v2.3.90

cookbook/tools/pubmed.py

@@ -1,10 +1,8 @@
 from phi.assistant import Assistant
 from phi.tools.pubmed import Pubmed
 
-assistant = Assistant(tools=[Pubmed()], debug=True, show_tool_calls=True)
-res = assistant.print_response(
+assistant = Assistant(tools=[Pubmed()], debug_mode=True, show_tool_calls=True)
+assistant.print_response(
  "ulcerative colitis.",
  markdown=True,
 )
-
-print(res)

phi/tools/pubmed.py

@@ -8,29 +8,27 @@
 class Pubmed(Toolkit):
  def __init__(
  self,
- search_term: Optional[str] = None,
+ email: str = "[email protected]",
  max_results: Optional[int] = None,
- email: Optional[str] = "[email protected]",
  ):
  super().__init__(name="pubmed")
- self.search_term = search_term
- self.max_results = max_results
- self.email = email
+ self.max_results: Optional[int] = max_results
+ self.email: str = email
 
  self.register(self.search_pubmed)
 
- def fetch_pubmed_ids(self, search_term: str, max_results: int, email: str) -> List[str]:
+ def fetch_pubmed_ids(self, query: str, max_results: int, email: str) -> List[str]:
  url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
  params = {
  "db": "pubmed",
- "term": search_term,
+ "term": query,
  "retmax": max_results,
  "email": email,
  "usehistory": "y",
  }
  response = requests.get(url, params=params)
  root = ElementTree.fromstring(response.content)
- return [id_elem.text for id_elem in root.findall(".//Id")]
+ return [id_elem.text for id_elem in root.findall(".//Id") if id_elem.text is not None]
 
  def fetch_details(self, pubmed_ids: List[str]) -> ElementTree.Element:
  url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
@@ -54,11 +52,23 @@ def parse_details(self, xml_root: ElementTree.Element) -> List[Dict[str, Any]]:
  return articles
 
  def search_pubmed(self, query: str, max_results: int = 10) -> str:
- ids = self.fetch_pubmed_ids(query, max_results, self.email)
- details_root = self.fetch_details(ids)
- articles = self.parse_details(details_root)
- results = [
- f"Published: {article['Published']}\nTitle: {article['Title']}\nSummary:\n{article['Summary']}"
- for article in articles
- ]
- return json.dumps(results)
+ """Use this function to search PubMed for articles.
+
+ Args:
+ query (str): The search query.
+ max_results (int): The maximum number of results to return.
+
+ Returns:
+ str: A JSON string containing the search results.
+ """
+ try:
+ ids = self.fetch_pubmed_ids(query, self.max_results or max_results, self.email)
+ details_root = self.fetch_details(ids)
+ articles = self.parse_details(details_root)
+ results = [
+ f"Published: {article.get('Published')}\nTitle: {article.get('Title')}\nSummary:\n{article.get('Summary')}"
+ for article in articles
+ ]
+ return json.dumps(results)
+ except Exception as e:
+ return f"Cound not fetch articles. Error: {e}"

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phidata"
-version = "2.3.89"
+version = "2.3.90"
 description = "Add memory, knowledge and tools to LLMs."
 requires-python = ">=3.8"
 readme = "README.md"