Merge pull request #447 from niaid/fix/copy-zarrs-to-assets-brt-flow

Add missing zarr asset copy
niaid · Feb 7, 2024 · 752f0aa · 752f0aa
2 parents 1f6a2e2 + a574a17
commit 752f0aa
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/em_workflows/brt/flow.py b/em_workflows/brt/flow.py
@@ -473,7 +473,8 @@ def gen_ng_metadata(fp_in: FilePath, zarr: Path) -> Dict:
     # Working fp is actually used for getting the metadata
 
     file_path = fp_in
-    asset_fp = Path(f"{file_path.assets_dir}/{file_path.base}.zarr")
+    asset_fp = file_path.copy_to_assets_dir(fp_to_cp=Path(zarr))
+
     utils.log("Instantiating HWZarrImages")
     hw_images = HedwigZarrImages(zarr_path=zarr, read_only=False)
     utils.log("Accessing first HWZarrImage")
@@ -514,7 +515,6 @@ def get_callback_result(callback_data: list) -> list:
     return cb_data
 
 
-# run_config=LocalRun(labels=[utils.get_environment()]),
 @flow(
     name="BRT",
     flow_run_name=utils.generate_flow_run_name,

diff --git a/em_workflows/utils/neuroglancer.py b/em_workflows/utils/neuroglancer.py
@@ -115,6 +115,7 @@ def bioformats_gen_zarr(
 
     cmd.extend([input_fname, output_zarr])
     FilePath.run(cmd=cmd, log_file=log_fp)
+    return Path(output_zarr)
 
 
 def zarr_build_multiscales(file_path: FilePath) -> None: