improve connection with retry

sources/bin/shared.py

@@ -90,23 +90,39 @@ def read_suite_per_tool_id(tool_fp: str) -> Dict:
     return tools
 
 
-def get_request_json(url: str, headers: dict) -> dict:
-    """
-    Return JSON output using request
-
-    :param url: galaxy tool id
-    """
-
-    try:
-        r = requests.get(url, auth=None, headers=headers)
-        r.raise_for_status()  # Optional: Raises an HTTPError if the response was an unsuccessful status code
-    except ConnectionError as e:
-        raise ConnectionError("Connection aborted: Remote end closed connection without response") from e
-    except requests.exceptions.RequestException as e:
-        # This will handle other possible errors (e.g., timeout, HTTPError)
-        raise SystemExit(e)
-    else:
-        return r.json()
+def get_request_json(url: str, headers: dict, retries: int = 3, delay: float = 2.0) -> dict:
+    """
+    Perform a GET request to retrieve JSON output from a specified URL, with retry on ConnectionError.
+
+    :param url: URL to send the GET request to.
+    :param headers: Headers to include in the GET request.
+    :param retries: Number of retry attempts in case of a ConnectionError (default is 3).
+    :param delay: Delay in seconds between retries (default is 2.0 seconds).
+    :return: JSON response as a dictionary.
+    :raises ConnectionError: If all retry attempts fail due to a connection error.
+    :raises SystemExit: For any other request-related errors.
+    """
+    attempt = 0  # Track the number of attempts
+
+    while attempt < retries:
+        try:
+            r = requests.get(url, auth=None, headers=headers)
+            r.raise_for_status()  # Raises an HTTPError for unsuccessful status codes
+            return r.json()  # Attempt to parse JSON response if successful
+        except ConnectionError as e:
+            attempt += 1
+            if attempt == retries:
+                raise ConnectionError(
+                    "Connection aborted after multiple retries: Remote end closed connection without response"
+                ) from e
+            print(f"Connection error on attempt {attempt}/{retries}. Retrying in {delay} seconds...")
+            time.sleep(delay)  # Wait before retrying
+        except requests.exceptions.RequestException as e:
+            # Handles all other exceptions from the requests library
+            raise SystemExit(f"Request failed: {e}")
+        except ValueError as e:
+            # Handles cases where the response isn't valid JSON
+            raise ValueError("Response content is not valid JSON") from e
 
 
 def format_date(date: str) -> str: