diff gcp_batch_netcat.py @ 4:2ff4a39ea41b draft

planemo upload commit 1bf6938d35be8e67e317f504f43f281ce7dc06e6

--- a/gcp_batch_netcat.py	Mon Jul 21 15:13:09 2025 +0000
+++ b/gcp_batch_netcat.py	Tue Jul 22 14:47:47 2025 +0000
@@ -1,86 +1,192 @@
-
+import argparse
 import json
-import subprocess
-import argparse
+import logging
+import os
+import sys
+# import time
 import uuid
-import time
-import os
+from google.cloud import batch_v1
+
+# Configure logging to go to stdout instead of stderr to avoid Galaxy marking job as failed
+import sys
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(levelname)s - %(message)s',
+    stream=sys.stdout
+)
+logger = logging.getLogger(__name__)
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument('--nfs_address', required=True)
+    parser.add_argument('--nfs_address', required=False, help='NFS server address (if not provided, will be auto-detected from /galaxy/server/database/ mount)')
     parser.add_argument('--output', required=True)
-    parser.add_argument('--project', required=True)
+    parser.add_argument('--project', required=False, help='GCP Project ID (if not provided, will be extracted from service account key)')
     parser.add_argument('--region', required=True)
-    parser.add_argument('--port', default='2049')
+    parser.add_argument('--network', default='default', help='GCP Network name')
+    parser.add_argument('--subnet', default='default', help='GCP Subnet name')
     parser.add_argument('--service_account_key', required=True)
     args = parser.parse_args()
 
     # Set up authentication using the service account key
     os.environ['GOOGLE_APPLICATION_CREDENTIALS'] = args.service_account_key
+    logger.info(f"Authentication configured with service account: {args.service_account_key}")
 
-    # Ensure gcloud uses a writable config directory
-    os.environ['CLOUDSDK_CONFIG'] = '/tmp/gcloud-config'
+    # Extract GCP project ID from service account key if not provided
+    if args.project:
+        project_id = args.project
+        logger.info(f"Using provided project ID: {project_id}")
+    else:
+        try:
+            with open(args.service_account_key, 'r') as f:
+                service_account_data = json.load(f)
+            project_id = service_account_data.get('project_id')
+            if not project_id:
+                raise ValueError("project_id not found in service account key file")
+            logger.info(f"Extracted project ID from service account key: {project_id}")
+        except Exception as e:
+            logger.error(f"Failed to extract project ID from service account key: {e}")
+            raise
+
+    # Extract NFS server address if not provided
+    if args.nfs_address:
+        nfs_address = args.nfs_address
+        logger.info(f"Using provided NFS address: {nfs_address}")
+    else:
+        try:
+            # Try to detect NFS server from /galaxy/server/database/ mount
+            import subprocess
+            result = subprocess.run(['mount'], capture_output=True, text=True)
+            nfs_address = None
 
-    # Create the temp config directory if it doesn't exist
-    os.makedirs('/tmp/gcloud-config', exist_ok=True)
+            for line in result.stdout.split('\n'):
+                if '/galaxy/server/database' in line and ':' in line:
+                    # Look for NFS mount pattern: server:/path on /galaxy/server/database
+                    parts = line.split()
+                    for part in parts:
+                        if ':' in part and part.count(':') == 1:
+                            nfs_address = part.split(':')[0]
+                            break
+                    if nfs_address:
+                        logger.info(f"Detected NFS address from mount: {nfs_address}")
+                        break
+
+            if not nfs_address:
+                # Fallback: try to parse /proc/mounts
+                try:
+                    with open('/proc/mounts', 'r') as f:
+                        for line in f:
+                            if '/galaxy/server/database' in line and ':' in line:
+                                parts = line.split()
+                                if len(parts) > 0 and ':' in parts[0]:
+                                    nfs_address = parts[0].split(':')[0]
+                                    logger.info(f"Detected NFS address from /proc/mounts: {nfs_address}")
+                                    break
+                except:
+                    pass
+
+            if not nfs_address:
+                raise ValueError("Could not auto-detect NFS server address from /galaxy/server/database/ mount")
+
+            logger.info(f"Auto-detected NFS address from mount: {nfs_address}")
+        except Exception as e:
+            logger.error(f"Failed to auto-detect NFS address: {e}")
+            raise
+
+    # time.sleep(10000)
 
     job_name = f'netcat-job-{uuid.uuid4()}'
+    logger.info(f"Generated job name: {job_name}")
 
-    job_spec = {
-        "taskGroups": [
-            {
-                "taskSpec": {
-                    "runnables": [
-                        {
-                            "script": {
-                                "text": f"/usr/bin/nc -z -v {args.nfs_address} {args.port}"
-                            }
-                        }
-                    ],
-                    "computeResource": {
-                        "cpuMilli": 1000,
-                        "memoryMib": 1024
-                    },
-                    "environment": {
-                        "imageUri": "afgane/gcp-batch-netcat:0.1.0"
-                    }
-                },
-                "taskCount": 1,
-                "parallelism": 1
-            }
-        ],
-        "logsPolicy": {
-            "destination": "CLOUD_LOGGING"
-        }
-    }
+    # Create Batch client
+    logger.info("Creating Batch client...")
+    client = batch_v1.BatchServiceClient()
+    logger.info("Batch client created successfully")
+
+    # Define the job using the Python client library objects
+    logger.info("Building job specification...")
+    runnable = batch_v1.Runnable()
+    runnable.container = batch_v1.Runnable.Container()
+    runnable.container.image_uri = "afgane/gcp-batch-netcat:0.2.0"
+    runnable.container.entrypoint = "/usr/bin/nc"
+    runnable.container.commands = ["-z", "-v", nfs_address, "2049"]
+    logger.debug(f"Container config: image={runnable.container.image_uri}, entrypoint={runnable.container.entrypoint}, commands={runnable.container.commands}")
+
+    task = batch_v1.TaskSpec()
+    task.runnables = [runnable]
+    task.compute_resource = batch_v1.ComputeResource()
+    task.compute_resource.cpu_milli = 1000
+    task.compute_resource.memory_mib = 1024
+    logger.debug(f"Compute resources: CPU={task.compute_resource.cpu_milli}m, Memory={task.compute_resource.memory_mib}MiB")
+
+    task_group = batch_v1.TaskGroup()
+    task_group.task_count = 1
+    task_group.parallelism = 1
+    task_group.task_spec = task
+    logger.debug(f"Task group: count={task_group.task_count}, parallelism={task_group.parallelism}")
+
+    # Network configuration: Batch job should run in the same network as the NFS server
+    network_interface = batch_v1.AllocationPolicy.NetworkInterface()
+    network_interface.network = f"global/networks/{args.network}"
+    network_interface.subnetwork = f"regions/{args.region}/subnetworks/{args.subnet}"
+    logger.debug(f"Network: {network_interface.network}")
+    logger.debug(f"Subnet: {network_interface.subnetwork}")
+
+    network_policy = batch_v1.AllocationPolicy.NetworkPolicy()
+    network_policy.network_interfaces = [network_interface]
+
+    allocation_policy = batch_v1.AllocationPolicy()
+    allocation_policy.network = network_policy
 
-    job_spec_file = 'job.json'
-    with open(job_spec_file, 'w') as f:
-        json.dump(job_spec, f)
+    job = batch_v1.Job()
+    job.task_groups = [task_group]
+    job.allocation_policy = allocation_policy
+    job.logs_policy = batch_v1.LogsPolicy()
+    job.logs_policy.destination = batch_v1.LogsPolicy.Destination.CLOUD_LOGGING
+    logger.info("Job specification built successfully")
 
-    command = [
-        'gcloud', 'batch', 'jobs', 'submit', job_name,
-        '--location', args.region,
-        '--project', args.project,
-        '--config', job_spec_file,
-        '--format=text',
-        '--verbosity=debug'
-    ]
+    create_request = batch_v1.CreateJobRequest()
+    create_request.parent = f"projects/{project_id}/locations/{args.region}"
+    create_request.job_id = job_name
+    create_request.job = job
+    logger.debug(f"Create request parent: {create_request.parent}")
+    logger.debug(f"Create request job_id: {create_request.job_id}")
+
+    logger.info(f"Submitting job with name: {job_name}")
+    logger.info(f"Target project: {project_id}")
+    logger.info(f"Target Batch region: {args.region}")
+    logger.info(f"NFS target: {nfs_address}:2049")
 
-    # Wait 4 minutes before submitting the job
-    time.sleep(240)
+    # Proceed with job submission
+    try:
+        logger.info("Calling client.create_job()...")
+        job_response = client.create_job(request=create_request)
+        logger.info("Job submitted successfully!")
+        logger.info(f"Job name: {job_response.name}")
+        logger.info(f"Job UID: {job_response.uid}")
 
-    try:
-        result = subprocess.run(command, capture_output=True, text=True, check=True)
         with open(args.output, 'w') as f:
-            f.write("Job output:\n")
-            f.write(result.stdout)
-            f.write(result.stderr)
-    except subprocess.CalledProcessError as e:
+            f.write("Job submitted successfully using Python client.\n")
+            f.write(f"Job name: {job_name}\n")
+            f.write(f"Job response name: {job_response.name}\n")
+            f.write(f"Job UID: {job_response.uid}\n")
+            f.write(f"Project: {project_id}\n")
+            f.write(f"Region: {args.region}\n")
+            f.write(f"NFS Address: {nfs_address}:2049\n")
+
+    except Exception as e:
+        logger.error(f"Error submitting job: {type(e).__name__}: {e}")
+        logger.error(f"Error details: {str(e)}")
+        import traceback
+        logger.error("Traceback:", exc_info=True)
+
         with open(args.output, 'w') as f:
-            f.write("Error submitting job:\n")
-            f.write(e.stderr)
+            f.write(f"Error submitting job: {type(e).__name__}: {e}\n")
+            f.write(f"Error details: {str(e)}\n")
+            f.write(f"Job name: {job_name}\n")
+            f.write(f"Project: {project_id}\n")
+            f.write(f"Region: {args.region}\n")
+            f.write(f"Traceback:\n")
+            f.write(traceback.format_exc())
 
 if __name__ == '__main__':
     main()