aiagents4pharma 1.42.0__py3-none-any.whl → 1.43.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tools/paper_download/download_medrxiv_input.py

@@ -1,114 +0,0 @@
-#!/usr/bin/env python3
-"""
-Tool for downloading medRxiv paper metadata and retrieving the PDF URL.
-"""
-
-import logging
-from typing import Annotated, Any
-
-import hydra
-import requests
-from langchain_core.messages import ToolMessage
-from langchain_core.tools import tool
-from langchain_core.tools.base import InjectedToolCallId
-from langgraph.types import Command
-from pydantic import BaseModel, Field
-
-# Configure logging
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
-
-
-class DownloadMedrxivPaperInput(BaseModel):
-    """Input schema for the medRxiv paper download tool."""
-
-    doi: str = Field(
-        description="""The medRxiv DOI, from search_helper or multi_helper or single_helper,
-    used to retrieve the paper details and PDF URL."""
-    )
-    tool_call_id: Annotated[str, InjectedToolCallId]
-
-
-# Fetching raw metadata from medRxiv API for a given DOI
-def fetch_medrxiv_metadata(doi: str, api_url: str, request_timeout: int) -> dict:
-    """
-    Fetch metadata for a medRxiv paper using its DOI and extract relevant fields.
-
-    Parameters:
-        doi (str): The DOI of the medRxiv paper.
-
-    Returns:
-        dict: A dictionary containing the title, authors, abstract, publication date, and URLs.
-    """
-    # Strip any version suffix (e.g., v1) since bioRxiv's API is version-sensitive
-    clean_doi = doi.split("v")[0]
-
-    api_url = f"{api_url}{clean_doi}"
-    logger.info("Fetching metadata from api url: %s", api_url)
-    response = requests.get(api_url, timeout=request_timeout)
-    response.raise_for_status()
-
-    data = response.json()
-    if not data.get("collection"):
-        raise ValueError(f"No entry found for medRxiv ID {doi}")
-
-    return data["collection"][0]
-
-
-# Extracting relevant metadata fields from the raw data
-def extract_metadata(paper: dict, doi: str) -> dict:
-    """
-    Extract relevant metadata fields from a medRxiv paper entry.
-    """
-    title = paper.get("title", "")
-    authors = paper.get("authors", "")
-    abstract = paper.get("abstract", "")
-    pub_date = paper.get("date", "")
-    doi_suffix = paper.get("doi", "").split("10.1101/")[-1]
-    pdf_url = f"https://www.medrxiv.org/content/10.1101/{doi_suffix}.full.pdf"
-    logger.info("PDF URL: %s", pdf_url)
-    return {
-        "Title": title,
-        "Authors": authors,
-        "Abstract": abstract,
-        "Publication Date": pub_date,
-        "URL": pdf_url,
-        "pdf_url": pdf_url,
-        "filename": f"{doi_suffix}.pdf",
-        "source": "medrxiv",
-        "medrxiv_id": doi,
-    }
-
-
-# Tool to download medRxiv paper metadata and PDF URL
-@tool(args_schema=DownloadMedrxivPaperInput, parse_docstring=True)
-def download_medrxiv_paper(
-    doi: str,
-    tool_call_id: Annotated[str, InjectedToolCallId],
-) -> Command[Any]:
-    """
-    Get metadata and PDF URL for a medRxiv paper using its doi or medrxiv id.
-    """
-    logger.info("Fetching metadata from medRxiv for DOI: %s", doi)
-
-    # Load configuration
-    with hydra.initialize(version_base=None, config_path="../../configs"):
-        cfg = hydra.compose(
-            config_name="config", overrides=["tools/download_medrxiv_paper=default"]
-        )
-        api_url = cfg.tools.download_medrxiv_paper.api_url
-        request_timeout = cfg.tools.download_medrxiv_paper.request_timeout
-        logger.info("API URL: %s", api_url)
-
-    raw_data = fetch_medrxiv_metadata(doi, api_url, request_timeout)
-    metadata = extract_metadata(raw_data, doi)
-    article_data = {doi: metadata}
-
-    content = f"Successfully retrieved metadata and PDF URL for medRxiv DOI {doi}"
-
-    return Command(
-        update={
-            "article_data": article_data,
-            "messages": [ToolMessage(content=content, tool_call_id=tool_call_id)],
-        }
-    )