From d6bb20ae7dcd9bc81e6b259b25e32ef8efa8aa36 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Juan=20Felipe=20Fl=C3=B3rez=20Ospina?= <juanflo16@gmail.com>
Date: Sat, 28 Jun 2025 14:45:06 +0200
Subject: [PATCH] Update pipelines/data_integration.py with new functionality.
 copy subtree and create hdf5 function now checks whether there is already a
 copy of the src directory to avoid replacing files and verifies there is
 enough free storage space to initiate data transfer and subsequent ingestion
 into hdf5.

---
 pipelines/data_integration.py | 49 ++++++++++++++++++++++++++++++-----
 1 file changed, 43 insertions(+), 6 deletions(-)

diff --git a/pipelines/data_integration.py b/pipelines/data_integration.py
index 66a5fca..2cfb013 100644
--- a/pipelines/data_integration.py
+++ b/pipelines/data_integration.py
@@ -18,8 +18,8 @@ if dimaPath not in sys.path:  # Avoid duplicate entries
 import yaml 
 import logging
 from datetime import datetime
-# Importing chain class from itertools 
-from itertools import chain 
+import shutil 
+
 
 # Import DIMA modules
 try:
@@ -196,11 +196,48 @@ def copy_subtree_and_create_hdf5(src, dst, select_dir_keywords, select_file_keyw
     """Helper function to copy directory with constraints and create HDF5."""
     src = src.replace(os.sep,'/')
     dst = dst.replace(os.sep,'/')
-    
-    logging.info("Creating constrained copy of the experimental campaign folder %s at: %s", src, dst)
 
-    path_to_files_dict = utils.copy_directory_with_contraints(src, dst, select_dir_keywords, select_file_keywords, allowed_file_extensions)
-    logging.info("Finished creating a copy of the experimental campaign folder tree at: %s", dst)
+    
+    # Dry run to see what needs copying
+    logging.info("Checking copy status for %s", src)
+    # Return path to files that are expected in the dst directory
+    path_to_expected_files = utils.copy_directory_with_contraints(src, dst, select_dir_keywords, 
+                                                        select_file_keywords, allowed_file_extensions, 
+                                                        dry_run=True)
+    
+    # Check existence and collect sizes
+    all_exist = True
+    total_size = 0
+    
+    for dir_path, filenames in path_to_expected_files.items():
+        for filename in filenames:
+            dst_file_path = os.path.join(dir_path, filename)
+            
+            if not os.path.exists(dst_file_path):
+                all_exist = False
+                # Get size from source file
+                src_file_path = os.path.join(src, os.path.relpath(dst_file_path, dst))
+
+                if os.path.exists(src_file_path):
+                    #print(os.path.getsize(src_file_path))
+                    total_size += os.path.getsize(src_file_path)
+
+    if all_exist:
+        logging.info(f"All files already exist at {dst}, skipping copy.")
+        print(f"[Notice] All files already exist at {dst}, skipping copy.")
+        path_to_files_dict = path_to_expected_files
+    else:
+        # Check available space for missing files only
+        dst_free = shutil.disk_usage(".").free # checks the free space in the current dir
+        if total_size > dst_free:
+            raise Exception(f"Insufficient space: need {total_size/1e9:.6f}GB, have {dst_free/1e9:.6f}GB")
+        else:
+            print(f"Campaign folder size: {total_size/1e9:.6f}GB")
+            print(f"Free space: {dst_free/1e9:.6f}GB")
+            
+        logging.info(f"Creating constrained copy of the experimental campaign folder {src} at: {dst}")#, src, dst)
+        path_to_files_dict = utils.copy_directory_with_contraints(src, dst, select_dir_keywords, select_file_keywords, allowed_file_extensions)
+        logging.info("Finished creating a copy of the experimental campaign folder tree at: %s", dst)
 
     
     logging.info("Creating HDF5 file at: %s", dst)