PubMed MCP Server

Instructions

Implementation Reference

• src/tool_handler.py:380-422 (handler)

  The main handler function that executes the search_by_journal tool logic. It extracts parameters, calls the PubMed client to search by journal, formats the results using _format_article_summary, and returns an MCPResponse.

  async def _handle_search_by_journal(self, arguments: Dict[str, Any]) -> MCPResponse:
      """Handle journal-based search."""
      try:
          journal_name = arguments.get("journal_name", "")
          if not journal_name:
              return MCPResponse(
                  content=[{"type": "text", "text": "Journal name is required"}], is_error=True
              )
  
          max_results = arguments.get("max_results", 20)
          date_from = arguments.get("date_from")
          date_to = arguments.get("date_to")
  
          search_result = await self.pubmed_client.search_articles(
              query=f'"{journal_name}"[Journal]',
              max_results=max_results,
              date_from=date_from,
              date_to=date_to,
              cache=self.cache,
          )
  
          content = []
          content.append(
              {
                  "type": "text",
                  "text": f"**Recent Articles from {journal_name}**\n\n"
                  f"Total Results: {search_result.total_results:,}\n"
                  f"Showing: {search_result.returned_results}\n",
              }
          )
  
          for i, article_data in enumerate(search_result.articles, 1):
              article_text = self._format_article_summary(article_data, i)
              content.append({"type": "text", "text": article_text})
  
          return MCPResponse(content=content)
  
      except Exception as e:
          logger.error(f"Error in search_by_journal: {e}")
          return MCPResponse(
              content=[{"type": "text", "text": f"Error: {str(e)}"}], is_error=True
          )

• src/tools.py:205-224 (schema)

  The JSON schema definition for the search_by_journal tool, including input parameters and validation rules.

  {
      "name": "search_by_journal",
      "description": "Search articles from a specific journal",
      "inputSchema": {
          "type": "object",
          "properties": {
              "journal_name": {"type": "string", "description": "Journal name or abbreviation"},
              "max_results": {
                  "type": "integer",
                  "minimum": 1,
                  "maximum": 100,
                  "default": 20,
                  "description": "Maximum number of results",
              },
              "date_from": {"type": "string", "description": "Start date (YYYY/MM/DD)"},
              "date_to": {"type": "string", "description": "End date (YYYY/MM/DD)"},
          },
          "required": ["journal_name"],
      },
  },

• src/tool_handler.py:65-78 (registration)

  The handler_map dictionary that registers the _handle_search_by_journal function for the 'search_by_journal' tool name in the handle_tool_call method.

  handler_map = {
      "search_pubmed": self._handle_search_pubmed,
      "get_article_details": self._handle_get_article_details,
      "search_by_author": self._handle_search_by_author,
      "find_related_articles": self._handle_find_related_articles,
      "export_citations": self._handle_export_citations,
      "search_mesh_terms": self._handle_search_mesh_terms,
      "search_by_journal": self._handle_search_by_journal,
      "get_trending_topics": self._handle_get_trending_topics,
      "analyze_research_trends": self._handle_analyze_research_trends,
      "compare_articles": self._handle_compare_articles,
      "get_journal_metrics": self._handle_get_journal_metrics,
      "advanced_search": self._handle_advanced_search,
  }