aiagents4pharma 1.13.1__tar.gz → 1.14.1__tar.gz

{aiagents4pharma-1.13.1 → aiagents4pharma-1.14.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.13.1
+Version: 1.14.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License

aiagents4pharma-1.14.1/aiagents4pharma/configs/config.yaml

@@ -0,0 +1,4 @@
+defaults:
+  - _self_
+  - talk2biomodels/agents/t2b_agent: default
+  - talk2biomodels/tools/ask_question: default

{aiagents4pharma-1.13.1 → aiagents4pharma-1.14.1}/aiagents4pharma/configs/talk2biomodels/__init__.py

@@ -3,3 +3,4 @@ Import all the modules in the package
 '''
 
 from . import agents
+from . import tools

{aiagents4pharma-1.13.1 → aiagents4pharma-1.14.1}/aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml

@@ -4,6 +4,5 @@ state_modifier: >
   If the user asks for the uploaded model, 
   then pass the use_uploaded_model argument
   as True. If the user asks for simulation
-  or steady state, suggest a value for the
-  `simulation_name` or `steadystate_name`
-  argument.
+  or param_scan or steady state, suggest a
+  value for the `experiment_name` argument.

aiagents4pharma-1.14.1/aiagents4pharma/configs/talk2biomodels/tools/__init__.py

@@ -0,0 +1,4 @@
+'''
+Import all the modules in the package
+'''
+from . import ask_question

aiagents4pharma-1.14.1/aiagents4pharma/configs/talk2biomodels/tools/ask_question/__init__.py

@@ -0,0 +1,3 @@
+'''
+Import all the modules in the package
+'''

{aiagents4pharma-1.13.1 → aiagents4pharma-1.14.1}/aiagents4pharma/talk2biomodels/__init__.py

@@ -5,3 +5,4 @@ from . import models
 from . import tools
 from . import agents
 from . import states
+from . import api

{aiagents4pharma-1.13.1 → aiagents4pharma-1.14.1}/aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -15,6 +15,7 @@ from ..tools.search_models import SearchModelsTool
 from ..tools.get_modelinfo import GetModelInfoTool
 from ..tools.simulate_model import SimulateModelTool
 from ..tools.custom_plotter import CustomPlotterTool
+from ..tools.get_annotation import GetAnnotationTool
 from ..tools.ask_question import AskQuestionTool
 from ..tools.parameter_scan import ParameterScanTool
 from ..tools.steady_state import SteadyStateTool
@@ -44,8 +45,9 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
                     SearchModelsTool(),
                     GetModelInfoTool(),
                     SteadyStateTool(),
-                    ParameterScanTool()
-                    ])
+                    ParameterScanTool(),
+                    GetAnnotationTool()
+                ])
 
     # Define the model
     llm = ChatOpenAI(model=llm_model, temperature=0)

aiagents4pharma-1.14.1/aiagents4pharma/talk2biomodels/api/__init__.py

@@ -0,0 +1,6 @@
+'''
+This file is used to import the modules in the package.
+'''
+from . import uniprot
+from . import ols
+from . import kegg

aiagents4pharma-1.14.1/aiagents4pharma/talk2biomodels/api/kegg.py

@@ -0,0 +1,83 @@
+"""
+This module contains the API for fetching Kegg database
+"""
+import re
+from typing import List, Dict
+import requests
+
+def fetch_from_api(base_url: str, query: str) -> str:
+    """Fetch data from the given API endpoint."""
+    try:
+        response = requests.get(base_url + query, timeout=10)
+        response.raise_for_status()
+        return response.text
+    except requests.exceptions.RequestException as e:
+        print(f"Error fetching data for query {query}: {e}")
+        return ""
+
+def fetch_kegg_names(ids: List[str], batch_size: int = 10) -> Dict[str, str]:
+    """
+    Fetch the names of multiple KEGG entries using the KEGG REST API in batches.
+
+    Args:
+        ids (List[str]): List of KEGG IDs.
+        batch_size (int): Maximum number of IDs to include in a single request.
+
+    Returns:
+        Dict[str, str]: A mapping of KEGG IDs to their names.
+    """
+    if not ids:
+        return {}
+
+    base_url = "https://rest.kegg.jp/get/"
+    entry_name_map = {}
+
+    # Process IDs in batches
+    for i in range(0, len(ids), batch_size):
+        batch = ids[i:i + batch_size]
+        query = "+".join(batch)
+        entry_data = fetch_from_api(base_url, query)
+
+        # if not entry_data:
+        #     continue
+        entries = entry_data.split("///")
+        for entry in entries:
+            if not entry.strip():
+                continue
+            lines = entry.strip().split("\n")
+            entry_line = next((line for line in lines
+                                if line.startswith("ENTRY")), None)
+            name_line = next((line for line in lines
+                                if line.startswith("NAME")), None)
+
+            # if not entry_line and not name_line:
+            #     continue
+            entry_id = entry_line.split()[1]
+            # Split multiple names in the NAME field and clean them
+            names = [
+                re.sub(r'[^a-zA-Z0-9\s]', '', name).strip()
+                for name in name_line.replace("NAME", "").strip().split(";")
+            ]
+            # Join cleaned names into a single string
+            entry_name_map[entry_id] = " ".join(names).strip()
+
+    return entry_name_map
+
+def fetch_kegg_annotations(data: List[Dict[str, str]],
+                           batch_size: int = 10) -> Dict[str, Dict[str, str]]:
+    """Fetch KEGG entry descriptions grouped by database type."""
+    grouped_data = {}
+    for entry in data:
+        db_type = entry["Database"].lower()
+        grouped_data.setdefault(db_type, []).append(entry["Id"])
+
+    results = {}
+    for db_type, ids in grouped_data.items():
+        results[db_type] = fetch_kegg_names(ids, batch_size=batch_size)
+
+    return results
+
+# def get_protein_name_or_label(data: List[Dict[str, str]],
+#                               batch_size: int = 10) -> Dict[str, Dict[str, str]]:
+#     """Fetch descriptions for KEGG-related identifiers."""
+#     return fetch_kegg_annotations(data, batch_size=batch_size)

aiagents4pharma-1.14.1/aiagents4pharma/talk2biomodels/api/ols.py

@@ -0,0 +1,72 @@
+"""
+This module contains the API for fetching ols database
+"""
+from typing import List, Dict
+import requests
+
+def fetch_from_ols(term: str) -> str:
+    """
+    Fetch the label for a single term from OLS.
+
+    Args:
+        term (str): The term in the format "ONTOLOGY:TERM_ID".
+
+    Returns:
+        str: The label for the term or an error message.
+    """
+    try:
+        ontology, _ = term.split(":")
+        base_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology.lower()}/terms"
+        params = {"obo_id": term}
+        response = requests.get(
+            base_url,
+            params=params,
+            headers={"Accept": "application/json"},
+            timeout=10
+        )
+        response.raise_for_status()
+        data = response.json()
+        label = '-'
+        # Extract and return the label
+        if "_embedded" in data and "terms" in data["_embedded"] \
+             and len(data["_embedded"]["terms"]) > 0:
+            label = data["_embedded"]["terms"][0].get("label", "Label not found")
+        return label
+    except (requests.exceptions.RequestException, KeyError, IndexError) as e:
+        return f"Error: {str(e)}"
+
+def fetch_ols_labels(terms: List[str]) -> Dict[str, str]:
+    """
+    Fetch labels for multiple terms from OLS.
+
+    Args:
+        terms (List[str]): A list of terms in the format "ONTOLOGY:TERM_ID".
+
+    Returns:
+        Dict[str, str]: A mapping of term IDs to their labels or error messages.
+    """
+    results = {}
+    for term in terms:
+        results[term] = fetch_from_ols(term)
+    return results
+
+def search_ols_labels(data: List[Dict[str, str]]) -> Dict[str, Dict[str, str]]:
+    """
+    Fetch OLS annotations grouped by ontology type.
+
+    Args:
+        data (List[Dict[str, str]]): A list of dictionaries containing 'Id' and 'Database'.
+
+    Returns:
+        Dict[str, Dict[str, str]]: A mapping of ontology type to term labels.
+    """
+    grouped_data = {}
+    for entry in data:
+        ontology = entry["Database"].lower()
+        grouped_data.setdefault(ontology, []).append(entry["Id"])
+
+    results = {}
+    for ontology, terms in grouped_data.items():
+        results[ontology] = fetch_ols_labels(terms)
+
+    return results

aiagents4pharma-1.14.1/aiagents4pharma/talk2biomodels/api/uniprot.py

@@ -0,0 +1,35 @@
+"""
+This module contains the API for fetching uniprot database
+"""
+from typing import List, Dict
+import requests
+
+def search_uniprot_labels(identifiers: List[str]) -> Dict[str, str]:
+    """
+    Fetch protein names or labels for a list of UniProt identifiers by making sequential requests.
+
+    Args:
+        identifiers (List[str]): A list of UniProt identifiers.
+
+    Returns:
+        Dict[str, str]: A mapping of UniProt identifiers to their protein names or error messages.
+    """
+    results = {}
+    base_url = "https://www.uniprot.org/uniprot/"
+
+    for identifier in identifiers:
+        url = f"{base_url}{identifier}.json"
+        try:
+            response = requests.get(url, timeout=10)
+            response.raise_for_status()
+            data = response.json()
+            protein_name = (
+                data.get('proteinDescription', {})
+                .get('recommendedName', {})
+                .get('fullName', {})
+                .get('value', 'Name not found')
+            )
+            results[identifier] = protein_name
+        except requests.exceptions.RequestException as e:
+            results[identifier] = f"Error: {str(e)}"
+    return results

aiagents4pharma-1.14.1/aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+
+'''
+This is the state file for the Talk2BioModels agent.
+'''
+
+from typing import Annotated
+import operator
+from langgraph.prebuilt.chat_agent_executor import AgentState
+
+def add_data(data1: dict, data2: dict) -> dict:
+    """
+    A reducer function to merge two dictionaries.
+    """
+    left_idx_by_name = {data['name']: idx for idx, data in enumerate(data1)}
+    merged = data1.copy()
+    for data in data2:
+        idx = left_idx_by_name.get(data['name'])
+        if idx is not None:
+            merged[idx] = data
+        else:
+            merged.append(data)
+    return merged
+
+class Talk2Biomodels(AgentState):
+    """
+    The state for the Talk2BioModels agent.
+    """
+    llm_model: str
+    # A StateGraph may receive a concurrent updates
+    # which is not supported by the StateGraph. Hence,
+    # we need to add a reducer function to handle the
+    # concurrent updates.
+    # https://langchain-ai.github.io/langgraph/troubleshooting/errors/INVALID_CONCURRENT_GRAPH_UPDATE/
+    model_id: Annotated[list, operator.add]
+    sbml_file_path: Annotated[list, operator.add]
+    dic_simulated_data: Annotated[list[dict], add_data]
+    dic_scanned_data: Annotated[list[dict], add_data]
+    dic_steady_state_data: Annotated[list[dict], add_data]
+    dic_annotations_data : Annotated[list[dict], add_data]

aiagents4pharma-1.14.1/aiagents4pharma/talk2biomodels/tests/test_api.py

@@ -0,0 +1,57 @@
+'''
+Test cases for Talk2Biomodels.
+'''
+
+from ..api.uniprot import search_uniprot_labels
+from ..api.ols import fetch_from_ols
+from ..api.kegg import fetch_kegg_names, fetch_from_api
+
+def test_search_uniprot_labels():
+    '''
+    Test the search_uniprot_labels function.
+    '''
+    # "P61764" = Positive result, "P0000Q" = negative result
+    identifiers = ["P61764", "P0000Q"]
+    results = search_uniprot_labels(identifiers)
+    assert results["P61764"] == "Syntaxin-binding protein 1"
+    assert results["P0000Q"].startswith("Error: 400")
+
+def test_fetch_from_ols():
+    '''
+    Test the fetch_from_ols function.
+    '''
+    term_1 = "GO:0005886" #Positive result
+    term_2 = "GO:ABC123" #Negative result
+    label_1 = fetch_from_ols(term_1)
+    label_2 = fetch_from_ols(term_2)
+    assert isinstance(label_1, str), f"Expected string, got {type(label_1)}"
+    assert isinstance(label_2, str), f"Expected string, got {type(label_2)}"
+    assert label_1 == "plasma membrane"
+    assert label_2.startswith("Error: 404")
+
+def test_fetch_kegg_names():
+    '''
+    Test the fetch_kegg_names function.
+    '''
+    ids = ["C00001", "C00002"]
+    results = fetch_kegg_names(ids)
+    assert results["C00001"] == "H2O"
+    assert results["C00002"] == "ATP"
+
+    # Try with an empty list
+    results = fetch_kegg_names([])
+    assert not results
+
+def test_fetch_from_api():
+    '''
+    Test the fetch_from_api function.
+    '''
+    base_url = "https://rest.kegg.jp/get/"
+    query = "C00001"
+    entry_data = fetch_from_api(base_url, query)
+    assert entry_data.startswith("ENTRY       C00001")
+
+    # Try with an invalid query
+    query = "C0000Q"
+    entry_data = fetch_from_api(base_url, query)
+    assert not entry_data

aiagents4pharma-1.14.1/aiagents4pharma/talk2biomodels/tests/test_ask_question.py

@@ -0,0 +1,44 @@
+'''
+Test cases for Talk2Biomodels.
+'''
+
+from langchain_core.messages import HumanMessage, ToolMessage
+from ..agents.t2b_agent import get_app
+
+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"

aiagents4pharma-1.14.1/aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

@@ -0,0 +1,171 @@
+'''
+Test cases for Talk2Biomodels get_annotation tool.
+'''
+
+import random
+import pytest
+from langchain_core.messages import HumanMessage, ToolMessage
+from ..agents.t2b_agent import get_app
+from ..tools.get_annotation import prepare_content_msg
+
+@pytest.fixture(name="make_graph")
+def make_graph_fixture():
+    '''
+    Create an instance of the talk2biomodels agent.
+    '''
+    unique_id = random.randint(1000, 9999)
+    graph = get_app(unique_id)
+    config = {"configurable": {"thread_id": unique_id}}
+    return graph, config
+
+def test_no_model_provided(make_graph):
+    '''
+    Test the tool by not specifying any model.
+    We are testing a condition where the user
+    asks for annotations of all species without
+    specifying a model.
+    '''
+    app, config = make_graph
+    prompt = "Extract annotations of all species. Call the tool get_annotation."
+    app.invoke({"messages": [HumanMessage(content=prompt)]},
+                        config=config
+                    )
+    current_state = app.get_state(config)
+    # Assert that the state key model_id is empty.
+    assert current_state.values["model_id"] == []
+
+def test_specific_species_provided(make_graph):
+    '''
+    Test the tool by providing a specific species name.
+    We are testing a condition where the user asks for annotations
+    of a specific species in a specific model.
+    '''
+    # Test with a valid species name
+    app, config = make_graph
+    prompt = "Extract annotations of species IL6 in model 537."
+    app.invoke(
+                {"messages": [HumanMessage(content=prompt)]},
+                config=config
+            )
+    current_state = app.get_state(config)
+    # print (current_state.values["dic_annotations_data"])
+    dic_annotations_data = current_state.values["dic_annotations_data"]
+
+    # The assert statement checks if IL6 is present in the returned annotations.
+    assert dic_annotations_data[0]['data']["Species Name"][0] == "IL6"
+
+    # Test with an invalid species name
+    app, config = make_graph
+    prompt = "Extract annotations of species NADH in model 537."
+    app.invoke(
+        {"messages": [HumanMessage(content=prompt)]},
+        config=config
+    )
+    current_state = app.get_state(config)
+    reversed_messages = current_state.values["messages"][::-1]
+    # Loop through the reversed messages until a
+    # ToolMessage is found.
+
+    test_condition = False
+    for msg in reversed_messages:
+        # Assert that the one of the messages is a ToolMessage
+        # and its artifact is None.
+        if isinstance(msg, ToolMessage) and msg.name == "get_annotation":
+            #If a ToolMessage exists and artifact is None (meaning no valid annotation was found)
+            #and the rejected species (NADH) is mentioned, the test passes.
+            if msg.artifact is None and 'NADH' in msg.content:
+                #If artifact is None, it means no annotation was found
+                # (likely due to an invalid species).
+                #If artifact contains data, the tool successfully retrieved annotations.
+                test_condition = True
+                break
+    # assert test_condition
+    assert test_condition, "Expected rejection message for NADH but did not find it."
+
+    # Test with an invalid species name and a valid species name
+    app, config = make_graph
+    prompt = "Extract annotations of species NADH, NAD, and IL7 in model 64."
+    app.invoke(
+        {"messages": [HumanMessage(content=prompt)]},
+        config=config
+    )
+    current_state = app.get_state(config)
+    # dic_annotations_data = current_state.values["dic_annotations_data"]
+    reversed_messages = current_state.values["messages"][::-1]
+    # Loop through the reversed messages until a
+    # ToolMessage is found.
+    artifact_was_none = False
+    for msg in reversed_messages:
+        # Assert that the one of the messages is a ToolMessage
+        # and its artifact is None.
+        if isinstance(msg, ToolMessage) and msg.name == "get_annotation":
+            # print (msg.artifact, msg.content)
+
+            if msg.artifact is True and 'IL7' in msg.content:
+                artifact_was_none = True
+                break
+    assert artifact_was_none
+
+def test_all_species_annotations(make_graph):
+    '''
+    Test the tool by asking for annotations of all species is specific models.
+    Here, we test the tool with three models since they have different use cases:
+        - model 12 contains a species with no URL provided.
+        - model 20 contains a species without description.
+        - model 56 contains a species with database outside of KEGG, UniProt, and OLS.
+
+    We are testing a condition where the user asks for annotations
+    of all species in a specific model.
+    '''
+    # Loop through the models and test the tool
+    # for each model's unique use case.
+    for model_id in [12, 20, 56]:
+        app, config = make_graph
+        prompt = f"Extract annotations of all species model {model_id}."
+        # Test the tool get_modelinfo
+        app.invoke({"messages": [HumanMessage(content=prompt)]},
+                            config=config
+                        )
+        current_state = app.get_state(config)
+
+        reversed_messages = current_state.values["messages"][::-1]
+        # Coveres all of the use cases for the expecetd sting on all the species
+        test_condition = False
+        for msg in reversed_messages:
+            # Skip messages that are not ToolMessages and those that are not
+            # from the get_annotation tool.
+            if not isinstance(msg, ToolMessage) or msg.name != "get_annotation":
+                continue
+            if model_id == 12:
+                # Extact the first and second description of the LacI protein
+                # We already know that the first or second description is missing ('-')
+                dic_annotations_data = current_state.values["dic_annotations_data"][0]
+                first_descp_laci_protein = dic_annotations_data['data']['Description'][0]
+                second_descp_laci_protein = dic_annotations_data['data']['Description'][1]
+
+                # Expect a successful extraction (artifact is True) and that the content
+                # matches what is returned by prepare_content_msg for species.
+                # And that the first or second description of the LacI protein is missing.
+                if (msg.artifact is True and msg.content == prepare_content_msg([],[])
+                    and msg.status=="success" and (first_descp_laci_protein == '-' or
+                                                    second_descp_laci_protein == '-')):
+                    test_condition = True
+                    break
+
+            if model_id == 20:
+                # Expect an error message containing a note
+                # that species extraction failed.
+                if ("Unable to extract species from the model"
+                    in msg.content and msg.status == "error"):
+                    test_condition = True
+                    break
+
+            if model_id == 56:
+                # Expect a successful extraction (artifact is True) and that the content
+                # matches for for missing description ['ORI'].
+                if (msg.artifact is True and
+                msg.content == prepare_content_msg([],['ORI'])
+                and msg.status == "success"):
+                    test_condition = True
+                    break
+        assert test_condition # Expected output is validated

aiagents4pharma-1.14.1/aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py

@@ -0,0 +1,26 @@
+'''
+Test cases for Talk2Biomodels get_modelinfo tool.
+'''
+
+from langchain_core.messages import HumanMessage
+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)