argument("--output_dir", type=str, default="./outputs", help="Output directory for results")
args = parser.parse_args()
# Define relative paths for assets within the mounted data directory
# Updated based on user feedback:
# ground truth: validation/validation_superset_term.tsv
# obo: go_info/go-basic.obo
# ia: IA.tsv
gt_rel_path = "validation/validation_superset_term.tsv"
obo_rel_path = "go_info/go-basic.obo"
ia_rel_path = "IA.tsv"
# Construct absolute paths
data_dir = Path(args.data_dir)
ground_truth_path = data_dir / gt_rel_path
ontology_path = data_dir / obo_rel_path
ia_path = data_dir / ia_rel_path
prediction_dir = data_dir / args.prediction_path
output_dir = Path(args.output_dir)
# basic validation
missing = []
if not ground_truth_path.exists(): missing.append(f"Ground truth: {ground_truth_path}")
if not ontology_path.exists(): missing.append(f"Ontology: {ontology_path}")
if not ia_path.exists(): missing.append(f"IA file: {ia_path}")
if not prediction_dir.exists(): missing.append(f"Predictions: {prediction_dir}")
if missing:
print("="*60)
print("❌ Critical Input Files Missing:")
for m in missing: print(f" - {m}")
print("Listing data dir contents for debugging:")
try:
for root, dirs, files in os.walk(data_dir):
level = root.replace(str(data_dir), '').count(os.sep)
if level < 2:
indent = ' ' * 4 * (level)
print(f'{indent}{os.path.basename(root)}/')
for f in files: print(f'{indent} {f}')
except: pass
print("="*60)
sys.exit(1)
# Ensure output directory exists (though CAFA evaluator might create it, good practice)
output_dir.mkdir(parents=True, exist_ok=True)
# Resolve script path
# We assume this script is running from the root of the source directory where CAFA-evaluator-PK is located.
script_path = Path("CAFA-evaluator-PK/src/cafaeval/__main__.py")
if not script_path.exists():
if Path("src/CAFA-evaluator-PK/src/cafaeval/__main__.py").exists():
script_path = Path("src/CAFA-evaluator-PK/src/cafaeval/__main__.py")
else:
print(f"❌ Error: CAFA evaluator script not found at {script_path}")
sys.exit(1)
# Set PYTHONPATH to include the CAFA-evaluator source
# The module is in CAFA-evaluator-PK/src
cafa_src_path = script_path.parent.parent.resolve()
env = os.environ.copy()
env["PYTHONPATH"] = str(cafa_src_path) + os.pathsep + env.get("PYTHONPATH", "")
cmd = [
sys.executable,
str(script_path),
str(ontology_path),
str(prediction_dir),
str(ground_truth_path),
"-ia", str(ia_path),
"-out_dir", str(output_dir),
"-no_orphans", # often good practice for stable evaluation, can remove if not desired
"-th_step", "0.01"
]
print("="*60)
print("🚀 Starting CAFA Evaluator Wrapper")
print(f"📂 Predictions: {prediction_dir}")
print(f"📂 Outputs: {output_dir}")
print(f"🔧 PYTHONPATH: {env['PYTHONPATH']}")
print(f"📜 Command: {' '.join(cmd)}")
print("="*60)
try:
# Run subprocess and stream output
# Using check=True to raise exception on non-zero exit code
process = subprocess.run(
cmd,
check=True,
stdout=sys.stdout,
stderr=sys.stderr, # Pipe stderr to sys.stderr so it shows up in AML logs
text=True,
env=env # Pass modified env
)
print("="*60)
print("✅ CAFA Evaluator completed successfully.")
print("="*60)
except subprocess.CalledProcessError as e:
print("="*60)
print("❌ CAFA EVALUATOR ERROR")
print(f"Command failed with exit code {e.returncode}")
print("See stderr above for details.")
print("="*60)
sys.exit(e.returncode)
except Exception as e:
print("="*60)
print(f"❌ UNEXPECTED ERROR: {e}")
print("="*60)
sys.exit(1)
if __name__ == "__main__":
main()
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