fixed FileNotFoundError

multi_species_genomes.py

@@ -15,10 +15,13 @@
 """Script for the multi-species genomes dataset. This dataset contains the genomes
 from 850 different species."""
 
+from concurrent.futures import ThreadPoolExecutor, as_completed
 from typing import List
 import datasets
 import pandas as pd
 from Bio import SeqIO
+import requests
+
 
 
 # Find for instance the citation on arxiv or on the dataset repo/website
@@ -71,6 +74,28 @@ def clean_sequence(seq: str) -> str:
     seq = ''.join(list(seq))
     return seq
 
+def validate_url(url: str) -> bool:
+    """Check if the URL is valid by sending a HEAD request."""
+    try:
+        response = requests.head(url, allow_redirects=True)
+        return response.status_code == 200
+    except requests.RequestException as e:
+        print(f"Error validating URL {url}: {e}")
+        return False
+        
+def validate_urls_concurrently(urls: List[str], max_workers: int = 10) -> List[str]:
+    """Validate URLs concurrently and return a list of valid URLs."""
+    valid_urls = []
+    with ThreadPoolExecutor(max_workers=max_workers) as executor:
+        future_to_url = {executor.submit(validate_url, url): url for url in urls}
+        for future in as_completed(future_to_url):
+            url = future_to_url[future]
+            try:
+                if future.result():
+                    valid_urls.append(url)
+            except Exception as e:
+                print(f"Error processing URL {url}: {e}")
+    return valid_urls
 
 class MultiSpeciesGenomesConfig(datasets.BuilderConfig):
     """BuilderConfig for The Human Reference Genome."""
@@ -131,7 +156,10 @@ class MultiSpeciesGenomes(datasets.GeneratorBasedBuilder):
         urls_filepath = dl_manager.download_and_extract('urls.txt')
         with open(urls_filepath) as urls_file:
             urls = [line.rstrip() for line in urls_file]
-        
+
+        # Validate URLs
+        urls=validate_urls_concurrently(urls)
+
         test_urls = urls[-50:]   # 50 genomes for test set
         validation_urls = urls[-100:-50]  # 50 genomes for validation set
         train_urls = urls[:-100]  # 800 genomes for training