tooluniverse 1.0.4__py3-none-any.whl → 1.0.6__py3-none-any.whl

tooluniverse/pubmed_tool.py

@@ -0,0 +1,110 @@
+import requests
+from .base_tool import BaseTool
+from .tool_registry import register_tool
+
+
+@register_tool("PubMedTool")
+class PubMedTool(BaseTool):
+    """
+    Search PubMed using NCBI E-utilities (esearch + esummary) and return
+    articles.
+    """
+
+    def __init__(self, tool_config):
+        super().__init__(tool_config)
+        self.esearch_url = (
+            "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
+        )
+        self.esummary_url = (
+            "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
+        )
+
+    def run(self, arguments):
+        query = arguments.get("query")
+        limit = int(arguments.get("limit", 10))
+        api_key = arguments.get("api_key")  # optional NCBI API key
+        if not query:
+            return {"error": "`query` parameter is required."}
+        return self._search(query, limit, api_key)
+
+    def _search(self, query, limit, api_key=None):
+        params = {
+            "db": "pubmed",
+            "term": query,
+            "retmax": max(1, min(limit, 200)),
+            "retmode": "json",
+        }
+        if api_key:
+            params["api_key"] = api_key
+
+        try:
+            r = requests.get(self.esearch_url, params=params, timeout=20)
+        except requests.RequestException as e:
+            return {
+                "error": "Network error calling PubMed esearch",
+                "reason": str(e),
+            }
+        if r.status_code != 200:
+            return {
+                "error": f"PubMed esearch error {r.status_code}",
+                "reason": r.reason,
+            }
+
+        data = r.json()
+        id_list = data.get("esearchresult", {}).get("idlist", [])
+        if not id_list:
+            return []
+
+        summary_params = {
+            "db": "pubmed",
+            "id": ",".join(id_list),
+            "retmode": "json",
+        }
+        if api_key:
+            summary_params["api_key"] = api_key
+
+        try:
+            s = requests.get(
+                self.esummary_url,
+                params=summary_params,
+                timeout=20,
+            )
+        except requests.RequestException as e:
+            return {
+                "error": "Network error calling PubMed esummary",
+                "reason": str(e),
+            }
+        if s.status_code != 200:
+            return {
+                "error": f"PubMed esummary error {s.status_code}",
+                "reason": s.reason,
+            }
+
+        result = s.json().get("result", {})
+        uids = result.get("uids", [])
+        articles = []
+        for uid in uids:
+            rec = result.get(uid, {})
+            title = rec.get("title")
+            journal = rec.get("fulljournalname") or rec.get("source")
+            year = None
+            pubdate = rec.get("pubdate")
+            if pubdate and len(pubdate) >= 4 and pubdate[:4].isdigit():
+                year = int(pubdate[:4])
+            doi = None
+            for id_obj in rec.get("articleids", []):
+                if id_obj.get("idtype") == "doi":
+                    doi = id_obj.get("value")
+                    break
+            url = f"https://pubmed.ncbi.nlm.nih.gov/{uid}/"
+            articles.append(
+                {
+                    "title": title,
+                    "journal": journal,
+                    "year": year,
+                    "doi": doi,
+                    "url": url,
+                }
+            )
+
+        return articles

tooluniverse/remote/boltz/boltz_mcp_server.py

@@ -17,7 +17,7 @@ except FileNotFoundError as e:
     )
     sys.exit(1)
 
-server = FastMCP("Your MCP Server", stateless_http=True)
+server = FastMCP("Your MCP Server")
 agents = {}
 for tool_config in boltz_tools:
     agents[tool_config["name"]] = Boltz2DockingTool(tool_config=tool_config)
@@ -47,4 +47,4 @@ def run_boltz2(query: dict):
 
 
 if __name__ == "__main__":
-    server.run(transport="streamable-http", host="0.0.0.0", port=8080)
+    server.run(transport="streamable-http", host="0.0.0.0", port=8080, stateless_http=True)

tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py

@@ -18,7 +18,7 @@ except FileNotFoundError as e:
     )
     sys.exit(1)
 
-server = FastMCP("Your MCP Server", stateless_http=True)
+server = FastMCP("Your MCP Server")
 agents = {}
 for tool_config in uspto_downloader_tools:
     agents[tool_config["name"]] = USPTOPatentDocumentDownloader(tool_config=tool_config)
@@ -58,4 +58,4 @@ def download_full_text(query: dict):
 
 
 if __name__ == "__main__":
-    server.run(transport="streamable-http", host="0.0.0.0", port=8081)
+    server.run(transport="streamable-http", host="0.0.0.0", port=8081, stateless_http=True)