Tool unit tests

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

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):

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):

swarm_copy_tests/data/get_traces.json

@@ -0,0 +1,201 @@
+{
+  "hits": {
+    "hits": [
+      {
+        "_id": "https://bbp.epfl.ch/data/demo/morpho-demo/1761e604-03fc-452b-9bf2-2214782bb751",
+        "_index": "nexus_search_d067e019-1398-4eb8-9e28-3af8a717dcd7_41b1545a-cb2e-4848-8c74-195ec79f7bd3_18",
+        "_score": 6.0860696,
+        "_source": {
+          "@id": "https://bbp.epfl.ch/data/demo/morpho-demo/1761e604-03fc-452b-9bf2-2214782bb751",
+          "@type": [
+            "https://neuroshapes.org/Trace",
+            "https://bbp.epfl.ch/ontologies/core/bmo/ExperimentalTrace"
+          ],
+          "brainRegion": {
+            "@id": "http://api.brain-map.org/api/v2/data/Structure/382",
+            "idLabel": "http://api.brain-map.org/api/v2/data/Structure/382|Field CA1",
+            "identifier": "http://api.brain-map.org/api/v2/data/Structure/382",
+            "label": "Field CA1"
+          },
+          "contributors": [
+            {
+              "@id": "https://bbp.epfl.ch/neurosciencegraph/data/859a20a2-9eea-4ab5-9504-d080c3c79311",
+              "@type": [
+                "http://www.w3.org/ns/prov#Agent",
+                "http://schema.org/Person"
+              ],
+              "idLabel": "https://bbp.epfl.ch/neurosciencegraph/data/859a20a2-9eea-4ab5-9504-d080c3c79311|Zsolt Kohus",
+              "label": "Zsolt Kohus"
+            }
+          ],
+          "createdAt": "2024-04-09T21:47:08.569Z",
+          "createdBy": "https://bbp.epfl.ch/nexus/v1/realms/bbp/users/budd",
+          "deprecated": false,
+          "derivation": [
+            {
+              "@type": [
+                "http://www.w3.org/ns/prov#Entity",
+                "https://neuroshapes.org/PatchedCell"
+              ],
+              "identifier": "https://bbp.epfl.ch/data/data/demo/morpho-demo/7173ea54-8e59-478d-85f3-ff86246ef22b",
+              "label": "s160106_0201"
+            }
+          ],
+          "distribution": [
+            {
+              "contentSize": 4919928,
+              "contentUrl": "https://bbp.epfl.ch/nexus/v1/files/demo/morpho-demo/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdata%2Fdemo%2Fmorpho-demo%2F01dffb7b-1122-4e1a-9acf-837e683da4ba",
+              "encodingFormat": "application/nwb",
+              "label": "s160106_02.nwb"
+            }
+          ],
+          "generation": {
+            "@id": "https://bbp.epfl.ch/data/demo/morpho-demo/d857ff82-b558-4117-b643-74d44dbda5e6",
+            "endedAt": "2016-01-06T23:59:00.000Z",
+            "startedAt": "2016-01-06T00:00:00.000Z"
+          },
+          "image": [
+            {
+              "@id": "https://bbp.epfl.ch/neurosciencegraph/data/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdata%2Fdemo%2Fmorpho-demo%2Fc1ef69e4-0073-481d-9446-fcfd7b5b5f7a",
+              "about": "https://neuroshapes.org/StimulationTrace",
+              "identifier": "https://bbp.epfl.ch/neurosciencegraph/data/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdata%2Fdemo%2Fmorpho-demo%2Fc1ef69e4-0073-481d-9446-fcfd7b5b5f7a",
+              "repetition": 0,
+              "stimulusType": "square"
+            },
+            {
+              "@id": "https://bbp.epfl.ch/neurosciencegraph/data/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdata%2Fdemo%2Fmorpho-demo%2F6fd03e92-b2ae-4ab8-8c9e-f0ff52d20a0d",
+              "about": "https://neuroshapes.org/ResponseTrace",
+              "identifier": "https://bbp.epfl.ch/neurosciencegraph/data/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdata%2Fdemo%2Fmorpho-demo%2F6fd03e92-b2ae-4ab8-8c9e-f0ff52d20a0d",
+              "repetition": 0,
+              "stimulusType": "square"
+            }
+          ],
+          "name": "s160106_02",
+          "project": {
+            "@id": "https://bbp.epfl.ch/nexus/v1/projects/demo/morpho-demo",
+            "identifier": "https://bbp.epfl.ch/nexus/v1/projects/demo/morpho-demo",
+            "label": "demo/morpho-demo"
+          },
+          "subjectAge": {
+            "label": "59 days Post-natal",
+            "period": "Post-natal",
+            "unit": "days",
+            "value": 59
+          },
+          "subjectSpecies": {
+            "@id": "http://purl.obolibrary.org/obo/NCBITaxon_10090",
+            "identifier": "http://purl.obolibrary.org/obo/NCBITaxon_10090",
+            "label": "Mus musculus"
+          },
+          "updatedAt": "2024-04-10T08:40:23.039Z",
+          "updatedBy": "https://bbp.epfl.ch/nexus/v1/realms/bbp/users/cgonzale",
+          "_self": "https://bbp.epfl.ch/nexus/v1/resources/demo/morpho-demo/_/https:%2F%2Fbbp.epfl.ch%2Fdata%2Fdemo%2Fmorpho-demo%2F1761e604-03fc-452b-9bf2-2214782bb751"
+        }
+      },
+      {
+        "_id": "https://bbp.epfl.ch/data/demo/morpho-demo/5f710291-9aac-45d0-94ff-d3d318c6ba2f",
+        "_index": "nexus_search_d067e019-1398-4eb8-9e28-3af8a717dcd7_41b1545a-cb2e-4848-8c74-195ec79f7bd3_18",
+        "_score": 6.0860696,
+        "_source": {
+          "@id": "https://bbp.epfl.ch/data/demo/morpho-demo/5f710291-9aac-45d0-94ff-d3d318c6ba2f",
+          "@type": [
+            "https://neuroshapes.org/Trace",
+            "https://bbp.epfl.ch/ontologies/core/bmo/ExperimentalTrace"
+          ],
+          "brainRegion": {
+            "@id": "http://api.brain-map.org/api/v2/data/Structure/382",
+            "idLabel": "http://api.brain-map.org/api/v2/data/Structure/382|Field CA1",
+            "identifier": "http://api.brain-map.org/api/v2/data/Structure/382",
+            "label": "Field CA1"
+          },
+          "contributors": [
+            {
+              "@id": "https://bbp.epfl.ch/neurosciencegraph/data/859a20a2-9eea-4ab5-9504-d080c3c79311",
+              "@type": [
+                "http://www.w3.org/ns/prov#Agent",
+                "http://schema.org/Person"
+              ],
+              "idLabel": "https://bbp.epfl.ch/neurosciencegraph/data/859a20a2-9eea-4ab5-9504-d080c3c79311|Zsolt Kohus",
+              "label": "Zsolt Kohus"
+            }
+          ],
+          "createdAt": "2024-04-10T13:58:37.803Z",
+          "createdBy": "https://bbp.epfl.ch/nexus/v1/realms/bbp/users/budd",
+          "deprecated": false,
+          "derivation": [
+            {
+              "@type": [
+                "https://neuroshapes.org/PatchedCell",
+                "http://www.w3.org/ns/prov#Entity"
+              ],
+              "identifier": "https://bbp.epfl.ch/data/demo/morpho-demo/c5c68107-39e5-4124-8681-8a644ab0f8ce",
+              "label": "s160106_0201"
+            }
+          ],
+          "distribution": [
+            {
+              "contentSize": 4919928,
+              "contentUrl": "https://bbp.epfl.ch/nexus/v1/files/demo/morpho-demo/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdemo%2Fmorpho-demo%2Ff759098b-3db5-4236-a577-eac23191e063",
+              "encodingFormat": "application/nwb",
+              "label": "s160106_02.nwb"
+            }
+          ],
+          "generation": {
+            "@id": "https://bbp.epfl.ch/data/demo/morpho-demo/d47968ad-7644-4153-9bf5-a68277f9e17e",
+            "endedAt": "2016-01-06T23:59:00.000Z",
+            "startedAt": "2016-01-06T00:00:00.000Z"
+          },
+          "image": [
+            {
+              "@id": "https://bbp.epfl.ch/neurosciencegraph/data/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdemo%2Fmorpho-demo%2F835b1f06-c688-4771-9e45-c9c091666a8d",
+              "about": "https://neuroshapes.org/ResponseTrace",
+              "identifier": "https://bbp.epfl.ch/neurosciencegraph/data/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdemo%2Fmorpho-demo%2F835b1f06-c688-4771-9e45-c9c091666a8d",
+              "repetition": 0,
+              "stimulusType": "square"
+            },
+            {
+              "@id": "https://bbp.epfl.ch/neurosciencegraph/data/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdemo%2Fmorpho-demo%2Fde25efaf-6f6a-4245-a5a5-eeed4eddc83e",
+              "about": "https://neuroshapes.org/StimulationTrace",
+              "identifier": "https://bbp.epfl.ch/neurosciencegraph/data/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fdemo%2Fmorpho-demo%2Fde25efaf-6f6a-4245-a5a5-eeed4eddc83e",
+              "repetition": 0,
+              "stimulusType": "square"
+            }
+          ],
+          "name": "s160106_02",
+          "project": {
+            "@id": "https://bbp.epfl.ch/nexus/v1/projects/demo/morpho-demo",
+            "identifier": "https://bbp.epfl.ch/nexus/v1/projects/demo/morpho-demo",
+            "label": "demo/morpho-demo"
+          },
+          "subjectAge": {
+            "label": "59 days Post-natal",
+            "period": "Post-natal",
+            "unit": "days",
+            "value": 59
+          },
+          "subjectSpecies": {
+            "@id": "http://purl.obolibrary.org/obo/NCBITaxon_10090",
+            "identifier": "http://purl.obolibrary.org/obo/NCBITaxon_10090",
+            "label": "Mus musculus"
+          },
+          "updatedAt": "2024-04-10T13:58:37.803Z",
+          "updatedBy": "https://bbp.epfl.ch/nexus/v1/realms/bbp/users/budd",
+          "_self": "https://bbp.epfl.ch/nexus/v1/resources/demo/morpho-demo/_/https:%2F%2Fbbp.epfl.ch%2Fdata%2Fdemo%2Fmorpho-demo%2F5f710291-9aac-45d0-94ff-d3d318c6ba2f"
+        }
+      }
+    ],
+    "max_score": 6.0860696,
+    "total": {
+      "relation": "eq",
+      "value": 1905
+    }
+  },
+  "timed_out": false,
+  "took": 65,
+  "_shards": {
+    "failed": 0,
+    "skipped": 664,
+    "successful": 742,
+    "total": 742
+  }
+}