Merge pull request #83 from davidkastner/cluster-submit-bug

Fixed a bug for the cluster submitter

Author: davidkastner

pyqmmm/io/submit_clustering.py

@@ -1,63 +1,67 @@
 import os
 import subprocess
 
-# Get the current working directory
-cwd = os.getcwd()
+def main():
+    # Get the current working directory
+    cwd = os.getcwd()
 
-# Function to check if a directory contains any .out file
-def has_out_file(dir_path):
-    for file in os.listdir(dir_path):
-        if file.endswith('.out'):
-            return True
-    return False
+    # Function to check if a directory contains any .out file
+    def has_out_file(dir_path):
+        for file in os.listdir(dir_path):
+            if file.endswith('.out'):
+                return True
+        return False
 
-# Iterate over all items in the cwd
-for item in os.listdir(cwd):
-    item_path = os.path.join(cwd, item)
-    
-    # Check if it's a directory and not "1_cluster"
-    if os.path.isdir(item_path) and item != "1_cluster":
-        # Path to 2_analysis
-        analysis_dir = os.path.join(item_path, "2_analysis")
+    # Iterate over all items in the cwd
+    for item in os.listdir(cwd):
+        item_path = os.path.join(cwd, item)
 
-        # Check if 2_analysis exists
-        if os.path.exists(analysis_dir) and os.path.isdir(analysis_dir):
-            # Path to 1_cluster inside 2_analysis
-            cluster_dir = os.path.join(analysis_dir, "1_cluster")
+        # Check if it's a directory and not "1_cluster"
+        if os.path.isdir(item_path) and item != "1_cluster":
+            # Path to 2_analysis
+            analysis_dir = os.path.join(item_path, "2_analysis")
 
-            # Check if 1_cluster exists
-            if os.path.exists(cluster_dir) and os.path.isdir(cluster_dir):
-                # Iterate over subdirectories in 1_cluster
-                for sub_item in os.listdir(cluster_dir):
-                    sub_item_path = os.path.join(cluster_dir, sub_item)
-                    
-                    # Check if it's a directory
-                    if os.path.isdir(sub_item_path):
-                        # Path to cluster.sh
-                        sh_file = os.path.join(sub_item_path, "cluster.sh")
+            # Check if 2_analysis exists
+            if os.path.exists(analysis_dir) and os.path.isdir(analysis_dir):
+                # Path to 1_cluster inside 2_analysis
+                cluster_dir = os.path.join(analysis_dir, "1_cluster")
+                
+                # Check if 1_cluster exists
+                if os.path.exists(cluster_dir) and os.path.isdir(cluster_dir):
+                    # Iterate over subdirectories in 1_cluster
+                    for sub_item in os.listdir(cluster_dir):
+                        sub_item_path = os.path.join(cluster_dir, sub_item)
 
-                        # Check if cluster.sh exists
-                        if os.path.exists(sh_file):
-                            # Check for .out files
-                            if has_out_file(sub_item_path):
-                                # Prompt user
-                                response = input(f"Job might be running in {sub_item_path}. Resubmit? (y/N): ").strip().lower()
-                                if response != 'y':
-                                    print(f"Skipping resubmission for {sub_item_path}")
-                                    continue
+                        # Check if it's a directory
+                        if os.path.isdir(sub_item_path):
+                            # Path to cluster.sh
+                            sh_file = os.path.join(sub_item_path, "cluster.sh")
 
-                            # Submit the job
-                            try:
-                                result = subprocess.run(['sbatch', sh_file], capture_output=True, text=True, cwd=sub_item_path)
-                                if result.returncode == 0:
-                                    print(f"Submitted job for {sub_item_path}: {result.stdout.strip()}")
-                                else:
-                                    print(f"Error submitting job for {sub_item_path}: {result.stderr.strip()}")
-                            except Exception as e:
-                                print(f"Exception submitting job for {sub_item_path}: {str(e)}")
-                        else:
-                            print(f"cluster.sh not found in {sub_item_path}")
+                            # Check if cluster.sh exists
+                            if os.path.exists(sh_file):
+                                # Check for .out files
+                                if has_out_file(sub_item_path):
+                                    # Prompt user
+                                    response = input(f"Job might be running in {sub_item_path}. Resubmit? (y/N): ").strip().lower()
+                                    if response != 'y':
+                                        print(f"Skipping resubmission for {sub_item_path}")
+                                        continue
+                                
+                                # Submit the job
+                                try:
+                                    result = subprocess.run(['sbatch', sh_file], capture_output=True, text=True, cwd=sub_item_path)
+                                    if result.returncode == 0:
+                                        print(f"Submitted job for {sub_item_path}: {result.stdout.strip()}")
+                                    else:
+                                        print(f"Error submitting job for {sub_item_path}: {result.stderr.strip()}")
+                                except Exception as e:
+                                    print(f"Exception submitting job for {sub_item_path}: {str(e)}")
+                            else:
+                                print(f"cluster.sh not found in {sub_item_path}")
+                else:
+                    print(f"1_cluster not found in {analysis_dir}")
             else:
-                print(f"1_cluster not found in {analysis_dir}")
-        else:
-            print(f"2_analysis not found in {item_path}")
+                print(f"2_analysis not found in {item_path}")
+
+if __name__ == "__main__":
+    main()