add dependencies, and config

src/neuroagent/app/config.py

@@ -121,6 +121,13 @@ class SettingsGetMEModel(BaseModel):
 
     model_config = ConfigDict(frozen=True)
 
+class SettingsBlueNaaS(BaseModel):
+    """BlueNaaS settings."""
+
+    url: str
+
+    model_config = ConfigDict(frozen=True)
+
 
 class SettingsKnowledgeGraph(BaseModel):
     """Knowledge graph API settings."""
@@ -166,6 +173,7 @@ class SettingsTools(BaseModel):
     trace: SettingsTrace = SettingsTrace()
     kg_morpho_features: SettingsKGMorpho = SettingsKGMorpho()
     me_model: SettingsGetMEModel = SettingsGetMEModel()
+    blue_naas: SettingsBlueNaaS = SettingsBlueNaaS()
 
     model_config = ConfigDict(frozen=True)
 

src/neuroagent/app/dependencies.py

@@ -35,6 +35,7 @@
     LiteratureSearchTool,
     MorphologyFeatureTool,
     ResolveBrainRegionTool,
+    BlueNaaSTool,
 )
 from neuroagent.utils import RegionMeta, get_file_from_KG
 
@@ -323,6 +324,23 @@ def get_me_model_tool(
     )
     return tool
 
+def run_single_cell_sim_tool(
+    settings: Annotated[Settings, Depends(get_settings)],
+    token: Annotated[str, Depends(get_kg_token)],
+    httpx_client: Annotated[AsyncClient, Depends(get_httpx_client)],
+) -> BlueNaaSTool:
+    """Load BlueNaaS tool."""
+    tool = BlueNaaSTool(
+        metadata={
+            "url": settings.bluenaas.url,
+            "token": token,
+            "httpx_client": httpx_client,
+        }
+    )
+    return tool
+
+def get_project_id():
+    pass
 
 def get_language_model(
     settings: Annotated[Settings, Depends(get_settings)],

src/neuroagent/app/main.py

@@ -23,6 +23,7 @@
     get_kg_token,
     get_settings,
     get_update_kg_hierarchy,
+    get_project_id,
 )
 from neuroagent.app.middleware import strip_path_prefix
 from neuroagent.app.routers import qa
@@ -125,7 +126,8 @@ async def lifespan(fastapi_app: FastAPI) -> AsyncContextManager[None]:  # type:
     title="Agents",
     summary=(
         "Use an AI agent to answer queries based on the knowledge graph, literature"
-        " search and neuroM."
+        " search and neuroM. Extract statistical information from morphologies and electrophysiology."
+        "Run single cell simulations with BlueNaaS API."
     ),
     version=__version__,
     swagger_ui_parameters={"tryItOutEnabled": True},

src/neuroagent/tools/__init__.py

@@ -2,6 +2,7 @@
 
 from neuroagent.tools.electrophys_tool import ElectrophysFeatureTool, FeaturesOutput
 from neuroagent.tools.get_me_model_tool import GetMEModelTool
+from neuroagent.tools.bluenaas_tool import BlueNaaSTool
 from neuroagent.tools.get_morpho_tool import GetMorphoTool, KnowledgeGraphOutput
 from neuroagent.tools.kg_morpho_features_tool import (
     KGMorphoFeatureOutput,
@@ -37,4 +38,5 @@
     "ResolveBrainRegionTool",
     "TracesOutput",
     "GetMEModelTool",
+    "BlueNaaSTool",
 ]

src/neuroagent/tools/bluenaas_tool.py

@@ -0,0 +1,78 @@
+"""BlueNaaS single cell stimulation, simulation and synapse placement tool."""
+from typing import List, Literal, Optional
+from pydantic import BaseModel, Field
+
+import logging
+from typing import Any, Type
+from pydantic import BaseModel
+from neuroagent.tools.base_tool import BaseToolOutput, BasicTool
+from neuroagent.utils import get_kg_data
+
+logger = logging.getLogger(__name__)
+
+class SynapseConfig(BaseModel):
+    id: str
+    delay: int
+    duration: int
+    frequency: int
+    weightScalar: float
+
+class StimulusConfig(BaseModel):
+    stimulusType: Literal["current_clamp", "voltage_clamp"]
+    stimulusProtocol: Literal["ap_waveform", "idrest", "iv", "fire_pattern", "pos_cheops", "neg_cheops"]
+    amplitudes: List[float]
+
+class CurrentInjectionConfig(BaseModel):
+    injectTo: str
+    stimulus: StimulusConfig
+
+class RecordFromConfig(BaseModel):
+    section: str
+    offset: float
+
+class ConditionsConfig(BaseModel):
+    celsius: float
+    vinit: float
+    hypamp: float
+    max_time: int
+    time_step: float
+    seed: int
+
+class InputBlueNaaS(BaseModel):
+    model_id: str
+    synapses: List[SynapseConfig]
+    currentInjection: CurrentInjectionConfig
+    recordFrom: List[RecordFromConfig]
+    conditions: ConditionsConfig
+    type: Literal["single-neuron-simulation"]
+    simulationDuration: int
+
+class BlueNaaSOutput(BaseModel):
+    status: str
+    result: Optional[dict]
+    error: Optional[str]
+
+
+class BlueNaaSTool(BasicTool):
+    name: str = "blue-naas-tool"
+    description: str = """Runs a single-neuron simulation using the BlueNaaS service.
+    Requires a 'model_id' which can be fetched using the 'get-me-model-tool'.
+    The input configuration should be provided by the user otherwise agent will probe the user
+    with the selected default values."""
+    metadata: dict[str, Any]
+    args_schema: Type[BaseModel] = InputBlueNaaS
+
+    async def _arun(self, **kwargs) -> BlueNaaSOutput:
+        """Run a single-neuron simulation using the BlueNaaS service."""
+        logger.info(f"Running BlueNaaS tool with inputs: {kwargs}")
+        try:
+            response = await self.metadata["httpx_client"].post(
+                url=self.metadata["url"],
+                headers={"Authorization": f"Bearer {self.metadata['token']}"},
+                json=kwargs,
+            )
+            response_data = response.json()
+            return BlueNaaSOutput(status="success", result=response_data)
+        except Exception as e:
+            logger.error(f"Error running BlueNaaS tool: {e}")
+            return BlueNaaSOutput(status="error", error=str(e))