aiagents4pharma 1.13.1__py3-none-any.whl → 1.14.1__py3-none-any.whl

{aiagents4pharma-1.13.1.dist-info → aiagents4pharma-1.14.1.dist-info}/RECORD

@@ -1,31 +1,47 @@
 aiagents4pharma/__init__.py,sha256=5muWWIg89VHPybfxonO_5xOMJPasKNsGdQRhozDaEmk,177
 aiagents4pharma/configs/__init__.py,sha256=hNkSrXw1Ix1HhkGn_aaidr2coBYySfM0Hm_pMeRcX7k,76
-aiagents4pharma/configs/config.yaml,sha256=8y8uG6Dzx4-9jyb6hZ8r4lOJz5gA_sQhCiSCgXL5l7k,65
-aiagents4pharma/configs/talk2biomodels/__init__.py,sha256=5ah__-8XyRblwT0U1ByRigNjt_GyCheu7zce4aM-eZE,68
+aiagents4pharma/configs/config.yaml,sha256=4t7obD0gOSfqnDDZZBB53ZC7zsmk7QDcM7T_1Hf1wIQ,112
+aiagents4pharma/configs/talk2biomodels/__init__.py,sha256=safyFKhkd5Wlirl9dMZIHWDLTpY2oLw9wjIM7ZtLIHk,88
 aiagents4pharma/configs/talk2biomodels/agents/__init__.py,sha256=_ZoG8snICK2bidWtc2KOGs738LWg9_r66V9mOMnEb-E,71
 aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml,sha256=Oi89_BbxfQc6SGW1pC-hyZMqOIkiAMOlNwpCa4VCXk0,327
-aiagents4pharma/talk2biomodels/__init__.py,sha256=qUw3qXrENqSCLIKSLy_qtNPwPDTb1wdZ8fZispcHb3g,141
+aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml,sha256=w0ES09GSuY61x7C9FSx9auwhoGc6xVeG51roe6tT4Bk,317
+aiagents4pharma/configs/talk2biomodels/tools/__init__.py,sha256=WxK7h5n39l-NSMvjLZyxDqzwWlVA6mQ69gzsbJ17vEk,72
+aiagents4pharma/configs/talk2biomodels/tools/ask_question/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
+aiagents4pharma/talk2biomodels/__init__.py,sha256=2ICwVh1u07SZv31Jd2DKHobauOxWNWY29_Gqq3kOnNQ,159
 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
-aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=8_2D3uknPjYbzKj7IDhC8xnz_HEvXck0b4RCJxoAxRs,3276
+aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=13aSlBZBWtjXOLq7c99u33c923fi2Ab0VW--eX5gF-o,3366
+aiagents4pharma/talk2biomodels/api/__init__.py,sha256=_GmDQqDLYpsUPUeE1nBNlT5AI9oTXIcqgOfNfvmonqA,123
+aiagents4pharma/talk2biomodels/api/kegg.py,sha256=QzYDAfJ16E7tbHGxP8ZNWRizMkMRS_HJuucueXEC1Gg,2943
+aiagents4pharma/talk2biomodels/api/ols.py,sha256=qq0Qy-gJDxanQW-HfCChDsTQsY1M41ua8hMlTnfuzrA,2202
+aiagents4pharma/talk2biomodels/api/uniprot.py,sha256=aPUAVBR7UYXDuuhDpKezAK2aTMzo-NxFYFq6C0W5u6U,1175
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
 aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=PH25FTOuUjsmw_UUxoRb-4kptOYpicEn4GqS0phS3nk,4807
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=JeoiGQAvQABHnG0wKR2XBmmxqQdtgO6kxaLDUTUmr1s,2001
 aiagents4pharma/talk2biomodels/states/__init__.py,sha256=YLg1-N0D9qyRRLRqwqfLCLAqZYDtMVZTfI8Y0b_4tbA,139
-aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=XcrCsBbQgc4LCZ7ihpY5tcLQ82Mq17XhRXD1DW8Ep7U,887
+aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=WriIk_MH9XyUD-WAcIFVjHZMegwrh2-zQpXleTzpHEU,1332
 aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
+aiagents4pharma/talk2biomodels/tests/test_api.py,sha256=7Kz2r5F5tjmn3F0LoM33oP-21W633936YHiyf5toGg0,1716
+aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=yRkKK9HLB1bGGWm_WwOckwaUmmRfRAD9z2NFFGLIGTY,1560
 aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=y82fpTJMPHwtXxlle1cGQ_2Bewwpxi0aJSVrVAYLhN0,2060
-aiagents4pharma/talk2biomodels/tests/test_langgraph.py,sha256=QLAL4nmHrioTD-w-9OE0wQi5JdWJJ59PejNbDzCSvw4,15170
+aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=mKOacH28OB6xpFPygAlhBUQS93gnI5j-jAfSGu6uQMI,7465
+aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=6kChSc_MCnzXlDao_R8pKdhIELlg3MZrUa7hg8piJ4E,883
+aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=ZsBXWSFLIcdzrO8obLJx8Ib2f9AAW3BI7H9Eqjdc5to,5057
+aiagents4pharma/talk2biomodels/tests/test_param_scan.py,sha256=vRbnn4uVWFbfZbU4gVCjHi5WDCUrErut8ElzAPE5y84,2648
+aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=8ODFubLxWYD3I3KQWuUnJ2GZRzMjFpXInFBLxKxG_ME,929
+aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=GjLE1DZpcKUAFSmoHD86vkfK0b5LJPM8a4WYyraazig,1487
+aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=zt15KQoQku6jyzvpJXwINGTyhEnQl8wX81ueHlxnUCA,3467
 aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=HSmBBViMi0jYf4gWX21IbppAfDzG0nr_S3KtKS9fZVQ,2165
-aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=-Fz3TryG3ZgBMwfF3v2ZMNSM_-g9vywjKBrGJgVQuYY,293
-aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=qpltsgyLFFwLYQeapQHASFRDCNiWsJkmTH_sUrfJ_Fg,3708
+aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=ZiOdSFaeHW6y3hdtBfsKf0vSb3MuCLuy9MDyjARggb4,322
+aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=hWXg7o0sTMDWH1ZnxtashTALvXpvNoaomfcniEhw-Bw,4684
 aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=HWwKTX3o4dk0GcRVTO2hPrFSu98mtJ4TKC_hbHXOe1c,4018
+aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=jCGkidvafuk1YzAH9GFwaVUF35maXTjg6XqBg_zLk44,12475
 aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=qA-4FOI-O728Nmn7s8JJ8HKwxvA9MZbst7NkPKTAMV4,5391
+aiagents4pharma/talk2biomodels/tools/load_arguments.py,sha256=bffNIlBDTCSFYiZprA73yi8Jbb8z3Oh2decVNh1UnZc,4162
 aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=pyVzLQoMnuJYEwsjeOlqcUrbU1F1Z-pNlgkhFaoKpy0,689
-aiagents4pharma/talk2biomodels/tools/parameter_scan.py,sha256=aIyL_m46s3Q74ieJOZjZBM34VCjBKSMpEtckhdZofbE,12139
+aiagents4pharma/talk2biomodels/tools/parameter_scan.py,sha256=aNh94LgBgVXBIczuNkbSsOZ9j54YVEdZWmZbZr7Nk8k,12465
 aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=Iq2ddofOOfZYtAurCISq3bAq5rbwB3l_rL1lgEFyFCI,2653
-aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=sWmFVnVvJbdXXTqn_7gQl5UW0tv4FyU5yLXWLweLs_M,7059
-aiagents4pharma/talk2biomodels/tools/steady_state.py,sha256=itUXFTYO525D695LQlGb1ObwSuvHk0A5mXtgdCproqo,8102
+aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=qXs9lg9XgA7EaRiX3wBS8w_ug8tI-G3pzhcRg6dTRio,5060
+aiagents4pharma/talk2biomodels/tools/steady_state.py,sha256=j3ckuNlUtv7lT922MbN0JhT9H0JpWAdx2mLPwao6uu8,7123
 aiagents4pharma/talk2cells/__init__.py,sha256=zmOP5RAhabgKIQP-W4P4qKME2tG3fhAXM3MeO5_H8kE,120
 aiagents4pharma/talk2cells/agents/__init__.py,sha256=38nK2a_lEFRjO3qD6Fo9a3983ZCYat6hmJKWY61y2Mo,128
 aiagents4pharma/talk2cells/agents/scp_agent.py,sha256=gDMfhUNWHa_XWOqm1Ql6yLAdI_7bnIk5sRYn43H2sYk,3090
@@ -77,8 +93,8 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sh
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py,sha256=tW426knki2DBIHcWyF_K04iMMdbpIn_e_TpPmTgz2dI,113
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py,sha256=Bx8x6zzk5614ApWB90N_iv4_Y_Uq0-KwUeBwYSdQMU4,924
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py,sha256=8eoxR-VHo0G7ReQIwje7xEhE-SJlHdef7_wJRpnvFIc,4116
-aiagents4pharma-1.13.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.13.1.dist-info/METADATA,sha256=HCfDwV_-IF_1yQccq0COSwj9C_Hr1wTtETFJOSP44ec,8609
-aiagents4pharma-1.13.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-aiagents4pharma-1.13.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.13.1.dist-info/RECORD,,
+aiagents4pharma-1.14.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.14.1.dist-info/METADATA,sha256=zwewL1DN0qEv3L7l901tNdc6PaX1wrKvRIkZ0dFIqHU,8609
+aiagents4pharma-1.14.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+aiagents4pharma-1.14.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.14.1.dist-info/RECORD,,

aiagents4pharma/talk2biomodels/tests/test_langgraph.py

@@ -1,384 +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 model 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_param_scan_tool():
-    '''
-    In this test, we will test the parameter_scan tool.
-    We will prompt it to scan the parameter `kIL6RBind`
-    from 1 to 100 in steps of 10, record the changes
-    in the concentration of the species `Ab{serum}` in
-    model 537.
-
-    We will pass the inaccuarate parameter (`KIL6Rbind`)
-    and species names (just `Ab`) to the tool to test
-    if it can deal with it.
-
-    We expect the agent to first invoke the parameter_scan
-    tool and raise an error. It will then invoke another
-    tool get_modelinfo to get the correct parameter
-    and species names. Finally, the agent will reinvoke
-    the parameter_scan tool with the correct parameter
-    and species names.
-
-    '''
-    unique_id = 123
-    app = get_app(unique_id)
-    config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
-    prompt = """How will the value of Ab in model 537 change
-            if the param kIL6Rbind is varied from 1 to 100 in steps of 10?
-            Set the initial `DoseQ2W` concentration to 300. Also, reset
-            the IL6{serum} concentration to 100 every 500 hours and assume
-            that the model is simulated for 2016 hours with an interval of 2016."""
-    # Invoke the agent
-    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.
-    df = pd.DataFrame(columns=['name', 'status', 'content'])
-    names = []
-    statuses = []
-    contents = []
-    for msg in reversed_messages:
-        # Assert that the message is a ToolMessage
-        # and its status is "error"
-        if not isinstance(msg, ToolMessage):
-            continue
-        names.append(msg.name)
-        statuses.append(msg.status)
-        contents.append(msg.content)
-    df = pd.DataFrame({'name': names, 'status': statuses, 'content': contents})
-    # print (df)
-    assert any((df["status"] == "error") &
-               (df["name"] == "parameter_scan") &
-               (df["content"].str.startswith("Error: ValueError('Invalid parameter name:")))
-    assert any((df["status"] == "success") &
-               (df["name"] == "parameter_scan") &
-               (df["content"].str.startswith("Parameter scan results of")))
-    assert any((df["status"] == "success") &
-               (df["name"] == "get_modelinfo"))
-
-def test_steady_state_tool():
-    '''
-    Test the steady_state tool.
-    '''
-    unique_id = 123
-    app = get_app(unique_id)
-    config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
-    #########################################################
-    # In this case, we will test if the tool returns an error
-    # when the model does not achieve a steady state. The tool
-    # status should be "error".
-    prompt = """Run a steady state analysis of model 537."""
-    # Invoke the agent
-    app.invoke(
-        {"messages": [HumanMessage(content=prompt)]},
-        config=config
-    )
-    current_state = app.get_state(config)
-    reversed_messages = current_state.values["messages"][::-1]
-    tool_msg_status = None
-    for msg in reversed_messages:
-        # Assert that the status of the
-        # ToolMessage is "error"
-        if isinstance(msg, ToolMessage):
-            # print (msg)
-            tool_msg_status = msg.status
-            break
-    assert tool_msg_status == "error"
-    #########################################################
-    # In this case, we will test if the tool is indeed invoked
-    # successfully
-    prompt = """Run a steady state analysis of model 64.
-    Set the initial concentration of `Pyruvate` to 0.2. The
-    concentration of `NAD` resets to 100 every 2 time units."""
-    # Invoke the agent
-    app.invoke(
-        {"messages": [HumanMessage(content=prompt)]},
-        config=config
-    )
-    # Loop through the reversed messages until a
-    # ToolMessage is found.
-    current_state = app.get_state(config)
-    reversed_messages = current_state.values["messages"][::-1]
-    steady_state_invoked = False
-    for msg in reversed_messages:
-        # Assert that the message is a ToolMessage
-        # and its status is "error"
-        if isinstance(msg, ToolMessage):
-            print (msg)
-            if msg.name == "steady_state" and msg.status != "error":
-                steady_state_invoked = True
-                break
-    assert steady_state_invoked
-    #########################################################
-    # In this case, we will test if the `ask_question` tool is
-    # invoked upon asking a question about the already generated
-    # steady state results
-    prompt = """What is the Phosphoenolpyruvate concentration
-        at the steady state? Show onlyconcentration, rounded to
-        2 decimal places. For example, if the concentration is
-        0.123456, your response should be `0.12`. Do not return
-        any other information."""
-    # Invoke the agent
-    response = app.invoke(
-        {"messages": [HumanMessage(content=prompt)]},
-        config=config
-    )
-    assistant_msg = response["messages"][-1].content
-    current_state = app.get_state(config)
-    reversed_messages = current_state.values["messages"][::-1]
-    # Loop through the reversed messages until a
-    # ToolMessage is found.
-    ask_questool_invoked = False
-    for msg in reversed_messages:
-        # Assert that the message is a ToolMessage
-        # and its status is "error"
-        if isinstance(msg, ToolMessage):
-            if msg.name == "ask_question":
-                ask_questool_invoked = True
-                break
-    assert ask_questool_invoked
-    assert "0.06" in assistant_msg
-
-def test_integration():
-    '''
-    Test the integration of the tools.
-    '''
-    unique_id = 1234567
-    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 after 1000 time points?"""
-    # 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 = """Make a custom plot showing the
-        concentration of the species `TP53` over
-        time. Do not show any other 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
-    # 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