create a zip file

src/depiction_targeted_preproc/pipeline/store_outputs.py

@@ -0,0 +1,33 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import yaml
+from bfabric import Bfabric
+from bfabric.entities import Workunit
+
+
+def _get_outputs_spec(zip_file_path: Path, workunit: Workunit) -> dict[str, list[dict[str, str | int | bool]]]:
+    return {
+        "outputs": [
+            {
+                "type": "bfabric_copy_resource",
+                "local_path": str(zip_file_path.absolute()),
+                "store_entry_path": zip_file_path.name,
+                "workunit_id": workunit.id,
+                "storage_id": workunit.application.storage.id,
+            }
+        ]
+    }
+
+
+def write_outputs_spec(zip_file_path: Path, workunit: Workunit) -> None:
+    output_spec = _get_outputs_spec(zip_file_path=zip_file_path, workunit=workunit)
+    outputs_yaml = zip_file_path.parent / f"{zip_file_path.stem}_outputs_spec.yml"
+    with outputs_yaml.open("w") as file:
+        yaml.safe_dump(output_spec, file)
+
+
+def store_outputs(client: Bfabric, zip_file_path: Path, workunit_id: int):
+    workunit = Workunit.find(id=workunit_id, client=client)
+    write_outputs_spec(zip_file_path=zip_file_path, workunit=workunit)

src/depiction_targeted_preproc/workflow/snakemake_invoke.py

@@ -80,7 +80,7 @@ def _invoke_subprocess(self, work_dir: Path, result_files: list[Path], extra_arg
             command = self.get_command_create_report(
                 base_command=base_command, result_files=result_files, work_dir=work_dir
             )
-            logger.info("Executing {command}", command=command)
+            logger.info("Executing {command}", command=self._args_to_shell_command(command))
             subprocess.run(
                 command,
                 cwd=self.workflow_dir,