Check GitHub API rate limit in `get_alternative_versions`, skip test if hit

Fix the following mulled unit test random failure:

```
    @external_dependency_management
    def test_get_alternative_versions():
>       versions = get_alternative_versions("recipes/bioblend", "meta.yaml")

test/unit/tool_util/mulled/test_get_tests.py:79:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy/tool_util/deps/mulled/get_tests.py:178: in get_alternative_versions
    r.raise_for_status()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <Response [403]>

                f"{self.status_code} Server Error: {reason} for url: {self.url}"
            )

        if http_error_msg:
>           raise HTTPError(http_error_msg, response=self)
E           requests.exceptions.HTTPError: 403 Client Error: rate limit exceeded for url: https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/bioblend

.tox/mulled/lib/python3.7/site-packages/requests/models.py:1021: HTTPError
------------------------------ Captured log call -------------------------------
DEBUG    urllib3.connectionpool:connectionpool.py:1007 Starting new HTTPS connection (1): api.github.com:443
DEBUG    urllib3.connectionpool:connectionpool.py:465 https://api.github.com:443 "GET /repos/bioconda/bioconda-recipes/contents/recipes/bioblend HTTP/1.1" 403 277
```

lib/galaxy/tool_util/deps/mulled/get_tests.py

@@ -20,6 +20,7 @@ except ImportError:
     Template = None  # type: ignore[assignment,misc]
     UndefinedError = Exception  # type: ignore[assignment,misc]
 
+from galaxy.util import check_github_api_response_rate_limit
 from .util import (
     get_file_from_recipe_url,
     MULLED_SOCKET_TIMEOUT,
@@ -175,6 +176,7 @@ def get_alternative_versions(filepath, filename, recipes_path=None, github_repo=
     # else use the GitHub API:
     versions = []
     r = requests.get(f"https://api.github.com/repos/{github_repo}/contents/{filepath}", timeout=MULLED_SOCKET_TIMEOUT)
+    check_github_api_response_rate_limit(r)
     r.raise_for_status()
     for subfile in json.loads(r.text):
         if subfile["type"] == "dir":

lib/galaxy/tool_util/deps/mulled/mulled_search.py

@@ -5,15 +5,14 @@ import json
 import logging
 import sys
 import tempfile
-from datetime import (
-    datetime,
-    timezone,
-)
 
 import requests
 
 from galaxy.tool_util.deps.conda_util import CondaContext
-from galaxy.util import which
+from galaxy.util import (
+    check_github_api_response_rate_limit,
+    which,
+)
 from .mulled_list import get_singularity_containers
 from .util import (
     build_target,
@@ -147,17 +146,6 @@ class GitHubSearch:
     Tool to search the GitHub bioconda-recipes repo
     """
 
-    @staticmethod
-    def _check_response_rate_limit(response):
-        if response.status_code == 403 and "API rate limit exceeded" in response.json()["message"]:
-            # It can take tens of minutes before the rate limit window resets
-            message = "GitHub API rate limit exceeded."
-            rate_limit_reset_UTC_timestamp = response.headers.get("X-RateLimit-Reset")
-            if rate_limit_reset_UTC_timestamp:
-                rate_limit_reset_datetime = datetime.fromtimestamp(int(rate_limit_reset_UTC_timestamp), tz=timezone.utc)
-                message += f" The rate limit window will reset at {rate_limit_reset_datetime.isoformat()}."
-            raise Exception(message)
-
     def get_json(self, search_string):
         """
         Takes search_string variable and return results from the bioconda-recipes github repository in JSON format
@@ -169,7 +157,7 @@ class GitHubSearch:
             f"https://api.github.com/search/code?q={search_string}+in:path+repo:bioconda/bioconda-recipes+path:recipes",
             timeout=MULLED_SOCKET_TIMEOUT,
         )
-        self._check_response_rate_limit(response)
+        check_github_api_response_rate_limit(response)
         response.raise_for_status()
         return response.json()
 
@@ -188,7 +176,7 @@ class GitHubSearch:
             f"https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/{search_string}",
             timeout=MULLED_SOCKET_TIMEOUT,
         )
-        self._check_response_rate_limit(response)
+        check_github_api_response_rate_limit(response)
         return response.status_code == 200
 
 

lib/galaxy/util/__init__.py

@@ -25,7 +25,10 @@ import threading
 import time
 import unicodedata
 import xml.dom.minidom
-from datetime import datetime
+from datetime import (
+    datetime,
+    timezone,
+)
 from email.mime.multipart import MIMEMultipart
 from email.mime.text import MIMEText
 from hashlib import md5
@@ -1806,6 +1809,17 @@ def is_url(uri, allow_list=None):
     return any(uri.startswith(scheme) for scheme in allow_list)
 
 
+def check_github_api_response_rate_limit(response):
+    if response.status_code == 403 and "API rate limit exceeded" in response.json()["message"]:
+        # It can take tens of minutes before the rate limit window resets
+        message = "GitHub API rate limit exceeded."
+        rate_limit_reset_UTC_timestamp = response.headers.get("X-RateLimit-Reset")
+        if rate_limit_reset_UTC_timestamp:
+            rate_limit_reset_datetime = datetime.fromtimestamp(int(rate_limit_reset_UTC_timestamp), tz=timezone.utc)
+            message += f" The rate limit window will reset at {rate_limit_reset_datetime.isoformat()}."
+        raise Exception(message)
+
+
 def download_to_file(url, dest_file_path, timeout=30, chunk_size=2**20):
     """Download a URL to a file in chunks."""
     with requests.get(url, timeout=timeout, stream=True) as r, open(dest_file_path, "wb") as f:

test/unit/tool_util/mulled/test_get_tests.py

@@ -1,3 +1,5 @@
+from unittest import SkipTest
+
 from galaxy.tool_util.deps.mulled.get_tests import (
     deep_test_search,
     find_anaconda_versions,
@@ -76,7 +78,12 @@ def test_open_recipe_file():
 
 @external_dependency_management
 def test_get_alternative_versions():
-    versions = get_alternative_versions("recipes/bioblend", "meta.yaml")
+    try:
+        versions = get_alternative_versions("recipes/bioblend", "meta.yaml")
+    except Exception as e:
+        if "API rate limit" in str(e):
+            raise SkipTest("Hitting GitHub API rate limit")
+        raise
     assert versions == ["recipes/bioblend/0.7.0/meta.yaml"]