Fixed ncbi timeout

CHANGELOG.md

@@ -10,7 +10,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Added
 
 - Checks for MIBiG and Rhea IDs (implemented as warnings in mite_validation)
-- Timeout for UniProt, NCBI connection
+- Timeout for UniProt using requests
+- Timeout for NCBI using concurrent.futures (Biopython Entrez lacks timeout, requests blocked by NCBI servers)
 
 ### Fixed
 

mite_data/modules/fasta_manager.py

@@ -123,10 +123,11 @@
     this CC0 or use of the Work.
 """
 
+import concurrent.futures
 import json
 import logging
 from pathlib import Path
-from typing import Self
+from typing import Any, Self
 
 import requests
 from Bio import Entrez
@@ -201,22 +202,29 @@ def download_ncbi(self: Self, mite_acc: str, genpept_acc: str) -> tuple:
 
         Returns:
             Tuple of path and data for storage
+
+        Notes:
+            concurrent.futures needed to implement timeout since Biopythons Entrez lacks it and requests is blocked by NCBI
         """
-        url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
-        params = {
-            "db": "protein",
-            "id": genpept_acc,
-            "rettype": "fasta",
-            "retmode": "text",
-        }
-        try:
-            response = requests.get(url, params, timeout=self.timeout)
-        except requests.exceptions.ConnectTimeout as e:
-            raise RuntimeError("Warning: could not connect to NCBI: Timeout") from e
 
-        if response is None:
-            raise RuntimeError(f"{mite_acc}: NCBI download failed on ID {genpept_acc}")
-        lines = response.text.strip().splitlines()
+        def fetch_ncbi(acc: str) -> Any:
+            """Fetch data from NCBI"""
+            handle = Entrez.efetch(
+                db="protein", id=genpept_acc, rettype="fasta", retmode="text"
+            )
+            data = handle.read().strip()
+            handle.close()
+            return data
+
+        with concurrent.futures.ThreadPoolExecutor() as ex:
+            future = ex.submit(fetch_ncbi, genpept_acc)
+
+            try:
+                fasta_data = future.result(timeout=self.timeout)
+            except concurrent.futures.TimeoutError as e:
+                raise RuntimeError("Warning: could not connect to NCBI: Timeout") from e
+
+        lines = fasta_data.splitlines()
 
         if not lines or len(lines) == 1:
             raise ValueError(

tests/test_fasta_manager.py

@@ -42,13 +42,6 @@ def test_download_ncbi(fasta_manager):
     assert content
 
 
-def test_download_ncbi_timeout(fasta_manager):
-    mngr = copy.deepcopy(fasta_manager)
-    mngr.timeout = 0.000001
-    with pytest.raises(RuntimeError):
-        mngr.download_ncbi(mite_acc="MITE9999999", genpept_acc="AAD28496.1")
-
-
 def test_download_uniprot(fasta_manager):
     path, content = fasta_manager.download_uniprot(
         mite_acc="MITE9999999", uniprot_acc="Q9X2V9"
@@ -57,6 +50,13 @@ def test_download_uniprot(fasta_manager):
     assert content
 
 
+def test_download_ncbi_timeout(fasta_manager):
+    mngr = copy.deepcopy(fasta_manager)
+    mngr.timeout = 0.000001
+    with pytest.raises(RuntimeError):
+        mngr.download_ncbi(mite_acc="MITE9999999", genpept_acc="AAD28496.1")
+
+
 def test_download_uniprot_timeout(fasta_manager):
     mngr = copy.deepcopy(fasta_manager)
     mngr.timeout = 0.000001