add bellavista prepare #6946
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add bellavista prepare #6946
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bgruening
reviewed
May 2, 2025
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| while sleep 1; do | ||
| if grep -q "OME-Zarr image saved successfully" './bellavista.log'; then | ||
| echo "Bella Vista input files created! Stopping the tool..." |
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I think you need an additional safe-guards here.
What happens if this string never appears? Should we kill the tool after X hours? The X hours can be taken optionally from an ENV var, so the admin can overwrite it?
Also would it make sense to actually check if the result file exist?
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I added a timeout to the script.
For the output I'm not sure how to check. the main output would be the image in zarr format.
Now I just check if the directory and .zgroup file exists
bgruening
reviewed
May 2, 2025
bgruening
reviewed
May 2, 2025
Co-authored-by: Björn Grüning <[email protected]>
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Large spatial transcriptomic images take a long time to prepare for bellavista interactive tool.
This tool will prepare inputs in advance to reduce computation time.
FOR CONTRIBUTOR: