Pqa tool

.env.example

@@ -4,8 +4,5 @@
 # OpenAI API Key
 OPENAI_API_KEY=YOUR_OPENAI_API_KEY_GOES_HERE  # pragma: allowlist secret
 
-# PQA API Key
-PQA_API_KEY=YOUR_PQA_API_KEY_GOES_HERE  # pragma: allowlist secret
-
 # Serp API key
 SERP_API_KEY=YOUR_SERP_API_KEY_GOES_HERE  # pragma: allowlist secret

.github/workflows/build.yml

@@ -13,10 +13,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python "3.9"
+    - name: Set up Python "3.11"
       uses: actions/setup-python@v2
       with:
-        python-version: "3.9"
+        python-version: "3.11"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/tests.yml

@@ -23,10 +23,10 @@ jobs:
         environment-file: environment.yaml
         python-version: ${{ matrix.python-version }}
         auto-activate-base: true
-    - name: Install openmm pdbfixer mdanalysis with conda
+    - name: Install pdbfixer with conda
       shell: bash -l {0}
       run: |
-        conda install -c conda-forge openmm pdbfixer mdanalysis
+        conda install -c conda-forge pdbfixer
     - name: Install dependencies
       shell: bash -l {0}
       run: |
@@ -45,6 +45,5 @@ jobs:
       env:
         OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
         SEMANTIC_SCHOLAR_API_KEY: ${{ secrets.SEMANTIC_SCHOLAR_API_KEY }}
-        PQA_API_KEY : ${{ secrets.PQA_API_TOKEN }}
       run: |
          pytest -m "not skip" tests

.secrets.baseline

@@ -3,8 +3,5 @@
 # Rule for detecting OpenAI API keys
 OpenAI API Key: \b[secrets]{3}_[a-zA-Z0-9]{32}\b
 
-# Rule for detecting pqa API keys
-PQA API Key: "pqa[a-zA-Z0-9-._]+"
-
 # Rule for detecting serp API keys
 # Serp API Key: "[a-zA-Z0-9]{64}"

README.md

@@ -7,8 +7,8 @@ To use the OpenMM features in the agent, please set up a conda environment, foll
 - Create conda environment: `conda env create -n mdagent -f environment.yaml`
 - Activate your environment: `conda activate mdagent`
 
-If you already have a conda environment, you can install the necessary dependencies with the following steps.
-- Install the necessary conda dependencies: `conda install -c conda-forge openmm pdbfixer mdanalysis`
+If you already have a conda environment, you can install, pdbfixer, a necessary dependency with the following steps.
+- Install the necessary conda dependencies: `conda install -c conda-forge pdbfixer`
 
 
 ## Installation

dev-requirements.txt

@@ -1,2 +1,3 @@
 pre-commit
 pytest
+pytest-mock

mdagent/tools/base_tools/util_tools/search_tools.py

@@ -1,26 +1,75 @@
-import pqapi
+import os
+import re
+
+import langchain
+import paperqa
+import paperscraper
+from langchain.base_language import BaseLanguageModel
 from langchain.tools import BaseTool
+from pypdf.errors import PdfReadError
+
+
+def paper_scraper(search: str, pdir: str = "query") -> dict:
+    try:
+        return paperscraper.search_papers(search, pdir=pdir)
+    except KeyError:
+        return {}
+
+
+def paper_search(llm, query):
+    prompt = langchain.prompts.PromptTemplate(
+        input_variables=["question"],
+        template="""
+        I would like to find scholarly papers to answer
+        this question: {question}. Your response must be at
+        most 10 words long.
+        'A search query that would bring up papers that can answer
+        this question would be: '""",
+    )
+
+    query_chain = langchain.chains.llm.LLMChain(llm=llm, prompt=prompt)
+    if not os.path.isdir("./query"):  # todo: move to ckpt
+        os.mkdir("query/")
+    search = query_chain.run(query)
+    print("\nSearch:", search)
+    papers = paper_scraper(search, pdir=f"query/{re.sub(' ', '', search)}")
+    return papers
+
+
+def scholar2result_llm(llm, query, k=5, max_sources=2):
+    """Useful to answer questions that require
+    technical knowledge. Ask a specific question."""
+    papers = paper_search(llm, query)
+    if len(papers) == 0:
+        return "Not enough papers found"
+    docs = paperqa.Docs(llm=llm)
+    not_loaded = 0
+    for path, data in papers.items():
+        try:
+            docs.add(path, data["citation"])
+        except (ValueError, FileNotFoundError, PdfReadError):
+            not_loaded += 1
+
+    print(f"\nFound {len(papers.items())} papers but couldn't load {not_loaded}")
+    answer = docs.query(query, k=k, max_sources=max_sources).formatted_answer
+    return answer
 
 
 class Scholar2ResultLLM(BaseTool):
     name = "LiteratureSearch"
-    description = """Input a specific question,
-                returns an answer from literature search."""
+    description = (
+        "Useful to answer questions that require technical "
+        "knowledge. Ask a specific question."
+    )
+    llm: BaseLanguageModel = None
 
-    pqa_key: str = ""
-
-    def __init__(self, pqa_key: str):
+    def __init__(self, llm):
         super().__init__()
-        self.pqa_key = pqa_key
+        self.llm = llm
 
-    def _run(self, question: str) -> str:
-        """Use the tool"""
-        try:
-            response = pqapi.agent_query("default", question)
-            return response.answer
-        except Exception:
-            return "Literature search failed."
-
-    async def _arun(self, question: str) -> str:
-        """Use the tool asynchronously"""
-        raise NotImplementedError
+    def _run(self, query) -> str:
+        return scholar2result_llm(self.llm, query)
+
+    async def _arun(self, query) -> str:
+        """Use the tool asynchronously."""
+        raise NotImplementedError("this tool does not support async")

mdagent/tools/maketools.py

@@ -76,6 +76,7 @@ def make_all_tools(
 
     # add base tools
     base_tools = [
+        Scholar2ResultLLM(llm=llm),
         CleaningToolFunction(path_registry=path_instance),
         ListRegistryPaths(path_registry=path_instance),
         ProteinName2PDBTool(path_registry=path_instance),
@@ -108,14 +109,6 @@ def make_all_tools(
         learned_tools = get_learned_tools(subagent_settings.ckpt_dir)
 
     all_tools += base_tools + subagents_tools + learned_tools
-
-    # add other tools depending on api keys
-    os.getenv("SERP_API_KEY")
-    pqa_key = os.getenv("PQA_API_KEY")
-    # if serp_key:
-    #    all_tools.append(SerpGitTool(serp_key))  # github issues search
-    if pqa_key:
-        all_tools.append(Scholar2ResultLLM(pqa_key))  # literature search
     return all_tools
 
 

notebooks/lit_search.ipynb

@@ -0,0 +1,121 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
+      "  from .autonotebook import tqdm as notebook_tqdm\n"
+     ]
+    }
+   ],
+   "source": [
+    "from mdagent import MDAgent"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#until we update to new version\n",
+    "import nest_asyncio\n",
+    "nest_asyncio.apply()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mda = MDAgent()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prompt = \"Are there any studies that show that the use of a mask can reduce the spread of COVID-19?\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\"Masks COVID-19 transmission reduction studies\"\n",
+      "Search: \"Masks COVID-19 transmission reduction studies\"\n",
+      "\n",
+      "Found 14 papers but couldn't load 0\n",
+      "Yes, there are studies that show that the use of a mask can reduce the spread of COVID-19. The review by Howard et al. (2021) indicates that mask-wearing reduces the transmissibility of COVID-19 by limiting the spread of infected respiratory particles. This conclusion is supported by evidence from both laboratory and clinical studies."
+     ]
+    }
+   ],
+   "source": [
+    "answer = mda.run(prompt)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'Yes, there are studies that show that the use of a mask can reduce the spread of COVID-19. The review by Howard et al. (2021) indicates that mask-wearing reduces the transmissibility of COVID-19 by limiting the spread of infected respiratory particles. This conclusion is supported by evidence from both laboratory and clinical studies.'"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "answer"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "mdagent",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.8"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

setup.py

@@ -17,22 +17,21 @@
     license="MIT",
     packages=find_packages(),
     install_requires=[
-        "paper-scraper @ git+https://github.com/blackadad/paper-scraper.git",
         "chromadb==0.3.29",
         "google-search-results",
         "langchain==0.0.336",
         "langchain_experimental",
         "matplotlib",
         "nbformat",
         "openai",
-        "paper-qa",
-        "python-dotenv",
-        "pqapi",
         "requests",
-        "rmrkl",
         "tiktoken",
         "rdkit",
         "streamlit",
+        "paper-qa",
+        "openmm",
+        "MDAnalysis",
+        "paper-scraper @ git+https://github.com/blackadad/paper-scraper.git",
     ],
     test_suite="tests",
     long_description=long_description,

tests/test_fxns.py

@@ -5,9 +5,11 @@
 from unittest.mock import MagicMock, mock_open, patch
 
 import pytest
+from langchain.chat_models import ChatOpenAI
 
 from mdagent.tools.base_tools import (
     CleaningTools,
+    Scholar2ResultLLM,
     SimulationFunctions,
     VisFunctions,
     get_pdb,
@@ -438,3 +440,24 @@ def test_init_path_registry(path_registry_with_mocked_fs):
     # you may need to check the internal state or the contents of the JSON file.
     # For example:
     assert "water_000000" in path_registry_with_mocked_fs.list_path_names()
+
+
+@pytest.fixture
+def questions():
+    qs = [
+        "What are the effects of norhalichondrin B in mammals?",
+    ]
+    return qs[0]
+
+
+@pytest.mark.skip(reason="This requires an API call")
+def test_litsearch(questions):
+    llm = ChatOpenAI()
+
+    searchtool = Scholar2ResultLLM(llm=llm)
+    for q in questions:
+        ans = searchtool._run(q)
+        assert isinstance(ans, str)
+        assert len(ans) > 0
+    if os.path.exists("../query"):
+        os.rmdir("../query")