Merged main

CHANGELOG.md

@@ -14,6 +14,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Unit tests for the migrated tools
 - CRUDs.
 - BlueNaas CRUD tools
+- app unit tests
+- Tests of AgentsRoutine.
 - Unit tests for database
 
 ### Fixed

pyproject.toml

@@ -75,6 +75,7 @@ convention = "numpy"
 
 [tool.ruff.lint.per-file-ignores]
 "tests/*" = ["D"]
+"swarm_copy_tests/*" = ["D"]
 
 [tool.mypy]
 mypy_path = "src"

swarm_copy/run.py → swarm_copy/agent_routine.py

@@ -222,7 +222,7 @@ async def astream(
     ) -> AsyncIterator[str | Response]:
         """Stream the agent response."""
         active_agent = agent
-        context_variables = copy.deepcopy(context_variables)
+
         history = copy.deepcopy(messages)
         init_len = len(messages)
         is_streaming = False
@@ -251,7 +251,7 @@ async def astream(
                 stream=True,
             )
             async for chunk in completion:  # type: ignore
-                delta = json.loads(chunk.choices[0].delta.json())
+                delta = json.loads(chunk.choices[0].delta.model_dump_json())
 
                 # Check for tool calls
                 if delta["tool_calls"]:

swarm_copy/app/dependencies.py

@@ -13,12 +13,12 @@
 from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession
 from starlette.status import HTTP_401_UNAUTHORIZED
 
+from swarm_copy.agent_routine import AgentsRoutine
 from swarm_copy.app.app_utils import validate_project
 from swarm_copy.app.config import Settings
 from swarm_copy.app.database.sql_schemas import Threads
 from swarm_copy.cell_types import CellTypesMeta
 from swarm_copy.new_types import Agent
-from swarm_copy.run import AgentsRoutine
 from swarm_copy.tools import (
     ElectrophysFeatureTool,
     GetMorphoTool,
@@ -204,9 +204,7 @@ async def get_vlab_and_project(
         if not thread:
             raise HTTPException(
                 status_code=404,
-                detail={
-                    "detail": "Thread not found.",
-                },
+                detail="Thread not found.",
             )
         if thread and thread.vlab_id and thread.project_id:
             vlab_and_project = {

swarm_copy/app/routers/qa.py

@@ -7,6 +7,7 @@
 from fastapi.responses import StreamingResponse
 from sqlalchemy.ext.asyncio import AsyncSession
 
+from swarm_copy.agent_routine import AgentsRoutine
 from swarm_copy.app.database.db_utils import get_history, get_thread, save_history
 from swarm_copy.app.database.sql_schemas import Threads
 from swarm_copy.app.dependencies import (
@@ -17,7 +18,6 @@
     get_user_id,
 )
 from swarm_copy.new_types import Agent, AgentRequest, AgentResponse
-from swarm_copy.run import AgentsRoutine
 from swarm_copy.stream import stream_agent_response
 
 router = APIRouter(prefix="/qa", tags=["Run the agent"])

swarm_copy/stream.py

@@ -5,9 +5,9 @@
 from openai import AsyncOpenAI
 from sqlalchemy.ext.asyncio import AsyncSession
 
+from swarm_copy.agent_routine import AgentsRoutine
 from swarm_copy.app.database.db_utils import save_history
 from swarm_copy.new_types import Agent, Response
-from swarm_copy.run import AgentsRoutine
 
 
 async def stream_agent_response(

swarm_copy_tests/__init__.py

@@ -0,0 +1 @@
+"""Sarm copy tests."""

swarm_copy_tests/app/test_app_utils.py

@@ -0,0 +1,75 @@
+"""Test app utils."""
+
+from unittest.mock import AsyncMock, patch
+
+import pytest
+from fastapi.exceptions import HTTPException
+from httpx import AsyncClient
+
+from swarm_copy.app.app_utils import setup_engine, validate_project
+from swarm_copy.app.config import Settings
+
+
+@pytest.mark.asyncio
+async def test_validate_project(patch_required_env, httpx_mock, monkeypatch):
+    monkeypatch.setenv("NEUROAGENT_KEYCLOAK__VALIDATE_TOKEN", "true")
+    httpx_client = AsyncClient()
+    token = "fake_token"
+    test_vp = {"vlab_id": "test_vlab_DB", "project_id": "project_id_DB"}
+    vlab_url = "https://openbluebrain.com/api/virtual-lab-manager/virtual-labs"
+
+    # test with bad config
+    httpx_mock.add_response(
+        url=f'{vlab_url}/{test_vp["vlab_id"]}/projects/{test_vp["project_id"]}',
+        status_code=404,
+    )
+    with pytest.raises(HTTPException) as error:
+        await validate_project(
+            httpx_client=httpx_client,
+            vlab_id=test_vp["vlab_id"],
+            project_id=test_vp["project_id"],
+            token=token,
+            vlab_project_url=vlab_url,
+        )
+    assert error.value.status_code == 401
+
+    # test with good config
+    httpx_mock.add_response(
+        url=f'{vlab_url}/{test_vp["vlab_id"]}/projects/{test_vp["project_id"]}',
+        json="test_project_ID",
+    )
+    await validate_project(
+        httpx_client=httpx_client,
+        vlab_id=test_vp["vlab_id"],
+        project_id=test_vp["project_id"],
+        token=token,
+        vlab_project_url=vlab_url,
+    )
+    # we jsut want to assert that the httpx_mock was called.
+
+
+@patch("neuroagent.app.app_utils.create_async_engine")
+def test_setup_engine(create_engine_mock, monkeypatch, patch_required_env):
+    create_engine_mock.return_value = AsyncMock()
+
+    monkeypatch.setenv("NEUROAGENT_DB__PREFIX", "prefix")
+
+    settings = Settings()
+
+    connection_string = "postgresql+asyncpg://user:password@localhost/dbname"
+    retval = setup_engine(settings=settings, connection_string=connection_string)
+    assert retval is not None
+
+
+@patch("neuroagent.app.app_utils.create_async_engine")
+def test_setup_engine_no_connection_string(
+    create_engine_mock, monkeypatch, patch_required_env
+):
+    create_engine_mock.return_value = AsyncMock()
+
+    monkeypatch.setenv("NEUROAGENT_DB__PREFIX", "prefix")
+
+    settings = Settings()
+
+    retval = setup_engine(settings=settings, connection_string=None)
+    assert retval is None

swarm_copy_tests/app/test_config.py

@@ -0,0 +1,71 @@
+"""Test config"""
+
+import pytest
+from pydantic import ValidationError
+
+from swarm_copy.app.config import Settings
+
+
+def test_required(monkeypatch, patch_required_env):
+    settings = Settings()
+
+    assert settings.tools.literature.url == "https://fake_url"
+    assert settings.knowledge_graph.base_url == "https://fake_url/api/nexus/v1"
+    assert settings.openai.token.get_secret_value() == "dummy"
+
+    # make sure not case sensitive
+    monkeypatch.delenv("NEUROAGENT_TOOLS__LITERATURE__URL")
+    monkeypatch.setenv("neuroagent_tools__literature__URL", "https://new_fake_url")
+
+    settings = Settings()
+    assert settings.tools.literature.url == "https://new_fake_url"
+
+
+def test_no_settings():
+    # We get an error when no custom variables provided
+    with pytest.raises(ValidationError):
+        Settings()
+
+
+def test_setup_tools(monkeypatch, patch_required_env):
+    monkeypatch.setenv("NEUROAGENT_TOOLS__TRACE__SEARCH_SIZE", "20")
+    monkeypatch.setenv("NEUROAGENT_TOOLS__MORPHO__SEARCH_SIZE", "20")
+    monkeypatch.setenv("NEUROAGENT_TOOLS__KG_MORPHO_FEATURES__SEARCH_SIZE", "20")
+
+    monkeypatch.setenv("NEUROAGENT_KEYCLOAK__USERNAME", "user")
+    monkeypatch.setenv("NEUROAGENT_KEYCLOAK__PASSWORD", "pass")
+
+    settings = Settings()
+
+    assert settings.tools.morpho.search_size == 20
+    assert settings.tools.trace.search_size == 20
+    assert settings.tools.kg_morpho_features.search_size == 20
+    assert settings.keycloak.username == "user"
+    assert settings.keycloak.password.get_secret_value() == "pass"
+
+
+def test_check_consistency(monkeypatch):
+    # We get an error when no custom variables provided
+    url = "https://fake_url"
+    monkeypatch.setenv("NEUROAGENT_TOOLS__LITERATURE__URL", url)
+    monkeypatch.setenv("NEUROAGENT_KNOWLEDGE_GRAPH__URL", url)
+
+    with pytest.raises(ValueError):
+        Settings()
+
+    monkeypatch.setenv("NEUROAGENT_GENERATIVE__OPENAI__TOKEN", "dummy")
+    monkeypatch.setenv("NEUROAGENT_KEYCLOAK__VALIDATE_TOKEN", "true")
+
+    with pytest.raises(ValueError):
+        Settings()
+
+    monkeypatch.setenv("NEUROAGENT_KEYCLOAK__VALIDATE_TOKEN", "false")
+
+    with pytest.raises(ValueError):
+        Settings()
+
+    monkeypatch.setenv("NEUROAGENT_KNOWLEDGE_GRAPH__BASE_URL", "http://fake_nexus.com")
+    monkeypatch.setenv("NEUROAGENT_KEYCLOAK__VALIDATE_TOKEN", "true")
+    monkeypatch.setenv("NEUROAGENT_KEYCLOAK__PASSWORD", "Hello")
+
+    Settings()