feat: use Path or str type (#24)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "aind-data-transformation"
-description = "Generated from aind-library-template"
+description = "Generic Etl Job template that can be imported"
 license = {text = "MIT"}
 requires-python = ">=3.8"
 authors = [

src/aind_data_transformation/core.py

@@ -9,6 +9,8 @@
 from pydantic import BaseModel, ConfigDict, Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
+PathLike = TypeVar("PathLike", str, Path)
+
 
 def get_parser() -> argparse.ArgumentParser:
     """
@@ -49,8 +51,8 @@ class BasicJobSettings(BaseSettings):
     """Model to define Transformation Job Configs"""
 
     model_config = SettingsConfigDict(env_prefix="TRANSFORMATION_JOB_")
-    input_source: Path
-    output_directory: Path
+    input_source: PathLike
+    output_directory: PathLike
 
     @classmethod
     def from_config_file(cls, config_file_location: Path):
@@ -92,7 +94,16 @@ def __init__(self, job_settings: _T):
         job_settings : _T
           Generic type that is bound by the BaseSettings class.
         """
-        self.job_settings = job_settings
+        self.job_settings = job_settings.model_copy(deep=True)
+        # Parse str into Paths
+        if isinstance(self.job_settings.input_source, str):
+            self.job_settings.input_source = Path(
+                self.job_settings.input_source
+            )
+        if isinstance(self.job_settings.output_directory, str):
+            self.job_settings.output_directory = Path(
+                self.job_settings.output_directory
+            )
 
     @abstractmethod
     def run_job(self) -> JobResponse:

tests/test_core.py

@@ -48,12 +48,22 @@ def setUpClass(cls) -> None:
         """Set up tests with basic job settings and etl job"""
         basic_settings = ExampleJobSettings(
             param=2,
-            input_source=Path("some_input_dir"),
-            output_directory=Path("some_output_dir"),
+            input_source="some_input_dir",
+            output_directory="some_output_dir",
         )
         cls.basic_settings = basic_settings
         cls.basic_job = ExampleJob(job_settings=basic_settings)
 
+    def test_settings_with_paths(self):
+        """Tests JobSettings can be set with Path types if desired."""
+        basic_settings = ExampleJobSettings(
+            param=2,
+            input_source=Path("some_input_dir"),
+            output_directory=Path("some_out_dir"),
+        )
+        self.assertEqual(Path("some_input_dir"), basic_settings.input_source)
+        self.assertEqual(Path("some_out_dir"), basic_settings.output_directory)
+
     def test_load_cli_args_json_str(self):
         """Tests loading json string defined in command line args"""
         job_settings_json = self.basic_settings.model_dump_json()