aiagents4pharma 1.45.1__py3-none-any.whl → 1.46.1__py3-none-any.whl

aiagents4pharma/talk2biomodels/api/kegg.py

@@ -1,87 +0,0 @@
-"""
-This module contains the API for fetching Kegg database
-"""
-
-import re
-
-import requests
-
-
-def fetch_from_api(base_url: str, query: str) -> str:
-    """Fetch data from the given API endpoint."""
-    try:
-        response = requests.get(base_url + query, timeout=10)
-        response.raise_for_status()
-        return response.text
-    except requests.exceptions.RequestException as e:
-        print(f"Error fetching data for query {query}: {e}")
-        return ""
-
-
-def fetch_kegg_names(ids: list[str], batch_size: int = 10) -> dict[str, str]:
-    """
-    Fetch the names of multiple KEGG entries using the KEGG REST API in batches.
-
-    Args:
-        ids (List[str]): List of KEGG IDs.
-        batch_size (int): Maximum number of IDs to include in a single request.
-
-    Returns:
-        Dict[str, str]: A mapping of KEGG IDs to their names.
-    """
-    if not ids:
-        return {}
-
-    base_url = "https://rest.kegg.jp/get/"
-    entry_name_map = {}
-
-    # Process IDs in batches
-    for i in range(0, len(ids), batch_size):
-        batch = ids[i : i + batch_size]
-        query = "+".join(batch)
-        entry_data = fetch_from_api(base_url, query)
-
-        # if not entry_data:
-        #     continue
-        entries = entry_data.split("///")
-        for entry in entries:
-            if not entry.strip():
-                continue
-            lines = entry.strip().split("\n")
-            entry_line = next((line for line in lines if line.startswith("ENTRY")), None)
-            name_line = next((line for line in lines if line.startswith("NAME")), None)
-
-            # if not entry_line and not name_line:
-            #     continue
-            entry_id = entry_line.split()[1]
-            # Split multiple names in the NAME field and clean them
-            names = [
-                re.sub(r"[^a-zA-Z0-9\s]", "", name).strip()
-                for name in name_line.replace("NAME", "").strip().split(";")
-            ]
-            # Join cleaned names into a single string
-            entry_name_map[entry_id] = " ".join(names).strip()
-
-    return entry_name_map
-
-
-def fetch_kegg_annotations(
-    data: list[dict[str, str]], batch_size: int = 10
-) -> dict[str, dict[str, str]]:
-    """Fetch KEGG entry descriptions grouped by database type."""
-    grouped_data = {}
-    for entry in data:
-        db_type = entry["Database"].lower()
-        grouped_data.setdefault(db_type, []).append(entry["Id"])
-
-    results = {}
-    for db_type, ids in grouped_data.items():
-        results[db_type] = fetch_kegg_names(ids, batch_size=batch_size)
-
-    return results
-
-
-# def get_protein_name_or_label(data: List[Dict[str, str]],
-#                               batch_size: int = 10) -> Dict[str, Dict[str, str]]:
-#     """Fetch descriptions for KEGG-related identifiers."""
-#     return fetch_kegg_annotations(data, batch_size=batch_size)