Remove bypass method

Author: bruno-f-cruz

src/aind_behavior_vr_foraging/data_mappers/__init__.py

@@ -21,6 +21,7 @@ class DataMapperCli(BaseSettings, cli_kebab_case=True):
         default=None,
         description="End time of the session in ISO format. If not provided, will use the time the data mapping is run.",
     )
+    suffix: t.Optional[str] = Field(default="vrforaging", description="Suffix to append to the output filenames.")
 
     def cli_cmd(self):
         """Generate aind-data-schema metadata for the VR Foraging dataset located at the specified path."""
@@ -41,8 +42,8 @@ def cli_cmd(self):
         assert rig_mapper.mapped is not None
 
         session_mapper.mapped.instrument_id = rig_mapper.mapped.instrument_id
-        session_mapper.write_standard_file()
-        rig_mapper.write_standard_file()
+        session_mapper.mapped.write_standard_file(output_directory=Path(self.data_path), filename_suffix=self.suffix)
+        rig_mapper.mapped.write_standard_file(output_directory=Path(self.data_path), filename_suffix=self.suffix)
         logger.info(
             "Mapping completed! Saved acquisition.json and instrument.json to %s",
             self.data_path,

src/aind_behavior_vr_foraging/data_mappers/_rig.py

@@ -55,9 +55,6 @@ def rig_schema(self):
     def session_name(self):
         raise NotImplementedError("Method not implemented.")
 
-    def write_standard_file(self) -> None:
-        self.mapped.write_standard_file(self._data_path, filename_suffix="vrforaging")
-
     def map(self) -> instrument.Instrument:
         logger.info("Mapping aind-data-schema Rig.")
         self._mapped = self._map(self._data_path)

src/aind_behavior_vr_foraging/data_mappers/_session.py

@@ -124,9 +124,6 @@ def _map(self) -> acquisition.Acquisition:
         )
         return aind_data_schema_session
 
-    def write_standard_file(self) -> None:
-        self.mapped.write_standard_file(Path(self._data_path), filename_suffix="vrforaging")
-
     def _get_subject_details(self) -> acquisition.AcquisitionSubjectDetails:
         return acquisition.AcquisitionSubjectDetails(
             mouse_platform_name=TrackedDevices.WHEEL,