aiagents4pharma 1.9.0__py3-none-any.whl → 1.11.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- aiagents4pharma/__init__.py +9 -6
- aiagents4pharma/talk2biomodels/agents/t2b_agent.py +7 -10
- aiagents4pharma/talk2biomodels/models/basico_model.py +29 -32
- aiagents4pharma/talk2biomodels/models/sys_bio_model.py +9 -6
- aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py +3 -3
- aiagents4pharma/talk2biomodels/tests/test_basico_model.py +7 -8
- aiagents4pharma/talk2biomodels/tests/test_langgraph.py +64 -2
- aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py +13 -7
- aiagents4pharma/talk2biomodels/tools/__init__.py +1 -0
- aiagents4pharma/talk2biomodels/tools/get_modelinfo.py +5 -3
- aiagents4pharma/talk2biomodels/tools/parameter_scan.py +292 -0
- aiagents4pharma/talk2biomodels/tools/simulate_model.py +9 -11
- aiagents4pharma/talk2competitors/__init__.py +5 -0
- aiagents4pharma/talk2competitors/agents/__init__.py +6 -0
- aiagents4pharma/talk2competitors/agents/main_agent.py +130 -0
- aiagents4pharma/talk2competitors/agents/s2_agent.py +75 -0
- aiagents4pharma/talk2competitors/config/__init__.py +5 -0
- aiagents4pharma/talk2competitors/config/config.py +110 -0
- aiagents4pharma/talk2competitors/state/__init__.py +5 -0
- aiagents4pharma/talk2competitors/state/state_talk2competitors.py +32 -0
- aiagents4pharma/talk2competitors/tests/__init__.py +3 -0
- aiagents4pharma/talk2competitors/tests/test_langgraph.py +274 -0
- aiagents4pharma/talk2competitors/tools/__init__.py +7 -0
- aiagents4pharma/talk2competitors/tools/s2/__init__.py +8 -0
- aiagents4pharma/talk2competitors/tools/s2/display_results.py +25 -0
- aiagents4pharma/talk2competitors/tools/s2/multi_paper_rec.py +132 -0
- aiagents4pharma/talk2competitors/tools/s2/search.py +119 -0
- aiagents4pharma/talk2competitors/tools/s2/single_paper_rec.py +141 -0
- {aiagents4pharma-1.9.0.dist-info → aiagents4pharma-1.11.0.dist-info}/METADATA +39 -23
- {aiagents4pharma-1.9.0.dist-info → aiagents4pharma-1.11.0.dist-info}/RECORD +33 -17
- {aiagents4pharma-1.9.0.dist-info → aiagents4pharma-1.11.0.dist-info}/LICENSE +0 -0
- {aiagents4pharma-1.9.0.dist-info → aiagents4pharma-1.11.0.dist-info}/WHEEL +0 -0
- {aiagents4pharma-1.9.0.dist-info → aiagents4pharma-1.11.0.dist-info}/top_level.txt +0 -0
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#!/usr/bin/env python3
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"""
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This tool is used to return recommendations for a single paper.
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"""
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import logging
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from typing import Annotated, Any, Dict, Optional
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import pandas as pd
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import requests
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from langchain_core.messages import ToolMessage
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from langchain_core.tools import tool
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from langchain_core.tools.base import InjectedToolCallId
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from langgraph.types import Command
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from pydantic import BaseModel, Field
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# Configure logging
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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class SinglePaperRecInput(BaseModel):
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"""Input schema for single paper recommendation tool."""
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paper_id: str = Field(
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description="Semantic Scholar Paper ID to get recommendations for (40-character string)"
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)
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limit: int = Field(
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default=2,
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description="Maximum number of recommendations to return",
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ge=1,
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le=500,
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)
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year: Optional[str] = Field(
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default=None,
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description="Year range in format: YYYY for specific year, "
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"YYYY- for papers after year, -YYYY for papers before year, or YYYY:YYYY for range",
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)
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tool_call_id: Annotated[str, InjectedToolCallId]
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model_config = {"arbitrary_types_allowed": True}
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@tool(args_schema=SinglePaperRecInput)
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def get_single_paper_recommendations(
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paper_id: str,
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tool_call_id: Annotated[str, InjectedToolCallId],
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limit: int = 2,
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year: Optional[str] = None,
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) -> Dict[str, Any]:
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"""
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Get paper recommendations based on a single paper.
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Args:
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paper_id (str): The Semantic Scholar Paper ID to get recommendations for.
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tool_call_id (Annotated[str, InjectedToolCallId]): The tool call ID.
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limit (int, optional): The maximum number of recommendations to return. Defaults to 2.
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year (str, optional): Year range for papers.
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Supports formats like "2024-", "-2024", "2024:2025". Defaults to None.
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Returns:
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Dict[str, Any]: The recommendations and related information.
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"""
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logger.info("Starting single paper recommendations search.")
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endpoint = (
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f"https://api.semanticscholar.org/recommendations/v1/papers/forpaper/{paper_id}"
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)
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params = {
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"limit": min(limit, 500), # Max 500 per API docs
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"fields": "paperId,title,abstract,year,authors,citationCount,url",
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"from": "all-cs", # Using all-cs pool as specified in docs
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}
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# Add year parameter if provided
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if year:
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params["year"] = year
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response = requests.get(endpoint, params=params, timeout=10)
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data = response.json()
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papers = data.get("data", [])
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response = requests.get(endpoint, params=params, timeout=10)
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# print(f"API Response Status: {response.status_code}")
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logging.info(
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"API Response Status for recommendations of paper %s: %s",
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paper_id,
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response.status_code,
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)
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# print(f"Request params: {params}")
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logging.info("Request params: %s", params)
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data = response.json()
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recommendations = data.get("recommendedPapers", [])
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# Extract paper ID and title from recommendations
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filtered_papers = {
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paper["paperId"]: {
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"Title": paper.get("title", "N/A"),
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"Abstract": paper.get("abstract", "N/A"),
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"Year": paper.get("year", "N/A"),
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"Citation Count": paper.get("citationCount", "N/A"),
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"URL": paper.get("url", "N/A"),
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# "Publication Type": paper.get("publicationTypes", ["N/A"])[0]
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# if paper.get("publicationTypes")
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# else "N/A",
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# "Open Access PDF": paper.get("openAccessPdf", {}).get("url", "N/A")
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# if paper.get("openAccessPdf") is not None
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# else "N/A",
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}
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for paper in recommendations
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if paper.get("title") and paper.get("authors")
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}
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# Create a DataFrame for pretty printing
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df = pd.DataFrame(filtered_papers)
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# Format papers for state update
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papers = [
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f"Paper ID: {paper_id}\n"
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f"Title: {paper_data['Title']}\n"
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f"Abstract: {paper_data['Abstract']}\n"
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f"Year: {paper_data['Year']}\n"
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f"Citations: {paper_data['Citation Count']}\n"
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f"URL: {paper_data['URL']}\n"
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# f"Publication Type: {paper_data['Publication Type']}\n"
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# f"Open Access PDF: {paper_data['Open Access PDF']}"
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for paper_id, paper_data in filtered_papers.items()
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]
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# Convert DataFrame to markdown table
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markdown_table = df.to_markdown(tablefmt="grid")
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logging.info("Search results: %s", papers)
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return Command(
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update={
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"papers": filtered_papers, # Now sending the dictionary directly
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"messages": [
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ToolMessage(content=markdown_table, tool_call_id=tool_call_id)
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],
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}
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)
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Metadata-Version: 2.2
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Name: aiagents4pharma
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Version: 1.
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Version: 1.11.0
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Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
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Classifier: Programming Language :: Python :: 3
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Requires-Python: >=3.
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Requires-Python: >=3.12
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: copasi_basico==0.78
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[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
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[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
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[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml)
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<h1 align="center" style="border-bottom: none;">🤖 AIAgents4Pharma</h1>
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@@ -56,9 +59,9 @@ Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://
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Our toolkit currently consists of three intelligent agents, each designed to simplify and enhance access to specialized data in biology:
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- **Talk2BioModels**: Engage directly with mathematical models in systems biology.
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- **Talk2Cells**
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- **Talk2KnowledgeGraphs**
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- **Talk2Competitors**
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- **Talk2Cells** _(Work in progress)_: Query and analyze sequencing data with ease.
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- **Talk2KnowledgeGraphs** _(Work in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
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- **Talk2Competitors** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
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---
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- Forward simulation of both internal and open-source models (BioModels).
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- Adjust parameters within the model to simulate different conditions.
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- Query simulation results.
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- Extract model information such as species, parameters, units and description.
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### 2. Talk2Cells
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### 2. Talk2Cells _(Work in Progress)_
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**Talk2Cells** is being developed to provide direct access to and analysis of sequencing data, such as RNA-Seq or DNA-Seq, using natural language.
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### 3. Talk2KnowledgeGraphs
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### 3. Talk2KnowledgeGraphs _(Work in Progress)_
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**Talk2KnowledgeGraphs** is an agent designed to enable interaction with biological knowledge graphs (KGs). KGs integrate vast amounts of structured biological data into a format that highlights relationships between entities, such as proteins, genes, and diseases.
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### 4.
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### 4. Talk2Competitors _(Coming soon)_
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## Getting Started
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- Required libraries specified in `requirements.txt`
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### Installation
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#### Option 1: PyPI
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```bash
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```
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#### Option 2: git
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```
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2. **Install dependencies:**
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```
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3. **Initialize OPENAI_API_KEY**
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4. **[Optional] Set up login credentials**
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```
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5. **[Optional] Initialize LANGSMITH_API_KEY**
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```
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Please note that this will create a new tracing project in your Langsmith
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account with the name `<user_name>@<uuid>`, where `user_name` is the name
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5. **Open a pull request**
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### Current Needs
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- **Beta testers** for Talk2BioModels.
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- **Developers** with experience in natural language processing, bioinformatics, or knowledge graphs for contributions to AIAgents4Pharma.
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## Roadmap
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### Completed
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### Planned
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- **User Interface**: Interactive web UI for all agents.
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- **Talk2Cells**: Integration of sequencing data analysis tools.
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**Get Started** with AIAgents4Pharma today and transform the way you interact with biological data.
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## Feedback
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Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use the `Isssues` tab 😀
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