aiagents4pharma 1.9.0__py3-none-any.whl → 1.15.0__py3-none-any.whl

aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py

@@ -0,0 +1,123 @@
+#!/usr/bin/env python3
+
+"""
+Enrichment class using Ollama model based on LangChain Enrichment class.
+"""
+
+import time
+from typing import List
+import subprocess
+import ast
+import ollama
+from langchain_ollama import ChatOllama
+from langchain_core.prompts import ChatPromptTemplate
+from langchain_core.output_parsers import StrOutputParser
+from .enrichments import Enrichments
+
+class EnrichmentWithOllama(Enrichments):
+    """
+    Enrichment class using Ollama model based on the Enrichment abstract class.
+    """
+    def __init__(
+        self,
+        model_name: str,
+        prompt_enrichment: str,
+        temperature: float,
+        streaming: bool,
+    ):
+        """
+        Initialize the EnrichmentWithOllama class.
+
+        Args:
+            model_name: The name of the Ollama model to be used.
+            prompt_enrichment: The prompt enrichment template.
+            temperature: The temperature for the Ollama model.
+            streaming: The streaming flag for the Ollama model.
+        """
+        # Setup the Ollama server
+        self.__setup(model_name)
+
+        # Set parameters
+        self.model_name = model_name
+        self.prompt_enrichment = prompt_enrichment
+        self.temperature = temperature
+        self.streaming = streaming
+
+        # Prepare prompt template
+        self.prompt_template = ChatPromptTemplate.from_messages(
+            [
+                ("system", self.prompt_enrichment),
+                ("human", "{input}"),
+            ]
+        )
+
+        # Prepare model
+        self.model = ChatOllama(
+            model=self.model_name,
+            temperature=self.temperature,
+            streaming=self.streaming,
+        )
+
+    def __setup(self, model_name: str) -> None:
+        """
+        Check if the Ollama model is available and run the Ollama server if needed.
+
+        Args:
+            model_name: The name of the Ollama model to be used.
+        """
+        try:
+            models_list = ollama.list()["models"]
+            if model_name not in [m['model'].replace(":latest", "") for m in models_list]:
+                ollama.pull(model_name)
+                time.sleep(30)
+                raise ValueError(f"Pulled {model_name} model")
+        except Exception as e:
+            with subprocess.Popen(
+                "ollama serve", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE
+            ):
+                time.sleep(10)
+            raise ValueError(f"Error: {e} and restarted Ollama server.") from e
+
+    def enrich_documents(self, texts: List[str]) -> List[str]:
+        """
+        Enrich a list of input texts with additional textual features using OLLAMA model.
+        Important: Make sure the input is a list of texts based on the defined prompt template
+        with 'input' as the variable name.
+
+        Args:
+            texts: The list of texts to be enriched.
+
+        Returns:
+            The list of enriched texts.
+        """
+
+        # Perform enrichment
+        chain = self.prompt_template | self.model | StrOutputParser()
+
+        # Generate the enriched node
+        # Important: Make sure the input is a list of texts based on the defined prompt template
+        # with 'input' as the variable name
+        enriched_texts = chain.invoke({"input": "[" + ", ".join(texts) + "]"})
+
+        # Convert the enriched nodes to a list of dictionary
+        enriched_texts = ast.literal_eval(enriched_texts.replace("```", ""))
+
+        # Final check for the enriched texts
+        assert len(enriched_texts) == len(texts)
+
+        return enriched_texts
+
+    def enrich_documents_with_rag(self, texts, docs):
+        """
+        Enrich a list of input texts with additional textual features using OLLAMA model with RAG.
+        As of now, we don't have a RAG model to test this method yet.
+        Thus, we will just call the enrich_documents method instead.
+
+        Args:
+            texts: The list of texts to be enriched.
+            docs: The list of reference documents to enrich the input texts.
+        
+        Returns:
+            The list of enriched texts
+        """
+        return self.enrich_documents(texts)

{aiagents4pharma-1.9.0.dist-info → aiagents4pharma-1.15.0.dist-info}/METADATA

@@ -1,11 +1,11 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.9.0
+Version: 1.15.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: copasi_basico==0.78
@@ -20,13 +20,16 @@ Requires-Dist: langchain-community==0.3.5
 Requires-Dist: langchain-core==0.3.31
 Requires-Dist: langchain-experimental==0.3.3
 Requires-Dist: langchain-openai==0.2.5
+Requires-Dist: langchain_ollama==0.2.2
 Requires-Dist: langgraph==0.2.66
 Requires-Dist: matplotlib==3.9.2
 Requires-Dist: openai==1.59.4
+Requires-Dist: ollama==0.4.6
 Requires-Dist: pandas==2.2.3
 Requires-Dist: plotly==5.24.1
 Requires-Dist: pydantic==2.9.2
 Requires-Dist: pylint==3.3.1
+Requires-Dist: pypdf==5.2.0
 Requires-Dist: pytest==8.3.3
 Requires-Dist: pytest-asyncio==0.25.2
 Requires-Dist: streamlit==1.39.0
@@ -48,6 +51,9 @@ Requires-Dist: streamlit-feedback
 [![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
 [![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
 [![Talk2Competitors](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
 
 <h1 align="center" style="border-bottom: none;">🤖 AIAgents4Pharma</h1>
 
@@ -56,9 +62,9 @@ Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://
 Our toolkit currently consists of three intelligent agents, each designed to simplify and enhance access to specialized data in biology:
 
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
-- **Talk2Cells** *(Work in progress)*: Query and analyze sequencing data with ease.
-- **Talk2KnowledgeGraphs** *(Work in progress)*: Access and explore complex biological knowledge graphs for insightful data connections.
-- **Talk2Competitors** *(Coming soon)*: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(Work in progress)_: Query and analyze sequencing data with ease.
+- **Talk2KnowledgeGraphs** _(Work in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Competitors** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
 
 ---
 
@@ -71,68 +77,77 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - Forward simulation of both internal and open-source models (BioModels).
 - Adjust parameters within the model to simulate different conditions.
 - Query simulation results.
+- Extract model information such as species, parameters, units and description.
 
-### 2. Talk2Cells *(Work in Progress)*
+### 2. Talk2Cells _(Work in Progress)_
 
 **Talk2Cells** is being developed to provide direct access to and analysis of sequencing data, such as RNA-Seq or DNA-Seq, using natural language.
 
-### 3. Talk2KnowledgeGraphs *(Work in Progress)*
+### 3. Talk2KnowledgeGraphs _(Work in Progress)_
 
 **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.
 
-### 4. Talk2KnowledgeGraphs *(Coming soon)*
+### 4. Talk2Competitors _(Coming soon)_
 
 ## Getting Started
 
-### Prerequisites
-
-- **Python 3.10+**
-- **Git**
-- Required libraries specified in `requirements.txt`
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
 
 ### Installation
+
 #### Option 1: PyPI
-   ```bash
-   pip install aiagents4pharma
-   ```
+
+```bash
+pip install aiagents4pharma
+```
 
 Check out the tutorials on each agent for detailed instrcutions.
 
 #### Option 2: git
+
 1. **Clone the repository:**
+
    ```bash
    git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
    cd AIAgents4Pharma
    ```
 
 2. **Install dependencies:**
+
    ```bash
    pip install .
    ```
 
 3. **Initialize OPENAI_API_KEY**
+
    ```bash
-   export OPENAI_API_KEY = ....
+   export OPENAI_API_KEY=....
    ```
 
 4. **[Optional] Set up login credentials**
+
    ```bash
    vi .streamlit/secrets.toml
    ```
+
    and enter
+
    ```
    password='XXX'
    ```
-   Please note that the passowrd will be same for all the users.
+
+   Please note that the passoword will be same for all the users.
 
 5. **[Optional] Initialize LANGSMITH_API_KEY**
+
    ```bash
    export LANGCHAIN_TRACING_V2=true
    export LANGCHAIN_API_KEY=<your-api-key>
    ```
-   Please note that this will create a new tracing project in your Langsmith 
-   account with the name `<user_name>@<uuid>`, where `user_name` is the name 
-   you provided in the previous step. If you skip the previous step, it will 
+
+   Please note that this will create a new tracing project in your Langsmith
+   account with the name `<user_name>@<uuid>`, where `user_name` is the name
+   you provided in the previous step. If you skip the previous step, it will
    default to `default`. <uuid> will be the 128 bit unique ID created for the
    session.
 
@@ -164,6 +179,7 @@ We welcome contributions to AIAgents4Pharma! Here’s how you can help:
 5. **Open a pull request**
 
 ### Current Needs
+
 - **Beta testers** for Talk2BioModels.
 - **Developers** with experience in natural language processing, bioinformatics, or knowledge graphs for contributions to AIAgents4Pharma.
 
@@ -174,19 +190,22 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 ## Roadmap
 
 ### Completed
+
 - **Talk2BioModels**: Initial release with core capabilities for interacting with systems biology models.
 
 ### Planned
+
 - **User Interface**: Interactive web UI for all agents.
 - **Talk2Cells**: Integration of sequencing data analysis tools.
 - **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
-- **Talk2Competitors**
+- **Talk2Competitors**: Interface for exploring articles
 
-We’re excited to bring AIAgents4Pharma to the bioinformatics and pharmaceutical research community. Together, let’s make data-driven biological research more accessible and insightful. 
+We’re excited to bring AIAgents4Pharma to the bioinformatics and pharmaceutical research community. Together, let’s make data-driven biological research more accessible and insightful.
 
 **Get Started** with AIAgents4Pharma today and transform the way you interact with biological data.
 
 ---
 
 ## Feedback
+
 Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use the `Isssues` tab 😀

aiagents4pharma-1.15.0.dist-info/RECORD

@@ -0,0 +1,102 @@
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aiagents4pharma/talk2biomodels/tests/test_langgraph.py

@@ -1,240 +0,0 @@
-'''
-Test cases for Talk2Biomodels.
-'''
-
-import pandas as pd
-from langchain_core.messages import HumanMessage, ToolMessage
-from ..agents.t2b_agent import get_app
-
-def test_get_modelinfo_tool():
-    '''
-    Test the get_modelinfo tool.
-    '''
-    unique_id = 12345
-    app = get_app(unique_id)
-    config = {"configurable": {"thread_id": unique_id}}
-    # Update state
-    app.update_state(config,
-      {"sbml_file_path": ["aiagents4pharma/talk2biomodels/tests/BIOMD0000000449_url.xml"]})
-    prompt = "Extract all relevant information from the uploaded model."
-    # Test the tool get_modelinfo
-    response = app.invoke(
-                        {"messages": [HumanMessage(content=prompt)]},
-                        config=config
-                    )
-    assistant_msg = response["messages"][-1].content
-    # Check if the assistant message is a string
-    assert isinstance(assistant_msg, str)
-
-def test_search_models_tool():
-    '''
-    Test the search_models tool.
-    '''
-    unique_id = 12345
-    app = get_app(unique_id)
-    config = {"configurable": {"thread_id": unique_id}}
-    # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
-    prompt = "Search for models on Crohn's disease."
-    # Test the tool get_modelinfo
-    response = app.invoke(
-                        {"messages": [HumanMessage(content=prompt)]},
-                        config=config
-                    )
-    assistant_msg = response["messages"][-1].content
-    # Check if the assistant message is a string
-    assert isinstance(assistant_msg, str)
-    # Check if the assistant message contains the
-    # biomodel id BIO0000000537
-    assert "BIOMD0000000537" in assistant_msg
-
-def test_ask_question_tool():
-    '''
-    Test the ask_question tool without the simulation results.
-    '''
-    unique_id = 12345
-    app = get_app(unique_id, llm_model='gpt-4o-mini')
-    config = {"configurable": {"thread_id": unique_id}}
-
-    ##########################################
-    # Test ask_question tool when simulation
-    # results are not available i.e. the
-    # simulation has not been run. In this
-    # case, the tool should return an error
-    ##########################################
-    # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
-    # Define the prompt
-    prompt = "Call the ask_question tool to answer the "
-    prompt += "question: What is the concentration of CRP "
-    prompt += "in serum at 1000 hours? The simulation name "
-    prompt += "is `simulation_name`."
-    # Invoke the tool
-    app.invoke(
-            {"messages": [HumanMessage(content=prompt)]},
-            config=config
-        )
-    # Get the messages from the current state
-    # and reverse the order
-    current_state = app.get_state(config)
-    reversed_messages = current_state.values["messages"][::-1]
-    # Loop through the reversed messages until a
-    # ToolMessage is found.
-    for msg in reversed_messages:
-        # Assert that the message is a ToolMessage
-        # and its status is "error"
-        if isinstance(msg, ToolMessage):
-            assert msg.status == "error"
-
-def test_simulate_model_tool():
-    '''
-    Test the simulate_model tool when simulating
-    multiple models.
-    '''
-    unique_id = 123
-    app = get_app(unique_id)
-    config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
-    # Upload a model to the state
-    app.update_state(config,
-        {"sbml_file_path": ["aiagents4pharma/talk2biomodels/tests/BIOMD0000000449_url.xml"]})
-    prompt = "Simulate models 64 and the uploaded model"
-    # Invoke the agent
-    app.invoke(
-        {"messages": [HumanMessage(content=prompt)]},
-        config=config
-    )
-    current_state = app.get_state(config)
-    dic_simulated_data = current_state.values["dic_simulated_data"]
-    # Check if the dic_simulated_data is a list
-    assert isinstance(dic_simulated_data, list)
-    # Check if the length of the dic_simulated_data is 2
-    assert len(dic_simulated_data) == 2
-    # Check if the source of the first model is 64
-    assert dic_simulated_data[0]['source'] == 64
-    # Check if the source of the second model is upload
-    assert dic_simulated_data[1]['source'] == "upload"
-    # Check if the data of the first model contains
-    assert '1,3-bisphosphoglycerate' in dic_simulated_data[0]['data']
-    # Check if the data of the second model contains
-    assert 'mTORC2' in dic_simulated_data[1]['data']
-
-def test_integration():
-    '''
-    Test the integration of the tools.
-    '''
-    unique_id = 123
-    app = get_app(unique_id)
-    config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
-    # ##########################################
-    # ## Test simulate_model tool
-    # ##########################################
-    prompt = "Simulate the model 537 for 2016 hours and intervals"
-    prompt += " 2016 with an initial concentration of `DoseQ2W` "
-    prompt += "set to 300 and `Dose` set to 0. Reset the concentration"
-    prompt += " of `NAD` to 100 every 500 hours."
-    # Test the tool get_modelinfo
-    response = app.invoke(
-                        {"messages": [HumanMessage(content=prompt)]},
-                        config=config
-                    )
-    assistant_msg = response["messages"][-1].content
-    print (assistant_msg)
-    # Check if the assistant message is a string
-    assert isinstance(assistant_msg, str)
-    ##########################################
-    # Test ask_question tool when simulation
-    # results are available
-    ##########################################
-    # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
-    prompt = "What is the concentration of CRP in serum at 1000 hours? "
-    # prompt += "Show only the concentration, rounded to 1 decimal place."
-    # prompt += "For example, if the concentration is 0.123456, "
-    # prompt += "your response should be `0.1`. Do not return any other information."
-    # Test the tool get_modelinfo
-    response = app.invoke(
-                        {"messages": [HumanMessage(content=prompt)]},
-                        config=config
-                    )
-    assistant_msg = response["messages"][-1].content
-    # print (assistant_msg)
-    # Check if the assistant message is a string
-    assert "1.7" in assistant_msg
-
-    ##########################################
-    # Test custom_plotter tool when the
-    # simulation results are available
-    ##########################################
-    prompt = "Plot only CRP related species."
-
-    # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"}
-                    )
-    # Test the tool get_modelinfo
-    response = app.invoke(
-                        {"messages": [HumanMessage(content=prompt)]},
-                        config=config
-                    )
-    assistant_msg = response["messages"][-1].content
-    current_state = app.get_state(config)
-    # Get the messages from the current state
-    # and reverse the order
-    reversed_messages = current_state.values["messages"][::-1]
-    # Loop through the reversed messages
-    # until a ToolMessage is found.
-    expected_header = ['Time', 'CRP[serum]', 'CRPExtracellular']
-    expected_header += ['CRP Suppression (%)', 'CRP (% of baseline)']
-    expected_header += ['CRP[liver]']
-    predicted_artifact = []
-    for msg in reversed_messages:
-        if isinstance(msg, ToolMessage):
-            # Work on the message if it is a ToolMessage
-            # These may contain additional visuals that
-            # need to be displayed to the user.
-            if msg.name == "custom_plotter":
-                predicted_artifact = msg.artifact
-                break
-    # Convert the artifact into a pandas dataframe
-    # for easy comparison
-    df = pd.DataFrame(predicted_artifact)
-    # Extract the headers from the dataframe
-    predicted_header = df.columns.tolist()
-    # Check if the header is in the expected_header
-    # assert expected_header in predicted_artifact
-    assert set(expected_header).issubset(set(predicted_header))
-    ##########################################
-    # Test custom_plotter tool when the
-    # simulation results are available but
-    # the species is not available
-    ##########################################
-    prompt = "Plot the species `TP53`."
-
-    # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"}
-                    )
-    # Test the tool get_modelinfo
-    response = app.invoke(
-                        {"messages": [HumanMessage(content=prompt)]},
-                        config=config
-                    )
-    assistant_msg = response["messages"][-1].content
-    # print (response["messages"])
-    current_state = app.get_state(config)
-    # Get the messages from the current state
-    # and reverse the order
-    reversed_messages = current_state.values["messages"][::-1]
-    # Loop through the reversed messages until a
-    # ToolMessage is found.
-    predicted_artifact = []
-    for msg in reversed_messages:
-        if isinstance(msg, ToolMessage):
-            # Work on the message if it is a ToolMessage
-            # These may contain additional visuals that
-            # need to be displayed to the user.
-            if msg.name == "custom_plotter":
-                predicted_artifact = msg.artifact
-                break
-    # Check if the the predicted artifact is `None`
-    assert predicted_artifact is None