pubmed tool added

Author: lucifertrj

src/openagi/actions/tools/pubmed_tool.py

@@ -0,0 +1,72 @@
+from openagi.actions.base import ConfigurableAction
+from openagi.exception import OpenAGIException
+from pydantic import Field
+
+try:
+	from Bio import Entrez
+except ImportError:
+	raise OpenAGIException("Install Biopython with cmd `pip install biopython`")
+
+class PubMedSearch(ConfigurableAction):
+	"""PubMed Search tool for querying biomedical literature.
+	
+	This action uses the Bio.Entrez module to search PubMed and retrieve
+	scientific articles based on user queries. Requires an email address
+	to be configured for NCBI's tracking purposes.
+	"""
+	
+	query: str = Field(..., description="Search query for PubMed")
+	max_results: int = Field(
+		default=5,
+		description="Maximum number of results to return (default: 5)"
+	)
+	sort: str = Field(
+		default="relevance",
+		description="Sort order: 'relevance', 'pub_date', or 'first_author'"
+	)
+
+	def execute(self) -> str:
+		email: str = self.get_config('email')
+		if not email:
+			raise OpenAGIException(
+				"Email not configured. Use PubMedSearch.set_config(email='[email protected]')"
+			)
+
+		Entrez.email = email
+		
+		try:
+			# Search PubMed
+			search_handle = Entrez.esearch(
+				db="pubmed",
+				term=self.query,
+				retmax=self.max_results,
+				sort=self.sort
+			)
+			search_results = Entrez.read(search_handle)
+			search_handle.close()
+
+			if not search_results["IdList"]:
+				return "No results found for the given query."
+
+			# Fetch details for found articles
+			ids = ",".join(search_results["IdList"])
+			fetch_handle = Entrez.efetch(
+				db="pubmed",
+				id=ids,
+				rettype="medline",
+				retmode="text"
+			)
+			
+			results = fetch_handle.read()
+			fetch_handle.close()
+
+			# Process and format results
+			formatted_results = (
+				f"Found {len(search_results['IdList'])} results for query: {self.query}\n\n"
+				f"{results}"
+			)
+
+			return formatted_results
+
+		except Exception as e:
+			return f"Error searching PubMed: {str(e)}"