Update genesis/providers.py

genesis/providers.py

@@ -1,163 +1,79 @@
+# genesis/providers.py
 import os
 import requests
-import logging
-import time
-from typing import Optional
+from genesis.api_clients.pubmed_api import search_pubmed
+from genesis.api_clients.chembl_api import search_chembl
+from genesis.api_clients.bioportal_api import search_bioportal
+from genesis.api_clients.umls_api import search_umls
+from genesis.api_clients.ncbi_api import search_ncbi
 
-# Setup logging
-logging.basicConfig(level=logging.INFO, format="[%(levelname)s] %(message)s")
-
-# Load API keys from environment
-DEEPSEEK_API_KEY = os.getenv("DEEPSEEK_API_KEY")
-GEMINI_API_KEY = os.getenv("GEMINI_API_KEY")
 OPENAI_API_KEY = os.getenv("OPENAI_API_KEY")
-HF_API_KEY = os.getenv("HF_API_KEY")
-
-# Retry decorator
-def retry_request(func):
-    def wrapper(*args, **kwargs):
-        retries = 3
-        delay = 2
-        for attempt in range(1, retries + 1):
-            try:
-                return func(*args, **kwargs)
-            except Exception as e:
-                logging.warning(f"{func.__name__} failed (attempt {attempt}): {e}")
-                if attempt < retries:
-                    time.sleep(delay)
-        return None
-    return wrapper
-
-
-# === DeepSeek Summarization ===
-@retry_request
-def run_deepseek_summary(prompt: str) -> str:
-    if not DEEPSEEK_API_KEY:
-        logging.error("Missing DeepSeek API key.")
-        return "[DeepSeek] API key missing."
-    
-    resp = requests.post(
-        "https://api.deepseek.com/v1/chat/completions",
-        headers={
-            "Authorization": f"Bearer {DEEPSEEK_API_KEY}",
-            "Content-Type": "application/json"
-        },
-        json={
-            "model": "deepseek-chat",
-            "messages": [{"role": "user", "content": prompt}],
-            "temperature": 0.3
-        },
-        timeout=60
-    )
-    resp.raise_for_status()
-    return resp.json()["choices"][0]["message"]["content"].strip()
-
-
-# === Gemini Polishing ===
-@retry_request
-def run_gemini_polish(text: str) -> str:
-    if not GEMINI_API_KEY:
-        logging.warning("No Gemini API key found, skipping polish.")
-        return text
-    
-    resp = requests.post(
-        f"https://generativelanguage.googleapis.com/v1beta/models/gemini-pro:generateContent?key={GEMINI_API_KEY}",
-        headers={"Content-Type": "application/json"},
-        json={
-            "contents": [{"parts": [{"text": f"Polish and refine this scientific text:\n\n{text}"}]}]
-        },
-        timeout=60
-    )
-    resp.raise_for_status()
-    candidates = resp.json().get("candidates", [])
-    if candidates and "content" in candidates[0]:
-        return candidates[0]["content"]["parts"][0]["text"].strip()
-    return text
+GEMINI_API_KEY = os.getenv("GEMINI_API_KEY")
+DEEPSEEK_API_KEY = os.getenv("DEEPSEEK_API_KEY")
+CLAUDE_API_KEY = os.getenv("CLAUDE_API_KEY")
+HUGGINGFACE_API_KEY = os.getenv("HUGGINGFACE_API_KEY")
 
+# ---------- LITERATURE ----------
+def run_pubmed_literature(query: str, max_results: int = 10):
+    """Fetch literature from PubMed."""
+    return search_pubmed(query, max_results=max_results)
 
-# === Gemini Image Generation ===
-@retry_request
-def run_gemini_image(prompt: str) -> Optional[str]:
-    if not GEMINI_API_KEY:
-        logging.warning("No Gemini API key found, skipping image generation.")
-        return None
-    
+# ---------- DEEPSEEK ----------
+def run_deepseek_summary(prompt: str):
+    """Summarize content using DeepSeek API."""
     try:
-        resp = requests.post(
-            f"https://generativelanguage.googleapis.com/v1beta/models/gemini-pro-vision:generateImage?key={GEMINI_API_KEY}",
-            headers={"Content-Type": "application/json"},
-            json={"prompt": prompt},
-            timeout=60
-        )
-        resp.raise_for_status()
-        data = resp.json()
-        if "imageUrl" in data:
-            return data["imageUrl"]
+        url = "https://api.deepseek.com/v1/chat/completions"
+        headers = {"Authorization": f"Bearer {DEEPSEEK_API_KEY}"}
+        data = {"model": "deepseek-chat", "messages": [{"role": "user", "content": prompt}]}
+        r = requests.post(url, headers=headers, json=data)
+        r.raise_for_status()
+        return r.json()["choices"][0]["message"]["content"]
     except Exception as e:
-        logging.error(f"[Gemini Image] Failed: {e}")
-    return None
-
-
-# === OpenAI Image Generation ===
-@retry_request
-def run_openai_image(prompt: str) -> Optional[str]:
-    if not OPENAI_API_KEY:
-        logging.warning("No OpenAI API key found, skipping OpenAI image.")
+        print(f"[DeepSeek] Failed: {e}")
         return None
-    
+
+# ---------- GEMINI ----------
+def run_gemini_polish(text: str):
+    """Polish text using Gemini."""
     try:
-        resp = requests.post(
-            "https://api.openai.com/v1/images/generations",
-            headers={
-                "Authorization": f"Bearer {OPENAI_API_KEY}",
-                "Content-Type": "application/json"
-            },
-            json={"model": "gpt-image-1", "prompt": prompt, "size": "1024x1024"},
-            timeout=60
-        )
-        resp.raise_for_status()
-        return resp.json()["data"][0]["url"]
+        url = f"https://generativelanguage.googleapis.com/v1beta/models/gemini-pro:generateContent?key={GEMINI_API_KEY}"
+        headers = {"Content-Type": "application/json"}
+        payload = {"contents": [{"parts": [{"text": text}]}]}
+        r = requests.post(url, headers=headers, json=payload)
+        r.raise_for_status()
+        return r.json()["candidates"][0]["content"]["parts"][0]["text"]
     except Exception as e:
-        logging.error(f"[OpenAI Image] Failed: {e}")
-        return None
-
+        print(f"[Gemini] Failed: {e}")
+        return text
 
-# === Hugging Face Fallback Image ===
-@retry_request
-def run_hf_image(prompt: str) -> Optional[str]:
-    if not HF_API_KEY:
-        logging.warning("No Hugging Face API key found, skipping HF image.")
-        return None
-    
+# ---------- GEMINI IMAGE (Fallback to OpenAI, then HuggingFace) ----------
+def run_image_generation(prompt: str):
+    """Generate image using Gemini > OpenAI > Hugging Face fallback."""
+    # Try Gemini first
     try:
-        resp = requests.post(
-            "https://api-inference.huggingface.co/models/stabilityai/stable-diffusion-2",
-            headers={"Authorization": f"Bearer {HF_API_KEY}"},
-            json={"inputs": prompt},
-            timeout=120
-        )
-        resp.raise_for_status()
-        output_file = "hf_image.png"
-        with open(output_file, "wb") as f:
-            f.write(resp.content)
-        logging.info(f"Hugging Face image saved to {output_file}")
-        return output_file
+        url = f"https://generativelanguage.googleapis.com/v1beta/models/gemini-pro-vision:generateImage?key={GEMINI_API_KEY}"
+        r = requests.post(url, json={"prompt": prompt})
+        r.raise_for_status()
+        return r.json().get("image_url")
+    except:
+        pass
+
+    # Try OpenAI
+    try:
+        import openai
+        openai.api_key = OPENAI_API_KEY
+        result = openai.Image.create(model="gpt-image-1", prompt=prompt, size="1024x1024")
+        return result["data"][0]["url"]
+    except:
+        pass
+
+    # Try Hugging Face
+    try:
+        hf_url = "https://api-inference.huggingface.co/models/stabilityai/stable-diffusion-2"
+        headers = {"Authorization": f"Bearer {HUGGINGFACE_API_KEY}"}
+        r = requests.post(hf_url, headers=headers, json={"inputs": prompt})
+        r.raise_for_status()
+        return r.json()
     except Exception as e:
-        logging.error(f"[HF Image] Failed: {e}")
+        print(f"[Image Generation] Failed: {e}")
         return None
-
-
-# === Master Image Generator ===
-def generate_image_with_fallback(prompt: str) -> Optional[str]:
-    """
-    Try Gemini → OpenAI → Hugging Face in order.
-    """
-    img_url = run_gemini_image(prompt)
-    if img_url:
-        return img_url
-
-    img_url = run_openai_image(prompt)
-    if img_url:
-        return img_url
-
-    return run_hf_image(prompt)