refactor

src/depiction_targeted_preprocbatch/job_export_results.py

@@ -14,10 +14,13 @@
 class JobExportResults:
     """Exports the results of the job to the output storage and registers it in B-Fabric."""
 
-    def __init__(self, client: Bfabric, work_dir: Path, workunit_config: WorkunitConfig) -> None:
+    def __init__(
+        self, client: Bfabric, work_dir: Path, workunit_config: WorkunitConfig, output_storage: Storage
+    ) -> None:
         self._client = client
         self._workunit_config = workunit_config
         self.output_dir = work_dir / "output"
+        self._output_storage = output_storage
 
     @classmethod
     def export(
@@ -30,41 +33,42 @@ def export(
         output_storage: Storage,
     ) -> None:
         """Exports the results of one job."""
-        instance = cls(client=client, work_dir=work_dir, workunit_config=workunit_config)
-        instance.export_results(sample_name, result_files, output_storage)
+        instance = cls(client=client, work_dir=work_dir, workunit_config=workunit_config, output_storage=output_storage)
+        instance.export_results(sample_name, result_files)
 
-    def export_results(self, sample_name: str, result_files: list[Path], output_storage: Storage) -> None:
+    def export_results(self, sample_name: str, result_files: list[Path]) -> None:
         """Exports the results of one job."""
         zip_file_path = self._create_zip_file(result_files, sample_name)
-        output_path_relative = self._copy_zip_to_storage(zip_file_path, output_storage)
-        self._register_zip_in_workunit(output_path_relative, output_storage, zip_file_path)
+        output_path_relative = self._copy_zip_to_storage(zip_file_path)
+        self._register_zip_in_workunit(output_path_relative, zip_file_path)
 
-    def _create_zip_file(self, result_files, sample_name):
+    def _create_zip_file(self, result_files: list[Path], sample_name: str) -> Path:
+        """Creates a ZIP file containing the results for one sample, and returns the zip file's path."""
         self.output_dir.mkdir(exist_ok=True, parents=True)
         zip_file_path = self.output_dir / f"{sample_name}.zip"
         with zipfile.ZipFile(zip_file_path, "w") as zip_file:
             for result_file in result_files:
                 zip_file.write(result_file, arcname=Path(sample_name) / result_file.name)
         return zip_file_path
 
-    def _register_zip_in_workunit(self, output_path_relative, output_storage, zip_file_path):
+    def _register_zip_in_workunit(self, output_path_relative: Path, zip_file_path: Path) -> None:
         checksum = FileChecksums(file_path=zip_file_path).checksum_md5
         self._client.save(
             "resource",
             {
                 "name": zip_file_path.name,
                 "workunitid": self._workunit_config.workunit_id,
-                "storageid": output_storage.id,
+                "storageid": self._output_storage.id,
                 "relativepath": output_path_relative,
                 "filechecksum": checksum,
                 "status": "available",
                 "size": zip_file_path.stat().st_size,
             },
         )
 
-    def _copy_zip_to_storage(self, zip_file_path, output_storage):
+    def _copy_zip_to_storage(self, zip_file_path: Path) -> Path:
         output_path = self._workunit_config.output_folder_absolute_path / zip_file_path.name
-        output_path_relative = output_path.relative_to(output_storage.base_path)
-        output_uri = f"{output_storage.scp_prefix}{output_path_relative}"
+        output_path_relative = output_path.relative_to(self._output_storage.base_path)
+        output_uri = f"{self._output_storage.scp_prefix}{output_path_relative}"
         scp(zip_file_path, output_uri)
         return output_path_relative