Install boto3 at runtime for authenticated S3 download (fix syntax error)

main.nf

@@ -56,74 +56,46 @@ process POCKETMINER {
             fi
         fi
 
-        # Method 3: Download from MinIO using python boto3/S3
+        # Method 3: Download from MinIO using python
         if [ -z "\$PDB_FILE" ]; then
             S3_PATH="${pdb_path}"
             ENDPOINT="\${AWS_ENDPOINT_URL:-http://datalake-hl.datalake.svc.cluster.local:9000}"
-            echo "Downloading via python S3 client from: \$ENDPOINT" >> run.log
+            echo "Downloading via python S3 from: \$ENDPOINT" >> run.log
             echo "S3 path: \$S3_PATH" >> run.log
             echo "AWS_ACCESS_KEY_ID: \${AWS_ACCESS_KEY_ID:+set}" >> run.log
             echo "AWS_SECRET_ACCESS_KEY: \${AWS_SECRET_ACCESS_KEY:+set}" >> run.log
             echo "AWS_ENDPOINT_URL: \${AWS_ENDPOINT_URL:-not set}" >> run.log
+
+            # Install boto3 if needed, then download
+            pip install -q boto3 2>> run.log || conda install -y -q boto3 2>> run.log || true
+
             python -c "
 import os, sys
-s3_path = '\$S3_PATH'
+s3_path = os.environ.get('S3_INPUT', '${pdb_path}')
-endpoint = '\$ENDPOINT'
+endpoint = os.environ.get('AWS_ENDPOINT_URL', 'http://datalake-hl.datalake.svc.cluster.local:9000')
-
-# Parse s3://bucket/key
 path = s3_path.replace('s3://', '')
 parts = path.split('/', 1)
-bucket = parts[0]
+bucket, key = parts[0], parts[1]
-key = parts[1] if len(parts) > 1 else ''
+print(f'Bucket: {bucket}, Key: {key}, Endpoint: {endpoint}')
-
+import boto3
-print(f'Bucket: {bucket}, Key: {key}')
+from botocore.client import Config
-print(f'Endpoint: {endpoint}')
+s3 = boto3.client('s3',
-
-try:
-    import boto3
-    from botocore.client import Config
-    s3 = boto3.client('s3',
     endpoint_url=endpoint,
     aws_access_key_id=os.environ.get('AWS_ACCESS_KEY_ID', ''),
     aws_secret_access_key=os.environ.get('AWS_SECRET_ACCESS_KEY', ''),
     config=Config(signature_version='s3v4'),
     region_name='us-east-1'
-    )
+)
-    s3.download_file(bucket, key, 'input.pdb')
+s3.download_file(bucket, key, 'input.pdb')
-    print(f'Downloaded via boto3 ({os.path.getsize(\"input.pdb\")} bytes)')
+size = os.path.getsize('input.pdb')
-except ImportError:
+print(f'Downloaded {size} bytes')
-    print('boto3 not available, trying urllib with signing...')
-    # Fallback: use subprocess to call python with hmac signing
-    import urllib.request, hmac, hashlib, datetime
-    access_key = os.environ.get('AWS_ACCESS_KEY_ID', '')
-    secret_key = os.environ.get('AWS_SECRET_ACCESS_KEY', '')
-    if access_key and secret_key:
-        # Simple S3 GET with AWS Signature V2
-        date_str = datetime.datetime.utcnow().strftime('%a, %d %b %Y %H:%M:%S GMT')
-        string_to_sign = f'GET\n\n\n{date_str}\n/{bucket}/{key}'
-        signature = hmac.new(secret_key.encode(), string_to_sign.encode(), hashlib.sha1)
-        import base64
-        sig_b64 = base64.b64encode(signature.digest()).decode()
-        url = f'{endpoint}/{bucket}/{key}'
-        req = urllib.request.Request(url)
-        req.add_header('Date', date_str)
-        req.add_header('Authorization', f'AWS {access_key}:{sig_b64}')
-        with urllib.request.urlopen(req) as resp:
-            with open('input.pdb', 'wb') as f:
-                f.write(resp.read())
-        print(f'Downloaded via signed URL ({os.path.getsize(\"input.pdb\")} bytes)')
-    else:
-        print('No AWS credentials available')
-        sys.exit(1)
-except Exception as e:
-    print(f'Download failed: {e}')
-    sys.exit(1)
 " >> run.log 2>&1
             if [ -f input.pdb ] && [ -s input.pdb ]; then
                 echo "S3 download successful (\$(wc -c < input.pdb) bytes)" >> run.log
                 PDB_FILE="input.pdb"
             else
-                echo "S3 download failed" >> run.log
+                echo "S3 download failed - check run.log" >> run.log
+                cat run.log
                 rm -f input.pdb
             fi
         fi