Tool unit tests (#44)

* Migrated bluenaas * Migration of the rest of the tools * Some pydantic fixes * Fixed error when calling agents * Removed references from neuroagent in swarm_copy * Remove changelog job * CR fixes * Review fixes * lint * lint * MR comments * Migrated electrophys tool tests * Added test for me_model_tool * Added tests for get_morpho tool * Added tests for kg_morpho_features_tool * Added morpho features test * Added test for resolve entitie tool * added traces tool tests * Added traces tool tests * Update ci.yaml * Run new tests * Fixed unit test problems after mergint main * lint * Removed unneeded imports * Use httpx_mock * Bring back changelog * lint * Update changelog.yml * Fixed fixture * Fixed fixtures * Fixed some failing tests * fix last tool tests * added test_create_query to morpho tool * Small changes --------- Co-authored-by: Csaba Zsolnai <[email protected]> Co-authored-by: Csaba Zsolnai <[email protected]> Co-authored-by: Boris-Bergsma <[email protected]> Co-authored-by: Nicolas Frank <[email protected]>
BlueBrain · Dec 19, 2024 · bc1ac9b · bc1ac9b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - LLM evaluation logic
 - Integrated Alembic for managing chat history migrations
 - Tool implementations without langchain or langgraph dependencies
+- Unit tests for the migrated tools
 - CRUDs.
 - BlueNaas CRUD tools
 - Cell types, resolving and utils tests

diff --git a/swarm_copy/tools/get_morpho_tool.py b/swarm_copy/tools/get_morpho_tool.py
@@ -1,6 +1,7 @@
 """Get Morpho tool."""
 
 import logging
+from pathlib import Path
 from typing import Any, ClassVar
 
 from pydantic import BaseModel, Field
@@ -30,8 +31,8 @@ class GetMorphoMetadata(BaseMetadata):
     knowledge_graph_url: str
     token: str
     morpho_search_size: int
-    brainregion_path: str
-    celltypes_path: str
+    brainregion_path: str | Path
+    celltypes_path: str | Path
 
 
 class KnowledgeGraphOutput(BaseModel):

diff --git a/swarm_copy/tools/kg_morpho_features_tool.py b/swarm_copy/tools/kg_morpho_features_tool.py
@@ -1,6 +1,7 @@
 """KG Morpho Feature tool."""
 
 import logging
+from pathlib import Path
 from typing import Any, ClassVar, Literal
 
 from pydantic import BaseModel, Field, model_validator
@@ -151,7 +152,7 @@ class KGMorphoFeatureMetadata(BaseMetadata):
     knowledge_graph_url: str
     token: str
     kg_morpho_feature_search_size: int
-    brainregion_path: str
+    brainregion_path: str | Path
 
 
 class KGMorphoFeatureOutput(BaseModel):

diff --git a/swarm_copy_tests/data/99111002.nwb b/swarm_copy_tests/data/99111002.nwb
diff --git a/swarm_copy_tests/data/get_traces.json b/swarm_copy_tests/data/get_traces.json
@@ -0,0 +1,201 @@
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