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.gitattributes

@@ -57,3 +57,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+pmc-vid_caption.csv filter=lfs diff=lfs merge=lfs -text
+pmc-vid_paper.csv filter=lfs diff=lfs merge=lfs -text

download_pmc.py

@@ -0,0 +1,220 @@
+#!/usr/bin/env python3
+"""
+PMC Paper Download Script
+Saves all files regardless of MP4 presence.
+
+Usage:
+    python download_pmc.py input.csv output_dir [--workers 4]
+
+Required CSV columns:
+    - File: Path to download file (e.g., oa_package/e6/58/PMC176545.tar.gz)
+"""
+
+import pandas as pd
+import os
+import subprocess
+import tarfile
+import glob
+import shutil
+import time
+import argparse
+from concurrent.futures import ThreadPoolExecutor, as_completed
+from tqdm import tqdm
+
+
+def download_and_process_file(file_name, base_url, output_dir):
+    """Download file and process if it's a tar.gz"""
+    url = os.path.join(base_url, file_name)
+    save_path = os.path.join(output_dir, file_name.split("/")[-1])
+    
+    # Download the file
+    subprocess.run([
+        "wget",
+        "-q",  # quiet mode
+        "--header=User-Agent: PMCImageDownloader/1.0",
+        "-O",
+        save_path,
+        url
+    ])
+    
+    # Process if it's a tar.gz file
+    if save_path.endswith('.tar.gz'):
+        has_mp4 = process_tar_gz(save_path, output_dir)
+        if has_mp4:
+            print(f"Found MP4 in {save_path} - extracted all files")
+        else:
+            print(f"No MP4 found in {save_path} - files still extracted")
+    
+    return save_path
+
+
+def process_tar_gz(file_path, output_dir):
+    """
+    Process tar.gz file and extract all files.
+    Flattens directory structure and places all files at top level.
+    Always removes the original tar.gz file.
+    """
+    try:
+        # Create subdirectory with same name as tar.gz (without .tar.gz extension)
+        base_name = os.path.basename(file_path).replace('.tar.gz', '')
+        extract_dir = os.path.join(output_dir, base_name)
+        temp_dir = os.path.join(output_dir, f"temp_{base_name}")
+        os.makedirs(extract_dir, exist_ok=True)
+        os.makedirs(temp_dir, exist_ok=True)
+        
+        # Extract to temporary directory
+        with tarfile.open(file_path, 'r:gz') as tar:
+            tar.extractall(path=temp_dir)
+        
+        # Check for MP4 files (for information only)
+        mp4_files = glob.glob(os.path.join(temp_dir, "**/*.mp4"), recursive=True)
+        has_mp4 = len(mp4_files) > 0
+        
+        # Move all files from nested directories to extract_dir
+        for root, dirs, files in os.walk(temp_dir):
+            for file in files:
+                src_path = os.path.join(root, file)
+                dst_path = os.path.join(extract_dir, file)
+                # Add number suffix if filename already exists
+                if os.path.exists(dst_path):
+                    base, ext = os.path.splitext(file)
+                    counter = 1
+                    while os.path.exists(dst_path):
+                        dst_path = os.path.join(extract_dir, f"{base}_{counter}{ext}")
+                        counter += 1
+                shutil.move(src_path, dst_path)
+        
+        # Cleanup
+        os.remove(file_path)  # Remove original tar.gz file
+        shutil.rmtree(temp_dir)  # Remove temporary directory
+        
+        return has_mp4
+        
+    except Exception as e:
+        print(f"Error processing {file_path}: {e}")
+        # Cleanup on error
+        if os.path.exists(file_path):
+            os.remove(file_path)
+        if os.path.exists(temp_dir):
+            shutil.rmtree(temp_dir)
+        return False
+
+
+def parallel_download(file_list, base_url, output_dir, max_workers=4):
+    """Execute parallel downloads"""
+    os.makedirs(output_dir, exist_ok=True)
+    start_time = time.time()
+    
+    # Check for File column
+    if 'File' not in file_list.columns:
+        raise ValueError("CSV must contain 'File' column")
+    
+    total_files = len(file_list['File'])
+    print(f"Starting download of {total_files} files...")
+    
+    with ThreadPoolExecutor(max_workers=max_workers) as executor:
+        futures = []
+        with tqdm(total=total_files) as progress_bar:
+            # Submit download and process tasks
+            for file_name in file_list['File']:
+                futures.append(
+                    executor.submit(download_and_process_file, file_name, base_url, output_dir)
+                )
+            
+            # Update progress
+            completed = 0
+            for future in as_completed(futures):
+                completed += 1
+                progress_bar.update(1)
+                elapsed_time = time.time() - start_time
+                remaining_files = total_files - completed
+                
+                # Calculate and display estimated remaining time
+                if completed > 0:
+                    time_per_file = elapsed_time / completed
+                    remaining_time = time_per_file * remaining_files
+                    hours = int(remaining_time // 3600)
+                    minutes = int((remaining_time % 3600) // 60)
+                    seconds = int(remaining_time % 60)
+                    progress_bar.set_description(
+                        f"Remaining: {hours:02d}:{minutes:02d}:{seconds:02d}"
+                    )
+    
+    total_time = time.time() - start_time
+    print(f"\nCompleted download of {total_files} files in {total_time:.2f} seconds")
+
+
+def main():
+    """Main function"""
+    parser = argparse.ArgumentParser(
+        description='Download PMC papers from NCBI FTP server'
+    )
+    parser.add_argument(
+        'csv_file',
+        help='Input CSV file containing File column with paths to download'
+    )
+    parser.add_argument(
+        'output_dir',
+        help='Output directory for downloaded and extracted files'
+    )
+    parser.add_argument(
+        '--workers',
+        type=int,
+        default=4,
+        help='Number of parallel download workers (default: 4)'
+    )
+    parser.add_argument(
+        '--base-url',
+        default='https://ftp.ncbi.nlm.nih.gov/pub/pmc',
+        help='Base URL for PMC FTP server (default: https://ftp.ncbi.nlm.nih.gov/pub/pmc)'
+    )
+    
+    args = parser.parse_args()
+    
+    # Read CSV file
+    try:
+        file_list = pd.read_csv(args.csv_file)
+    except FileNotFoundError:
+        print(f"Error: CSV file '{args.csv_file}' not found")
+        return 1
+    except Exception as e:
+        print(f"Error reading CSV file: {e}")
+        return 1
+    
+    # Check for File column
+    if 'File' not in file_list.columns:
+        print("Error: CSV must contain 'File' column")
+        print(f"Available columns: {', '.join(file_list.columns)}")
+        return 1
+    
+    # Remove NaN values
+    file_list = file_list.dropna(subset=['File'])
+    
+    if len(file_list) == 0:
+        print("Error: No valid files to download in CSV")
+        return 1
+    
+    print(f"Found {len(file_list)} files to download")
+    print(f"Output directory: {args.output_dir}")
+    print(f"Using {args.workers} parallel workers")
+    
+    # Execute download
+    try:
+        parallel_download(
+            file_list=file_list,
+            base_url=args.base_url,
+            output_dir=args.output_dir,
+            max_workers=args.workers
+        )
+    except KeyboardInterrupt:
+        print("\nDownload interrupted by user")
+        return 1
+    except Exception as e:
+        print(f"Error during download: {e}")
+        return 1
+    
+    return 0
+
+
+if __name__ == "__main__":
+    exit(main())

pmc-vid_caption.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:49d0c5429738d87d7d2927b3666e8c30c3a95596456001b45ea9e0a28134d352
+size 23488012

pmc-vid_paper.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cd018fd330339d3b140374cb28795016d052c463d3e8307859ca75fce4c5c25f
+size 57399963