Merge pull request #448 from AllenNeuralDynamics/feat-make-mapper-absolute

Use bonsai app to derive session mapper

Author: bruno-f-cruz

src/aind_behavior_vr_foraging/data_mappers/__init__.py

@@ -7,7 +7,7 @@
 import pydantic_settings
 from aind_behavior_services.session import AindBehaviorSessionModel
 from aind_behavior_services.utils import model_from_json_file
-from clabe.apps import CurriculumSuggestion
+from clabe.apps import BonsaiAppSettings, CurriculumSuggestion
 from git import Repo
 
 from aind_behavior_vr_foraging.rig import AindVrForagingRig
@@ -21,10 +21,6 @@
 
 class DataMapperCli(pydantic_settings.BaseSettings, cli_kebab_case=True):
     data_path: os.PathLike = pydantic.Field(description="Path to the session data directory.")
-    db_root: os.PathLike = pydantic.Field(
-        default=Path(r"\\allen\aind\scratch\AindBehavior.db\AindVrForaging"),
-        description="Root directory for the database for additional metadata.",
-    )
     repo_path: os.PathLike = pydantic.Field(
         default=Path("."), description="Path to the repository. By default it will use the current directory."
     )
@@ -45,15 +41,20 @@ def cli_cmd(self):
             curriculum_suggestion = None
 
         repo = Repo(self.repo_path)
+        settings = BonsaiAppSettings(
+            workflow=Path(repo.working_dir) / "src" / "main.bonsai",
+            executable=Path(repo.working_dir) / "bonsai/bonsai.exe",
+        )
+
         session_mapped = AindSessionDataMapper(
             session=session,
             rig=rig,
-            task_logic_model=task_logic,
+            task_logic=task_logic,
             repository=repo,
-            script_path=Path("./src/main.bonsai"),
+            bonsai_app_settings=settings,
             curriculum_suggestion=curriculum_suggestion,
         ).map()
-        rig_mapped = AindRigDataMapper(rig_schema_filename=f"{rig.rig_name}.json", db_root=Path(self.db_root)).map()
+        rig_mapped = AindRigDataMapper(rig=rig).map()
 
         assert session.session_name is not None
         assert session_mapped is not None

src/aind_behavior_vr_foraging/data_mappers/_session.py

@@ -14,7 +14,7 @@
 from aind_data_schema.core import acquisition
 from aind_data_schema_models import units
 from aind_data_schema_models.modalities import Modality
-from clabe.apps import CurriculumSuggestion
+from clabe.apps import BonsaiAppSettings, CurriculumSuggestion
 from clabe.data_mapper import aind_data_schema as ads
 from clabe.data_mapper import helpers as data_mapper_helpers
 
@@ -32,8 +32,8 @@ def __init__(
         session: AindBehaviorSessionModel,
         rig: AindVrForagingRig,
         task_logic: AindVrForagingTaskLogic,
+        bonsai_app_settings: BonsaiAppSettings = BonsaiAppSettings(workflow=Path("./src/main.bonsai")),
         repository: Union[os.PathLike, git.Repo] = Path("."),
-        script_path: os.PathLike = Path("./src/main.bonsai"),
         session_end_time: Optional[datetime.datetime] = None,
         curriculum_suggestion: Optional[CurriculumSuggestion] = None,
     ):
@@ -43,7 +43,7 @@ def __init__(
         self.repository = repository
         if isinstance(self.repository, os.PathLike | str):
             self.repository = git.Repo(Path(self.repository))
-        self.script_path = script_path
+        self.bonsai_app = bonsai_app_settings
         self._session_end_time = session_end_time
         self._mapped: Optional[acquisition.Acquisition] = None
         self.curriculum = curriculum_suggestion
@@ -260,7 +260,8 @@ def _map_compression(compression: AbsRig.cameras.VideoWriter) -> acquisition.Cod
         return list(map(_map_camera, cameras.keys(), cameras.values()))
 
     def _get_bonsai_as_code(self) -> acquisition.Code:
-        bonsai_env = data_mapper_helpers.snapshot_bonsai_environment(Path("./bonsai/bonsai.config"))
+        bonsai_folder = Path(self.bonsai_app.executable).parent
+        bonsai_env = data_mapper_helpers.snapshot_bonsai_environment(bonsai_folder / "bonsai.config")
         bonsai_version = bonsai_env.get("Bonsai", "unknown")
         assert isinstance(self.repository, git.Repo)
 
@@ -270,7 +271,7 @@ def _get_bonsai_as_code(self) -> acquisition.Code:
             version=self.repository.head.commit.hexsha,
             language="Bonsai",
             language_version=bonsai_version,
-            run_script=Path("./src/main.bonsai"),
+            run_script=Path(self.bonsai_app.workflow),
         )
 
     def _get_python_as_code(self) -> acquisition.Code:

src/aind_behavior_vr_foraging/launcher.py

@@ -84,7 +84,11 @@ def experiment(launcher: Launcher) -> None:
 
     # Mappers
     ads_session = AindSessionDataMapper(
-        rig=rig, session=session, task_logic=task_logic, curriculum_suggestion=suggestion
+        rig=rig,
+        session=session,
+        task_logic=task_logic,
+        curriculum_suggestion=suggestion,
+        bonsai_app_settings=bonsai_app.settings,
     ).map()
     ads_session.write_standard_file(launcher.session_directory)
     ads_rig = AindRigDataMapper(rig=rig).map()

tests/test_aind_data_mapper.py

@@ -6,6 +6,7 @@
 
 from aind_data_schema.core import acquisition, instrument
 from aind_data_schema.utils import compatibility_check
+from clabe.apps import BonsaiAppSettings
 from git import Repo
 
 from aind_behavior_vr_foraging.data_mappers import AindRigDataMapper, AindSessionDataMapper
@@ -22,7 +23,7 @@ def setUp(self):
         self.rig = rig
         self.task_logic = task_logic
         self.repository = Repo(Path("./"))
-        self.script_path = Path("./src/main.bonsai")
+        self.bonsai_app_settings = BonsaiAppSettings(workflow=Path("./src/main.bonsai"))
         self.session_end_time = datetime.now()
         self.session_directory = None
 
@@ -31,7 +32,7 @@ def setUp(self):
             rig=self.rig,
             task_logic=self.task_logic,
             repository=self.repository,
-            script_path=self.script_path,
+            bonsai_app_settings=self.bonsai_app_settings,
             session_end_time=self.session_end_time,
         )
 
@@ -84,12 +85,14 @@ def setUp(self):
         self.rig_mapper = AindRigDataMapper(
             rig=self.rig,
         )
+        self.bonsai_app_settings = BonsaiAppSettings(workflow=Path("./src/main.bonsai"))
+
         self.session_mapper = AindSessionDataMapper(
             session=self.session,
             rig=self.rig,
             task_logic=self.task_logic,
             repository=Repo(Path("./")),
-            script_path=Path("./src/main.bonsai"),
+            bonsai_app_settings=self.bonsai_app_settings,
             session_end_time=datetime.now(),
         )