aurelian 0.3.3__py3-none-any.whl → 0.3.4__py3-none-any.whl

aurelian/agents/paperqa/paperqa_mcp.py

@@ -0,0 +1,155 @@
+"""
+MCP tools for working with PaperQA for scientific literature search and analysis.
+"""
+import os
+from typing import Dict, List, Any, Optional
+
+from mcp.server.fastmcp import FastMCP
+
+import aurelian.agents.paperqa.paperqa_tools as pt
+from aurelian.agents.paperqa.paperqa_agent import paperqa_agent, PAPERQA_SYSTEM_PROMPT
+from aurelian.agents.paperqa.paperqa_config import PaperQADependencies
+from pydantic_ai import RunContext
+
+mcp = FastMCP("paperqa", instructions=PAPERQA_SYSTEM_PROMPT.strip())
+
+
+from aurelian.dependencies.workdir import WorkDir
+
+def deps() -> PaperQADependencies:
+    deps = PaperQADependencies()
+    loc = os.getenv("AURELIAN_WORKDIR", "/tmp/paperqa")
+    deps.workdir = WorkDir(loc)
+    
+    paper_dir = os.getenv("PAPERQA_PAPER_DIRECTORY", os.path.join(loc, "papers"))
+    deps.paper_directory = paper_dir
+    
+    if os.getenv("PAPERQA_LLM"):
+        deps.llm = os.getenv("PAPERQA_LLM")
+    
+    if os.getenv("PAPERQA_EMBEDDING"):
+        deps.embedding = os.getenv("PAPERQA_EMBEDDING")
+    
+    return deps
+
+def ctx() -> RunContext[PaperQADependencies]:
+    rc: RunContext[PaperQADependencies] = RunContext[PaperQADependencies](
+        deps=deps(),
+        model=None, usage=None, prompt=None,
+    )
+    return rc
+
+
+@mcp.tool()
+async def search_papers(query: str, max_papers: Optional[int] = None) -> Any:
+    """
+    Search for papers relevant to the query using PaperQA.
+    
+    Args:
+        query: The search query for scientific papers
+        max_papers: Maximum number of papers to return (overrides config)
+        
+    Returns:
+        The search results with paper information
+        
+    This searches for scientific papers based on your query. It returns papers 
+    that are most relevant to the topic you're searching for. You can optionally 
+    specify a maximum number of papers to return.
+    """
+    return await pt.search_papers(ctx(), query, max_papers)
+
+
+@mcp.tool()
+async def query_papers(query: str) -> Any:
+    """
+    Query the papers to answer a specific question using PaperQA.
+    
+    Args:
+        query: The question to answer based on the papers
+        
+    Returns:
+        Detailed answer with citations from the papers
+        
+    This tool analyzes the papers in your collection to provide an evidence-based 
+    answer to your question. It extracts relevant information from across papers 
+    and synthesizes a response with citations to the source papers.
+    """
+    return await pt.query_papers(ctx(), query)
+
+
+@mcp.tool()
+async def add_paper(path: str, citation: Optional[str] = None) -> Any:
+    """
+    Add a specific paper to the collection.
+    
+    Args:
+        path: Path to the paper file or URL
+        citation: Optional citation for the paper
+        
+    Returns:
+        Information about the added paper
+        
+    You can add a paper by providing its file path (PDF) or a URL to the paper 
+    (must be accessible). The paper will be added to your collection for searching 
+    and querying. You can optionally provide a citation string.
+    """
+    return await pt.add_paper(ctx(), path, citation)
+
+@mcp.tool()
+async def add_papers(path: str,) -> Any:
+    """
+    Add multiple papers to the collection.
+    Args:
+        path: Path to the paper file or URL
+        citation: Optional citation for the paper
+
+    Returns:
+        Informations about the added papers
+
+    You can add multiple papers by providing its file path (PDF) or a URL to the
+    paper (must be accessible). The paper will be added to your collection for
+    searching and querying.
+    """
+    return await pt.add_papers(ctx(), path)
+
+
+@mcp.tool()
+async def list_papers() -> Any:
+    """
+    List all papers in the current paper directory.
+    
+    Args:
+        None
+        
+    Returns:
+        Information about all papers in the paper directory
+        
+    This lists all papers currently in your collection, showing their file paths and 
+    any other available metadata. Use this to see what papers you have available 
+    for searching and querying.
+    """
+    return await pt.list_papers(ctx())
+
+
+@mcp.tool()
+async def build_index() -> Any:
+    """
+    Rebuild the search index for papers.
+    
+    Args:
+        None
+        
+    Returns:
+        Information about the indexing process
+        
+    This rebuilds the search index for all papers in your paper directory.
+    The index is required for searching and querying papers. You should run this
+    after adding new papers to make them searchable.
+    """
+    return await pt.build_index(ctx())
+
+
+if __name__ == "__main__":
+    print("Running the PaperQA MCP server")
+    print("Use Ctrl-C to exit")
+    mcp.run(transport='stdio')