Remove any trace of resolving

CHANGELOG.md

@@ -23,6 +23,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Tool selection remains when switching between pages.
 - Propagate temperature to the api call and set the seed.
 
+### Removed
+- Brain region and mtype resolving.
+
 ## [v0.6.4] - 02.07.2025
 
 ### Added

README.md

@@ -24,12 +24,6 @@ docker compose up
 docker exec -it neuroagent-minio-1 mc alias set myminio http://minio:9000 minioadmin minioadmin && docker exec -it neuroagent-minio-1 mc mb myminio/neuroagent
 ```
 
-To enable the brain region resolving tool, retrieve your bearer token and make sure to run the following script:
-```bash
-python backend/src/neuroagent/scripts/embed_hierarchies.py $token -e https://staging.openbraininstitute.org/api/entitycore/ -u http://localhost:9000 -b neuroagent -a minioadmin -s minioadmin
-```
-which stores a json file in your minio/s3 instance.
-
 4. Access the application at `http://localhost:3000`
 
 Notes:

backend/README.md

@@ -37,12 +37,6 @@ You'll need to create the `neuroagent` bucket. You can either:
 docker exec <container_id> mc mb /data/neuroagent
 ```
 
-You can compute and push the brain region hierarchy embedding to minio:
-```bash
-python src/neuroagent/scripts/embed_hierarchies.py $token -e https://staging.openbraininstitute.org/api/entitycore/ -u http://localhost:9000 -b neuroagent -a minioadmin -s minioadmin
-```
-You need to insert your bearer token corresponding to the environment defined in the `-e` arg.
-
 4. (Optional) Set up Redis for rate limiting:
 ```bash
 docker run -d -p 6379:6379 redis

backend/pyproject.toml

@@ -27,7 +27,6 @@ dependencies = [
     "pyyaml",
     "redis",
     "semantic-router",
-    "scikit-learn",
     "sqlalchemy[asyncio]",
     "tavily-python",
     "types-PyYAML",

backend/src/neuroagent/app/app_utils.py

@@ -2,7 +2,6 @@
 
 import json
 import logging
-import re
 import uuid
 from pathlib import Path
 from typing import Any, Literal, Sequence
@@ -34,7 +33,6 @@
     ToolCallPartVercel,
     ToolCallVercel,
 )
-from neuroagent.schemas import EmbeddedBrainRegions
 from neuroagent.tools.base_tool import BaseTool
 
 logger = logging.getLogger(__name__)
@@ -226,24 +224,6 @@ async def commit_messages(
         await session.close()
 
 
-def get_br_embeddings(
-    s3_client: Any, bucket_name: str, folder: str
-) -> list[EmbeddedBrainRegions]:
-    """Retrieve brain regions embeddings from s3."""
-    file_list = s3_client.list_objects_v2(Bucket=bucket_name, Prefix=folder)
-    pattern = re.compile(rf"^{folder}/.*_hierarchy_embeddings.json$")
-    output: list[EmbeddedBrainRegions] = []
-
-    if "Contents" in file_list:
-        for obj in file_list["Contents"]:
-            key = obj["Key"]
-            if pattern.match(key):
-                file_obj = s3_client.get_object(Bucket=bucket_name, Key=key)
-                content = json.loads(file_obj["Body"].read().decode("utf-8"))
-                output.append(EmbeddedBrainRegions(**content))
-    return output
-
-
 def format_messages_output(
     db_messages: Sequence[Messages],
     tool_hil_mapping: dict[str, bool],

backend/src/neuroagent/app/dependencies.py

@@ -71,8 +71,6 @@
     PlotMorphologyGetOneTool,
     ReconstructionMorphologyGetAllTool,
     ReconstructionMorphologyGetOneTool,
-    ResolveBrainRegionTool,
-    ResolveMtypeTool,
     SCSGetAllTool,
     SCSGetOneTool,
     SCSPlotTool,
@@ -354,8 +352,6 @@ def get_tool_list(
         LiteratureSearchTool,
         ReconstructionMorphologyGetAllTool,
         ReconstructionMorphologyGetOneTool,
-        ResolveBrainRegionTool,
-        ResolveMtypeTool,
         MorphometricsGetOneTool,
         EphysMetricsGetOneTool,
         OrganizationGetAllTool,
@@ -578,7 +574,6 @@ def get_s3_client(
 
 
 def get_context_variables(
-    request: Request,
     settings: Annotated[Settings, Depends(get_settings)],
     httpx_client: Annotated[AsyncClient, Depends(get_httpx_client)],
     thread: Annotated[Threads, Depends(get_thread)],
@@ -589,7 +584,6 @@ def get_context_variables(
     """Get the context variables to feed the tool's metadata."""
     return {
         "bluenaas_url": settings.tools.bluenaas.url,
-        "brainregion_embeddings": request.app.state.br_embeddings,
         "bucket_name": settings.storage.bucket_name,
         "entitycore_url": settings.tools.entitycore.url,
         "httpx_client": httpx_client,

backend/src/neuroagent/app/main.py

@@ -24,15 +24,13 @@
 
 from neuroagent import __version__
 from neuroagent.app.app_utils import (
-    get_br_embeddings,
     get_semantic_router,
     setup_engine,
 )
 from neuroagent.app.config import Settings
 from neuroagent.app.dependencies import (
     get_connection_string,
     get_mcp_tool_list,
-    get_s3_client,
     get_settings,
     get_tool_list,
 )
@@ -121,14 +119,6 @@ async def lifespan(fastapi_app: FastAPI) -> AsyncContextManager[None]:  # type:
     semantic_router = get_semantic_router(settings=app_settings)
     fastapi_app.state.semantic_router = semantic_router
 
-    s3_client = get_s3_client(app_settings)
-    br_embeddings = get_br_embeddings(
-        s3_client=s3_client,
-        bucket_name=app_settings.storage.bucket_name,
-        folder="shared",
-    )
-    fastapi_app.state.br_embeddings = br_embeddings
-
     async with aclosing(
         AsyncAccountingSessionFactory(
             base_url=app_settings.accounting.base_url,

backend/src/neuroagent/schemas.py

@@ -163,19 +163,3 @@ class JSONMultiLinechart(BaseObject):
         default="solid", description="Line style (e.g., 'solid', 'dashed', 'dotted')"
     )
     line_color: str | None = Field(None, description="Hex color code for the line")
-
-
-class EmbeddedBrainRegion(BaseModel):
-    """Brain region schema."""
-
-    id: str
-    name: str
-    hierarchy_level: int
-    name_embedding: list[float] | None = None
-
-
-class EmbeddedBrainRegions(BaseModel):
-    """Schema for dumping."""
-
-    regions: list[EmbeddedBrainRegion]
-    hierarchy_id: str