Delete utils/api_clients.py

utils/api_clients.py

@@ -1,194 +0,0 @@
-"""
-utils/api_clients.py
-------------------------------------------------
-Enhanced API clients for:
-- PubMed (NCBI)
-- ClinicalTrials.gov
-- FDA Open Data
-- WHO ICTRP
-------------------------------------------------
-Optimized for hybrid VAN-based query processing:
-- Automatically truncates long queries (top keywords only)
-- Resilient to API downtime or malformed responses
-- HTML formatted results for Gradio rendering
-"""
-
-import requests
-import html
-import re
-import traceback
-
-# ============================================================
-# 🔹 Query Normalization
-# ============================================================
-def _normalize_query(query: str, max_words: int = 5) -> str:
-    """
-    Cleans and shortens user query for API compatibility.
-    Removes filler phrases and limits to key words.
-    """
-    q = query.lower()
-    q = re.sub(
-        r"(what is|define|explain|describe|in clinical trials|the meaning of|tell me about|explanation of|concept of)\b",
-        "",
-        q,
-    )
-    q = re.sub(r"[^a-z0-9\s]", "", q)
-    q = re.sub(r"\s+", " ", q).strip()
-
-    # limit to first few words (avoid 404s from overlong queries)
-    words = q.split()
-    q = " ".join(words[:max_words])
-    return q or "clinical trial"
-
-# ============================================================
-# 🔹 PubMed API (NCBI E-Utilities)
-# ============================================================
-def fetch_pubmed(query: str, limit: int = 3) -> str:
-    try:
-        q = _normalize_query(query)
-        base = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
-        esearch = f"{base}esearch.fcgi?db=pubmed&term={q}&retmax={limit}&retmode=json"
-        res = requests.get(esearch, timeout=10)
-        res.raise_for_status()
-
-        ids = res.json().get("esearchresult", {}).get("idlist", [])
-        if not ids:
-            return f"<i>No PubMed results found for <b>{html.escape(q)}</b>.</i>"
-
-        summaries = []
-        for pmid in ids:
-            summary_url = f"{base}esummary.fcgi?db=pubmed&id={pmid}&retmode=json"
-            sres = requests.get(summary_url, timeout=10)
-            sres.raise_for_status()
-            doc = sres.json()["result"].get(pmid, {})
-            title = html.escape(doc.get("title", "Untitled"))
-            source = html.escape(doc.get("source", ""))
-            pubdate = html.escape(doc.get("pubdate", ""))
-            link = f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/"
-            summaries.append(
-                f"<b>{title}</b><br>{source} ({pubdate})<br>"
-                f"<a href='{link}' target='_blank'>[PubMed]</a>"
-            )
-
-        return "<br><br>".join(summaries)
-
-    except Exception as e:
-        traceback.print_exc()
-        return f"<i>PubMed fetch failed for <b>{html.escape(query)}</b>: {e}</i>"
-
-# ============================================================
-# 🔹 ClinicalTrials.gov API
-# ============================================================
-def fetch_clinicaltrials(query: str, limit: int = 3) -> str:
-    """
-    Retrieves brief summaries of matching trials from ClinicalTrials.gov.
-    Automatically truncates query to avoid 404s on long input.
-    """
-    try:
-        q = _normalize_query(query)
-        url = (
-            f"https://clinicaltrials.gov/api/query/study_fields?"
-            f"expr={q}&fields=NCTId,BriefTitle,Condition,OverallStatus"
-            f"&max_rnk={limit}&fmt=json"
-        )
-        res = requests.get(url, timeout=10)
-        res.raise_for_status()
-
-        studies = res.json().get("StudyFieldsResponse", {}).get("StudyFields", [])
-        if not studies:
-            return f"<i>No trials found for <b>{html.escape(q)}</b>.</i>"
-
-        formatted = []
-        for s in studies:
-            nct = s.get("NCTId", [""])[0]
-            title = html.escape(s.get("BriefTitle", [""])[0])
-            condition = html.escape(", ".join(s.get("Condition", [])))
-            status = html.escape(s.get("OverallStatus", ["Unknown"])[0])
-            link = f"https://clinicaltrials.gov/study/{nct}" if nct else "#"
-            formatted.append(
-                f"<b>{title}</b><br>"
-                f"Condition: {condition or 'N/A'}<br>"
-                f"Status: {status}<br>"
-                f"<a href='{link}' target='_blank'>[ClinicalTrials.gov]</a>"
-            )
-
-        return "<br><br>".join(formatted)
-
-    except Exception as e:
-        traceback.print_exc()
-        return f"<i>ClinicalTrials.gov fetch failed for <b>{html.escape(query)}</b>: {e}</i>"
-
-# ============================================================
-# 🔹 FDA Open Data API
-# ============================================================
-def fetch_fda(query: str, limit: int = 3) -> str:
-    """
-    Retrieves FDA label and safety data for a given compound/drug name.
-    """
-    try:
-        q = _normalize_query(query)
-        url = f"https://api.fda.gov/drug/label.json?search=openfda.brand_name:{q}&limit={limit}"
-        res = requests.get(url, timeout=10)
-
-        if res.status_code == 404:
-            return f"<i>No FDA data found for <b>{html.escape(q)}</b>.</i>"
-
-        res.raise_for_status()
-        data = res.json().get("results", [])
-        if not data:
-            return f"<i>No FDA label results found for <b>{html.escape(q)}</b>.</i>"
-
-        formatted = []
-        for entry in data:
-            brand = ", ".join(entry.get("openfda", {}).get("brand_name", []))
-            generic = ", ".join(entry.get("openfda", {}).get("generic_name", []))
-            purpose = html.escape(" ".join(entry.get("purpose", [])[:1]))
-            warnings = html.escape(" ".join(entry.get("warnings", [])[:1]))
-            link = "https://open.fda.gov/drug/label/"
-            formatted.append(
-                f"<b>{brand or q}</b> ({generic or 'N/A'})<br>"
-                f"<u>Purpose:</u> {purpose or 'N/A'}<br>"
-                f"<u>Warning:</u> {warnings or 'N/A'}<br>"
-                f"<a href='{link}' target='_blank'>[FDA Label]</a>"
-            )
-
-        return "<br><br>".join(formatted)
-
-    except Exception as e:
-        traceback.print_exc()
-        return f"<i>FDA fetch failed for <b>{html.escape(query)}</b>: {e}</i>"
-
-# ============================================================
-# 🔹 WHO ICTRP (Backup Trial Source)
-# ============================================================
-def fetch_who_trials(query: str, limit: int = 2) -> str:
-    """
-    Optional backup trial search from WHO ICTRP API.
-    Returns simplified summaries for readability.
-    """
-    try:
-        q = _normalize_query(query)
-        url = f"https://trialsearch.who.int/api/TrialSearch?query={q}"
-        res = requests.get(url, timeout=10)
-
-        if res.status_code != 200:
-            return "<i>WHO ICTRP API unavailable or throttled.</i>"
-
-        trials = res.json().get("TrialSearchResult", [])
-        if not trials:
-            return f"<i>No WHO trials found for <b>{html.escape(q)}</b>.</i>"
-
-        formatted = []
-        for t in trials[:limit]:
-            title = html.escape(t.get("Scientific_title", "Untitled"))
-            registry = html.escape(t.get("Register", ""))
-            country = html.escape(t.get("Recruitment_Country", ""))
-            formatted.append(
-                f"<b>{title}</b><br>{registry or 'Registry Unknown'} — {country or 'N/A'}"
-            )
-
-        return "<br><br>".join(formatted)
-
-    except Exception as e:
-        traceback.print_exc()
-        return f"<i>WHO ICTRP fetch failed for <b>{html.escape(query)}</b>: {e}</i>"