manubot#337 hunting requests without timeout.

manubot/cite/curie/__init__.py

@@ -50,7 +50,7 @@
     "synonyms",
 }
 
-
+default_timeout = 3
 bioregistry_path = pathlib.Path(__file__).parent.joinpath("bioregistry.json")
 
 
@@ -111,7 +111,7 @@ def _download_bioregistry() -> None:
     import requests
 
     url = "https://github.com/biopragmatics/bioregistry/raw/main/exports/registry/registry.json"
-    response = requests.get(url)
+    response = requests.get(url, timeout=default_timeout)
     response.raise_for_status()
     results = response.json()
     assert isinstance(results, dict)

manubot/process/metadata.py

@@ -8,6 +8,8 @@
 from typing import Optional
 from urllib.parse import urljoin
 
+default_timeout = 3
+
 
 def get_header_includes(variables: dict) -> str:
     """
@@ -160,7 +162,7 @@ def get_manuscript_urls(html_url: Optional[str] = None) -> dict:
         return urls
     urls["html_url_versioned"] = urljoin(html_url, "v/{commit}/".format(**ci_params))
     urls["pdf_url_versioned"] = urljoin(urls["html_url_versioned"], "manuscript.pdf")
-    response = requests.head(html_url, allow_redirects=True)
+    response = requests.head(html_url, allow_redirects=True, timeout=default_timeout)
     if not response.ok:
         logging.warning(
             "html_url is not web accessible. "

manubot/util.py

@@ -11,6 +11,8 @@
 import typing
 from types import ModuleType
 
+default_timeout = 3
+
 if typing.TYPE_CHECKING:
     # allow type annotations of lazy-imported packages
     import yaml
@@ -85,7 +87,7 @@ def read_serialized_data(path: str):
     suffixes = set(path_obj.suffixes)
     if is_http_url(path_str):
         headers = {"User-Agent": get_manubot_user_agent()}
-        response = requests.get(path_str, headers=headers)
+        response = requests.get(path_str, headers=headers, timeout=default_timeout)
         if not suffixes & supported_suffixes:
             # if URL has no supported suffixes, evaluate suffixes of final redirect
             suffixes = set(pathlib.Path(response.url).suffixes)